Nonadditive Monte Carlo Simulation of Liquid Hydrogen Chloride Difference Algorithm and Parallel Implementation

Abstract

This paper continues our Monte Carlo simulation study of liquid hydrogen chloride [1]. The importance of non-additive interactions is carefully analyzed. Computed atom pair correlation functions are compared to neutron scattering experiments [2]. A difference algorithm (“Δ—algorithm”) is developed, which makes non-additive Monte Carlo simulations practicable. We also report an implementation of this algorithm on a transputer network, taking advantage of the inherent parallelism of the Δ — algorithm.     

A Study of Conformational Equilibria in Chain Molecules. I. Liquid n-Butane

Abstract

We have performed molecular dynamics simulations for liquid n-butane in order to understand liquid structures in terms of both inter- and intra-molecular interactions. Each n-butane molecule consists of four sites interacting with LJ potential and only a dihedral angle is taken into account as the internal degree of freedom. The population of gauche conformations with respect to the ideal gas state is found to increase in the liquid state. To investigate how the intermolecular interaction affects the dihedral angle distribution, we also adopt the repulsive LJ potential (RLJ) model. It is found that the nearest neighbor packing of the methyl and/or methylene groups can be approximately represented by using only the repulsive interaction. From the dihedral angle distribution, however, the rate of the shift of RLJ model to gauche is larger than that of LJ model and the attractive force also plays a significant role in the conformational equilibrium.     

Molecular dynamics simulation of the atomistic monolayer structures of N-acyl amino acid-based surfactants

Abstract

Atomic molecular dynamics simulations have been performed on the monolayer systems of N-acyl amino acid-based surfactants. The role of intermolecular hydrogen bonds and ionic side chain length of dicarboxylate surfactants were investigated through radial and spatial distribution functions. It was found that the hydrogen bonding capability between surfactants was the major factor determining the surface area each surfactant could occupy. Tighter packing of surfactants would lead to a weaker interaction with water molecule, and the protonation of carboxylate groups resulted in stronger inter-surfactant interactions. The hydrogen bonds with water molecules were found to prevail between the carboxylate groups, and regular cage-like water distributions surrounding the surfactant headgroups were seen. The introduction of divalent ions leads to a significant increase of counterion binding, and their intramolecular and intermolecular bindings of calcium ions were also well characterised. The intramolecular chelation of calcium ions was found impossible between the carboxylate groups for N-acyl glutamate due to its flexible side chain.     

A combined experimental and computational study on the material properties of shape memory polyurethane

A type of shape memory polyurethane with 60 wt% hard segments (SMPU60) was prepared. Its material properties were tested by dynamic mechanical analysis (DMA) and Instron, and simulated using fully atomistic molecular dynamics (MD). The glass transition temperature (T _g) of SMPU60 determined by DMA is 316 K, which is slightly lower than that estimated through MD simulations (T _g = 328 K) , showing the calculated T _g is in good agreement with experimental data. A complex hydrogen bonding network was revealed with the calculation of radial distribution functions (RDFs). The C═O⋯H bond is the predominant hydrogen-bonding interaction. With increasing temperature, both the hydrogen bonding and the moduli decreased, and the dissociation of intermolecular hydrogen bonding induced the decrease of the moduli.     

Computer Simulation of the Dielectric Properties of Liquid Water

Abstract

Monte Carlo simulations of water in the NVT ensemble using three models (SPC, TIP4P and TIPS2) are reported. The internal energy, dielectric constant, and the site-site radial distribution functions of liquid water (temperature 300 K and mass density 1 gm cc^?1) were calculated and compared with experiment. It was found that of the three intermolecular potential models, SPC gives the best dielectric constant. Since SPC also yields acceptable results for the energy and structure, it is judged to be the best among the three models studied.     

Hydrogen bond analysis of confined water in mesoporous silica using the reactive force field

ABSTRACT

The structural and dynamical properties of water confined in nanoporous silica with a pore diameter of 2.7?nm were investigated by performing large-scale molecular dynamics simulations using the reactive force field. The radial distribution function and diffusion coefficient of water were calculated, and the values at the centre of the pore agreed well with experimental values for real water. In addition, the pore was divided into thin coaxial layers, and the average number of hydrogen bonds, hydrogen bond lifetime and hydrogen bond strength were calculated as a function of the radial distance from the pore central axis. The analysis showed that hydrogen bonds involving silanol (Si–OH) have a longer lifetime, although the average number of hydrogen bonds per atom does not change from that at the pore centre. The longer lifetime, as well as smaller diffusion coefficient, of these hydrogen bonds is attributed to their greater strength.     

Molecular dynamics simulations and 2H NMR study of the GalCer/DPPG lipid bilayer

Molecular dynamics simulations were performed on a two-component lipid bilayer system in the liquid crystalline phase at constant pressure and constant temperature. The lipid bilayers were composed of a mixture of neutral galactosylceramide (GalCer) and charged dipalmitoylphosphatidylglycerol (DPPG) lipid molecules. Two lipid bilayer systems were prepared with GalCer:DPPG ratio 9:1 (10%-DPPG system) and 3:1 (25%-DPPG system). The 10%-DPPG system represents a collapsed state lipid bilayer, with a narrow water space between the bilayers, and the 25%-DPPG system represents an expanded state with a fluid space of approximately 10 nm. The number of lipid molecules used in each simulation was 1024, and the length of the production run simulation was 10 ns. The simulations were validated by comparing the results with experimental data for several important aspects of the bilayer structure and dynamics. Deuterium order parameters obtained from (2)H NMR experiments for DPPG chains are in a very good agreement with those obtained from molecular dynamics simulations. The surface area per GalCer lipid molecule was estimated to be 0.608 +/- 0.011 nm(2). From the simulated electron density profiles, the bilayer thickness defined as the distance between the phosphorus peaks across the bilayer was calculated to be 4.21 nm. Both simulation systems revealed a tendency for cooperative bilayer undulations, as expected in the liquid crystalline phase. The interaction of water with the GalCer and DPPG oxygen atoms results in a strong water ordering in a spherical hydration shell and the formation of hydrogen bonds (H-bonds). Each GalCer lipid molecule makes 8.6 +/- 0.1 H-bonds with the surrounding water, whereas each DPPG lipid molecule makes 8.3 +/- 0.1 H-bonds. The number of water molecules per GalCer or DPPG in the hydration shell was estimated to be 10-11 from an analysis of the radial distribution functions. The formation of the intermolecular hydrogen bonds was observed between hydroxyl groups from the opposing GalCer sugar headgroups, giving an energy of adhesion in the range between -1.0 and -3.4 erg/cm(2). We suggest that this value is the contribution of the hydrogen-bond component to the net adhesion energy between GalCer bilayers in the liquid crystalline phase.     

On the Uniqueness of the Reverse Monte Carlo Simulation for Molecular Liquids

Abstract

A careful analysis of the three dimensional structures of liquid Chlorine produced by the Reverse Monte Carlo (RMC) and Molecular Dynamics (MD) techniques is presented. The analysis allows us to measure the degree of uniqueness between the potential and the atom-atom distribution functions, g _aa(r), in the case of pairwise potentials formed by isotropic and anisotropic site-site interactions. The g _aa(r) obtained from MD simulations are used as ‘experimental’ input data in the RMC procedure and the constraint of rigid molecules is imposed. The particle configurations produced by RMC are then studied by using a recently proposed general method for analysing the local order in liquids. The same analysis applied to the particle configurations produced by the conventional MD simulation yields a set of partial distribution functions which relates the main features of the g _aa(r) to microscopic pair geometries. The comparison between the partial centre-centre g _cc(r) shows that the three dimensional structures, produced by MD and RMC simulations, agree very well when only isotropic site-site interactions act. In this case RMC produces the same radial distribution function g(r, ω₁, ω₂) as that obtained from the original MD configurations; it is therefore a valid tool for deriving a complete information on the physical properties of a fluid. For anisotropic site-site interactions the partial g _cc(r) of MD and RMC differ significantly and show that the three dimensional structures, produced by MD and RMC simulations, differ too. The discrepancies are particularly evident for the T shaped configurations and affect the values of the potential energy. Therefore, even if the potential is purely pairwise additive, the use of the atomic radial distribution function as input data and the imposition of atomic constraints which model the molecules as hard dumbbells are not sufficient to bring the RMC procedure towards the ‘true’ microscopic structure of the liquid; the presence of non central forces between sites disrupts the bijective correspondence between the potential and the g _aa(r).     

Vapour-Liquid Phase Equilibria of n-alkanes by Direct Monte Carlo Simulations

Abstract

We report results of direct Monte Carlo simulations of n-pentane and n-decane at the liquidvapour interface for a number of temperatures. The intermolecular interactions are modeled using the last version of the anisotropic united atom model (AUA4). We have used the local long range correction energy and an algorithm allowing to select randomly with equal probability two different displacements. The liquid and vapour densities are in excellent agreement with experimental data and with those previously calculated using the GEMC method.     

The Calculation of 3D Solubility Parameters Using Molecular Models

Abstract

In this paper we describe the use of molecular mechanics models to examine detailed intermolecular interactions within the liquid state of a common nonionic surfactant system, nonyl phenol ethoxylate (NPE). Using constant energy molecular dynamics simulations we have studied the relative strengths of dispersive interactions versus polar interactions and have estimated three dimensional solubility parameters for NPE systems as a function of temperature and ethylene oxide content. The predictions at 300 K are in good agreement with three dimensional solubility parameters predicted using group contribution tables. Models of the amorphous liquid state were represented by single molecular structures of NPE in a periodic cell. The solubility parameters predicted with these models were in good agreement with those values derived from models having eight NPE molecules packed into a cell with the exception of the electrostatic interactions, which are the most sensitive to system size effects.     

Molecular properties of a bent-core nematic liquid crystal A131 by multi-level theory simulations

ABSTRACT

Multi-level theory simulations have been performed to model a number of important molecular properties of a bent-core nematic liquid crystal (LC) A131. These important properties include molecular conformations, molecular Raman spectra, differential polarisability ratios, molecular crystals packing, atomic LC structures, order parameters, and Raman depolarisation spectra. The simulations contain four theory levels, involving molecular quantum chemistry, molecular crystal packing, super cell density functional based tight binding optimisation, and super cell molecular dynamics calculations. To heat initial optimised super cell structures, molecular dynamics simulations reveal phase transitions to uniaxial and biaxial nematic phases from molecular crystals. LC atomic structures result in direct calculations on order parameters, which can be further applied to computations on Raman depolarisation spectra with differential polarisability ratios, obtained in the molecular quantum chemistry theory level. The good agreement of simulated Raman depolarisation spectra with the experiment provides a detailed analysis on the unusually low values of experimental uniaxial order parameters.     

Docking of a Series of Peptide-Based Interleukin-1β Converting Enzyme Inhibitors with Aspartyl Hemiacetals, α-((2,6-Dichlorobenzoyl)oxy)methyl and (Acyloxy)methyl Ketone Moieties

The enzyme-binding mode of a series of interleukin-1 converting enzyme (ICE) inhibitors has been analysed on the basis of the crystal structure of the complex between hICE and tetrapeptide aldehyde. The conformation of these ligands were explored by performing molecular dynamics simulations at 100 ps. The conformation adopted by these inhibitors was very similar to and could be superimposable onto the regions of crystal structure. The active and the low energy conformers were docked either by grid or manually into the binding site. The analysis of the resulting model indicated that O-benzylacyl group of aspartyl hemiacetals interact with Cys285 and the large substituents: semicarbazone, 2,6-bis(trifluoromethyl) benzoate, other leaving groups of (acyloxy)methyl and -((2,6-dichlorobenzoyl)oxy)methyl ketone series of P1 site protrude from the surface of Cys285 and interact with Val338, which is located below the binding pocket. The hydrogen bonding interaction between -NH of semicarbazone and Cys285 seems to have significant role. The total potential energy including intermolecular interaction energy, consisting of van der Waals and electrostatic energies were calculated. The resulting model is qualitatively consistent with the reported experimental data and can be useful for the design of more potent inhibitors of ICE.Electronic Supplementary Material available.     

Study on properties of liquid ammonia via molecular dynamics simulation based on ABEEMσπ polarisable force field

Abstract

The molecular dynamics simulation has been performed to investigate the charge distribution, structural and dynamical properties of liquid ammonia at 273 K using a polarisable force field of the atom-bond electronegativity equalisation method (ABEEMσπ). One ammonia molecule in this model has eight charge sites, one N atomic site, three H atomic sites, three N–H bond sites and one lone-pair electron site. ABEEMσπ model can present the quantitative site charges of molecular ammonias in liquid and their changing in response to their surroundings. The radial distribution functions and dynamical properties are in fair agreement with the available experimental data. The first peak of g_NN(r) appears at N–N distance of ~3.50 ± 0.05 Å where most hydrogen bonds are formed. The average coordination number of the first shell is 13.0 ± 0.1 among which a central ammonia molecule intimately connects 3 ~ 4 ammonia molecules by hydrogen bonds. The power spectrum shows the vibrations of hydrogen bonds. For a reference, a simple estimation of the average hydrogen bonding energy in liquid ammonia is 6.5 ± 0.1 kcal/mol larger than 3.8 ± 0.3 kcal/mol in dimer ammonia. Our simulation results provide more detailed information about liquid ammonia.     

Hydrogen-bonding propensities of sphingomyelin in solution and in a bilayer assembly: a molecular dynamics study

Sphingomyelin is enriched within lipid microdomains of the cell membrane termed lipid rafts. These microdomains play a part in regulating a variety of cellular events. Computer simulations of the hydrogen-bonding properties of sphingolipids, believed to be central to the organization of these domains, can delineate the possible molecular interactions that underlie this lipid structure. We have therefore used molecular dynamics simulations to unravel the hydrogen-bonding behavior of palmitoylsphingomyelin (PSM). A series of eight simulations of 3 ns each of a single PSM molecule in water showed that the sphingosine OH and NH groups can form hydrogen bonds with the phosphate oxygens of their own polar head, in agreement with NMR data. Simulations of PSM in a bilayer assembly were carried out for 8 ns with three different force field parameterizations. The major physico-chemical parameters of the simulated bilayer agree with those established experimentally. The sphingosine OH group was mainly involved in intramolecular hydrogen bonds, in contrast to the almost exclusive intermolecular hydrogen bonds formed by the amide NH moiety. During the bilayer simulations the intermolecular hydrogen bonds among lipids formed a dynamic network characterized by the presence of hydrogen-bonded lipid clusters of up to nine PSM molecules.     

A molecular dynamics study of liquid aliphatic alcohols: simulation of density and self-diffusion coefficient using a modified OPLS force field

A set of 13 aliphatic alcohols was modelled by molecular dynamics simulations at temperatures from 288 to 338 K using the optimised potential for liquid simulations (OPLS) united-atom force field, the OPLS all-atom force field and the OPLS all-atom force field with modified partial charges of the hydroxyl group. The set includes primary and secondary alcohols, and mono-, di- and trialcohols, and covers a broad range of polarities from log P = ? 0.74 (methanol) to log P = 2.9 (octanol). The density, the radial distribution function, the self-diffusion coefficient and the dielectric constant were evaluated. A long equilibration time of at least 50 ns and a large size of the molecular system of more than 75,000 atoms were used. Except for glycerol, the OPLS all-atom force field reliably reproduced the experimentally determined density with deviations of less than 4% over the whole temperature range. In contrast, the modelled self-diffusion coefficient deviated from its experimental value by up to 55%. To modify the force field, the partial charges of the hydroxyl group were varied by up to 3%. Using the modified OPLS force field, the deviation of the self-diffusion coefficients from their experimental values decreased to less than 19%, while the densities changed by less than 1%.     

Studying the structure of single-component ceramide bilayers with molecular dynamics simulations using different force fields

Molecular dynamics simulations are performed on a lipid bilayer that consists of ceramide NS 24:0 in an attempt to examine several structural and physicochemical properties of the specific system. The simulations are carried out with five different force fields (OPLS, GROMOS, BERGER, CHARMM and GAFF) in order to evaluate and compare their performance in modelling lipid systems that contain ceramides. The examined properties include bilayer thickness, chain tilt, density profiles, order parameters, chain conformation, area per lipid and (intermolecular or intramolecular) hydrogen bonding between the head groups. Special focus is given to the lateral lipid arrangement. To this purpose, a method is proposed that utilises the radial distribution functions of the alkyl chains to derive quantitative information about the lateral lipid packing. In most cases, all force fields lead to similar results. For a few properties (e.g. intramolecular hydrogen bonding), there is some discrepancy between the force fields but the lack of respective experimental data does not allow an unambiguous conclusion on which force field is the most reliable.     

Hydration of cis and trans N-methylformamide as revealed by the use of 17O-NMR,molecular mechanics,and ab initio calculations

The solvation of cis and trans N-methylformamide (NMF) by water was investigated using a combination of ¹⁷O-nmr spectroscopy, classical molecular mechanics [MM2(77) and MM2(87)] force field, and ab initio 4-31G* gradient optimization calculations. In dilute aqueous solution, the ¹⁷O-nmr spectra of NMF indicate strong shielding by 66.9 and 66.1 ppm for the cis and trans amide oxygens, respectively, compared to those values obtained in dilute toluene solution. This demonstrates that both isomers are equally solvated by molecules of water, which are further hydrogen bonded to molecules of water of the bulk solvent. Molecular mechanics simulations were carried out for cis and trans NMF in a cluster of water molecules. Radial distribution functions show structural contacts by several water molecules at the amide CO and NH group, which are significantly more pronounced with MM2 (87) calculations. Ab initio 4-31G* gradient optimization calculations on the supermolecule trans NMF-(H₂O)₃ indicates the presence of more than two hydrogen-bond contacts at the carbonyl oxygen. This is in agreement with MM2 calculations and provides further evidence for multiple acceptor properties of the amide oxygen and an out of the amide plane arrangement of the bound molecules of water. Comparison of the integration data to the first radial distribution function (rdf) minima shows that the local solvation of the CO and NH groups is very similar for both cis and trans isomers. The intermolecular geometric parameters of the supermolecule trans NMA–(H₂O)₃ and the first rdf maxima resulting from MM2 (87) and MM2 (77) calculations are compared with distribution of water molecules around the CO and NH groups of peptides and proteins resulting from x-ray and neutron diffraction experiments. The rdfs involving the methyl group of NMF demonstrate the nonrandom distribution of solvent sites with first maxima in reasonable agreement with distribution of water molecules around the apolar side chain of amino acid residues in proteins. © 1995 John Wiley & Sons, Inc.     

A New Potential Model for Carbon Dioxide from AB Initio Calculations

Abstract

Ab initio quantum chemical calculations have been carried out for carbon dioxide dimer and the results have been used to establish potential functions usable in molecular simulations. Since the intermolecular interaction in carbon dioxide is fairly weak, careful treatment is required: this study uses 6–31G* basis set and takes electron correlations by the 2nd order Møller-Plesset theory into account. The potential energy surface is elucidated using the four representative relative configurations of the dimer. A new potential function model has been proposed on the basis of these ab initio data. In the super-critical region, this model is used to calculate the PVT relation of carbon dioxide fluid by the Monte Carlo simulations and confirmed to reproduce reasonably well the experimental isotherms.     

Using DL_POLY to study the sensitivity of liquid structure to potential parameters

Two case studies are presented showing the local structure in liquids and how it responds to changes in the intermolecular potential. The idea is to use realistic and unrealistic potentials in order to determine the sensitivity of local liquid structure to potential parameters. The first case study concerns two families of modified water models. In the “hybrid” family, the hydrogen bond strength is reduced, but the geometry kept constant; in the second family, the molecular geometry is changed by reducing the bond angle, keeping a constant molecular dipole moment. The local structure is measured by radial distribution functions, three-dimensional probability distribution functions and three-body angular correlations. The second case study concerns the ionic liquid dimethylimidazolium chloride ([C₁mim]Cl). The effect of reducing the hydrogen bonding potential of the cations while maintaining their charge is examined.