Charge-on-spring polarizable water models revisited: from water clusters to liquid water to ice

The properties of two improved versions of charge-on-spring (COS) polarizable water models (COS/G2 and COS/G3) that explicitly include nonadditive polarization effects are reported. In COS models, the polarization is represented via a self-consistently induced dipole moment consisting of a pair of separated charges. A previous polarizable water model (COS/B2), upon which the improved versions are based, was developed by Yu, Hansson, and van Gunsteren. To improve the COS/B2 model, which overestimated the dielectric permittivity, one additional virtual atomic site was used to reproduce the water monomer quadrupole moments besides the water monomer dipole moment in the gas phase. The molecular polarizability, residing on the virtual atomic site, and Lennard-Jones parameters for oxygen-oxygen interactions were varied to reproduce the experimental values for the heat of vaporization and the density of liquid water at room temperature and pressure. The improved models were used to study the properties of liquid water at various thermodynamic states as well as gaseous water clusters and ice. Overall, good agreement is obtained between simulated properties and those derived from experiments and ab initio calculations. The COS/G2 and COS/G3 models may serve as simple, classical, rigid, polarizable water models for the study of organic solutes and biopolymers. Due to its simplicity, COS type of polarization can straightforwardly be used to introduce explicit polarization into (bio)molecular force fields.     

A transferable coarse-grained model for hydrogen-bonding liquids

We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations.     

The effect of solvent on the internal rotation of formamide: an ab initio study using a polarizable continuum model

The effect of solvent on the barrier to internal rotation of formamide has been studied using an ab initio 4-3IG method coupled with a polarizable continuum model. The trend of increasing rotation barrier with increasing solvent dielectric constant is reproduced. Conformational free energies were calculated by adding dispersion and cavitation terms to the electrostatic energy.     

Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation

Monte Carlo simulations of liquid methanol were performed using a refined ab initio derived potential which includes polarizability, nonadditivity, and intramolecular relaxation. The results present good agreement between the energetic and structural properties predicted by the model and those predicted by ab initio calculations of methanol clusters and experimental values of gas and condensed phases. The molecular level picture of methanol shows the existence of both rings and linear polymers in the methanol liquid phase.     

Spectroscopic characterization of a molecule with a weak bond: the BrOO radical

Pure rotational spectra of the BrOO radical for the 79Br and 81Br isotopomers have been observed using a Fourier transform microwave spectrometer. The radical was produced in a supersonic jet by discharging a mixture gas containing bromine and oxygen diluted in argon. A-type rotational transitions are observed for N" = 1-5, K(a) = 0 with spin doublings and hyperfine splittings due to the nuclear spin of the bromine atom. High-level ab initio calculations by RCCSD(T) and MRCI have also been performed, and results are compared with the experimental data. Molecular structure of BrOO has been discussed based on the present experimental data, supplemented by the tendency among the halogen peroxide series and the results of the ab initio calculations; the Br-O bond is found to be anomalously long and weak. Systematic comparisons with other halogen peroxides have revealed anomalous nature of the X-O (X = halogen atom) bonds for this series of radicals.     

Continuum treatment of electronic polarization effect

A continuum treatment of electronic polarization has been explored for in molecular mechanics simulations in implicit solvents. The dielectric constant for molecule interior is the only parameter in the continuum polarizable model. A value of 4 is found to yield optimal agreement with high-level ab initio quantum mechanical calculations for the tested molecular systems. Interestingly, its performance is not sensitive to the definition of molecular volume, in which the continuum electronic polarization is defined. In this model, quantum mechanical electrostatic field in different dielectric environments from vacuum, low-dielectric organic solvent, and water can be used simultaneously in atomic charge fitting to achieve consistent treatment of electrostatic interactions. The tests show that a single set of atomic charges can be used consistently in different dielectric environments and different molecular conformations, and the atomic charges transfer well from training monomers to tested dimers. The preliminary study gives us the hope of developing a continuum polarizable force field for more consistent simulations of proteins and nucleic acids in implicit solvents.     

Theoretical and experimental study of the acetohydroxamic acid protonation: the solvent effect

The mechanism of the protonation of acetohydroxamic acid is investigated comparing experimental results and ab initio calculations. Experimentally, the UV spectral curves were recorded at different temperatures, at constant dioxane/water concentration, and at very high concentrations of strong mineral acids. The process is followed by monitoring the changes in the UV curves with increasing acid concentration. The molecular structures and the solvation energies were calculated with the RHF, B3LYP, and MP2 methods. The solvent is treated as a continuum of uniform dielectric constant. The isolated molecule of acetohydroxamic acid exhibits two protonation sites, the carbonyl oxygen and the nitrogen atom. In dioxane/water mixture, the RHF calculations predict the existence of a third cation of low stability, where the proton is bonded to the OH oxygen. With the MP2 ab initio calculations, the free energies of the formation processes in solution of the two most stable cations, CH3COH-NHOH+ (O3H+) and CH3CO-NH2OH+ have been evaluated to be -160.2 kcalmol(-1) and -157.6 kcal mol(-1). The carbonyl site is the most active center in solution and in the gas phase. The carbonyl site is also the most active center in the UV measurements. Experimentally, the ionization constant was found to be pK(O3H+) = -2.21 at 298.15 K, after the elimination of the medium effects using the Cox-Yates equation for hight acidity levels. Experiments and ab initio calculations indicate that K(O3H+) decreases with the temperature.     

Accurate prediction of electron-paramagnetic-resonance tensors for spin probes dissolved in liquid crystals

High-level ab initio g and A tensor components have been calculated for PD-tempone and tempo-palmitate (TP) radical spin probes dissolved in n-pentyl and n-hexyl cyanobiphenyl liquid crystals. Solvent effects have been included in the proposed approach by means of the polarizable continuum model, allowing for solvent anisotropy. An in-depth analysis of the electronic structure of probes was performed to choose a suitable model for TP and make the calculations more accessible. Computed magnetic tensor components have been compared with corresponding values measured in the rigid limit. The quality of the results suggests the use of quantum-mechanical data to determine the order parameter of the nematic from experimental electron-spin resonance measurements.     

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 systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

In this work, parameters are optimized for a charge‐on‐spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico‐chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed‐phase polarizabilities, and starting from the non‐polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure‐liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure‐liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen‐bonding and non‐hydrogen‐bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.     

The DFT investigations of the electron injection in hydrazone-based sensitizers

A brief review of popular polarizable potentials for water, including both those parameterized to fit experimental properties, typically of the liquid, or electronic structure calculations on small clusters, is presented. The recently developed POLIR potential, which was parameterized to reproduce both ab initio calculations on clusters and the experimental liquid IR spectrum, is discussed, and some new results for both clusters and the liquid phase are shown, indicating its transferable nature.     

Sodium chloride in supercritical water as a function of density: potentials of mean force and an equation for the dissociation constant from 723 to 1073 K and from 0 to 0.9 g/cm(3)

The potential of mean force (PMF) of sodium chloride in water has been calculated by using the ab initio classical free-energy perturbation method at five state points: at 973 K with densities of 0.2796, 0.0935, and 0.0101 g/cm (3) and at 723 K with densities of 0.0897 and 0.0098 g/cm (3). The method is based on a QM-MM model in which Na-H 2O, Cl-H 2O, and Na-Cl interactions are calculated by ab initio methods. The water-water interactions are from the polarizable TIP4P-FQ model. The logarithm of the dissociation constant (log K c) has been calculated from the PMF. These predictions, together with experimental measurements, were used to derive an equation for log K c at densities from 0 to 0.9 g/cm (3) and temperatures from 723 to 1073 K, as well as from 600 to 1073 K for densities from 0.29 g/cm (3) to 0.9 g/cm (3). Extrapolation of the present equation below 723 K for densities less than 0.29 g/cm (3) does not fit the experimental results. This is attributed to long-range changes in the local dielectric constant due to the high compressibility. Comparisons with previous predictions and simulations are presented.     

Ab initio parametrized polarizable force field for rutile-type SnO<Subscript>2</Subscript>

We report a new, polarizable classical force field for the rutile-type phase of SnO₂, casserite. This force field has been parametrized using results from ab initio (density functional theory) calculations as a basis for fitting. The force field was found to provide structural, dynamical and thermodynamic properties of tin oxide that compare well with both ab initio and experimental results at ambient and high pressures.     

银表面甲醇氧化反应机理的ab initio计算研究 1: 银表面静态吸附物种的几何构型和吸附性质

本文用原子簇模型(CM)的从头计算方法, 计算了银表面甲醇氧化反应中的静态吸附物种的优化几何构型及吸附性质。计算表明在清洁银表面甲醇、甲醛只存在物理吸附; 当表面存在吸附氧原子时, 甲醇可在银表面形成两种分子态吸附;甲醛与表面羟基OH(a)或氢原子H(a)共存时在银表面能够形成化学吸附, 且CH2O(a)极易与O(a)反应生成深度氧化中间体η^2-甲二氧基; 中间产物甲氧基在无氧的银表面能够形成稳定吸附, 在富氧银表面极易进一步氧化脱氢生成产物甲醛。通过计算与实验结果的对照, 我们对反应机理作了初步讨论。     

Intermolecular interactions between halothane and dimethyl ether: a cryosolution infrared and Ab initio study.

The complex of halothane (CHClBrCF(3)) and dimethyl ether has been investigated experimentally in solutions of liquid krypton using infrared spectroscopy and theoretically using ab initio calculations at the MP2/6-311++G(d,p) level. The formation of a 1:1 complex was experimentally detected. The most stable ab initio geometry found is the one in which the C--H bond of halothane interacts with the oxygen atom of dimethyl ether. The complexes in which the chlorine or the bromine atom of halothane interacts with the oxygen atom of the ether were found to be local energy minima and were less stable by 14.5 and 9.3 kJ mol(-1), respectively, than the global minimum. The formation of a single complex species was observed in the infrared spectra; the standard complexation enthalpy of this complex was determined to be -12.3(8) kJ mol(-1). Analysis of the observed complexation shifts supports the identification of the complex as the hydrogen-bonded species. The C--H stretching vibration of halothane was found to show a redshift upon complexation of 19(2) cm(-1). The infrared intensity ratios epsilon(complex)/epsilon(monomer) for the fundamental and its first overtone were measured to be 6.5(1) and 0.31(1). The frequency shift was analyzed using Morokuma-type analysis, and the infrared intensity ratios were rationalized using a model including the mechanical and electric anharmonicity of the C--H stretching fundamental.     

Determination of structure and energetics for gibbs surface adsorption layers of binary liquid mixture 2. Methanol + water

Vapor/methanol and vapor/methanol-water mixture interfaces have been among the benchmark liquid interfaces under extensive experimental and theoretical investigation. In this report, we studied the orientation, structure and energetics of the vapor/methanol-water interface with newly developed techniques in sum frequency generation vibrational spectroscopy (SFG-VS). Different from the interpretations in previous SFG-VS studies for a more disordered interface at higher bulk methanol concentrations, we found that the methanol-water mixture interface is well ordered in the whole concentration region. We are able to do so because direct polarization null angle (PNA) measurement allowed us to accurately determine the CH3 orientation at the interface and to separate the orientational and interface density contributions to the SFG-VS signal. We found that the CH3 groups at the interface pointed out almost perpendicularly from the interface. We further found that this well-ordered vapor/methanol-water mixture interface has an antiparallel structure. With the double layer adsorption model (DAM) and Langmuir isotherm, the adsorption free energies for the first and second layer are obtained as -1.7 +/- 0.1 kcal/mol and 0.5 +/- 0.4 kcal/mol, respectively. Therefore, the second layer adsorption is slightly negative, and this means that replacement of the second layer water molecule with methanol molecule is energetically unfavorable. Comparing this interface with the vapor/acetone-water mixture interface reported previously, we are able to correlate the second layer adsorption free energy with the work of self-association using the pairwise self- and mutual interaction energies between the water and solute molecules. These results provided detailed microscopic structural evidences for understanding of liquid interfaces.     

Behavior of the Eigen form of hydronium at the air/water interface

Surface affinity of hydro-nium was explored using umbrella sampling molecular dynamics simulations with a refined polarizable potential. The polarizable interaction potential of H(3)O(+) was reparametrized against accurate ab initio calculations for geometries including a water molecule approaching the Eigen cation from its oxygen side. Although there is no true hydrogen bonding with H(3)O(+) acting as an acceptor, respecting in the force field the very shallow ab initio minimum corresponding to this interaction leads to a decrease in surface propensity of hydronium compared to previous results. Qualitatively, the mild surface affinity and strong surface orientation of hydronium is, nevertheless, robustly predicted by various computational approaches, as well as by spectroscopic experiments.     

A polarizable force field for water using an artificial neural network

A force field for liquid water including polarization effects has been constructed using an artificial neural network (ANN). It is essential to include a many-body polarization effect explicitly into a potential energy function in order to treat liquid water which is dense and highly polar. The new potential energy function is a combination of empirical and nonempirical potentials. The TIP4P model was used for the empirical part of the potential. For the nonempirical part, an ANN with a back-propagation of error algorithm (BPNN) was introduced to reproduce the complicated many-body interaction energy surface from ab initio quantum mechanical calculations. BPNN, described in terms of a matrix, provides enough flexibility to describe the complex potential energy surface (PES). The structural and thermodynamic properties, calculated by isobaric-isothermal (constant-NPT) Monte Carlo simulations with the new polarizable force field for water, are compatible with experimental results. Thus, the simulation establishes the validity of using our estimated PES with a polarization effect for accurate predictions of liquid state properties. Applications of this approach are simple and systematic so that it can easily be applied to the development of other force fields besides the water-water system.     

Critical and phase-equilibrium properties of an ab initio based potential model of methanol and 1-propanol using two-phase molecular dynamics simulations

Two-phase molecular dynamics simulations employing a Monte Carlo volume sampling method were performed using an ab initio based force field model parameterized to reproduce quantum-mechanical dimer energies for methanol and 1-propanol at temperatures approaching the critical temperature. The intermolecular potential models were used to obtain the binodal vapor-liquid phase dome at temperatures to within about 10 K of the critical temperature. The efficacy of two all-atom, site-site pair potential models, developed solely from the energy landscape obtained from high-level ab initio pair interactions, was tested for the first time. The first model was regressed from the ab initio landscape without point charges using a modified Morse potential to model the complete interactions; the second model included point charges to separate Coulombic and dispersion interactions. Both models produced equivalent phase domes and critical loci. The model results for the critical temperature, density, and pressure, in addition to the sub-critical equilibrium vapor and liquid densities and vapor pressures, are compared to experimental data. The model's critical temperature for methanol is 77 K too high while that for 1-propanol is 80 K too low, but the critical densities are in good agreement. These differences are likely attributable to the lack of multi-body interactions in the true pair potential models used here.