Hydrogen tunneling is central to many chemical and biological processes. Herein, we introduce the vibronic-SHAKE (V-SHAKE) approach to comprehensively sample energy-conserving molecular configurations enabling hydrogen tunneling. A constrained form of nuclear-electronic orbital multistate density functional theory (NEO-MSDFT) dynamics, where the tunneling hydrogen nucleus is quantized, is used to sample geometries in the diabatic seam space corresponding to the intersection of the reactant and product NEO-DFT diabatic vibronic surfaces. V-SHAKE is applied to hydrogen and deuterium tunneling in 4-cyanobutanolate and Z-4-hydroxybut-3-en-2-one. The vibronic coupling is found to vary significantly in the diabatic seam space, mainly due to changes in the donor-acceptor distance. The reaction coordinate and gradient of the vibronic coupling at the minimum energy crossing point are nearly orthogonal and are dominated by motions stabilizing the product relative to the reactant or decreasing the donor-acceptor distance, respectively. V-SHAKE provides fundamental insights and validation for assumptions underlying rate theories.
Joseph A. Dickinson, Eno Paenurk, Sharon Hammes-Schiffer· 0 citations
Hydrogen transfer is a critical component of many chemical and biological processes. The ratio of rate constants for hydrogen and deuterium transfer defines the H/D kinetic isotope effect (KIE), which is a powerful tool for elucidating hydrogen transfer mechanisms. Interpretation of experimental H/D KIEs relies on accurate and affordable computational methods. However, due to their light mass, hydrogen and deuterium can undergo tunneling, which is challenging to describe in multidimensional molecular systems. Herein, we introduce the nuclear–electronic orbital general rate theory (NEO-GRT), which enables the efficient prediction of H/D KIEs based on full-dimensional molecular quantum chemistry calculations. The NEO-GRT approach describes the hydrogen transfer rate constant with a general expression that spans the vibrationally adiabatic and nonadiabatic hydrogen tunneling regimes. The input quantities are computed using NEO density functional theory, which treats the transferring hydrogen or deuterium nucleus quantum mechanically on the same level as the electrons. We investigate two intramolecular proton transfer reactions in organic molecules at temperatures down to 50 K to evaluate the performance of NEO-GRT by comparison to transition state theory and ring-polymer instanton theory. The KIEs computed with NEO-GRT agree with those calculated using ring-polymer instanton theory for the full-dimensional molecular systems at the same level of electronic structure theory. This agreement indicates that NEO-GRT captures the deep hydrogen tunneling effects, in contrast to transition state theory, which neglects such effects. Given its relatively low computational cost, NEO-GRT is a promising approach for predicting H/D KIEs in large organic and organometallic systems.
Eno Paenurk, Jang-Kul Yoo, Sharon Hammes-Schiffer· Journal of Chemical Theory a...· 0 citations
Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides, utilizing a ∼32 Å chain of proton-coupled electron transfer (PCET) reactions spanning two protein subunits to generate a catalytic cysteine radical. Two cryogenic electron microscopy structures of the active complex of E. coli RNR are currently available. One structure was trapped in the preturnover state, prior to radical translocation, and the other structure was trapped in the midturnover state, with the radical in the active site. Herein, we use molecular dynamics simulations to investigate the differences in hydrogen-bonding interactions and conformational motions between the preturnover and midturnover states. Our simulations show that Y731, an interfacial tyrosine that participates in the PCET pathway, samples multiple conformations in both states, allowing it to participate in forward and reverse PCET between subunits. We also observe interfacial water channels between the protein subunits in both states. Moreover, our simulations show that E623, which is near Y730 in the preturnover structure and was shown by previous simulations to mediate PCET between Y731 and Y730, can also sample conformations distal to Y730 in the preturnover state, similar to its position in the midturnover structure. Our mixed quantum mechanical/molecular mechanical free energy simulations indicate that forward radical transfer from Y731 to Y730 is thermodynamically favorable with a reasonable free energy barrier, even in the absence of mediation by E623. These results provide insights into the critical role of conformational motions and flexibility in regulating PCET reactions at and near the protein subunit interface of RNR.
Matthew Tremblay, Sharon Hammes-Schiffer· Biochemistry· 0 citations
Protein stabilizers and denaturants can be used to elucidate the fundamental principles of hydration, which is crucial for biological functions and biotechnology. Despite decades of work, existing molecular models of such stabilizers and denaturants have not yet been fully validated because few experimental methods can detect water structures within the hydration shell in situ under ambient conditions. Here, we devise a molecular model guided by the application of chiral-selective vibrational sum frequency generation spectroscopy to a solvated protein. We show that urea disrupts the first hydration shell, weakening the protein’s hydrogen bonds. Conversely, trimethylamine N-oxide resides outside the shell and stabilizes the protein by strengthening water hydrogen bonds within the first hydration shell. In mixtures, trimethylamine N-oxide drives urea out of the shell, neutralizing urea’s destabilizing effect. We conclude that protein stability directly correlates with first hydration shell integrity. These insights have broad implications for understanding solvent effects on biocatalysis and heterogeneous cellular environments.
Zhi-Jie Wang, Matthew Tremblay, Nicholas Hatzis-Schoch et al.· Journal of the American Chem...· 0 citations
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