Stanford Advisors

All Publications

  • 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


    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

  • Correcting pi-delocalisation errors in conformational energies using density-corrected DFT, with application to crystal polymorphs MOLECULAR PHYSICS Rana, B., Beran, G. O., Herbert, J. M. 2022
  • Detection and Correction of Delocalization Errors for Electron and Hole Polarons Using Density-Corrected DFT. The journal of physical chemistry letters Rana, B., Coons, M. P., Herbert, J. M. 2022: 5275-5284


    Modeling polaron defects is an important aspect of computational materials science, but the description of unpaired spins in density functional theory (DFT) often suffers from delocalization error. To diagnose and correct the overdelocalization of spin defects, we report an implementation of density-corrected (DC-)DFT and its analytic energy gradient. In DC-DFT, an exchange-correlation functional is evaluated using a Hartree-Fock density, thus incorporating electron correlation while avoiding self-interaction error. Results for an electron polaron in models of titania and a hole polaron in Al-doped silica demonstrate that geometry optimization with semilocal functionals drives significant structural distortion, including the elongation of several bonds, such that subsequent single-point calculations with hybrid functionals fail to afford a localized defect even in cases where geometry optimization with the hybrid functional does localize the polaron. This has significant implications for traditional workflows in computational materials science, where semilocal functionals are often used for structure relaxation. DC-DFT calculations provide a mechanism to detect situations where delocalization error is likely to affect the results.

    View details for DOI 10.1021/acs.jpclett.2c01187

    View details for PubMedID 35674719

  • Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package JOURNAL OF CHEMICAL PHYSICS Epifanovsky, E., Gilbert, A. B., Feng, X., Lee, J., Mao, Y., Mardirossian, N., Pokhilko, P., White, A. F., Coons, M. P., Dempwolff, A. L., Gan, Z., Hait, D., Horn, P. R., Jacobson, L. D., Kaliman, I., Kussmann, J., Lange, A. W., Lao, K., Levine, D. S., Liu, J., McKenzie, S. C., Morrison, A. F., Nanda, K. D., Plasser, F., Rehn, D. R., Vidal, M. L., You, Z., Zhu, Y., Alam, B., Albrecht, B. J., Aldossary, A., Alguire, E., Andersen, J. H., Athavale, V., Barton, D., Begam, K., Behn, A., Bellonzi, N., Bernard, Y. A., Berquist, E. J., Burton, H. A., Carreras, A., Carter-Fenk, K., Chakraborty, R., Chien, A. D., Closser, K. D., Cofer-Shabica, V., Dasgupta, S., de Wergifosse, M., Deng, J., Diedenhofen, M., Do, H., Ehlert, S., Fang, P., Fatehi, S., Feng, Q., Friedhoff, T., Gayvert, J., Ge, Q., Gidofalvi, G., Goldey, M., Gomes, J., Gonzalez-Espinoza, C. E., Gulania, S., Gunina, A. O., Hanson-Heine, M. D., Harbach, P. P., Hauser, A., Herbst, M. F., Vera, M., Hodecker, M., Holden, Z. C., Houck, S., Huang, X., Hui, K., Huynh, B. C., Ivanov, M., Jasz, A., Ji, H., Jiang, H., Kaduk, B., Kaehler, S., Khistyaev, K., Kim, J., Kis, G., Klunzinger, P., Koczor-Benda, Z., Koh, J., Kosenkov, D., Koulias, L., Kowalczyk, T., Krauter, C. M., Kue, K., Kunitsa, A., Kus, T., Ladjanszki, I., Landau, A., Lawler, K., Lefrancois, D., Lehtola, S., Li, R. R., Li, Y., Liang, J., Liebenthal, M., Lin, H., Lin, Y., Liu, F., Liu, K., Loipersberger, M., Luenser, A., Manjanath, A., Manohar, P., Mansoor, E., Manzer, S. F., Mao, S., Marenich, A., Markovich, T., Mason, S., Maurer, S. A., McLaughlin, P. F., Menger, M. J., Mewes, J., Mewes, S. A., Morgante, P., Mullinax, J., Oosterbaan, K. J., Paran, G., Paul, A. C., Paul, S. K., Pavosevic, F., Pei, Z., Prager, S., Proynov, E., Rak, A., Ramos-Cordoba, E., Rana, B., Rask, A. E., Rettig, A., Richard, R. M., Rob, F., Rossomme, E., Scheele, T., Scheurer, M., Schneider, M., Sergueev, N., Sharada, S. M., Skomorowski, W., Small, D. W., Stein, C. J., Su, Y., Sundstrom, E. J., Tao, Z., Thirman, J., Tornai, G. J., Tsuchimochi, T., Tubman, N. M., Veccham, S., Vydrov, O., Wenzel, J., Witte, J., Yamada, A., Yao, K., Yeganeh, S., Yost, S. R., Zech, A., Zhang, I., Zhang, X., Zhang, Y., Zuev, D., Aspuru-Guzik, A., Bell, A. T., Besley, N. A., Bravaya, K. B., Brooks, B. R., Casanova, D., Chai, J., Coriani, S., Cramer, C. J., Cserey, G., DePrince, A., DiStasio, R. A., Dreuw, A., Dunietz, B. D., Furlani, T. R., Goddard, W. A., Hammes-Schiffer, S., Head-Gordon, T., Hehre, W. J., Hsu, C., Jagau, T., Jung, Y., Klamt, A., Kong, J., Lambrecht, D. S., Liang, W., Mayhall, N. J., McCurdy, C., Neaton, J. B., Ochsenfeld, C., Parkhill, J. A., Peverati, R., Rassolov, V. A., Shao, Y., Slipchenko, L., Stauch, T., Steele, R. P., Subotnik, J. E., Thom, A. W., Tkatchenko, A., Truhlar, D. G., Van Voorhis, T., Wesolowski, T. A., Whaley, K., Woodcock, H., Zimmerman, P. M., Faraji, S., Gill, P. W., Head-Gordon, M., Herbert, J. M., Krylov, A. 2021; 155 (8)

    View details for DOI 10.1063/5.0055522

    View details for Web of Science ID 000687352200007

  • Hidden Hemibonding in the Aqueous Hydroxyl Radical JOURNAL OF PHYSICAL CHEMISTRY LETTERS Rana, B., Herbert, J. M. 2021; 12 (33): 8053-8060


    The existence of a two-center, three-electron hemibond in the first solvation shell of •OH(aq) has long been a matter of debate. The hemibond manifests in ab initio molecular dynamics simulations as a small-r feature in the oxygen radial distribution function (RDF) for H2O···•OH, but that feature disappears when semilocal density functionals are replaced with hybrids, suggesting a self-interaction artifact. Using periodic simulations at the PBE0+D3 level, we demonstrate that the hemibond is actually still present (as evidenced by delocalization of the spin density) but is obscured by the hydrogen-bonded feature in the RDF due to a slight elongation of the hemibond. Computed electronic spectra for •OH(aq) are in excellent agreement with experiment and confirm that hemibond-like configurations play an outsized role in the spectroscopy due to an intense charge-transfer transition that is strongly attenuated in hydrogen-bonded configurations. Apparently, 25% exact exchange (as in PBE0) is insufficient to eliminate delocalization of unpaired spins.

    View details for DOI 10.1021/acs.jpclett.1c02283

    View details for Web of Science ID 000692014200020

    View details for PubMedID 34406021

  • Role of hemibonding in the structure and ultraviolet spectroscopy of the aqueous hydroxyl radical PHYSICAL CHEMISTRY CHEMICAL PHYSICS Rana, B., Herbert, J. M. 2020; 22 (47): 27829-27844


    The presence of a hemibond in the local solvation structure of the aqueous hydroxyl radical has long been debated, as its appearance in ab initio simulations based on density functional theory is sensitive to self-interaction error (favoring a two-center, three-electron hemibond) but also to finite-size effects. Simulations reported here use a mixed quantum mechanics/molecular mechanics (QM/MM) framework in a very large periodic simulation cell, in order to avoid finite-size artifacts and to facilitate testing of various density functionals, in order to probe the effects of delocalization error. The preponderance of hemibonded structures predicted by generalized gradient approximations persists in simulations using the hybrid functionals B3LYP and PBE0, but is reduced to a minor population if the fraction of exact exchange is increased to 50%. The hemibonded population is also small in simulations employing the long-range corrected functional LRC-ωPBE. Electronic spectra are computed using time-dependent density functional theory, and from these calculations emerges a consensus picture in which hemibonded configurations play an outsized role in the absorption spectrum, even when present as a minority species. An intense 1b2(H2O) → 2pπ(˙OH) charge-transfer transition in hemibonded configurations of the radical proves to be responsible for an absorption feature at 230 nm that is strongly shifted with respect to the gas-phase absorption at 307 nm, but this intense feature is substantially diminished in aqueous geometries where the hemibond is absent. Although not yet sufficient to quantitatively establish the population of hemibonded ˙OH(aq), these simulations do suggest that its presence is revealed by the strongly shifted ultraviolet absorption spectrum of the aqueous radical.

    View details for DOI 10.1039/d0cp05216g

    View details for Web of Science ID 000599460800034

    View details for PubMedID 33245735

  • Ab Initio Investigation of the Resonance Raman Spectrum of the Hydrated Electron JOURNAL OF PHYSICAL CHEMISTRY B Dasgupta, S., Rana, B., Herbert, J. M. 2019; 123 (38): 8074-8085


    According to the conventional picture, the aqueous or "hydrated" electron, e-(aq), occupies an excluded volume (cavity) in the structure of liquid water. However, simulations with certain one-electron models predict a more delocalized spin density for the unpaired electron, with no distinct cavity structure. It has been suggested that only the latter (non-cavity) structure can explain the hydrated electron's resonance Raman spectrum, although this suggestion is based on calculations using empirical frequency maps developed for neat liquid water, not for e-(aq). All-electron ab initio calculations presented here demonstrate that both cavity and non-cavity models of e-(aq) afford significant red-shifts in the O-H stretching region. This effect is nonspecific and arises due to electron penetration into frontier orbitals of the water molecules. Only the conventional cavity model, however, reproduces the splitting of the H-O-D bend (in isotopically mixed water) that is observed experimentally and arises due to the asymmetric environments of the hydroxyl moieties in the electron's first solvation shell. We conclude that the cavity model of e-(aq) is more consistent with the measured resonance Raman spectrum than is the delocalized, non-cavity model, despite previous suggestions to the contrary. Furthermore, calculations with hybrid density functionals and with Hartree-Fock theory predict that non-cavity liquid geometries afford only unbound (continuum) states for an extra electron, whereas in reality this energy level should lie more than 3 eV below vacuum level. As such, the non-cavity model of e-(aq) appears to be inconsistent with available vibrational spectroscopy, photoelectron spectroscopy, and quantum chemistry.

    View details for DOI 10.1021/acs.jpcb.9b04895

    View details for Web of Science ID 000488335100014

    View details for PubMedID 31442044

  • Variational Formulation of the Generalized Many-Body Expansion with Self-Consistent Charge Embedding: Simple and Correct Analytic Energy Gradient for Fragment-Based ab Initio Molecular Dynamics JOURNAL OF PHYSICAL CHEMISTRY LETTERS Liu, J., Rana, B., Liu, K., Herbert, J. M. 2019; 10 (14): 3877-3886


    The many-body expansion (MBE) and its extension to overlapping fragments, the generalized (G)MBE, constitute the theoretical basis for most fragment-based approaches for large-scale quantum chemistry. We reformulate the GMBE for use with embedding charges determined self-consistently from the fragment wave functions, in a manner that preserves the variational nature of the underlying self-consistent field method. As a result, the analytic gradient retains the simple "sum of fragment gradients" form that is often assumed in practice, sometimes incorrectly. This obviates (without approximation) the need to solve coupled-perturbed equations, and we demonstrate stable, fragment-based ab initio molecular dynamics simulations using this technique. Energy conservation fails when charge-response contributions to the Fock matrix are neglected, even while geometry optimizations and vibrational frequency calculations may yet be accurate. Stable simulations can be recovered by means of straightforward modifications introduced here, providing a general paradigm for fragment-based ab initio molecular dynamics.

    View details for DOI 10.1021/acs.jpclett.9b01214

    View details for Web of Science ID 000476694300009

    View details for PubMedID 31251619

  • Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron JOURNAL OF CHEMICAL PHYSICS Holden, Z. C., Rana, B., Herbert, J. M. 2019; 150 (14): 144115


    We report an implementation of periodic boundary conditions for mixed quantum mechanics/molecular mechanics (QM/MM) simulations, in which atomic partial charges are used to represent periodic images of the QM region. These charges are incorporated into the Fock matrix in a manner that preserves the variational nature of the self-consistent field procedure, and their interactions with the MM charges are summed using the conventional Ewald technique. To ensure that the procedure is stable in arbitrary basis sets, the atomic charges are derived by least-squares fit to the electrostatic potential generated by the QM region. We formulate and implement analytic energy gradients for the QM/MM-Ewald method and demonstrate that stable molecular dynamics simulations are thereby obtained. As a proof-of-concept application, we perform QM/MM simulations of a hydrated electron in bulk liquid water at the level of Hartree-Fock theory plus empirical dispersion. These simulations demonstrate that the "cavity model" of the aqueous electron, in which the spin density of the anionic defect is localized within an excluded volume in the liquid, is stable at room temperature on a time scale of at least several picoseconds. These results validate cavity-forming pseudopotential models of e-(aq) that have previously been derived from static-exchange Hartree-Fock calculations, and cast doubt upon whether non-cavity-forming pseudopotentials are faithful to the underlying Hartree-Fock calculation from which they were obtained.

    View details for DOI 10.1063/1.5089673

    View details for Web of Science ID 000464451300018

    View details for PubMedID 30981237