Transport and spectroscopy of the hydrated proton: A molecular dynamics study

Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package

Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system's bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.

Electronic Fingerprint of the Protonated Imidazole Dimer Probed by X-ray Absorption Spectroscopy

Protons in low-barrier superstrong hydrogen bonds are typically delocalized between two electronegative atoms. Conventional methods to characterize such superstrong hydrogen bonds are vibrational spectroscopy and diffraction techniques. We introduce soft X-ray spectroscopy to uncover the electronic fingerprints for proton sharing in the protonated imidazole dimer, a prototypical building block enabling effective proton transport in biology and high-temperature fuel cells. Using nitrogen core excitations as a sensitive probe for the protonation status, we identify the X-ray signature of a shared proton in the solvated imidazole dimer in a combined experimental and theoretical approach. The degree of proton sharing is examined as a function of structural variations that modify the shape of the low-barrier potential in the superstrong hydrogen bond. We conclude by showing how the sensitivity to the quantum distribution of proton motion in the double-well potential is reflected in the spectral signature of the shared proton.

Thermal dependence of the hydrated proton and optimal proton transfer in the protonated water hexamer

Water is a key ingredient for life and plays a central role as solvent in many biochemical reactions. However, the intrinsically quantum nature of the hydrogen nucleus, revealing itself in a large variety of physical manifestations, including proton transfer, gives rise to unexpected phenomena whose description is still elusive. Here we study, by a combination of state-of-the-art quantum Monte Carlo methods and path-integral molecular dynamics, the structure and hydrogen-bond dynamics of the protonated water hexamer, the fundamental unit for the hydrated proton. We report a remarkably low thermal expansion of the hydrogen bond from zero temperature up to 300 K, owing to the presence of short-Zundel configurations, characterised by proton delocalisation and favoured by the synergy of nuclear quantum effects and thermal activation. The hydrogen bond strength progressively weakens above 300 K, when localised Eigen-like configurations become relevant. Our analysis, supported by the instanton statistics of shuttling protons, reveals that the near-room-temperature range from 250 K to 300 K is optimal for proton transfer in the protonated water hexamer.

Developing machine-learned potentials to simultaneously capture the dynamics of excess protons and hydroxide ions in classical and path integral simulations

The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics simulations to model the bond breaking and formation involved in proton transfer and path-integral simulations to model the nuclear quantum effects relevant to light hydrogen atoms. These requirements result in a prohibitive computational cost, especially at the time and length scales needed to converge proton transport properties. Here, we present machine-learned potentials (MLPs) that can model both excess protons and hydroxide ions at the generalized gradient approximation and hybrid density functional theory levels of accuracy and use them to perform multiple nanoseconds of both classical and path-integral proton defect simulations at a fraction of the cost of the corresponding ab initio simulations. We show that the MLPs are able to reproduce ab initio trends and converge properties such as the diffusion coefficients of both excess protons and hydroxide ions. We use our multi-nanosecond simulations, which allow us to monitor large numbers of proton transfer events, to analyze the role of hypercoordination in the transport mechanism of the hydroxide ion and provide further evidence for the asymmetry in diffusion between excess protons and hydroxide ions.

Ultrafast Proton Transfer Pathways Mediated by Amphoteric Imidazole

Imidazole, being an amphoteric molecule, can act both as an acid and as a base. This property enables imidazole, as an essential building block, to effectively facilitate proton transport in high-temperature proton exchange membrane fuel cells and in proton channel transmembrane proteins, enabling those systems to exhibit high energy conversion yields and optimal biological function. We explore the amphoteric properties of imidazole by following the proton transfer exchange reaction dynamics with the bifunctional photoacid 7-hydroxyquinoline (7HQ). We show with ultrafast ultraviolet-mid-infrared pump-probe spectroscopy how for imidazole, in contrast to expectations based on textbook knowledge of acid-base reactivity, the preferential reaction pathway is that of an initial proton transfer from 7HQ to imidazole, and only at a later stage a transfer from imidazole to 7HQ, completing the 7HQ tautomerization reaction. An assessment of the molecular distribution functions and first-principles calculations of proton transfer reaction barriers reveal the underlying reasons for our observations.

Coarse-Graining of Imaginary Time Feynman Path Integrals: Inclusion of Intramolecular Interactions and Bottom-up Force-Matching

Feynman's imaginary time path integral formalism of quantum statistical mechanics and the corresponding quantum-classical isomorphism provide a tangible way of incorporating nuclear quantum effect (NQE) in the simulation of condensed matter systems using well-developed classical simulation techniques. Our previous work has presented the many-body coarse-graining of path integral (CG-PI) theory that builds an isomorphism between the quantum partition function of N distinguishable particles and the classical partition function of 2N pseudoparticles. In this present work, we develop a generalized version of the many-body CG-PI theory that incorporates many-body interactions in the force field. Based on the new derivation, we provide a numerical CG-PI (n-CG-PI) modeling strategy parametrized from the underlying path integral molecular dynamics (PIMD) trajectories using force matching and Boltzmann inversion. The n-CG-PI models for two liquid systems are shown to capture well both the intramolecular and intermolecular structural correlations of the reference PIMD simulations. The generalized derivation of the many-body CG-PI theory and the n-CG-PI model presented in this work extend the scope of the CG-PI formalism by generalizing the previously limited theory to incorporate force fields of realistic molecular systems.

Ultrafast Charge Relocation Dynamics in Enol-Keto Tautomerization Monitored with a Local Soft-X-ray Probe

Proton-coupled electron transfer (PCET) is the underlying mechanism governing important reactions ranging from water splitting in photosynthesis to oxygen reduction in hydrogen fuel cells. The interplay of proton and electronic charge distribution motions can vary from sequential to concerted schemes, with elementary steps occurring on ultrafast time scales. We demonstrate with a simulation study that femtosecond soft-X-ray spectroscopy provides key insights into the PCET mechanism of a photoinduced intramolecular enol* → keto* tautomerization reaction. A full quantum treatment of the electronic and nuclear dynamics of 2-(2'-hydroxyphenyl)benzothiazole upon electronic excitation reveals how spectral signatures of local excitations from core to frontier orbitals display the distinctly different stages of charge relocation for the H atom, donating, and accepting sites. Our findings indicate that ultraviolet/X-ray pump-probe spectroscopy provides a unique way to probe ultrafast electronic structure rearrangements in photoinduced chemical reactions essential to understanding the mechanism of PCET.

Graph-Theory-Based Molecular Fragmentation for Efficient and Accurate Potential Surface Calculations in Multiple Dimensions

We present a multitopology molecular fragmentation approach, based on graph theory, to calculate multidimensional potential energy surfaces in agreement with post-Hartree-Fock levels of theory but at the density functional theory cost. A molecular assembly is coarse-grained into a set of graph-theoretic nodes that are then connected with edges to represent a collection of locally interacting subsystems up to an arbitrary order. Each of the subsystems is treated at two levels of electronic structure theory, the result being used to construct many-body expansions that are embedded within an ONIOM scheme. These expansions converge rapidly with the many-body order (or graphical rank) of subsystems and capture many-body interactions accurately and efficiently. However, multiple graphs, and hence multiple fragmentation topologies, may be defined in molecular configuration space that may arise during conformational sampling or from reactive, bond breaking and bond formation, events. Obtaining the resultant potential surfaces is an exponential scaling proposition, given the number of electronic structure computations needed. We utilize a family of graph-theoretic representations within a variational scheme to obtain multidimensional potential surfaces at a reduced cost. The fast convergence of the graph-theoretic expansion with increasing order of many-body interactions alleviates the exponential scaling cost for computing potential surfaces, with the need to only use molecular fragments that contain a fewer number of quantum nuclear degrees of freedom compared to the full system. This is because the dimensionality of the conformational space sampled by the fragment subsystems is much smaller than the full molecular configurational space. Additionally, we also introduce a multidimensional clustering algorithm, based on physically defined criteria, to reduce the number of energy calculations by orders of magnitude. The molecular systems benchmarked include coupled proton motion in protonated water wires. The potential energy surfaces and multidimensional nuclear eigenstates obtained are shown to be in very good agreement with those from explicit post-Hartree-Fock calculations that become prohibitive as the number of quantum nuclear dimensions grows. The developments here provide a rigorous and efficient alternative to this important chemical physics problem.

Characterizing and Contrasting Structural Proton Transport Mechanisms in Azole Hydrogen Bond Networks Using Ab Initio Molecular Dynamics

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.

Proton Traffic Jam: Effect of Nanoconfinement and Acid Concentration on Proton Hopping Mechanism

The properties of the water network in concentrated HCl acid pools in nanometer-sized reverse non-ionic micelles were probed with TeraHertz absorption, dielectric relaxation spectroscopy, and reactive force field simulations capable of describing proton hopping mechanisms. We identify that only at a critical micelle size of W0=9 do solvated proton complexes form in the water pool, accompanied by a change in mechanism from Grotthuss forward shuttling to one that favors local oscillatory hopping. This is due to a preference for H+ and Cl- ions to adsorb to the micelle interface, together with an acid concentration effect that causes a "traffic jam" in which the short-circuiting of the hydrogen-bonding motif of the hydronium ion decreases the forward hopping rate throughout the water interior even as the micelle size increases. These findings have implications for atmospheric chemistry, biochemical and biophysical environments, and energy materials, as transport of protons vital to these processes can be suppressed due to confinement, aggregation, and/or concentration.

Switching between Proton Vacancy and Excess Proton Transfer Pathways in the Reaction between 7-Hydroxyquinoline and Formate

Bifunctional or amphoteric photoacids simultaneously present donor (acidic) and acceptor (basic) properties making them useful tools to analyze proton transfer reactions. In protic solvents, the proton exchange between the acid and the base is controlled by the acidity or basicity strength and typically occurs on two different pathways known as protolysis and hydrolysis. We report here how the addition of a formate base will alter the relative importance of the possible reaction pathways of the bifunctional photoacid 7-hydroxyquinoline (7HQ), which has been recently understood to predominantly involve a hydroxide/methoxide transport mechanism between the basic proton-accepting quinoline nitrogen site toward the proton-donating OH group with a time constant of 360 ps in deuterated methanol (CD₃OD). We follow the reaction dynamics by probing the IR-active marker modes of the different charged forms of photoexcited 7HQ, and of formic acid (HCOOD) in CD₃OD solution. A comparison of the transient IR spectra as a function of formate concentration, and classical molecular dynamics simulations enables us to identify distinct contributions of “tight” (meaning “contact”) and “loose” (i.e., “solvent-separated”) 7HQ–formate reaction pairs in our data. Our results suggest that depending on the orientation of the OH group with respect to the quinoline aromatic ring system, the presence of the formate molecule in a proton relay pathway facilitates a net proton transfer from the proton-donating OH group of 7HQ-N* via the methanol/formate bridge toward the quinoline N site.

An effective partial charge model for bulk and surface properties of cubic ZrO2, Y2O3 and yttrium-stabilised zirconia

In this work a newly parametrised Coulomb plus Buckingham potential formulation for cubic ZrO₂, Y₂O₃ and yttrium-stabilised zirconia (YSZ) is presented. The density and pair distributions obtained for neat ZrO₂ and Y₂O₃ under ambient conditions are in excellent agreement with experimental data, while the vibrational power spectra are highly similar compared to those obtained via ab initio molecular dynamics simulations at the PBEsol level. In addition, it is shown that the use of effective partial charges has several advantages compared to interaction potentials employing the oxidation states in the evaluation of the coulombic interactions: (i) the diffusion coefficient and the associated activation energy of oxygen ions evaluated for YSZn (n = 4 to 12) display the best agreement with experimental data; (ii) no unphysical reorganisation of the interface and the bulk are observed in simulations of the (110) and (111) surfaces of cubic ZrO₂ and Y₂O₃, while due to the strong coulombic contributions in the case of the tested full-charge models a pronounced restructuring of the interface and the bulk is observed in the ZrO₂ case, and (iii) the use of effective partial charges ensures compatibility with existing solvent models and force-fields for the treatment of molecular compounds.

The solvation effect on the rattling behaviour of the hydrated excess proton in water

The solvation effect on the kinetic rattling behaviour of the hydrated excess proton H⁺(aq) in water is theoretically modeled by using density functional theory (DFT) and the quantum chemical cluster model (CM). To test the solvation effects on the proton morphology and rattling kinetics, different solvation models for the proton are constructed based on the gas phase (GP) Zundel cation, which include the gas phase-polarizable continuum model (GP-PCM), the gas phase-supermolecule model (GP-SM), and the gas phase-supermolecule-polarizable continuum model (GP-SM-PCM). These solvation models consider either one or both of the short- and long-range solute-solvent interactions. Meanwhile, 1 to 6 explicit solvent water molecules (N_m' = 1-6) are added around the GP Zundel cation to test different explicit solvation environments. The calculation results show that the solvation environment has an important influence on the morphology and rattling kinetics of H⁺(aq). The proton rattling pathways are obtained only under the condition that both symmetrical explicit solvation environments and implicit bulk solvents are present. The zero-point contribution reduces the reaction energy barrier and enables the rattling to occur spontaneously at room temperature. The theoretical modeling results provide new insights into the microscopic kinetic behaviour of proton rattling in water at the molecular level, which are helpful in studying the proton transfer mechanism in aqueous systems.

Ultrafast Proton Transport between a Hydroxy Acid and a Nitrogen Base along Solvent Bridges Governed by the Hydroxide/Methoxide Transfer Mechanism

Aqueous proton transport plays a key role in acid–base neutralization and energy transport through biological membranes and hydrogen fuel cells. Extensive experimental and theoretical studies have resulted in a highly detailed elucidation of one of the underlying microscopic mechanisms for aqueous excess proton transport, known as the von Grotthuss mechanism, involving different hydrated proton configurations with associated high fluxional structural dynamics. Hydroxide transport, with approximately 2-fold-lower bulk diffusion rates compared to those of excess protons, has received much less attention. We present femtosecond UV/IR pump–probe experiments and ab initio molecular dynamics simulations of different proton transport pathways of bifunctional photoacid 7-hydroxyquinoline (7HQ) in water/methanol mixtures. For 7HQ solvent-dependent photoacidity, free-energy–reactivity correlation behavior and quantum mechanics/molecular mechanics (QM/MM) trajectories point to a dominant OH^–/CH₃O^– transport pathway for all water/methanol mixing ratios investigated. Our joint ultrafast infrared spectroscopic and ab initio molecular dynamics study provides conclusive evidence for the hydrolysis/methanolysis acid–base neutralization pathway, as formulated by Manfred Eigen half a century ago. Our findings on the distinctly different acid–base reactivities for aromatic hydroxyl and aromatic nitrogen functionalities suggest the usefulness of further exploration of these free-energy–reactivity correlations as a function of solvent polarity. Ultimately the determination of solvent-dependent acidities will contribute to a better understanding of proton-transport mechanisms at weakly polar surfaces and near polar or ionic regions in transmembrane proton pump proteins or hydrogen fuel cell materials.

Coarse-graining of many-body path integrals: Theory and numerical approximations

Feynman's imaginary time path integral approach to quantum statistical mechanics provides a theoretical formalism for including nuclear quantum effects (NQEs) in simulation of condensed matter systems. Sinitskiy and Voth [J. Chem. Phys. 143, 094104 (2015)] have presented the coarse-grained path integral (CG-PI) theory, which provides a reductionist coarse-grained representation of the imaginary time path integral based on the quantum-classical isomorphism. In this paper, the many-body generalization of the CG-PI theory is presented. It is shown that the N interacting particles obeying quantum Boltzmann statistics can be represented as a system of N pairs of classical-like pseudoparticles coupled to each other analogous to the pseudoparticle pair of the one-body theory. Moreover, we present a numerical CG-PI (n-CG-PI) method applying a simple approximation to the coupling scheme between the pseudoparticles due to numerical challenges of directly implementing the full many-body CG-PI theory. Structural correlations of two liquid systems are investigated to demonstrate the performance of the n-CG-PI method. Both the many-body CG-PI theory and the n-CG-PI method not only present reductionist views of the many-body quantum Boltzmann statistics but also provide theoretical and numerical insight into how to explicitly incorporate NQEs in the representation of condensed matter systems with minimal additional degrees of freedom.

Hydrated Excess Protons in Acetonitrile/Water Mixtures: Solvation Species and Ultrafast Proton Motions

The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond time scales with a direct impact on proton solvation. We use two-dimensional infrared (2D-IR) spectroscopy to follow proton dynamics in acetonitrile/water mixtures with the Zundel cation H₅O₂⁺ prepared in neat acetonitrile as a benchmark. The 2D-IR spectra of the proton transfer mode of H₅O₂⁺ demonstrate stochastic large-amplitude motions in the double-minimum proton potential, driven by fluctuating electric fields. In all cases, the excess proton is embedded in a water dimer, forming an H₅O₂⁺ complex as the major solvation species. This observation is rationalized by quantum mechanics/molecular mechanics molecular dynamics simulations including up to four water molecules embedded in acetonitrile. The Zundel motif interacts with its closest water neighbor in an H₇O₃⁺ unit without persistent proton localization.

Infrared Spectra of Deprotonated Dicarboxylic Acids: IRMPD Spectroscopy and Empirical Valence‐Bond Modeling

Experimental infrared multiple-photon dissociation (IRMPD) spectra recorded for a series of deprotonated dicarboxylic acids, HO₂ (CH₂ )_n CO 2 - (n=2-4), are interpreted using a variety of computational methods. The broad bands centered near 1600 cm^-1 can be reproduced neither by static vibrational calculations based on quantum chemistry nor by a dynamical description of individual structures using the many-body polarizable AMOEBA force field, strongly suggesting that these molecules experience dynamical proton sharing between the two carboxylic ends. To confirm this assumption, AMOEBA was combined with a two-state empirical valence-bond (EVB) model to allow for proton transfer in classical molecular dynamics simulations. Upon suitable parametrization based on ab initio reference data, the EVB-AMOEBA model satisfactorily reproduces the experimental infrared spectra, and the finite temperature dynamics reveals a significant amount of proton sharing in such systems.

Unprecedented O:⇔:O compression and H↔H fragilization in Lewis solutions

Charge injection in terms of protons, lone pairs, cations and anions by acid and base solvation mediates the HB network and properties of Lewis solutions through H↔H fragilization, O:⇔:O compression and polarization, ionic polarization and hydrating H₂O dipolar screen shielding, anion–anion repulsion, compressed solvent H–O bond elongation and undercoordinated solute H–O bond contraction.

IR spectral assignments for the hydrated excess proton in liquid water

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm^-1 for every local proton configuration, with the region 2000-2600 cm^-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H⁺⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H₅O2+moiety.

Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism

Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light–dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal.

Protein-bound water clusters play a key role for proton transport and storage in molecular biology. Here, the authors show by simulations and experiments that the orientation of non-spherical protonated water clusters in bacteriorhodopsin is unveiled by polarization-resolved infrared spectroscopy.

Towards a dissociative SPC-like water model II. The impact of Lennard-Jones and Buckingham non-coulombic forces

The dissociative water potential by Garofalini and coworkers has been re-formulated in the framework of the widely employed Lennard-Jones and Buckingham potentials, enhancing the transferability of the model to third party simulation programs.

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

Different H-bond structures of donor and acceptor water molecules significantly affect structure, H-bond lifetimes, and autodissociation via proton transfer.

Molecular modeling and assignment of IR spectra of the hydrated excess proton in isotopically dilute water

Infrared (IR) spectroscopy of the water O-H stretch has been widely used to probe both the local hydrogen-bonding structure and dynamics of aqueous systems. Although of significant interest, the IR spectroscopy of excess protons in water remains difficult to assign as a result of extensive and strong intermolecular interactions in hydrated proton complexes. As an alternate approach, we develop a mixed quantum-classical model for the vibrational spectroscopy of the excess proton in isotopically dilute water that draws on frozen proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multi-state empirical valence bond proton model (MS-EVB 3.2). A semi-empirical single oscillator spectroscopic map for the instantaneous transition frequency and transition dipole moment is constructed using potential energy surfaces for the O-H stretch coordinate of the excess proton using electronic structure calculations. Calculated spectra are compared with experimental spectra of dilute H⁺ in D₂O obtained from double-difference FTIR to demonstrate the validity of the map. The model is also used to decompose IR spectra into contributions from different aqueous proton configurations. We find that the O-H transition frequency continuously decreases as the oxygen-oxygen length for a special pair proton decreases, shifting from Eigen- to Zundel-like configurations. The same shift is accompanied by a shift of the flanking water stretches of the Zundel complex to higher frequency than the hydronium O-H vibrations.

Towards a dissociative SPC-like water model – probing the impact of intramolecular Coulombic contributions

A modification of the dissociative Garofalini water model towards an SPC-like Coulombic formulation proved to enhance accuracy and transferability of this successful force field approach.

The Hydrated Excess Proton in the Zundel Cation H5 O2 (+) : The Role of Ultrafast Solvent Fluctuations

The nature of the excess proton in liquid water has remained elusive after decades of extensive research. In view of ultrafast structural fluctuations of bulk water scrambling the structural motifs of excess protons in water, we selectively probe prototypical protonated water solvates in acetonitrile on the femtosecond time scale. Focusing on the Zundel cation H5 O2 (+) prepared in room-temperature acetonitrile, we unravel the distinct character of its vibrational absorption continuum and separate it from OH stretching and bending excitations in transient pump-probe spectra. The infrared absorption continuum originates from a strong ultrafast frequency modulation of the H(+) transfer vibration and its combination and overtones. Vibrational lifetimes of H5 O2 (+) are found to be in the sub-100 fs range, much shorter than those of unprotonated water. Theoretical results support a picture of proton hydration where fluctuating electrical interactions with the solvent and stochastic thermal excitations of low-frequency modes continuously modify the proton binding site while affecting its motions.

Protons and Hydroxide Ions in Aqueous Systems

Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.

Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels

Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 Å(-3) have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent. © 2016 Wiley Periodicals, Inc.

Proton transfer in liquid water confined inside graphene slabs

The microscopic structure and dynamics of an excess proton in water constrained in narrow graphene slabs between 0.7 and 3.1 nm wide has been studied by means of a series of molecular dynamics simulations. Interaction of water and carbon with the proton species was modeled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of confinement on proton solvation structure and on its dynamical properties has been considered for varying densities. The system is organized in one interfacial and a bulk-like region, both of variable size. In the widest interplate separations, the lone proton shows a marked tendency to place itself in the bulk phase of the system, due to the repulsive interaction with the carbon atoms. However, as the system is compressed and the proton is forced to move to the vicinity of graphene walls it moves closer to the interface, producing a neat enhancement of the local structure. We found a marked slowdown of proton transfer when the separation of the two graphene plates is reduced. In the case of lowest distances between graphene plates (0.7 and 0.9 nm), only one or two water layers persist and the two-dimensional character of water structure becomes evident. By means of spectroscopical analysis, we observed the persistence of Zundel and Eigen structures in all cases, although at low interplate separations a signature frequency band around 2500 cm^{-1} suffers a blue shift and moves to characteristic values of asymmetric hydronium ion vibrations, indicating some unstability of the typical Zundel-Eigen moieties and their eventual conversion to a single hydronium species solvated by water.

Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor

The proton permeation process of the stator complex MotA/B in the flagellar motor of Escherichia coli was investigated. The atomic model structure of the transmembrane part of MotA/B was constructed based on the previously published disulfide cross-linking and tryptophan scanning mutations. The dynamic permeation of hydronium/sodium ions and water molecule through the channel formed in MotA/B was observed using a steered molecular dynamics simulation. During the simulation, Leu46 of MotB acts as the gate for hydronium ion permeation, which induced the formation of water wire that may mediate the proton transfer to Asp32 on MotB. Free energy profiles for permeation were calculated by umbrella sampling. The free energy barrier for H3O(+) permeation was consistent with the proton transfer rate deduced from the flagellar rotational speed and number of protons per rotation, which suggests that the gating is the rate-limiting step. Structure and dynamics of the MotA/B with nonprotonated and protonated Asp32, Val43Met, and Val43Leu mutants in MotB were investigated using molecular dynamics simulation. A narrowing of the channel was observed in the mutants, which is consistent with the size-dependent ion selectivity. In MotA/B with the nonprotonated Asp32, the A3 segment in MotA maintained a kink whereas the protonation induced a straighter shape. Assuming that the cytoplasmic domain not included in the atomic model moves as a rigid body, the protonation/deprotonation of Asp32 is inferred to induce a ratchet motion of the cytoplasmic domain, which may be correlated to the motion of the flagellar rotor.