Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited

Machine-learning surrogate models for particle insertions and element substitutions

Two machine-learning-aided thermodynamic integration schemes to compute the chemical potentials of atoms and molecules have been developed and compared. One is the particle insertion method, and the other combines particle insertion with element substitution. In the former method, the species is gradually inserted into the liquid and its chemical potential is computed. In the latter method, after the particle insertion, the inserted species is substituted with another species, and the chemical potential of this new species is computed. In both methods, the thermodynamic integrations are conducted using machine-learned potentials trained on first-principles datasets. The errors of the machine-learned surrogate models are further corrected by performing thermodynamic integrations from the machine-learned potentials to the first-principles potentials, accurately providing the first-principles chemical potentials. These two methods are applied to compute the real potentials of proton, alkali metal cations, and halide anions in water. The applications indicate that these two entirely different thermodynamic pathways yield identical real potentials within statistical error bars, demonstrating that both methods provide reproducible real potentials. The computed real potentials and solvation structures are also in good agreement with past experiments and simulations. These results indicate that machine-learning surrogate models enabling particle insertion and element substitution provide a precise method for determining the chemical potentials of atoms and molecules.

Reparameterization of Polarizable Force Fields for Studying Ion Transfer across Liquid-Liquid Interfaces

We have developed a general scheme for refining classical polarizable molecular dynamics (MD) force fields that can accurately describe the molecular interactions in systems with liquid-liquid interfaces. While ab initio MD (AIMD) simulations can naturally describe molecular interactions, they are often so computationally expensive that simulating large system sizes and/or long time scales is usually infeasible. To resolve this, we parameterized efficient and accurate classical polarizable force fields that use AIMD reference data by minimizing both the relative entropy and the root mean squared deviation in atomic forces. We utilized our new multiscale models to study chloride ion transfer across the water-dichloromethane (DCM) interface with and without the tetraethylammonium cation as the phase-transfer catalyst. Our calculated free-energy barrier for the water-DCM interface is consistent with the other reported simulation results. We further analyzed the ion-transfer process by studying the hydration shell structures around the chloride ion and the ion-pair formation to better understand the mechanism. We observed that electronic polarizability is an important factor for the studied phase-transfer catalyst to lower the free-energy barrier of the ion transfer. Using the water-benzene interface system as an additional example, we show that our parameterization scheme provides a general route for modeling different liquid-liquid interface systems even when the experimental data or force field parameters are not readily available.

Multiscale simulation of fluids: coupling molecular and continuum

Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In molecular dynamics (MD) simulation, the length and time scales that can be captured are limited, while computational fluid dynamics (CFD) methods are built on a range of assumptions, from the continuum hypothesis itself, to a variety of closure assumptions. To address these issues, the coupling of different methodologies provides a way to retain the best of both methods. Here, we provide a perspective on multiscale simulation based on the coupling of MD and CFD with each a distinct part of the same simulation domain. This style of coupling allows molecular detail to be present only where it is needed, so CFD can model larger scales than possible with MD alone. We present a unified perspective of the literature, showing the links between the two main types of coupling, state and flux, and discuss the varying assumptions in their use. A unique challenge in such coupled simulation is obtaining averages and constraining local parts of a molecular simulation. We highlight that incorrect localisation has resulted in an error in the literature. We then finish with some applications, focused on the simulation of fluids. Thus, we hope to motivate further research in this exciting area with applications across the spectrum of scientific disciplines.

Tracking the Delocalized Proton in Concerted Proton Transfer in Bulk Water

A solvated proton in water is often characterized as a charge or structural defect, and it is important to track its evolution on-the-fly in certain dynamics simulations. Previously, we introduced the proton indicator, a pseudo-atom, whose position approximates the location of the excess proton modeled as a structural defect. The proton indicator generally yields a smooth trajectory of a hydrated proton diffusing in aqueous solutions, including in the events of stepwise proton transfer via the Grotthuss mechanism; however, the proton indicator did not perform well in the events of concerted proton transfer, for which it occasionally yielded large position displacements between two successive time steps. To overcome this hurdle, we develop a new algorithm of a proton indicator with greatly enhanced performance for concerted proton transfer in bulk water. A protocol is proposed to exhaustively explore the hydrogen-bonding network of the water wires over which the excess proton is delocalized and to properly account for the contributions of the water molecules in this network as the geometry evolves. The new proton indicator (called Indicator 2.0) is assessed in dynamics simulations of an excess proton in bulk water and in specially constructed model systems of more complex architectures. The results demonstrate that the new indicator yields a smooth trajectory in both stepwise and concerted proton transfers.

Structural and Dynamic Properties of Solvated Hydroxide and Hydronium Ions in Water from Ab Initio Modeling

Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient exchange-correlation functional in elucidating the amphiphilic nature and the ubiquitous proton transfer behaviors of the two ions. By adopting the strongly-constrained and appropriately normed (SCAN) meta-GGA functional in AIMD simulations, we systematically examine the amphiphilic properties, the solvation structures, the electronic structures, and the dynamic properties of the two water ions. In particular, we compare these results to those predicted by the PBE0-TS functional, which is an accurate yet computationally more expensive exchange-correlation functional. We demonstrate that the general-purpose SCAN functional provides a reliable choice in describing the two water ions. Specifically, in the SCAN picture of water ions, the appearance of the fourth and fifth hydrogen bonds near hydroxide stabilizes the pot-like shape solvation structure and suppresses the structural diffusion, while the hydronium stably donates three hydrogen bonds to its neighbors. We apply a detailed analysis of the proton transfer mechanism of the two ions and find the two ions exhibit substantially different proton transfer patterns. Our AIMD simulations indicate hydroxide diffuses slower than hydronium in water, which is consistent with the experiments.

Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation

Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.

The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water

In this work, a series of analyses are performed on ab initio molecular dynamics simulations of a hydrated excess proton in water to quantify the relative occurrence of concerted hopping events and "rattling" events and thus to further elucidate the hopping mechanism of proton transport in water. Contrary to results reported in certain earlier papers, the new analysis finds that concerted hopping events do occur in all simulations but that the majority of events are the product of proton rattling, where the excess proton will rattle between two or more waters. The results are consistent with the proposed "special-pair dance" model of the hydrated excess proton wherein the acceptor water molecule for the proton transfer will quickly change (resonate between three equivalent special pairs) until a decisive proton hop occurs. To remove the misleading effect of simple rattling, a filter was applied to the trajectory such that hopping events that were followed by back hops to the original water are not counted. A steep reduction in the number of multiple hopping events is found when the filter is applied, suggesting that many multiple hopping events that occur in the unfiltered trajectory are largely the product of rattling, contrary to prior suggestions. Comparing the continuous correlation function of the filtered and unfiltered trajectories, we find agreement with experimental values for the proton hopping time and Eigen-Zundel interconversion time, respectively.

Tautomeric Equilibrium in Condensed Phases

We present an ab initio molecular dynamics (MD) investigation of the tautomeric equilibrium for the aqueous solutions of glycine and acetone under realistic experimental conditions. Metadynamics is used to accelerate proton migration among tautomeric centers. Due to the formation of complex water-ion structures involved in the proton dynamics in the aqueous environment, standard enhanced sampling approaches may face severe limitations in providing a general description of the phenomenon. Recently, we have developed a set of collective variables (CVs) designed to study protons transfer reactions in complex condensed systems [Grifoni, E. Proc. Natl. Acad. Sci. U.S.A. 2019, 116, 4054 4057]. In this work, we applied this approach to study proton dissociation dynamics leading to tautomeric interconversion of biologically and chemically relevant prototypical systems, namely, glycine and acetone in water. Although relatively simple from a chemical point of view, the results show that even for these small systems, complex reaction pathways and nontrivial conversion dynamics are observed. The generality of our method allows obtaining these results without providing any prior information on the dissociation dynamics but only the atomic species that can exchange protons in the process. Our results agree with literature estimates and demonstrate the general applicability of this method in the study of tautomeric reactions.

Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.

Quantifying the Stability of the Hydronium Ion in Organic Solvents With Molecular Dynamics Simulations

The solution-phase stability of the hydronium ion catalyst significantly affects the rates of acid-catalyzed reactions, which are ubiquitously utilized to convert biomass to valuable chemicals. In this work, classical molecular dynamics simulations were performed to quantify the stability of hydronium and chloride ions by measuring their solvation free energies in water, 1,4-dioxane (DIOX), tetrahydrofuran (THF), γ-valerolactone (GVL), N-methyl-2-pyrrolidone (NMP), acetone (ACE), and dimethyl sulfoxide (DMSO). By measuring the free energy for transferring a hydronium ion from pure water to pure organic solvent, we found that the hydronium ion is destabilized in DIOX, THF, and GVL and stabilized in NMP, ACE, and DMSO relative to water. The distinction between these organic solvents can be used to predict the preference of the hydronium ion for specific regions in aqueous mixtures of organic solvents. We then incorporated the stability of the hydronium ion into a correlative model for the acid-catalyzed conversion of 1,2-propanediol to propanal. The revised model is able to predict experimental reaction rates across solvent systems with different organic solvents. These results demonstrate the ability of classical molecular dynamics simulations to screen solvent systems for improved acid-catalyzed reaction performance.

The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations

The hexapeptide glutathione disulfide (GSSG) has six ionizable groups with six associated dissociation constants. The experimentally measured pH-titration curve, however, does not exhibit the six corresponding equivalence points and bears little resemblance to standard textbook examples of acid-base pH-titration curves. The curve highlights the difficulties in determining multiple pKa values of polyprotic acids - typically proteins and peptides - from experiment. The six pKa values of GSSG can, however, be estimated using Car-Parrinello molecular dynamics (CPMD) simulations in conjunction with metadynamics sampling of the underlying free energy landscape of the dissociation reactions. Ab initio MD simulations were performed on a GSSG molecule solvated by 200 water molecules. Using the estimated pKa values the theoretical titration curve was calculated and found to be in good agreement with experiment. The results clearly highlight how dissociation constants estimated from ab initio MD simulations can facilitate the interpretation of the pH-titration curves of complex chemical and biological systems.

Correlated dynamics in aqueous proton diffusion

The aqueous proton displays an anomalously large diffusion coefficient that is up to 7 times that of similarly sized cations. There is general consensus that the proton achieves its high diffusion through the Grotthuss mechanism, whereby protons hop from one molecule to the next. A main assumption concerning the extraction of the timescale of the Grotthuss mechanism from experimental results has been that, on average, there is an equal probability for the proton to hop to any of its neighboring water molecules. Herein, we present ab initio simulations that show this assumption is not generally valid. Specifically, we observe that there is an increased probability for the proton to revert back to its previous location. These correlations indicate that the interpretation of the experimental results need to be re-examined and suggest that the timescale of the Grotthuss mechanism is significantly shorter than was previously thought.

Thermodynamic, structural, and dynamical properties of nano-confined water using SPC/E and TIP4P models by molecular dynamics simulations

Different morphologies of water molecules are confined between two parallel graphene surfaces.

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.

Interpretation of the à ← X̃ transition of hydrated protons in aqueous solutions observed in the far-UV region with quantum chemical calculations

A substantial blue-shift of the first electronic transition band of liquid water with a H₂SO₄ concentration (0–14.4 M) observed in the far-UV region.

A new algorithm for construction of coarse-grained sites of large biomolecules

The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials.

Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport

Results from condensed phase ab initio molecular dynamics (AIMD) simulations suggest a proton transfer reaction is facilitated by "presolvation" in which the hydronium is transiently solvated by four water molecules, similar to the typical solvation structure of water, by accepting a weak hydrogen bond from the fourth water molecule. A new version 3.2 multistate empirical valence bond (MS-EVB 3.2) model for the hydrated excess proton incorporating this presolvation behavior is therefore developed. The classical MS-EVB simulations show similar structural properties as those of the previous model but with significantly improved diffusive behavior. The inclusion of nuclear quantum effects in the MS-EVB also provides an even better description of the proton diffusion rate. To quantify the influence of anharmonicity, a second model (aMS-EVB 3.2) is developed using the anharmonic aSPC/Fw water model, which provides similar structural properties but improved spectroscopic responses at high frequencies.

Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue

The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pKa Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation-deprotonation reaction of the 20 canonical α amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metadynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pKa values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error, with respect to experimental results, of 0.2 pKa units.

Solvation-Dependent Latency of Photoacid Dissociation and Transient IR Signatures of Protonation Dynamics

We elucidate the characteristic proton pathways and the transient infrared signatures of intermediate complexes during the first picoseconds of photoinduced protonation dynamics of a photoacid (N-methyl-6-hydroxyquinolinium) in aqueous solution from first-principles molecular dynamics simulations. Our results indicate that the typical latency time between photoexcitation and proton dissociation ranges from 1 ps to longer time time scales (∼100 ps). The rate-limiting step for the actual dissociation of the proton into the solvent is the solvation structure of the first accepting water molecule. The nature of the proton pathway in water (stepwise or concerted) is not unique but determined by the coordination number of the accepting water molecules along the hydrogen bond chain. We find a characteristic uncommon infrared mode at ∼1300 cm(-1) of the transient photobase-Eigen cation complex immediately after photodissociation that we predict to be observable experimentally in time-resolved IR spectroscopy. A broad continuous absorption band from 1500 to 2000 cm(-1) arises from the acidic proton imminently before dissociation.

Estimating successive pKa values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

pKa values of polyprotic acids estimated from ab initio molecular dynamics computation of the change in free energy upon dissociation.

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel

The self-consistent charge density functional tight binding (SCC-DFTB) method has been increasingly applied to study proton transport (PT) in biological environments. However, recent studies revealing some significant limitations of SCC-DFTB for proton and hydroxide solvation and transport in bulk aqueous systems call into question its accuracy for simulating PT in biological systems. The current work benchmarks the SCC-DFTB/MM method against more accurate DFT/MM by simulating PT in a synthetic leucine-serine channel (LS2), which emulates the structure and function of biomolecular proton channels. It is observed that SCC-DFTB/MM produces over-coordinated and less structured pore water, an over-coordinated excess proton, weak hydrogen bonds around the excess proton charge defect and qualitatively different PT dynamics. Similar issues are demonstrated for PT in a carbon nanotube, indicating that the inaccuracies found for SCC-DFTB are not due to the point charge based QM/MM electrostatic coupling scheme, but rather to the approximations of the semiempirical method itself. The results presented in this work highlight the limitations of the present form of the SCC-DFTB/MM approach for simulating PT processes in biological protein or channel-like environments, while providing benchmark results that may lead to an improvement of the underlying method.

Proton transfer through the water gossamer

The diffusion of protons through water is understood within the framework of the Grotthuss mechanism, which requires that they undergo structural diffusion in a stepwise manner throughout the water network. Despite long study, this picture oversimplifies and neglects the complexity of the supramolecular structure of water. We use first-principles simulations and demonstrate that the currently accepted picture of proton diffusion is in need of revision. We show that proton and hydroxide diffusion occurs through periods of intense activity involving concerted proton hopping followed by periods of rest. The picture that emerges is that proton transfer is a multiscale and multidynamical process involving a broader distribution of pathways and timescales than currently assumed. To rationalize these phenomena, we look at the 3D water network as a distribution of closed directed rings, which reveals the presence of medium-range directional correlations in the liquid. One of the natural consequences of this feature is that both the hydronium and hydroxide ion are decorated with proton wires. These wires serve as conduits for long proton jumps over several hydrogen bonds.

Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer

The membrane potential at the water/phospholipid interfaces may play a key role for proton conduction of gramicidin A (gA). Here we address this issue by Density Functional Theory-based molecular dynamics and metadynamics simulations. The calculations, performed on gA embedded in a solvated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model membrane environment (about 2,000 atoms), indicate that (i) the membrane dipole potential rises at the channel mouth by ∼0.4 V. A similar value has been measured for gA embedded in a DMPC monolayer; (ii) the calculated free energy barrier is located at the channel entrance, consistent with experiments comparing gA proton conduction in different bilayers. The electronic structures of the proton ligands (water molecules and peptide units) are similar to those in the bulk solvent. Based on these results, we suggest an important role of the membrane dipole potential for the free energy barrier of proton permeation of gA. This may provide a rationale for the large increase in the rate of proton conduction under application of a transmembrane voltage, as observed experimentally. Our calculations might suggest also a role for proton desolvation for the permeation process. This role has already emerged from EVB calculations on gA embedded in a model membrane.

Multiscale reactive molecular dynamics

Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

Proton defect solvation and dynamics in aqueous acid and base

Easy come, easy go: LEWIS, a new model of reactive and polarizable water that enables the simulation of a statistically reliable number of proton hopping events in aqueous acid and base at concentrations of practical interest, is used to evaluate proton transfer intermediates in aqueous acid and base (picture, left and right, respectively).

Natural polarizability and flexibility via explicit valency: the case of water

As the dominant physiological solvent, water drives the folding of biological macromolecules, influences conformational changes, determines the ionization states of surface groups, actively participates in catalytic events, and provides "wires" for long-range proton transfer. Elucidation of all these roles calls for atomistic simulations. However, currently available methods do not lend themselves to efficient simulation of proton transfer events, or even polarizability and flexibility. Here, we report that an explicit account of valency can provide a unified description for the polarizability, flexibility, and dissociability of water in one intuitive and efficient setting. We call this approach LEWIS, after the chemical theory that inspires the use of valence electron pairs. In this paper, we provide details of the method, the choice of the training set, and predictions for the neat ambient liquid, with emphasis on structure, dynamics, and polarization. LEWIS water provides a good description of bulk properties, and dipolar and quadrupolar responses.

Proton transport in functionalised additives for PEM fuel cells: contributions from atomistic simulations

The conventional polymer electrolyte membrane (PEM) materials for fuel cell applications strongly rely on temperature and pressure conditions for optimal performance. In order to expand the range of operating conditions of these conventional PEM materials, mesoporous functionalised SiO(2) additives are developed. It has been demonstrated that these additives themselves achieve proton conductivities approaching those of conventional materials. However, the proton conduction mechanisms and especially factors influencing charge carrier mobility under different hydration conditions are not well known and difficult to separate from concentration effects in experiments. This tutorial review highlights contributions of atomistic computer simulations to the basic understanding and eventual design of these materials. Some basic introduction to the theoretical and computational framework is provided to introduce the reader to the field, the techniques are in principle applicable to a wide range of other situations as well. Simulation results are directly compared to experimental data as far as possible.