Monte Carlo simulation of polarizable systems: Early rejection scheme for improving the performance of adiabatic nuclear and electronic sampling Monte Carlo simulations

An early rejection scheme for trial moves in adiabatic nuclear and electronic sampling Monte Carlo simulation (ANES-MC) of polarizable intermolecular potential models is presented. The proposed algorithm is based on Swendsen–Wang filter functions for prediction of success or failure of trial moves in Monte Carlo simulations. The goal was to reduce the amount of calculations involved in ANES-MC electronic moves, by foreseeing the success of an attempt before making those moves. The new method was employed in Gibbs ensemble Monte Carlo (GEMC) simulations of the polarizable simple point charge-fluctuating charge (SPC-FQ) model of water. The overall improvement in GEMC depends on the number of swap attempts (transfer molecules between phases) in one Monte Carlo cycle. The proposed method allows this number to increase, enhancing the chemical potential equalization. For a system with 300 SPC-FQ water molecules, for example, the fractions of early rejected transfers were about 0.9998 and 0.9994 at 373 and 423 K, respectively. This means that the transfer moves consume only a very small part of the overall computing effort, making GEMC almost equivalent to a simulation in the canonical ensemble.     

Molecular dynamics simulation of the water|nitrobenzene interface

The structure and dynamics of the neat water|nitrobenzene liquid|liquid interface are studied at 300 K using molecular dynamics computer simulations. The water is modeled using the flexible SPC potential, and the nitrobenzene is modeled using an empirically determined nitrobenzene potential energy function. Although nitrobenzene is a polar liquid with a large dielectric constant, the structure of the interface is similar to other water|non-polar organic liquid interfaces. Among the main structural features we describe are an enhancement of interfacial water hydrogen bonds, the specific orientation of water dipoles and nitrobenzene molecules, and a rough surface that is locally sharp. Surface roughness is also characterized dynamically. The dynamics of molecular reorientation are shown to be only mildly modified at the interface. The effect due to the polarizable many-body potential energy functions of both liquids is investigated and is found to affect only mildly the above results.     

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH₂, CH₃, and CH₄ moieties. © 2014 Wiley Periodicals, Inc.     

A first-principles study of molecular oxygen dissociation at an electrode surface: a comparison of potential variation and coadsorption effects

Influences of coadsorbed sodium and water, aqueous solvent, and electrode potential on the kinetics of O(2) dissociation over Pt(111) are systematically investigated using density functional theory models of vacuum and electrochemical interfaces. Na coadsorption alters the electronic states of Pt to stabilize the reactant (O(2)*), transition, and product (2O*) states by facilitating electron donation to oxygen, causing a more exothermic reaction energy (-0.84 eV for Na and O(2), -0.81 eV for isolated O(2)) and a decrease in dissociation barrier (0.39 eV for Na and O(2), 0.57 eV for isolated O(2)). Solvation decreases the reaction energy (-0.67 eV) due to enhanced hydrogen bond stabilization of O(2)* compared to 2O*. The influence of Na is less pronounced at the solvated interface (barrier decreases by only 0.11 eV) because H(2)O screens Na charge-donation. In the electrochemical model system, the dissociation energy becomes more exothermic and the barrier decreases toward more positive potentials. Potential-dependent behavior results from changes in interfacial dipole moment and polarizability between O(2)*, the dissociation transition state, and 2O*; each are influenced by changes in adsorption and hydrogen bonding. Coadsorption of Na in the solvated system dampens the dipole moment change between O(2)* and 2O* and significantly increases the polarizability at the dissociation transition state and for 2O*; the combination causes little change in the reaction energy but reduces the activation barrier by 0.08 eV at 0 V versus NHE. The potential-dependent behavior contrasts that determined at a constant surface charge or from an applied electric field, illustrating the importance of considering the electrochemical potential at the fully-solvated interface in determining reaction energetics, even for non-redox reactions.     

Polarizable empirical force field for alkanes based on the classical Drude oscillator model

Recent extensions of potential energy functions used in empirical force field calculations have involved the inclusion of electronic polarizability. To properly include this extension into a potential energy function it is necessary to systematically and rigorously optimize the associated parameters based on model compounds for which extensive experimental data are available. In the present work, optimization of parameters for alkanes in a polarizable empirical force field based on a classical Drude oscillator is presented. Emphasis is placed on the development of parameters for CH3, CH2, and CH moieties that are directly transferable to long chain alkanes, as required for lipids and other biomolecules. It is shown that a variety of quantum mechanical and experimental target data are reproduced by the polarizable model. Notable is the proper treatment of the dielectric constant of pure alkanes by the polarizable force field, a property essential for the accurate treatment of, for example, hydrophobic solvation in lipid bilayers. The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.     

Polarizable solute in polarizable and flexible solvents: simulation study of electron transfer reaction systems

A polarizable solute model, based on the empirical valence bond approach, is developed and applied to electron transfer (ET) reactions in polarizable and flexible water solvents. The polarization effect is investigated in comparison with a nonpolarizable solute and solvent model. With free energy curves constructed by a molecular dynamics simulation, the activation energy barrier and the reorganization energy related to ET processes are investigated. The present simulation results show that the activation energy barrier becomes larger in the polarizable model than in the nonpolarizable model and that this makes the ET rate slower than that with the nonpolarizable model. It is shown that the effect of the electronic energy difference of solute molecule on free energy profiles is remarkable and that, corresponding to this effect, the reorganization energy is significantly modified. These results indicate that the process of solvent polarization by the polarized solute to enhance the solute-solvent interaction is a key factor and that treating the polarization of both solute and solvent at the same time is essential. Also, the polarization effect on the diffusive motion of the solute molecule in the polarization solvent is studied. The polarized solute molecule shows slower diffusive motion compared with that in the nonpolarizable model.     

Alignment of electronic energy levels at electrochemical interfaces

The position of electronic energy levels in a phase depends on the surface potentials at its boundaries. Bringing two phases in contact at an interface will alter the surface potentials shifting the energy levels relative to each other. Calculating such shifts for electrochemical interfaces requires a combination of methods from computational surface science and physical chemistry. The problem is closely related to the computation of potentials of electrochemically inactive electrodes. These so-called ideally polarizable interfaces are impossible to cross for electrons. In this perspective we review two density functional theory based methods that have been developed for this purpose, the workfunction method and the hydrogen insertion method. The key expressions of the two methods are derived from the formal theory of absolute electrode potentials. As an illustration of the workfunction method we review the computation of the potential of zero charge of the Pt(111)-water interface as recently published by a number of groups. The example of the hydrogen insertion method is from our own work on the rutile TiO(2)(110)-water interface at the point of zero proton charge. The calculations are summarized in level diagrams aligning the electronic energy levels of the solid electrode (Fermi level of the metal, valence band maximum and conduction band minimum of the semiconductor) to the band edges of liquid water and the standard potential for the reduction of the hydroxyl radical. All potentials are calculated at the same level of density functional theory using the standard hydrogen electrode as common energy reference. Comparison to experiment identifies the treatment of the valence band of water as a potentially dangerous source of error for application to electrocatalysis and photocatalysis.     

润湿特性对超级电容器储能动力学的影响机理

润湿特性对超级电容器储能性能有着至关重要的影响。借助分子动力学模拟,本文研究了润湿特性对超级电容器储能动力学行为的影响。以石墨烯和晶体铜作为疏电解液和亲电解液电极材料。结果表明,在充电过程中,亲电解液铜电极呈现出非对称的U型微分电容曲线,负极电容是正极的～5.77倍,不同于经典双电层理论Gouy-Chapman-Stern(对称U型)和疏电解液型。该现象与离子自由能阻力分布密切相关,负极自由能阻力远小于正极(～2倍)和疏电解液电极,进而有利于强化双电层结构对电极电压的响应能力,导致更高微分电容。通过微分离子电荷密度,本文再现了微分电容演变规律,并发现改善润湿性会显著降低双电层厚度。最后,我们指出润湿性直接影响储能微观机理,将电荷储存机制从离子吸附和交换共同主导(疏电解液)转变到离子吸附主导(亲电解液)。本文所得结论揭示了润湿特性对储能动力学行为影响的原子层级机理,对超级电容器材料设计、构筑与润湿特性调控具有重要指导意义。     

Specific adsorption of chloride ions on liquid Ga electrode from N-methylformamide solutions with constant ionic strength

Differential capacitance curves are measured by mans of an ac-bridge in the system Ga/[N-MF + 0.1m M KCl + 0.1(1 − m) M KClO₄] with the surface-active anion taken in the following molar fractions m: 0, 0.01, 0.02, 0.05, 0.1, 0.2, 0.5, and 1. As compared with the other solvents, N-methylformamide (N-MF) makes it possible to realize the highest positive charges of the Ga electrode at which the electrode remains ideally polarizable (up to 20 μC/cm²). The data on the specific adsorption of Cl⁻ ions in the mentioned system can be described qualitatively by the Frumkin isotherm in which the free energy is considered as a linear function of the electrode charge.     

Polarizable coarse‐grained models for molecular dynamics simulation of liquid cyclohexane

Force field parameters for polarizable coarse‐grained (CG) supra‐atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine‐grained (FG) CH₂r united atoms of the cyclohexane ring, and one representing three FG CH₂r united atoms. Electronic polarizability is represented by a massless charge‐on‐spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self‐diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.     

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Condensed‐phase computational studies of molecules using molecular mechanics approaches require the use of force fields to describe the energetics of the systems as a function of structure. The advantage of polarizable force fields over nonpolarizable (or additive) models lies in their ability to vary their electronic distribution as a function of the environment. Toward development of a polarizable force field for biological molecules, parameters for a series of sulfur‐containing molecules are presented. Parameter optimization was performed to reproduce quantum mechanical and experimental data for gas phase properties including geometries, conformational energies, vibrational spectra, and dipole moments as well as for condensed phase properties such as heats of vaporization, molecular volumes, and free energies of hydration. Compounds in the training set include methanethiol, ethanethiol, propanethiol, ethyl methyl sulfide, and dimethyl disulfide. The molecular volumes and heats of vaporization are in good accordance with experimental values, with the polarizable model performing better than the CHARMM22 nonpolarizable force field. Improvements with the polarizable model were also obtained for molecular dipole moments and in the treatment of intermolecular interactions as a function of orientation, in part due to the presence of lone pairs and anisotropic atomic polarizability on the sulfur atoms. Significant advantage of the polarizable model was reflected in calculation of the dielectric constants, a property that CHARMM22 systematically underestimates. The ability of this polarizable model to accurately describe a range of gas and condensed phase properties paves the way for more accurate simulation studies of sulfur‐containing molecules including cysteine and methionine residues in proteins. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Electrolysis with electrolyte dropping electrode: II. Basic properties of the system

In a theoretical discussion the conditions have been pointed out where an interface of two immiscible electrolyte solution behaves as an equilibrium system metal ion-metallic electrode, as an ideally polarized electrode and as an electrode under faradaic current flow. The basic equations for current-electrical potential difference across the interface have been deduced for the cases of ion as well as electron transfer.Experimentally, various base electrolyte systems were studied, the most advantageous among these are LiCl in water+tetrabutylammonium tetraphenylborate in nitrobenzene and MgCl₂ in water+tetrabutylammonium dicarbollyl cobaltate in nitrobenzene. S-shaped polarographic curves were observed with the tetramethylammonium ion. The limiting current is directly proportional to concentration. The limiting currents are somewhat higher than those predicted by the Ilkovi? equation which has been ascribed to the tangential movement of the interface.     

Calculation of adiabatic free energy surfaces in the case of electrochemical tunneling microscopy of redox systems

A method of adiabatic (infinitely slow) switching-on of interaction of the reactant with the electrode and the tip of a tunneling microscope at a bias voltage other than zero is used to derive expressions for the average number of electrons in the valence orbital of the reactant, the current passing through the valence orbital of the reactant at fixed values of coordinates of the slow subsystem of the solvent, and the electronic contribution to an expression that describes the adiabatic free energy surface (AFES) of the electrode-reactant-tip of the tunneling microscope system. The derived expressions are the same that had already been obtained in a Kuznetsov-Schmickler work, by a not-quite-correct method, though. Relationships that link the AFES corresponding to the opposite signs of the bias voltage are deduced. Examples of calculations of AFES and a current for a number of characteristic sets of parameters of the system are presented.Translated from Elektrokhimiya, Vol. 41, No. 3, 2005, pp. 259–272.Original Russian Text Copyright © 2005 by Medvedev.     

Water polarizability in condensed phase: ab initio evaluation by cluster approach

The polarizability of a water molecule in liquid is evaluated via ab initio and density functional calculations for water clusters. This work has considerably improved our previous effort [J Chem Phys 1999, 110, 11987] to attain quantitative accuracy for polarizability. The calculations revealed that the water polarizability in the liquid is reduced from that in the gaseous phase by 7-9%. These results suggest significant implications for polarizable water models.     

An efficient parallelization scheme for molecular dynamics simulations with many-body, flexible, polarizable empirical potentials: application to water

An efficient parallelization scheme for classical molecular dynamics simulations with flexible, polarizable empirical potentials is presented. It is based on the standard Ewald summation technique to handle the long-range electrostatic and induction interactions. The algorithm for this parallelization scheme is designed for systems containing several thousands of polarizable sites in the simulation box. Its performance is evaluated during molecular dynamics simulations under periodic boundary conditions with unit cell sizes ranging from 128 to 512 molecules employing two flexible polarizable water models [DC(F) and TTM2.1-F] containing 1 and 3 polarizable sites, respectively. The time-to-solution for these two polarizable models is compared with the one for a flexible, pairwise-additive water model (TIP4F). The benchmarks were performed on both shared and distributed memory platforms. As a result of the efficient calculation of the induced dipole moments, a superlinear scaling as a function of the number of the processors is observed. To the best of our knowledge, this is the first reported results of parallel scaling and performance for simulations of liquid water with a polarizable potential under periodic boundary conditions.     

Chemical reactivity of the compressed noble gas atoms and their reactivity dynamics during collisions with protons

Attempts are made to gain insights into the effect of confinement of noble gas atoms on their various reactivity indices. Systems become harder, less polarizable and difficult to excite as the compression increases. Ionization also causes similar effects. A quantum fluid density functional technique is adopted in order to study the dynamics of reactivity parameters during a collision between protons and He atoms in different electronic states for various projectile velocities and impact parameters. Dynamical variants of the principles of maximum hardness, minimum polarizability and maximum entropy are found to be operative.