Todd Martinez

All Publications

• Attosecond Probing of Coherent Vibrational Dynamics in CBr4. The journal of physical chemistry. A Ou, J. H., Hait, D., Rupprecht, P., Beetar, J. E., Martínez, T. J., Leone, S. R. 2024

  Abstract

  A coherent vibrational wavepacket is launched and manipulated in the symmetric stretch (a1) mode of CBr4, by impulsive stimulated Raman scattering (ISRS) from nonresonant 400 nm laser pump pulses with various peak intensities on the order of tens of 1012 W/cm2. Extreme ultraviolet (XUV) attosecond transient absorption spectroscopy (ATAS) records the wavepacket dynamics as temporal oscillations in XUV absorption energy at the bromine M4,5 3d3/2,5/2 edges around 70 eV. The results are augmented by nuclear time-dependent Schrödinger equation simulations. Slopes of the (Br 3d3/2,5/2)-110a1* core-excited state potential energy surface (PES) along the a1 mode are calculated to be -9.4 eV/Å from restricted open-shell Kohn-Sham calculations. Using analytical relations derived for the small-displacement limit and the calculated slopes of the core-excited state PES, a deeper insight into the vibrational dynamics is obtained by retrieving the experimental excursion amplitude of the vibrational wavepacket and the amount of population transferred to the vibrational first-excited state as a function of pump-pulse peak intensity. Experimentally, the results show that XUV ATAS is capable of resolving oscillations in the XUV absorption energy on the order of a few to tens of meV with tens of femtosecond time precision. This corresponds to change in C-Br bond length on the order of 10-4 to 10-3 Å. The results and the analytic relationships offer a clear physical picture, on multiple levels of understanding, of how the pump-pulse peak intensity controls the vibrational dynamics launched by nonresonant ISRS in the small-displacement limit.

  View details for DOI 10.1021/acs.jpca.4c05210

  View details for PubMedID 39401297

• Prediction of photodynamics of 200 nm excited cyclobutanone with linear response electronic structure and ab initio multiple spawning. The Journal of chemical physics Hait, D., Lahana, D., Fajen, O. J., Paz, A. S., Unzueta, P. A., Rana, B., Lu, L., Wang, Y., Kjønstad, E. F., Koch, H., Martínez, T. J. 2024; 160 (24)

  Abstract

  Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming ultrafast diffraction experiment on the photodynamics of cyclobutanone after excitation to the lowest lying Rydberg state (S2). A picosecond of nonadiabatic dynamics is described with ab initio multiple spawning. We use both time dependent density functional theory (TDDFT) and equation-of-motion coupled cluster singles and doubles (EOM-CCSD) theory for the underlying electronic structure theory. We find that the lifetime of the S2 state is more than a picosecond (with both TDDFT and EOM-CCSD). The predicted ultrafast electron diffraction spectrum exhibits numerous structural features, but weak time dependence over the course of the simulations.

  View details for DOI 10.1063/5.0203800

  View details for PubMedID 38912674

• Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins. Journal of the American Chemical Society Pieri, E., Walker, A. R., Zhu, M., Martínez, T. J. 2024

  Abstract

  Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).

  View details for DOI 10.1021/jacs.4c00458

  View details for PubMedID 38885641

• Photo-induced structural dynamics of o-nitrophenol by ultrafast electron diffraction. Physical chemistry chemical physics : PCCP Nunes, J. P., Williams, M., Yang, J., Wolf, T. J., Rankine, C. D., Parrish, R., Moore, B., Wilkin, K., Shen, X., Lin, M. F., Hegazy, K., Li, R., Weathersby, S., Martinez, T. J., Wang, X. J., Centurion, M. 2024

  Abstract

  The photo-induced dynamics of o-nitrophenol, particularly its photolysis, has garnered significant scientific interest as a potential source of nitrous acid in the atmosphere. Although the photolysis products and preceding photo-induced electronic structure dynamics have been investigated extensively, the nuclear dynamics accompanying the non-radiative relaxation of o-nitrophenol on the ultrafast timescale, which include an intramolecular proton transfer step, have not been experimentally resolved. Herein, we present a direct observation of the ultrafast nuclear motions mediating photo-relaxation using ultrafast electron diffraction. This work spatiotemporally resolves the loss of planarity which enables access to a conical intersection between the first excited state and the ground state after the proton transfer step, on the femtosecond timescale and with sub-Angstrom resolution. Our observations, supported by ab initio multiple spawning simulations, provide new insights into the proton transfer mediated relaxation mechanism in o-nitrophenol.

  View details for DOI 10.1039/d3cp06253h

  View details for PubMedID 38764355

• Massively scalable workflows for quantum chemistry: BigChem and ChemCloud. The Journal of chemical physics Hicks, C. B., Martinez, T. J. 2024; 160 (14)

  Abstract

  Electronic structure theory, i.e., quantum chemistry, is the fundamental building block for many problems in computational chemistry. We present a new distributed computing framework (BigChem), which allows for an efficient solution of many quantum chemistry problems in parallel. BigChem is designed to be easily composable and leverages industry-standard middleware (e.g., Celery, RabbitMQ, and Redis) for distributed approaches to large scale problems. BigChem can harness any collection of worker nodes, including ones on cloud providers (such as AWS or Azure), local clusters, or supercomputer centers (and any mixture of these). BigChem builds upon MolSSI packages, such as QCEngine to standardize the operation of numerous computational chemistry programs, demonstrated here with Psi4, xtb, geomeTRIC, and TeraChem. BigChem delivers full utilization of compute resources at scale, offers a programable canvas for designing sophisticated quantum chemistry workflows, and is fault tolerant to node failures and network disruptions. We demonstrate linear scalability of BigChem running computational chemistry workloads on up to 125 GPUs. Finally, we present ChemCloud, a web API to BigChem and successor to TeraChem Cloud. ChemCloud delivers scalable and secure access to BigChem over the Internet.

  View details for DOI 10.1063/5.0190834

  View details for PubMedID 38591672

• QuTree: A tree tensor network package. The Journal of chemical physics Ellerbrock, R., Johnson, K. G., Seritan, S., Hoppe, H., Zhang, J. H., Lenzen, T., Weike, T., Manthe, U., Martinez, T. J. 2024; 160 (11)

  Abstract

  We present QuTree, a C++ library for tree tensor network approaches. QuTree provides class structures for tensors, tensor trees, and related linear algebra functions that facilitate the fast development of tree tensor network approaches such as the multilayer multiconfigurational time-dependent Hartree approach or the density matrix renormalization group approach and its various extensions. We investigate the efficiency of relevant tensor and tensor network operations and show that the overhead for managing the network structure is negligible, even in cases with a million leaves and small tensors. QuTree focuses on providing simple, high-level routines while retaining easy access to the backend to facilitate novel developments. We demonstrate the capabilities of the package by computing the eigenstates of coupled harmonic oscillator Hamiltonians and performing random circuit simulations on a virtual quantum computer.

  View details for DOI 10.1063/5.0180233

  View details for PubMedID 38497471

• Tensor Hypercontraction of Cluster Perturbation Theory: Quartic Scaling Perturbation Series for the Coupled Cluster Singles and Doubles Ground-State Energies. Journal of chemical theory and computation Hillers-Bendtsen, A. E., Mikkelsen, K. V., Martinez, T. J. 2024

  Abstract

  Even though cluster perturbation theory has been shown to be a robust noniterative alternative to coupled cluster theory, it is still plagued by high order polynomial computational scaling and the storage of higher order tensors. We present a proof-of-concept strategy for implementing a cluster perturbation theory ground-state energy series for the coupled cluster singles and doubles energy with N4 computational scaling using tensor hypercontraction (THC). The reduction in computational scaling by two orders is achieved by decomposing two electron repulsion integrals, doubles amplitudes and multipliers, as well as selected double intermediates to the THC format. Using the outlined strategy, we showcase that the THC pilot implementations retain numerical accuracy to within 1 kcal/mol relative to corresponding conventional and density fitting implementations, and we empirically verify the N4 scaling.

  View details for DOI 10.1021/acs.jctc.3c01038

  View details for PubMedID 38380846

• Chemical control of excited-state reactivity of the anionic green fluorescent protein chromophore. Communications chemistry List, N. H., Jones, C. M., Martinez, T. J. 2024; 7 (1): 25

  Abstract

  Controlling excited-state reactivity is a long-standing challenge in photochemistry, as a desired pathway may be inaccessible or compete with other unwanted channels. An important example is internal conversion of the anionic green fluorescent protein (GFP) chromophore where non-selective progress along two competing torsional modes (P: phenolate and I: imidazolinone) impairs and enables Z-to-E photoisomerization, respectively. Developing strategies to promote photoisomerization could drive new areas of applications of GFP-like proteins. Motivated by the charge-transfer dichotomy of the torsional modes, we explore chemical substitution on the P-ring of the chromophore as a way to control excited-state pathways and improve photoisomerization. As demonstrated by methoxylation, selective P-twisting appears difficult to achieve because the electron-donating potential effects of the substituents are counteracted by inertial effects that directly retard the motion. Conversely, these effects act in concert to promote I-twisting when introducing electron-withdrawing groups. Specifically, 2,3,5-trifluorination leads to both pathway selectivity and a more direct approach to the I-twisted intersection which, in turn, doubles the photoisomerization quantum yield. Our results suggest P-ring engineering as an effective approach to boost photoisomerization of the anionic GFP chromophore.

  View details for DOI 10.1038/s42004-024-01099-1

  View details for PubMedID 38316834

• Predicting the X-ray Absorption Spectrum of Ozone with Single Configuration State Functions. Journal of chemical theory and computation Hait, D., Martínez, T. J. 2024

  Abstract

  X-ray absorption spectra (XAS) of biradicaloid species are often thought to represent a challenge to theoretical methods. This has led to the testing of recently developed multireference techniques on the XAS of ozone, but reproduction of the experimental spectral profile has proven difficult. We utilize a minimal model consisting of a single configuration state function (CSF) per excited state to model core-level excitations of ozone, with the orbitals of each CSF optimized using the restricted open-shell Kohn-Sham (ROKS) method. This protocol leads to semiquantitative agreement with experimental XAS. In fact, we find that low-lying core-hole excited states in biradicaloids can be approximated with individual CSFs, despite the presence of multireference character in the ground state. We also report that the 1s → π* and 1s → σ* transitions have quite distinct widths for O3. This reveals the importance of sampling over a representative range of geometries from the vibrational ground state for properly assessing the accuracy of electronic structure methods against experiments instead of the popular procedure of uniformly broadening stick spectra at the equilibrium geometry.

  View details for DOI 10.1021/acs.jctc.3c01035

  View details for PubMedID 38175153

• Mechanochemistry of Pterodactylane. Journal of the American Chemical Society Horst, M., Meisner, J., Yang, J., Kouznetsova, T. B., Craig, S. L., Martínez, T. J., Xia, Y. 2023

  Abstract

  Pterodactylane is a [4]-ladderane with substituents on the central rung. Comparing the mechanochemistry of the [4]-ladderane structure when pulled from the central rung versus the end rung revealed a striking difference in the threshold force of mechanoactivation: the threshold force is dramatically lowered from 1.9 nN when pulled on the end rung to 0.7 nN when pulled on the central rung. We investigated the bicyclic products formed from the mechanochemical activation of pterodactylane experimentally and computationally, which are distinct from the mechanochemical products of ladderanes being activated from the end rung. We compared the products of pterodactylane's mechanochemical and thermal activation to reveal differences and similarities in the mechanochemical and thermal pathways of pterodactylane transformation. Interestingly, we also discovered the presence of elementary steps that are accelerated or suppressed by force within the same mechanochemical reaction of pterodactylane, suggesting rich mechanochemical manifolds of multicyclic structures. We rationalized the greatly enhanced mechanochemical reactivity of the central rung of pterodactylane and discovered force-free ground state bond length to be a good low-cost predictor of the threshold force for cyclobutane-based mechanophores. These findings advance our understanding of mechanochemical reactivities and pathways, and they will guide future designs of mechanophores with low threshold forces to facilitate their applications in force-responsive materials.

  View details for DOI 10.1021/jacs.3c11293

  View details for PubMedID 38131266

• Simulating the Excited-State Dynamics of Polaritons with Ab Initio Multiple Spawning. The journal of physical chemistry. A Rana, B., Hohenstein, E. G., Martínez, T. J. 2023

  Abstract

  Over the past decade, there has been a growth of interest in polaritonic chemistry, where the formation of hybrid light-matter states (polaritons) can alter the course of photochemical reactions. These hybrid states are created by strong coupling between molecules and photons in resonant optical cavities and can even occur in the absence of light when the molecule is strongly coupled with the electromagnetic fluctuations of the vacuum field. We present a first-principles model to simulate nonadiabatic dynamics of such polaritonic states inside optical cavities by leveraging graphical processing units (GPUs). Our first implementation of this model is specialized for a single molecule coupled to a single-photon mode confined inside the optical cavity but with any number of excited states computed using complete active space configuration interaction (CASCI) and a Jaynes-Cummings-type Hamiltonian. Using this model, we have simulated the excited-state dynamics of a single salicylideneaniline (SA) molecule strongly coupled to a cavity photon with the ab initio multiple spawning (AIMS) method. We demonstrate how the branching ratios of the photodeactivation pathways for this molecule can be manipulated by coupling to the cavity. We also show how one can stop the photoreaction from happening inside of an optical cavity. Finally, we also investigate cavity-based control of the ordering of two excited states (one optically bright and the other optically dark) inside a cavity for a set of molecules, where the dark and bright states are close in energy.

  View details for DOI 10.1021/acs.jpca.3c06607

  View details for PubMedID 38110364

• Simulation-guided engineering of split GFPs with efficient β-strand photodissociation. Nature communications Shamsudin, Y., Walker, A. R., Jones, C. M., Martínez, T. J., Boxer, S. G. 2023; 14 (1): 7401

  Abstract

  Green fluorescent proteins (GFPs) are ubiquitous for protein tagging and live-cell imaging. Split-GFPs are widely used to study protein-protein interactions by fusing proteins of interest to split GFP fragments that create a fluorophore upon typically irreversible complementation. Thus, controlled dissociation of the fragments is desirable. Although we have found that split strands can be photodissociated, the quantum efficiency of light-induced photodissociation of split GFPs is low. Traditional protein engineering approaches to increase efficiency, including extensive mutagenesis and screening, have proved difficult to implement. To reduce the search space, key states in the dissociation process are modeled by combining classical and enhanced sampling molecular dynamics with QM/MM calculations, enabling the rational design and engineering of split GFPs with up to 20-fold faster photodissociation rates using non-intuitive amino acid changes. This demonstrates the feasibility of modeling complex molecular processes using state-of-the-art computational methods, and the potential of integrating computational methods to increase the success rate in protein engineering projects.

  View details for DOI 10.1038/s41467-023-42954-4

  View details for PubMedID 37973981

  View details for PubMedCentralID 6537611

• Efficient Acceleration of Reaction Discovery in the Ab Initio Nanoreactor: Phenyl Radical Oxidation Chemistry. The journal of physical chemistry. A Chang, A. M., Meisner, J., Xu, R., Martínez, T. J. 2023

  Abstract

  Over the years, many computational strategies have been employed to elucidate reaction networks. One of these methods is accelerated molecular dynamics, which can circumvent the expense required in dynamics to find all reactants and products (local minima) and transition states (first-order saddle points) on a potential energy surface (PES) by using fictitious forces that promote reaction events. The ab initio nanoreactor uses these accelerating forces to study large chemical reaction networks from first-principles quantum mechanics. In the initial nanoreactor studies, this acceleration was done through a piston periodic compression potential, which pushes molecules together to induce entropically unfavorable bimolecular reactions. However, the piston is not effective for discovering intramolecular and dissociative reactions, such as those integral to the decomposition channels of phenyl radical oxidation. In fact, the choice of accelerating forces dictates not only the rate of reaction discovery but also the types of reactions discovered; thus, it is critical to understand the biases and efficacies of these forces. In this study, we examine forces using metadynamics, attractive potentials, and local thermostats for accelerating reaction discovery. For each force, we construct a separate phenyl radical combustion reaction network using solely that force in discovery trajectories. We elucidate the enthalpic and entropic trends of each accelerating force and highlight their efficiency in reaction discovery. Comparing the nanoreactor-constructed reaction networks with literature renditions of the phenyl radical combustion PES shows that a combination of accelerating forces is best suited for reaction discovery.

  View details for DOI 10.1021/acs.jpca.3c05484

  View details for PubMedID 37934692

• Sparse adaptive basis set methods for solution of the time dependent Schrodinger equation MOLECULAR PHYSICS Thompson, K. C., Martinez, T. J. 2023

  View details for DOI 10.1080/00268976.2023.2268221

  View details for Web of Science ID 001084926300001

• Femtosecond Electronic and Hydrogen Structural Dynamics in Ammonia Imaged with Ultrafast Electron Diffraction. Physical review letters Champenois, E. G., List, N. H., Ware, M., Britton, M., Bucksbaum, P. H., Cheng, X., Centurion, M., Cryan, J. P., Forbes, R., Gabalski, I., Hegazy, K., Hoffmann, M. C., Howard, A. J., Ji, F., Lin, M. F., Nunes, J. P., Shen, X., Yang, J., Wang, X., Martinez, T. J., Wolf, T. J. 2023; 131 (14): 143001

  Abstract

  Directly imaging structural dynamics involving hydrogen atoms by ultrafast diffraction methods is complicated by their low scattering cross sections. Here we demonstrate that megaelectronvolt ultrafast electron diffraction is sufficiently sensitive to follow hydrogen dynamics in isolated molecules. In a study of the photodissociation of gas phase ammonia, we simultaneously observe signatures of the nuclear and corresponding electronic structure changes resulting from the dissociation dynamics in the time-dependent diffraction. Both assignments are confirmed by ab initio simulations of the photochemical dynamics and the resulting diffraction observable. While the temporal resolution of the experiment is insufficient to resolve the dissociation in time, our results represent an important step towards the observation of proton dynamics in real space and time.

  View details for DOI 10.1103/PhysRevLett.131.143001

  View details for PubMedID 37862660

• Photo-actuators via epitaxial growth of microcrystal arrays in polymer membranes. Nature materials Xu, W., Sanchez, D. M., Raucci, U., Zhou, H., Dong, X., Hu, M., Bardeen, C. J., Martinez, T. J., Hayward, R. C. 2023

  Abstract

  Photomechanical crystals composed of three-dimensionally ordered and densely packed photochromes hold promise for high-performance photochemical actuators. However, bulk crystals with high structural ordering are severely limited in their flexibility, resulting in poor processibility and a tendency to fragment upon light exposure, while previous nano- or microcrystalline composites have lacked global alignment. Here we demonstrate a photon-fuelled macroscopic actuator consisting of diarylethene microcrystals in a polyethylene terephthalate host matrix. These microcrystals survive large deformations and show a high degree of three-dimensional ordering dictated by the anisotropic polyethylene terephthalate, which critically also has a similar stiffness. Overall, these ordered and compliant composites exhibit rapid response times, sustain a performance of over at least hundreds of cycles and generate work densities exceeding those of single crystals. Our composites represent the state-of-the-art for photochemical actuators and enable properties unattainable by single crystals, such as controllable, reversible and abrupt jumping (photosalient behaviour).

  View details for DOI 10.1038/s41563-023-01610-4

  View details for PubMedID 37500960

• First principles reaction discovery: from the Schrodinger equation to experimental prediction for methane pyrolysis. Chemical science Xu, R., Meisner, J., Chang, A. M., Thompson, K. C., Martínez, T. J. 2023; 14 (27): 7447-7464

  Abstract

  Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of the methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling.

  View details for DOI 10.1039/d3sc01202f

  View details for PubMedID 37449065

  View details for PubMedCentralID PMC10337770

• Geometric phase in coupled cluster theory. The Journal of chemical physics Williams, D. M., Kjonstad, E. F., Martinez, T. J. 2023; 158 (21)

  Abstract

  It has been well-established that the topography around conical intersections between excited electronic states is incorrectly described by coupled cluster and many other single reference theories (the intersections are "defective"). Despite this, we show both analytically and numerically that the geometric phase effect (GPE) is correctly reproduced upon traversing a path around a defective excited-state conical intersection (CI) in coupled cluster theory. The theoretical analysis is carried out by using a non-Hermitian generalization of the linear vibronic coupling approach. Interestingly, the approach qualitatively explains the characteristic (incorrect) shape of the defective CIs and CI seams. Moreover, the validity of the approach and the presence of the GPE indicate that defective CIs are local (and not global) artifacts. This implies that a sufficiently accurate coupled cluster method could predict nuclear dynamics, including geometric phase effects, as long as the nuclear wavepacket never gets too close to the conical intersections.

  View details for DOI 10.1063/5.0151856

  View details for PubMedID 37283267

• Rehybridization dynamics into the pericyclic minimum of an electrocyclic reaction imaged in real-time. Nature communications Liu, Y., Sanchez, D. M., Ware, M. R., Champenois, E. G., Yang, J., Nunes, J. P., Attar, A., Centurion, M., Cryan, J. P., Forbes, R., Hegazy, K., Hoffmann, M. C., Ji, F., Lin, M., Luo, D., Saha, S. K., Shen, X., Wang, X. J., Martinez, T. J., Wolf, T. J. 2023; 14 (1): 2795

  Abstract

  Electrocyclic reactions are characterized by the concerted formation and cleavage of both sigma and pi bonds through a cyclic structure. This structure is known as a pericyclic transition state for thermal reactions and a pericyclic minimum in the excited state for photochemical reactions. However, the structure of the pericyclic geometry has yet to be observed experimentally. We use a combination of ultrafast electron diffraction and excited state wavepacket simulations to image structural dynamics through the pericyclic minimum of a photochemical electrocyclic ring-opening reaction in the molecule alpha-terpinene. The structural motion into the pericyclic minimum is dominated by rehybridization of two carbon atoms, which is required for the transformation from two to three conjugated pi bonds. The sigma bond dissociation largely happens after internal conversion from the pericyclic minimum to the electronic ground state. These findings may be transferrable to electrocyclic reactions in general.

  View details for DOI 10.1038/s41467-023-38513-6

  View details for PubMedID 37202402

• Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning. Journal of chemical theory and computation Holm, S., Unzueta, P. A., Thompson, K., Martínez, T. J. 2023

  Abstract

  Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. The test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.

  View details for DOI 10.1021/acs.jctc.2c01298

  View details for PubMedID 37192428

• A Nitrogen Out-of-Plane (NOOP) Mechanism for Imine-Based Light-Driven Molecular Motors. Journal of the American Chemical Society Liu, L., Fang, W., Martinez, T. J. 2023

  Abstract

  Light-driven molecular motors have generated considerable interest due to their potential applications in material and biological systems. Recently, Greb and Lehn reported a new class of molecular motors, chiral N-alkyl imines, which undergo unidirectional rotation induced by light and heat. The mechanism of unidirectional motion in molecular motors containing a C═N group has been assumed to consist of photoinduced torsion about the double bond. In this work, we present a computational study of the photoisomerization dynamics of a chiral N-alkyl imine motor. We find that the location and energetics of minimal energy conical intersections (MECIs) alone are insufficient to understand the mechanism of the motor. Furthermore, a key part of the mechanism consists of out-of-plane distortions of the N atom (followed by isomerization about the double bond). Dynamic effects and out-of-plane distortions are critical to understand the observed (rather low) quantum yield for photoisomerization. Our results provide hints as to how the photoisomerization quantum yield might be increased, improving the efficiency of this class of molecular motors.

  View details for DOI 10.1021/jacs.3c00275

  View details for PubMedID 36920260

• SQMBox: Interfacing a semiempirical integral library to modular ab initio electronic structure enables new semiempirical methods. The Journal of chemical physics Bannwarth, C., Martinez, T. J. 2023; 158 (7): 074109

  Abstract

  Ab initio and semiempirical electronic structure methods are usually implemented in separate software packages or use entirely different code paths. As a result, it can be time-consuming to transfer an established ab initio electronic structure scheme to a semiempirical Hamiltonian. We present an approach to unify ab initio and semiempirical electronic structure code paths based on a separation of the wavefunction ansatz and the needed matrix representations of operators. With this separation, the Hamiltonian can refer to either an ab initio or semiempirical treatment of the resulting integrals. We built a semiempirical integral library and interfaced it to the GPU-accelerated electronic structure code TeraChem. Equivalency between ab initio and semiempirical tight-binding Hamiltonian terms is assigned according to their dependence on the one-electron density matrix. The new library provides semiempirical equivalents of the Hamiltonian matrix and gradient intermediates, corresponding to those provided by the ab initio integral library. This enables the straightforward combination of semiempirical Hamiltonians with the full pre-existing ground and excited state functionality of the ab initio electronic structure code. We demonstrate the capability of this approach by combining the extended tight-binding method GFN1-xTB with both spin-restricted ensemble-referenced Kohn-Sham and complete active space methods. We also present a highly efficient GPU implementation of the semiempirical Mulliken-approximated Fock exchange. The additional computational cost for this term becomes negligible even on consumer-grade GPUs, enabling Mulliken-approximated exchange in tight-binding methods for essentially no additional cost.

  View details for DOI 10.1063/5.0132776

  View details for PubMedID 36813714

• 2021 JCP Emerging Investigator Special Collection. The Journal of chemical physics Ceriotti, M., Jensen, L., Manolopoulos, D. E., Martinez, T., Reichman, D. R., Sciortino, F., Sherrill, C. D., Shi, Q., Vega, C., Wang, L., Weiss, E. A., Zhu, X., Stein, J., Lian, T. 2023; 158 (6): 060401

  View details for DOI 10.1063/5.0143234

  View details for PubMedID 36792492

• TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model THE JOURNAL OF CHEMICAL PHYSICS Cruzeiro, V. D., Wang, Y., Pieri, E., Hohenstein, E. G., Martínez, T. J. 2023; 158 (044801)

  View details for DOI 10.1063/5.0130886

• Enhanced Sampling Aided Design of Molecular Photoswitches. Journal of the American Chemical Society Raucci, U., Sanchez, D. M., Martinez, T. J., Parrinello, M. 2022

  Abstract

  Advances in the evolving field of atomistic simulations promise important insights for the design and fundamental understanding of novel molecular photoswitches. Here, we use state-of-the-art enhanced simulation techniques to unravel the complex, multistep chemistry of donor-acceptor Stenhouse adducts (DASAs). Our reaction discovery workflow consists of enhanced sampling for efficient chemical space exploration, refinement of newly observed pathways with more accurate ab initio electronic structure calculations, and structural modifications to introduce design principles within future generations of DASAs. We showcase our discovery workflow by not only recovering the full photoswitching mechanism of DASA but also predicting a plethora of new plausible thermal pathways and suggesting a way for their experimental validation. Furthermore, we illustrate the tunability of these newly discovered reactions, leading to a potential avenue for controlling DASA dynamics through multiple external stimuli. Overall, these insights could offer alternative routes to increase the efficiency and control of DASA's photoswitching mechanism, providing new elements to design more complex light-responsive materials.

  View details for DOI 10.1021/jacs.2c04419

  View details for PubMedID 36222799

• Multinode Multi-GPU Two-Electron Integrals: Code Generation Using the Regent Language. Journal of chemical theory and computation Johnson, K. G., Mirchandaney, S., Hoag, E., Heirich, A., Aiken, A., Martinez, T. J. 2022

  Abstract

  The computation of two-electron repulsion integrals (ERIs) is often the most expensive step of integral-direct self-consistent field methods. Formally it scales as O(N4), where N is the number of Gaussian basis functions used to represent the molecular wave function. In practice, this scaling can be reduced to O(N2) or less by neglecting small integrals with screening methods. The contributions of the ERIs to the Fock matrix are of Coulomb (J) and exchange (K) type and require separate algorithms to compute matrix elements efficiently. We previously implemented highly efficient GPU-accelerated J-matrix and K-matrix algorithms in the electronic structure code TeraChem. Although these implementations supported the use of multiple GPUs on a node, they did not support the use of multiple nodes. This presents a key bottleneck to cutting-edge ab initio simulations of large systems, e.g., excited state dynamics of photoactive proteins. We present our implementation of multinode multi-GPU J- and K-matrix algorithms in TeraChem using the Regent programming language. Regent directly supports distributed computation in a task-based model and can generate code for a variety of architectures, including NVIDIA GPUs. We demonstrate multinode scaling up to 45 GPUs (3 nodes) and benchmark against hand-coded TeraChem integral code. We also outline our metaprogrammed Regent implementation, which enables flexible code generation for integrals of different angular momenta.

  View details for DOI 10.1021/acs.jctc.2c00414

  View details for PubMedID 36200649

• Steric and Electronic Origins of Fluorescence in GFP and GFP-like Proteins. Journal of the American Chemical Society Jones, C. M., List, N. H., Martinez, T. J. 2022

  Abstract

  Fluorescent proteins have become routine tools for biological imaging. However, their nanosecond lifetimes on the excited state present computational hurdles to a full understanding of these photoactive proteins. In this work, we simulate approximately 0.5 nanoseconds of ab initio molecular dynamics to elucidate steric and electronic features responsible for fluorescent protein behavior. Using green fluorescent protein (GFP) and Dronpa2─widely used fluorescent proteins with contrasting functionality─as case studies, we leverage previous findings in the gas phase and solution to explore the deactivation mechanisms available to these proteins. Starting with ground-state analyses, we identify steric (the distribution of empty pockets near the chromophore) and electronic (electric fields exerted on chromophore moieties) factors that offer potential avenues for rational design. Picosecond timescale simulations on the excited state reveal that the chromophore can access twisted structures in Dronpa2, while the chromophore is largely confined to planarity in GFP. We couple ab initio multiple spawning (AIMS) and enhanced sampling simulations to discover and characterize conical intersection seams that facilitate internal conversion, which is a rare event in both systems. Our AIMS simulations correctly capture the relative fluorescence profiles of GFP and Dronpa2 within the first few picoseconds, and we attribute the diminished fluorescence intensity of Dronpa2, relative to GFP, to flexible chromophore intermediates on the excited state. Furthermore, we predict that twisted chromophore intermediates produce red-shifted intensities in the Dronpa2 fluorescence spectrum. If confirmed experimentally, this spectroscopic signature would provide valuable insights when screening and developing novel fluorescent proteins.

  View details for DOI 10.1021/jacs.2c02946

  View details for PubMedID 35786916

• A multi-stage single photochrome system for controlled photoswitching responses. Nature chemistry Stricker, F., Sanchez, D. M., Raucci, U., Dolinski, N. D., Zayas, M. S., Meisner, J., Hawker, C. J., Martinez, T. J., Read de Alaniz, J. 2022

  Abstract

  The ability of molecular photoswitches to convert on/off responses into large macroscale property change is fundamental to light-responsive materials. However, moving beyond simple binary responses necessitates the introduction of new elements that control the chemistry of the photoswitching process at the molecular scale. To achieve this goal, we designed, synthesized and developed a single photochrome, based on a modified donor-acceptor Stenhouse adduct (DASA), capable of independently addressing multiple molecular states. The multi-stage photoswitch enables complex switching phenomena. To demonstrate this, we show spatial control of the transformation of a three-stage photoswitch by tuning the population of intermediates along the multi-step reaction pathway of the DASAs without interfering with either the first or final stage. This allows for a photonic three-stage logic gate where the secondary wavelength solely negates the input of the primary wavelength. These results provide a new strategy to move beyond traditional on/off binary photochromic systems and enable the design of future molecular logic systems.

  View details for DOI 10.1038/s41557-022-00947-8

  View details for PubMedID 35681046

• InteraChem: Exploring Excited States in Virtual Reality with Ab Initio Interactive Molecular Dynamics. Journal of chemical theory and computation Wang, Y., Seritan, S., Lahana, D., Ford, J. E., Valentini, A., Hohenstein, E. G., Martinez, T. J. 2022

  Abstract

  InteraChem is an ab initio interactive molecular dynamics (AI-IMD) visualizer that leverages recent advances in virtual reality hardware and software, as well as the graphical processing unit (GPU)-accelerated TeraChem electronic structure package, in order to render quantum chemistry in real time. We introduce the exploration of electronically excited states via AI-IMD using the floating occupation molecular orbital-complete active space configuration interaction method. The optimization tools in InteraChem enable identification of excited state minima as well as minimum energy conical intersections for further characterization of excited state chemistry in small- to medium-sized systems. We demonstrate that finite-temperature Hartree-Fock theory is an efficient method to perform ground state AI-IMD. InteraChem allows users to track electronic properties such as molecular orbitals and bond order in real time, resulting in an interactive visualization tool that aids in the interpretation of excited state chemistry data and makes quantum chemistry more accessible for both research and educational purposes.

  View details for DOI 10.1021/acs.jctc.2c00005

  View details for PubMedID 35649124

• Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry. The Journal of chemical physics Sakshuwong, S., Weir, H., Raucci, U., Martinez, T. J. 2022; 156 (20): 204801

  Abstract

  Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, an open-source mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or protein data bank ID and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.

  View details for DOI 10.1063/5.0090482

  View details for PubMedID 35649841

• Chiral photochemistry of achiral molecules. Nature communications Raucci, U., Weir, H., Bannwarth, C., Sanchez, D. M., Martinez, T. J. 2022; 13 (1): 2091

  Abstract

  Chirality is a molecular property governed by the topography of the potential energy surface (PES). Thermally achiral molecules interconvert rapidly when the interconversion barrier between the two enantiomers is comparable to or lower than the thermal energy, in contrast to thermally stable chiral configurations. In principle, a change in the PES topography on the excited electronic state may diminish interconversion, leading to electronically prochiral molecules that can be converted from achiral to chiral by electronic excitation. Here we report that this is the case for two prototypical examples - cis-stilbene and cis-stiff stilbene. Both systems exhibit unidirectional photoisomerization for each enantiomer as a result of their electronic prochirality. We simulate an experiment to demonstrate this effect in cis-stilbene based on its interaction with circularly polarized light. Our results highlight the drastic change in chiral behavior upon electronic excitation, opening up the possibility for asymmetric photochemistry from an effectively nonchiral starting point.

  View details for DOI 10.1038/s41467-022-29662-1

  View details for PubMedID 35440559

• Dissociative electron attachment to 5-bromo-uracil: non-adiabatic dynamics on complex-valued potential energy surfaces. Physical chemistry chemical physics : PCCP Cornetta, L. M., Martinez, T. J., Varella, M. T. 2022

  Abstract

  Electron induced dissociation reactions are relevant to many fields, ranging from prebiotic chemistry to cancer treatments. However, the simulation of dissociation electron attachment (DEA) dynamics is very challenging because the auto-ionization widths of the transient negative ions must be accounted for. We propose an adaptation of the ab initio multiple spawning (AIMS) method for complex-valued potential energy surfaces, along the lines of recent developments based on surface hopping dynamics. Our approach combines models for the energy dependence of the auto-ionization widths, obtained from scattering calculations, with survival probabilities computed for the trajectory basis functions employed in the AIMS dynamics. The method is applied to simulate the DEA dynamics of 5-bromo-uracil in full dimensionality, i.e., taking all the vibrational modes into consideration. The propagation starts on the resonance state and describes the formation of Br- anions mediated by non-adiabatic couplings. The potential energies, gradients and non-adiabatic couplings were computed with the fractional-occupancy molecular orbital complete-active-space configuration-interaction method, and the calculated DEA cross section are consistent with the observed DEA intensities.

  View details for DOI 10.1039/d1cp05663h

  View details for PubMedID 35253036

• Rank-reduced coupled-cluster. III. Tensor hypercontraction of the doubles amplitudes. The Journal of chemical physics Hohenstein, E. G., Fales, B. S., Parrish, R. M., Martinez, T. J. 2022; 156 (5): 054102

  Abstract

  We develop a quartic-scaling implementation of coupled-cluster singles and doubles (CCSD) based on low-rank tensor hypercontraction (THC) factorizations of both the electron repulsion integrals (ERIs) and the doubles amplitudes. This extends our rank-reduced (RR) coupled-cluster method to incorporate higher-order tensor factorizations. The THC factorization of the doubles amplitudes accounts for most of the gain in computational efficiency as it is sufficient, in conjunction with a Cholesky decomposition of the ERIs, to reduce the computational complexity of most contributions to the CCSD amplitude equations. Further THC factorization of the ERIs reduces the complexity of certain terms arising from nested commutators between the doubles excitation operator and the two-electron operator. We implement this new algorithm using graphical processing units and demonstrate that it enables CCSD calculations for molecules with 250 atoms and 2500 basis functions using a single computer node. Furthermore, we show that the new method computes correlation energies with comparable accuracy to the underlying RR-CCSD method.

  View details for DOI 10.1063/5.0077770

  View details for PubMedID 35135289

• Interactive Quantum Chemistry Enabled by Machine Learning, Graphical Processing Units, and Cloud Computing. Annual review of physical chemistry Raucci, U., Weir, H., Sakshuwong, S., Seritan, S., Hicks, C. B., Vannucci, F., Rea, F., Martínez, T. J. 2022

  Abstract

  Modern quantum chemistry algorithms are increasingly able to accurately predict molecular properties that are useful for chemists in research and education. Despite this progress, performing such calculations is currently unattainable to the wider chemistry community, as they often require domain expertise, computer programming skills, and powerful computer hardware. In this review, we outline methods to eliminate these barriers using cutting-edge technologies. We discuss the ingredients needed to create accessible platforms that can compute quantum chemistry properties in real time, including graphical processing units-accelerated quantum chemistry in the cloud, artificial intelligence-driven natural molecule input methods, and extended reality visualization. We end by highlighting a series of exciting applications that assemble these components to create uniquely interactive platforms for computing and visualizing spectra, 3D structures, molecular orbitals, and many other chemical properties. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 74 is April 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  View details for DOI 10.1146/annurev-physchem-061020-053438

  View details for PubMedID 36750410

• Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S1/S0 conical intersection seam. Chemical science List, N. H., Jones, C. M., Martínez, T. J. 2022; 13 (2): 373-385

  Abstract

  The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI-). Its ability to undergo Z/E-isomerization is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. Yet, key dynamical features of the underlying internal conversion process in the native HBDI- chromophore remain largely elusive. We investigate the intrinsic excited-state behavior of isolated HBDI- to resolve competing decay pathways and map out the factors governing efficiency and the stereochemical outcome of photoisomerization. Based on non-adiabatic dynamics simulations, we demonstrate that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways accounts for the three decay constants reported experimentally, leading to competing ultrafast relaxation primarily along the I-twisted pathway and S1 trapping along the P-torsion. The majority of the population (∼70%) is transferred to S0 in the vicinity of two approximately enantiomeric minima on the I-twisted intersection seam (MECI-Is). Despite their sloped, reactant-biased topographies (suggesting low photoproduct yields), we find that decay through these intersections leads to products with a surprisingly high quantum yield of ∼30%. This demonstrates that E-isomer generation results at least in part from direct isomerization on the excited state. A photoisomerization committor analysis reveals a difference in intrinsic photoreactivity of the two MECI-Is and that the observed photoisomerization is the combined result of two effects: early, non-statistical dynamics around the less reactive intersection followed by later, near-statistical behavior around the more reactive MECI-I. Our work offers new insight into internal conversion of HBDI- that both establishes the intrinsic properties of the chromophore and enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.

  View details for DOI 10.1039/d1sc05849e

  View details for PubMedID 35126970

  View details for PubMedCentralID PMC8729814

• 2020 JCP Emerging Investigator Special Collection. The Journal of chemical physics Ceriotti, M., Jensen, L., Manolopoulos, D. E., Martinez, T. J., Michaelides, A., Ogilvie, J. P., Reichman, D. R., Shi, Q., Straub, J. E., Vega, C., Wang, L., Weiss, E., Zhu, X., Stein, J. L., Lian, T. 1800; 155 (23): 230401

  View details for DOI 10.1063/5.0078934

  View details for PubMedID 34937385

• Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S-1/S-0 conical intersection seam CHEMICAL SCIENCE List, N. H., Jones, C. M., Martinez, T. J. 2021

  View details for DOI 10.1039/d1sc05849e

  View details for Web of Science ID 000728080400001

• Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. The Journal of chemical physics Smith, D. G., Lolinco, A. T., Glick, Z. L., Lee, J., Alenaizan, A., Barnes, T. A., Borca, C. H., Di Remigio, R., Dotson, D. L., Ehlert, S., Heide, A. G., Herbst, M. F., Hermann, J., Hicks, C. B., Horton, J. T., Hurtado, A. G., Kraus, P., Kruse, H., Lee, S. J., Misiewicz, J. P., Naden, L. N., Ramezanghorbani, F., Scheurer, M., Schriber, J. B., Simmonett, A. C., Steinmetzer, J., Wagner, J. R., Ward, L., Welborn, M., Altarawy, D., Anwar, J., Chodera, J. D., Dreuw, A., Kulik, H. J., Liu, F., Martinez, T. J., Matthews, D. A., Schaefer, H. F., Sponer, J., Turney, J. M., Wang, L., De Silva, N., King, R. A., Stanton, J. F., Gordon, M. S., Windus, T. L., Sherrill, C. D., Burns, L. A. 2021; 155 (20): 204801

  Abstract

  Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

  View details for DOI 10.1063/5.0059356

  View details for PubMedID 34852489

• In Silico Discovery of Multistep Chemistry Initiated by a Conical Intersection: The Challenging Case of Donor-Acceptor Stenhouse Adducts. Journal of the American Chemical Society Sanchez, D. M., Raucci, U., Martinez, T. J. 2021

  Abstract

  Detailed mechanistic understanding of multistep chemical reactions triggered by internal conversion via a conical intersection is a challenging task that emphasizes limitations in theoretical and experimental techniques. We present a discovery-based, hypothesis-free computational approach based on first-principles molecular dynamics to discover and refine the switching mechanism of donor-acceptor Stenhouse adducts (DASAs). We simulate the photochemical experiment in silico, following the "hot" ground state dynamics for 10 ps after photoexcitation. Using state-of-the-art graphical processing units-enabled electronic structure calculations we performed in total 2 ns of nonadiabatic ab initio molecular dynamics discovering (a) critical intermediates that are involved in the open-to-closed transformation, (b) several competing pathways which lower the overall switching yield, and (c) key elements for future design strategies. Our dynamics describe the natural evolution of both the nuclear and electronic degrees of freedom that govern the interconversion between DASA ground-state intermediates, exposing significant elements for future design strategies of molecular switches.

  View details for DOI 10.1021/jacs.1c06648

  View details for PubMedID 34761899

• InteraChem: Virtual Reality Visualizer for Reactive Interactive Molecular Dynamics JOURNAL OF CHEMICAL EDUCATION Seritan, S., Wang, Y., Ford, J. E., Valentini, A., Gold, T., Martinez, T. J. 2021; 98 (11): 3486-3492

  View details for DOI 10.1021/acs.jchemed.1c00654

  View details for Web of Science ID 000718185800010

• Proton Transfer from a Photoacid to a Water Wire: First Principles Simulations and Fast Fluorescence Spectroscopy. The journal of physical chemistry. B Walker, A. R., Wu, B., Meisner, J., Fayer, M. D., Martinez, T. J. 2021

  Abstract

  Proton transfer reactions are ubiquitous in chemistry, especially in aqueous solutions. We investigate photoinduced proton transfer between the photoacid 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) and water using fast fluorescence spectroscopy and ab initio molecular dynamics simulations. Photoexcitation causes rapid proton release from the HPTS hydroxyl. Previous experiments on HPTS/water described the progress from photoexcitation to proton diffusion using kinetic equations with two time constants. The shortest time constant has been interpreted as protonated and photoexcited HPTS evolving into an "associated" state, where the proton is "shared" between the HPTS hydroxyl and an originally hydrogen bonded water. The longer time constant has been interpreted as indicating evolution to a "solvent separated" state where the shared proton undergoes long distance diffusion. In this work, we refine the previous experimental results using very pure HPTS. We then use excited state ab initio molecular dynamics to elucidate the detailed molecular mechanism of aqueous excited state proton transfer in HPTS. We find that the initial excitation results in rapid rearrangement of water, forming a strong hydrogen bonded network (a "water wire") around HPTS. HPTS then deprotonates in ≤3 ps, resulting in a proton that migrates back and forth along the wire before localizing on a single water molecule. We find a near linear relationship between the emission wavelength and proton-HPTS distance over the simulated time scale, suggesting that the emission wavelength can be used as a ruler for the proton distance. Our simulations reveal that the "associated" state corresponds to a water wire with a mobile proton and that the diffusion of the proton away from this water wire (to a generalized "solvent-separated" state) corresponds to the longest experimental time constant.

  View details for DOI 10.1021/acs.jpcb.1c07254

  View details for PubMedID 34743512

• Predictions of Pre-edge Features in Time-Resolved Near-Edge X-ray Absorption Fine Structure Spectroscopy from Hole-Hole Tamm-Dancoff-Approximated Density Functional Theory. Journal of chemical theory and computation Hohenstein, E. G., Yu, J. K., Bannwarth, C., List, N. H., Paul, A. C., Folkestad, S. D., Koch, H., Martinez, T. J. 2021

  Abstract

  Time-resolved near-edge X-ray absorption fine structure (TR-NEXAFS) spectroscopy is a powerful technique for studying photochemical reaction dynamics with femtosecond time resolution. In order to avoid ambiguity in TR-NEXAFS spectra from nonadiabatic dynamics simulations, core- and valence-excited states must be evaluated on equal footing and those valence states must also define the potential energy surfaces used in the nonadiabatic dynamics simulation. In this work, we demonstrate that hole-hole Tamm-Dancoff-approximated density functional theory (hh-TDA) is capable of directly simulating TR-NEXAFS spectroscopies. We apply hh-TDA to the excited-state dynamics of acrolein. We identify two pre-edge features in the oxygen K-edge TR-NEXAFS spectrum associated with the S2 (pipi*) and S1 (npi*) excited states. We show that these features can be used to follow the internal conversion dynamics between the lowest three electronic states of acrolein. Due to the low, O(N2) apparent computational complexity of hh-TDA and our GPU-accelerated implementation, this method is promising for the simulation of pre-edge features in TR-NEXAFS spectra of large molecules and molecules in the condensed phase.

  View details for DOI 10.1021/acs.jctc.1c00478

  View details for PubMedID 34623139

• Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water. Chemical science Jones, C. M., List, N. H., Martínez, T. J. 2021; 12 (34): 11347-11363

  Abstract

  The chromophore of the green fluorescent protein (GFP) is critical for probing environmental influences on fluorescent protein behavior. Using the aqueous system as a bridge between the unconfined vacuum system and a constricting protein scaffold, we investigate the steric and electronic effects of the environment on the photodynamical behavior of the chromophore. Specifically, we apply ab initio multiple spawning to simulate five picoseconds of nonadiabatic dynamics after photoexcitation, resolving the excited-state pathways responsible for internal conversion in the aqueous chromophore. We identify an ultrafast pathway that proceeds through a short-lived (sub-picosecond) imidazolinone-twisted (I-twisted) species and a slower (several picoseconds) channel that proceeds through a long-lived phenolate-twisted (P-twisted) intermediate. The molecule navigates the non-equilibrium energy landscape via an aborted hula-twist-like motion toward the one-bond-flip dominated conical intersection seams, as opposed to following the pure one-bond-flip paths proposed by the excited-state equilibrium picture. We interpret our simulations in the context of time-resolved fluorescence experiments, which use short- and long-time components to describe the fluorescence decay of the aqueous GFP chromophore. Our results suggest that the longer time component is caused by an energetically uphill approach to the P-twisted intersection seam rather than an excited-state barrier to reach the twisted intramolecular charge-transfer species. Irrespective of the location of the nonadiabatic population events, the twisted intersection seams are inefficient at facilitating isomerization in aqueous solution. The disordered and homogeneous nature of the aqueous solvent environment facilitates non-selective stabilization with respect to I- and P-twisted species, offering an important foundation for understanding the consequences of selective stabilization in heterogeneous and rigid protein environments.

  View details for DOI 10.1039/d1sc02508b

  View details for PubMedID 34667545

  View details for PubMedCentralID PMC8447926

• ChemPix: automated recognition of hand-drawn hydrocarbon structures using deep learning. Chemical science Weir, H., Thompson, K., Woodward, A., Choi, B., Braun, A., Martínez, T. J. 2021; 12 (31): 10622-10633

  Abstract

  Inputting molecules into chemistry software, such as quantum chemistry packages, currently requires domain expertise, expensive software and/or cumbersome procedures. Leveraging recent breakthroughs in machine learning, we develop ChemPix: an offline, hand-drawn hydrocarbon structure recognition tool designed to remove these barriers. A neural image captioning approach consisting of a convolutional neural network (CNN) encoder and a long short-term memory (LSTM) decoder learned a mapping from photographs of hand-drawn hydrocarbon structures to machine-readable SMILES representations. We generated a large auxiliary training dataset, based on RDKit molecular images, by combining image augmentation, image degradation and background addition. Additionally, a small dataset of ∼600 hand-drawn hydrocarbon chemical structures was crowd-sourced using a phone web application. These datasets were used to train the image-to-SMILES neural network with the goal of maximizing the hand-drawn hydrocarbon recognition accuracy. By forming a committee of the trained neural networks where each network casts one vote for the predicted molecule, we achieved a nearly 10 percentage point improvement of the molecule recognition accuracy and were able to assign a confidence value for the prediction based on the number of agreeing votes. The ensemble model achieved an accuracy of 76% on hand-drawn hydrocarbons, increasing to 86% if the top 3 predictions were considered.

  View details for DOI 10.1039/d1sc02957f

  View details for PubMedID 34447555

  View details for PubMedCentralID PMC8365825

• Direct observation of ultrafast hydrogen bond strengthening in liquid water. Nature Yang, J., Dettori, R., Nunes, J. P., List, N. H., Biasin, E., Centurion, M., Chen, Z., Cordones, A. A., Deponte, D. P., Heinz, T. F., Kozina, M. E., Ledbetter, K., Lin, M., Lindenberg, A. M., Mo, M., Nilsson, A., Shen, X., Wolf, T. J., Donadio, D., Gaffney, K. J., Martinez, T. J., Wang, X. 2021; 596 (7873): 531-535

  Abstract

  Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network1, including unusually efficient vibrational energy redistribution and relaxation2. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments2-7. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here, we measure the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04A on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of approximately 1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on femtosecond timescales. Our experiment and simulations unveil the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

  View details for DOI 10.1038/s41586-021-03793-9

  View details for PubMedID 34433948

• Understanding the Mechanochemistry of Ladder-Type Cyclobutane Mechanophores by Single Molecule Force Spectroscopy. Journal of the American Chemical Society Horst, M., Yang, J., Meisner, J., Kouznetsova, T. B., Martinez, T. J., Craig, S. L., Xia, Y. 2021

  Abstract

  We have recently reported a series of ladder-type cyclobutane mechanophores, polymers of which can transform from nonconjugated structures to conjugated structures and change many properties at once. These multicyclic mechanophores, namely, exo-ladderane/ene, endo-benzoladderene, and exo-bicyclohexene-peri-naphthalene, have different ring structures fused to the first cyclobutane, significantly different free energy changes for ring-opening, and different stereochemistry. To better understand their mechanochemistry, we used single molecule force spectroscopy (SMFS) to characterize their force-extension behavior and measure the threshold forces. The threshold forces correlate with the activation energy of the first bond, but not with the strain of the fused rings distal to the polymer main chain, suggesting that the activation of these ladder-type mechanophores occurs with similar early transition states, which is supported by force-modified potential energy surface calculations. We further determined the stereochemistry of the mechanically generated dienes and observed significant and variable contour length elongation for these mechanophores both experimentally and computationally. The fundamental understanding of ladder-type mechanophores will facilitate future design of multicyclic mechanophores with amplified force-response and their applications as mechanically responsive materials.

  View details for DOI 10.1021/jacs.1c05857

  View details for PubMedID 34310875

• A diagrammatic approach for automatically deriving analytical gradients of tensor hyper-contracted electronic structure methods. The Journal of chemical physics Song, C., Martinez, T. J., Neaton, J. B. 2021; 155 (2): 024108

  Abstract

  We introduce a diagrammatic approach to facilitate the automatic derivation of analytical nuclear gradients for tensor hyper-contraction (THC) based electronic structure methods. The automatically derived gradients are guaranteed to have the same scaling in terms of both operation count and memory footprint as the underlying energy calculations, and the computation of a gradient is roughly three times as costly as the underlying energy. The new diagrammatic approach enables the first cubic scaling implementation of nuclear derivatives for THC tensors fitted in molecular orbital basis (MO-THC). Furthermore, application of this new approach to THC-MP2 analytical gradients leads to an implementation, which is at least four times faster than the previously reported, manually derived implementation. Finally, we apply the new approach to the 14 tensor contraction patterns appearing in the supporting subspace formulation of multireference perturbation theory, laying the foundation for developments of analytical nuclear gradients and nonadiabatic coupling vectors for multi-state CASPT2.

  View details for DOI 10.1063/5.0055914

  View details for PubMedID 34266268

• Resolving the ultrafast dynamics of the anionic green fluorescent protein chromophore in water CHEMICAL SCIENCE Jones, C. M., List, N. H., Martinez, T. J. 2021

  View details for DOI 10.1039/d1sc02508b

  View details for Web of Science ID 000678833800001

• Flyby reaction trajectories: Chemical dynamics under extrinsic force. Science (New York, N.Y.) Liu, Y., Holm, S., Meisner, J., Jia, Y., Wu, Q., Woods, T. J., Martinez, T. J., Moore, J. S. 2021; 373 (6551): 208-212

  Abstract

  Dynamic effects are an important determinant of chemical reactivity and selectivity, but the deliberate manipulation of atomic motions during a chemical transformation is not straightforward. Here, we demonstrate that extrinsic force exerted upon cyclobutanes by stretching pendant polymer chains influences product selectivity through force-imparted nonstatistical dynamic effects on the stepwise ring-opening reaction. The high product stereoselectivity is quantified by carbon-13 labeling and shown to depend on external force, reactant stereochemistry, and intermediate stability. Computational modeling and simulations show that, besides altering energy barriers, the mechanical force activates reactive intramolecular motions nonstatistically, setting up "flyby trajectories" that advance directly to product without isomerization excursions. A mechanistic model incorporating nonstatistical dynamic effects accounts for isomer-dependent mechanochemical stereoselectivity.

  View details for DOI 10.1126/science.abi7609

  View details for PubMedID 34244412

• Unmasking the cis-Stilbene Phantom State via Vacuum Ultraviolet Time-Resolved Photoelectron Spectroscopy and Ab Initio Multiple Spawning. The journal of physical chemistry letters Williams, M., Forbes, R., Weir, H., Veyrinas, K., MacDonell, R. J., Boguslavskiy, A. E., Schuurman, M. S., Stolow, A., Martinez, T. J. 2021: 6363-6369

  Abstract

  We present the first vacuum ultraviolet time-resolved photoelectron spectroscopy (VUV-TRPES) study of photoisomerization dynamics in the paradigmatic molecule cis-stilbene. A key reaction intermediate in its dynamics, known as the phantom state, has often been invoked but never directly detected in the gas phase. We report direct spectral signatures of the phantom state in isolated cis-stilbene, observed and characterized through a combination of VUV-TRPES and ab initio multiple spawning (AIMS) nonadiabatic dynamics simulations of the channel-resolved observable. The high VUV probe photon energy tracks the complete excited-state dynamics via multiple photoionization channels, from initial excitation to its return to the "hot" ground state. The TRPES was compared with AIMS simulations of the dynamics from initial excitation, to the phantom-state intermediate (an S1 minimum), through to the ultimate electronic decay to the ground state. This combination revealed the unique spectral signatures and time-dependent dynamics of the phantom-state intermediate, permitting us to report here its direct observation.

  View details for DOI 10.1021/acs.jpclett.1c01227

  View details for PubMedID 34231356

• Chemical physics software. The Journal of chemical physics Sherrill, C. D., Manolopoulos, D. E., Martinez, T. J., Ceriotti, M., Michaelides, A. 2021; 155 (1): 010401

  View details for DOI 10.1063/5.0059886

  View details for PubMedID 34241402

• ChemPix: automated recognition of hand-drawn hydrocarbon structures using deep learning CHEMICAL SCIENCE Weir, H., Thompson, K., Woodward, A., Choi, B., Braun, A., Martinez, T. J. 2021

  View details for DOI 10.1039/d1sc02957f

  View details for Web of Science ID 000673126700001

• The non-adiabatic nanoreactor: towards the automated discovery of photochemistry CHEMICAL SCIENCE Pieri, E., Lahana, D., Chang, A. M., Aldaz, C. R., Thompson, K. C., Martinez, T. J. 2021

  View details for DOI 10.1039/d1sc00775k

  View details for Web of Science ID 000648669700001

• The non-adiabatic nanoreactor: towards the automated discovery of photochemistry. Chemical science Pieri, E., Lahana, D., Chang, A. M., Aldaz, C. R., Thompson, K. C., Martínez, T. J. 2021; 12 (21): 7294-7307

  Abstract

  The ab initio nanoreactor has previously been introduced to automate reaction discovery for ground state chemistry. In this work, we present the nonadiabatic nanoreactor, an analogous framework for excited state reaction discovery. We automate the study of nonadiabatic decay mechanisms of molecules by probing the intersection seam between adiabatic electronic states with hyper-real metadynamics, sampling the branching plane for relevant conical intersections, and performing seam-constrained path searches. We illustrate the effectiveness of the nonadiabatic nanoreactor by applying it to benzene, a molecule with rich photochemistry and a wide array of photochemical products. Our study confirms the existence of several types of S0/S1 and S1/S2 conical intersections which mediate access to a variety of ground state stationary points. We elucidate the connections between conical intersection energy/topography and the resulting photoproduct distribution, which changes smoothly along seam space segments. The exploration is performed with minimal user input, and the protocol requires no previous knowledge of the photochemical behavior of a target molecule. We demonstrate that the nonadiabatic nanoreactor is a valuable tool for the automated exploration of photochemical reactions and their mechanisms.

  View details for DOI 10.1039/d1sc00775k

  View details for PubMedID 34163820

  View details for PubMedCentralID PMC8171323

• Electrostatic Control of Photoisomerization in Channelrhodopsin 2. Journal of the American Chemical Society Liang, R., Yu, J. K., Meisner, J., Liu, F., Martinez, T. J. 2021

  Abstract

  Channelrhodopsin 2 (ChR2) is the most commonly used tool in optogenetics. Because of its faster photocycle compared to wild-type (WT) ChR2, the E123T mutant of ChR2 is a useful optogenetic tool when fast neuronal stimulation is needed. Interestingly, in spite of its faster photocycle, the initial step of the photocycle in E123T (photoisomerization of retinal protonated Schiff base or RPSB) was found experimentally to be much slower than that of WT ChR2. The E123T mutant replaces the negatively charged E123 residue with a neutral T123 residue, perturbing the electric field around the RPSB. Understanding the RPSB photoisomerization mechanism in ChR2 mutants will provide molecular-level insights into how ChR2 photochemical reactivity can be controlled, which will lay the foundation for improving the design of optogenetic tools. In this work, we combine ab initio nonadiabatic dynamics simulation, excited state free energy calculation, and reaction path search to comprehensively characterize the RPSB photoisomerization mechanism in the E123T mutant of ChR2. Our simulation agrees with previous experiments in predicting a red-shifted absorption spectrum and significant slowdown of photoisomerization in the E123T mutant. Interestingly, our simulations predict similar photoisomerization quantum yields for the mutant and WT despite the differences in excited-state lifetime and absorption maximum. Upon mutation, the neutralization of the negative charge on the E123 residue increases the isomerization barrier, alters the reaction pathway, and changes the relative stability of two fluorescent states. Our findings provide new insight into the intricate role of the electrostatic environment on the RPSB photoisomerization mechanism in microbial rhodopsins.

  View details for DOI 10.1021/jacs.1c00058

  View details for PubMedID 33794085

• Parallel molecular mechanisms for enzyme temperature adaptation. Science (New York, N.Y.) Pinney, M. M., Mokhtari, D. A., Akiva, E., Yabukarski, F., Sanchez, D. M., Liang, R., Doukov, T., Martinez, T. J., Babbitt, P. C., Herschlag, D. 2021; 371 (6533)

  Abstract

  The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.

  View details for DOI 10.1126/science.aay2784

  View details for PubMedID 33674467

• Substituent Effects in Mechanochemical Allowed and Forbidden Cyclobutene Ring-Opening Reactions. Journal of the American Chemical Society Brown, C. L., Bowser, B. H., Meisner, J., Kouznetsova, T. B., Seritan, S., Martinez, T. J., Craig, S. L. 2021

  Abstract

  Woodward and Hoffman once jested that a very powerful Maxwell demon could seize a molecule of cyclobutene at its methylene groups and tear it open in a disrotatory fashion to obtain butadiene (Woodward, R. B.; Hoffmann, R. The Conservation of Orbital Symmetry. Angew. Chem., Int. Ed. 1969, 8, 781-853). Nearly 40 years later, that demon was discovered, and the field of covalent polymer mechanochemistry was born. In the decade since our demon was befriended, many fundamental investigations have been undertaken to build up our understanding of force-modified pathways for electrocyclic ring-opening reactions. Here, we seek to extend that fundamental understanding by exploring substituent effects in allowed and forbidden ring-opening reactions of cyclobutene (CBE) and benzocyclobutene (BCB) using a combination of single-molecule force spectroscopy (SMFS) and computation. We show that, while the forbidden ring-opening of cis-BCB occurs at a lower force than the allowed ring-opening of trans-BCB on the time scale of the SMFS experiment, the opposite is true for cis- and trans-CBE. Such a reactivity flip is explained through computational analysis and discussion of the so-called allowed/forbidden gap.

  View details for DOI 10.1021/jacs.0c12088

  View details for PubMedID 33667078

• Nitromethane Decomposition via Automated Reaction Discovery and an Ab Initio Corrected Kinetic Model. The journal of physical chemistry. A Ford, J., Seritan, S., Zhu, X., Sakano, M. N., Islam, M. M., Strachan, A., Martinez, T. J. 2021

  Abstract

  We explore the systematic construction of kinetic models from in silico reaction data for the decomposition of nitromethane. Our models are constructed in a computationally affordable manner by using reactions discovered through accelerated molecular dynamics simulations using the ReaxFF reactive force field. The reaction paths are then optimized to determine reaction rate parameters. We introduce a reaction barrier correction scheme that combines accurate thermochemical data from density functional theory with ReaxFF minimal energy paths. We validate our models across different thermodynamic regimes, showing predictions of gas phase CO and NO concentrations and high-pressure induction times that are similar to experimental data. The kinetic models are analyzed to find fundamental decomposition reactions in different thermodynamic regimes.

  View details for DOI 10.1021/acs.jpca.0c09168

  View details for PubMedID 33569957

• Transient resonant Auger-Meitner spectra of photoexcited thymine. Faraday discussions Wolf, T. J., Paul, A. C., Folkestad, S. D., Myhre, R. H., Cryan, J. P., Berrah, N., Bucksbaum, P. H., Coriani, S., Coslovich, G., Feifel, R., Martinez, T. J., Moeller, S. P., Mucke, M., Obaid, R., Plekan, O., Squibb, R. J., Koch, H., Guhr, M. 2021

  Abstract

  We present the first investigation of excited state dynamics by resonant Auger-Meitner spectroscopy (also known as resonant Auger spectroscopy) using the nucleobase thymine as an example. Thymine is photoexcited in the UV and probed with X-ray photon energies at and below the oxygen K-edge. After initial photoexcitation to a pipi* excited state, thymine is known to undergo internal conversion to an npi* excited state with a strong resonance at the oxygen K-edge, red-shifted from the ground state pi* resonances of thymine (see our previous study Wolf, et al., Nat. Commun., 2017, 8, 29). We resolve and compare the Auger-Meitner electron spectra associated both with the excited state and ground state resonances, and distinguish participator and spectator decay contributions. Furthermore, we observe simultaneously with the decay of the npi* state signatures the appearance of additional resonant Auger-Meitner contributions at photon energies between the npi* state and the ground state resonances. We assign these contributions to population transfer from the npi* state to a pipi* triplet state via intersystem crossing on the picosecond timescale based on simulations of the X-ray absorption spectra in the vibrationally hot triplet state. Moreover, we identify signatures from the initially excited pipi* singlet state which we have not observed in our previous study.

  View details for DOI 10.1039/d0fd00112k

  View details for PubMedID 33566045

• Comparing (stochastic-selection) ab initio multiple spawning with trajectory surface hopping for the photodynamics of cyclopropanone, fulvene, and dithiane. The Journal of chemical physics Ibele, L. M., Lassmann, Y. n., Martínez, T. J., Curchod, B. F. 2021; 154 (10): 104110

  Abstract

  Ab Initio Multiple Spawning (AIMS) simulates the excited-state dynamics of molecular systems by representing nuclear wavepackets in a basis of coupled traveling Gaussian functions, called trajectory basis functions (TBFs). New TBFs are spawned when nuclear wavepackets enter regions of strong nonadiabaticity, permitting the description of non-Born-Oppenheimer processes. The spawning algorithm is simultaneously the blessing and the curse of the AIMS method: it allows for an accurate description of the transfer of nuclear amplitude between different electronic states, but it also dramatically increases the computational cost of the AIMS dynamics as all TBFs are coupled. Recently, a strategy coined stochastic-selection AIMS (SSAIMS) was devised to limit the ever-growing number of TBFs and tested on simple molecules. In this work, we use the photodynamics of three different molecules-cyclopropanone, fulvene, and 1,2-dithiane-to investigate (i) the potential of SSAIMS to reproduce reference AIMS results for challenging nonadiabatic dynamics, (ii) the compromise achieved by SSAIMS in obtaining accurate results while using the smallest average number of TBFs as possible, and (iii) the performance of SSAIMS in comparison to the mixed quantum/classical method trajectory surface hopping (TSH)-both in terms of its accuracy and computational cost. We show that SSAIMS can accurately reproduce the AIMS results for the three molecules considered at a much cheaper computational cost, often close to that of TSH. We deduce from these tests that an overlap-based criterion for the stochastic-selection process leads to the best agreement with the reference AIMS dynamics for the smallest average number of TBFs.

  View details for DOI 10.1063/5.0045572

  View details for PubMedID 33722031

• Voice-controlled quantum chemistry. Nature computational science Raucci, U., Valentini, A., Pieri, E., Weir, H., Seritan, S., Martínez, T. J. 2021; 1 (1): 42-45

  Abstract

  Over the past decade, artificial intelligence has been propelled forward by advances in machine learning algorithms and computational hardware, opening up myriads of new avenues for scientific research. Nevertheless, virtual assistants and voice control have yet to be widely used in the natural sciences. Here, we present ChemVox, an interactive Amazon Alexa skill that uses speech recognition to perform quantum chemistry calculations. This new application interfaces Alexa with cloud computing and returns the results through a capable device. ChemVox paves the way to making computational chemistry routinely accessible to the wider community.

  View details for DOI 10.1038/s43588-020-00012-9

  View details for PubMedID 38217155

• GPU acceleration of rank-reduced coupled-cluster singles and doubles. The Journal of chemical physics Hohenstein, E. G., Martínez, T. J. 2021; 155 (18): 184110

  Abstract

  We have developed a graphical processing unit (GPU) accelerated implementation of our recently introduced rank-reduced coupled-cluster singles and doubles (RR-CCSD) method. RR-CCSD introduces a low-rank approximation of the doubles amplitudes. This is combined with a low-rank approximation of the electron repulsion integrals via Cholesky decomposition. The result of these two low-rank approximations is the replacement of the usual fourth-order CCSD tensors with products of second- and third-order tensors. In our implementation, only a single fourth-order tensor must be constructed as an intermediate during the solution of the amplitude equations. Owing in large part to the compression of the doubles amplitudes, the GPU-accelerated implementation shows excellent parallel efficiency (95% on eight GPUs). Our implementation can solve the RR-CCSD equations for up to 400 electrons and 1550 basis functions-roughly 50% larger than the largest canonical CCSD computations that have been performed on any hardware. In addition to increased scalability, the RR-CCSD computations are faster than the corresponding CCSD computations for all but the smallest molecules. We test the accuracy of RR-CCSD for a variety of chemical systems including up to 1000 basis functions and determine that accuracy to better than 0.1% error in the correlation energy can be achieved with roughly 95% compression of the ov space for the largest systems considered. We also demonstrate that conformational energies can be predicted to be within 0.1 kcal mol-1 with efficient compression applied to the wavefunction. Finally, we find that low-rank approximations of the CCSD doubles amplitudes used in the similarity transformation of the Hamiltonian prior to a conventional equation-of-motion CCSD computation will not introduce significant errors (on the order of a few hundredths of an electronvolt) into the resulting excitation energies.

  View details for DOI 10.1063/5.0063467

  View details for PubMedID 34773962

• Voice-controlled quantum chemistry NATURE COMPUTATIONAL SCIENCE Raucci, U., Valentini, A., Pieri, E., Weir, H., Seritan, S., Martinez, T. J. 2021; 1 (1): 42-45

  View details for DOI 10.1038/s43588-020-00012-9

  View details for Web of Science ID 000888550400016

• Reduced scaling formulation of CASPT2 analytical gradients using the supporting subspace method. The Journal of chemical physics Song, C. n., Neaton, J. B., Martínez, T. J. 2021; 154 (1): 014103

  Abstract

  We present a reduced scaling and exact reformulation of state specific complete active space second-order perturbation (CASPT2) analytical gradients in terms of the MP2 and Fock derivatives using the supporting subspace method. This work follows naturally from the supporting subspace formulation of the CASPT2 energy in terms of the MP2 energy using dressed orbitals and Fock builds. For a given active space configuration, the terms corresponding to the MP2-gradient can be evaluated with O(N5) operations, while the rest of the calculations can be computed with O(N3) operations using Fock builds, Fock gradients, and linear algebra. When tensor-hyper-contraction is applied simultaneously, the computational cost can be further reduced to O(N4) for a fixed active space size. The new formulation enables efficient implementation of CASPT2 analytical gradients by leveraging the existing graphical processing unit (GPU)-based MP2 and Fock routines. We present benchmark results that demonstrate the accuracy and performance of the new method. Example applications of the new method in ab initio molecular dynamics simulation and constrained geometry optimization are given.

  View details for DOI 10.1063/5.0035233

  View details for PubMedID 33412861

• A Tribute to Emily A. Carter. The journal of physical chemistry. A Zhuang, H. n., Keith, J. n., Martinez, T. n. 2021; 125 (8): 1669–70

  View details for DOI 10.1021/acs.jpca.0c10468

  View details for PubMedID 33657811

• Analytical derivatives of the individual state energies in ensemble density functional theory. II. Implementation on graphical processing units (GPUs). The Journal of chemical physics Liu, F. n., Filatov, M. n., Martínez, T. J. 2021; 154 (10): 104108

  Abstract

  Conical intersections control excited state reactivity, and thus, elucidating and predicting their geometric and energetic characteristics are crucial for understanding photochemistry. Locating these intersections requires accurate and efficient electronic structure methods. Unfortunately, the most accurate methods (e.g., multireference perturbation theories such as XMS-CASPT2) are computationally challenging for large molecules. The state-interaction state-averaged restricted ensemble referenced Kohn-Sham (SI-SA-REKS) method is a computationally efficient alternative. The application of SI-SA-REKS to photochemistry was previously hampered by a lack of analytical nuclear gradients and nonadiabatic coupling matrix elements. We have recently derived analytical energy derivatives for the SI-SA-REKS method and implemented the method effectively on graphical processing units. We demonstrate that our implementation gives the correct conical intersection topography and energetics for several examples. Furthermore, our implementation of SI-SA-REKS is computationally efficient, with observed sub-quadratic scaling as a function of molecular size. This demonstrates the promise of SI-SA-REKS for excited state dynamics of large molecular systems.

  View details for DOI 10.1063/5.0041389

  View details for PubMedID 33722027

• Nonadiabatic Dynamics Simulation of the Wavelength-Dependent Photochemistry of Azobenzene Excited to the npi* and pipi* Excited States. Journal of the American Chemical Society Yu, J. K., Bannwarth, C., Liang, R., Hohenstein, E. G., Martinez, T. J. 2020

  Abstract

  Azobenzene is one of the most ubiquitous photoswitches in photochemistry and a prototypical model for photoisomerizing systems. Despite this, its wavelength-dependent photochemistry has puzzled researchers for decades. Upon excitation to the higher energy pipi* excited state instead of the dipole-forbidden npi* state, the quantum yield of isomerization from trans- to cis-azobenzene is halved. The difficulties associated with unambiguously resolving this effect both experimentally and theoretically have contributed to lasting controversies regarding the photochemistry of azobenzene. Here, we systematically characterize the dynamic photoreaction pathways of azobenzene by performing first-principles simulations of the nonadiabatic dynamics following excitation to both the pipi* and the npi* states. We demonstrate that ground-state recovery is mediated by two distinct S1 decay pathways: a reactive twisting pathway and an unreactive planar pathway. Increased preference for the unreactive pathway upon pipi* excitation largely accounts for the wavelength-dependent behavior observed in azobenzene.

  View details for DOI 10.1021/jacs.0c09056

  View details for PubMedID 33228358

• An ab initio exciton model for singlet fission. The Journal of chemical physics Li, X., Parrish, R. M., Martinez, T. J. 2020; 153 (18): 184116

  Abstract

  We present an ab initio exciton model that extends the Frenkel exciton model and includes valence, charge-transfer, and multiexcitonic excited states. It serves as a general, parameter-free, yet computationally efficient and scalable approach for simulation of singlet fission processes in multichromophoric systems. A comparison with multiconfigurational methods confirms that our exciton model predicts consistent energies and couplings for the pentacene dimer and captures the correct physics. Calculations of larger pentacene clusters demonstrate the computational scalability of the exciton model and suggest that the mixing between local and charge-transfer excitations narrows the gap between singlet and multiexcitonic states. Local vibrations of pentacene molecules are found to facilitate singlet-multiexcitonic state-crossing and hence are important for understanding singlet fission. The exciton model developed in this work also sets the stage for further implementation of the nuclear gradients and nonadiabatic couplings needed for first principles nonadiabatic quantum molecular dynamics simulations of singlet fission.

  View details for DOI 10.1063/5.0028605

  View details for PubMedID 33187442

• The Mechanics of the Bicycle Pedal Photoisomerization in Crystalline cis,cis-1,4-Diphenyl-1,3-butadiene. The journal of physical chemistry. A Aldaz, C. R., Martinez, T. J., Zimmerman, P. M. 2020

  Abstract

  Direct irradiation of crystalline cis,cis-1,4-diphenyl-1,3-butadiene (cc-DPB) forms trans,trans-1,4-diphenyl-1,3,-butadiene via a concerted two-bond isomerization called the bicycle pedal (BP) mechanism. However, little is known about photoisomerization pathways in the solid state and there has been much debate surrounding the interpretation of volume-conserving isomerization mechanisms. The bicycle pedal photoisomerization is investigated using the quantum mechanics/molecular mechanics complete active space self-consistent field/Amber force-field method. Important details about how the steric environment influences isomerization mechanisms are revealed including how the one-bond flip and hula-twist mechanisms are suppressed by the crystal cavity, the nature of the seam space in steric environments, and the features of the bicycle pedal mechanism. Specifically, in the bicycle pedal, the phenyl rings of cc-DPB are locked in place and the intermolecular packing allows a passageway for rotation of the central diene in a volume-conserving manner. In contrast, the bicycle pedal rotation in the gas phase is not a stable pathway, so single-bond rotation mechanisms become operative instead. Furthermore, the crystal BP mechanism is an activated process that occurs completely on the excited state; the photoproduct can decay to the ground state through radiative and non-radiative pathways. The present models, however, do not capture the quantitative activation barriers, and more work is needed to better model reactions in crystals. Last, the reaction barriers of the different crystalline conformations within the unit cell of cc-DPB are compared to investigate the possibility for conformation-dependent isomerization. Although some difference in reaction barriers is observed, the difference is most likely not responsible for the experimentally observed periods of fast and slow conversion.

  View details for DOI 10.1021/acs.jpca.0c05803

  View details for PubMedID 33064471

• JCP Emerging Investigator Special Collection 2019. The Journal of chemical physics Ediger, M. D., Jensen, L., Manolopoulos, D. E., Martinez, T. J., Michaelides, A., Reichman, D. R., Sherrill, C. D., Shi, Q., Straub, J. E., Vega, C., Wang, L., Brigham, E. C., Lian, T. 2020; 153 (11): 110402

  View details for DOI 10.1063/5.0021946

  View details for PubMedID 32962387

• Proton Transfer Dynamics in the Aprotic Proton Accepting Solvent 1-Methylimidazole. The journal of physical chemistry. B Thomaz, J. E., Walker, A. R., Van Wyck, S. J., Meisner, J., Martinez, T. J., Fayer, M. D. 2020

  Abstract

  The dynamics of proton transfer to the aprotic solvent 1-methylimidazole (MeIm, proton acceptor) from the photoacid 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) was investigated using fast fluorescence measurements. The closely related molecule, 8-methoxypyrene-1,3,6-trisulfonic acid trisodium salt (MPTS), which is not a photoacid, was also studied for comparison. Following optical excitation, the wavelength-dependent population dynamics of HPTS in MeIm resulting from the deprotonation process were collected over the entire fluorescence emission window. Analysis of the time-dependent fluorescence spectra revealed four distinct fluorescence bands that appear and decay on different time scales. We label these four states as protonated (P), associated I (AI), associated II (AII), and deprotonated (D). We find that the simple kinetic scheme of P AI AII D is not consistent with the data. Instead, the kinetic scheme that describes the data has P decaying into AI, which mainly goes on to deprotonation (D), but AI can also feed into AII. AII can return to AI or decay to the ground state, but does not deprotonate within experimental error. Quantum chemistry and excited state QM/MM Born-Oppenheimer molecular dynamics simulations indicate that AI and AII are two H-bonding conformations of MeIm to the HPTS hydroxyl, axial, and equatorial, respectively.

  View details for DOI 10.1021/acs.jpcb.0c05525

  View details for PubMedID 32790382

• A multilayer multi-configurational approach to efficiently simulate large-scale circuit-based quantum computers on classical machines. The Journal of chemical physics Ellerbrock, R., Martinez, T. J. 2020; 153 (5): 051101

  Abstract

  A multilayer multi-configurational theory framework is adapted to simulate circuit-based quantum computers. Quantum addition of superpositions of an exponential number of summands is performed in polynomial time with high accuracy. We demonstrate numerically accurate calculations including up to one million qubits for entangling benchmarks. Simulation cost can be assessed by entropy-based entanglement measures. For the considered systems, we show that the entanglement only grows weakly with the system size. The present simulations demonstrate how quantum algorithms in low-entropy regimes can be used efficiently on classically simulated quantum computers.

  View details for DOI 10.1063/5.0013123

  View details for PubMedID 32770887

• TeraChem: A graphical processing unit-acceleratedelectronic structure package forlarge-scaleab initio molecular dynamics WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE Seritan, S., Bannwarth, C., Fales, B. S., Hohenstein, E. G., Isborn, C. M., Kokkila-Schumacher, S. L., Li, X., Liu, F., Luehr, N., Snyder, J. W., Song, C., Titov, A., Ufimtsev, I. S., Wang, L., Martinez, T. J. 2020

  View details for DOI 10.1002/wcms.1494

  View details for Web of Science ID 000552279200001

• SSAIMS-Stochastic-Selection Ab Initio Multiple Spawning for Efficient Nonadiabatic Molecular Dynamics. The journal of physical chemistry. A Curchod, B. F., Glover, W. J., Martinez, T. J. 2020

  Abstract

  Ab initio multiple spawning provides a powerful and accurate way of describing the excited-state dynamics of molecular systems, whose strength resides in the proper description of coherence effects during nonadiabatic processes thanks to the coupling of trajectory basis functions. However, the simultaneous propagation of a large number of trajectory basis functions can be numerically inconvenient. We propose here an elegant and simple solution to this issue, which consists of (i) detecting uncoupled groups of coupled trajectory basis functions and (ii) selecting stochastically one of these groups to continue the ab initio multiple spawning dynamics. We show that this procedure can reproduce the results of full ab initio multiple spawning dynamics in cases where the uncoupled groups of trajectory basis functions stay uncoupled throughout the dynamics (which is often the case in high-dimensional problems). We present and discuss the aforementioned idea in detail and provide simple numerical applications on indole, ethylene, and protonated formaldimine, highlighting the potential of stochastic-selection ab initio multiple spawning.

  View details for DOI 10.1021/acs.jpca.0c04113

  View details for PubMedID 32580552

• Strong, Nonresonant Radiation Enhances Cis-Trans Photoisomerization of Stilbene in Solution. The journal of physical chemistry. A van den Berg, J. L., Neumann, K. I., Harrison, J. A., Weir, H., Hohenstein, E. G., Martinez, T. J., Zare, R. N. 2020

  Abstract

  Previously, it has been demonstrated that external electric fields may be used to exert control over chemical reactivity. In this study, the impact of a strong, nonresonant IR field (1064 nm) on the photoisomerization of cis-stilbene is investigated in cyclohexane solution. The design of a suitable reaction vessel for characterization of this effect is presented. The electric field supplied by the pulsed, near-IR radiation (epsilonl = 4.5 * 107 V/cm) enhances the cis trans photoisomerization yield at the red edge of the absorption spectrum (wavelengths between 337 and 340 nm). Within the microliter focal volume, up to 75% of all cis-stilbene molecules undergo isomerization to trans-stilbene in the strong electric-field environment, indicating a significant increase relative to the 35% yield of trans-stilbene under field-free conditions. This result correlates with a 1-3% enhancement in the trans-stilbene concentration throughout the bulk solution. Theoretical analysis suggests that the observed change is the result of dynamic Stark shifting of the ground and first excited states, leading to a significant redshift in cis-stilbene's absorption spectrum. The predicted increase in the absorption cross section in this range of excitation wavelengths is qualitatively consistent with the experimental increase in trans-stilbene production.

  View details for DOI 10.1021/acs.jpca.0c02732

  View details for PubMedID 32585098

• Performance of Coupled-Cluster Singles and Doubles on Modern Stream Processing Architectures. Journal of chemical theory and computation Fales, B. S., Curtis, E. R., Johnson, K. G., Lahana, D., Seritan, S., Wang, Y., Weir, H., Martinez, T. J., Hohenstein, E. G. 2020

  Abstract

  We develop a new implementation of coupled-cluster singles and doubles (CCSD) optimized for the most recent graphical processing unit (GPU) hardware. We find that a single node with 8 NVIDIA V100 GPUs is capable of performing CCSD computations on roughly 100 atoms and 1300 basis functions in less than 1 day. Comparisons against massively parallel implementations of CCSD suggest that more than 64 CPU-based nodes (each with 16 cores) are required to match this performance.

  View details for DOI 10.1021/acs.jctc.0c00336

  View details for PubMedID 32567305

• Reduced scaling extended multi-state CASPT2 (XMS-CASPT2) using supporting subspaces and tensor hyper-contraction. The Journal of chemical physics Song, C., Martinez, T. J. 2020; 152 (23): 234113

  Abstract

  We present a reduced scaling formulation of the extended multi-state CASPT2 (XMS-CASPT2) method, which is based on our recently developed state-specific CASPT2 (SS-CASPT2) formulation using supporting subspaces and tensor hyper-contraction. By using these two techniques, the off-diagonal elements of the effective Hamiltonian can be computed with only O(N3) operations and O(N2) memory, where N is the number of basis functions. This limits the overall computational scaling to O(N4) operations and O(N2) memory. Thus, excited states can now be obtained at the same reduced (relative to previous algorithms) scaling we achieved for SS-CASPT2. In addition, we also investigate how the energy denominators can be factorized with the Laplace quadrature when some of the denominators are negative, which is critical for excited state calculations. An efficient implementation of the method has been developed using graphical processing units while also exploiting spatial sparsity in tensor operations. We benchmark the accuracy of the new method by comparison to non-THC formulated XMS-CASPT2 for the excited states of various molecules. In our tests, the THC approximation introduces negligible errors (0.01 eV) compared to the non-THC reference method. Scaling behavior and computational timings are presented to demonstrate performance. The new method is also interfaced with quantum mechanics/molecular mechanics (QM/MM). In an example study of green fluorescent protein, we show how the XMS-CASPT2 potential energy surfaces and excitation energies are affected by increasing the size of the QM region up to 278 QM atoms with more than 2300 basis functions.

  View details for DOI 10.1063/5.0007417

  View details for PubMedID 32571032

• Fast transformations between configuration state function and Slater determinant bases for direct configuration interaction. The Journal of chemical physics Fales, B. S., Martinez, T. J. 2020; 152 (16): 164111

  Abstract

  A hybrid configuration state function (CSF) and Slater determinant (SD) basis full configuration interaction (CI) program was developed to simultaneously take advantage of fast SD basis algorithms for sigma = Hc formation and the smaller CI vector length and more robust convergence offered by a CSF basis. Graphical processing unit acceleration of the direct CSF-SD and SD-CSF basis transformation algorithms ensures that the combined transformation time per iteration relative to sigma formation is small (15%). In addition to the obvious benefits of reducing the memory footprint of the CI vector, additional computational savings are demonstrated that rely directly on the size of the CI basis, in one particular case reducing the CI time-to-solution of a HF-CAS-(16,16)-CI/6-31G calculation of ethylene from 1954.79 s to 956 s by using a CSF basis, a 2.0* speedup.

  View details for DOI 10.1063/5.0005155

  View details for PubMedID 32357800

• Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy CHEMICAL SCIENCE List, N. H., Dempwolff, A. L., Dreuw, A., Norman, P., Martinez, T. J. 2020; 11 (16): 4180–93

  View details for DOI 10.1039/d0sc00840k

  View details for Web of Science ID 000530491400012

• Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy. Chemical science List, N. H., Dempwolff, A. L., Dreuw, A., Norman, P., Martínez, T. J. 2020; 11 (16): 4180-4193

  Abstract

  Excited-state intramolecular hydrogen transfer (ESIHT) is a fundamental reaction relevant to chemistry and biology. Malonaldehyde is the simplest example of ESIHT, yet only little is known experimentally about its excited-state dynamics. Several competing relaxation pathways have been proposed, including internal conversion mediated by ESIHT and C[double bond, length as m-dash]C torsional motion as well as intersystem crossing. We perform an in silico transient X-ray absorption spectroscopy (TRXAS) experiment at the oxygen K-edge to investigate its potential to monitor the proposed ultrafast decay pathways in malonaldehyde upon photoexcitation to its bright S2(ππ*) state. We employ both restricted active space perturbation theory and algebraic-diagrammatic construction for the polarization propagator along interpolated reaction coordinates as well as representative trajectories from ab initio multiple spawning simulations to compute the TRXAS signals from the lowest valence states. Our study suggests that oxygen K-edge TRXAS can distinctly fingerprint the passage through the H-transfer intersection and the concomitant population transfer to the S1(nπ*) state. Potential intersystem crossing to T1(ππ*) is detectable from reappearance of the double pre-edge signature and reversed intensities. Moreover, the torsional deactivation pathway induces transient charge redistribution from the enol side towards the central C-atom and manifests itself as substantial shifts of the pre-edge features. Given the continuous advances in X-ray light sources, our study proposes an experimental route to disentangle ultrafast excited-state decay channels in this prototypical ESIHT system and provides a pathway-specific mapping of the TRXAS signal to facilitate the interpretation of future experiments.

  View details for DOI 10.1039/d0sc00840k

  View details for PubMedID 34122881

  View details for PubMedCentralID PMC8152795

• The cascade unzipping of ladderane reveals dynamic effects in mechanochemistry. Nature chemistry Chen, Z., Zhu, X., Yang, J., Mercer, J. A., Burns, N. Z., Martinez, T. J., Xia, Y. 2020

  Abstract

  Force can induce remarkable non-destructive transformations along a polymer, but we have a limited understanding of the energy transduction and product distribution in tandem mechanochemical reactions. Ladderanes consist of multiple fused cyclobutane rings and have recently been used as monomeric motifs to develop polymers that drastically change their properties in response to force. Here we show that [4]-ladderane always exhibits 'all-or-none' cascade mechanoactivations and the same stereochemical distribution of the generated dienes under various conditions and within different polymer backbones. Transition state theory fails to capture the reaction kinetics and explain the observed stereochemical distributions. Ab initio steered molecular dynamics reveals unique non-equilibrium dynamic effects: energy transduction from the first cycloreversion substantially accelerates the second cycloreversion, and bifurcation on the force-modified potential energy surface leads to the product distributions. Our findings illustrate the rich chemistry in closely coupled multi-mechanophores and an exciting potential for effective energy transduction in tandem mechanochemical reactions.

  View details for DOI 10.1038/s41557-019-0396-5

  View details for PubMedID 31907403

• Hole-hole Tamm-Dancoff-approximated density functional theory: A highly efficient electronic structure method incorporating dynamic and static correlation. The Journal of chemical physics Bannwarth, C. n., Yu, J. K., Hohenstein, E. G., Martínez, T. J. 2020; 153 (2): 024110

  Abstract

  The study of photochemical reaction dynamics requires accurate as well as computationally efficient electronic structure methods for the ground and excited states. While time-dependent density functional theory (TDDFT) is not able to capture static correlation, complete active space self-consistent field methods neglect much of the dynamic correlation. Hence, inexpensive methods that encompass both static and dynamic electron correlation effects are of high interest. Here, we revisit hole-hole Tamm-Dancoff approximated (hh-TDA) density functional theory for this purpose. The hh-TDA method is the hole-hole counterpart to the more established particle-particle TDA (pp-TDA) method, both of which are derived from the particle-particle random phase approximation (pp-RPA). In hh-TDA, the N-electron electronic states are obtained through double annihilations starting from a doubly anionic (N+2 electron) reference state. In this way, hh-TDA treats ground and excited states on equal footing, thus allowing for conical intersections to be correctly described. The treatment of dynamic correlation is introduced through the use of commonly employed density functional approximations to the exchange-correlation potential. We show that hh-TDA is a promising candidate to efficiently treat the photochemistry of organic and biochemical systems that involve several low-lying excited states-particularly those with both low-lying ππ* and nπ* states where inclusion of dynamic correlation is essential to describe the relative energetics. In contrast to the existing literature on pp-TDA and pp-RPA, we employ a functional-dependent choice for the response kernel in pp- and hh-TDA, which closely resembles the response kernels occurring in linear response and collinear spin-flip TDDFT.

  View details for DOI 10.1063/5.0003985

  View details for PubMedID 32668944

• TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units. The Journal of chemical physics Seritan, S. n., Bannwarth, C. n., Fales, B. S., Hohenstein, E. G., Kokkila-Schumacher, S. I., Luehr, N. n., Snyder, J. W., Song, C. n., Titov, A. V., Ufimtsev, I. S., Martínez, T. J. 2020; 152 (22): 224110

  Abstract

  Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

  View details for DOI 10.1063/5.0007615

  View details for PubMedID 32534542

• Simultaneous observation of nuclear and electronic dynamics by ultrafast electron diffraction. Science (New York, N.Y.) Yang, J. n., Zhu, X. n., F Nunes, J. P., Yu, J. K., Parrish, R. M., Wolf, T. J., Centurion, M. n., Gühr, M. n., Li, R. n., Liu, Y. n., Moore, B. n., Niebuhr, M. n., Park, S. n., Shen, X. n., Weathersby, S. n., Weinacht, T. n., Martinez, T. J., Wang, X. n. 2020; 368 (6493): 885–89

  Abstract

  Simultaneous observation of nuclear and electronic motion is crucial for a complete understanding of molecular dynamics in excited electronic states. It is challenging for a single experiment to independently follow both electronic and nuclear dynamics at the same time. Here we show that ultrafast electron diffraction can be used to simultaneously record both electronic and nuclear dynamics in isolated pyridine molecules, naturally disentangling the two components. Electronic state changes (S1→S0 internal conversion) were reflected by a strong transient signal in small-angle inelastic scattering, and nuclear structural changes (ring puckering) were monitored by large-angle elastic diffraction. Supported by ab initio nonadiabatic molecular dynamics and diffraction simulations, our experiment provides a clear view of the interplay between electronic and nuclear dynamics of the photoexcited pyridine molecule.

  View details for DOI 10.1126/science.abb2235

  View details for PubMedID 32439793

• Ab Initio Nonadiabatic Molecular Dynamics with Hole-Hole Tamm-Dancoff Approximated Density Functional Theory. Journal of chemical theory and computation Yu, J. K., Bannwarth, C. n., Hohenstein, E. G., Martínez, T. J. 2020

  Abstract

  The study of photoinduced dynamics in chemical systems necessitates accurate and computationally efficient electronic structure methods, especially as the systems of interest grow larger. The linear response hole-hole Tamm-Dancoff approximated (hh-TDA) density functional theory method was recently proposed to satisfy such demands. The N-electron electronic states are obtained by means of double annihilations on a doubly anionic (N + 2)-electron reference state, allowing for the ground and excited states to be formed on the same footing and thus enabling the correct description of conical intersections. Dynamic electron correlation effects are incorporated by means of the exchange-correlation functional. The accuracy afforded by the simultaneous treatment of static and dynamic correlation in addition to the relatively low computational cost, comparable to that of time-dependent density functional theory (TDDFT), makes it a promising ab initio electronic structure method for on-the-fly generation of potential energy surfaces in nonadiabatic dynamics simulations of photochemical systems, particularly those for which the nπ* and ππ* electronic excitations are most relevant. Here, we apply the hh-TDA method to nonadiabatic dynamics simulations of prototypical photochemical processes. First, we demonstrate the ability of hh-TDA to adequately describe conical intersection geometries. We next examine its ability to describe the ultrafast excited state dynamics of photoexcited ethylene through an ab initio multiple spawning (AIMS) dynamics simulation. Finally, we present an alternative variant of the hh-TDA method, which uses orbitals from a fractional occupation number Kohn-Sham (FON-KS) calculation applied to an ensemble with N-electrons. The resulting method is termed floating occupation molecular orbital hh-TDA (FOMO-hh-TDA). This scheme allows us to combine hh-TDA with global hybrid functionals and allows us to avoid unbound valence orbitals that may result from an (N + 2)-electron self-consistent field (SCF) procedure. FOMO-hh-TDA-BHLYP faithfully reproduces the nonadiabatic dynamics of trans-azobenzene (TAB) and is used to characterize the excited state decay pathways from the first (nπ*) excited state.

  View details for DOI 10.1021/acs.jctc.0c00644

  View details for PubMedID 32786902

• TeraChem Cloud: A High-Performance Computing Service for Scalable Distributed GPU-Accelerated Electronic Structure Calculations. Journal of chemical information and modeling Seritan, S. n., Thompson, K. n., Martínez, T. J. 2020

  Abstract

  The encapsulation and commoditization of electronic structure arise naturally as interoperability, and the use of nontraditional compute resources (e.g., new hardware accelerators, cloud computing) remains important for the computational chemistry community. We present TeraChem Cloud, a high-performance computing service (HPCS) that offers on-demand electronic structure calculations on both traditional HPC clusters and cloud-based hardware. The framework is designed using off-the-shelf web technologies and containerization to be extremely scalable and portable. Within the HPCS model, users can quickly develop new methods and algorithms in an interactive environment on their laptop while allowing TeraChem Cloud to distribute ab initio calculations across all available resources. This approach greatly increases the accessibility of hardware accelerators such as graphics processing units (GPUs) and flexibility for the development of new methods as additional electronic structure packages are integrated into the framework as alternative backends. Cost-performance analysis indicates that traditional nodes are the most cost-effective long-term solution, but commercial cloud providers offer cutting-edge hardware with competitive rates for short-term large-scale calculations. We demonstrate the power of the TeraChem Cloud framework by carrying out several showcase calculations, including the generation of 300,000 density functional theory energy and gradient evaluations on medium-sized organic molecules and reproducing 300 fs of nonadiabatic dynamics on the B800-B850 antenna complex in LH2, with the latter demonstration using over 50 Tesla V100 GPUs in a commercial cloud environment in 8 h for approximately $1250.

  View details for DOI 10.1021/acs.jcim.9b01152

  View details for PubMedID 32267693

• Strictly non-adiabatic quantum control of the acetylene dication using an infrared field. The Journal of chemical physics Liekhus-Schmaltz, C. n., Zhu, X. n., McCracken, G. A., Cryan, J. P., Martinez, T. J., Bucksbaum, P. H. 2020; 152 (18): 184302

  Abstract

  We demonstrate the existence of a strictly non-adiabatic control pathway in deprotonation of the acetylene dication. This pathway is identified experimentally by measuring a kinetic energy shift in an ion coincidence experiment. We use a time dependent Schrödinger equation simulation to identify which properties most strongly affect our control. We find that resonant control around conical intersections is limited by the speed of non-adiabatic dynamics.

  View details for DOI 10.1063/5.0007058

  View details for PubMedID 32414271

• Intermolecular vibrations mediate ultrafast singlet fission. Science advances Duan, H. G., Jha, A. n., Li, X. n., Tiwari, V. n., Ye, H. n., Nayak, P. K., Zhu, X. L., Li, Z. n., Martinez, T. J., Thorwart, M. n., Miller, R. J. 2020; 6 (38)

  Abstract

  Singlet fission is a spin-allowed exciton multiplication process in organic semiconductors that converts one spin-singlet exciton to two triplet excitons. It offers the potential to enhance solar energy conversion by circumventing the Shockley-Queisser limit on efficiency. We study the primary steps of singlet fission in a pentacene film by using a combination of TG and 2D electronic spectroscopy complemented by quantum chemical and nonadiabatic dynamics calculations. We show that the coherent vibrational dynamics induces the ultrafast transition from the singlet excited electronic state to the triplet-pair state via a degeneracy of potential energy surfaces, i.e., a multidimensional conical intersection. Significant vibronic coupling of the electronic wave packet to a few key intermolecular rocking modes in the low-frequency region connect the excited singlet and triplet-pair states. Along with high-frequency local vibrations acting as tuning modes, they open a new channel for the ultrafast exciton transfer through the resulting conical intersection.

  View details for DOI 10.1126/sciadv.abb0052

  View details for PubMedID 32948583

• PySpawn: Software for Nonadiabatic Quantum Molecular Dynamics. Journal of chemical theory and computation Fedorov, D. A., Seritan, S. n., Fales, B. S., Martínez, T. J., Levine, B. G. 2020

  Abstract

  The ab initio multiple spawning (AIMS) method enables nonadiabatic quantum molecular dynamics simulations in an arbitrary number of dimensions, with potential energy surfaces provided by electronic structure calculations performed on-the-fly. However, the intricacy of the AIMS algorithm complicates software development, deployment on modern shared computer resources, and post-simulation data analysis. PySpawn is a nonadiabatic molecular dynamics software package that addresses these issues. The program is designed to be easily interfaced with electronic structure software, and an interface to the TeraChem software package is described here. PySpawn introduces a task-based reorganization of the AIMS algorithm, allowing fine-grained restart capability and setting the stage for efficient parallelization in a future release. PySpawn includes a user-friendly and interactive Python analysis module that will enable novice users to painlessly adopt AIMS. As a demonstration of PySpawn's simulation capability and analysis module, we report complete active space self-consistent field-based AIMS simulations of the 1,2-dithienyl-1,2-dicyanoethene molecule, a promising molecular photoswitch.

  View details for DOI 10.1021/acs.jctc.0c00575

  View details for PubMedID 32687710

• Efficient Treatment of Large Active Spaces through Multi-GPU Parallel Implementation of Direct Configuration Interaction. Journal of chemical theory and computation Fales, B. S., Martínez, T. J. 2020

  Abstract

  We have extended our graphical processing unit (GPU) accelerated direct configuration interaction program to multiple devices, reducing iteration times for configuration spaces of 165 million determinants to only 3 seconds using NVIDIA P100 GPUs. Similar improvements in the one- and two-particle reduced density matrix (RDM) formation allow for fast analytical energy gradients and electronic properties. Our parallel algorithm enables the calculation of arbitrarily large configuration spaces (limited only by available system memory), with iteration times of 13 minutes for an active space of 18 electrons in 18 orbitals (2.4 billion determinants) using six consumer grade NVIDIA 1080Ti GPUs. These advances enable routine molecular dynamics simulations, geometry optimizations, and absorption spectrum calculations for molecules with large configuration spaces, a task which has heretofore required massive computational effort. In this work, we demonstrate the utility of our program by generating the absorption spectrum for diphenyl acetylene (DPA) at the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) level of theory. Several active spaces were investigated to assess the dependence of spectral features on orbital space dimension.

  View details for DOI 10.1021/acs.jctc.9b01165

  View details for PubMedID 31995369

• Putting Photomechanical Switches to Work: An Ab Initio Multiple Spawning Study of Donor-Acceptor Stenhouse Adducts. The journal of physical chemistry letters Sanchez, D. M., Raucci, U. n., Ferreras, K. N., Martínez, T. J. 2020: 7901–7

  Abstract

  Photomechanical switches are light sensitive molecules capable of transducing the energy of a photon into mechanical work via photodynamics. In this Letter, we present the first atomistic investigation of the photodynamics of a novel class of photochromes called donor-acceptor Stenhouse adducts (DASA) using state-of-the-art ab initio multiple spawning interfaced with state-averaged complete active-space self-consistent field theory. Understanding the Z/E photoisomerization mechanism in DASAs at the molecular level is crucial in designing new derivatives with improved photoswitching capabilities. Our dynamics simulations show that the actinic step consists of competing nonradiative relaxation pathways that collectively contribute to DASAs' low (21% in toluene) photoisomerization quantum yield. Furthermore, we highlight the important role the intramolecular hydrogen bond plays in the selectivity of photoisomerization in DASAs, identifying it as a possible structural element to tune DASA properties. Our fully ab initio simulations reveal the key degrees of freedom involved in the actinic step, paving the way for the rational design of new generations of DASAs with improved quantum yield and efficiency.

  View details for DOI 10.1021/acs.jpclett.0c02401

  View details for PubMedID 32864975

• Electronic structure software. The Journal of chemical physics Sherrill, C. D., Manolopoulos, D. E., Martínez, T. J., Michaelides, A. n. 2020; 153 (7): 070401

  View details for DOI 10.1063/5.0023185

  View details for PubMedID 32828107

• Nonadiabatic Dynamics of Photoexcited cis-Stilbene Using Ab Initio Multiple Spawning. The journal of physical chemistry. B Weir, H. n., Williams, M. n., Parrish, R. M., Hohenstein, E. G., Martínez, T. J. 2020

  Abstract

  The photochemistry of cis-stilbene proceeds through two pathways: cis-trans isomerization and ring closure to 4a,4b-dihydrophenanthrene (DHP). Despite serving for many decades as a model system for photoisomerization, the photodynamics of cis-stilbene is still not fully understood. We use ab initio multiple spawning on a SA-2-CASSCF(2,2) potential energy surface to simulate the nonadiabatic dynamics of isolated cis-stilbene. We find the cyclization (to DHP and cis-stilbene) and isomerization (to trans- and cis-stilbene) reaction coordinates to be orthogonal; branching between the two pathways is determined on the S1 excited state within 150 fs of photoexcitation. Trajectory basis functions (TBFs) undergoing cyclization decay rapidly to the ground state in 250 fs, while TBFs moving along the isomerization coordinate remain on the excited state longer, with the majority decaying between 300 and 500 fs. We observe three avoided crossing regions in the dynamics: two along the isomerization coordinate (displaying pyramidalization and migration of an ethylenic hydrogen or phenyl group), and one DHP-like conical intersection along the cyclization coordinate. The isomeric form of the vibrationally hot photoproducts (as determined by measurement 2 ps after photoexcitation) is determined within less than 50 fs of decay to the ground state mediated by passage through a conical intersection. Excess vibrational energy of ground state cis- and trans-stilbene is channelled into phenyl torsions (with mostly opposing directionality). Our simulations are validated by direct comparison to experiment for the absorption spectrum, branching ratio of the three photoproducts (44:52:4 cis-stilbene:trans-stilbene:DHP), and excited state lifetime (520 ± 40 fs).

  View details for DOI 10.1021/acs.jpcb.0c03344

  View details for PubMedID 32428407

• First-Principles Characterization of the Elusive I Fluorescent State and the Structural Evolution of Retinal Protonated Schiff Base in Bacteriorhodopsin. Journal of the American Chemical Society Yu, J. K., Liang, R., Liu, F., Martinez, T. J. 2019

  Abstract

  The conversion of light energy into work is essential to life on earth. Bacteriorhodopsin (bR), a light-activated proton pump in Archae, has served for many years as a model system for the study of this process in photoactive proteins. Upon absorption of a photon, its chromophore, the retinal protonated Schiff base (RPSB), isomerizes from its native all-trans form to a 13-cis form and pumps a proton out of the cell in a process that is coupled to eventual ATP synthesis. Despite numerous time-resolved spectroscopic studies over the years, the details of the photodynamics of bR on the excited state, particularly the characterization of the I fluorescent state, the time-resolved reaction mechanism, and the role of the counterion cluster of RPSB, remain uncertain. Here, we use ab initio multiple spawning (AIMS) with spin-restricted ensemble Kohn-Sham (REKS) theory to simulate the nonadiabatic dynamics of the ultrafast photoreaction in bR. The excited state dynamics can be partitioned into three distinct phases: (1) relaxation away from the Franck-Condon region dominated by changes in retinal bond length alternation, (2) dwell time on the excited state in the I fluorescent state featuring an untwisted, bond length inverted RPSB, and (3) rapid torsional evolution to the conical intersection after overcoming a small excited state barrier. We fully characterize the I fluorescent state and the excited state barrier that hinders direct evolution to the conical intersection following photoexcitation. We also find that photoisomerization is accompanied by weakening of the interaction between RPSB and its counterion cluster. However, in contradiction with a recent time-resolved X-ray experiment, hydrogen bond cleavage is not necessary to reproduce the observed photoisomerization dynamics.

  View details for DOI 10.1021/jacs.9b08941

  View details for PubMedID 31621314

• Rank reduced coupled cluster theory. II. Equation-of-motion coupled-cluster singles and doubles. The Journal of chemical physics Hohenstein, E. G., Zhao, Y., Parrish, R. M., Martinez, T. J. 2019; 151 (16): 164121

  Abstract

  Equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) is a reliable and popular approach to the determination of electronic excitation energies. Recently, we have developed a rank-reduced CCSD (RR-CCSD) method that allows the ground-state coupled-cluster energy to be determined with low-rank cluster amplitudes. Here, we extend this approach to excited-state energies through a RR-EOM-CCSD method. We start from the EOM-CCSD energy functional and insert low-rank approximations to the doubles amplitudes. The result is an approximate EOM-CCSD method with only a quadratic number (in the molecular size) of free parameters in the wavefunction. Importantly, our formulation of RR-EOM-CCSD preserves the size intensivity of the excitation energy and size extensivity of the total energy. Numerical tests of the method suggest that accuracy on the order of 0.05-0.01 eV in the excitation energy is possible with 1% or less of the original number of wavefunction coefficients; accuracy of better than 0.01 eV can be achieved with about 4% or less of the free parameters. The amount of compression at a given accuracy level is expected to increase with the size of the molecule. The RR-EOM-CCSD method is a new path toward the efficient determination of accurate electronic excitation energies.

  View details for DOI 10.1063/1.5121867

  View details for PubMedID 31675873

• Computational Discovery of the Origins of Life. ACS central science Meisner, J., Zhu, X., Martinez, T. J. 2019; 5 (9): 1493–95

  View details for DOI 10.1021/acscentsci.9b00832

  View details for PubMedID 31572775

• Reaction Dynamics of Cyanohydrins with Hydrosulfide in Water. The journal of physical chemistry. A Valleau, S., Martinez, T. J. 2019

  Abstract

  We studied the reaction dynamics of a proposed prebiotic reaction theoretically. The chemical process involves acetone cyanohydrin or formalcyanohydrin reacting with hydrosulfide in an aqueous environment. Rate constants and populations of reactant and product bimolecular geometric orientations for the reactions were obtained by using density functional theory for the energies, transition-state theory for the rates, and matrix exponentiation as well as the hybrid tau-leaping algorithm for the population dynamics. The role of including the solvent explicitly versus implicitly was also investigated. We found that adding explicit water or hydrogen sulfide molecules lowers the activation energy barrier and leads to a more efficient reaction pathway. In particular, hydrogen sulfide was a better proton donor. Finally, we studied the role of including more than one reactant and product bimolecular orientation geometry in the dynamics. Including all initial pathways, reactant to reactant, product to product, reactant to product, and product to reactant led to a larger reaction rate constant compared to the single minimum energy pathway approach. Overall, we found that most reactions which involve formalcyanohydrin occur more rapidly or at the same speed as reactions which involve acetone cyanohydrin at room temperature.

  View details for DOI 10.1021/acs.jpca.9b05735

  View details for PubMedID 31348667

• Diffractive imaging of dissociation and ground-state dynamics in a complex molecule PHYSICAL REVIEW A Wilkin, K. J., Parrish, R. M., Yang, J., Wolf, T. A., Nunes, J. F., Guehr, M., Li, R., Shen, X., Zheng, Q., Wang, X., Martinez, T. J., Centurion, M. 2019; 100 (2)

  View details for DOI 10.1103/PhysRevA.100.023402

  View details for Web of Science ID 000478952200002

• Disentangling conical intersection and coherent molecular dynamics in methyl bromide with attosecond transient absorption spectroscopy. Nature communications Timmers, H., Zhu, X., Li, Z., Kobayashi, Y., Sabbar, M., Hollstein, M., Reduzzi, M., Martinez, T. J., Neumark, D. M., Leone, S. R. 2019; 10 (1): 3133

  Abstract

  Attosecond probing of core-level electronic transitions provides a sensitive tool for studying valence molecular dynamics with atomic, state, and charge specificity. In this report, we employ attosecond transient absorption spectroscopy to follow the valence dynamics of strong-field initiated processes in methyl bromide. By probing the 3d core-to-valence transition, we resolve the strong field excitation and ensuing fragmentation of the neutralsigma* excited states of methyl bromide. The results provide a clear signature of the non-adiabatic passage of the excited state wavepacket through a conical intersection. We additionally observe competing, strong field initiated processes arising in both the ground state and ionized molecule corresponding to vibrational and spin-orbit motion, respectively. The demonstrated ability to resolve simultaneous dynamics with few-femtosecond resolution presents a clear path forward in the implementation of attosecond XUV spectroscopy as a general tool for probing competing and complex molecular phenomena with unmatched temporal resolution.

  View details for DOI 10.1038/s41467-019-10789-7

  View details for PubMedID 31311933

• Quantum Computation of Electronic Transitions Using a Variational Quantum Eigensolver. Physical review letters Parrish, R. M., Hohenstein, E. G., McMahon, P. L., Martínez, T. J. 2019; 122 (23): 230401

  Abstract

  We develop an extension of the variational quantum eigensolver (VQE) algorithm-multistate contracted VQE (MC-VQE)-that allows for the efficient computation of the transition energies between the ground state and several low-lying excited states of a molecule, as well as the oscillator strengths associated with these transitions. We numerically simulate MC-VQE by computing the absorption spectrum of an ab initio exciton model of an 18-chromophore light-harvesting complex from purple photosynthetic bacteria.

  View details for DOI 10.1103/PhysRevLett.122.230401

  View details for PubMedID 31298869

• Quantum Computation of Electronic Transitions Using a Variational Quantum Eigensolver PHYSICAL REVIEW LETTERS Parrish, R. M., Hohenstein, E. G., McMahon, P. L., Martinez, T. J. 2019; 122 (23)

  View details for DOI 10.1103/PhysRevLett.122.230401

  View details for Web of Science ID 000471988500002

• Nonadiabatic Photodynamics of Retinal Protonated Schiff Base in Channelrhodopsin 2 JOURNAL OF PHYSICAL CHEMISTRY LETTERS Liang, R., Liu, F., Martinez, T. J. 2019; 10 (11): 2862–68

  View details for DOI 10.1021/acs.jpclett.9b00701

  View details for Web of Science ID 000471079400033

• On combining the conductor-like screening model and optimally tuned range-separated hybrid density functionals. The Journal of chemical physics Sachse, T., Martinez, T. J., Presselt, M. 2019; 150 (17): 174117

  Abstract

  Range-separated hybrid functionals whose range-separation parameter gamma has been nonempirically tuned to a particular molecule have been shown to yield frontier orbital energies and other properties in very good agreement with experiments. However, many cases, such as organic optoelectronic devices, require the description of molecules embedded in an environment. This can be done by combining the gamma-tuning procedure with polarizable continuum models in general and the very versatile conductor-like screening model in particular. There are at least two different ways of performing this combination. The partially vertical gamma-tuning employs equilibrium solvation throughout. The strictly vertical gamma-tuning, on the other hand, employs nonequilibrium solvation to obtain ionization energies. In this article, we compare ground-state and excited-state properties of several different molecules relevant to organic optoelectronics that were obtained using both of the two different tuning procedures. While there are significant differences in the ground-state properties, we see virtually no difference in the excited-state properties. Given these results, we conclude that both tuning procedures have to be used in conjunction for the correct description of both ground-state and excited-state properties.

  View details for PubMedID 31067895

• Ab initio Computation of Rotationally-Averaged Pump-Probe X-ray and Electron Diffraction Signals JOURNAL OF CHEMICAL THEORY AND COMPUTATION Parrish, R. M., Martinez, T. J. 2019; 15 (3): 1523-1537

  View details for DOI 10.1021/acs.jctc.8b01051

  View details for Web of Science ID 000461533000006

• Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses JOURNAL OF PHYSICAL CHEMISTRY LETTERS Mignolet, B., Curchod, B. E., Remacle, F., Martinez, T. J. 2019; 10 (4): 742-747

  View details for DOI 10.1021/acs.jpclett.8b03814

  View details for Web of Science ID 000459948800007

• Ab Initio Computation of Rotationally-Averaged Pump-Probe X-ray and Electron Diffraction Signals. Journal of chemical theory and computation Parrish, R. M., Martinez, T. J. 2019

  Abstract

  We develop a new algorithm for the computation of the rotationally averaged elastic molecular diffraction signal for the cases of perpendicular or parallel pump-probe geometries. The algorithm first collocates the charge density from an arbitrary ab initio wave function onto a Becke quadrature grid [A. Becke, J. Chem. Phys. 1988 , 88 , 2457 ], providing a high-fidelity multiresolution representation of the charge density. A double sum is then performed over the Becke grid points, and the interaction between points computed using the scattering kernels of Williamson and Zewail [J. C. Williamson and A. H. Zewail, J. Phys. Chem. 1994 , 98 , 2766 ]. These kernels analytically average over the molecular orientations with the cos2 gamma selection factor appropriate for one-photon dipole absorption in a perpendicular pump-probe geometry. We show that the method is converged with small grids containing <500 points/atom. We implement the algorithm on a GPU for increased efficiency and emonstrate the algorithm for molecules with up to a few dozen atoms. We explore the accuracy of the independent atom model (IAM) by comparison with our new and more accurate method. We also investigate the possibility of detecting signatures of electronic transitions in polyatomic pump-probe diffraction experiments.

  View details for PubMedID 30702882

• Multicolor Mechanochromism of a Polymer/Silica Composite with Dual Distinct Mechanophores JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kosuge, T., Zhu, X., Lau, V. M., Aoki, D., Martinez, T. J., Moore, J. S., Otsuka, H. 2019; 141 (5): 1898-1902

  View details for DOI 10.1021/jacs.8b13310

  View details for Web of Science ID 000458348300018

• Sub-Femtosecond Stark Control of Molecular Photoexcitation with Near Single-Cycle Pulses. The journal of physical chemistry letters Mignolet, B., Curchod, B. F., Remacle, F., Martinez, T. J. 2019: 742–47

  Abstract

  Electric fields can tailor molecular potential energy surfaces by interaction with the electronic state-dependent molecular dipole moment. Recent developments in optics have enabled the creation of ultrashort few-cycle optical pulses with precise control of the carrier envelope phase (CEP) that determines the offset of the maxima in the field and the pulse envelope. This opens news ways of controlling ultrafast molecular dynamics by exploiting the CEP. In this work, we show that the photoabsorption efficiency of oriented H2CSO (sulfine) can be controlled by tuning the CEP. We further show that this control emanates from a resonance condition related to Stark shifting of the electronic energy levels.

  View details for PubMedID 30695646

• Multicolor Mechanochromism of a Polymer/Silica Composite with Dual Distinct Mechanophores. Journal of the American Chemical Society Kosuge, T., Zhu, X., Lau, V. M., Aoki, D., Martinez, T. J., Moore, J. S., Otsuka, H. 2019

  Abstract

  The development of a multicolor mechanochromic polymer/silica composite is achieved by using two distinct types of mechanochromophores. The multicolor mechanochromism of the composite containing diarylbibenzofuranone in silica-rich domains and naphthopyran in the polymer-rich domain is observed. The obtained composite shows blue, green, and orange colors according to the intensity of applied mechanical stimuli, solvent addition, and lapse of time. This unique multicolor mechanochromic behavior is evaluated by solid-state UV-vis absorption spectroscopy, ab initio steered molecular dynamics simulations, and computed minimum energy paths on force-modified potential energy surfaces. The unique mechanochromism is attributed to the difference in properties, activated colors, and domain locations between the two mechanochromophores.

  View details for PubMedID 30676738

• Exploiting graphical processing units to enable quantum chemistry calculation of large solvated molecules with conductor-like polarizable continuum models Liu, F., Sanchez, D. M., Kulik, H. J., Martinez, T. J. WILEY. 2019

  View details for DOI 10.1002/qua.25760

  View details for Web of Science ID 000451038100006

• Geodesic interpolation for reaction pathways. The Journal of chemical physics Zhu, X. n., Thompson, K. C., Martínez, T. J. 2019; 150 (16): 164103

  Abstract

  The development of high throughput reaction discovery methods such as the ab initio nanoreactor demands massive numbers of reaction rate calculations through the optimization of minimum energy reaction paths. These are often generated from interpolations between the reactant and product endpoint geometries. Unfortunately, straightforward interpolation in Cartesian coordinates often leads to poor approximations that lead to slow convergence. In this work, we reformulate the problem of interpolation between endpoint geometries as a search for the geodesic curve on a Riemannian manifold. We show that the perceived performance difference of interpolation methods in different coordinates is the result of an implicit metric change. Accounting for the metric explicitly allows us to obtain good results in Cartesian coordinates, bypassing the difficulties caused by redundant coordinates. Using only geometric information, we are able to generate paths from reactants to products which are remarkably close to the true minimum energy path. We show that these geodesic paths are excellent starting guesses for minimum energy path algorithms.

  View details for PubMedID 31042909

• Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy. The journal of physical chemistry. A Erickson, B. A., Heim, Z. N., Pieri, E. n., Liu, E. n., Martinez, T. J., Neumark, D. M. 2019

  Abstract

  The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.

  View details for DOI 10.1021/acs.jpca.9b08258

  View details for PubMedID 31756106

• Imaging the ring opening reaction of 1,3-cyclohexadiene with MeV ultrafast electron diffraction Wolf, T. A., Yang, J., Sanchez, D. M., Nunes, J. F., Parrish, R. M., Shen, X., Centurion, M., Coffee, R., Gyan, J. P., Guhr, M., Kareem, H., Kirrander, A., Li, R., Ruddock, J., Veccione, T., Weathersby, S. P., Weber, P. M., Wilkin, K., Yong, H., Zheng, Q., Martinez, T. J., Wang, X., Minitti, M. P., Cerullo, G., Ogilvie, J., Kartner, F., Khalil, M., Li, R. E D P SCIENCES. 2019

  View details for DOI 10.1051/epjconf/201920507006

  View details for Web of Science ID 000570451400143

• Nonadiabatic Photodynamics of Retinal Protonated Schiff Base in Channelrhodopsin 2. The journal of physical chemistry letters Liang, R. n., Liu, F. n., Martínez, T. J. 2019: 2862–68

  Abstract

  Channelrhodopsin 2 (ChR2) is a light-gated ion channel and an important tool in optogenetics. Photoisomerization of retinal protonated Schiff base (RPSB) in ChR2 triggers channel activation. Despite the importance of ChR2 in optogenetics, the detailed mechanism for photoisomerization and channel activation is still not fully understood. Here, we report on computer simulations to investigate the photoisomerization mechanism and its effect on the activation of ChR2. Nonadiabatic dynamics simulation of ChR2 was carried out using the ab initio multiple spawning (AIMS) method and quantum mechanics/molecular mechanics (QM/MM) with a restricted ensemble Kohn-Sham (REKS) treatment of the QM region. Our results agree well with spectroscopic measurements and reveal that the RPSB isomerization is highly specific around the C13=C14 bond and follows the "aborted bicycle-pedal" mechanism. In addition, RPSB photoisomerization facilitates its deprotonation and partially increases the hydration level in the channel, which could trigger subsequent channel opening and ion conduction.

  View details for PubMedID 31083920

• Observation of Ultrafast Intersystem Crossing in Thymine by Extreme Ultraviolet Time-Resolved Photoelectron Spectroscopy. The journal of physical chemistry. A Wolf, T. J., Parrish, R. M., Myhre, R. H., Martínez, T. J., Koch, H. n., Gühr, M. n. 2019

  Abstract

  We studied the photoinduced ultrafast relaxation dynamics of the nucleobase thymine using gas-phase time-resolved photoelectron spectroscopy. By employing extreme ultraviolet pulses from high harmonic generation for photoionization, we substantially extend our spectral observation window with respect to previous studies. This enables us to follow relaxation of the excited state population all the way to low-lying electronic states including the ground state. In thymine, we observe relaxation from the optically bright 1ππ* state of thymine to a dark 1nπ* state within 80 ± 30 fs. The 1nπ* state relaxes further within 3.5 ± 0.3 ps to a low-lying electronic state. By comparison with quantum chemical simulations, we can unambiguously assign its spectroscopic signature to the 3ππ* state. Hence, our study draws a comprehensive picture of the relaxation mechanism of thymine including ultrafast intersystem crossing to the triplet manifold.

  View details for DOI 10.1021/acs.jpca.9b05573

  View details for PubMedID 31319031

• Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation. The journal of physical chemistry. B Thomson, B. n., Both, J. n., Wu, Y. n., Parrish, R. M., Martínez, T. J., Boxer, S. G. 2019

  Abstract

  Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.

  View details for DOI 10.1021/acs.jpcb.9b01571

  View details for PubMedID 31117606

• Rank reduced coupled cluster theory. I. Ground state energies and wavefunctions. The Journal of chemical physics Parrish, R. M., Zhao, Y. n., Hohenstein, E. G., Martínez, T. J. 2019; 150 (16): 164118

  Abstract

  We propose a compression of the opposite-spin coupled cluster doubles amplitudes of the form τijab≡UiaVTVWUjbW, where UiaV are the nV-highest magnitude eigenvectors of the MP2 or MP3 doubles amplitudes. Together with a corresponding parameterization of the opposite-spin coupled cluster Lagrange multipliers of the form λabij≡UiaVLVWUjbW, this yields a fully self-consistent parameterization of reduced-rank coupled cluster equations in terms of the Lagrangian L0TVW,LVW. Making this Lagrangian stationary with respect to the LVW parameters yields a perfectly determined set of equations for the TVW equations and coupled cluster energy. These equations can be solved using a Lyapunov equation for the first-order amplitude updates. We test this "rank-reduced coupled cluster" method for coupled cluster singles and doubles in medium sized molecules and find that substantial compression of the T^2 amplitudes is possible with acceptable accuracy.

  View details for PubMedID 31042891

• Ab lnitio Prediction of Fluorescence Lifetimes Involving Solvent Environments by Means of COSMO and Vibrational Broadening JOURNAL OF PHYSICAL CHEMISTRY A Preiss, J., Kage, D., Hoffmann, K., Martinez, T. J., Resch-Genger, U., Presselt, M. 2018; 122 (51): 9813–20

  Abstract

  The fluorescence lifetime is a key property of fluorophores that can be utilized for microenvironment probing, analyte sensing, and multiplexing as well as barcoding applications. For the rational design of lifetime probes and barcodes, theoretical methods have been developed to enable the ab initio prediction of this parameter, which depends strongly on interactions with solvent molecules and other chemical species in the emitter´s immediate environment. In this work, we investigate how a conductor-like screening model (COSMO) can account for variations in fluorescence lifetimes that are caused by such fluorophore-solvent interactions. Therefore, we calculate vibrationally broadened fluorescence spectra using the nuclear ensemble method to obtain distorted molecular geometries to sample the electronic transitions with time-dependent density functional theory (TDDFT). The influence of the solvent on fluorescence lifetimes is accounted for with COSMO. For an example 4-hydroxythiazole fluorophore containing different heteroatoms and acidic and basic moieties in aprotic and protic solvents of varying polarity, this approach was compared to experimentally determined lifetimes in the same solvents. Our results demonstrate a good correlation between theoretically predicted and experimentally measured fluorescence lifetimes except for the polar solvents ethanol and acetonitrile that can specifically interact with the heteroatoms and the carboxylic acid of the thiazole derivative.

  View details for PubMedID 30507127

• Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Pinney, M. M., Natarajan, A., Yabukarski, F., Sanchez, D. M., Liu, F., Liang, R., Doukov, T., Schwans, J. P., Martinez, T. J., Herschlag, D. 2018; 140 (31): 9827–43

  Abstract

  Hydrogen bonds are fundamental to biological systems and are regularly found in networks implicated in folding, molecular recognition, catalysis, and allostery. Given their ubiquity, we asked the fundamental questions of whether, and to what extent, hydrogen bonds within networks are structurally coupled. To address these questions, we turned to three protein systems, two variants of ketosteroid isomerase and one of photoactive yellow protein. We perturbed their hydrogen bond networks via a combination of site-directed mutagenesis and unnatural amino acid substitution, and we used 1H NMR and high-resolution X-ray crystallography to determine the effects of these perturbations on the lengths of the two oxyanion hole hydrogen bonds that are donated to negatively charged transition state analogs. Perturbations that lengthened or shortened one of the oxyanion hole hydrogen bonds had the opposite effect on the other. The oxyanion hole hydrogen bonds were also affected by distal hydrogen bonds in the network, with smaller perturbations for more remote hydrogen bonds. Across 19 measurements in three systems, the length change in one oxyanion hole hydrogen bond was propagated to the other, by a factor of -0.30 ± 0.03. This common effect suggests that hydrogen bond coupling is minimally influenced by the remaining protein scaffold. The observed coupling is reproduced by molecular mechanics and quantum mechanics/molecular mechanics (QM/MM) calculations for changes to a proximal oxyanion hole hydrogen bond. However, effects from distal hydrogen bonds are reproduced only by QM/MM, suggesting the importance of polarization in hydrogen bond coupling. These results deepen our understanding of hydrogen bonds and their networks, providing strong evidence for long-range coupling and for the extent of this coupling. We provide a broadly predictive quantitative relationship that can be applied to and can be further tested in new systems.

  View details for DOI 10.1021/jacs.8b01596

  View details for Web of Science ID 000441475800011

  View details for PubMedID 29990421

• Reduced scaling CASPT2 using supporting subspaces and tensor hyper-contraction. The Journal of chemical physics Song, C., Martinez, T. J. 2018; 149 (4): 044108

  Abstract

  We present a reduced scaling formulation of the state specific complete active space second-order perturbation method (CASPT2) requiring O(N4) operations and O(N2) memory for a fixed active space, where N is proportional to system size. Motivated by the properties of the Kronecker sum, we introduce the supporting subspace technique (SST), which decomposes the CASPT2 linear equations into two parts: a single-reference MP2 energy term using dressed orbitals, plus a reduced linear system with dimension scaling as O(N2). Together with Laplace quadrature, the SST allows us to reformulate CASPT2 using a MP2 energy computation and Fock builds. By further applying the tensor hyper-contraction (THC) approximation, the MP2-like term can be computed with O(N4) operations, and the remainder can be solved with O(N3) operations using the preconditioned conjugate gradient method. This is the first application of THC in the context of multi-reference methods. We also developed an efficient implementation of the method by utilizing graphical processing units and exploiting spatial sparsity in tensor operations. We benchmark the accuracy of the new method against conventional CASPT2 for reactions in the gas phase. We apply the new method to Menshutkin SN2 reactions in carbon nanotubes, demonstrating the feasibility of CASPT2 calculations with O(100) atoms.

  View details for PubMedID 30068209

• Reduced scaling CASPT2 using supporting subspaces and tensor hyper-contraction JOURNAL OF CHEMICAL PHYSICS Song, C., Martinez, T. J. 2018; 149 (4)

  View details for DOI 10.1063/1.5037283

  View details for Web of Science ID 000440586200012

• Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction. Science (New York, N.Y.) Yang, J., Zhu, X., Wolf, T. J., Li, Z., Nunes, J. P., Coffee, R., Cryan, J. P., Gühr, M., Hegazy, K., Heinz, T. F., Jobe, K., Li, R., Shen, X., Veccione, T., Weathersby, S., Wilkin, K. J., Yoneda, C., Zheng, Q., Martinez, T. J., Centurion, M., Wang, X. 2018; 361 (6397): 64-67

  Abstract

  Conical intersections play a critical role in excited-state dynamics of polyatomic molecules because they govern the reaction pathways of many nonadiabatic processes. However, ultrafast probes have lacked sufficient spatial resolution to image wave-packet trajectories through these intersections directly. Here, we present the simultaneous experimental characterization of one-photon and two-photon excitation channels in isolated CF3I molecules using ultrafast gas-phase electron diffraction. In the two-photon channel, we have mapped out the real-space trajectories of a coherent nuclear wave packet, which bifurcates onto two potential energy surfaces when passing through a conical intersection. In the one-photon channel, we have resolved excitation of both the umbrella and the breathing vibrational modes in the CF3 fragment in multiple nuclear dimensions. These findings benchmark and validate ab initio nonadiabatic dynamics calculations.

  View details for DOI 10.1126/science.aat0049

  View details for PubMedID 29976821

• A Program for Automatically Predicting Supramolecular Aggregates and Its Application to Urea and Porphin JOURNAL OF COMPUTATIONAL CHEMISTRY Sachse, T., Martinez, T. J., Dietzek, B., Presselt, M. 2018; 39 (13): 763–72

  Abstract

  Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open-source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom-up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected. We crossvalidate this approach by predicting both literature-known and heretofore unreported geometries of the urea dimer. We also predict a diverse set of dimers of the less intensely studied case of porphin, which we investigate further using quantum chemistry. For several dimers, we find strong deviations from a reference absorption spectrum, which we explain using computed transition densities. This proof of principle clearly shows that EnergyScan successfully predicts aggregates exhibiting large structural and spectral diversity. © 2018 Wiley Periodicals, Inc.

  View details for PubMedID 29297589

• Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations JOURNAL OF CHEMICAL PHYSICS Glover, W. J., Mori, T., Schuurman, M. S., Boguslavskiy, A. E., Schalk, O., Stolow, A., Martinez, T. J. 2018; 148 (16): 164303

  Abstract

  The excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene (BD), has long been the subject of controversy due to its strong coupling, ultrafast time scales and the difficulties that theory faces in describing the relevant electronic states in a balanced fashion. Here we apply Ab Initio Multiple Spawning (AIMS) using state-averaged complete active space multistate second order perturbation theory [SA-3-CAS(4/4)-MSPT2] which describes both static and dynamic electron correlation effects, providing a balanced description of both the initially prepared bright 11Bu (ππ*) state and non-adiabatically coupled dark 21Ag state of BD. Importantly, AIMS allows for on-the-fly calculations of experimental observables. We validate our approach by directly simulating the time resolved photoelectron-photoion coincidence spectroscopy results presented in Paper I [A. E. Boguslavskiy et al., J. Chem. Phys. 148, 164302 (2018)], demonstrating excellent agreement with experiment. Our simulations reveal that the initial excitation to the 11Bu state rapidly evolves via wavepacket dynamics that follow both bright- and dark-state pathways as well as mixtures of these. In order to test the sensitivity of the AIMS results to the relative ordering of states, we considered two hypothetical scenarios biased toward either the bright 1Bu or the dark 21Ag state. In contrast with AIMS/SA-3-CAS(4/4)-MSPT2 simulations, neither of these scenarios yields favorable agreement with experiment. Thus, we conclude that the excited state non-adiabatic dynamics in BD involves both of these ultrafast pathways.

  View details for PubMedID 29716209

• Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy JOURNAL OF CHEMICAL PHYSICS Boguslavskiy, A. E., Schalk, O., Gador, N., Glover, W. J., Mori, T., Schultz, T., Schuurman, M. S., Martinez, T. J., Stolow, A. 2018; 148 (16): 164302

  Abstract

  The ultrafast excited state dynamics of the smallest polyene, trans-1,3-butadiene, were studied by femtosecond time-resolved photoelectron-photoion coincidence (TRPEPICO) spectroscopy. The evolution of the excited state wavepacket, created by pumping the bright 1Bu (ππ*) electronic state at its origin of 216 nm, is projected via one- and two-photon ionization at 267 nm onto several ionization continua. The results are interpreted in terms of Koopmans' correlations and Franck-Condon factors for the excited and cationic states involved. The known predissociative character of the cation excited states is utilized to assign photoelectron bands to specific continua using TRPEPICO spectroscopy. This permits us to report the direct observation of the famously elusive S1(21Ag) dark electronic state during the internal conversion of trans 1,3-butadiene. Our phenomenological analysis permits the spectroscopic determination of several important time constants. We report the overall decay lifetimes of the 11Bu and 21Ag states and observe the re-appearance of the hot ground state molecule. We argue that the apparent dephasing time of the S2(11Bu) state, which leads to the extreme breadth of the absorption spectrum, is principally due to large amplitude torsional motion on the 1Bu surface in conjunction with strong non-adiabatic couplings via conical intersections, whereupon nuclear wavepacket revivals to the initial Franck-Condon region become effectively impossible. In Paper II [W. J. Glover et al., J. Chem. Phys. 148, 164303 (2018)], ab initio multiple spawning is used for on-the-fly computations of the excited state non-adiabatic wavepacket dynamics and their associated TRPEPICO observables, allowing for direct comparisons of experiment with theory.

  View details for PubMedID 29716221

• Ab Initio Nonadiabatic Quantum Molecular Dynamics CHEMICAL REVIEWS Curchod, B. E., Martinez, T. J. 2018; 118 (7): 3305–36

  Abstract

  The Born-Oppenheimer approximation underlies much of chemical simulation and provides the framework defining the potential energy surfaces that are used for much of our pictorial understanding of chemical phenomena. However, this approximation breaks down when the dynamics of molecules in excited electronic states are considered. Describing dynamics when the Born-Oppenheimer approximation breaks down requires a quantum mechanical description of the nuclei. Chemical reaction dynamics on excited electronic states is critical for many applications in renewable energy, chemical synthesis, and bioimaging. Furthermore, it is necessary in order to connect with many ultrafast pump-probe spectroscopic experiments. In this review, we provide an overview of methods that can describe nonadiabatic dynamics, with emphasis on those that are able to simultaneously address the quantum mechanics of both electrons and nuclei. Such ab initio quantum molecular dynamics methods solve the electronic Schrödinger equation alongside the nuclear dynamics and thereby avoid the need for precalculation of potential energy surfaces and nonadiabatic coupling matrix elements. Two main families of methods are commonly employed to simulate nonadiabatic dynamics in molecules: full quantum dynamics, such as the multiconfigurational time-dependent Hartree method, and classical trajectory-based approaches, such as trajectory surface hopping. In this review, we describe a third class of methods that is intermediate between the two: Gaussian basis set expansions built around trajectories.

  View details for PubMedID 29465231

• Mixed quantum-classical electrodynamics: Understanding spontaneous decay and zero-point energy PHYSICAL REVIEW A Li, T. E., Nitzan, A., Sukharev, M., Martinez, T., Chen, H., Subotnik, J. E. 2018; 97 (3)

  View details for DOI 10.1103/PhysRevA.97.032105

  View details for Web of Science ID 000427110600003

• Large-Scale Functional Group Symmetry-Adapted Perturbation Theory on Graphical Processing Units JOURNAL OF CHEMICAL THEORY AND COMPUTATION Parrish, R. M., Thompson, K. C., Martinez, T. J. 2018; 14 (3): 1737–53

  Abstract

  Symmetry-adapted perturbation theory (SAPT) is a valuable method for analyzing intermolecular interactions. The functional group SAPT partition (F-SAPT) has been introduced to provide additional insight into the origins of noncovalent interactions. Until now, SAPT analysis has been too costly for large ligand-protein complexes where it could provide key insights for chemical modifications that might improve ligand binding. In this paper, we present a large-scale implementation of a variant of F-SAPT. Two pragmatic choices are made from the outset to render the problem tractable: (1) Ab initio computation of dispersion and exchange-dispersion is replaced with Grimme's empirical dispersion correction. (2) Basis sets with augmented functions are avoided to allow for efficient integral screening. These choices allow the F-SAPT analysis to be written largely in terms of Coulomb and exchange matrix builds which have been implemented efficiently on graphical processing units (GPUs). Our formulation of F-SAPT is routinely applicable to molecules with well over 3000 atoms and 25,000 basis functions and is particularly optimized for the case where one monomer is significantly larger than the other. This is demonstrated explicitly with results from F-SAPT analysis of the full indinavir @ HIV-II protease complex (PDB ID 1HSG ) in a polarized double-ζ basis.

  View details for PubMedID 29345933

• Rational Protein Design via Structure-Energetics-Function Relationships in the Photoactive Yellow Protein (PYP) Model System Both, J. H., Parrish, R. M., Martinez, T. J., Boxer, S. G. CELL PRESS. 2018: 410A

  View details for Web of Science ID 000430450000539

• Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method JOURNAL OF CHEMICAL THEORY AND COMPUTATION Hollas, D., Sistik, L., Hohenstein, E. G., Martinez, T. J., Slavicek, P. 2018; 14 (1): 339–50

  Abstract

  We show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest that the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.

  View details for PubMedID 29207238

• Large Scale Electron Correlation Calculations: Rank-Reduced Full Configuration Interaction. Journal of chemical theory and computation Fales, B. S., Seritan, S. n., Settje, N. F., Levine, B. G., Koch, H. n., Martínez, T. J. 2018

  Abstract

  We present the rank-reduced full configuration interaction (RR-FCI) method, a variational approach for the calculation of extremely large full configuration interaction (FCI) wavefunctions. In this report we show that RR-FCI can provide ground state singlet and triplet energies within kcal/mol accuracy of full CI (FCI) with computational effort scaling as the square root of the number of determinants in the CI space (compared to conventional FCI methods which scale linearly with the number of determinants). Fast graphical processing unit (GPU) accelerated projected σ=Hc matrix-vector product formation enables calculations with configuration spaces as large as 30 electrons in 30 orbitals, corresponding to an FCI calculation with over 2.4x1016 configurations. We apply this method in the context of complete active space configuration interaction calculations to acenes with 2-5 aromatic rings, comparing absolute energies against FCI when possible and singlet/triplet excitation energies against both density matrix renormalization group (DMRG) and experimental results. The dissociation of molecular nitrogen was also examined using both FCI and RR-FCI. In each case we found that RR-FCI provides a low cost alternative to FCI, with particular advantages when relative energies are desired.

  View details for PubMedID 29889519

• Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction Science Yang, J., Zhu, X., Wolf, T. J., Li, Z., Nunes, J. F., Coffee, R., Cryan, J. P., Gühr, M., Hegazy, K., Heinz, T. F., Jobe, K., Li, R., Shen, X., Veccione, T., Weathersby, S., Wilkin, K. J., Yoneda, C., Zheng, Q., Martinez, T. J., Centurion, M., Wang, X. 2018; 361 (6397): 64-67

  View details for DOI 10.1126/science.aat0049

• The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein JOURNAL OF CHEMICAL THEORY AND COMPUTATION Nabo, L. J., Olsen, J., Martinez, T. J., Kongsted, J. 2017; 13 (12): 6230–36

  Abstract

  The calculation of spectral properties for photoactive proteins is challenging because of the large cost of electronic structure calculations on large systems. Mixed quantum mechanical (QM) and molecular mechanical (MM) methods are typically employed to make such calculations computationally tractable. This study addresses the connection between the minimal QM region size and the method used to model the MM region in the calculation of absorption properties-here exemplified for calculations on the green fluorescent protein. We find that polarizable embedding is necessary for a qualitatively correct description of the MM region, and that this enables the use of much smaller QM regions compared to fixed charge electrostatic embedding. Furthermore, absorption intensities converge very slowly with system size and inclusion of effective external field effects in the MM region through polarizabilities is therefore very important. Thus, this embedding scheme enables accurate prediction of intensities for systems that are too large to be treated fully quantum mechanically.

  View details for PubMedID 29099597

• Pomeranz-Fritsch Synthesis of Isoquinoline: Gas-Phase Collisional Activation Opens Additional Reaction Pathways JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Banerjee, S., Liu, F., Sanchez, D. M., Martinez, T. J., Zare, R. N. 2017; 139 (41): 14352–55

  Abstract

  We have investigated the gas-phase production of isoquinoline by performing collisional activation on benzalaminoacetal, the first intermediate in the classic solution-phase Pomeranz-Fritsch synthesis of isoquinoline. We have elucidated the reaction pathways in the gas phase using tandem mass spectrometry. Unlike the corresponding condensed-phase reaction, where catalytic proton exchange between intermediate(s) and solvent (Brønsted-Lowry base) is known to drive the reaction, the gas-phase reaction follows the "mobile proton model" to form the products via a number of intermediates, some the same as in their condensed-phase counterparts. Energy-resolved mass spectrometry, deuterium labeling experiments, and theoretical calculations (B3LYP/6-31G**) identified 27 different reaction routes in the gas phase, forming a complex interlinked reaction network. The experimental measurements and theoretical calculations confirm the proton hopping onto different basic sites of the precursors and intermediates to transform them ultimately into isoquinoline.

  View details for DOI 10.1021/jacs.7b06813

  View details for Web of Science ID 000413503300006

  View details for PubMedID 28949532

• Ultrafast isomerization in acetylene dication after carbon K-shell ionization NATURE COMMUNICATIONS Li, Z., Inhester, L., Liekhus-Schmaltz, C., Curchod, B. E., Snyder, J. W., Medvedev, N., Cryan, J., Osipov, T., Pabst, S., Vendrell, O., Bucksbaum, P., Martinez, T. J. 2017; 8: 453

  Abstract

  Ultrafast proton migration and isomerization are key processes for acetylene and its ions. However, the mechanism for ultrafast isomerization of acetylene [HCCH]2+ to vinylidene [H2CC]2+ dication remains nebulous. Theoretical studies show a large potential barrier ( > 2 eV) for isomerization on low-lying dicationic states, implying picosecond or longer isomerization timescales. However, a recent experiment at a femtosecond X-ray free-electron laser suggests sub-100 fs isomerization. Here we address this contradiction with a complete theoretical study of the dynamics of acetylene dication produced by Auger decay after X-ray photoionization of the carbon atom K shell. We find no sub-100 fs isomerization, while reproducing the salient features of the time-resolved Coulomb imaging experiment. This work resolves the seeming contradiction between experiment and theory and also calls for careful interpretation of structural information from the widely applied Coulomb momentum imaging method.The timescale of isomerization in molecules involving ultrafast migration of constituent atoms is difficult to measure. Here the authors report that sub-100 fs isomerization time on acetylene dication in lower electronic states is not possible and point to misinterpretation of recent experimental results.

  View details for PubMedID 28878226

• The Spin-Flip Variant of the Algebraic-Diagrammatic Construction Yields the Correct Topology of s(1)/S-0 Conical Intersections JOURNAL OF CHEMICAL THEORY AND COMPUTATION Lefrancois, D., Tuna, D., Martinez, T. J., Dreuw, A. 2017; 13 (9): 4436–41

  Abstract

  While the conventional variants of the algebraic-diagrammatic construction (ADC) scheme for the polarization propagator are generally incapable of correctly describing the topology of S1/S0 conical intersections (CIs), its corresponding spin-flip (SF) variant of third-order ADC (ADC(3)) is herein demonstrated to successfully reproduce the S1/S0 minimum-energy CI (MECI) of twisted formaldinium (H2C═NH2+). Analytical nuclear excited-state gradients of ADC have been used in combination with the CIOpt program for the optimization of the MECI without the need for nonadiabatic-coupling vectors. For comparison, MS-CASPT2 calculations were performed via conventional CI optimization employing analytical nonadiabatic-coupling vectors. It is shown that SF-ADC(3) yields the correct dimensionality of the CI and overall compares very favorably to the MS-CASPT2 results.

  View details for PubMedID 28742963

• Understanding the mechanochemistry of molecular ladders Chen, Z., Chen, L., Mercer, J., Zhu, X., Martinez, T., Burns, N., Xia, Y. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000429556704155

• Mechanochemical unzipping of insulating polyladderene to semiconducting polyacetylene. Science (New York, N.Y.) Chen, Z., Mercer, J. A., Zhu, X., Romaniuk, J. A., Pfattner, R., Cegelski, L., Martinez, T. J., Burns, N. Z., Xia, Y. 2017; 357 (6350): 475-479

  Abstract

  Biological systems sense and respond to mechanical stimuli in a complex manner. In an effort to develop synthetic materials that transduce mechanical force into multifold changes in their intrinsic properties, we report on a mechanochemically responsive nonconjugated polymer that converts to a conjugated polymer via an extensive rearrangement of the macromolecular structure in response to force. Our design is based on the facile mechanochemical unzipping of polyladderene, a polymer inspired by a lipid natural product structure and prepared via direct metathesis polymerization. The resultant polyacetylene block copolymers exhibit long conjugation length and uniform trans-configuration and self-assemble into semiconducting nanowires. Calculations support a tandem unzipping mechanism of the ladderene units.

  View details for DOI 10.1126/science.aan2797

  View details for PubMedID 28774923

• An Ab Initio Exciton Model Including Charge-Transfer Excited States JOURNAL OF CHEMICAL THEORY AND COMPUTATION Li, X., Parrish, R. M., Liu, F., Schumacher, S., Martinez, T. J. 2017; 13 (8): 3493–3504

  Abstract

  The Frenkel exciton model is a useful tool for theoretical studies of multichromophore systems. We recently showed that the exciton model could be used to coarse-grain electronic structure in multichromophoric systems, focusing on singly excited exciton states [ Acc. Chem. Res. 2014 , 47 , 2857 - 2866 ]. However, our previous implementation excluded charge-transfer excited states, which can play an important role in light-harvesting systems and near-infrared optoelectronic materials. Recent studies have also emphasized the significance of charge-transfer in singlet fission, which mediates the coupling between the locally excited states and the multiexcitonic states. In this work, we report on an ab initio exciton model that incorporates charge-transfer excited states and demonstrate that the model provides correct charge-transfer excitation energies and asymptotic behavior. Comparison with TDDFT and EOM-CC2 calculations shows that our exciton model is robust with respect to system size, screening parameter, and different density functionals. Inclusion of charge-transfer excited states makes the exciton model more useful for studies of singly excited states and provides a starting point for future construction of a model that also includes double-exciton states.

  View details for PubMedID 28617595

• Analytical derivatives of the individual state energies in ensemble density functional theory method. I. General formalism JOURNAL OF CHEMICAL PHYSICS Filatov, M., Liu, F., Martinez, T. J. 2017; 147 (3): 034113

  Abstract

  The state-averaged (SA) spin restricted ensemble referenced Kohn-Sham (REKS) method and its state interaction (SI) extension, SI-SA-REKS, enable one to describe correctly the shape of the ground and excited potential energy surfaces of molecules undergoing bond breaking/bond formation reactions including features such as conical intersections crucial for theoretical modeling of non-adiabatic reactions. Until recently, application of the SA-REKS and SI-SA-REKS methods to modeling the dynamics of such reactions was obstructed due to the lack of the analytical energy derivatives. In this work, the analytical derivatives of the individual SA-REKS and SI-SA-REKS energies are derived. The final analytic gradient expressions are formulated entirely in terms of traces of matrix products and are presented in the form convenient for implementation in the traditional quantum chemical codes employing basis set expansions of the molecular orbitals. The implementation and benchmarking of the derived formalism will be described in a subsequent article of this series.

  View details for PubMedID 28734302

• Observing Femtosecond Fragmentation Using Ultrafast X-ray-Induced Auger Spectra APPLIED SCIENCES-BASEL Wolf, T. A., Holzmeier, F., Wagner, I., Berrah, N., Bostedt, C., Bozek, J., Bucksbaum, P., Coffee, R., Cryan, J., Farrell, J., Feifel, R., Martinez, T. J., McFarland, B., Mucke, M., Nandi, S., Tarantelli, F., Fischer, I., Guhr, M. 2017; 7 (7)

  View details for DOI 10.3390/app7070681

  View details for Web of Science ID 000407700400038

• a-CASSCF: An Efficient, Empirical Correction for SA-CASSCF To Closely Approximate MS-CASPT2 Potential Energy Surfaces. journal of physical chemistry letters Snyder, J. W., Parrish, R. M., Martínez, T. J. 2017; 8 (11): 2432-2437

  Abstract

  Because of its computational efficiency, the state-averaged complete active-space self-consistent field (SA-CASSCF) method is commonly employed in nonadiabatic ab initio molecular dynamics. However, SA-CASSCF does not effectively recover dynamical correlation. As a result, there can be qualitative differences between SA-CASSCF potential energy surfaces (PESs) and more accurate reference surfaces computed using multistate complete active space second-order perturbation theory (MS-CASPT2). Here we introduce an empirical correction to SA-CASSCF that scales the splitting between individual states and the state-averaged energy. We call this the α-CASSCF method, and we show here that it significantly improves the accuracy of relative energies and PESs compared with MS-CASPT2 for the chromophores of green fluorescent and photoactive yellow proteins. As such, this method may prove to be quite valuable for nonadiabatic dynamics.

  View details for DOI 10.1021/acs.jpclett.7b00940

  View details for PubMedID 28513165

• A direct-compatible formulation of the coupled perturbed complete active space self-consistent field equations on graphical processing units JOURNAL OF CHEMICAL PHYSICS Snyder, J. W., Fales, B. S., Hohenstein, E. G., Levine, B. G., Martinez, T. J. 2017; 146 (17)

  Abstract

  We recently developed an algorithm to compute response properties for the state-averaged complete active space self-consistent field method (SA-CASSCF) that capitalized on sparsity in the atomic orbital basis. Our original algorithm was limited to treating small to moderate sized active spaces, but the recent development of graphical processing unit (GPU) based direct-configuration interaction algorithms provides an opportunity to extend this to large active spaces. We present here a direct-compatible version of the coupled perturbed equations, enabling us to compute response properties for systems treated with arbitrary active spaces (subject to available memory and computation time). This work demonstrates that the computationally demanding portions of the SA-CASSCF method can be formulated in terms of seven fundamental operations, including Coulomb and exchange matrix builds and their derivatives, as well as, generalized one- and two-particle density matrix and σ vector constructions. As in our previous work, this algorithm exhibits low computational scaling and is accelerated by the use of GPUs, making possible optimizations and nonadiabatic dynamics on systems with O(1000) basis functions and O(100) atoms, respectively.

  View details for DOI 10.1063/1.4979844

  View details for Web of Science ID 000400625800014

  View details for PubMedID 28477593

• Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15 JOURNAL OF PHYSICAL CHEMISTRY B Wang, L., McKiernan, K. A., Gomes, J., Beauchamp, K. A., Head-Gordon, T., Rice, J. E., Swope, W. C., Martinez, T. J., Pande, V. S. 2017; 121 (16): 4023-4039

  Abstract

  The increasing availability of high-quality experimental data and first-principles calculations creates opportunities for developing more accurate empirical force fields for simulation of proteins. We developed the AMBER-FB15 protein force field by building a high-quality quantum chemical data set consisting of comprehensive potential energy scans and employing the ForceBalance software package for parameter optimization. The optimized potential surface allows for more significant thermodynamic fluctuations away from local minima. In validation studies where simulation results are compared to experimental measurements, AMBER-FB15 in combination with the updated TIP3P-FB water model predicts equilibrium properties with equivalent accuracy, and temperature dependent properties with significantly improved accuracy, in comparison with published models. We also discuss the effect of changing the protein force field and water model on the simulation results.

  View details for DOI 10.1021/acs.jpcb.7b02320

  View details for Web of Science ID 000400534200012

  View details for PubMedID 28306259

• Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. Physical chemistry chemical physics : PCCP Sisto, A., Stross, C., van der Kamp, M. W., O'Connor, M., McIntosh-Smith, S., Johnson, G. T., Hohenstein, E. G., Manby, F. R., Glowacki, D. R., Martinez, T. J. 2017

  Abstract

  We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail - enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-chlorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores. Using snapshots obtained from equilibrium molecular dynamics simulations (MD) of LH2, we tune the values of both δ and ε through fitting to the thermally broadened experimental absorption spectrum, giving a linear absorption spectrum that agrees reasonably well with experiment. In part two of this article, we construct a time-resolved picture of the coupled vibrational and excitation energy transfer (EET) dynamics in the sub-picosecond regime following photo-excitation. Assuming Franck-Condon excitation of a narrow eigenstate band centred at 800 nm, we use surface hopping to follow a single nonadiabatic dynamics trajectory within the full eigenstate manifold. Consistent with experimental data, this trajectory gives timescales for B800→B850 population transfer (τB800→B850) between 650-1050 fs, and B800 population decay (τ800→) between 10-50 fs. The dynamical picture that emerges is one of rapidly fluctuating LH2 eigenstates that are delocalized over multiple chromophores and undergo frequent crossing on a femtosecond timescale as a result of the atomic vibrations of the constituent chromophores. The eigenstate fluctuations arise from disorder that is driven by vibrational dynamics with multiple characteristic timescales. The scalability of our ab initio excitonic computational framework across massively parallel architectures opens up the possibility of addressing a wide range of questions, including how specific dynamical motions impact both the pathways and efficiency of electronic energy-transfer within large supramolecular systems.

  View details for DOI 10.1039/c7cp00492c

  View details for PubMedID 28430270

• Reduced-order formulation of multi-reference perturbation theory via tensor hyper-contraction Song, C., Martinez, T. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000430568507099

• Development of pressure-sensitive amorphous materials bearing TCAQ motifs Ren, Y., Lee, S., Christensen, J., Plotnikov, N., Burgess, M., Martinez, T., Dlott, D., Moore, J. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000430569107421

• GPU-accelerated state-averaged complete active space self-consistent field and derivative methods enable accurate, large-scale nonadiabatic dynamics simulations Snyder, J., Hohenstein, E., Curchod, B., Fales, B., Parrish, R., Martinez, T. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000430568507173

• Large-scale selected configuration interaction based on a Davidson-Liu flow Parrish, R., Martinez, T. AMER CHEMICAL SOC. 2017

  View details for Web of Science ID 000430568507645

• Atomic orbital-based SOS-MP2 with tensor hypercontraction. II. Local tensor hypercontraction. journal of chemical physics Song, C., Martínez, T. J. 2017; 146 (3): 034104-?

  Abstract

  In the first paper of the series [Paper I, C. Song and T. J. Martinez, J. Chem. Phys. 144, 174111 (2016)], we showed how tensor-hypercontracted (THC) SOS-MP2 could be accelerated by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs). This reduced the formal scaling of the SOS-MP2 energy calculation to cubic with respect to system size. The computational bottleneck then becomes the THC metric matrix inversion, which scales cubically with a large prefactor. In this work, the local THC approximation is proposed to reduce the computational cost of inverting the THC metric matrix to linear scaling with respect to molecular size. By doing so, we have removed the primary bottleneck to THC-SOS-MP2 calculations on large molecules with O(1000) atoms. The errors introduced by the local THC approximation are less than 0.6 kcal/mol for molecules with up to 200 atoms and 3300 basis functions. Together with the graphical processing unit techniques and locality-exploiting approaches introduced in previous work, the scaled opposite spin MP2 (SOS-MP2) calculations exhibit O(N(2.5)) scaling in practice up to 10 000 basis functions. The new algorithms make it feasible to carry out SOS-MP2 calculations on small proteins like ubiquitin (1231 atoms/10 294 atomic basis functions) on a single node in less than a day.

  View details for DOI 10.1063/1.4973840

  View details for PubMedID 28109237

• Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs JOURNAL OF PHYSICAL CHEMISTRY A Curchod, B. F., Sisto, A., Martinez, T. J. 2017; 121 (1): 265-276

  Abstract

  The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S2 (the initially populated bright state) to S1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S1 and acquires locally excited electronic character. Our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S1).

  View details for DOI 10.1021/acs.jpca.6b09962

  View details for Web of Science ID 000392035800029

  View details for PubMedID 27976899

• Crossing conditions in coupled cluster theory. The Journal of chemical physics Kjønstad, E. F., Myhre, R. H., Martínez, T. J., Koch, H. n. 2017; 147 (16): 164105

  Abstract

  We derive the crossing conditions at conical intersections between electronic states in coupled cluster theory and show that if the coupled cluster Jacobian matrix is nondefective, two (three) independent conditions are correctly placed on the nuclear degrees of freedom for an inherently real (complex) Hamiltonian. Calculations using coupled cluster theory on a 21A'/31A' conical intersection in hypofluorous acid illustrate the nonphysical artifacts associated with defects at accidental same-symmetry intersections. In particular, the observed intersection seam is folded about a space of the correct dimensionality, indicating that minor modifications to the theory are required for it to provide a correct description of conical intersections in general. We find that an accidental symmetry allowed 11A″/21A″ intersection in hydrogen sulfide is properly described, showing no artifacts as well as linearity of the energy gap to first order in the branching plane.

  View details for PubMedID 29096474

• Mechanochemical unzipping of insulating polyladderene to semiconducting polyacetylene Science Chen, Z., Mercer, J. A., Zhu, X., Romaniuk, J. A., Pfattner, R., Cegelski, L., Martinez, T. J., Burns, N. Z., Xia, Y. 2017; 357 (6350): 475-479

  Abstract

  Biological systems sense and respond to mechanical stimuli in a complex manner. In an effort to develop synthetic materials that transduce mechanical force into multifold changes in their intrinsic properties, we report on a mechanochemically responsive nonconjugated polymer that converts to a conjugated polymer via an extensive rearrangement of the macromolecular structure in response to force. Our design is based on the facile mechanochemical unzipping of polyladderene, a polymer inspired by a lipid natural product structure and prepared via direct metathesis polymerization. The resultant polyacetylene block copolymers exhibit long conjugation length and uniform trans-configuration and self-assemble into semiconducting nanowires. Calculations support a tandem unzipping mechanism of the ladderene units.

  View details for DOI 10.1126/science.aan2797

• Description of ground and excited electronic states by ensemble density functional method with extended active space. The Journal of chemical physics Filatov, M. n., Martínez, T. J., Kim, K. S. 2017; 147 (6): 064104

  Abstract

  An extended variant of the spin-restricted ensemble-referenced Kohn-Sham (REKS) method, the REKS(4,4) method, designed to describe the ground electronic states of strongly multireference systems is modified to enable calculation of excited states within the time-independent variational formalism. The new method, the state-interaction state-averaged REKS(4,4), i.e., SI-SA-REKS(4,4), is capable of describing several excited states of a molecule involving double bond cleavage, polyradical character, or multiple chromophoric units. We demonstrate that the new method correctly describes the ground and the lowest singlet excited states of a molecule (ethylene) undergoing double bond cleavage. The applicability of the new method for excitonic states is illustrated with π stacked ethylene and tetracene dimers. We conclude that the new method can describe a wide range of multireference phenomena.

  View details for PubMedID 28810777

• Analytical gradients for tensor hyper-contracted MP2 and SOS-MP2 on graphical processing units. The Journal of chemical physics Song, C. n., Martínez, T. J. 2017; 147 (16): 161723

  Abstract

  Analytic energy gradients for tensor hyper-contraction (THC) are derived and implemented for second-order Møller-Plesset perturbation theory (MP2), with and without the scaled-opposite-spin (SOS)-MP2 approximation. By exploiting the THC factorization, the formal scaling of MP2 and SOS-MP2 gradient calculations with respect to system size is reduced to quartic and cubic, respectively. An efficient implementation has been developed that utilizes both graphics processing units and sparse tensor techniques exploiting spatial sparsity of the atomic orbitals. THC-MP2 has been applied to both geometry optimization and ab initio molecular dynamics (AIMD) simulations. The resulting energy conservation in micro-canonical AIMD demonstrates that the implementation provides accurate nuclear gradients with respect to the THC-MP2 potential energy surfaces.

  View details for PubMedID 29096499

• Ab Initio Reactive Computer Aided Molecular Design. Accounts of chemical research Martínez, T. J. 2017; 50 (3): 652–56

  Abstract

  Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. We argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.

  View details for PubMedID 28945420

• Absorption and Fluorescence Features of an Amphiphilic meso-Pyrimidinylcorrole: Experimental Study and Quantum Chemical Calculations. The journal of physical chemistry. A Preiß, J. n., Herrmann-Westendorf, F. n., Ngo, T. H., Martínez, T. n., Dietzek, B. n., Hill, J. P., Ariga, K. n., Kruk, M. M., Maes, W. n., Presselt, M. n. 2017; 121 (45): 8614–24

  Abstract

  Corroles are emerging as an important class of macrocycles with numerous applications because of their peculiar photophysical and metal chelating properties. meso-Pyrimidinylcorroles are easily deprotonated in certain solvents, which changes their absorption and emission spectra as well as their accessible supramolecular structures. To enable control over the formation of supramolecular structures, the dominant corrole species, i.e., the deprotonated form or one of the two NH-tautomers, needs to be identified. Therefore, we focus in the present article on the determination of the UV-vis spectroscopic properties of the free-base NH-tautomers and the deprotonated form of a new amphiphilic meso-pyrimidinylcorrole that can assemble to supramolecular structures at heterointerfaces as utilized in the Langmuir-Blodgett and liquid-liquid interface precipitation techniques. After quantification of the polarities of the free-base NH-tautomers and the deprotonated form by means of quantum chemically derived electrostatic potential distributions at the corroles' van der Waals surfaces, the preferential stabilization of (some of) the considered species in solvents of different polarity is identified by means of absorption spectroscopy. For the solutions with complex mixtures of species, we applied fluorescence excitation spectroscopy to estimate the relative weights of the individual corrole species. This technique might also be applied to identify dominating species in molecularly thin films directly on the subphase' surface of Langmuir-Blodgett troughs. Supported by quantum chemical calculations we were able to differentiate between the spectral signatures of the individual NH-tautomers by means of fluorescence excitation spectroscopy.

  View details for PubMedID 29068684

• Self-consistent implementation of ensemble density functional theory method for multiple strongly correlated electron pairs JOURNAL OF CHEMICAL PHYSICS Filatov, M., Liu, F., Kim, K. S., Martinez, T. J. 2016; 145 (24)

  Abstract

  The spin-restricted ensemble-referenced Kohn-Sham (REKS) method is based on an ensemble representation of the density and is capable of correctly describing the non-dynamic electron correlation stemming from (near-)degeneracy of several electronic configurations. The existing REKS methodology describes systems with two electrons in two fractionally occupied orbitals. In this work, the REKS methodology is extended to treat systems with four fractionally occupied orbitals accommodating four electrons and self-consistent implementation of the REKS(4,4) method with simultaneous optimization of the orbitals and their fractional occupation numbers is reported. The new method is applied to a number of molecular systems where simultaneous dissociation of several chemical bonds takes place, as well as to the singlet ground states of organic tetraradicals 2,4-didehydrometaxylylene and 1,4,6,9-spiro[4.4]nonatetrayl.

  View details for DOI 10.1063/1.4972174

  View details for Web of Science ID 000392174800007

  View details for PubMedID 28010071

• Communication: XFAIMS-eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses JOURNAL OF CHEMICAL PHYSICS Mignolet, B., Curchod, B. F., Martinez, T. J. 2016; 145 (19)

  Abstract

  Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments "on-the-fly," from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. We then show the ability of XFAIMS to model the dynamics in polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H2CSO).

  View details for DOI 10.1063/1.4967761

  View details for Web of Science ID 000388956900004

  View details for PubMedID 27875877

• How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase. journal of physical chemistry. B Kulik, H. J., Zhang, J., Klinman, J. P., Martínez, T. J. 2016: -?

  Abstract

  Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in studies of enzymatic catalysis. Until recently, it has been cost prohibitive to determine the asymptotic limit of key energetic and structural properties with respect to increasingly large QM regions. Leveraging recent advances in electronic structure efficiency and accuracy, we investigate catalytic properties in catechol O-methyltransferase, a prototypical methyltransferase critical to human health. Using QM regions ranging in size from reactants-only (64 atoms) to nearly one-third of the entire protein (940 atoms), we show that properties such as the activation energy approach within chemical accuracy of the large-QM asymptotic limits rather slowly, requiring approximately 500-600 atoms if the QM residues are chosen simply by distance from the substrate. This slow approach to asymptotic limit is due to charge transfer from protein residues to the reacting substrates. Our large QM/MM calculations enable identification of charge separation for fragments in the transition state as a key component of enzymatic methyl transfer rate enhancement. We introduce charge shift analysis that reveals the minimum number of protein residues (approximately 11-16 residues or 200-300 atoms for COMT) needed for quantitative agreement with large-QM simulations. The identified residues are not those that would be typically selected using criteria such as chemical intuition or proximity. These results provide a recipe for a more careful determination of QM region sizes in future QM/MM studies of enzymes.

  View details for PubMedID 27704827

• Rich Athermal Ground-State Chemistry Triggered by Dynamics through a Conical Intersection. Angewandte Chemie (International ed. in English) Mignolet, B., Curchod, B. F., Martínez, T. J. 2016

  Abstract

  A fundamental tenet of statistical rate theories (such as transition state theory and RRKM) is the rapidity of vibrational relaxation. Excited-state reactions happen quite quickly (sub-picosecond) and thus can exhibit nonstatistical behavior. However, it is often thought that any diversity of photoproducts results from different conical intersections connecting the excited and ground electronic states. It is also conceivable that the large energy of the photon, which is converted to vibrational energy after electronic transitions could lead to athermal hot ground state reactions and that these might be responsible for the diversity of photoproducts. Here we show that this is the case for sulfines, where a single conical intersection is implicated in the electronic transition but the excited state reaction leads to nine different products within less than a picosecond.

  View details for DOI 10.1002/anie.201607633

  View details for PubMedID 27781367

• Pressure-Induced Neutral-to-Ionic Transition in an Amorphous Organic Material CHEMISTRY OF MATERIALS Ren, Y., Lee, S., Christensen, J. M., Plotnikov, N. V., Burgess, M., Martinez, T. J., Dlott, D. D., Moore, J. S. 2016; 28 (18): 6446-6449

  View details for DOI 10.1021/acs.chemmater.6b02703

  View details for Web of Science ID 000384399000005

• Toward fully quantum modelling of ultrafast photodissociation imaging experiments. Treating tunnelling in the ab initio multiple cloning approach. Faraday discussions Makhov, D. V., Martinez, T. J., Shalashilin, D. V. 2016: -?

  Abstract

  We present an account of our recent effort to improve simulation of the photodissociation of small heteroaromatic molecules using the Ab Initio Multiple Cloning (AIMC) algorithm. The ultimate goal is to create a quantitative and converged technique for fully quantum simulations which treats both electrons and nuclei on a fully quantum level. We calculate and analyse the total kinetic energy release (TKER) spectra and Velocity Map Images (VMI), and compare the results directly with experimental measurements. In this work, we perform new extensive calculations using an improved AIMC algorithm that now takes into account the tunnelling of hydrogen atoms. This can play an extremely important role in photodissociation dynamics.

  View details for PubMedID 27711808

• Using the GVB Ansatz to develop ensemble DFT method for describing multiple strongly correlated electron pairs PHYSICAL CHEMISTRY CHEMICAL PHYSICS Filatov, M., Martinez, T. J., Kim, K. S. 2016; 18 (31): 21040-21050

  Abstract

  Ensemble density functional theory (DFT) furnishes a rigorous theoretical framework for describing the non-dynamic electron correlation arising from (near) degeneracy of several electronic configurations. Ensemble DFT naturally leads to fractional occupation numbers (FONs) for several Kohn-Sham (KS) orbitals, which thereby become variational parameters of the methodology. The currently available implementation of ensemble DFT in the form of the spin-restricted ensemble-referenced KS (REKS) method was originally designed for systems with only two fractionally occupied KS orbitals, which was sufficient to accurately describe dissociation of a single chemical bond or the singlet ground state of biradicaloid species. To extend applicability of the method to systems with several dissociating bonds or to polyradical species, more fractionally occupied orbitals must be included in the ensemble description. Here we investigate a possibility of developing the extended REKS methodology with the help of the generalized valence bond (GVB) wavefunction theory. The use of GVB enables one to derive a simple and physically transparent energy expression depending explicitly on the FONs of several KS orbitals. In this way, a version of the REKS method with four electrons in four fractionally occupied orbitals is derived and its accuracy in the calculation of various types of strongly correlated molecules is investigated. We propose a possible scheme to ameliorate the partial size-inconsistency that results from perfect spin-pairing. We conjecture that perfect pairing natural orbital (NO) functionals of reduced density matrix functional theory (RDMFT) should also display partial size-inconsistency.

  View details for DOI 10.1039/c6cp00236f

  View details for Web of Science ID 000381418000015

  View details for PubMedID 26947515

• Ground and excited state ab initio molecular dynamics using graphical processing units Martinez, T. AMER CHEMICAL SOC. 2016

  View details for Web of Science ID 000431460402486

• Molecular Origin of Mechanical Sensitivity of the Reaction Rate in Anthracene Cyclophane Isomerization Reveals Structural Motifs for Rational Design of Mechanophores JOURNAL OF PHYSICAL CHEMISTRY C Plotnikov, N. V., Martinez, T. J. 2016; 120 (32): 17898-17908

  View details for DOI 10.1021/acs.jpcc.6b04924

  View details for Web of Science ID 000381778000005

• Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness. journal of physical chemistry. A Kulik, H. J., Seelam, N., Mar, B. D., Martínez, T. J. 2016; 120 (29): 5939-5949

  Abstract

  Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors.

  View details for DOI 10.1021/acs.jpca.6b04527

  View details for PubMedID 27383567

• Comment on "Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure" [J. Chem. Phys. 143, 064103 (2015)]. journal of chemical physics Parrish, R. M., Hohenstein, E. G., Martínez, T. J. 2016; 145 (2): 027101-?

  View details for DOI 10.1063/1.4955316

  View details for PubMedID 27421428

• GPU-Accelerated State-Averaged Complete Active Space Self-Consistent Field Interfaced with Ab Initio Multiple Spawning Unravels the Photodynamics of Provitamin D-3 JOURNAL OF PHYSICAL CHEMISTRY LETTERS Snyder, J. W., Curchod, B. F., Martinez, T. J. 2016; 7 (13): 2444-2449

  Abstract

  Excited-state molecular dynamics is essential to the study of photochemical reactions, which occur under nonequilibrium conditions. However, the computational cost of such simulations has often dictated compromises between accuracy and efficiency. The need for an accurate description of both the molecular electronic structure and nuclear dynamics has historically stymied the simulation of medium- to large-size molecular systems. Here, we show how to alleviate this problem by combining ab initio multiple spawning (AIMS) for the nuclear dynamics and GPU-accelerated state-averaged complete active space self-consistent field (SA-CASSCF) for the electronic structure. We demonstrate the new approach by first-principles SA-CASSCF/AIMS nonadiabatic dynamics simulation of photoinduced electrocyclic ring-opening in the 51-atom provitamin D3 molecule.

  View details for DOI 10.1021/acs.jpclett.6b00970

  View details for Web of Science ID 000379457400026

  View details for PubMedID 27266759

• "Balancing" the Block Davidson-Liu Algorithm JOURNAL OF CHEMICAL THEORY AND COMPUTATION Parrish, R. M., Hohenstein, E. G., Martinez, T. J. 2016; 12 (7): 3003-3007

  Abstract

  We describe a simple modification ("balancing") of the block Davidson-Liu eigenvalue algorithm which allows the norms of the Krylov search directions to decrease naturally as convergence is approached. In the context of integral-direct configuration interaction singles and time-dependent density functional theory, this provides for efficient utilization of density-based screening. Tests within the TeraChem GPGPU code exhibit speedups of ∼2× on systems with up to 1500 atoms, with negligible loss in accuracy.

  View details for DOI 10.1021/acs.jctc.6b00459

  View details for Web of Science ID 000379703800001

  View details for PubMedID 27253494

• Correction to "Toward Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable GPU-Accelerated Exciton Framework. Accounts of chemical research Sisto, A., Glowacki, D. R., Martinez, T. J. 2016; 49 (6): 1331-?

  View details for DOI 10.1021/acs.accounts.6b00217

  View details for PubMedID 27251301

• Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity JOURNAL OF CHEMICAL PHYSICS Song, C., Martinez, T. J. 2016; 144 (17)

  Abstract

  We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N(2.6) for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

  View details for DOI 10.1063/1.4948438

  View details for Web of Science ID 000377711300015

  View details for PubMedID 27155629

• Communication: A difference density picture for the self-consistent field ansatz. journal of chemical physics Parrish, R. M., Liu, F., Martínez, T. J. 2016; 144 (13): 131101-?

  Abstract

  We formulate self-consistent field (SCF) theory in terms of an interaction picture where the working variable is the difference density matrix between the true system and a corresponding superposition of atomic densities. As the difference density matrix directly represents the electronic deformations inherent in chemical bonding, this "difference self-consistent field (dSCF)" picture provides a number of significant conceptual and computational advantages. We show that this allows for a stable and efficient dSCF iterative procedure with wholly single-precision Coulomb and exchange matrix builds. We also show that the dSCF iterative procedure can be performed with aggressive screening of the pair space. These approximations are tested and found to be accurate for systems with up to 1860 atoms and >10 000 basis functions, providing for immediate overall speedups of up to 70% in the heavily optimized TeraChem SCF implementation.

  View details for DOI 10.1063/1.4945277

  View details for PubMedID 27059555

• Communication: GAIMS-Generalized Ab Initio Multiple Spawning for both internal conversion and intersystem crossing processes JOURNAL OF CHEMICAL PHYSICS Curchod, B. F., Rauer, C., Marquetand, P., Gonzalez, L., Martinez, T. J. 2016; 144 (10)

  Abstract

  Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.

  View details for DOI 10.1063/1.4943571

  View details for Web of Science ID 000372974600002

• Systematic improvement of intramolecular parameters for protein force fields from quantum chemistry data Wang, L., Beauchamp, K., Swope, W., Rice, J., Head-Gordon, T., Martinez, T., Pande, V. AMER CHEMICAL SOC. 2016

  View details for Web of Science ID 000431903806020

• Development of organic charge transfer complexes for shock wave energy dissipation (SWED) Ren, Y., Lee, S., Christensen, J., Shaw, W., Plotnikov, N., Martinez, T., Dlott, D., Moore, J. AMER CHEMICAL SOC. 2016

  View details for Web of Science ID 000431905707218

• Automated code engine for generation and optimization of electronic integrals on graphics processing hardware Song, C., Wang, L., Martinez, T. AMER CHEMICAL SOC. 2016

  View details for Web of Science ID 000431903806157

• Dynamical Correlation Effects on Photoisomerization: Ab Initio Multiple Spawning Dynamics with MS-CASPT2 for a Model trans-Protonated Schiff Base JOURNAL OF PHYSICAL CHEMISTRY B Liu, L., Liu, J., Martinez, T. J. 2016; 120 (8): 1940-1949

  Abstract

  We investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multistate second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well-described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerization are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.

  View details for DOI 10.1021/acs.jpcb.5b09838

  View details for Web of Science ID 000371562700059

  View details for PubMedID 26679298

• Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways JOURNAL OF CHEMICAL THEORY AND COMPUTATION Wang, L., McGibbon, R. T., Pande, V. S., Martinez, T. J. 2016; 12 (2): 638-649

  Abstract

  We describe a flexible and broadly applicable energy refinement method, "nebterpolation," for identifying and characterizing the reaction events in a molecular dynamics (MD) simulation. The new method is applicable to ab initio simulations with hundreds of atoms containing complex and multimolecular reaction events. A key aspect of nebterpolation is smoothing of the reactive MD trajectory in internal coordinates to initiate the search for the reaction path on the potential energy surface. We apply nebterpolation to analyze the reaction events in an ab initio nanoreactor simulation that discovers new molecules and mechanisms, including a C-C coupling pathway for glycolaldehyde synthesis. We find that the new method, which incorporates information from the MD trajectory that connects reactants with products, produces a dramatically distinct set of minimum energy paths compared to existing approaches that start from information for the reaction end points alone. The energy refinement method described here represents a key component of an emerging simulation paradigm where molecular dynamics simulations are applied to discover the possible reaction mechanisms.

  View details for DOI 10.1021/acs.jctc.5b00830

  View details for Web of Science ID 000370112900018

  View details for PubMedID 26683346

• Automated Code Engine for Graphical Processing Units: Application to the Effective Core Potential Integrals and Gradients. Journal of chemical theory and computation Song, C., Wang, L. P., Martínez, T. J. 2016; 12 (1): 92-106

  Abstract

  We present an automated code engine (ACE) that automatically generates optimized kernels for computing integrals in electronic structure theory on a given graphical processing unit (GPU) computing platform. The code generator in ACE creates multiple code variants with different memory and floating point operation trade-offs. A graph representation is created as the foundation of the code generation, which allows the code generator to be extended to various types of integrals. The code optimizer in ACE determines the optimal code variant and GPU configurations for a given GPU computing platform by scanning over all possible code candidates and then choosing the best-performing code candidate for each kernel. We apply ACE to the optimization of effective core potential integrals and gradients. It is observed that the best code candidate varies with differing angular momentum, floating point precision, and type of GPU being used, which shows that the ACE may be a powerful tool in adapting to fast evolving GPU architectures.

  View details for DOI 10.1021/acs.jctc.5b00790

  View details for PubMedID 26586267

• Automated Code Engine for Graphical Processing Units: Application to the Effective Core Potential Integrals and Gradients JOURNAL OF CHEMICAL THEORY AND COMPUTATION Song, C., Wang, L., Martinez, T. J. 2016; 12 (1): 92-106

  Abstract

  We present an automated code engine (ACE) that automatically generates optimized kernels for computing integrals in electronic structure theory on a given graphical processing unit (GPU) computing platform. The code generator in ACE creates multiple code variants with different memory and floating point operation trade-offs. A graph representation is created as the foundation of the code generation, which allows the code generator to be extended to various types of integrals. The code optimizer in ACE determines the optimal code variant and GPU configurations for a given GPU computing platform by scanning over all possible code candidates and then choosing the best-performing code candidate for each kernel. We apply ACE to the optimization of effective core potential integrals and gradients. It is observed that the best code candidate varies with differing angular momentum, floating point precision, and type of GPU being used, which shows that the ACE may be a powerful tool in adapting to fast evolving GPU architectures.

  View details for DOI 10.1021/acs.jctc.5b00790

  View details for Web of Science ID 000368322500010

• Evidence of Hydrogen Migration rather than Isomerization in the Acetylene Dication Liekhus-Schmaltz, C. E., Li, Z., Petrovic, V., Martinez, T., Bucksbaum, P. H., IEEE IEEE. 2016

  View details for Web of Science ID 000391286401261

• Catch and Release: Orbital Symmetry Guided Reaction Dynamics from a Freed "Tension Trapped Transition State" JOURNAL OF ORGANIC CHEMISTRY Wang, J., Ong, M. T., Kouznetsova, T. B., Lenhardt, J. M., Martinez, T. J., Craig, S. L. 2015; 80 (23): 11773-11778

  Abstract

  The dynamics of reactions at or in the immediate vicinity of transition states are critical to reaction rates and product distributions, but direct experimental probes of those dynamics are rare. Here, s-trans, s-trans 1,3-diradicaloid transition states are trapped by tension along the backbone of purely cis-substituted gem-difluorocyclopropanated polybutadiene using the extensional forces generated by pulsed sonication of dilute polymer solutions. Once released, the branching ratio between symmetry-allowed disrotatory ring closing (of which the trapped diradicaloid structure is the transition state) and symmetry-forbidden conrotatory ring closing (whose transition state is nearby) can be inferred. Net conrotatory ring closing occurred in 5.0 ± 0.5% of the released transition states, in excellent agreement with ab initio molecular dynamics simulations.

  View details for DOI 10.1021/acs.joc.5b01493

  View details for PubMedID 26322681

• An atomic orbital-based formulation of analytical gradients and nonadiabatic coupling vector elements for the state-averaged complete active space self-consistent field method on graphical processing units JOURNAL OF CHEMICAL PHYSICS Snyder, J. W., Hohenstein, E. G., Luehr, N., Martinez, T. J. 2015; 143 (15)

  Abstract

  We recently presented an algorithm for state-averaged complete active space self-consistent field (SA-CASSCF) orbital optimization that capitalizes on sparsity in the atomic orbital basis set to reduce the scaling of computational effort with respect to molecular size. Here, we extend those algorithms to calculate the analytic gradient and nonadiabatic coupling vectors for SA-CASSCF. Combining the low computational scaling with acceleration from graphical processing units allows us to perform SA-CASSCF geometry optimizations for molecules with more than 1000 atoms. The new approach will make minimal energy conical intersection searches and nonadiabatic dynamics routine for molecular systems with O(10(2)) atoms.

  View details for DOI 10.1063/1.4932613

  View details for Web of Science ID 000363418400008

  View details for PubMedID 26493897

• Ab initio interactive molecular dynamics on graphical processing units (GPUs). Journal of chemical theory and computation Luehr, N., Jin, A. G., Martínez, T. J. 2015; 11 (10): 4536-44

  Abstract

  A virtual molecular modeling kit is developed based on GPU-enabled interactive ab initio molecular dynamics (MD). The code uses the TeraChem and VMD programs with a modified IMD interface. Optimization of the GPU accelerated TeraChem program specifically for small molecular systems is discussed, and a robust multiple time step integrator is employed to accurately integrate strong user-supplied pulling forces. Smooth and responsive visualization techniques are developed to allow interactive manipulation at minimum simulation rates below five MD steps per second. Representative calculations at the Hartree-Fock level of theory are demonstrated for molecular systems containing up to a few dozen atoms.

  View details for DOI 10.1021/acs.jctc.5b00419

  View details for PubMedID 26574246

• Ab lnitio Interactive Molecular Dynamics on Graphical Processing Units (GPUs) JOURNAL OF CHEMICAL THEORY AND COMPUTATION Luehr, N., Jin, A. G., Martinez, T. J. 2015; 11 (10): 4536-4544

  Abstract

  A virtual molecular modeling kit is developed based on GPU-enabled interactive ab initio molecular dynamics (MD). The code uses the TeraChem and VMD programs with a modified IMD interface. Optimization of the GPU accelerated TeraChem program specifically for small molecular systems is discussed, and a robust multiple time step integrator is employed to accurately integrate strong user-supplied pulling forces. Smooth and responsive visualization techniques are developed to allow interactive manipulation at minimum simulation rates below five MD steps per second. Representative calculations at the Hartree-Fock level of theory are demonstrated for molecular systems containing up to a few dozen atoms.

  View details for DOI 10.1021/acs.jctc.5b00419

  View details for Web of Science ID 000362921700003

• Preface: Special Topic Section on Advanced Electronic Structure Methods for Solids and Surfaces JOURNAL OF CHEMICAL PHYSICS Michaelides, A., Martinez, T. J., Alavi, A., Kresse, G., Manby, F. R. 2015; 143 (10)

  Abstract

  This Special Topic section on Advanced Electronic Structure Methods for Solids and Surfaces contains a collection of research papers that showcase recent advances in the high accuracy prediction of materials and surface properties. It provides a timely snapshot of a growing field that is of broad importance to chemistry, physics, and materials science.

  View details for DOI 10.1063/1.4930182

  View details for Web of Science ID 000361572900005

  View details for PubMedID 26373993

• Ab initio multiple spawning on laser-dressed states: a study of 1,3-cyclohexadiene photoisomerization via light-induced conical intersections JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS Kim, J., Tao, H., Martinez, T. J., Bucksbaum, P. 2015; 48 (16)

  View details for DOI 10.1088/0953-4075/48/16/164003

  View details for Web of Science ID 000358623500003

• Energy refinement of reactive molecular dynamics pathways Wang, L., McGibbon, R., Pande, V., Martinez, T. AMER CHEMICAL SOC. 2015

  View details for Web of Science ID 000432475502791

• Molecular dynamics investigation of deeply supercooled water using a direct polarization model Wang, L., Schwantes, C., Lane, T., Sellberg, J., Nilsson, A., Martinez, T., Pande, V. AMER CHEMICAL SOC. 2015

  View details for Web of Science ID 000432475504058

• Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models. Journal of chemical theory and computation Liu, F., Luehr, N., Kulik, H. J., Martínez, T. J. 2015; 11 (7): 3131-44

  Abstract

  The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10× faster than that with a conventional CPU-based implementation. Our improvements to the linear solver provide a further 3× acceleration. The overall calculations including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril.

  View details for DOI 10.1021/acs.jctc.5b00370

  View details for PubMedID 26575750

• Tensor Hypercontraction Second-Order Møller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies. Journal of chemical theory and computation Schumacher, S. I., Hohenstein, E. G., Parrish, R. M., Wang, L. P., Martínez, T. J. 2015; 11 (7): 3042-52

  Abstract

  We have recently introduced the tensor hypercontraction (THC) method for electronic structure, including MP2. Here, we present an algorithm for THC-MP2 that lowers the memory requirements as well as the prefactor while maintaining the formal quartic scaling that we demonstrated previously. We also describe a procedure to optimize quadrature grids used in grid-based least-squares (LS) THC-MP2. We apply this algorithm to generate grids for first-row atoms with less than 100 points/atom while incurring negligible errors in the computed energies. We benchmark the LS-THC-MP2 method using optimized grids for a wide variety of tests sets including conformational energies and reaction barriers in both the cc-pVDZ and cc-pVTZ basis sets. These tests demonstrate that the THC methodology is not limited to small basis sets and that it incurs negligible errors in both absolute and relative energies.

  View details for DOI 10.1021/acs.jctc.5b00272

  View details for PubMedID 26575741

• Efficient implementation of effective core potential integrals and gradients on graphical processing units. journal of chemical physics Song, C., Wang, L., Sachse, T., Preiss, J., Presselt, M., Martínez, T. J. 2015; 143 (1): 014114-?

  Abstract

  Effective core potential integral and gradient evaluations are accelerated via implementation on graphical processing units (GPUs). Two simple formulas are proposed to estimate the upper bounds of the integrals, and these are used for screening. A sorting strategy is designed to balance the workload between GPU threads properly. Significant improvements in performance and reduced scaling with system size are observed when combining the screening and sorting methods, and the calculations are highly efficient for systems containing up to 10 000 basis functions. The GPU implementation preserves the precision of the calculation; the ground state Hartree-Fock energy achieves good accuracy for CdSe and ZnTe nanocrystals, and energy is well conserved in ab initio molecular dynamics simulations.

  View details for DOI 10.1063/1.4922844

  View details for PubMedID 26156472

• Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units. journal of chemical physics Hohenstein, E. G., Bouduban, M. E., Song, C., Luehr, N., Ufimtsev, I. S., Martínez, T. J. 2015; 143 (1): 014111-?

  Abstract

  The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.

  View details for DOI 10.1063/1.4923259

  View details for PubMedID 26156469

• Origin of the Individual Basicity of Corrole NH-Tautomers: A Quantum Chemical Study on Molecular Structure and Dynamics, Kinetics, and Thermodynamics JOURNAL OF PHYSICAL CHEMISTRY A Beenken, W., Maes, W., Kruk, M., Martinez, T., Presselt, M. 2015; 119 (26): 6875-6883

  Abstract

  Free-base corroles exist as individual NH-tautomers that may differ in their spectral and chemical properties. The present paper focuses on the origin of the basicity difference between two AB2-pyrimidinylcorrole NH-tautomers, which has been tentatively attributed to differences in the weak out-of-plane distortions of the pyrrolenic ring between two NH-tautomers. Using DFT-geometry optimizations, we show that the pyrroles involved in the NH-tautomerization process are approximately in-plane, whereas the other two pyrroles are tilted out-of-plane in opposite directions. Alternative out-of-plane distortion patterns play a minor role, as revealed by ab initio molecular dynamics simulations. Given that the protonated corrole is a unique species, the energy difference between the two NH-tautomers equals the difference in protonation driving force between them. This energy difference increases with improved theoretical level of accounting for intermolecular interactions and dielectric screening of surface charges. The different charge distributions of the two NH-tautomers result in electrostatic potential distributions that effect a larger proton attraction in the case of the T1 tautomer than in the case of the T2 tautomer. In summary, our quantum chemical results show clearly a higher basicity of the T1 tautomer as compared to the T2 tautomer: The previously assumed pronounced out-of-plane tilt of the T1-nonprotonated nitrogen is verified by ab initio molecular dynamics simulations. Together with analysis of the electrostatic potential distribution we show that the nonprotonated nitrogen is not only tilted stronger but also significantly more accessible for protons in the case of T1 as compared to T2. Additionally, the thermodynamic basicity is higher for T1 than for T2.

  View details for DOI 10.1021/acs.jpca.5b02869

  View details for Web of Science ID 000357623600013

  View details for PubMedID 26052732

• Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models JOURNAL OF CHEMICAL THEORY AND COMPUTATION Liu, F., Luehr, N., Kulik, H. J., Martinez, T. J. 2015; 11 (7): 3131-3144

  Abstract

  The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10× faster than that with a conventional CPU-based implementation. Our improvements to the linear solver provide a further 3× acceleration. The overall calculations including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril.

  View details for DOI 10.1021/acs.jctc.5b00370

  View details for Web of Science ID 000358104800024

• Tensor Hypercontraction Second-Order Moller-Plesset Perturbation Theory: Grid Optimization and Reaction Energies JOURNAL OF CHEMICAL THEORY AND COMPUTATION Schumacher, S. I., Hohenstein, E. G., Parrish, R. M., Wang, L., Martinez, T. J. 2015; 11 (7): 3042-3052

  Abstract

  We have recently introduced the tensor hypercontraction (THC) method for electronic structure, including MP2. Here, we present an algorithm for THC-MP2 that lowers the memory requirements as well as the prefactor while maintaining the formal quartic scaling that we demonstrated previously. We also describe a procedure to optimize quadrature grids used in grid-based least-squares (LS) THC-MP2. We apply this algorithm to generate grids for first-row atoms with less than 100 points/atom while incurring negligible errors in the computed energies. We benchmark the LS-THC-MP2 method using optimized grids for a wide variety of tests sets including conformational energies and reaction barriers in both the cc-pVDZ and cc-pVTZ basis sets. These tests demonstrate that the THC methodology is not limited to small basis sets and that it incurs negligible errors in both absolute and relative energies.

  View details for DOI 10.1021/acs.jctc.5b00272

  View details for Web of Science ID 000358104800015

• Mediation of donor-acceptor distance in an enzymatic methyl transfer reaction PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Zhang, J., Kulik, H. J., Martinez, T. J., Klinman, J. P. 2015; 112 (26): 7954-7959

  Abstract

  Enzymatic methyl transfer, catalyzed by catechol-O-methyltransferase (COMT), is investigated using binding isotope effects (BIEs), time-resolved fluorescence lifetimes, Stokes shifts, and extended graphics processing unit (GPU)-based quantum mechanics/molecular mechanics (QM/MM) approaches. The WT enzyme is compared with mutants at Tyr68, a conserved residue that is located behind the reactive sulfur of cofactor. Small (>1) BIEs are observed for an S-adenosylmethionine (AdoMet)-binary and abortive ternary complex containing 8-hydroxyquinoline, and contrast with previously reported inverse (<1) kinetic isotope effects (KIEs). Extended GPU-based computational studies of a ternary complex containing catecholate show a clear trend in ground state structures, from noncanonical bond lengths for WT toward solution values with mutants. Structural and dynamical differences that are sensitive to Tyr68 have also been detected using time-resolved Stokes shift measurements and molecular dynamics. These experimental and computational results are discussed in the context of active site compaction that requires an ionization of substrate within the enzyme ternary complex.

  View details for DOI 10.1073/pnas.1506792112

  View details for Web of Science ID 000357079400037

  View details for PubMedID 26080432

  View details for PubMedCentralID PMC4491759

• An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2015; 142 (22)

  Abstract

  Despite its importance, state-of-the-art algorithms for performing complete active space self-consistent field (CASSCF) computations have lagged far behind those for single reference methods. We develop an algorithm for the CASSCF orbital optimization that uses sparsity in the atomic orbital (AO) basis set to increase the applicability of CASSCF. Our implementation of this algorithm uses graphical processing units (GPUs) and has allowed us to perform CASSCF computations on molecular systems containing more than one thousand atoms. Additionally, we have implemented analytic gradients of the CASSCF energy; the gradients also benefit from GPU acceleration as well as sparsity in the AO basis.

  View details for DOI 10.1063/1.4921956

  View details for Web of Science ID 000356176600005

  View details for PubMedID 26071697

• How Does Peripheral Functionalization of Ruthenium(II)-Terpyridine Complexes Affect Spatial Charge Redistribution after Photoexcitation at the Franck-Condon Point? CHEMPHYSCHEM Preiss, J., Jaeger, M., Rau, S., Dietzek, B., Popp, J., Martinez, T., Presselt, M. 2015; 16 (7): 1395-1404

  Abstract

  Ruthenium polypyridine-type complexes are extensively used sensitizers to convert solar energy into chemical and/or electrical energy, and they can be tailored through their metal-to-ligand charge-transfer (MLCT) properties. Much work has been directed at harnessing the triplet MLCT state in photoinduced processes, from sophisticated molecular architectures to dye-sensitized solar cells. In dye-sensitized solar cells, strong coupling to the semiconductor exploits the high reactivity of the (hot) singlet/triplet MLCT state. In this work, we explore the nature of the (1) MLCT states of remotely substituted Ru(II) model complexes by both experimental and theoretical techniques. Two model complexes with electron-withdrawing (i.e. NO2 ) and electron-donating (i.e. NH2 ) groups were synthesized; these complexes contained a phenylene spacer to serve as a spectroscopic handle and to confirm the contribution of the remote substituent to the (1) MLCT transition. [Ru(tpy)2 ](2+) -based complexes (tpy=2,2':6',2''-terpyridine) were further desymmetrized by tert-butyl groups to yield unidirectional (1) MLCTs with large transition dipole moments, which are beneficial for related directional charge-transfer processes. Detailed comparison of experimental spectra (deconvoluted UV/Vis and resonance Raman spectroscopy data) with theoretical calculations based on density functional theory (including vibronic broadening) revealed different properties of the optically active bright (1) MLCT states already at the Franck-Condon point.

  View details for DOI 10.1002/cphc.201500223

  View details for Web of Science ID 000354367500013

  View details for PubMedID 25898828

• Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Sigala, P. A., Ruben, E. A., Liu, C. W., Piccoli, P. M., Hohenstein, E. G., Martinez, T. J., Schultz, A. J., Herschlag, D. 2015; 137 (17): 5730-5740

  Abstract

  Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (ΔGf) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to ΔGf, but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond ΔGf are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

  View details for DOI 10.1021/ja512980h

  View details for Web of Science ID 000354338500017

  View details for PubMedID 25871450

• Inducing and quantifying forbidden reactivity with single-molecule polymer mechanochemistry NATURE CHEMISTRY Wang, J., Kouznetsova, T. B., Niu, Z., Ong, M. T., Klukovich, H., Rheingold, A. L., Martinez, T. J., Craig, S. L. 2015; 7 (4): 323-327

  Abstract

  Forbidden reactions, such as those that violate orbital symmetry effects as captured in the Woodward-Hoffmann rules, remain an ongoing challenge for experimental characterization, because when the competing allowed pathway is available the reactions are intrinsically difficult to trigger. Recent developments in covalent mechanochemistry have opened the door to activating otherwise inaccessible reactions. Here we report single-molecule force spectroscopy studies of three mechanically induced reactions along both their symmetry-allowed and symmetry-forbidden pathways, which enables us to quantify just how 'forbidden' each reaction is. To induce reactions on the ~0.1 s timescale of the experiments, the forbidden ring-opening reactions of benzocyclobutene, gem-difluorocyclopropane and gem-dichlorocyclopropane require approximately 130 pN less, 560 pN more and 1,000 pN more force, respectively, than their corresponding allowed analogues. The results provide the first experimental benchmarks for mechanically induced forbidden reactions, and in some cases suggest revisions to prior computational predictions.

  View details for DOI 10.1038/NCHEM.2185

  View details for Web of Science ID 000351756200012

  View details for PubMedID 25803470

• Understanding mechanochemistry from first principles Martinez, T. AMER CHEMICAL SOC. 2015

  View details for Web of Science ID 000411186504229

• Ab initio exciton model for nonadiabatic dynamics of multichromophoric systems on GPUs Sisto, A., Glowacki, D., Martinez, T. AMER CHEMICAL SOC. 2015

  View details for Web of Science ID 000411186503571

• Ab initio multiple cloning simulations of pyrrole photodissociation: TKER spectra and velocity map imaging. Physical chemistry chemical physics Makhov, D. V., Saita, K., Martinez, T. J., Shalashilin, D. V. 2015; 17 (5): 3316-3325

  Abstract

  We report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropic component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.

  View details for DOI 10.1039/c4cp04571h

  View details for PubMedID 25523235

• Direct QM/MM Excited-State Dynamics of Retinal Protonated Schiff Base in Isolation and Methanol Solution. journal of physical chemistry. B Punwong, C., Owens, J., Martínez, T. J. 2015; 119 (3): 704-714

  Abstract

  We use the full multiple spawning (FMS) dynamics approach with a hybrid quantum mechanics/molecular mechanics (QM/MM) reparameterized semiempirical method to investigate the excited-state dynamics of retinal protonated Schiff base (RPSB) in isolation, in neat methanol solution, and in methanol solution with a Cl(-) counterion. The excited-state lifetime is dramatically affected by MeOH solvent, which slows down the photoisomerization by an order of magnitude. We show that this is due to charge migration in the RPSB chromophore and the concomitant solvent friction in polar media. Simulation results are compared to experiments where available, with good agreement for excited-state lifetimes, bond selectivity of isomerization, and the time/energy-resolved fluorescence spectrum. We find that the inclusion of a Cl(-) counterion in the simulations has little effect on lifetimes, mechanism, or bond selectivity. In contrast to previous studies limited to RPSB and a surrounding counterion, we find that the placement of the counterion has little effect on bond selectivity. This suggests that dielectric screening can spoil the effect of a counterion in directing excited-state reactivity.

  View details for DOI 10.1021/jp5038798

  View details for PubMedID 25178510

• Ultrafast isomerization initiated by X-ray core ionization. Nature communications Liekhus-Schmaltz, C. E., Tenney, I., Osipov, T., Sanchez-Gonzalez, A., Berrah, N., Boll, R., Bomme, C., Bostedt, C., Bozek, J. D., Carron, S., Coffee, R., Devin, J., Erk, B., Ferguson, K. R., Field, R. W., Foucar, L., Frasinski, L. J., Glownia, J. M., Gühr, M., Kamalov, A., Krzywinski, J., Li, H., Marangos, J. P., Martinez, T. J., McFarland, B. K., Miyabe, S., Murphy, B., Natan, A., Rolles, D., Rudenko, A., Siano, M., Simpson, E. R., Spector, L., Swiggers, M., Walke, D., Wang, S., Weber, T., Bucksbaum, P. H., Petrovic, V. S. 2015; 6: 8199-?

  Abstract

  Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a 'molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

  View details for DOI 10.1038/ncomms9199

  View details for PubMedID 26354002

• Ultrafast isomerization initiated by X-ray core ionization. Nature communications Liekhus-Schmaltz, C. E., Tenney, I., Osipov, T., Sanchez-Gonzalez, A., Berrah, N., Boll, R., Bomme, C., Bostedt, C., Bozek, J. D., Carron, S., Coffee, R., Devin, J., Erk, B., Ferguson, K. R., Field, R. W., Foucar, L., Frasinski, L. J., Glownia, J. M., Gühr, M., Kamalov, A., Krzywinski, J., Li, H., Marangos, J. P., Martinez, T. J., McFarland, B. K., Miyabe, S., Murphy, B., Natan, A., Rolles, D., Rudenko, A., Siano, M., Simpson, E. R., Spector, L., Swiggers, M., Walke, D., Wang, S., Weber, T., Bucksbaum, P. H., Petrovic, V. S. 2015; 6: 8199-?

  View details for DOI 10.1038/ncomms9199

  View details for PubMedID 26354002

• Quantum chemical insights into the dependence of porphyrin basicity on the meso-aryl substituents: thermodynamics, buckling, reaction sites and molecular flexibility PHYSICAL CHEMISTRY CHEMICAL PHYSICS Presselt, M., Dehaen, W., Maes, W., Klamt, A., Martinez, T., Beenken, W. J., Kruk, M. 2015; 17 (21): 14096-14106

  Abstract

  The chemical and sensing properties of porphyrins are frequently tuned via the introduction of peripheral substituents. In the context of the exceptionally fast second protonation step in the case of 5,10,15,20-tetraphenylporphyrin (TPP), as compared to porphin and 5,10,15,20-tetramesitylporphyrin (TMesP), we investigated the macrocycle-substituent interactions of these three porphyrin derivatives in detail. Using quantum chemical thermodynamics calculations, the analysis of geometric structures, torsional profiles, electrostatic potential distributions, and particularly the analysis of molecular flexibilities via ab initio molecular dynamics simulations, we obtained a comprehensive picture of the reactivities of the studied porphyrins and how these are influenced by the meso-substituents. As compared to porphin and TMesP the second protonation of TPP is energetically more favorable and is particularly energetically comparable to its first protonation, instead of being significantly less favorable like in the case of porphyrin and TMesP. Additionally, the second TPP protonation is facilitated by an interplay between out-of-plane (oop) distortion of the protonation site and a pronounced electrostatic binding spot at the protonation site. Furthermore, the second protonation is particularly facilitated in the case of TPP by the large oop-flexibility of the diprotonated species as unraveled by ab initio molecular dynamics simulations.

  View details for DOI 10.1039/c5cp01808k

  View details for Web of Science ID 000354946200036

  View details for PubMedID 25959745

• Discovering chemistry with an ab initio nanoreactor NATURE CHEMISTRY Wang, L., Titov, A., McGibbon, R., Liu, F., Pande, V. S., Martinez, T. J. 2014; 6 (12): 1044-1048

  Abstract

  Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  View details for DOI 10.1038/NCHEM.2099

  View details for Web of Science ID 000345429200008

  View details for PubMedCentralID PMC4239668

• Discovering chemistry with an ab initio nanoreactor (vol 6, pg 1044, 2014) NATURE CHEMISTRY Wang, L., Titov, A., McGibbon, R., Liu, F., Pande, V. S., Martinez, T. J. 2014; 6 (12)

  View details for Web of Science ID 000345429200009

• Interfacing the Ab Initio Multiple Spawning Method with Electronic Structure Methods in GAMESS: Photodecay of trans-Azonnethane JOURNAL OF PHYSICAL CHEMISTRY A Gaenko, A., DeFusco, A., Varganov, S. A., Martinez, T. J., Gordon, M. S. 2014; 118 (46): 10902-10908

  Abstract

  This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitation on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ∼60-200 fs. These short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.

  View details for DOI 10.1021/jp508242j

  View details for Web of Science ID 000345474500004

• A remote stereochemical lever arm effect in polymer mechanochemistry. Journal of the American Chemical Society Wang, J., Kouznetsova, T. B., Kean, Z. S., Fan, L., Mar, B. D., Martínez, T. J., Craig, S. L. 2014; 136 (43): 15162-15165

  Abstract

  Molecular mechanisms by which to increase the activity of a mechanophore might provide access to new chemical reactions and enhanced stress-responsive behavior in mechanochemically active polymeric materials. Here, single-molecule force spectroscopy reveals that the force-induced acceleration of the electrocyclic ring opening of gem-dichlorocyclopropanes (gDCC) is sensitive to the stereochemistry of an α-alkene substituent on the gDCC. On the ∼0.1 s time scale of the experiment, the force required to open the E-alkene-substituted gDCC was found to be 0.4 nN lower than that required in the corresponding Z-alkene isomer, despite the effectively identical force-free reactivities of the two isomers and the distance between the stereochemical permutation and the scissile bond of the mechanophore. Fitting the experimental data with a cusp model provides force-free activation lengths of 1.67 ± 0.05 and 1.20 ± 0.05 Å for the E and Z isomers, respectively, as compared to 1.65 and 1.24 Å derived from computational modeling.

  View details for DOI 10.1021/ja509585g

  View details for PubMedID 25322470

• Ab initio nonadiabatic dynamics of multichromophore complexes: a scalable graphical-processing-unit-accelerated exciton framework. Accounts of chemical research Sisto, A., Glowacki, D. R., Martinez, T. J. 2014; 47 (9): 2857-66

  Abstract

  Conspectus Although advances in computer hardware and algorithms tuned for novel computer architectures are leading to significant increases in the size and time scale for molecular simulations, it remains true that new methods and algorithms will be needed to address some of the problems in complex chemical systems, such as electrochemistry, excitation energy transport, proton transport, and condensed phase reactivity. Ideally, these new methods would exploit the strengths of emerging architectures. Fragment based approaches for electronic structure theory decompose the problem of solving the electronic Schrodinger equation into a series of much smaller problems. Because each of these smaller problems is largely independent, this strategy is particularly well-suited to parallel architectures. It appears that the most significant advances in computer architectures will be toward increased parallelism, and therefore fragment-based approaches are an ideal match to these trends. When the computational effort involved scales with the third (or higher) power of the molecular size, there is a large benefit to fragment-based approaches even on serial architectures. This is the case for many of the well-known methods for solving the electronic structure theory problem, especially when wave function-based approaches including electron correlation are considered. A major issue in fragment-based approaches is determining or improving their accuracy. Since the Achilles' heel of any such method lies in the approximations used to stitch the smaller problems back together (i.e., in the treatment of the cross-fragment interactions), it can often be important to ensure that the size of the smaller problems is "large enough." Thus, there are two frontiers that need to be extended in order to enable molecular simulations for large systems and long times: the strongly coupled problem of medium sized molecules (100-500 atoms) and the more weakly coupled problem of decomposing ("fragmenting") a molecular system and then stitching it back together. In this Account, we address both of these problems, the first by using graphical processing units (GPUs) and electronic structure algorithms tuned for these architectures and the second by using an exciton model as a framework in which to stitch together the solutions of the smaller problems. The multitiered parallel framework outlined here is aimed at nonadiabatic dynamics simulations on large supramolecular multichromophoric complexes in full atomistic detail. In this framework, the lowest tier of parallelism involves GPU-accelerated electronic structure theory calculations, for which we summarize recent progress in parallelizing the computation and use of electron repulsion integrals (ERIs), which are the major computational bottleneck in both density functional theory (DFT) and time-dependent density functional theory (TDDFT). The topmost tier of parallelism relies on a distributed memory framework, in which we build an exciton model that couples chromophoric units. Combining these multiple levels of parallelism allows access to ground and excited state dynamics for large multichromophoric assemblies. The parallel excitonic framework is in good agreement with much more computationally demanding TDDFT calculations of the full assembly.

  View details for DOI 10.1021/ar500229p

  View details for PubMedID 25186064

• Ab Initio Nonadiabatic Dynamics of Multichromophore Complexes: A Scalable Graphical-Processing-Unit-Accelerated Exciton Framework ACCOUNTS OF CHEMICAL RESEARCH Sisto, A., Glowacki, D. R., Martinez, T. J. 2014; 47 (9): 2857-2866

  Abstract

  Conspectus Although advances in computer hardware and algorithms tuned for novel computer architectures are leading to significant increases in the size and time scale for molecular simulations, it remains true that new methods and algorithms will be needed to address some of the problems in complex chemical systems, such as electrochemistry, excitation energy transport, proton transport, and condensed phase reactivity. Ideally, these new methods would exploit the strengths of emerging architectures. Fragment based approaches for electronic structure theory decompose the problem of solving the electronic Schrodinger equation into a series of much smaller problems. Because each of these smaller problems is largely independent, this strategy is particularly well-suited to parallel architectures. It appears that the most significant advances in computer architectures will be toward increased parallelism, and therefore fragment-based approaches are an ideal match to these trends. When the computational effort involved scales with the third (or higher) power of the molecular size, there is a large benefit to fragment-based approaches even on serial architectures. This is the case for many of the well-known methods for solving the electronic structure theory problem, especially when wave function-based approaches including electron correlation are considered. A major issue in fragment-based approaches is determining or improving their accuracy. Since the Achilles' heel of any such method lies in the approximations used to stitch the smaller problems back together (i.e., in the treatment of the cross-fragment interactions), it can often be important to ensure that the size of the smaller problems is "large enough." Thus, there are two frontiers that need to be extended in order to enable molecular simulations for large systems and long times: the strongly coupled problem of medium sized molecules (100-500 atoms) and the more weakly coupled problem of decomposing ("fragmenting") a molecular system and then stitching it back together. In this Account, we address both of these problems, the first by using graphical processing units (GPUs) and electronic structure algorithms tuned for these architectures and the second by using an exciton model as a framework in which to stitch together the solutions of the smaller problems. The multitiered parallel framework outlined here is aimed at nonadiabatic dynamics simulations on large supramolecular multichromophoric complexes in full atomistic detail. In this framework, the lowest tier of parallelism involves GPU-accelerated electronic structure theory calculations, for which we summarize recent progress in parallelizing the computation and use of electron repulsion integrals (ERIs), which are the major computational bottleneck in both density functional theory (DFT) and time-dependent density functional theory (TDDFT). The topmost tier of parallelism relies on a distributed memory framework, in which we build an exciton model that couples chromophoric units. Combining these multiple levels of parallelism allows access to ground and excited state dynamics for large multichromophoric assemblies. The parallel excitonic framework is in good agreement with much more computationally demanding TDDFT calculations of the full assembly.

  View details for DOI 10.1021/ar500229p

  View details for Web of Science ID 000341800800018

• Direct QM/MM simulation of photoexcitation dynamics in bacteriorhodopsin and halorhodopsin CHEMICAL PHYSICS LETTERS Punwong, C., Martinez, T. J., HANNONGBUA, S. 2014; 610: 213-218

  View details for DOI 10.1016/j.cplett.2014.07.037

  View details for Web of Science ID 000342527500040

• Theoretical insight on mechanical sensitivity of chemical reactions rates from ab initio molecular dynamics free energy modeling Plotnikov, N. V., Martinez, T. J. AMER CHEMICAL SOC. 2014

  View details for Web of Science ID 000349167403806

• Reduced scaling in electronic structure theory via tensor hypercontraction Hohenstein, E. G., Parrish, R. M., Martinez, T. J. AMER CHEMICAL SOC. 2014

  View details for Web of Science ID 000349167403826

• Building force fields: An automatic, systematic and reproducible approach Wang, L., Martinez, T. J., Pande, V. S. AMER CHEMICAL SOC. 2014

  View details for Web of Science ID 000349167403776

• Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics. journal of chemical physics Makhov, D. V., Glover, W. J., Martinez, T. J., Shalashilin, D. V. 2014; 141 (5): 054110-?

  Abstract

  We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  View details for DOI 10.1063/1.4891530

  View details for PubMedID 25106573

• Mechanically triggered heterolytic unzipping of a low-ceiling-temperature polymer NATURE CHEMISTRY Diesendruck, C. E., Peterson, G. I., Kulik, H. J., Kaitz, J. A., Mar, B. D., May, P. A., White, S. R., Martinez, T. J., Boydston, A. J., Moore, J. S. 2014; 6 (7): 624-629

  Abstract

  Biological systems rely on recyclable materials resources such as amino acids, carbohydrates and nucleic acids. When biomaterials are damaged as a result of aging or stress, tissues undergo repair by a depolymerization-repolymerization sequence of remodelling. Integration of this concept into synthetic materials systems may lead to devices with extended lifetimes. Here, we show that a metastable polymer, end-capped poly(o-phthalaldehyde), undergoes mechanically initiated depolymerization to revert the material to monomers. Trapping experiments and steered molecular dynamics simulations are consistent with a heterolytic scission mechanism. The obtained monomer was repolymerized by a chemical initiator, effectively completing a depolymerization-repolymerization cycle. By emulating remodelling of biomaterials, this model system suggests the possibility of smart materials where aging or mechanical damage triggers depolymerization, and orthogonal conditions regenerate the polymer when and where necessary.

  View details for DOI 10.1038/NCHEM.1938

  View details for Web of Science ID 000338444600015

• Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations. Physical chemistry chemical physics Wolf, T. J., Kuhlman, T. S., Schalk, O., Martínez, T. J., Møller, K. B., Stolow, A., Unterreiner, A. 2014; 16 (23): 11770-11779

  Abstract

  Progress in our understanding of ultrafast light-induced processes in molecules is best achieved through a close combination of experimental and theoretical approaches. Direct comparison is obtained if theory is able to directly reproduce experimental observables. Here, we present a joint approach comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay of the photoelectron signal and an induction time prior to excited state depopulation in dynamics simulations. As a benchmark molecule, we have chosen hexamethylcyclopentadiene, which shows an unprecedentedly large spectral delay of (310 ± 20) fs in TRPES experiments. For the dynamics simulations, methyl groups were replaced by "hydrogen atoms" having mass 15 and TRPES spectra were calculated. These showed an induction time of (108 ± 10) fs which could directly be assigned to progress along a torsional mode leading to the intersection seam with the molecular ground state. In a stepladder-type approach, the close connection between the two phenomena could be elucidated, allowing for a comparison with other polyenes and supporting the general validity of this finding for their excited state dynamics. Thus, the combination of TRPES and AIMS proves to be a powerful tool for a thorough understanding of ultrafast excited state dynamics in polyenes.

  View details for DOI 10.1039/c4cp00977k

  View details for PubMedID 24817114

• Steric and electrostatic effects on photoisomerization dynamics using QM/MM ab initio multiple spawning THEORETICAL CHEMISTRY ACCOUNTS Virshup, A. M., Levine, B. G., Martinez, T. J. 2014; 133 (7)

  View details for DOI 10.1007/s00214-014-1506-5

  View details for Web of Science ID 000337047700001

• Building Force Fields: An Automatic, Systematic, and Reproducible Approach JOURNAL OF PHYSICAL CHEMISTRY LETTERS Wang, L., Martinez, T. J., Pande, V. S. 2014; 5 (11): 1885-1891

  Abstract

  The development of accurate molecular mechanics force fields is a significant challenge that must be addressed for the continued success of molecular simulation. We developed the ForceBalance method to automatically derive accurate force field parameters using flexible combinations of experimental and theoretical reference data. The method is demonstrated in the parametrization of two rigid water models, yielding new parameter sets (TIP3P-FB and TIP4P-FB) that accurately describe many physical properties of water.

  View details for DOI 10.1021/jz500737m

  View details for Web of Science ID 000337012500017

• Ultrafast X-ray Auger probing of photoexcited molecular dynamics NATURE COMMUNICATIONS McFarland, B. K., Farrell, J. P., Miyabe, S., Tarantelli, F., Aguilar, A., Berrah, N., Bostedt, C., Bozek, J. D., Bucksbaum, P. H., Castagna, J. C., Coffee, R. N., Cryan, J. P., Fang, L., Feifel, R., Gaffney, K. J., Glownia, J. M., Martinez, T. J., Mucke, M., Murphy, B., Natan, A., Osipov, T., Petrovic, V. S., Schorb, S., Schultz, T., SPECTOR, L. S., Swiggers, M., Tenney, I., Wang, S., WHITE, J. L., White, W., Guehr, M. 2014; 5

  View details for DOI 10.1038/ncomms5235

  View details for Web of Science ID 000338840000004

• Steric and electronic contributions to the core reactivity of monoprotonated 5-phenylporphyrin: A DFT study CHEMICAL PHYSICS LETTERS Presselt, M., Wojdyr, M., Beenken, W. J., Kruk, M., Martinez, T. J. 2014; 603: 21-27

  View details for DOI 10.1016/j.cplett.2014.04.011

  View details for Web of Science ID 000336485400005

• Communication: Acceleration of coupled cluster singles and doubles via orbital-weighted least-squares tensor hypercontraction. journal of chemical physics Parrish, R. M., Sherrill, C. D., Hohenstein, E. G., Kokkila, S. I., Martínez, T. J. 2014; 140 (18): 181102-?

  View details for DOI 10.1063/1.4876016

  View details for PubMedID 24832246

• Photochemical Dynamics of Ethylene Cation C2H4+ JOURNAL OF PHYSICAL CHEMISTRY LETTERS Joalland, B., Mori, T., Martinez, T. J., Suits, A. G. 2014; 5 (8): 1467-1471

  Abstract

  We present a theoretical study of the nonadiabatic effects in ethylene cation C2H4(+), the simplest π radical cation, after photoexcitation to its three lowest doublet excited states. Two families of conical intersections are found, with minimum energy structures characterized by planar and twisted geometries. Ab initio multiple spawning dynamical calculations suggest that the competition between these relaxation pathways depends strongly on the initial excited state, with excited state lifetimes in the 30-60 fs range. Ultrafast decay via planar geometries deposits the molecule near a bridged minimum on the ground state, allowing prompt H migration events. The alternative pathway mediated by torsional motion induces important backspawned population transfer promoted by hindered rotations. The results allow us to revisit earlier vibrationally-mediated photodissociation experiments and shed light on the electronic relaxation dynamics of a prototypical radical cation subject to strong vibronic interactions.

  View details for DOI 10.1021/jz500352x

  View details for Web of Science ID 000334731700028

• Multiple time step integrators in ab initio molecular dynamics. journal of chemical physics Luehr, N., Markland, T. E., Martínez, T. J. 2014; 140 (8): 084116-?

  Abstract

  Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  View details for DOI 10.1063/1.4866176

  View details for PubMedID 24588157

• Axis-dependence of molecular high harmonic emission in three dimensions. Nature communications Spector, L. S., Artamonov, M., Miyabe, S., Martinez, T., Seideman, T., Guehr, M., Bucksbaum, P. H. 2014; 5: 3190-?

  Abstract

  High-order harmonic generation in an atomic or molecular gas is a promising source of sub-femtosecond vacuum ultraviolet coherent radiation for transient scattering, absorption, metrology and imaging applications. High harmonic spectra are sensitive to Ångstrom-scale structure and motion of laser-driven molecules, but interference from radiation produced by random molecular orientations obscures this in all but the simplest cases, such as linear molecules. Here we show how to extract full body-frame high harmonic generation information for molecules with more complicated geometries by utilizing the methods of coherent transient rotational spectroscopy. To demonstrate this approach, we obtain the relative strength of harmonic emission along the three principal axes in the asymmetric-top sulphur dioxide. This greatly simplifies the analysis task of high harmonic spectroscopy and extends its usefulness to more complex molecules.

  View details for DOI 10.1038/ncomms4190

  View details for PubMedID 24504181

• Modeling mechanophore activation within a viscous rubbery network JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS Silberstein, M. N., Cremar, L. D., Beiermann, B. A., Kramer, S. B., Martinez, T. J., White, S. R., Sottos, N. R. 2014; 63: 141-153

  View details for DOI 10.1016/j.jmps.2013.09.014

  View details for Web of Science ID 000331006900010

• Systematic Improvement on the Classical Molecular Model of Water Wang, L., Head-Gordon, T., Ponder, J., Ren, P., Chodera, J., Eastman, P., Martinez, T. J., Pande, V. S. CELL PRESS. 2014: 403A

  View details for DOI 10.1016/j.bpj.2013.11.2273

  View details for Web of Science ID 000337000402271

• Ultrafast X-ray Auger probing of photoexcited molecular dynamics. Nature communications McFarland, B. K., Farrell, J. P., Miyabe, S., Tarantelli, F., Aguilar, A., Berrah, N., Bostedt, C., Bozek, J. D., Bucksbaum, P. H., Castagna, J. C., Coffee, R. N., Cryan, J. P., Fang, L., Feifel, R., Gaffney, K. J., Glownia, J. M., Martinez, T. J., Mucke, M., Murphy, B., Natan, A., Osipov, T., Petrovic, V. S., Schorb, S., Schultz, T., SPECTOR, L. S., Swiggers, M., Tenney, I., Wang, S., WHITE, J. L., White, W., Gühr, M. 2014; 5: 4235-?

  Abstract

  Molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation--X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towards high kinetic energies, resulting from a particular C-O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.

  View details for DOI 10.1038/ncomms5235

  View details for PubMedID 24953740

• Enhancement of strong-field multiple ionization in the vicinity of the conical intersection in 1,3-cyclohexadiene ring opening JOURNAL OF CHEMICAL PHYSICS Petrovic, V. S., Schorb, S., Kim, J., White, J., Cryan, J. P., Glownia, J. M., Zipp, L., Broege, D., Miyabe, S., Tao, H., Martinez, T., Bucksbaum, P. H. 2013; 139 (18)

  Abstract

  Nonradiative energy dissipation in electronically excited polyatomic molecules proceeds through conical intersections, loci of degeneracy between electronic states. We observe a marked enhancement of laser-induced double ionization in the vicinity of a conical intersection during a non-radiative transition. We measured double ionization by detecting the kinetic energy of ions released by laser-induced strong-field fragmentation during the ring-opening transition between 1,3-cyclohexadiene and 1,3,5-hexatriene. The enhancement of the double ionization correlates with the conical intersection between the HOMO and LUMO orbitals.

  View details for DOI 10.1063/1.4829766

  View details for Web of Science ID 000327712800032

  View details for PubMedID 24320276

• Tensor Hypercontraction Equation-of-Motion Second-Order Approximate Coupled Cluster: Electronic Excitation Energies in O(N-4) Time JOURNAL OF PHYSICAL CHEMISTRY B Hohenstein, E. G., Kokkila, S. I., Parrish, R. M., Martinez, T. J. 2013; 117 (42): 12972-12978

  Abstract

  The tensor hypercontraction (THC) formalism is applied to equation-of-motion second-order approximate coupled cluster singles and doubles (EOM-CC2). The resulting method, THC-EOM-CC2, is shown to scale as [Formula: see text], a reduction of one order from the formal [Formula: see text] scaling of conventional EOM-CC2. Numerical tests for a variety of molecules show that errors of less than 0.02 eV are introduced into the excitation energies.

  View details for DOI 10.1021/jp4021905

  View details for Web of Science ID 000326259800032

• The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules JOURNAL OF PHYSICAL CHEMISTRY B Isborn, C. M., Mar, B. D., Curchod, B. F., Tavernelli, I., Martinez, T. J. 2013; 117 (40): 12189-12201

  Abstract

  Recent advances in algorithms and computational hardware have enabled the calculation of excited states with time-dependent density functional theory (TDDFT) for large systems of O(1000) atoms. Unfortunately, the aqueous charge transfer problem in TDDFT (whereby many spuriously low-lying charge transfer excited states are predicted) seems to become more severe as the system size is increased. In this work, we concentrate on the common case where a chromophore is embedded in aqueous solvent. We examine the role of exchange-correlation functionals, basis set effects, ground state geometries, and the treatment of the external environment in order to assess the root cause of this problem. We conclude that the problem rests largely on water molecules at the boundary of a finite cluster model, i.e., "edge waters." We also demonstrate how the TDDFT problem can be related directly to ground state problems. These findings demand caution in the commonly employed strategy that rests on "snapshot" cutout geometries taken from ground state dynamics with molecular mechanics. We also find that the problem is largely ameliorated when the range-separated hybrid functional LC-ωPBEh is used.

  View details for DOI 10.1021/jp4058274

  View details for Web of Science ID 000326367000031

  View details for PubMedID 23964865

• Exact Tensor Hypercontraction: A Universal Technique for the Resolution of Matrix Elements of Local Finite-Range N-Body Potentials in Many-Body Quantum Problems PHYSICAL REVIEW LETTERS Parrish, R. M., Hohenstein, E. G., Schunck, N. F., Sherrill, C. D., Martinez, T. J. 2013; 111 (13)

  Abstract

  Configuration-space matrix elements of N-body potentials arise naturally and ubiquitously in the Ritz-Galerkin solution of many-body quantum problems. For the common specialization of local, finite-range potentials, we develop the exact tensor hypercontraction method, which provides a quantized renormalization of the coordinate-space form of the N-body potential, allowing for a highly separable tensor factorization of the configuration-space matrix elements. This representation allows for substantial computational savings in chemical, atomic, and nuclear physics simulations, particularly with respect to difficult "exchangelike" contractions.

  View details for DOI 10.1103/PhysRevLett.111.132505

  View details for Web of Science ID 000325364600001

  View details for PubMedID 24116775

• Photochemical dynamics on excited states in ethylene cation Joalland, B. Y., Mori, T., Martinez, T. J., Suits, A. G. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618406314

• Tensor hypercontraction and graphical processing units for electronic structure and ab initio molecular dynamics Martinez, T. J., Hohenstein, E., Kokkila, S. L., Ufimtsev, I. S., Luehr, N., Parrish, R. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618406015

• Enhanced strong-field multiple ionization in the vicinity of S-1/S-0 conical intersection in 1,3-cyclohexadiene Petrovic, V., Schorb, S., Kim, J., White, J., Cryan, J., Glownia, J. M., Zipp, L., Broege, D., Miyabe, S., Tao, H., Martinez, T., Bucksbaum, P. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618406281

• ForceBalance, a method for developing better force fields Wang, L., Van Voorhis, T., Martinez, T. J., Pande, V. S. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618402575

• Systematic improvement on the classical molecular model of water Wang, L., Head-Gordon, T., Ponder, J. W., Ren, P., Chodera, J. D., Eastman, P. K., Martinez, T. J., Pande, V. S. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618402611

• Interactive ab initio molecular dynamics Luehr, N., Jin, A., Martinez, T. J. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618402672

• Rotational dynamics of water near protein binding sites: Insights from ab initio molecular dynamics simulation Ufimtsev, I. S., Martinez, T. J. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000329618406119

• Systematic improvement of a classical molecular model of water. journal of physical chemistry. B Wang, L., Head-Gordon, T., Ponder, J. W., Ren, P., Chodera, J. D., Eastman, P. K., Martinez, T. J., Pande, V. S. 2013; 117 (34): 9956-9972

  Abstract

  We report the iAMOEBA ("inexpensive AMOEBA") classical polarizable water model. The iAMOEBA model uses a direct approximation to describe electronic polarizability, in which the induced dipoles are determined directly from the permanent multipole electric fields and do not interact with one another. The direct approximation reduces the computational cost relative to a fully self-consistent polarizable model such as AMOEBA. The model is parameterized using ForceBalance, a systematic optimization method that simultaneously utilizes training data from experimental measurements and high-level ab initio calculations. We show that iAMOEBA is a highly accurate model for water in the solid, liquid, and gas phases, with the ability to fully capture the effects of electronic polarization and predict a comprehensive set of water properties beyond the training data set including the phase diagram. The increased accuracy of iAMOEBA over the fully polarizable AMOEBA model demonstrates ForceBalance as a method that allows the researcher to systematically improve empirical models by efficiently utilizing the available data.

  View details for DOI 10.1021/jp403802c

  View details for PubMedID 23750713

  View details for PubMedCentralID PMC3770532

• Relation of exact Gaussian basis methods to the dephasing representation: Theory and application to time-resolved electronic spectra JOURNAL OF CHEMICAL PHYSICS Sulc, M., Hernandez, H., Martinez, T. J., Vanicek, J. 2013; 139 (3)

  Abstract

  We recently showed that the dephasing representation (DR) provides an efficient tool for computing ultrafast electronic spectra and that further acceleration is possible with cellularization [M. Šulc and J. Vaníček, Mol. Phys. 110, 945 (2012)]. Here, we focus on increasing the accuracy of this approximation by first implementing an exact Gaussian basis method, which benefits from the accuracy of quantum dynamics and efficiency of classical dynamics. Starting from this exact method, the DR is derived together with ten other methods for computing time-resolved spectra with intermediate accuracy and efficiency. These methods include the Gaussian DR, an exact generalization of the DR, in which trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. The newly obtained methods are tested numerically on time correlation functions and time-resolved stimulated emission spectra in the harmonic potential, pyrazine S0∕S1 model, and quartic oscillator. Numerical results confirm that both the Gaussian basis method and the Gaussian DR increase the accuracy of the DR. Surprisingly, in chaotic systems the Gaussian DR can outperform the presumably more accurate Gaussian basis method, in which the two bases are evolved separately.

  View details for DOI 10.1063/1.4813124

  View details for Web of Science ID 000322203000014

• Modeling mechanophore activation within a crosslinked glassy matrix JOURNAL OF APPLIED PHYSICS Silberstein, M. N., Min, K., Cremar, L. D., Degen, C. M., Martinez, T. J., Aluru, N. R., White, S. R., Sottos, N. R. 2013; 114 (2)

  View details for DOI 10.1063/1.4812581

  View details for Web of Science ID 000321761600011

• Discrete variable representation in electronic structure theory: Quadrature grids for least-squares tensor hypercontraction JOURNAL OF CHEMICAL PHYSICS Parrish, R. M., Hohenstein, E. G., Martinez, T. J., Sherrill, C. D. 2013; 138 (19)

  Abstract

  We investigate the application of molecular quadratures obtained from either standard Becke-type grids or discrete variable representation (DVR) techniques to the recently developed least-squares tensor hypercontraction (LS-THC) representation of the electron repulsion integral (ERI) tensor. LS-THC uses least-squares fitting to renormalize a two-sided pseudospectral decomposition of the ERI, over a physical-space quadrature grid. While this procedure is technically applicable with any choice of grid, the best efficiency is obtained when the quadrature is tuned to accurately reproduce the overlap metric for quadratic products of the primary orbital basis. Properly selected Becke DFT grids can roughly attain this property. Additionally, we provide algorithms for adopting the DVR techniques of the dynamics community to produce two different classes of grids which approximately attain this property. The simplest algorithm is radial discrete variable representation (R-DVR), which diagonalizes the finite auxiliary-basis representation of the radial coordinate for each atom, and then combines Lebedev-Laikov spherical quadratures and Becke atomic partitioning to produce the full molecular quadrature grid. The other algorithm is full discrete variable representation (F-DVR), which uses approximate simultaneous diagonalization of the finite auxiliary-basis representation of the full position operator to produce non-direct-product quadrature grids. The qualitative features of all three grid classes are discussed, and then the relative efficiencies of these grids are compared in the context of LS-THC-DF-MP2. Coarse Becke grids are found to give essentially the same accuracy and efficiency as R-DVR grids; however, the latter are built from explicit knowledge of the basis set and may guide future development of atom-centered grids. F-DVR is found to provide reasonable accuracy with markedly fewer points than either Becke or R-DVR schemes.

  View details for DOI 10.1063/1.4802773

  View details for Web of Science ID 000319291600009

  View details for PubMedID 23697409

• Time resolved photoelectron spectroscopy from first principles nonadiabatic dynamics Martinez, T. J. AMER CHEMICAL SOC. 2013

  View details for Web of Science ID 000324303603618

• Quartic scaling second-order approximate coupled cluster singles and doubles via tensor hypercontraction: THC-CC2 JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Kokkila, S. I., Parrish, R. M., Martinez, T. J. 2013; 138 (12)

  Abstract

  The second-order approximate coupled cluster singles and doubles method (CC2) is a valuable tool in electronic structure theory. Although the density fitting approximation has been successful in extending CC2 to larger molecules, it cannot address the steep O(N(5)) scaling with the number of basis functions, N. Here, we introduce the tensor hypercontraction (THC) approximation to CC2 (THC-CC2), which reduces the scaling to O(N(4)) and the storage requirements to O(N(2)). We present an algorithm to efficiently evaluate the THC-CC2 correlation energy and demonstrate its quartic scaling. This implementation of THC-CC2 uses a grid-based least-squares THC (LS-THC) approximation to the density-fitted electron repulsion integrals. The accuracy of the CC2 correlation energy under these approximations is shown to be suitable for most practical applications.

  View details for DOI 10.1063/1.4795514

  View details for Web of Science ID 000316969500064

  View details for PubMedID 23556713

• Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method. Journal of chemical theory and computation Mori, T., Martínez, T. J. 2013; 9 (2): 1155-63

  Abstract

  Conical intersections (CIs) play a fundamental role in photoreactions. Although it is widely known that CIs are not isolated points but rather multidimensional seams, there is a dearth of techniques to explore and characterize these seams beyond the immediate vicinity of minimum energy points within the intersection space (minimum energy conical intersections or MECIs). Here, we develop a method that connects these MECIs by minimal energy paths within the space of geometries that maintain the electronic degeneracy (the "seam space") in order to obtain a more general picture of a CI seam. This method, the seam space nudged elastic band (SS-NEB) method, combines the nudged elastic band method with gradient projected MECI optimization. It provides a very efficient way of finding minimum energy seam paths in the conical intersection seam. The method is demonstrated by application to two molecules: ethylene and the green fluorescent protein (GFP) chromophore. The results show that previously known MECIs for these molecules are connected within a single seam, adding further support to previous conjectures that all MECIs are topologically connected in the seam space. Analysis of the nonadiabatic dynamics further suggests that a broad range of seam geometries, not only the vicinity of MECIs, is involved in the nonadiabatic transition events. The current method provides a tool to characterize CI seams in different environments and to explore the importance of the seam in the dynamics.

  View details for DOI 10.1021/ct300892t

  View details for PubMedID 26588758

• Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method JOURNAL OF CHEMICAL THEORY AND COMPUTATION Mori, T., Martinez, T. J. 2013; 9 (2): 1155-1163

  Abstract

  Conical intersections (CIs) play a fundamental role in photoreactions. Although it is widely known that CIs are not isolated points but rather multidimensional seams, there is a dearth of techniques to explore and characterize these seams beyond the immediate vicinity of minimum energy points within the intersection space (minimum energy conical intersections or MECIs). Here, we develop a method that connects these MECIs by minimal energy paths within the space of geometries that maintain the electronic degeneracy (the "seam space") in order to obtain a more general picture of a CI seam. This method, the seam space nudged elastic band (SS-NEB) method, combines the nudged elastic band method with gradient projected MECI optimization. It provides a very efficient way of finding minimum energy seam paths in the conical intersection seam. The method is demonstrated by application to two molecules: ethylene and the green fluorescent protein (GFP) chromophore. The results show that previously known MECIs for these molecules are connected within a single seam, adding further support to previous conjectures that all MECIs are topologically connected in the seam space. Analysis of the nonadiabatic dynamics further suggests that a broad range of seam geometries, not only the vicinity of MECIs, is involved in the nonadiabatic transition events. The current method provides a tool to characterize CI seams in different environments and to explore the importance of the seam in the dynamics.

  View details for DOI 10.1021/ct300892t

  View details for Web of Science ID 000315018300033

• Generating Efficient Quantum Chemistry Codes for Novel Architectures. Journal of chemical theory and computation Titov, A. V., Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2013; 9 (1): 213-21

  Abstract

  We describe an extension of our graphics processing unit (GPU) electronic structure program TeraChem to include atom-centered Gaussian basis sets with d angular momentum functions. This was made possible by a "meta-programming" strategy that leverages computer algebra systems for the derivation of equations and their transformation to correct code. We generate a multitude of code fragments that are formally mathematically equivalent, but differ in their memory and floating-point operation footprints. We then select between different code fragments using empirical testing to find the highest performing code variant. This leads to an optimal balance of floating-point operations and memory bandwidth for a given target architecture without laborious manual tuning. We show that this approach is capable of similar performance compared to our hand-tuned GPU kernels for basis sets with s and p angular momenta. We also demonstrate that mixed precision schemes (using both single and double precision) remain stable and accurate for molecules with d functions. We provide benchmarks of the execution time of entire self-consistent field (SCF) calculations using our GPU code and compare to mature CPU based codes, showing the benefits of the GPU architecture for electronic structure theory with appropriately redesigned algorithms. We suggest that the meta-programming and empirical performance optimization approach may be important in future computational chemistry applications, especially in the face of quickly evolving computer architectures.

  View details for DOI 10.1021/ct300321a

  View details for PubMedID 26589024

• Generating Efficient Quantum Chemistry Codes for Novel Architectures JOURNAL OF CHEMICAL THEORY AND COMPUTATION Titov, A. V., Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2013; 9 (1): 213-221

  Abstract

  We describe an extension of our graphics processing unit (GPU) electronic structure program TeraChem to include atom-centered Gaussian basis sets with d angular momentum functions. This was made possible by a "meta-programming" strategy that leverages computer algebra systems for the derivation of equations and their transformation to correct code. We generate a multitude of code fragments that are formally mathematically equivalent, but differ in their memory and floating-point operation footprints. We then select between different code fragments using empirical testing to find the highest performing code variant. This leads to an optimal balance of floating-point operations and memory bandwidth for a given target architecture without laborious manual tuning. We show that this approach is capable of similar performance compared to our hand-tuned GPU kernels for basis sets with s and p angular momenta. We also demonstrate that mixed precision schemes (using both single and double precision) remain stable and accurate for molecules with d functions. We provide benchmarks of the execution time of entire self-consistent field (SCF) calculations using our GPU code and compare to mature CPU based codes, showing the benefits of the GPU architecture for electronic structure theory with appropriately redesigned algorithms. We suggest that the meta-programming and empirical performance optimization approach may be important in future computational chemistry applications, especially in the face of quickly evolving computer architectures.

  View details for DOI 10.1021/ct300321a

  View details for Web of Science ID 000313378700025

• Probing nucleobase photoprotection with soft x-rays 18th International Conference on Ultrafast Phenomena McFarland, B. K., Farrell, J. P., Berrah, N., Bostedt, C., Bozek, J., Bucksbaum, P. H., Coffee, R., Cryan, J., Fang, L., Feifel, R., Gaffney, K., Glownia, J., Martinez, T., Mucke, M., Murphy, B., Miyabe, S., Natan, A., Osipov, T., Petrovic, V., Schorb, S., Schultz, T., Spector, L., Tarantelli, F., Tenney, I., Wang, S., White, W., WHITE, J., Guehr, M. E D P SCIENCES. 2013

  View details for DOI 10.1051/epjconf/20134107004

  View details for Web of Science ID 000320558600179

• Communication: Tensor hypercontraction. III. Least-squares tensor hypercontraction for the determination of correlated wavefunctions JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Parrish, R. M., Sherrill, C. D., Martinez, T. J. 2012; 137 (22)

  Abstract

  The manipulation of the rank-four tensor of double excitation amplitudes represents a challenge to the efficient implementation of many electronic structure methods. We present a proof of concept for the approximation of doubles amplitudes in the tensor hypercontraction (THC) representation. In particular, we show how THC can be used to both reduce the scaling with respect to molecular size of coupled cluster singles and doubles (CCSD) (and related methods) by two orders [from O(N(6)) to O(N(4))] and remove the memory bottleneck associated with storage of the doubles amplitudes. The accuracy of correlated methods as integral and amplitude approximations are introduced is examined. For a set of 20 small molecules, single and double-excitation configuration interaction (CISD), quadratic CISD (QCISD), and CCSD correlation energies could be reproduced with millihartree accuracy after the introduction of these approximations. Our approach exploits otherwise hidden factorizable tensor structure in both the electron repulsion integrals and the wavefunction coefficients and should be applicable with suitable modifications to many methods in electronic structure theory.

  View details for DOI 10.1063/1.4768241

  View details for Web of Science ID 000312491400055

  View details for PubMedID 23248980

• Nonlinear dimensionality reduction for nonadiabatic dynamics: The influence of conical intersection topography on population transfer rates JOURNAL OF CHEMICAL PHYSICS Virshup, A. M., Chen, J., Martinez, T. J. 2012; 137 (22)

  Abstract

  Conical intersections play a critical role in the nonadiabatic relaxation of excited electronic states. However, there are an infinite number of these intersections and it is difficult to predict which are actually relevant. Furthermore, traditional descriptors such as intrinsic reaction coordinates and steepest descent paths often fail to adequately characterize excited state reactions due to their highly nonequilibrium nature. To address these deficiencies in the characterization of excited state mechanisms, we apply a nonlinear dimensionality reduction scheme (diffusion mapping) to generate reaction coordinates directly from ab initio multiple spawning dynamics calculations. As illustrated with various examples of photoisomerization dynamics, excited state reaction pathways can be derived directly from simulation data without any a priori specification of relevant coordinates. Furthermore, diffusion maps also reveal the influence of intersection topography on the efficiency of electronic population transfer, providing further evidence that peaked intersections promote nonadiabatic transitions more effectively than sloped intersections. Our results demonstrate the usefulness of nonlinear dimensionality reduction techniques as powerful tools for elucidating reaction mechanisms beyond the statistical description of processes on ground state potential energy surfaces.

  View details for DOI 10.1063/1.4742066

  View details for Web of Science ID 000312491400020

  View details for PubMedID 23249056

• Tensor hypercontraction. II. Least-squares renormalization JOURNAL OF CHEMICAL PHYSICS Parrish, R. M., Hohenstein, E. G., Martinez, T. J., Sherrill, C. D. 2012; 137 (22)

  Abstract

  The least-squares tensor hypercontraction (LS-THC) representation for the electron repulsion integral (ERI) tensor is presented. Recently, we developed the generic tensor hypercontraction (THC) ansatz, which represents the fourth-order ERI tensor as a product of five second-order tensors [E. G. Hohenstein, R. M. Parrish, and T. J. Martínez, J. Chem. Phys. 137, 044103 (2012)]. Our initial algorithm for the generation of the THC factors involved a two-sided invocation of overlap-metric density fitting, followed by a PARAFAC decomposition, and is denoted PARAFAC tensor hypercontraction (PF-THC). LS-THC supersedes PF-THC by producing the THC factors through a least-squares renormalization of a spatial quadrature over the otherwise singular 1∕r(12) operator. Remarkably, an analytical and simple formula for the LS-THC factors exists. Using this formula, the factors may be generated with O(N(5)) effort if exact integrals are decomposed, or O(N(4)) effort if the decomposition is applied to density-fitted integrals, using any choice of density fitting metric. The accuracy of LS-THC is explored for a range of systems using both conventional and density-fitted integrals in the context of MP2. The grid fitting error is found to be negligible even for extremely sparse spatial quadrature grids. For the case of density-fitted integrals, the additional error incurred by the grid fitting step is generally markedly smaller than the underlying Coulomb-metric density fitting error. The present results, coupled with our previously published factorizations of MP2 and MP3, provide an efficient, robust O(N(4)) approach to both methods. Moreover, LS-THC is generally applicable to many other methods in quantum chemistry.

  View details for DOI 10.1063/1.4768233

  View details for Web of Science ID 000312491400061

  View details for PubMedID 23248986

• Electronic Absorption Spectra from MM and ab Initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein JOURNAL OF CHEMICAL THEORY AND COMPUTATION Isborn, C. M., Goetz, A. W., Clark, M. A., Walker, R. C., Martinez, T. J. 2012; 8 (12): 5092-5106

  Abstract

  We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.

  View details for DOI 10.1021/ct3006826

  View details for Web of Science ID 000312122200025

  View details for PubMedCentralID PMC3590007

• Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. Journal of chemical theory and computation Isborn, C. M., Götz, A. W., Clark, M. A., Walker, R. C., Martínez, T. J. 2012; 8 (12): 5092-5106

  Abstract

  We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.

  View details for DOI 10.1021/ct3006826

  View details for PubMedID 23476156

  View details for PubMedCentralID PMC3590007

• Ab Initio Quantum Chemistry for Protein Structures JOURNAL OF PHYSICAL CHEMISTRY B Kulik, H. J., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2012; 116 (41): 12501-12509

  Abstract

  Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio "force fields" to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to carry out systematic optimization of ab initio protein structures, which we compare against experimental and molecular mechanics force field references. We show that the quality of the ab initio optimized structures, as judged by conventional protein health metrics, increases with increasing basis set size. On the other hand, there is little evidence for a significant improvement of predicted structures using density functional theory as compared to Hartree-Fock methods. Although occasional pathologies of minimal basis sets are observed, these are easily alleviated with even the smallest double-ζ basis sets.

  View details for DOI 10.1021/jp307741u

  View details for Web of Science ID 000309902400013

  View details for PubMedID 22974088

• Charge-transfer states in the nonadiabatic dynamics of photoexcited trans-butadiene Glover, W. J., Martinez, T. J. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324621807620

• Predictive enzyme catalysis and protein structure with quantum chemistry on the GPU Kulik, H. J., Martinez, T. J. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324621803286

• Ab initio QM/MM molecular dynamics using TeraChem and AMBER: Exploring environmental effects on the absorption spectrum of photoactive yellow protein Isborn, C. M., Goetz, A. W., Clark, M., Martinez, T. J., Walker, R. C. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324621803368

• Photodynamics and spectroscopy in chemical and biological systems: The full multiple spawning method with thermal statistics Liu, J., Martinez, T. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324621807208

• Excitation and charge transport with first principles dynamics Martinez, T. J. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324621807314

• Tensor hypercontraction density fitting. I. Quartic scaling second- and third-order Moller-Plesset perturbation theory JOURNAL OF CHEMICAL PHYSICS Hohenstein, E. G., Parrish, R. M., Martinez, T. J. 2012; 137 (4)

  Abstract

  Many approximations have been developed to help deal with the O(N(4)) growth of the electron repulsion integral (ERI) tensor, where N is the number of one-electron basis functions used to represent the electronic wavefunction. Of these, the density fitting (DF) approximation is currently the most widely used despite the fact that it is often incapable of altering the underlying scaling of computational effort with respect to molecular size. We present a method for exploiting sparsity in three-center overlap integrals through tensor decomposition to obtain a low-rank approximation to density fitting (tensor hypercontraction density fitting or THC-DF). This new approximation reduces the 4th-order ERI tensor to a product of five matrices, simultaneously reducing the storage requirement as well as increasing the flexibility to regroup terms and reduce scaling behavior. As an example, we demonstrate such a scaling reduction for second- and third-order perturbation theory (MP2 and MP3), showing that both can be carried out in O(N(4)) operations. This should be compared to the usual scaling behavior of O(N(5)) and O(N(6)) for MP2 and MP3, respectively. The THC-DF technique can also be applied to other methods in electronic structure theory, such as coupled-cluster and configuration interaction, promising significant gains in computational efficiency and storage reduction.

  View details for DOI 10.1063/1.4732310

  View details for Web of Science ID 000307611500004

  View details for PubMedID 22852593

• Transient X-Ray Fragmentation: Probing a Prototypical Photoinduced Ring Opening PHYSICAL REVIEW LETTERS Petrovic, V. S., Siano, M., White, J. L., Berrah, N., Bostedt, C., Bozek, J. D., Broege, D., Chalfin, M., Coffee, R. N., Cryan, J., Fang, L., Farrell, J. P., Frasinski, L. J., Glownia, J. M., Guehr, M., Hoener, M., Holland, D. M., Kim, J., Marangos, J. P., Martinez, T., McFarland, B. K., Minns, R. S., Miyabe, S., Schorb, S., Sension, R. J., Spector, L. S., Squibb, R., Tao, H., Underwood, J. G., Bucksbaum, P. H. 2012; 108 (25)

  Abstract

  We report the first study of UV-induced photoisomerization probed via core ionization by an x-ray laser. We investigated x-ray ionization and fragmentation of the cyclohexadiene-hexatriene system at 850 eV during the ring opening. We find that the ion-fragmentation patterns evolve over a picosecond, reflecting a change in the state of excitation and the molecular geometry: the average kinetic energy per ion fragment and H(+)-ion count increase as the ring opens and the molecule elongates. We discuss new opportunities for molecular photophysics created by optical pump x-ray probe experiments.

  View details for DOI 10.1103/PhysRevLett.108.253006

  View details for Web of Science ID 000305569100005

  View details for PubMedID 23004597

• Ultrafast internal conversion in ethylene. II. Mechanisms and pathways for quenching and hydrogen elimination JOURNAL OF CHEMICAL PHYSICS Allison, T. K., Tao, H., Glover, W. J., Wright, T. W., Stooke, A. M., Khurmi, C., van Tilborg, J., Liu, Y., Falcone, R. W., Martinez, T. J., Belkacem, A. 2012; 136 (12)

  Abstract

  Through a combined experimental and theoretical approach, we study the nonadiabatic dynamics of the prototypical ethylene (C(2)H(4)) molecule upon π → π(∗) excitation with 161 nm light. Using a novel experimental apparatus, we combine femtosecond pulses of vacuum ultraviolet and extreme ultraviolet (XUV) radiation with variable delay to perform time resolved photo-ion fragment spectroscopy. In this second part of a two part series, the XUV (17 eV < hν < 23 eV) probe pulses are sufficiently energetic to break the C-C bond in photoionization, or to photoionize the dissociation products of the vibrationally hot ground state. The experimental data is directly compared to excited state ab initio molecular dynamics simulations explicitly accounting for the probe step. Enhancements of the CH(2)(+) and CH(3)(+) photo-ion fragment yields, corresponding to molecules photoionized in ethylene (CH(2)CH(2)) and ethylidene (CH(3)CH) like geometries are observed within 100 fs after π → π(∗) excitation. Quantitative agreement between theory and experiment on the relative CH(2)(+) and CH(3)(+) yields provides experimental confirmation of the theoretical prediction of two distinct conical intersections and their branching ratio [H. Tao, B. G. Levine, and T. J. Martinez, J. Phys. Chem. A. 113, 13656 (2009)]. Evidence for fast, non-statistical, elimination of H(2) molecules and H atoms is observed in the time resolved H(2)(+) and H(+) signals.

  View details for DOI 10.1063/1.3697760

  View details for Web of Science ID 000302216200043

  View details for PubMedID 22462867

• Converging to the basis set limit using empirical correction potentials Wang, L., Martinez, T., Pande, V. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324475104627

• Markov-state model analysis of systems containing identical and exchangable components using an optimally permuted RMSD metric Wang, L., Pande, V., Martinez, T. AMER CHEMICAL SOC. 2012

  View details for Web of Science ID 000324475104448

• Role of Rydberg States in the Photochemical Dynamics of Ethylene JOURNAL OF PHYSICAL CHEMISTRY A Mori, T., Glover, W. J., Schuurman, M. S., Martinez, T. J. 2012; 116 (11): 2808-2818

  Abstract

  We use the ab initio multiple spawning method with potential energy surfaces and nonadiabatic coupling vectors computed from multistate multireference perturbation theory (MSPT2) to follow the dynamics of ethylene after photoexcitation. We introduce an analytic formulation for the nonadiabatic coupling vector in the context of MSPT2 calculations. We explicitly include the low-lying 3s Rydberg state which has been neglected in previous ab initio molecular dynamics studies of this process. We find that although the 3s Rydberg state lies below the optically bright ππ* state, little population gets trapped on this state. Instead, the 3s Rydberg state is largely a spectator in the photodynamics, with little effect on the quenching mechanism or excited state lifetime. We predict the time-resolved photoelectron spectrum for ethylene and point out the signature of Rydberg state involvement that should be easily observed.

  View details for DOI 10.1021/jp2097185

  View details for Web of Science ID 000301766500027

  View details for PubMedID 22148837

• Control of 1,3-Cyclohexadiene Photoisomerization Using Light-Induced Conical Intersections JOURNAL OF PHYSICAL CHEMISTRY A Kim, J., Tao, H., White, J. L., Petrovic, V. S., Martinez, T. J., Bucksbaum, P. H. 2012; 116 (11): 2758-2763

  Abstract

  We have studied the photoinduced isomerization from 1,3-cyclohexadiene to 1,3,5-hexatriene in the presence of an intense ultrafast laser pulse. We find that the laser field maximally suppresses isomerization if it is both polarized parallel to the excitation dipole and present 50 fs after the initial photoabsorption, at the time when the system is expected to be in the vicinity of a conical intersection that mediates this structural transition. A modified ab initio multiple spawning (AIMS) method shows that the laser induces a resonant coupling between the excited state and the ground state, i.e., a light-induced conical intersection. The theory accounts for the timing and direction of the effect.

  View details for DOI 10.1021/jp208384b

  View details for Web of Science ID 000301766500022

  View details for PubMedID 22082319

• Between ethylene and polyenes - the non-adiabatic dynamics of cis-dienes FARADAY DISCUSSIONS Kuhlman, T. S., Glover, W. J., Mori, T., Moller, K. B., Martinez, T. J. 2012; 157: 193-212

  Abstract

  Using Ab Initio Multiple Spawning (AIMS) with a Multi-State Multi-Reference Perturbation theory (MS-MR-CASPT2) treatment of the electronic structure, we have simulated the non-adiabatic excited state dynamics of cyclopentadiene (CPD) and 1,2,3,4-tetramethyl-cyclopentadiene (Me4-CPD) following excitation to S1. It is observed that torsion around the carbon-carbon double bonds is essential in reaching a conical intersection seam connecting S1 and S0. We identify two timescales; the induction time from excitation to the onset of population transfer back to S0 (CPD: -25 fs, Me4-CPD: -71 fs) and the half-life of the subsequent population transfer (CPD: -28 fs, Me4-CPD: -48 fs). The longer timescales for Me4-CPD are a kinematic consequence of the inertia of the substituents impeding the essential out-of-plane motion that leads to the conical intersection seam. A bifurcation is observed on S1 leading to population transfer being attributable, in a 5 : 2 ratio for CPD and 7 : 2 ratio for Me4-CPD, to two closely related conical intersections. Calculated time-resolved photoelectron spectra are in excellent agreement with experimental spectra validating the simulation results.

  View details for DOI 10.1039/c2fd20055d

  View details for Web of Science ID 000309137600011

  View details for PubMedID 23230770

• Ultrafast X-ray probe of Nucleobase Photoprotection Conference on Lasers and Electro-Optics (CLEO) Farrell, J. P., McFarland, B. K., Berrah, N., Bostedt, C., Bozek, J., Bucksbaum, P. H., Coffee, R., Cryan, J., Fang, L., Feifel, R., Gaffney, K., Glownia, J., Martinez, T., Mucke, M., Murphy, B., Miyabe, S., Natan, A., Osipov, T., Petrovic, V., Schorb, S., Schultz, T., Spector, L., Tarantelli, F., Tenney, I., Wang, S., White, W., WHITE, J., Guehr, M. IEEE. 2012

  View details for Web of Science ID 000310362403286

• A scheme to interpolate potential energy surfaces and derivative coupling vectors without performing a global diabatization JOURNAL OF CHEMICAL PHYSICS Evenhuis, C., Martinez, T. J. 2011; 135 (22)

  Abstract

  Simulation of non-adiabatic molecular dynamics requires the description of multiple electronic state potential energy surfaces and their couplings. Ab initio molecular dynamics approaches provide an attractive avenue to accomplish this, but at great computational expense. Interpolation approaches provide a possible route to achieve flexible descriptions of the potential energy surfaces and their couplings at reduced expense. A previously developed approach based on modified Shepard interpolation required global diabatization, which can be problematic. Here, we extensively revise this previous approach, avoiding the need for global diabatization. The resulting interpolated potentials provide only adiabatic energies, gradients, and derivative couplings. This new interpolation approach has been integrated with the ab initio multiple spawning method and it has been rigorously validated against direct dynamics. It is shown that, at least for small molecules, constructing an interpolated PES can be more efficient than performing direct dynamics as measured by the total number of ab initio calculations that are required for a given accuracy.

  View details for DOI 10.1063/1.3660686

  View details for Web of Science ID 000298250600011

  View details for PubMedID 22168683

• Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics JOURNAL OF PHYSICAL CHEMISTRY LETTERS Ufimtsev, I. S., Luehr, N., Martinez, T. J. 2011; 2 (14): 1789-1793

  View details for DOI 10.1021/jz200697c

  View details for Web of Science ID 000293191800027

• Ultrafast internal conversion in ethylene. I. The excited state lifetime JOURNAL OF CHEMICAL PHYSICS Tao, H., Allison, T. K., Wright, T. W., Stooke, A. M., Khurmi, C., van Tilborg, J., Liu, Y., Falcone, R. W., Belkacem, A., Martinez, T. J. 2011; 134 (24)

  Abstract

  Using a combined theoretical and experimental approach, we investigate the non-adiabatic dynamics of the prototypical ethylene (C(2)H(4)) molecule upon π → π∗ excitation. In this first part of a two part series, we focus on the lifetime of the excited electronic state. The femtosecond time-resolved photoelectron spectrum (TRPES) of ethylene is simulated based on our recent molecular dynamics simulation using the ab initio multiple spawning method with multi-state second order perturbation theory [H. Tao, B. G. Levine, and T. J. Martinez, J. Phys. Chem. A 113, 13656 (2009)]. We find excellent agreement between the TRPES calculation and the photoion signal observed in a pump-probe experiment using femtosecond vacuum ultraviolet (hν = 7.7 eV) pulses for both pump and probe. These results explain the apparent discrepancy over the excited state lifetime between theory and experiment that has existed for ten years, with experiments [e.g., P. Farmanara, V. Stert, and W. Radloff, Chem. Phys. Lett. 288, 518 (1998) and K. Kosma, S. A. Trushin, W. Fuss, and W. E. Schmid, J. Phys. Chem. A 112, 7514 (2008)] reporting much shorter lifetimes than predicted by theory. Investigation of the TRPES indicates that the fast decay of the photoion yield originates from both energetic and electronic factors, with the energetic factor playing a larger role in shaping the signal.

  View details for DOI 10.1063/1.3604007

  View details for Web of Science ID 000292331900027

  View details for PubMedID 21721629

• Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units JOURNAL OF CHEMICAL THEORY AND COMPUTATION Isborn, C. M., Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2011; 7 (6): 1814-1823

  View details for DOI 10.1021/ct200030k

  View details for Web of Science ID 000291500400022

• Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs). Journal of chemical theory and computation Luehr, N., Ufimtsev, I. S., Martínez, T. J. 2011; 7 (4): 949-54

  Abstract

  It has recently been demonstrated that novel streaming architectures found in consumer video gaming hardware such as graphical processing units (GPUs) are well-suited to a broad range of computations including electronic structure theory (quantum chemistry). Although recent GPUs have developed robust support for double precision arithmetic, they continue to provide 2-8× more hardware units for single precision. In order to maximize performance on GPU architectures, we present a technique of dynamically selecting double or single precision evaluation for electron repulsion integrals (ERIs) in Hartree-Fock and density functional self-consistent field (SCF) calculations. We show that precision error can be effectively controlled by evaluating only the largest integrals in double precision. By dynamically scaling the precision cutoff over the course of the SCF procedure, we arrive at a scheme that minimizes the number of double precision integral evaluations for any desired accuracy. This dynamic precision scheme is shown to be effective for an array of molecules ranging in size from 20 to nearly 2000 atoms.

  View details for DOI 10.1021/ct100701w

  View details for PubMedID 26606344

• Dynamic Precision for Electron Repulsion Integral Evaluation on Graphical Processing Units (GPUs) JOURNAL OF CHEMICAL THEORY AND COMPUTATION Luehr, N., Ufimtsev, I. S., Martinez, T. J. 2011; 7 (4): 949-954

  Abstract

  It has recently been demonstrated that novel streaming architectures found in consumer video gaming hardware such as graphical processing units (GPUs) are well-suited to a broad range of computations including electronic structure theory (quantum chemistry). Although recent GPUs have developed robust support for double precision arithmetic, they continue to provide 2-8× more hardware units for single precision. In order to maximize performance on GPU architectures, we present a technique of dynamically selecting double or single precision evaluation for electron repulsion integrals (ERIs) in Hartree-Fock and density functional self-consistent field (SCF) calculations. We show that precision error can be effectively controlled by evaluating only the largest integrals in double precision. By dynamically scaling the precision cutoff over the course of the SCF procedure, we arrive at a scheme that minimizes the number of double precision integral evaluations for any desired accuracy. This dynamic precision scheme is shown to be effective for an array of molecules ranging in size from 20 to nearly 2000 atoms.

  View details for DOI 10.1021/ct100701w

  View details for Web of Science ID 000289315700018

• Reactive Cross-Talk between Adjacent Tension-Trapped Transition States JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Lenhardt, J. M., Ogle, J. W., Ong, M. T., Choe, R., Martinez, T. J., Craig, S. L. 2011; 133 (10): 3222-3225

  Abstract

  Tension along a polymer chain traps neighboring s-trans/s-trans-1,3-diradicals from the mechanically induced ring opening of gem-difluorocyclopropanes (gDFCs). The diradicals correspond to the transition states of the force-free thermal isomerization reactions of gDFCs, and the tension trapping allows a new disproportionation reaction between two simultaneously trapped diradicals to take place.

  View details for DOI 10.1021/ja107645c

  View details for Web of Science ID 000288410100002

  View details for PubMedID 21341786

• Conformationally selective photodissociation dynamics of propanal cation JOURNAL OF CHEMICAL PHYSICS Tao, H., Shen, L., Kim, M. H., Suits, A. G., Martinez, T. J. 2011; 134 (5)

  Abstract

  We have previously reported experimental evidence for conformationally selective dissociation of propanal cation that was interpreted, on the basis of ab initio multiple spawning calculations, as arising from distinct dynamics in the excited state manifold of the cation. Two conical intersections (CIs) are accessible from Franck-Condon points on the dark state; however, different conformers prefer different CIs and quench to different regions on the ground state. In this paper, we extend our initial report to include experimental results for the partially deuterated propanal cation as well as detailed characterization of the ground state potential energy surface and statistical calculations of the ground state dissociation dynamics. The DC slice imaging experiments show a bimodal velocity distribution for H elimination with the observed branching ratio of the two channels different for the cis and gauche conformers. H(D)-elimination experiments from deuterated propanal cation support the dissociation mechanism proposed in the earlier report. We further investigate reaction rates on the ground state using Rice-Ramsperger-Kassel-Marcus theory. We find that the experimental results are consistent with a mechanistic picture where the ground state dissociation is statistical, and conformer specificity of the dissociation products arises because of the different populations in distinct ground state isomers after photoexcitation due to ultrafast quenching to the ground state.

  View details for DOI 10.1063/1.3540659

  View details for Web of Science ID 000287095500042

  View details for PubMedID 21303126

• Time-resolved photoelectron spectroscopy from first principles: Excited state dynamics of benzene FARADAY DISCUSSIONS Thompson, A. L., Martinez, T. J. 2011; 150: 293-311

  Abstract

  We use the ab initio multiple spawning (AIMS) method to follow the dynamics of benzene after excitation to the second singlet excited state (S2). The results are validated by comparison to potential energy surfaces including dynamical electron correlation effects. Time-resolved photoelectron spectra are computed and compared to experimental results. Simulations agree with experiment that there are both short-lived and long-lived components of the excited state population. We show that these components both originate from quenching through the same S2/S1 conical intersection and that the difference between them comes from their behavior immediately after decay to S1. This is presumed to be a function of the details of the way in which the S2/S1 intersection region is accessed; for example, the momentum distribution and the topology of the seam in the relevant region.

  View details for DOI 10.1039/c1fd00003a

  View details for Web of Science ID 000292977100015

  View details for PubMedID 22457953

• PHYSICAL CHEMISTRY Seaming is believing NATURE Martinez, T. J. 2010; 467 (7314): 412-413

  View details for Web of Science ID 000282090200032

  View details for PubMedID 20864993

• Trapping a Diradical Transition State by Mechanochemical Polymer Extension SCIENCE Lenhardt, J. M., Ong, M. T., Choe, R., Evenhuis, C. R., Martinez, T. J., Craig, S. L. 2010; 329 (5995): 1057-1060

  Abstract

  Transition state structures are central to the rates and outcomes of chemical reactions, but their fleeting existence often leaves their properties to be inferred rather than observed. By treating polybutadiene with a difluorocarbene source, we embedded gem-difluorocyclopropanes (gDFCs) along the polymer backbone. We report that mechanochemical activation of the polymer under tension opens the gDFCs and traps a 1,3-diradical that is formally a transition state in their stress-free electrocyclic isomerization. The trapped diradical lives long enough that we can observe its noncanonical participation in bimolecular addition reactions. Furthermore, the application of a transient tensile force induces a net isomerization of the trans-gDFC into its less-stable cis isomer, leading to the counterintuitive result that the gDFC contracts in response to a transient force of extension.

  View details for DOI 10.1126/science.1193412

  View details for Web of Science ID 000281253500035

  View details for PubMedID 20798315

• Calculating molecular integrals of d and higher angular momentum functions on GPUs Titov, A. V., Ufimtsev, I., Martinez, T., Dunning, T. H. AMER CHEMICAL SOC. 2010

  View details for Web of Science ID 000208164706294

• High-Performance Computing with Accelerators INTRODUCTION COMPUTING IN SCIENCE & ENGINEERING Kindratenko, V., Wilhelmson, R., Brunner, R., Martinez, T. J., Hwu, W. 2010; 12 (4): 12-16

  View details for Web of Science ID 000279582400002

• Ab initio floating occupation molecular orbital-complete active space configuration interaction: An efficient approximation to CASSCF JOURNAL OF CHEMICAL PHYSICS Slavicek, P., Martinez, T. J. 2010; 132 (23)

  Abstract

  We have implemented a complete active space configuration interaction method (CASCI) based on floating occupation molecular orbitals (FOMOs) at the ab initio level. The performance of this FOMO-CASCI method was investigated for potential applications in photochemistry and photodynamics. We found that FOMO-CASCI often represents a good approximation to the state-averaged complete active space self-consistent field (SA-CASSCF) method. FOMO-CASCI is therefore an attractive alternative for use in ab initio photodynamics. The method is more efficient and more stable than SA-CASSCF. We also discuss some problematic cases for the FOMO-CASCI approach. Possible extensions of the FOMO-CASCI approach are discussed briefly.

  View details for DOI 10.1063/1.3436501

  View details for Web of Science ID 000279032000005

  View details for PubMedID 20572684

• Optimization of width parameters for quantum dynamics with frozen Gaussian basis sets CHEMICAL PHYSICS Thompson, A. L., Punwong, C., Martinez, T. J. 2010; 370 (1-3): 70-77

  View details for DOI 10.1016/j.chemphys.2010.03.020

  View details for Web of Science ID 000277468900010

• Masked Cyanoacrylates Unveiled by Mechanical Force JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kryger, M. J., Ong, M. T., Odom, S. A., Sottos, N. R., White, S. R., Martinez, T. J., Moore, J. S. 2010; 132 (13): 4558-?

  Abstract

  Mechanical damage of polymers is often a destructive and irreversible process. However, desirable outcomes may be achieved by controlling the location of chain cleavage events through careful design and incorporation of mechanically active chemical moieties known as mechanophores. It is possible that mechanophores can be used to generate reactive intermediates that can autopolymerize or cross-link, thus healing mechanically induced damage. Herein we report the generation of reactive cyanoacrylate units from a dicyanocyclobutane mechanophore located near the center of a polymer chain. Because cyanoacrylates (which are used as monomers in the preparation of superglue) autopolymerize, the generated cyanoacrylate-terminated polymers may be useful in self-healing polymers. Sonication studies of polymers with the mechanophore incorporated into the chain center have shown that selective cleavage of the mechanophore occurs. Trapping experiments with an amine-based chromophore support cyanoacrylate formation. Additionally, computational studies of small-molecule models predict that force-induced bond cleavage should occur with greater selectivity for the dicyanocyclobutane mechanophore than for a control molecule.

  View details for DOI 10.1021/ja1008932

  View details for Web of Science ID 000276553600028

  View details for PubMedID 20232911

• Variational geminal-augmented multireference self-consistent field theory: Two-electron systems JOURNAL OF CHEMICAL PHYSICS Varganov, S. A., Martinez, T. J. 2010; 132 (5)

  Abstract

  We introduce a geminal-augmented multiconfigurational self-consistent field method for describing electron correlation effects. The approach is based on variational optimization of a MCSCF-type wave function augmented by a single geminal. This wave function is able to account for some dynamic correlation without explicit excitations to virtual molecular orbitals. Test calculations on two-electron systems demonstrate the ability of the proposed method to describe ionic and covalent electronic states in a balanced way, i.e., including the effects of both static and dynamic correlation simultaneously. Extension of the theory to larger systems will potentially provide an alternative to standard multireference methods.

  View details for DOI 10.1063/1.3303203

  View details for Web of Science ID 000274319900004

  View details for PubMedID 20136301

• Protonic Gating of Excited-State Twisting and Charge Localization in GFP Chromophores: A Mechanistic Hypothesis for Reversible Photoswitching JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Olsen, S., Lamothe, K., Martinez, T. J. 2010; 132 (4): 1192-?

  Abstract

  Reversible photoswitching fluorescent proteins can be photoswitched between fluorescent and nonfluorescent states by different irradiation regimes. Accumulating spectroscopic and crystallographic evidence suggest a correlated change in protonation state and methine bridge isomerism of the chromophore. The anion can decay by photoisomerization of either of the methine bonds, but only one channel can act as a switch. Using ab initio multiple spawning dynamics simulations, we show that protonation is sufficient to change the photoisomerization channel in the chromophore. We propose that this behavior can underlie a switch given certain other conditions. We also propose a basis for coupling between excited-state basicity changes and selection of the photoisomerization channel based on the polarity of twisted charge-transfer states for neutral and anionic forms of the chromophore.

  View details for DOI 10.1021/ja907447k

  View details for Web of Science ID 000275084800006

  View details for PubMedID 20067241

• Ab Initio Multiple Spawning Dynamics Using Multi-State Second-Order Perturbation Theory JOURNAL OF PHYSICAL CHEMISTRY A Tao, H., Levine, B. G., Martinez, T. J. 2009; 113 (49): 13656-13662

  Abstract

  We have implemented multi-state second-order perturbation theory (MS-CASPT2) in the ab initio multiple spawning (AIMS) method for first-principles molecular dynamics including nonadiabatic effects. The nonadiabatic couplings between states are calculated numerically using an efficient method which requires only two extra energy calculations per time step. As a representative example, we carry out AIMS-MSPT2 calculations of the excited state dynamics of ethylene. Two distinct types of conical intersections, previously denoted as the twisted-pyramidalized and ethylidene intersections, are responsible for ultrafast population transfer from the excited state to the ground state. Although these two pathways have been observed in prior dynamics simulations, we show here that the branching ratio is affected by dynamic correlation with the twisted-pyramidalized intersection overweighting the ethylidene-like intersection during the decay process at the AIMS-MSPT2 level of description.

  View details for DOI 10.1021/jp9063565

  View details for Web of Science ID 000272338600004

  View details for PubMedID 19888736

• Ab Initio Multiple Spawning Dynamics of Excited Butadiene: Role of Charge Transfer JOURNAL OF PHYSICAL CHEMISTRY A Levine, B. G., Martinez, T. J. 2009; 113 (46): 12815-12824

  Abstract

  Ab initio multiple spawning simulations of the photochemical reaction dynamics of s-trans-1,3-butadiene were performed. It is found that nonadiabatic events involving two low-lying excited states begin as early as 10 fs after excitation, resulting in the population being split between the bright 1(1)B(u) state and the dark 2(1)A(g) state. The molecule subsequently twists about a terminal carbon-carbon bond regardless of whether it is on the 1(1)B(u) or 2(1)A(g) electronic state. This twisting motion leads to conical intersections between S(1) and S(0). Several regions of the intersection seam involving states of differing character are accessed. The regions of the seam involving intersection between a state of charge-transfer character and a state of covalent character dominate the quenching dynamics, but intersections between two covalent states are also accessed a small percentage of the time. The existence and relative energies of these intersections are validated by optimization at the multistate complete active space second-order perturbation level of theory (MS-CASPT2). Our results point to a new mechanism for photoisomerization of butadiene that emphasizes the role of charge-transfer states.

  View details for DOI 10.1021/jp907111u

  View details for Web of Science ID 000271583100008

  View details for PubMedID 19813720

• Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field (SCF) Implementation. Journal of chemical theory and computation Ufimtsev, I. S., Martinez, T. J. 2009; 5 (11): 3138-?

  View details for DOI 10.1021/ct900433g

  View details for PubMedID 26609993

• Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics. Journal of chemical theory and computation Ufimtsev, I. S., Martinez, T. J. 2009; 5 (10): 2619-28

  Abstract

  We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

  View details for DOI 10.1021/ct9003004

  View details for PubMedID 26631777

• Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2009; 5 (10): 2619-2628

  Abstract

  We demonstrate that a video gaming machine containing two consumer graphical cards can outpace a state-of-the-art quad-core processor workstation by a factor of more than 180× in Hartree-Fock energy + gradient calculations. Such performance makes it possible to run large scale Hartree-Fock and Density Functional Theory calculations, which typically require hundreds of traditional processor cores, on a single workstation. Benchmark Born-Oppenheimer molecular dynamics simulations are performed on two molecular systems using the 3-21G basis set - a hydronium ion solvated by 30 waters (94 atoms, 405 basis functions) and an aspartic acid molecule solvated by 147 waters (457 atoms, 2014 basis functions). Our GPU implementation can perform 27 ps/day and 0.7 ps/day of ab initio molecular dynamics simulation on a single desktop computer for these systems.

  View details for DOI 10.1021/ct9003004

  View details for Web of Science ID 000270595800005

• Observation of a Zundel-like transition state during proton transfer in aqueous hydroxide solutions PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Roberts, S. T., Petersen, P. B., Ramasesha, K., Tokmakoff, A., Ufimtsev, I. S., Martinez, T. J. 2009; 106 (36): 15154-15159

  Abstract

  It is generally accepted that the anomalous diffusion of the aqueous hydroxide ion results from its ability to accept a proton from a neighboring water molecule; yet, many questions exist concerning the mechanism for this process. What is the solvation structure of the hydroxide ion? In what way do water hydrogen bond dynamics influence the transfer of a proton to the ion? We present the results of femtosecond pump-probe and 2D infrared experiments that probe the O-H stretching vibration of a solution of dilute HOD dissolved in NaOD/D(2)O. Upon the addition of NaOD, measured pump-probe transients and 2D IR spectra show a new feature that decays with a 110-fs time scale. The calculation of 2D IR spectra from an empirical valence bond molecular dynamics simulation of a single NaOH molecule in a bath of H(2)O indicates that this fast feature is due to an overtone transition of Zundel-like H(3)O(2)(-) states, wherein a proton is significantly shared between a water molecule and the hydroxide ion. Given the frequency of vibration of shared protons, the observations indicate the shared proton state persists for 2-3 vibrational periods before the proton localizes on a hydroxide. Calculations based on the EVB-MD model argue that the collective electric field in the proton transfer direction is the appropriate coordinate to describe the creation and relaxation of these Zundel-like transition states.

  View details for DOI 10.1073/pnas.0901571106

  View details for Web of Science ID 000269632400014

  View details for PubMedID 19666493

  View details for PubMedCentralID PMC2741221

• Charge conservation in electronegativity equalization and its implications for the electrostatic properties of fluctuating-charge models JOURNAL OF CHEMICAL PHYSICS Chen, J., Martinez, T. J. 2009; 131 (4)

  Abstract

  An analytical solution of fluctuating-charge models using Gaussian elimination allows us to isolate the contribution of charge conservation effects in determining the charge distribution. We use this analytical solution to calculate dipole moments and polarizabilities and show that charge conservation plays a critical role in maintaining the correct translational invariance of the electrostatic properties predicted by these models.

  View details for DOI 10.1063/1.3183167

  View details for Web of Science ID 000268613700015

  View details for PubMedID 19655844

• First Principles Dynamics and Minimum Energy Pathways for Mechanochemical Ring Opening of Cyclobutene JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ong, M. T., Leiding, J., Tao, H., Virshup, A. M., Martinez, T. J. 2009; 131 (18): 6377-?

  Abstract

  We use ab initio steered molecular dynamics to investigate the mechanically induced ring opening of cyclobutene. We show that the dynamical results can be considered in terms of a force-modified potential energy surface (FMPES). We show how the minimal energy paths for the two possible competing conrotatory and disrotatory ring-opening reactions are affected by external force. We also locate minimal energy pathways in the presence of applied external force and show that the reactant, product, and transition state geometries are altered by the application of external force. The largest effects are on the transition state geometries and barrier heights. Our results provide a framework for future investigations of the role of external force on chemical reactivity.

  View details for DOI 10.1021/ja8095834

  View details for Web of Science ID 000265939200034

  View details for PubMedID 19378993

• Force-induced activation of covalent bonds in mechanoresponsive polymeric materials NATURE Davis, D. A., Hamilton, A., Yang, J., Cremar, L. D., Van Gough, D., Potisek, S. L., Ong, M. T., Braun, P. V., Martinez, T. J., White, S. R., Moore, J. S., Sottos, N. R. 2009; 459 (7243): 68-72

  Abstract

  Mechanochemical transduction enables an extraordinary range of physiological processes such as the sense of touch, hearing, balance, muscle contraction, and the growth and remodelling of tissue and bone. Although biology is replete with materials systems that actively and functionally respond to mechanical stimuli, the default mechanochemical reaction of bulk polymers to large external stress is the unselective scission of covalent bonds, resulting in damage or failure. An alternative to this degradation process is the rational molecular design of synthetic materials such that mechanical stress favourably alters material properties. A few mechanosensitive polymers with this property have been developed; but their active response is mediated through non-covalent processes, which may limit the extent to which properties can be modified and the long-term stability in structural materials. Previously, we have shown with dissolved polymer strands incorporating mechanically sensitive chemical groups-so-called mechanophores-that the directional nature of mechanical forces can selectively break and re-form covalent bonds. We now demonstrate that such force-induced covalent-bond activation can also be realized with mechanophore-linked elastomeric and glassy polymers, by using a mechanophore that changes colour as it undergoes a reversible electrocyclic ring-opening reaction under tensile stress and thus allows us to directly and locally visualize the mechanochemical reaction. We find that pronounced changes in colour and fluorescence emerge with the accumulation of plastic deformation, indicating that in these polymeric materials the transduction of mechanical force into the ring-opening reaction is an activated process. We anticipate that force activation of covalent bonds can serve as a general strategy for the development of new mechanophore building blocks that impart polymeric materials with desirable functionalities ranging from damage sensing to fully regenerative self-healing.

  View details for DOI 10.1038/nature07970

  View details for Web of Science ID 000265801300030

  View details for PubMedID 19424152

• Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation. Journal of chemical theory and computation Ufimtsev, I. S., Martinez, T. J. 2009; 5 (4): 1004-15

  Abstract

  We demonstrate the use of graphical processing units (GPUs) to carry out complete self-consistent-field calculations for molecules with as many as 453 atoms (2131 basis functions). Speedups ranging from 28× to 650× are achieved as compared to a mature third-party quantum chemistry program (GAMESS) running on a traditional CPU. The computational organization used to construct the Coulomb and exchange operators is discussed. We also present results using three GPUs in parallel, combining coarse and fine-grained parallelism.

  View details for DOI 10.1021/ct800526s

  View details for PubMedID 26609609

• Revisiting Molecular Dissociation in Density Functional Theory: A Simple Model. Journal of chemical theory and computation Tempel, D. G., Martínez, T. J., Maitra, N. T. 2009; 5 (4): 770-80

  Abstract

  A two-electron one-dimensional model of a heteroatomic molecule composed of two open-shell atoms is considered. Including only two electrons isolates and examines the effect that the highest occupied molecular orbital has on the Kohn-Sham potential as the molecule dissociates. We reproduce the characteristic step and peak that previous high-level wave function methods have shown to exist for real molecules in the low-density internuclear region. The simplicity of our model enables us to investigate in detail their development as a function of bond-length, with little computational effort, and derive properties of their features in the dissociation limit. We show that the onset of the step is coincident with the internuclear separation at which an avoided crossing between the ground-state and lowest charge-transfer excited-state is approached. Although the step and peak features have little effect on the ground-state energetics, we discuss their important consequences for dynamics and response.

  View details for DOI 10.1021/ct800535c

  View details for PubMedID 26609582

• An "optimal" spawning algorithm for adaptive basis set expansion in nonadiabatic dynamics JOURNAL OF CHEMICAL PHYSICS Yang, S., Coe, J. D., Kaduk, B., Martinez, T. J. 2009; 130 (13)

  Abstract

  The full multiple spawning (FMS) method has been developed to simulate quantum dynamics in the multistate electronic problem. In FMS, the nuclear wave function is represented in a basis of coupled, frozen Gaussians, and a "spawning" procedure prescribes a means of adaptively increasing the size of this basis in order to capture population transfer between electronic states. Herein we detail a new algorithm for specifying the initial conditions of newly spawned basis functions that minimizes the number of spawned basis functions needed for convergence. "Optimally" spawned basis functions are placed to maximize the coupling between parent and child trajectories at the point of spawning. The method is tested with a two-state, one-mode avoided crossing model and a two-state, two-mode conical intersection model.

  View details for DOI 10.1063/1.3103930

  View details for Web of Science ID 000265053200014

  View details for PubMedID 19355723

• Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2009; 5 (4): 1004-1015

  Abstract

  We demonstrate the use of graphical processing units (GPUs) to carry out complete self-consistent-field calculations for molecules with as many as 453 atoms (2131 basis functions). Speedups ranging from 28× to 650× are achieved as compared to a mature third-party quantum chemistry program (GAMESS) running on a traditional CPU. The computational organization used to construct the Coulomb and exchange operators is discussed. We also present results using three GPUs in parallel, combining coarse and fine-grained parallelism.

  View details for DOI 10.1021/ct800526s

  View details for Web of Science ID 000265268800039

• Revisiting Molecular Dissociation in Density Functional Theory: A Simple Model JOURNAL OF CHEMICAL THEORY AND COMPUTATION Tempel, D. G., Martinez, T. J., Maitra, N. T. 2009; 5 (4): 770-780

  Abstract

  A two-electron one-dimensional model of a heteroatomic molecule composed of two open-shell atoms is considered. Including only two electrons isolates and examines the effect that the highest occupied molecular orbital has on the Kohn-Sham potential as the molecule dissociates. We reproduce the characteristic step and peak that previous high-level wave function methods have shown to exist for real molecules in the low-density internuclear region. The simplicity of our model enables us to investigate in detail their development as a function of bond-length, with little computational effort, and derive properties of their features in the dissociation limit. We show that the onset of the step is coincident with the internuclear separation at which an avoided crossing between the ground-state and lowest charge-transfer excited-state is approached. Although the step and peak features have little effect on the ground-state energetics, we discuss their important consequences for dynamics and response.

  View details for DOI 10.1021/ct800535c

  View details for Web of Science ID 000265268800012

• Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics JOURNAL OF PHYSICAL CHEMISTRY B Virshup, A. M., Punwong, C., Pogorelov, T. V., Lindquist, B. A., Ko, C., Martinez, T. J. 2009; 113 (11): 3280-3291

  Abstract

  Our picture of reactions on electronically excited states has evolved considerably in recent years, due to advances in our understanding of points of degeneracy between different electronic states, termed "conical intersections" (CIs). CIs serve as funnels for population transfer between different electronic states, and play a central role in ultrafast photochemistry. Because most practical photochemistry occurs in solution and protein environments, it is important to understand the role complex environments play in directing excited-state dynamics generally, as well as specific environmental effects on CI geometries and energies. In order to model such effects, we employ the full multiple spawning (FMS) method for multistate quantum dynamics, together with hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy surfaces using both semiempirical and ab initio QM methods. In this article, we present an overview of these methods, and a comparison of the excited-state dynamics of several biological chromophores in solvent and protein environments. Aqueous solvation increases the rate of quenching to the ground state for both the photoactive yellow protein (PYP) and green fluorescent protein (GFP) chromophores, apparently by energetic stabilization of their respective CIs. In contrast, solvation in methanol retards the quenching process of the retinal protonated Schiff base (RPSB), the rhodopsin chromophore. Protein environments serve to direct the excited-state dynamics, leading to higher quantum yields and enhanced reaction selectivity.

  View details for DOI 10.1021/jp8073464

  View details for Web of Science ID 000264111200006

  View details for PubMedID 19090684

• Nonclassical Phase Space Jumps and Optimal Spawning 13th International Workshop on Quantum Systems in Chemistry and Physics Yang, S., Martinez, T. J. SPRINGER. 2009: 35–45

  View details for DOI 10.1007/978-90-481-2985-0_2

  View details for Web of Science ID 000281727000002

• Implementation of scientific computing applications on the Cell Broadband Engine SCIENTIFIC PROGRAMMING Shi, G., Kindratenko, V. V., Ufimtsev, I. S., Martinez, T. J., Phillips, J. C., Gottlieb, S. A. 2009; 17 (1-2): 135-151

  View details for DOI 10.3233/SPR-2009-0273

  View details for Web of Science ID 000272227800009

• A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions PHYSICAL CHEMISTRY CHEMICAL PHYSICS Ufimtsev, I. S., Kalinichev, A. G., Martinez, T. J., Kirkpatrick, R. J. 2009; 11 (41): 9420-9430

  Abstract

  We describe a new multistate empirical valence bond (MS-EVB) model of OH(-) in aqueous solutions. This model is based on the recently proposed "charged ring" parameterization for the intermolecular interaction of hydroxyl ion with water [Ufimtsev, et al., Chem. Phys. Lett., 2007, 442, 128] and is suitable for classical molecular simulations of OH(-) solvation and transport. The model reproduces the hydration structure of OH(-)(aq) in good agreement with experimental data and the results of ab initio molecular dynamics simulations. It also accurately captures the major structural, energetic, and dynamic aspects of the proton transfer processes involving OH(-) (aq). The model predicts an approximately two-fold increase of the OH(-) mobility due to proton exchange reactions.

  View details for DOI 10.1039/b907859b

  View details for Web of Science ID 000270795500014

  View details for PubMedID 19830325

• The Dissociation Catastrophe in Fluctuating-Charge Models and its Implications for the Concept of Atomic Electronegativity 13th International Workshop on Quantum Systems in Chemistry and Physics Chen, J., Martinez, T. J. SPRINGER. 2009: 397–415

  View details for DOI 10.1007/978-90-481-2596-8_19

  View details for Web of Science ID 000285958500019

• On the Extent and Connectivity of Conical Intersection Seams and the Effects of Three-State Intersections JOURNAL OF PHYSICAL CHEMISTRY A Coe, J. D., Ong, M. T., Levine, B. G., Martinez, T. J. 2008; 112 (49): 12559-12567

  Abstract

  We discuss the connectivity of intersection spaces and the role of minimal energy points within these intersection spaces (minimal energy conical intersections or MECIs) in promoting nonadiabatic transitions. We focus on malonaldeyde as a specific example, where there is a low-lying three-state conical intersection. This three-state intersection is the global minimum on the bright excited electronic state, but it plays a limited role in population transfer in our ab initio multiple spawning (AIMS) simulations because the molecule must traverse a series of two-state conical intersections to reach the three-state intersection. Due to the differences in seam space dimensionality separating conventional (two-state) and three-state intersections, we suggest that dynamical effects arising directly from a three-state intersection may prove difficult to observe in general. We also use a newly developed method for intersection optimization with geometric constraints to demonstrate the connectivity of all the stationary points in the intersection spaces for malonaldehyde. This supports the conjecture that all intersection spaces are connected, and that three-state intersections play a key role in extending this connectivity to all pairs of states, e.g. the S1/S0 and S2/S1 intersection spaces.

  View details for DOI 10.1021/jp806072k

  View details for Web of Science ID 000261426300005

  View details for PubMedID 19012385

• A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space JOURNAL OF CHEMICAL PHYSICS Chen, J., Hundertmark, D., Martinez, T. J. 2008; 129 (21)

  Abstract

  Our previously introduced QTPIE (charge transfer with polarization current equilibration) model [J. Chen and T. J. Martínez, Chem. Phys. Lett. 438, 315 (2007)] is a fluctuating-charge model with correct asymptotic behavior. Unlike most other fluctuating-charge models, QTPIE is formulated in terms of charge-transfer variables and pairwise electronegativities, not atomic charge variables and electronegativities. The pairwise character of the electronegativities in QTPIE allows us to avoid spurious charge transfer when bonds are broken. However, the increased number of variables leads to considerable computational expense and a rank-deficient set of working equations, which is numerically inconvenient. Here, we show that QTPIE can be exactly reformulated in terms of atomic charge variables, leading to a considerable reduction in computational complexity. The transformation between atomic and bond variables is generally applicable to arbitrary fluctuating charge models and uncovers an underlying topological framework that can be used to understand the relation between fluctuating-charge models and the classical theory of electrical circuits.

  View details for DOI 10.1063/1.3021400

  View details for Web of Science ID 000261430900014

  View details for PubMedID 19063550

• Excited-State Dynamics of Cytosine Reveal Multiple Intrinsic Subpicosecond Pathways CHEMPHYSCHEM Hudock, H. R., Martinez, T. J. 2008; 9 (17): 2486-2490

  View details for DOI 10.1002/cphc.200800649

  View details for Web of Science ID 000261721700008

  View details for PubMedID 19006165

• Graphical Processing Units for Quantum Chemistry COMPUTING IN SCIENCE & ENGINEERING Ufimtsev, I. S., Martinez, T. J. 2008; 10 (6): 26-34

  View details for Web of Science ID 000260130800007

• QTPIE: Charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics (vol 438, pg 315, 2007) CHEMICAL PHYSICS LETTERS Chen, J., Martinez, T. J. 2008; 463 (1-3): 288-288

  View details for DOI 10.1016/j.cplett.2008.08.060

  View details for Web of Science ID 000259150400057

• Electrostatic control of photoisomerization in the photoactive yellow protein chromophore: Ab initio multiple spawning dynamics CHEMICAL PHYSICS LETTERS Ko, C., Virshup, A. M., Martinez, T. J. 2008; 460 (1-3): 272-277

  View details for DOI 10.1016/j.cplett.2008.05.029

  View details for Web of Science ID 000257596300056

• Implementation of ab initio multiple spawning in the MOLPRO quantum chemistry package CHEMICAL PHYSICS Levine, B. G., Coe, J. D., Virshup, A. M., Martinez, T. J. 2008; 347 (1-3): 3-16

  View details for DOI 10.1016/j.chemphys.2008.01.014

  View details for Web of Science ID 000256866700002

• Ultrafast photoinduced processes in polyatomic molecules: Electronic structure, dynamics and spectroscopy (in honour of Wolfgang Domcke) - Preface CHEMICAL PHYSICS Thoss, M., Stock, G., Martinez, T. J. 2008; 347 (1-3): 1-2

  View details for DOI 10.1016/j.chemphys.2008.03.029

  View details for Web of Science ID 000256866700001

• Pseudospectral time-dependent density functional theory JOURNAL OF CHEMICAL PHYSICS Ko, C., Malick, D. K., Braden, D. A., Friesner, R. A., Martinez, T. J. 2008; 128 (10)

  Abstract

  Time-dependent density functional theory (TDDFT) is implemented within the Tamm-Dancoff approximation (TDA) using a pseudospectral approach to evaluate two-electron repulsion integrals. The pseudospectral approximation uses a split representation with both spectral basis functions and a physical space grid to achieve a reduction in the scaling behavior of electronic structure methods. We demonstrate here that exceptionally sparse grids may be used in the excitation energy calculation, following earlier work employing the pseudospectral approximation for determining correlation energies in wavefunction-based methods with similar conclusions. The pseudospectral TDA-TDDFT method is shown to be up to ten times faster than a conventional algorithm for hybrid functionals without sacrificing chemical accuracy.

  View details for DOI 10.1063/1.2834222

  View details for Web of Science ID 000254025300005

  View details for PubMedID 18345873

• Quantum chemistry on graphical processing units. 1. Strategies for two-electron integral evaluation JOURNAL OF CHEMICAL THEORY AND COMPUTATION Ufimtsev, I. S., Martinez, T. J. 2008; 4 (2): 222-231

  Abstract

  Modern videogames place increasing demands on the computational and graphical hardware, leading to novel architectures that have great potential in the context of high performance computing and molecular simulation. We demonstrate that Graphical Processing Units (GPUs) can be used very efficiently to calculate two-electron repulsion integrals over Gaussian basis functions [Formula: see text] the first step in most quantum chemistry calculations. A benchmark test performed for the evaluation of approximately 10(6) (ss|ss) integrals over contracted s-orbitals showed that a naïve algorithm implemented on the GPU achieves up to 130-fold speedup over a traditional CPU implementation on an AMD Opteron. Subsequent calculations of the Coulomb operator for a 256-atom DNA strand show that the GPU advantage is maintained for basis sets including higher angular momentum functions.

  View details for DOI 10.1021/ct700268q

  View details for Web of Science ID 000253166000002

• Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation. Journal of chemical theory and computation Ufimtsev, I. S., Martínez, T. J. 2008; 4 (2): 222-31

  Abstract

  Modern videogames place increasing demands on the computational and graphical hardware, leading to novel architectures that have great potential in the context of high performance computing and molecular simulation. We demonstrate that Graphical Processing Units (GPUs) can be used very efficiently to calculate two-electron repulsion integrals over Gaussian basis functions [Formula: see text] the first step in most quantum chemistry calculations. A benchmark test performed for the evaluation of approximately 10(6) (ss|ss) integrals over contracted s-orbitals showed that a naïve algorithm implemented on the GPU achieves up to 130-fold speedup over a traditional CPU implementation on an AMD Opteron. Subsequent calculations of the Coulomb operator for a 256-atom DNA strand show that the GPU advantage is maintained for basis sets including higher angular momentum functions.

  View details for DOI 10.1021/ct700268q

  View details for PubMedID 26620654

• Optimizing conical intersections without derivative coupling vectors: Application to multistate multireference second-order perturbation theory (MS-CASPT2) JOURNAL OF PHYSICAL CHEMISTRY B Levine, B. G., Coe, J. D., Martinez, T. J. 2008; 112 (2): 405-413

  Abstract

  We introduce a new method for optimizing minimal energy conical intersections (MECIs), based on a sequential penalty constrained optimization in conjunction with a smoothing function. The method is applied to optimize MECI geometries using the multistate formulation of second-order multireference perturbation theory (MS-CASPT2). Resulting geometries and energetics for conjugated molecules including ethylene, butadiene, stilbene, and the green fluorescent protein chromophore are compared with state-averaged complete active space self-consistent field (SA-CASSCF) and, where possible, benchmark multireference single- and double-excitation configuration interaction (MRSDCI) optimizations. Finally, we introduce the idea of "minimal distance conical intersections", which are points on the intersection seam that lie closest to some specified geometry such as the Franck-Condon point or a local minimum on the excited state.

  View details for DOI 10.1021/jp0761618

  View details for Web of Science ID 000252287200026

  View details for PubMedID 18081339

• Ab initio multiple spawning dynamics of excited state intramolecular proton transfer: the role of spectroscopically dark states MOLECULAR PHYSICS Coe, J. D., Martinez, T. J. 2008; 106 (2-4): 537-545

  View details for DOI 10.1080/00268970801901514

  View details for Web of Science ID 000256058400032

• Substituent effects on dynamics at conical intersections: alpha,beta-enones JOURNAL OF PHYSICAL CHEMISTRY A Lee, A. M., Coe, J. D., Ullrich, S., Ho, M., Lee, S., Cheng, B., Zgierski, M. Z., Chen, I., Martinez, T. J., Stolow, A. 2007; 111 (47): 11948-11960

  Abstract

  Femtosecond time-resolved photoelectron spectroscopy and high-level theoretical calculations were used to study the effects of methyl substitution on the electronic dynamics of the alpha,beta-enones acrolein (2-propenal), crotonaldehyde (2-butenal), methylvinylketone (3-buten-2-one), and methacrolein (2-methyl-2-propenal) following excitation to the S2(pipi*) state at 209 and 200 nm. We determine that following excitation the molecules move rapidly away from the Franck-Condon region, reaching a conical intersection promoting relaxation to the S1(npi*) state. Once on the S1 surface, the trajectories access another conical intersection, leading them to the ground state. Only small variations between molecules are seen in their S2 decay times. However, the position of methyl group substitution greatly affects the relaxation rate from the S1 surface and the branching ratios to the products. Ab initio calculations used to compare the geometries, energies, and topographies of the S1/S0 conical intersections of the molecules are not able to satisfactorily explain the variations in relaxation behavior. We propose that the S1 lifetime differences are caused by specific dynamical factors that affect the efficiency of passage through the S1/S0 conical intersection.

  View details for DOI 10.1021/jp074622j

  View details for Web of Science ID 000251140700002

  View details for PubMedID 17985850

• Ab initio molecular dynamics of excited-state intramolecular proton transfer using multireference perturbation theory JOURNAL OF PHYSICAL CHEMISTRY A Coe, J. D., Levine, B. G., Martinez, T. J. 2007; 111 (44): 11302-11310

  Abstract

  We present the first calculations of excited-state dynamics using ab initio molecular dynamics with a multireference perturbation theory description of the electronic structure. The new AIMS-CASPT2 method is applied to a paradigmatic excited-state intramolecular proton-transfer reaction in methyl salicylate, and the results are compared with previous ultrafast spectroscopic experiments. Agreement of AIMS-CASPT2 and experimental results is quantitative. The results demonstrate that the lack of an observed isotope effect in the reaction is due to multidimensionality of the reaction coordinate, which largely involves heavy-atom bond alternation instead of proton transfer. Using the dynamics results as a guide, we also characterize relevant minima on the ground and first singlet excited state using CASPT2 electronic structure theory. We further locate an S1/S0 minimal energy conical intersection, whose presence explains experimental observations of a sharp decrease in fluorescence quantum yield at excitation energies more than 1,300 cm-1 above the excited-state origin.

  View details for DOI 10.1021/jp072027b

  View details for Web of Science ID 000250646400018

  View details for PubMedID 17602455

• Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb(3) oxidase) of heme-copper oxygen reductases BIOCHEMISTRY Hemp, J., Han, H., Roh, J. H., Kaplan, S., Martinez, T. J., Gennis, R. B. 2007; 46 (35): 9963-9972

  Abstract

  Oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. The protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules along with polar amino acid side chains. Recent analyses identified eight oxygen reductase families in the superfamily: the A-, B-, C-, D-, E-, F-, G-, and H-families of oxygen reductases. Two proton input channels, the K-channel and the D-channel, are well established in the A-family of oxygen reductases (exemplified by the mitochondrial cytochrome c oxidases and by the respiratory oxidases from Rhodobacter sphaeroides and Paracoccus denitrificans). Each of these channels can be identified by the pattern of conserved polar amino acid residues within the protein. The C-family (cbb3 oxidases) is the second most abundant oxygen reductase family after the A-family, making up more than 20% of the sequences of the heme-copper superfamily. In this work, sequence analyses and structural modeling have been used to identify likely proton channels in the C-family. The pattern of conserved polar residues supports the presence of only one proton input channel, which is spatially analogous to the K-channel in the A-family. There is no pattern of conserved residues that could form a D-channel analogue or an alternative proton channel. The functional importance of the residues proposed to be part of the K-channel was tested by site-directed mutagenesis using the cbb3 oxidases from R. sphaeroides and Vibrio cholerae. Several of the residues proposed to be part of the putative K-channel had significantly reduced catalytic activity upon mutation: T219V, Y227F/Y228F, N293D, and Y321F. The data strongly suggest that in the C-family only one channel functions for the delivery of both catalytic and pumped protons. In addition, it is also proposed that a pair of acidic residues, which are totally conserved among the C-family, may be part of a proton-conducting exit channel for pumped protons. The residues homologous to these acidic amino acids are highly conserved in the cNOR family of nitric oxide reductases and have previously been implicated as part of a proton-conducting channel delivering protons from the periplasmic side of the membrane to the enzyme active site in the cNOR family. It is possible that the C-family contains a homologous proton-conducting channel that delivers pumped protons in the opposite direction, from the active site to the periplasm.

  View details for DOI 10.1021/bi700659y

  View details for Web of Science ID 000249021100010

  View details for PubMedID 17676874

• Ab initio molecular dynamics and time-resolved photoelectron spectroscopy of electronically excited uracil and thymine JOURNAL OF PHYSICAL CHEMISTRY A Hudock, H. R., Levine, B. G., Thompson, A. L., Satzger, H., Townsend, D., Gador, N., Ullrich, S., Stolow, A., Martinez, T. J. 2007; 111 (34): 8500-8508

  Abstract

  The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multicomponent decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and first principles quantum molecular dynamics methods we show that a true minimum on the bright S2 electronic state is responsible for the first step that occurs on a femtosecond time scale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S2/S1 conical intersection is responsible for the picosecond decay.

  View details for DOI 10.1021/jp0723665

  View details for Web of Science ID 000248929600028

  View details for PubMedID 17685594

• A charged ring model for classical OH-(aq) simulations CHEMICAL PHYSICS LETTERS Ufimtsev, I. S., Kalinichev, A. G., Martinez, T. J., Kirkpatrick, R. J. 2007; 442 (1-3): 128-133

  View details for DOI 10.1016/j.cplett.2007.05.042

  View details for Web of Science ID 000248247300023

• The vibrationally adiabatic torsional potential energy surface of trans-stilbene CHEMICAL PHYSICS LETTERS Chowdary, P. D., Martinez, T. J., Gruebele, M. 2007; 440 (1-3): 7-11

  View details for DOI 10.1016/j.cplett.2007.03.109

  View details for Web of Science ID 000246836600002

• QTPIE: Charge transfer with polarization current equalization. A fluctuating charge model with correct asymptotics CHEMICAL PHYSICS LETTERS Chen, J., Martinez, T. J. 2007; 438 (4-6): 315-320

  View details for DOI 10.1016/j.cplett.2007.02.065

  View details for Web of Science ID 000246060000032

• Conformationally controlled chemistry: Excited-state dynamics dictate ground-state reaction SCIENCE Kim, M. H., Shen, L., Tao, H., Martinez, T. J., Suits, A. G. 2007; 315 (5818): 1561-1565

  Abstract

  Ion imaging reveals distinct photodissociation dynamics for propanal cations initially prepared in either the cis or gauche conformation, even though these isomers differ only slightly in energy and face a small interconversion barrier. The product kinetic energy distributions for the hydrogen atom elimination channels are bimodal, and the two peaks are readily assigned to propanoyl cation or hydroxyallyl cation coproducts. Ab initio multiple spawning dynamical calculations suggest that distinct ultrafast dynamics in the excited state deposit each conformer in isolated regions of the ground-state potential energy surface, and, from these distinct regions, conformer interconversion does not effectively compete with dissociation.

  View details for DOI 10.1126/science.1136453

  View details for Web of Science ID 000244934800048

  View details for PubMedID 17363670

• A continuous spawning method for nonadiabatic dynamics and validation for the zero-temperature spin-boson problem ISRAEL JOURNAL OF CHEMISTRY Ben-Nun, M., Martinez, T. J. 2007; 47 (1): 75-88

  View details for Web of Science ID 000254385000011

• Optimization of semiempirical quantum chemistry methods via multiobjective genetic algorithms: Accurate photodynamics for larger molecules and longer time scales MATERIALS AND MANUFACTURING PROCESSES Sastry, K., Johnson, D. D., Thompson, A. L., Goldberg, D. E., Martinez, T. J., Leiding, J., Owens, J. 2007; 22 (5-6): 553-561

  View details for DOI 10.1080/10426910701319506

  View details for Web of Science ID 000248794900004

• The evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases 51st Annual Meeting of the Biophysical-Society Robinson, D., Hemp, J., Kelleher, N. L., Martinez, T. J., Gennis, R. B. CELL PRESS. 2007: 502A–502A

  View details for Web of Science ID 000243972403196

• Isomerization through conical intersections ANNUAL REVIEW OF PHYSICAL CHEMISTRY Levine, B. G., Martinez, T. J. 2007; 58: 613-634

  Abstract

  The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.

  View details for DOI 10.1146/annurev.physchem.57.032905.104612

  View details for Web of Science ID 000246652300024

  View details for PubMedID 17291184

• First principles dynamics of photoexcited DNA and RNA bases International Conference on Computational Methods in Science and Engineering Hudock, H. R., Levine, B. G., Thompson, A. L., Martinez, T. J. AMER INST PHYSICS. 2007: 219–222

  View details for Web of Science ID 000252602900054

• Evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases BIOCHEMISTRY Hemp, J., Robinson, D. E., Ganesan, K. B., Martinez, T. J., Kelleher, N. L., Gennis, R. B. 2006; 45 (51): 15405-15410

  Abstract

  In the respiratory chains of aerobic organisms, oxygen reductase members of the heme-copper superfamily couple the reduction of O2 to proton pumping, generating an electrochemical gradient. There are three distinct families of heme-copper oxygen reductases: A, B, and C types. The A- and B-type oxygen reductases have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. In the C-type oxygen reductases (also called cbb3 oxidases), an analogous active-site tyrosine has recently been predicted by molecular modeling to be located within a different transmembrane helix in comparison to the A- and B-type oxygen reductases. In this work, Fourier-transform mass spectrometry is used to show that the predicted tyrosine forms a histidine-tyrosine cross-linked cofactor in the active site of the C-type oxygen reductases. This is the first known example of the evolutionary migration of a post-translationally modified active-site residue. It also verifies the presence of a unique cofactor in all three families of proton-pumping respiratory oxidases, demonstrating that these enzymes likely share a common reaction mechanism and that the histidine-tyrosine cofactor may be a required component for proton pumping.

  View details for DOI 10.1021/bi062026u

  View details for Web of Science ID 000242935600028

  View details for PubMedID 17176062

  View details for PubMedCentralID PMC2535580

• Conical intersections and double excitations in time-dependent density functional theory MOLECULAR PHYSICS Levine, B. G., Ko, C., Quenneville, J., Martinez, T. J. 2006; 104 (5-7): 1039-1051

  View details for DOI 10.1080/00268970500417762

  View details for Web of Science ID 000236853100034

• Multicentered valence electron effective potentials: A solution to the link atom problem for ground and excited electronic states JOURNAL OF CHEMICAL PHYSICS Slavicek, P., Martinez, T. J. 2006; 124 (8)

  Abstract

  We introduce a multicentered valence electron effective potential (MC-VEEP) description of functional groups which succeeds even in the context of excited electronic states. The MC-VEEP is formulated within the ansatz which is familiar for effective core potentials in quantum chemistry, and so can be easily incorporated in any quantum chemical calculation. By demanding that both occupied and virtual orbitals are described correctly on the MC-VEEP, we are able to ensure correct behavior even when the MC-VEEP borders an electronically excited region. However, the present formulation does require that the electrons represented by the MC-VEEP are primarily spectators and not directly participating in the electronic excitation. We point out the importance of separating the electrostatic and exchange-repulsion components of the MC-VEEP in order that interactions between the effective potential and other nuclei can be modeled correctly. We present a MC-VEEP for methyl radical with one active electron which is tested in several conjugated molecules. We discuss the use of the MC-VEEP as a solution to the "link atom" problem in hybrid quantum mechanical/molecular mechanical methods. We also discuss the limitations and further development of this approach.

  View details for DOI 10.1063/1.2173992

  View details for Web of Science ID 000235663300014

  View details for PubMedID 16512708

• Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores ACCOUNTS OF CHEMICAL RESEARCH Martinez, T. J. 2006; 39 (2): 119-126

  Abstract

  We discuss the basic process of photoinduced isomerization as a building block for the design of complex, multifunctional molecular devices. The excited-state dynamics associated with isomerization is detailed through application of the ab initio multiple spawning (AIMS) method, which solves the electronic and nuclear Schrödinger equations simultaneously. This first-principles molecular dynamics approach avoids the uncertainties and extraordinary effort associated with fitting of potential energy surfaces and allows for bond rearrangement processes with no special input. Furthermore, the AIMS method allows for the breakdown of the Born-Oppenheimer approximation and thus can correctly model chemistry occurring on multiple electronic states. We show that charge-transfer states play an important role in photoinduced isomerization and argue that this provides an essential "design rule" for multifunctional devices based on isomerizing chromophores.

  View details for DOI 10.1021/ar040202q

  View details for Web of Science ID 000235662800007

  View details for PubMedID 16489731

• Ab initio molecular dynamics of excited-state intramolecular proton transfer around a three-state conical intersection in malonaldehyde JOURNAL OF PHYSICAL CHEMISTRY A Coe, J. D., Martinez, T. J. 2006; 110 (2): 618-630

  Abstract

  Excited-state potential energy surface (PES) characterization is carried out at the CASSCF and MRSDCI levels, followed by ab initio dynamics simulation of excited-state intramolecular proton transfer (ESIPT) on the S2(pipi*) state in malonaldehyde. The proton-transfer transition state lies close to an S2/S1 conical intersection, leading to substantial coupling of proton transfer with electronic relaxation. Proton exchange proceeds freely on S2, but its duration is limited by competition with twisting out of the molecular plane. This rotamerization pathway leads to an intersection of the three lowest singlet states, providing the first detailed report of ab initio dynamics around a three-state intersection (3SI). There is a significant energy barrier to ESIPT on S1, and further pyramidalization of the twisted structure leads to the minimal energy S1/S0 intersection and energetic terminal point of excited-state dynamics. Kinetics and additional mechanistic details of these pathways are discussed. Significant depletion of the spectroscopic state and recovery of the ground state is seen within the first 250 fs after photoexcitation.

  View details for DOI 10.1021/jp0535339

  View details for Web of Science ID 000234699000030

  View details for PubMedID 16405334

• Multiobjective genetic algorithms for multiscaling excited state direct dynamics in photochemistry 8th Annual Genetic and Evolutionary Computation Conference Sastry, K., Johnson, D. D., Thompson, A. L., Goldberg, D. E., Martinez, T. J., Leiding, J., Owens, J. ASSOC COMPUTING MACHINERY. 2006: 1745–1752

  View details for Web of Science ID 000249917300257

• Simulation of the photodynamics of azobenzene on its first excited state: Comparison of full multiple spawning and surface hopping treatments JOURNAL OF CHEMICAL PHYSICS Toniolo, A., Ciminelli, C., Persico, M., Martinez, T. J. 2005; 123 (23)

  Abstract

  We have studied the cis-->trans and trans-->cis photoisomerization of azobenzene after n-->pi* excitation using the full multiple spawning (FMS) method for nonadiabatic wave-packet dynamics with potential-energy surfaces and couplings determined "on the fly" from a reparametrized multiconfigurational semiempirical method. We compare the FMS results with a previous direct dynamics treatment using the same potential-energy surfaces and couplings, but with the nonadiabatic dynamics modeled using a semiclassical surface hopping (SH) method. We concentrate on the dynamical effects that determine the photoisomerization quantum yields, namely, the rate of radiationless electronic relaxation and the character of motion along the reaction coordinate. The quantal and semiclassical results are in good general agreement, confirming our previous analysis of the photodynamics. The SH method slightly overestimates the rate of excited state decay, leading in this case to lower quantum yields.

  View details for DOI 10.1063/1.2134705

  View details for Web of Science ID 000234145900019

  View details for PubMedID 16392921

• Using meta conjugation to enhance charge separation versus charge recombination in phenylacetylene donor-bridge-acceptor complexes JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Thompson, A. L., Ahn, T. S., Thomas, K. R., Thayumanavan, S., Martinez, T. J., Bardeen, C. J. 2005; 127 (47): 16348-16349

  Abstract

  A pair of donor-bridge-acceptor electron-transfer complexes, with a carbazole donor and a naphthalimide acceptor connected by either a para- or meta-conjugated phenylacetylene bridge, are synthesized and studied using time-resolved and steady-state spectroscopy. These experiments show that the charge separation times, which depend on the coupling of the donor and acceptor through the excited bridge moiety, are similar for the two molecules (Meta and Para). The charge recombination time, however, is a factor of 10 slower for Meta than for Para. These results are related to changes in the electronic coupling of the bridge depending on its electronic state, and show that meta-conjugated bridges provide a possible motif for the design of asymmetric molecular wires.

  View details for DOI 10.1021/ja054543q

  View details for Web of Science ID 000233617900004

  View details for PubMedID 16305193

• Meta- and para-substitution in aromatic systems: Insights from first-principles dynamics and ultrafast spectroscopy 230th National Meeting of the American-Chemical-Society Thompson, A. L., Gaab, K. M., Thomas, K. R., Thayumanavan, S., Bardeen, C. J., Martinez, T. J. AMER CHEMICAL SOC. 2005: U2968–U2969

  View details for Web of Science ID 000236797305881

• Helix switching of a key active-site residue in the cytochrome cbb(3) oxidases BIOCHEMISTRY Hemp, J., Christian, C., Barquera, B., Gennis, R. B., Martinez, T. J. 2005; 44 (32): 10766-10775

  Abstract

  In the respiratory chains of mitochondria and many aerobic prokaryotes, heme-copper oxidases are the terminal enzymes that couple the reduction of molecular oxygen to proton pumping, contributing to the protonmotive force. The cbb(3) oxidases belong to the superfamily of enzymes that includes all of the heme-copper oxidases. Sequence analysis indicates that the cbb(3) oxidases are missing an active-site tyrosine residue that is absolutely conserved in all other known heme-copper oxidases. In the other heme-copper oxidases, this tyrosine is known to be subject to an unusual post-translational modification and to play a critical role in the catalytic mechanism. The absence of this tyrosine in the cbb(3) oxidases raises the possibility that the cbb(3) oxidases utilize a different catalytic mechanism from that of the other members of the superfamily. Using homology modeling, quantum chemistry, and molecular dynamics, a model of the structure of subunit I of a cbb(3) oxidase (Vibrio cholerae) was constructed. The model predicts that a tyrosine residue structurally analogous to the active-site tyrosine in other oxidases is present in the cbb(3) oxidases but that the tyrosine originates from a different transmembrane helix within the protein. The predicted active-site tyrosine is conserved in the sequences of all of the known cbb(3) oxidases. Mutagenesis of the tyrosine to phenylalanine in the V. cholerae oxidase resulted in a fully assembled enzyme with nativelike structure but lacking catalytic activity. These findings strongly suggest that all of the heme-copper oxidases utilize the same catalytic mechanism and provide an unusual example in which a critical active-site residue originates from different places within the primary sequence for different members of the same superfamily.

  View details for DOI 10.1021/bi050464f

  View details for Web of Science ID 000231339600003

  View details for PubMedID 16086579

• Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Coe, J. D., Martinez, T. J. 2005; 127 (13): 4560-4561

  Abstract

  We demonstrate the existence of a simultaneous degeneracy (not required by symmetry) of three electronic states in malonaldehyde. This is one of the first reports of such a triple degeneracy involving S0, S1, and S2 in a molecule with a closed-shell ground state. We further report on a two-state S2/S1 conical intersection which is higher in energy than the three-state intersection, but closer to the Franck-Condon point. First-principles quantum dynamics calculations of the photochemistry after excitation to S2 show that there is a competition between these intersections, with more than half of the population decaying to S1 through the higher energy S2/S1 intersection. Surprisingly, much of the population which makes it to the triple degeneracy point is not funneled directly to S0, but rather remains trapped on S1. We attribute this to the large dimensionality of the branching plane at a three-state intersection (the degeneracy is lifted along at least five distinct molecular displacements).

  View details for DOI 10.1021/ja043093j

  View details for Web of Science ID 000228089300009

  View details for PubMedID 15796506

• Direct QM/MM Simulations of the photodynamics of retinal protonated Schiff base in isolation and solvated environments 49th Annual Meeting of the Biophysical-Society Punwong, C., Owens, J., Martinez, T. J. CELL PRESS. 2005: 530A–530A

  View details for Web of Science ID 000226378502595

• Computation of Reaction Mechanisms and Dynamics in Photobiology COMPUTATIONAL PHOTOCHEMISTRY Olsen, S., Toniolo, A., Ko, C., Manohar, L., Lamothe, K., Martinez, T. J., Olivucci, M. 2005; 16: 225-253

  View details for Web of Science ID 000311096100009

• Ab initio investigation of ionic hydration with the polarizable continuum model ASME Heat Transfer Summer Conference Karampinos, D. C., Georgiadis, J. G., Martinez, T. J. AMER SOC MECHANICAL ENGINEERS. 2005: 473–480

  View details for Web of Science ID 000243378100060

• Ab initio equation-of-motion coupled-cluster molecular dynamics with 'on-the-fly' diabatization: the doublet-like feature in the photoabsorption spectrum of ethylene CHEMICAL PHYSICS LETTERS Choi, H. C., Baeck, K. K., Martinez, T. J. 2004; 398 (4-6): 407-413

  View details for DOI 10.1016/j.cplett.2004.09.084

  View details for Web of Science ID 000224852800023

• Excited state direct dynamics of benzene with reparameterized multi-reference semiempirical configuration interaction methods CHEMICAL PHYSICS Toniolo, A., Thompson, A. L., Martinez, T. J. 2004; 304 (1-2): 133-145

  View details for DOI 10.1016/j.chemphys.2004.04.018

  View details for Web of Science ID 000223585700011

• Energy and charge transport through conjugated phenylacetylene networks. Bardeen, C. J., Thompson, A. L., Martinez, T., Thayumanavan, S., Thomas, K. R. AMER CHEMICAL SOC. 2004: U18

  View details for Web of Science ID 000223713800071

• A new approach to reactive potentials with fluctuating charges: Quadratic valence-bond model JOURNAL OF PHYSICAL CHEMISTRY A Morales, J., Martinez, T. J. 2004; 108 (15): 3076-3084

  View details for DOI 10.1021/jp0369342

  View details for Web of Science ID 000220724300035

• Variable electronic coupling in phenylacetylene dendrimers: The role of forster, dexter, and charge-transfer interactions JOURNAL OF PHYSICAL CHEMISTRY A Thompson, A. L., Gaab, K. M., Xu, J. J., Bardeen, C. J., Martinez, T. J. 2004; 108 (4): 671-682

  View details for DOI 10.1021/jp030953u

  View details for Web of Science ID 000188535600019

• Conical intersection dynamics in solution: the chromophore of Green Fluorescent Protein General Meeting on Non-Adiabiatic Effects in Chemical Dynamics Toniolo, A., Olsen, S., Manohar, L., Martinez, T. J. ROYAL SOC CHEMISTRY. 2004: 149–163

  Abstract

  We use ab initio results to reparameterize a multi-reference semiempirical method to reproduce the ground and excited state potential energy surfaces (PESs) for the chromophore of Green Fluorescent Protein (GFP). The validity of the new parameter set is tested, and the new method is combined with a quantum mechanical/molecular mechanical (QM/MM) treatment so that it can be applied in the solution phase. Solvent effects on the energetics of the relevant conical intersections are explored. We then combine this representation of the ground and excited state PESs with the full multiple spawning (FMS) nonadiabatic wavepacket dynamics method to simulate the photodynamics of the neutral GFP chromophore in both gas and solution phases. In these calculations, the PESs and their nonadiabatic couplings are evaluated simultaneously with the nuclear dynamics, ie. "on-the-fly". The effect of solvation is seen to be quite dramatic, resulting in an order of magnitude decrease in the excited state lifetime. We observe a correlated torsion about a double bond and its adjacent single bond in both gas and solution phases. This is discussed in the context of previous proposals about minimal volume isomerization mechanisms in protein environments.

  View details for DOI 10.1039/b401167h

  View details for Web of Science ID 000223139400010

  View details for PubMedID 15471344

• Helix switching of a key active site residue in the cytochrome cbb(3) oxidases Hemp, J., Martinez, T., Gennis, R. BIOPHYSICAL SOCIETY. 2004: 305A-306A

  View details for Web of Science ID 000187971201569

• Azobenzene photoisomerization: Two states and two relaxation pathways explain the violation of Kasha's rule. 6th International Conference on Femtochemistry Schultz, T., Ullrich, S., Quenneville, J., Martinez, T. J., Zgierski, M. Z., Stolow, A. ELSEVIER SCIENCE BV. 2004: 45–48

  View details for Web of Science ID 000222945300008

• Ultrafast excited state dynamics in the green fluorescent protein chromophore 6th International Conference on Femtochemistry Toniolo, A., Olsen, S., Manohar, L., Martinez, T. J. ELSEVIER SCIENCE BV. 2004: 425–432

  View details for Web of Science ID 000222945300083

• Quantum energy flow and trans-stilbene photoisomerization: an example of a non-RRKM reaction JOURNAL OF PHYSICAL CHEMISTRY A Leitner, D. M., Levine, B., Quenneville, J., Martinez, T. J., Wolynes, P. G. 2003; 107 (49): 10706-10716

  View details for DOI 10.1021/jp0305180

  View details for Web of Science ID 000187009500030

• Ab initio excited-state dynamics of the photoactive yellow protein chromophore JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ko, C., Levine, B., Toniolo, A., Manohar, L., Olsen, S., Werner, H. J., Martinez, T. J. 2003; 125 (42): 12710-12711

  Abstract

  The photoisomerization mechanism of the neutral form of the photoactive yellow protein (PYP) chromophore is investigated using ab initio quantum chemistry and first-principles nonadiabatic molecular dynamics (ab initio multiple spawning or AIMS). We identify the nature of the two lowest-lying excited states, characterize the short-time behavior of molecules excited directly to S2, and explain the origin of the experimentally observed wavelength-dependent photoisomerization quantum yield.

  View details for DOI 10.1021/ja0365025

  View details for Web of Science ID 000185990300022

  View details for PubMedID 14558810

• Hijacking the playstation2 for computational chemistry. 226th National Meeting of the American-Chemical-Society Levine, B., Martinez, T. J. AMER CHEMICAL SOC. 2003: U426–U426

  View details for Web of Science ID 000187062401973

• Meta-conjugation and excited-state coupling in phenylacetylene dendrimers JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Gaab, K. M., Thompson, A. L., Xu, J. J., Martinez, T. J., Bardeen, C. J. 2003; 125 (31): 9288-9289

  Abstract

  Traditional pictures of optical properties in phenylacetylene dendrimers view the molecule as a collection of independent chromophores, linked by meta-substitution at the central phenyl ring. While this picture is reasonable for explaining the observed absorption trends, it breaks down in describing the emission behavior. We utilize a combination of ab initio theory and experiment to demonstrate that differences in the absorbing and emitting states can be described using an exciton model with very weak chromophore coupling for the absorption geometry and strong coupling for the emission geometry. This result may have significant implications for the design of energy-funneling dendrimeric molecules.

  View details for DOI 10.1021/ja029489h

  View details for Web of Science ID 000184515300025

  View details for PubMedID 12889946

• Mechanism and dynamics of azobenzene photoisomerization JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Schultz, T., Quenneville, J., Levine, B., Toniolo, A., Martinez, T. J., Lochbrunner, S., Schmitt, M., Shaffer, J. P., Zgierski, M. Z., Stolow, A. 2003; 125 (27): 8098-8099

  Abstract

  The excited-state dynamics of trans-azobenzene were investigated by femtosecond time-resolved photoelectron spectroscopy and ab initio molecular dynamics. Two near-degenerate pipi* excited states, S2 and S3,4, were identified in a region hitherto associated with only one excited state. These results help to explain contradictory reports about the photoisomerization mechanism and the wavelength dependence of the quantum yield. A new model for the isomerization mechanism is proposed.

  View details for DOI 10.1021/ja021363x

  View details for Web of Science ID 000183938900015

  View details for PubMedID 12837068

• Ab initio molecular dynamics with equation-of-motion coupled-cluster theory: electronic absorption spectrum of ethylene CHEMICAL PHYSICS LETTERS Baeck, K. K., Martinez, T. J. 2003; 375 (3-4): 299-308

  View details for DOI 10.1016/S0009-2614(03)00847-9

  View details for Web of Science ID 000183966200008

• The construction of semi-diabatic potential energy surfaces of excited states for use in excited state AIMD studies by the equation-of-motion coupled-cluster method 10th Korea/Japan Joint Symposium on Theoretical/Computational Chemistry Molecular Structure, Properties, and Design Baeck, K. K., Martinez, T. J. KOREAN CHEMICAL SOC. 2003: 712–16

  View details for Web of Science ID 000183819300005

• Electronic structure of solid 1,3,5-triamino-2,4,6-trinitrobenzene under uniaxial compression: Possible role of pressure-induced metallization in energetic materials PHYSICAL REVIEW B Wu, C. J., Yang, L. H., Fried, L. E., Quenneville, J., Martinez, T. J. 2003; 67 (23)

  View details for DOI 10.1103/PhysRevB.67.235101

  View details for Web of Science ID 000184040700019

• Conical intersections in solution: A QM/MM study using floating occupation semiempirical configuration interaction wave functions JOURNAL OF PHYSICAL CHEMISTRY A Toniolo, A., Granucci, G., Martinez, T. J. 2003; 107 (19): 3822-3830

  View details for DOI 10.1021/jp022468p

  View details for Web of Science ID 000182893900032

• Ab initio study of cis-trans photoisomerization in stilbene and ethylene JOURNAL OF PHYSICAL CHEMISTRY A Quenneville, J., Martinez, T. J. 2003; 107 (6): 829-837

  View details for DOI 10.1021/jp021210w

  View details for Web of Science ID 000182533500011

• Solvation of the fluoride anion by methanol JOURNAL OF PHYSICAL CHEMISTRY A Corbett, C. A., Martinez, T. J., Lisy, J. M. 2002; 106 (42): 10015-10021

  View details for DOI 10.1021/jp020892k

  View details for Web of Science ID 000178792000048

• Optimization of conical intersections with floating occupation semiempirical configuration interaction wave functions JOURNAL OF PHYSICAL CHEMISTRY A Toniolo, A., Ben-Nun, M., Martinez, T. J. 2002; 106 (18): 4679-4689

  View details for DOI 10.1021/jp014289y

  View details for Web of Science ID 000175488400030

• The role of intersection topography in bond selectivity of cis-trans photoisomerization PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ben-Nun, M., Molnar, F., Schulten, K., Martinez, T. J. 2002; 99 (4): 1769-1773

  Abstract

  Ab initio methods are used to characterize the ground and first excited state of the chromophore in the rhodopsin family of proteins: retinal protonated Schiff base. Retinal protonated Schiff base has five double bonds capable of undergoing isomerization. Upon absorption of light, the chromophore isomerizes and the character of the photoproducts (e.g., 13-cis and 11-cis) depends on the environment, protein vs. solution. Our ab initio calculations show that, in the absence of any specific interactions with the environment (e.g., discrete ordered charges in a protein), energetic considerations cannot explain the observed bond selectivity. We instead attribute the origin of bond selectivity to the shape (topography) of the potential energy surfaces in the vicinity of points of true degeneracy (conical intersections) between the ground and first excited electronic states. This provides a molecular example where a competition between two distinct but nearly isoenergetic photochemical reaction pathways is resolved by a topographical difference between two conical intersections.

  View details for DOI 10.1073/pnas.032658099

  View details for Web of Science ID 000174031100006

  View details for PubMedID 11854479

  View details for PubMedCentralID PMC122268

• Ab initio quantum molecular dynamics ADVANCES IN CHEMICAL PHYSICS, VOLUME 121 Ben-Nun, M., Martinez, T. J. 2002; 121: 439-512

  View details for Web of Science ID 000175129800007

• Features of interest on the S-0 and S-1 potential energy surfaces of a model green fluorescent protein chromophore Olsen, S., Manohar, L., Martinez, T. J. CELL PRESS. 2002: 359A–359A

  View details for Web of Science ID 000173252701763

• Photochemistry from first principles - advances and future prospects 18th IUPAC Symposium on Photochemistry Quenneville, J., Ben-Nun, M., Martinez, T. J. ELSEVIER SCIENCE SA. 2001: 229–35

  View details for Web of Science ID 000172314000022

• Comparison of full multiple spawning, trajectory surface hopping, and converged quantum mechanics for electronically nonadiabatic dynamics JOURNAL OF CHEMICAL PHYSICS Hack, M. D., Wensmann, A. M., Truhlar, D. G., Ben-Nun, M., Martinez, T. J. 2001; 115 (3): 1172-1186

  View details for Web of Science ID 000169776100007

• Classical fluctuating charge theories: The maximum entropy valence bond formalism and relationships to previous models JOURNAL OF PHYSICAL CHEMISTRY A Morales, J., Martinez, T. J. 2001; 105 (12): 2842-2850

  View details for DOI 10.1021/jp003823j

  View details for Web of Science ID 000167766600045

• HYDRA: A program for QM/MM and dynamics calculations Kim, A. J., Olsen, S., Hemp, J., Martinez, T. J. CELL PRESS. 2001: 322A–322A

  View details for Web of Science ID 000166692201477

• Photodynamics of ethylene: ab initio studies of conical intersections CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 2000; 259 (2-3): 237-248

  View details for Web of Science ID 000089261600010

• Characterization of a conical intersection between the ground and first excited state for a retinal analog 5th World Congress of Theoretically Oriented Chemists (WATOC) Molnar, F., Ben-Nun, M., Martinez, T. J., Schulten, K. ELSEVIER SCIENCE BV. 2000: 169–178

  View details for Web of Science ID 000088054600015

• Direct observation of disrotatory ring-opening in photoexcited cyclobutene using ab initio molecular dynamics JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Ben-Nun, M., Martinez, T. J. 2000; 122 (26): 6299-6300

  View details for Web of Science ID 000088126600026

• Ab initio multiple spawning: Photochemistry from first principles quantum molecular dynamics JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Quenneville, J., Martinez, T. J. 2000; 104 (22): 5161-5175

  View details for DOI 10.1021/jp994174i

  View details for Web of Science ID 000088943500001

• A multiple spawning approach to tunneling dynamics JOURNAL OF CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 2000; 112 (14): 6113-6121

  View details for Web of Science ID 000086231600003

• Ab initio study of coupled electron transfer/proton transfer in cytochrome c oxidase JOURNAL OF PHYSICAL CHEMISTRY A Moore, D. B., Martinez, T. J. 2000; 104 (11): 2367-2374

  View details for Web of Science ID 000086025300029

• Electronic absorption and resonance Raman spectroscopy from ab initio quantum molecular dynamics JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Martinez, T. J. 1999; 103 (49): 10517-10527

  View details for Web of Science ID 000084318700059

• Semiclassical tunneling rates from ab initio molecular dynamics JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Martinez, T. J. 1999; 103 (31): 6055-6059

  View details for Web of Science ID 000082099000001

• The solvation of chloride by methanol - surface versus interior cluster ion states JOURNAL OF CHEMICAL PHYSICS Cabarcos, O. M., Weinheimer, C. J., Martinez, T. J., Lisy, J. M. 1999; 110 (19): 9516-9526

  View details for Web of Science ID 000080154000022

• Exploiting temporal nonlocality to remove scaling bottlenecks in nonadiabatic quantum dynamics JOURNAL OF CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 1999; 110 (9): 4134-4140

  View details for Web of Science ID 000078686400006

• Ab initio interpolated quantum dynamics on coupled electronic states with full configuration interaction wave functions JOURNAL OF CHEMICAL PHYSICS Thompson, K., Martinez, T. J. 1999; 110 (3): 1376-1382

  View details for Web of Science ID 000078030500008

• Ab initio molecular dynamics study of cis-trans photoisomerization in ethylene CHEMICAL PHYSICS LETTERS Ben-Nun, M., Martinez, T. J. 1998; 298 (1-3): 57-65

  View details for Web of Science ID 000077607700009

• Electronic energy funnels in cis-trans photoisomerization of retinal protonated Schiff base JOURNAL OF PHYSICAL CHEMISTRY A Ben-Nun, M., Martinez, T. J. 1998; 102 (47): 9607-9617

  View details for Web of Science ID 000078514000042

• Direct evaluation of the Pauli repulsion energy using 'classical' wavefunctions in hybrid quantum/classical potential energy surfaces CHEMICAL PHYSICS LETTERS Ben-Nun, M., Martinez, T. J. 1998; 290 (1-3): 289-295

  View details for Web of Science ID 000074466600045

• Nonadiabatic molecular dynamics: Validation of the multiple spawning method for a multidimensional problem JOURNAL OF CHEMICAL PHYSICS Ben-Nun, M., Martinez, T. J. 1998; 108 (17): 7244-7257

  View details for Web of Science ID 000073315200023

• Quantum dynamics of the femtosecond photoisomerization of retinal in bacteriorhodopsin FARADAY DISCUSSIONS Ben-Nun, M., Molnar, F., Lu, H., Phillips, J. C., Martinez, T. J., Schulten, K. 1998; 110: 447-462

  Abstract

  The membrane protein bacteriorhodopsin contains all-trans-retinal in a binding site lined by amino acid side groups and water molecules that guide the photodynamics of retinal. Upon absorption of light, retinal undergoes a subpicosecond all-trans-->13-cis phototransformation involving torsion around a double bond. The main reaction product triggers later events in the protein that induce pumping of a proton through bacteriorhodopsin. Quantum-chemical calculations suggest that three coupled electronic states, the ground state and two closely lying excited states, are involved in the motion along the torsional reaction coordinate phi. The evolution of the protein-retinal system on these three electronic surfaces has been modelled using the multiple spawning method for non-adiabatic dynamics. We find that, although most of the population transfer occurs on a timescale of 300 fs, some population transfer occurs on a longer timescale, occasionally extending well beyond 1 ps.

  View details for Web of Science ID 000077492000025

  View details for PubMedID 10822594

• Nonstationary electronic states and site-selective reactivity JOURNAL OF PHYSICAL CHEMISTRY A Weinkauf, R., Schlag, E. W., Martinez, T. J., Levine, R. D. 1997; 101 (42): 7702-7710

  View details for Web of Science ID A1997YB79500004

• Dynamical stereochemistry on several electronic states: A computational study of Na*+H-2 JOURNAL OF PHYSICAL CHEMISTRY A Bennun, M., Martinez, T. J., Levine, R. D. 1997; 101 (41): 7522-7529

  View details for Web of Science ID A1997YA48400010

• Molecular collision dynamics on several electronic states JOURNAL OF PHYSICAL CHEMISTRY A Martinez, T. J., Bennun, M., Levine, R. D. 1997; 101 (36): 6389-6402

  View details for Web of Science ID A1997XV73400006

• Ab initio molecular dynamics around a conical intersection: Li(2p)+H-2 CHEMICAL PHYSICS LETTERS Martinez, T. J. 1997; 272 (3-4): 139-147

  View details for Web of Science ID A1997XH44000001

• Multiple traversals of a conical intersection: electronic quenching in Na*+H-2 CHEMICAL PHYSICS LETTERS Bennun, M., Martinez, T. J., Levine, R. D. 1997; 270 (3-4): 319-326

  View details for Web of Science ID A1997XA80400012

• Non-adiabatic molecular dynamics: Split-operator multiple spawning with applications to photodissociation JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS Martinez, T. J., Levine, R. D. 1997; 93 (5): 941-947

  View details for Web of Science ID A1997WP01200034

• Direct imaging of excited electronic states using diffraction techniques: Theoretical considerations CHEMICAL PHYSICS LETTERS Bennun, M., Martinez, T. J., Weber, P. M., Wilson, K. R. 1996; 262 (3-4): 405-414

  View details for Web of Science ID A1996VT11700038

• First-principles molecular dynamics on multiple electronic states: A case study of NaI JOURNAL OF CHEMICAL PHYSICS Martinez, T. J., Levine, R. D. 1996; 105 (15): 6334-6341

  View details for Web of Science ID A1996VM55400023

• Dynamics of the collisional electron transfer and femtosecond photodissociation of NaI on ab initio electronic energy curves CHEMICAL PHYSICS LETTERS Martinez, T. J., Levine, R. D. 1996; 259 (3-4): 252-260

  View details for Web of Science ID A1996VF84100003

• Multi-electronic-state molecular dynamics: A wave function approach with applications JOURNAL OF PHYSICAL CHEMISTRY Martinez, T. J., Bennun, M., Levine, R. D. 1996; 100 (19): 7884-7895

  View details for Web of Science ID A1996UK16900017

• Classical quantal method for multistate dynamics: A computational study JOURNAL OF CHEMICAL PHYSICS Martinez, T. J., Bennun, M., Ashkenazi, G. 1996; 104 (8): 2847-2856

  View details for Web of Science ID A1996TV78700013