Reactive force fields for proton transfer dynamics

A force field-inspired method based on fitted, high-quality multidimensional potential energy surfaces to follow proton transfer (PT) reactions in molecular dynamics simulations is presented. In molecular mechanics with proton transfer (MMPT) a system is partitioned into a region where proton transfer takes place and the remaining degrees of freedom which are treated with a conventional force field. The implementation of the method and applications to specific chemically and biologically relevant scenarios are presented. MMPT is developed in view of two primary areas in mind: to follow the molecular dynamics of proton transfer in the condensed phase on realistic time scales and to adapt the shape (morphing) of the potential energy surface for specific applications. MMPT is applied to PT in protonated ammonia dimer, double proton transfer in 2-pyridone-2-hydroxypyridine, and the first step of PT from a protein side-chain towards a buried [3Fe4S] cluster in ferredoxin I. Specific findings of the work include the fundamental role of the N-N vibration as the gating mode for PT in NH4+...NH3 and the qualitative understanding of PT from the protein to a metastable active-site water molecule in Ferredoxin I.     

Different Protonation Equilibria of 4‐Methylimidazole and Acetic Acid

Dynamic protonation equilibria in water of one 4‐methylimidazole molecule as well as for pairs and groups consisting of 4‐methylimidazole, acetic acid and bridging water molecules are studied using Q‐HOP molecular dynamics simulation. We find a qualitatively different protonation behavior of 4‐methylimidazole compared to that of acetic acid. On one hand, deprotonated, neutral 4‐methylimidazole cannot as easily attract a freely diffusing extra proton from solution. Once the proton is bound, however, it remains tightly bound on a time scale of tens of nanoseconds. In a linear chain composed of acetic acid, a separating water molecule and 4‐methylimidazole, an excess proton is equally shared between 4‐methylimidazole and water. When a water molecule is linearly placed between two acetic acid molecules, the excess proton is always found on the central water. On the other hand, an excess proton in a 4‐methylimidazole‐water‐4‐methylimidazole chain is always localized on one of the two 4‐methylimidazoles. These findings are of interest to the discussion of proton transfer along chains of amino acids and water molecules in biomolecules.     

Potential of mean force of water–proton bath and molecular dynamic simulation of proteins at constant pH

An advanced implicit solvent model of water–proton bath for protein simulations at constant pH is presented. The implicit water–proton bath model approximates the potential of mean force of a protein in water solvent in a presence of hydrogen ions. Accurate and fast computational implementation of the implicit water–proton bath model is developed using the continuum electrostatic Poisson equation model for calculation of ionization equilibrium and the corrected MSR6 generalized Born model for calculation of the electrostatic atom–atom interactions and forces. Molecular dynamics (MD) method for protein simulation in the potential of mean force of water–proton bath is developed and tested on three proteins. The model allows to run MD simulations of proteins at constant pH, to calculate pH‐dependent properties and free energies of protein conformations. The obtained results indicate that the developed implicit model of water–proton bath provides an efficient way to study thermodynamics of biomolecular systems as a function of pH, pH‐dependent ionization‐conformation coupling, and proton transfer events. © 2012 Wiley Periodicals, Inc.     

Effects of water nanochannel diameter on proton transport in proton‐exchange membranes

The effects of water nanochannel diameter on proton transport pathways and properties have been studied using reactive molecular dynamics simulations. The proton distributions and diffusivities have been evaluated using the cylinder model of water domains at various diameters that is the most typical proposed morphological model in proton‐exchange membranes. The proton distributions are analyzed to clarify proton pathways by classifying the water channel into two regions in parallel: an inner channel (free water) and an outer channel (bound water). For all the water contents, the nonmonotonic trends that show a peak at a certain diameter are found to be observed in the proton diffusivity, which is dominated by the proton diffusivity in the free water region and has a strong correlation with the proton distribution that is controlled by the balance between the volume fraction of free water and the surface density of sulfonate groups. The electroosmotic drag coefficients are found to increase monotonically with increasing channel diameter as a result of the increase in the volume fraction of free water. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 867–878     

Ab initio parameterization of an all-atom polarizable and dissociable force field for water

A novel all-atom, dissociative, and polarizable force field for water is presented. The force field is parameterized based on forces, stresses, and energies obtained form ab initio calculations of liquid water at ambient conditions. The accuracy of the force field is tested by calculating structural and dynamical properties of liquid water and the energetics of small water clusters. The transferability of the force field to dissociated states is studied by considering the solvation of a proton and the ionization of water at extreme conditions of pressure and temperature. In the case of the solvated proton, the force field properly describes the presence of both Eigen and Zundel configurations. In the case of the pressure-induced ice VIII/ice X transition and the temperature-induced transition to a superionic phase, the force field is found to describe accurately the proton symmetrization and the melting of the proton sublattice, respectively.     

How Does a Membrane Protein Achieve a Vectorial Proton Transfer Via Water Molecules?

We present a detailed mechanism for the proton transfer from a protein‐bound protonated water cluster to the bulk water directed by protein side chains in the membrane protein bacteriorhodopsin. We use a combined approach of time‐resolved Fourier transform infrared spectroscopy, molecular dynamics simulations, and X‐ray structure analysis to elucidate the functional role of a hydrogen bond between Ser193 and Glu204. These two residues seal the internal protonated water cluster from the bulk water and the protein surface. During the photocycle of bacteriorhodopsin, a transient protonation of Glu204 leads to a breaking of this hydrogen bond. This breaking opens the gate to the extracellular bulk water, leading to a subsequent proton release from the protonated water cluster. We show in detail how the protein achieves vectorial proton transfer via protonated water clusters in contrast to random proton transfer in liquid water.     

Exploration on regulating factors for proton transfer along hydrogen-bonded water chains.

Proton transfer along a single-file hydrogen-bonded water chain is elucidated with a special emphasis on the investigation of chain length, side water, and solvent effects, as well as the temperature and pressure dependences. The number of water molecules in the chain varies from one to nine. The proton can be transported to the acceptor fragment through the single-file hydrogen-bonded water wire which contains at most five water molecules. If the number of water molecule is more than five, the proton is trapped by the chain in the hydroxyl-centered H(7)O(3) (+) state. The farthest water molecule involved in the formation of H(7)O(3) (+) is the fifth one away from the donor fragment. These phenomena reappear in the molecular dynamics simulations. The energy of the system is reduced along with the proton conduction. The proton transfer mechanism can be altered by excess proton. The augmentation of the solvent dielectric constant weakens the stability of the system, but favors the proton transfer. NMR spin-spin coupling constants can be used as a criterion in judging whether the proton is transferred or not. The enhancement of temperature increases the thermal motion of the molecule, augments the internal energy of the system, and favors the proton transfer. The lengthening of the water wire increases the entropy of the system, concomitantly, the temperature dependence of the Gibbs free energy increases. The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature.     

A Protonated Water Cluster as a Transient Proton‐Loading Site in Cytochrome c Oxidase

Cytochrome c oxidase (CcO) is a redox‐driven proton pump that powers aerobic respiratory chains. We show here by multi‐scale molecular simulations that a protonated water cluster near the active site is likely to serve as the transient proton‐loading site (PLS) that stores a proton during the pumping process. The pK_a of this water cluster is sensitive to the redox states of the enzyme, showing distinct similarities to other energy converting proton pumps.     

Potential Proton‐Release Channels in Bacteriorhodopsin

The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton‐transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen‐bonded networks, which may include internal water molecules. The terminal step of the proton‐transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton‐release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen‐bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.     

Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

Gating Mechanism of the Voltage-Gated Proton Channel Studied by Molecular Dynamics Simulations

The voltage-gated proton channel Hv1 has important roles in proton extrusion, pH homeostasis, sperm motility, and cancer progression. The Hv1 channel has also been found to be highly expressed in cell lines and tissue samples from patients with breast cancer. A high-resolution closed-state structure has been reported for the mouse Hv1 chimera channel (mHv1cc), solved by X-ray crystallography, but the open-state structure of Hv1 has not been solved. Since Hv1 is a promising drug target, various groups have proposed open conformations by molecular modeling and simulation studies. However, the gating mechanism and the open-state conformation under the membrane potential are still debate. Here, we present a molecular dynamics study considering membrane potential and pH conditions. The closed-state structure of mHv1cc was used to run molecular dynamics (MD) simulations with respect to electric field and pH conditions in order to investigate the mechanism of proton transfer. We observed a continuous hydrogen bond chain of water molecules called a water-wire to be formed through the channel pore in the channel opening, triggered by downward displacement of the S2 helix and upward movement of the S4 helix relative to other helices. Due to the movement of the S2 and S4 helices, the internal salt bridge network was rearranged, and the hydrophobic gating layers were destroyed. In line with previous experimental and simulation observations, our simulation results led us to propose a new gating mechanism for the Hv1 proton channel, and may provide valuable information for novel drug discovery.     

Proton transfer 200 years after von Grotthuss: insights from ab initio simulations.

In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.     

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H7+O3 Complex in Solution

Infrared (IR) absorption in the 1000–3700 cm⁻¹ range and ¹H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H₇⁺O_3, in acetonitrile. The core H₇⁺O₃ motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H₇⁺O₃ structure in solution. The QM/MM calculations allow for the successful simulation of the measured IR absorption spectra of H₇⁺O₃ in the OH stretch region, which reaffirms the assignment of the H₇⁺O₃ spectra to a hybrid-complex structure: a protonated water dimer strongly hydrogen-bonded to a third water molecule with the proton exchanging between the two possible shared-proton Zundel-like centers. The H₇⁺O₃ structure lends itself to promoting irreversible proton transport in presence of even one additional water molecule. We demonstrate how continuously evolving H₇⁺O₃ structures may support proton transport within larger water solvates.     

Can a Proton be Encapsulated in Tetraamido/Diamino Quaternized Macrocycles in Aqueous Solution and Electric Field?

The proton‐binding behavior of solvated tetraamido/diamino quaternized macrocyclic compounds with rigid phenyl and flexible phenyl bridges in the absence or presence of an external electric field is investigated by molecular dynamics simulation. The proton can be held through H‐bonding interactions with the two carbonyl oxygen atoms in macrocycles containing rigid (phenyl) and flexible (propyl) bridges. The solute–solvent H‐bonding interactions cause the macrocyclic backbones to twist to different extents, depending on the different bridges. The macrocycle with the rigid phenyl linkages folds into a cuplike shape due to π–π interaction, while the propyl analogue still maintains the ellipsoidal ringlike shape with just a slight distortion. The potential energy required for proton transfer is larger in the phenyl‐containing macrocycle than in the compound with propyl units. When an external electric field with a strength of 2.5 V nm^?1 is exerted along the carbonyl oxygen atoms, a difference in proton encircling is exhibited for macrocycles with rigid and flexible bridges. In contrast to encapsulation of a proton in the propyl analogue, the intermolecular solute–solvent H‐bonding and intramolecular π–π stacking between the two rigid phenyl spacers leads to loss of the proton from the highly distorted cuplike macrocycle with phenyl bridges. The competition between intra‐ and intermolecular interactions governs the behavior of proton encircling in macrocycles.     

Water sorption and diffusion coefficients of protons and water in PVDF-g-PSSA polymer electrolyte membranes

Water sorption properties, proton NMR spectra, and diffusion of water and protons in poly(vinylidene fluoride)-graft-polystyrene sulfonic acid (PVDF-g-PSSA) polymer electrolyte membranes were studied. Sorption curves for the membranes with different degrees of grafting in protonated and Na⁺ form were measured by equilibrating the membranes over saturated salt solutions. The membrane water content was found to be sensitive to changes in relative humidity (RH). The water/sulfonic acid ratio λ for the protonated samples was around 2 at 20% RH and increased to λ ∼ 30 at 100%. Proton NMR, pulsed field gradient proton NMR (PFG-NMR), and impedance measurements were made on membranes with different λ. In the proton NMR spectra only one peak was found, originating from the water in the membrane. The chemical shift of the peak was found to be dependent on the counterion and the water content. The water self-diffusion coefficients D_H2O, measured by PFG-NMR, increased with degree of grafting and water content of the membranes. The proton conductivity and the calculated proton mobility decreased more steeply than the D_H2O with decreasing water content. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 2893–2900, 1999     

2-取代咪唑衍生物掺杂高温非水用Nafion质子交换膜的制备和性能

高温质子交换膜燃料电池所面临的一个主要技术障碍是高温低湿度环境下能够具有满足电池工作条件的膜的制备.本文通过所合成的2-取代咪唑衍生物与全氟磺酸树脂的掺杂,采用溶液重铸法制备了可以在高温无水条件下工作的质子交换膜.通过2-位疏水基团的接枝,实现了非水质子传导介质的咪唑环在膜内的固定,所制备的复合质子交换膜的导质子率在160℃无水条件下达到6.8×10^-3Scm^-1;而且相比全氟磺酸均质膜,其热稳定性也有所提高.采用静电力显微镜观察到了所制备的复合质子交换膜内相互连接的离子团簇的形成;结合其质子传导活化能,提出了所制备的复合质子交换膜在120℃以下质子传导以跳跃方式为主;在120℃以上,则以咪唑环的＂钟摆＂形式实现质子在膜内的传输.     

Simulation of slow reaction with quantum character: Neutral hydrolysis of carboxylic ester

By computer simulation, using both quantum and classical dynamics, we determined the rate constant and the kinetic isotope effect of the rate-determining step in the neutral hydrolysis of p-methoxyphenyl dichloroacetate in aqueous solution. This step involves a proton transfer concerted with the formation of a C O bond. A method of biased sampling was used; the Gibbs free energy of the biased configuration from which proton transfer is likely to occur was determined by a combination of semiempirical quantum calculations and thermodynamic integration. The proton dynamics was modeled with the quantum-dynamical density matrix evolution method that includes nonadiabatic pathways. The proton dynamics is driven by a fluctuating proton potential that was derived from a classical molecular dynamics simulation of the system including solvent. The calculated rate constant of 3×10⁻² s⁻¹ agrees within the error of the calculation with the experimentally observed value of 2.78×10⁻³. The calculated pseudo-first-order kinetic isotope effect of 3.9 is in good agreement with the experimentally observed value of 3.2. The results show the feasibility of computational approaches to slow reactions in complex environments, where proton transfer with an essential quantum-dynamical nature is the rate-limiting step. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 886–895, 1999     

DNA Nucleobase under Ionizing Radiation: Unexpected Proton Transfer by Thymine Cation in Water Nanodroplets

The effect of ionizing radiation on DNA constituents is a widely studied fundamental process using experimental and computational techniques. In particular, radiation effects on nucleobases are usually tackled by mass spectrometry in which the nucleobase is embedded in a water nanodroplet. Here, we present a multiscale theoretical study revealing the effects and the dynamics of water droplets towards neutral and ionized thymine. In particular, by using both hybrid quantum mechanics/molecular mechanics and full ab initio molecular dynamics, we reveal an unexpected proton transfer from thymine cation to a nearby water molecule. This leads to the formation of a neutral radical thymine and a Zundel structure, while the hydrated proton localizes at the interface between the deprotonated thymine and the water droplet. This observation opens entirely novel perspectives concerning the reactivity and further fragmentation of ionized nucleobases.     

Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II

We present, for the first time, how transient changes in the coordination number of zinc ion affects the rate determining step in the enzyme human carbonic anhydrase (HCA) II. The latter involves an intramolecular proton transfer between a zinc-bound water and a distant histidine residue (His-64). In the absence of time-resolved experiments, results from classical and QM-MM molecular dynamics and transition path sampling simulations are presented. The catalytic zinc ion is found to be present in two possible coordination states; viz. a stable tetra-coordinated state, T and a less stable penta-coordinated state, P with tetrahedral and trigonal bipyramidal coordination geometries, respectively. A fast dynamical inter-conversion occurs between T and P due to reorganization of active site water molecules making the zinc ion more positively charged in state P. When initiated from different coordination environments, the most probable mechanism of proton transfer is found to be deprotonation of the equatorial water molecule from state P and transfer of the excess proton via a short path formed by hydrogen bonded network of active site water molecules. We estimate the rate constant of proton transfer as from P and from T. A quantitative match of estimated k_P with the experimental value, ( ) suggests that dynamics of Zn coordination triggers the rate determining proton transfer step in HCA II.