Quantum Mechanical Enhancement of Rate Constants and Kinetic Isotope Effects for Water-Mediated Proton Transfer in a Model Biological System

Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins

Transition state theory (TST) is widely employed for estimating the transition rate of a reaction when combined with free energy sampling techniques. A derivation of the transition theory rate expression for a general n-dimensional case is presented in this work which specifically focuses on water-assisted proton transfer/transport reactions, especially for protein systems. Our work evaluates the TST prefactor calculated at the transition state dividing surface compared to one sampled, as an approximation, in the reactant state in four case studies of water-assisted proton transport inside membrane proteins and highlights the significant impact of the prefactor position dependence in proton transport processes.

Enhancement of the Tetrel Bond by the Effects of Substituents, Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond

The T⋅⋅⋅N tetrel bond (TB) formed between TX₃ OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH₃ OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF₃ OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T-O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl₂ to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.

Isotopic separation of helium through graphyne membranes: a ring polymer molecular dynamics study

Microscopic-level understanding of the separation mechanism for two-dimensional (2D) membranes is an active area of research due to potential implications of this class of membranes for various technological processes. Helium (He) purification from the natural resources is of particular interest due to the shortfall in its production. In this work, we applied the ring polymer molecular dynamics (RPMD) method to graphdiyne (Gr2) and graphtriyne (Gr3) 2D membranes having variable pore sizes for the separation of He isotopes, and compare for the first time with rigorous quantum calculations. We found that the transmission rate through Gr3 is many orders of magnitude greater than Gr2. The selectivity of either isotope at low temperatures is a consequence of a delicate balance between the zero-point energy effect and tunneling of ⁴He and ³He. In particular, a remarkable tunneling effect is reported on the Gr2 membrane at 10 K, leading to a much larger permeation of the lighter species as compared to the heavier isotope. RPMD provides an efficient approach for studying the separation of He isotopes, taking into account quantum effects of light nuclei motions at low temperatures, which classical methods fail to capture.

Hydrogen-Bond Dynamics and Energetics of Biological Water

Water molecules in the immediate vicinity of biomacromolecules and biomimetic organized assemblies often exhibit a markedly distinct behavior from that of their bulk counterparts. The overall sluggish behavior of biological water substantially affects the stability and integrity of biomolecules, as well as the successful execution of various crucial water-mediated biochemical phenomena. In this Minireview, insights are provided into the features of truncated hydrogen-bond networks that grant biological water its unique characteristics. In particular, experimental results and theoretical investigations, based on chemical kinetics, are presented that have shed light on the dynamics and energetics governing such characteristics. It is emphasized how such details help us to understand the energetics of biological water, an aspect relatively less explored than its dynamics. For instance, when biological water at hydrophilic or charged protein surfaces was explored, the free energy of H-bond breakage was found to be of the order of 0.4 kcal mol^-1 higher than that of bulk water.

Quantitative analysis of the coupling between proton and electron transport in peptide/manganese oxide hybrid films

A novel platform is proposed to quantify the coupling phenomenon between electrons and protons in tyrosine-rich peptide/manganese oxide hybrid films at room temperature.

Theoretical description of quantum mechanical permeation of graphene membranes by charged hydrogen isotopes

It has been recently shown that in the presence of an applied voltage, hydrogen and deuterium nuclei can be separated from one another using graphene membranes as a nuclear sieve, resulting in a 10-fold enhancement in the concentration of the lighter isotope. While previous studies, both experimental and theoretical, have attributed this effect mostly to differences in vibrational zero point energy (ZPE) of the various isotopes near the membrane surface, we propose that multi-dimensional quantum mechanical tunneling of nuclei through the graphene membrane influences this proton permeation process in a fundamental way. We perform ring polymer molecular dynamics calculations in which we include both ZPE and tunneling effects of various hydrogen isotopes as they permeate the graphene membrane and compute rate constants across a range of temperatures near 300 K. While capturing the experimentally observed separation factor, our calculations indicate that the transverse motion of the various isotopes across the surface of the graphene membrane is an essential part of this sieving mechanism. An understanding of the multi-dimensional quantum mechanical nature of this process could serve to guide the design of other such isotopic enrichment processes for a variety of atomic and molecular species of interest.

The role of charge and proton transfer in fragmentation of hydrogen-bonded nanosystems: the breakup of ammonia clusters upon single photon multi-ionization

The charge and proton dynamics in hydrogen-bonded networks are investigated using ammonia as a model system. The fragmentation dynamics of medium-sized clusters (1-2 nm) upon single photon multi-ionization is studied, by analyzing the momenta of small ionic fragments. The observed fragmentation pattern of the doubly- and triply-charged clusters reveals a spatial anisotropy of emission between fragments (back-to-back). Protonated fragments exhibit a distinct kinematic correlation, indicating a delay between ionization and fragmentation (fission). The different kinematics observed for channels containing protonated and unprotonated species provides possible insights into the prime mechanisms of charge and proton transfer, as well as proton hopping, in such a nanoscale system.