Molecular dynamics simulation of the reciprocal fused LiF–KBr mixture: local structure and self-diffusion coefficients

This paper describes the molecular dynamics simulation of the reciprocal fused LiF–KBr mixture, which is located above the critical mixing point, in the temperature range 1280–1450 K. The first coordination sphere is found to form as follows: a smaller ion is formed around a smaller counter-ion, and a larger ion is formed around a larger counter-ion. The calculated concentration dependence of the self-diffusion coefficients and the radial distribution functions of all ion pairs indicate that the degree of association of the Li–F pair increases as the lithium fluoride fraction in the mixture decreases.     

On the Physical Basis of the Amino Acid Polar Requirement

Understanding how codons became associated with their specific amino acids is fundamental to deriving a theory for the origin of the genetic code. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and nucleobases that may have played a role in establishing the genetic code. Through these experiments it was found that a property of amino acids called the polar requirement (PR) is correlated with the organization of the codon table. No other property of amino acids has been found that correlates with the codon table as well as PR, indicating that PR is uniquely related to the modern genetic code. Using molecular dynamics simulations of amino acids in solutions of water and dimethylpyridine used to experimentally measure PR, we show that variations in the partitioning between the two phases as described by radial distribution functions correlate well with the measured PRs. Partition coefficients based on probability densities of the amino acids in each phase have the linear behavior with base concentration as suggested by PR experiments.     

Structural and dynamical properties predicted by reactive force fields simulations for four common pure fluids at liquid and gaseous non-reactive conditions

Four common pure fluids were chosen to elucidate the reliability of reactive force fields in estimating bulk properties of selected molecular systems: CH₄, H₂O, CO₂ and H₂. The pure fluids are not expected to undergo chemical reactions at the conditions chosen for these simulations. The ‘combustion’ ReaxFF was chosen as reactive force field. In the case of water, we also considered the ‘aqueous’ ReaxFF model. The results were compared to data obtained implementing popular classic force fields. In the gas phase, it was found that simulations conducted using the ‘combustion’ ReaxFF formalism yield structural properties in reasonable good agreement with classic simulations for CO₂ and H₂, but not for CH₄ and H₂O. In the liquid phase, ‘combustion’ ReaxFF simulations reproduce reasonably well the structure obtained from classic simulations for CH₄, degrade for CO₂ and H₂, and are rather poor for H₂O. In the gas phase, the simulation results are compared to experimental second virial coefficient data. The ‘combustion’ ReaxFF simulations yield second virial coefficients that are not sufficiently negative for CH₄ and CO₂, and slightly too negative for H₂. The ‘combustion’ ReaxFF parameterisation induces too strong an effective attraction between water molecules, while the ‘aqueous’ ReaxFF yields a second virial coefficient that is in reasonable agreement with experiments. The ‘combustion’ ReaxFF parameterisation yields acceptable self-diffusion coefficients for gas-phase properties of CH₄, CO₂ and H₂. In the liquid phase, the results are good for CO₂, while the self-diffusion coefficient predicted for liquid CH₄ is slower, and that predicted for liquid H₂ is about nine times faster than those expected based on classic simulations. The ‘aqueous’ ReaxFF parameterisation yields good results for both the structure and the diffusion of both liquid and vapour water.     

Influence of the conservative force on transport coefficients in the DPD method

The transport coefficients of a dissipative particle dynamics system are investigated numerically taking into account the conservative force. The influence of the conservative force parameter on kinetic and dissipative viscosity is considered and compared with theoretical predictions. The analytical solution of the potential term that arises from the conservative force is generally very complicated; therefore, this term has been ignored in most previous work and deemed negligible. In the present work, an expression for the effect of the conservative force on potential viscosity is semi-empirically obtained revealing the dependence of the latter on various parameters such as conservative force strength, density number and temperature. This relation offers a proper approximation of conservative force impact on potential viscosity.     

Rotation-Vibration Coupling in Liquid Water Investigated by Molecular Dynamics Simulation

Abstract

The standard rotation-vibration decoupling approximation for liquid water is tested using a method based on the split of the molecular dipole fluctuation correlation function into pure rotational, pure vibrational and crossed terms. Our results corroborate the total decoupling between vibrational and rotational motions in liquid water at ambient conditions and provide a tool able to test the reliability of this approximation for molecular liquids at different states.     

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.     

Differences in the adsorption and diffusion behaviour of water and non-polar gases in nanoporous carbon: role of cooperative effects of pore confinement and hydrogen bonding

We investigate the effect of pore confinement and molecular geometry on the adsorption and self-diffusion of H₂O, CO₂, Ar, CH₄, C₃H₆, SF₆ and C₅H₁₂, in a realistic model of nanoporous silicon carbide derived carbon (SiC-DC), constructed using hybrid reverse Monte Carlo simulation. Adsorption isotherms, adsorbate–adsorbate and adsorbate–adsorbent contributions to the isosteric heat of adsorption are determined to study the effect of pore confinement, microporosity and molecular geometry on adsorption of these gases. We describe the cooperative effect of pore confinement and hydrogen bonding on the formation of water clusters and anomalous adsorption behaviour of water compared with non-polar gases. We find that, in contrast to literature results based on the slit-pore model, pore-filling does not occur below the saturation pressure in hydrophobic amorphous carbon materials such as SiC-DC and activated carbon fibre. We also compare self-diffusivities and activation energy barriers of water and non-polar gases in the microporous structure of SiC-DC to identify underlying correlations with molecular properties. We demonstrate that the self-diffusivity of water deviates considerably from the correlation between diffusivity and molecular kinetic diameter observed for non-polar gases. This is attributed to the reduced diffusivity of water, and its relatively large energy barrier at high loadings despite its small kinetic diameter, which is due to the blocking effect of water clusters at pore entries.     

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%.     

Self-Diffusion in Electrostatically Stabilized Colloidal Suspensions Using Brownian Dynamics

Abstract

Brownian dynamics is applied to suspended colloidal particles interacting through a screened Coulombic pair potential in the dilute region where the hydrodynamics is approximated by Stokes drag. Calculated properties include the osmotic pressure, the radial distribution function, and the self-diffusion coefficient. Verification is obtained by comparing the results to independently evaluated properties. Self-diffusion coefficicents are compared to approximate theories in the literature. The self-diffusion coefficient is observed to depend strongly on the local structure but only slightly on the longer range structure.     

Reverse Monte Carlo Simulation: A New Technique for the Determination of Disordered Structures

Abstract

We have developed a new technique, based on the standard Monte Carlo simulation method with Markov chain sampling, in which a set of three dimensional particle configurations are generated that are consistent with the experimentally measured structure factor. A(Q), and radial distribution function, g(r), of a liquid or other disordered system. Consistency is determined by a standard χ² test using the experimental errors. No input potential is required, we present initial results for liquid argon. Since the technique can work directly from the structure factor it promises to be useful for modelling the structures of glasses or amorphous materials. It also has other advantages in multicomponent systems and as a tool for experimental data analysis.     

The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol.     

Investigating water and framework dynamics in pillared MOFs

In this work we highlight the use of molecular simulation to study the behaviour of water inside isostructural Zn-DMOF structures. Among the Zn-DMOF structures, the parent DMOF, and the DMOF-DM and DMOF-TF variants are known to be less stable than the DMOF-A and DMOF-TM structures in the presence of water. We apply tools such as radial distribution functions, rotational auto-correlation functions and the visualisation of adsorbate density distributions to investigate the differences in water behaviour within these structures. We also study properties that are inherent to the frameworks themselves such as thermal expansion and ligand flexibility. Our results indicate that water is only able to get 0.5 Å closer to the metal hydrolysis site in the water unstable structures than in the more water stable structures. The results can be somewhat sensitive to the details of the modelling of the electrostatic potential energy surface and, for dynamical properties, modelling of framework flexibility.     

Molecular Dynamics Simulations with Interaction Potentials Including Polarization Development of a Noniterative Method and Application to Water

A general method is suggested for the implementation of polarization in molecular dynamics simulations of small molecules. Induced dipole moments are evaluated on selected polarizability centers and represented by separation of charges. The positive polarization charges reside on the selected atoms. The negative polarization charges are treated as additional particles. The positions of these polarization charges are determined from the electrical fields due to the permanent charges of the system. Thus the induction is treated explicitly, while the higher order contributions, the polarization due to induced dipoles, are taken into account in an average way by modification of potential parameters. The forces can be evaluated for the new charge distribution in the conventional way. As an illustration of this approach initial results are reported for the development of a polarizable water model. The higher order polarization is treated in an average way by slight increase of the permanent charges as compared to the values that would give the gas phase dipole moment. The increase in CPU time is comparable to the addition of one atom per polarizable center.     

Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis

Data from polyphenylalanine [poly(Phe)] synthesis determination in the presence and in the absence of erythromycin have been used in conjunction with Molecular Dynamics Simulation analysis, in order to localize the functional sites affected by mutations of Thermus thermophilus ribosomal protein L4 incorporated in Escherichia coli ribosomes. We observed that alterations in ribosome capability to synthesize poly(Phe) in the absence of erythromycin were mainly correlated to shifts of A2062 and C2612 of 23S rRNA, while in the presence of erythromycin they were correlated to shifts of A2060 and U2584 of 23S rRNA. Our results suggest a means of understanding the role of the extended loop of L4 ribosomal protein in ribosomal peptidyltransferase center.     

Rare events out of equilibrium: mobility through the liquid–liquid interface

Transition state theory provides a well established means to compute the rate at which rare events occur; however, this is strictly an equilibrium approach. Here we consider a nonequilibrium problem of this nature in the form of transport through a liquid–liquid interface. When two immiscible liquids are coexisting in equilibrium, there will be a certain amount of mixing between the two phases, resulting in a finite linear mobility across the liquid–liquid interface. We derive an exact relationship between the mobility and the local diffusion in the direction perpendicular to the interface. We compute the mobility using both nonequilibrium molecular dynamics and a variety of linear response type approaches, with accurate agreement being obtained for the best of these. Our analysis makes it clear how the local diffusion is influenced by the inhomogeneities of the interface, even when at a distance from it. This nonlocal character to the mobility has not been appreciated before and results in a strong variation in the local diffusion, which is formally coupled to the variation in the potential of mean force. The nonlocal aspect of the diffusion requires the velocity autocorrelation function to be integrated out to far longer times than is the case for homogeneous liquids, and requires special care with regard to the choice of numerical approach.