All Publications

  • An accurate and efficient Ehrenfest dynamics approach for calculating linear and nonlinear electronic spectra. The Journal of chemical physics Atsango, A. O., Montoya-Castillo, A., Markland, T. E. 2023; 158 (7): 074107


    Linear and nonlinear electronic spectra provide an important tool to probe the absorption and transfer of electronic energy. Here, we introduce a pure state Ehrenfest approach to obtain accurate linear and nonlinear spectra that is applicable to systems with large numbers of excited states and complex chemical environments. We achieve this by representing the initial conditions as sums of pure states and unfolding multi-time correlation functions into the Schrodinger picture. By doing this, we show that one can obtain significant improvements in accuracy over the previously used projected Ehrenfest approach and that these benefits are particularly pronounced in cases where the initial condition is a coherence between excited states. While such initial conditions do not arise when calculating linear electronic spectra, they play a vital role in capturing multidimensional spectroscopies. We demonstrate the performance of our method by showing that it is able to quantitatively capture the exact linear, 2D electronic spectroscopy, and pump-probe spectra for a Frenkel exciton model in slow bath regimes and is even able to reproduce the main spectral features in fast bath regimes.

    View details for DOI 10.1063/5.0138671

    View details for PubMedID 36813724

  • A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site. Nature chemistry Zheng, C., Mao, Y., Kozuch, J., Atsango, A. O., Ji, Z., Markland, T. E., Boxer, S. G. 2022


    The catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C-D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that, despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active-site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, which provides direct evidence for the fundamental difference between the electrostatic environment of solvents and that of a preorganized enzyme active site.

    View details for DOI 10.1038/s41557-022-00937-w

    View details for PubMedID 35513508

  • A two-directional vibrational probe reveals the distinct electric field orientation at the active site of liver alcohol dehydrogenase Zheng, C., Mao, Y., Kozuch, J. A., Atsango, A. O., Ji, Z., Markland, T. E., Boxer, S. G. CELL PRESS. 2022: 441A
  • Characterizing and Contrasting Structural Proton Transport Mechanisms in Azole Hydrogen Bond Networks Using Ab Initio Molecular Dynamics. The journal of physical chemistry letters Atsango, A. O., Tuckerman, M. E., Markland, T. E. 2021: 8749-8756


    Imidazole and 1,2,3-triazole are promising hydrogen-bonded heterocycles that conduct protons via a structural mechanism and whose derivatives are present in systems ranging from biological proton channels to proton exchange membrane fuel cells. Here, we leverage multiple time-stepping to perform ab initio molecular dynamics of imidazole and 1,2,3-triazole at the nanosecond time scale. We show that despite the close structural similarities of these compounds, their proton diffusion constants vary by over an order of magnitude. Our simulations reveal the reasons for these differences in diffusion constants, which range from the degree of hydrogen-bonded chain linearity to the effect of the central nitrogen atom in 1,2,3-triazole on proton transport. In particular, we uncover evidence of two "blocking" mechanisms in 1,2,3-triazole, where covalent and hydrogen bonds formed by the central nitrogen atom limit the mobility of protons. Our simulations thus provide insights into the origins of the experimentally observed 10-fold difference in proton conductivity.

    View details for DOI 10.1021/acs.jpclett.1c02266

    View details for PubMedID 34478302

  • Interfacial properties of pure and doped CdS/graphene composites: CdS (0001)/graphene and a CdS/graphene bilayer COMPUTATIONAL MATERIALS SCIENCE Bendavid, L., Atsango, A. O., Smith, R. W. 2020; 177
  • Elucidating the Proton Transport Pathways in Liquid Imidazole with First-Principles Molecular Dynamics. The journal of physical chemistry letters Long, Z. n., Atsango, A. O., Napoli, J. A., Markland, T. E., Tuckerman, M. E. 2020: 6156–63


    Imidazole is a promising anhydrous proton conductor with a high conductivity comparable to that of water at a similar temperature relative to its melting point. Previous theoretical studies of the mechanism of proton transport in imidazole have relied either on empirical models or on ab initio trajectories that have been too short to draw significant conclusions. Here, we present the results of multiple time-step ab initio molecular dynamics simulations of an excess proton in liquid imidazole reaching 1 ns in total simulation time. We find that the proton transport is dominated by structural diffusion, with the diffusion constant of the proton defect being ∼8 times higher than that of self-diffusion of the imidazole molecules. By using correlation function analysis, we decompose the mechanism for proton transport into a series of first-order processes and show that the proton transport mechanism occurs over three distinct time and length scales. Although the mechanism at intermediate times is dominated by hopping along pseudo-one-dimensional chains, at longer times the overall rate of diffusion is limited by the re-formation of these chains. These results provide a more complete picture of the traditional idealized Grotthuss structural diffusion mechanism.

    View details for DOI 10.1021/acs.jpclett.0c01744

    View details for PubMedID 32633523