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1. Structural aspects of the topological model of the hydrogen bond in water on auto-dissociation via proton transfer

   https://doi.org/10.1039/c8cp02592d  

   Lentz, Jesse ; Garofalini, Stephen H. ( January 2018 , Physical Chemistry Chemical Physics)

   Molecular dynamics (MD) simulations were used to investigate the structure and lifetimes of hydrogen bonds and auto dissociation via proton transfer in bulk water using a reactive and dissociative all-atom potential that has previously been shown to match a variety of water properties and proton transfer. Using the topological model, each molecule's donated and accepted hydrogen bonds were labeled relative to the other hydrogen bonds on neighboring waters, providing a description of the effect of these details on the structure, dynamics and autoionization of water molecules. In agreement with prior data, asymmetric bonding at the sub-100 femtosecond timescale is observed, as well as the existence of linear, bifurcated, and dangling hydrogen bonds. The lifetime of the H-bond, 2.1 ps, is consistent with experimental data, with short time librations on the order of femtoseconds. The angular correlation functions, the presence of a second shell water entering the first shell, and OH vibrational stretch frequencies were all consistent with experiment or ab initio calculations. The simulations show short-lived (femtoseconds) dissociation of a small fraction of water molecules followed by rapid recombination. The role of the other H-bonds to the acceptor and on the donor plays an important part in proton transfer betweenmore »the molecules in auto dissociation and is consistent with the role of a strong electric field caused by local (first and second shell) waters on initiating dissociation. The number of H-bonds to the donor water is 4.3 per molecule in the simulations, consistent with previous data regarding the number of hydrogen bonds required to generate this strong local electric field that enhances dissociation. The continuous lifetime autocorrelation function of the H-bond for those molecules that experience dissociation is considerably longer than that for all molecules that show no proton transfer.« less
2. Hydronium ion diffusion in model proton exchange membranes at low hydration: insights from ab initio molecular dynamics

   https://doi.org/10.1039/d0ta10565a  

   Zelovich, Tamar ; Winey, Karen I. ; Tuckerman, Mark E. ( February 2021 , Journal of Materials Chemistry A)

   Fuel-cell deployable proton exchange membranes (PEMs) are considered to be a promising technology for clean and efficient power generation. However, a fundamental atomistic understanding of the hydronium diffusion process in the PEM environment is an ongoing challenge. In this work, we employ fully atomistic ab initio molecular dynamics to simulate diffusion mechanisms of the hydronium ion in a model PEM. In order to mimic a precise polymer with a layered morphology, as recently introduced by Trigg, et al. , Nat. Mater. , 2018, 17 , 725, a nano-confined environment was created composed of graphane bilayers to which sulfonate end groups (SO 3 − ) are attached, and the space between the bilayers was subsequently filled with water and hydronium ions up to λ values of 3 and 4, where λ denotes the water-to-anion ratio. We find that for the low λ value, the water distribution is not homogeneous, which results in an incomplete second solvation shell for H 3 O + , fewer water molecules in the vicinity of SO 3 − , and a higher probability of obtaining a coordination number of ∼1 for the nearest oxygen neighbor to SO 3 − . These conditions increase the probability thatmore »H 3 O + will react with SO 3 − according to the reaction SO 3 − + H 3 O + ↔ SO 3 H + H 2 O, which was found to be an essential part of the hydronium diffusion mechanism. This suggests there are optimal hydration conditions that allow the sulfonate end groups to take an active part in the hydronium diffusion mechanism, resulting in high hydronium conductivity. We expect that the results of this study could help guide synthesis and experimental characterization used to design new PEM materials with high hydronium conductivity.« less
3. Thermodynamic and Transport Properties of Tetrabutylphosphonium Hydroxide and Tetrabutylphosphonium Chloride–Water Mixtures via Molecular Dynamics Simulation

   https://doi.org/10.3390/polym12010249  

   Crawford, Brad ; Ismail, Ahmed ( January 2020 , Polymers)

   Thermodynamic, structural, and transport properties of tetrabutylphosphonium hydroxide (TBPH) and tetrabutylphosphonium chloride (TBPCl)–water mixtures have been investigated using all-atom molecular dynamics simulations in response to recent experimental work showing the TBPH–water mixtures capability as a cellulose solvent. Multiple transitional states exist for the water—ionic liquid (IL) mixture between 70 and 100 mol% water, which corresponds to a significant increase in water hydrogen bonds. The key transitional region, from 85 to 92.5 mol% water, which coincides with the mixture’s maximum cellulose solubility, reveals small and distinct water veins with cage structures formed by the TBP+ ions, while the hydroxide and chloride ions have moved away from the P atom of TBP+ and are strongly hydrogen bonded to the water. The maximum cellulose solubility of the TBPH–water solution at approximately 91.1 mol% water, appears correlated with the destruction of the TBP’s interlocking structure in the simulations, allowing the formation of water veins and channeling structures throughout the system, as well as changing from a subdiffusive to a near-normal diffusive regime, increasing the probability of the IL’s interaction with the cellulose polymer. A comparison is made between the solution properties of TBPH and TBPCl with those of alkylimidazolium-based ILs, for which water appearsmore »to act as anti-solvent rather than a co-solvent.« less
4. Evaluating Simple Ab Initio Models of the Hydrated Electron: The Role of Dynamical Fluctuations

   https://doi.org/10.1021/acs.jpcb.0c6356  

   Park, S. J. ; Schwartz, B. J. ( January 2020 , The journal of physical chemistry)

   Despite its importance in electron transfer reactions and radiation chemistry, there has been disagreement over the fundamental nature of the hydrated electron, such as whether or not it resides in a cavity. Mixed quantum/classical simulations of the hydrated electron give different structures depending on the pseudopotential employed, and ab initio models of computational necessity use small numbers of water molecules and/or provide insufficient statistics to compare to experimental observables. A few years ago, Kumar et al. (J. Phys. Chem. A 2015, 119, 9148) proposed a minimalist ab initio model of the hydrated electron with only a small number of explicitly treated water molecules plus a polarizable continuum model (PCM). They found that the optimized geometry had four waters arranged tetrahedrally around a central cavity, and that the calculated vertical detachment energy and radius of gyration agreed well with experiment, results that were largely independent of the level of theory employed. The model, however, is based on a fixed structure at 0 K and does not explicitly incorporate entropic contributions or the thermal fluctuations that should be associated with the room-temperature hydrated electron. Thus, in this paper, we extend the model of Kumar et al. by running Born−Oppenheimer molecular dynamics (BOMD)more »of a small number of water molecules with an excess electron plus PCM at room temperature. We find that when thermal fluctuations are introduced, the level of theory chosen becomes critical enough when only four waters are used that one of the waters dissociates from the cluster with certain density functionals. Moreover, even with an optimally tuned range-separated hybrid functional, at room temperature the tetrahedral orientation of the 0 K first-shell waters is entirely lost and the central cavity collapses, a process driven by the fact that the explicit water molecules prefer to make H-bonds with each other more than with the excess electron. The resulting average structure is quite similar to that produced by a noncavity mixed quantum/classical model, so that the minimalist 4-water BOMD models suffer from problems similar to those of noncavity models, such as predicting the wrong sign of the hydrated electron’s molar solvation volume. We also performed BOMD with 16 explicit water molecules plus an extra electron and PCM. We find that the inclusion of an entire second solvation shell of explicit water leads to little change in the outcome from when only four waters were used. In fact, the 16-water simulations behave much like those of water cluster anions, in which the electron localizes at the cluster surface, showing that PCM is not acceptable for use in minimalist models to describe the behavior of the bulk hydrated electron. For both the 4- and 16-water models, we investigate how the introduction of thermal motions alters the predicted absorption spectrum, vertical detachment energy, and resonance Raman spectrum of the simulated hydrated electron. We also present a set of structural criteria that can be used to numerically determine how cavity-like (or not) a particular hydrated electron model is. All of the results emphasize that the hydrated electron is a statistical object whose properties are inadequately captured using only a small number of explicit waters, and that a proper treatment of thermal fluctuations is critical to understanding the hydrated electron’s chemical and physical behavior.« less
5. Collision-induced dissociation of homodimeric and heterodimeric radical cations of 9-methylguanine and 9-methyl-8-oxoguanine: correlation between intra-base pair proton transfer originating from the N1–H at a Watson–Crick edge and non-statistical dissociation

   https://doi.org/10.1039/d2cp00312k  

   Moe, May Myat ; Benny, Jonathan ; Liu, Jianbo ( April 2022 , Physical Chemistry Chemical Physics)

   It has been shown previously in protonated, deprotonated and ionized guanine–cytosine base pairs that intra-base pair proton transfer from the N1–H at the Watson–Crick edge of guanine to the complementary nucleobase prompts non-statistical dissociation of the base-pair system, and the dissociation of a proton-transferred base-pair structure is kinetically more favored than that of the starting, conventional base-pair structure. However, the fundamental chemistry underlying this anomalous and intriguing kinetics has not been completely revealed, which warrants the examination of more base-pair systems in different structural contexts in order to derive a generalized base-pair structure–kinetics correlation. The purpose of the present work is to expand the investigation to the non-canonical homodimeric and heterodimeric radical cations of 9-methylguanine (9MG) and 9-methyl-8-oxoguanine (9MOG), i.e. , [9MG·9MG]˙ + , [9MOG·9MG]˙ + and [9MOG·9MOG]˙ + . Experimentally, collision-induced dissociation tandem mass spectrometry coupled with an electrospray ionization (ESI) source was used for the formation of base-pair radical cations, followed by detection of dissociation product ions and cross sections in the collisions with Xe gas under single ion–molecule collision conditions and as a function of the center-of-mass collision energy. Computationally, density functional theory and coupled cluster theory were used to calculate and identify probable base-pair structures andmore »intra-base pair proton transfer and hydrogen transfer reactions, followed by kinetics modeling to explore the properties of dissociation transition states and kinetic factors. The significance of this work is twofold: it provides insight into base-pair opening kinetics in three biologically-important, non-canonical systems upon oxidative and ionization damage; and it links non-statistical dissociation to intra-base pair proton-transfer originating from the N1–H at the Watson–Crick edge of 8-oxoguanine, enhancing understanding towards the base-pair fragmentation assisted by proton transfer.« less