Joseph Kelly

All Publications

• Accelerating CCSD(T) on Graphical Processing Units (GPUs). The journal of physical chemistry. A Fajen, O. J., Kelly, J. E., Hohenstein, E. G., Martinez, T. J. 2026

  Abstract

  Coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) often provides ground state correlation energies within ″chemical accuracy", but it suffers from high computational cost and steep scaling with system size. We present a GPU-accelerated implementation of CCSD(T) in the TeraChem software package. The new implementation achieves state-of-the-art performance, enabling the calculation of the (T) correction for a system with 63 atoms and more than 1000 basis functions in a little under 8 h on a single node. Additionally, we demonstrate the utility of our optimized implementation for the rapid calculation of full CCSD(T)/CBS stacking energies for all ten unique DNA base pair stacked tetramers. We expect that the TeraChem CCSD(T) implementation will enable the rapid calculation of high-level data that was not previously accessible in a reasonable time frame.

  View details for DOI 10.1021/acs.jpca.5c08113

  View details for PubMedID 41747765

• Two-dimensional electronic spectra from trajectory-based dynamics: Pure-state Ehrenfest, spin-mapping, and mean classical path approaches. The Journal of chemical physics Lieberherr, A. Z., Kelly, J., Runeson, J. E., Markland, T. E., Manolopoulos, D. E. 2025; 163 (21)

  Abstract

  Two-dimensional electronic spectroscopy (2DES) provides a detailed picture of electronically nonadiabatic dynamics that can be interpreted with the aid of simulations. Here, we develop and contrast trajectory-based nonadiabatic dynamics approaches for simulating 2DES spectra. First, we argue that an improved pure-state Ehrenfest approach can be constructed by decomposing the initial coherence into a sum of equatorial pure states that contain equal contributions from the states in the coherence. We then use this framework to show how one can obtain a more accurate, but computationally more expensive, approximation to the third-order 2DES response function by replacing Ehrenfest dynamics with spin mapping during the pump-probe delay time. We end by comparing and contrasting the accuracy of these methods and the simpler mean classical path approximation in reproducing the exact linear, pump-probe, and 2DES spectra of two Frenkel exciton models: a coupled dimer system and the Fenna-Matthews-Olson complex.

  View details for DOI 10.1063/5.0299204

  View details for PubMedID 41328970

• Proton-Transfer Kinetics at Liquid-Liquid Interfaces. Journal of the American Chemical Society D'Antona, N., Kelly, J., Barnard, N., Ardo, S., Wang, Y., Surendranath, Y., Markland, T. E., Kempler, P. A., Boettcher, S. W. 2025

  Abstract

  Proton transfer at electrochemical interfaces is fundamentally important across science and technology, yet kinetic measurements of this elementary step at electrode|electrolyte interfaces are convoluted with other electron-transfer steps and by inhomogeneous electrode surfaces. We use facilitated proton transfer at the interface between two immiscible electrolyte solutions (ITIES) as a platform to study proton-transfer kinetics in the absence of interfacial electron transfer and without the defects at solid|electrolyte interfaces. Diffusion-controlled micropipette voltammetry revealed that 2,6-diphenylpyridine (DPP) facilitates proton transfer across the HCl(aq)|trifluorotoluene interface, while voltammetry at nanopipette-supported interfaces yielded activation-controlled ion-transfer currents. We extract kinetic parameters kapp0 and αapp, 3.0 ± 1.8 cm/s and 0.3 ± 0.2, respectively, for DPP-facilitated proton transfer by fitting quasi-reversible voltammograms to a mixed diffusive-kinetic model. Finite-element simulations highlighted regimes of direct proton transfer and sequential proton transfer, where the current divided between these two possible pathways was shown to favor direct proton transfer when the neutral partitioning step DPP(org) → DPP(aq) was rate-determining. Atomistic molecular-dynamics simulations were used to compute the free energy change to move DPP and its protonated analogue within, and across, the liquid|liquid interface. The most-likely location for proton transfer is predicted to be in the surface region where significant interpenetration of the two liquids occurs. Understanding the kinetics of ion transfer at the ITIES illustrated here is important in the development of general theories of ion transfer in electrochemical science and technology.

  View details for DOI 10.1021/jacs.4c18349

  View details for PubMedID 40498631

• Two-Dimensional Electronic Spectroscopy in the Condensed Phase Using Equivariant Transformer Accelerated Molecular Dynamics Simulations. The journal of physical chemistry letters Kelly, J., Hu, F., Damiani, A., Chen, M. S., Snider, A., Son, M., Lee, A., Gupta, P., Montoya-Castillo, A., Zuehlsdorff, T. J., Schlau-Cohen, G. S., Isborn, C. M., Markland, T. E. 2025: 5561-5569

  Abstract

  Two-dimensional electronic spectroscopy (2DES) provides rich information about how the electronic states of molecules, proteins, and solid-state materials interact with each other and their surrounding environment. Atomistic molecular dynamics simulations offer an appealing route to uncover how nuclear motions mediate electronic energy relaxation and their manifestation in electronic spectroscopies but are computationally expensive. Here we show that by using an equivariant transformer-based machine learning architecture trained with only 2500 ground state and 100 excited state electronic structure calculations, one can construct accurate machine-learned potential energy surfaces for both the ground-state electronic surface and excited-state energy gap. We demonstrate the utility of this approach for simulating the dynamics of Nile blue in ethanol, where we experimentally validate and decompose the simulated 2DES to establish the nuclear motions of the chromophore and the solvent that couple to the excited state, connecting the spectroscopic signals to their molecular origin.

  View details for DOI 10.1021/acs.jpclett.5c00911

  View details for PubMedID 40434198

• Electron transfer at electrode interfaces via a straightforward quasiclassical fermionic mapping approach. The Journal of chemical physics Jung, K. A., Kelly, J., Markland, T. E. 2023; 159 (1)

  Abstract

  Electron transfer at electrode interfaces to molecules in solution or at the electrode surface plays a vital role in numerous technological processes. However, treating these processes requires a unified and accurate treatment of the fermionic states of the electrode and their coupling to the molecule being oxidized or reduced in the electrochemical processes and, in turn, the way the molecular energy levels are modulated by the bosonic nuclear modes of the molecule and solvent. Here we present a physically transparent quasiclassical scheme to treat these electrochemical electron transfer processes in the presence of molecular vibrations by using an appropriately chosen mapping of the fermionic variables. We demonstrate that this approach, which is exact in the limit of non-interacting fermions in the absence of coupling to vibrations, is able to accurately capture the electron transfer dynamics from the electrode even when the process is coupled to vibrational motions in the regimes of weak coupling. This approach, thus, provides a scalable strategy to explicitly treat electron transfer from electrode interfaces in condensed-phase molecular systems.

  View details for DOI 10.1063/5.0156136

  View details for PubMedID 37409707