A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site.
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
CELL PRESS. 2022: 441A
View details for Web of Science ID 000759523002685
Characterizing and Contrasting Structural Proton Transport Mechanisms in Azole Hydrogen Bond Networks Using Ab Initio Molecular Dynamics.
The journal of physical chemistry letters
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
View details for DOI 10.1016/j.commatsci.2020.109537
View details for Web of Science ID 000519576300023
Elucidating the Proton Transport Pathways in Liquid Imidazole with First-Principles Molecular Dynamics.
The journal of physical chemistry letters
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