Temperature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations

We applied the multibaric-multithermal (MUBATH) molecular dynamics (MD) algorithm to an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of conformational space and sampled the states of PII, C5, alphaR, alphaP, alphaL, and C7(ax). On the other hand, the conventional isobaric-isothermal simulation was trapped in local-minimum free-energy states and sampled only a few of them. We calculated the partial molar enthalpy difference DeltaH and partial molar volume difference DeltaV among these states by the MUBATH simulation using the AMBER parm99 and AMBER parm96 force fields and two sets of initial conditions. We compared these results with those from Raman spectroscopy experiments. The Raman spectroscopy data of DeltaH for the C5 state against the PII state agreed with both MUBATH data with the AMBER parm96 and parm99 force fields. The partial molar enthalpy difference DeltaH for the alphaR state and the partial molar volume difference DeltaV for the C5 state by the Raman spectroscopy agreed with those for the AMBER parm96 force field. On the other hand, DeltaV for the alphaR state by the Raman spectroscopy was consistent with our AMBER-parm99 force-field result. All the experimental results fall between those of simulations using AMBER parm96 and parm99 force fields, suggesting that the ideal force-field parameters lie between those of AMBER parm96 and parm99.     

Composition dependence of glass transition temperature of sulfonated-polystrene ionomers

The glass transition temperatures of alkali (Na, K, Rb, Cs) and alkaline-earth (Ba, Sr, Ca, Mg) ionomers of sulfonated polystyrenes (PSSA) with 3.4, 6.9, 12.7, and 16.7% of the styrene moieties sulfonated are reported. For the alkali-metal PSSA ionomers, T_g depends on the degree of sulfonation, at least up to 13%, but not strongly on the nature of the cation. For the alkaline-earth analogs T_g does not depend strongly on either the cation or the degree of sulfonation until the 16.7% level is reached. These and other reported data are discussed in terms of the role of cations in determining morphology.     

Gas diffusion in glasses via a probabilistic molecular dynamics

A probabilistic protocol which makes possible the calculation of the diffusivity of light gases in amorphous materials from limited Monte Carlo and molecular dynamics data is presented. Diffusion coefficients are calculated for helium and methane in polystyrene, and for helium, neon, and methane in three pairs of polysulfone isomers. Results include diffusion coefficients as small as 10(-9) cm2/s and are in good agreement with results obtained from traditional molecular dynamics and with available experimental data.     

Kinetics and dynamics in physisorption of CH3Cl on HOPG: surface temperature and molecular orientation dependence

We report a study of kinetics and dynamics in physisorption of CH(3)Cl on a highly-oriented pyrolytic graphite (HOPG). Thermal energy atom scattering (TEAS) was used to probe the kinetics of thermal CH(3)Cl adsorption on HOPG during the coverage evolution. The desorption energy of CH(3)Cl on HOPG changes from 0.25 to 0.30 eV with increasing surface coverage, suggesting the attractive interaction between CH(3)Cl molecules on the surface. On the other hand, the oriented molecular beam scattering was used to monitor the dynamical interaction of CH(3)Cl with HOPG at zero coverage, demonstrating that the CH(3)Cl scattering intensity depends on the molecular orientation of the incident CH(3)Cl. The observed steric preference is not sensitive to the surface temperature. These results suggest that the moderate anisotropy in the interaction potential induces the molecular-orientation dependence of energy dissipation during the transient trapping into the physisorption well.     

A molecular dynamics computer simulation study of the temperature dependence of hydration of 1,4-dioxane and 1,3-dioxane

This paper describes a study of the hydration of 1,3-dioxane and 1,4-dioxane at two different temperatures using different molecular dynamics (MD) computer simulation techniques. Three major conclusions have been drawn. Firstly, the simulations of 1,4-dioxane—water and 1,3-dioxane—water at constant pressure lead essentially to the same conclusions as earlir MD studies at constant volume. Secondly, the numerical values of dynamic properties depend critically on the density of the system. Simulations at constant pressure provide densities which are dependent on the periodicity requirement imposed on the system by the periodic boundary conditions. The smaller the periodic box, the stronger this effect is. Thirdly, in 1,4-dioxane—water an increase in temperature results in an enhanced mobility of water molecules in the solvation shell, whereas in the case of 1,3-dioxane—water these water molecules become more strongly bound by the solute. This effect is entirely due to a reduction of the mobility of water molecules in the 1,3-dioxane oxygen hydration subshells. The contrasting behavior is explained in terms of a situation where solvent—solvent interactions dominate solute—solvent interactions in 1,4-dioxane—water at both temperatures and in 1,3-dioxane—water at the lower temperature, while the opposite situation holds for 1,3-dioxane—water at the higher temperature.     

Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations

The temperature dependence of thermodynamic quantities, such as heat capacity, entropy and free enthalpy, may be obtained by using well-known equations that relate these quantities to the enthalpy of the molecular system of interest at a range of temperatures. In turn, the enthalpy of a molecular system can be estimated from molecular dynamics simulations of an appropriate model. To demonstrate this, we have investigated the temperature dependence of the enthalpy, heat capacity, entropy and free enthalpy of a system that consists of a beta-heptapeptide in methanol and have used the statistical mechanics relationships to describe the thermodynamics of the folding/unfolding equilibrium of the peptide. The results illustrate the power of current molecular simulation force fields and techniques in establishing the link between thermodynamic quantities and conformational distributions.     

Simulation analysis of the temperature dependence of lignin structure and dynamics

Lignins are hydrophobic, branched polymers that regulate water conduction and provide protection against chemical and biological degradation in plant cell walls. Lignins also form a residual barrier to effective hydrolysis of plant biomass pretreated at elevated temperatures in cellulosic ethanol production. Here, the temperature-dependent structure and dynamics of individual softwood lignin polymers in aqueous solution are examined using extensive (17 μs) molecular dynamics simulations. With decreasing temperature the lignins are found to transition from mobile, extended to glassy, compact states. The polymers are composed of blobs, inside which the radius of gyration of a polymer segment is a power-law function of the number of monomers comprising it. In the low temperature states the blobs are interpermeable, the polymer does not conform to Zimm/Stockmayer theory, and branching does not lead to reduction of the polymer size, the radius of gyration being instead determined by shape anisotropy. At high temperatures the blobs become spatially separated leading to a fractal crumpled globule form. The low-temperature collapse is thermodynamically driven by the increase of the translational entropy and density fluctuations of water molecules removed from the hydration shell, thus distinguishing lignin collapse from enthalpically driven coil-globule polymer transitions and providing a thermodynamic role of hydration water density fluctuations in driving hydrophobic polymer collapse. Although hydrophobic, lignin is wetted, leading to locally enhanced chain dynamics of solvent-exposed monomers. The detailed characterization obtained here provides insight at atomic detail into processes relevant to biomass pretreatment for cellulosic ethanol production and general polymer coil-globule transition phenomena.     

Langevin model of the temperature and hydration dependence of protein vibrational dynamics

The modification of internal vibrational modes in a protein due to intraprotein anharmonicity and solvation effects is determined by performing molecular dynamics (MD) simulations of myoglobin, analyzing them using a Langevin model of the vibrational dynamics and comparing the Langevin results to a harmonic, normal mode model of the protein in vacuum. The diagonal and off-diagonal Langevin friction matrix elements, which model the roughness of the vibrational potential energy surfaces, are determined together with the vibrational potentials of mean force from the MD trajectories at 120 K and 300 K in vacuum and in solution. The frictional properties are found to be describable using simple phenomenological functions of the mode frequency, the accessible surface area, and the intraprotein interaction (the displacement vector overlap of any given mode with the other modes in the protein). The frictional damping of a vibrational mode in vacuum is found to be directly proportional to the intraprotein interaction of the mode, whereas in solution, the friction is proportional to the accessible surface area of the mode. In vacuum, the MD frequencies are lower than those of the normal modes, indicating intramolecular anharmonic broadening of the associated potential energy surfaces. Solvation has the opposite effect, increasing the large-amplitude vibrational frequencies relative to in vacuum and thus vibrationally confining the protein atoms. Frictional damping of the low-frequency modes is highly frequency dependent. In contrast to the damping effect of the solvent, the vibrational frequency increase due to solvation is relatively temperature independent, indicating that it is primarily a structural effect. The MD-derived vibrational dynamic structure factor and density of states are well reproduced by a model in which the Langevin friction and potential of mean force parameters are applied to the harmonic normal modes.     

The temperature dependence of the electron mobility in molecular crystals

We show that a hopping model may explain the experimental temperature dependence of the electron mobility in molecular crystals. The flat, higher temperature portion is obtained if anharmonic effects are included in a simple manner. The low temperature part is obtained if coherent effects are added to the diffusional ones.     

The mixed alkali effect in ionically conducting glasses revisited: a study by molecular dynamics simulation

When more than two kinds of mobile ions are mixed in ionic conducting glasses and crystals, there is a non-linear decrease of the transport coefficients of either type of ion. This phenomenon is known as the mixed mobile ion effect or Mixed Alkali Effect (MAE), and remains an unsolved problem. We use molecular dynamics simulation to study the complex ion dynamics in ionically conducting glasses including the MAE. In the mixed alkali lithium-potassium silicate glasses and related systems, a distinct part of the van Hove functions reveals that jumps from one kind of site to another are suppressed. Although, consensus for the existence of preferential jump paths for each kind of mobile ions seems to have been reached amongst researchers, the role of network formers and the number of unoccupied ion sites remain controversial in explaining the MAE. In principle, these factors when incorporated into a theory can generate the MAE, but in reality they are not essential for a viable explanation of the ion dynamics and the MAE. Instead, dynamical heterogeneity and "cooperativity blockage" originating from ion-ion interaction and correlation are fundamental for the observed ion dynamics and the MAE. Suppression of long range motion with increased back-correlated motions is shown to be a cause of the large decrease of the diffusivity especially in dilute foreign alkali regions. Support for our conclusion also comes from the fact that these features of ion dynamics are common to other ionic conductors, which have no glassy networks, and yet they all exhibit the MAE.     

不同温度下熔融NaCl的分子动态学计算机模拟

用分子动态学方法对不同温度下的熔融NaCl进行了模拟计算, 得到了被模拟系统的偏径向分布函数、结构因子、配位数、马德隆常数以及Na^+和Cl^-的自扩散系数等。计算值与实验值大体符合。据此,还讨论了熔体的结构。     

Tight-binding molecular dynamics simulation of ZnSe liquid within the local environment dependence

We investigate the structural, electronic and dynamical properties of ZnSe liquid using tight-binding molecular dynamics (TBMD) simulations. We report the TBMD calculations for the solid and liquid forms of the ZnSe compound. To produce more realistic results the TB model includes the local environment dependence in the Hamiltonian matrix at finite temperature for ZnSe. To further demonstrate the efficiency of the TBMD approach, we present results for finite temperature physical properties of ZnSe liquid. We are able to show good agreement with experiment for the atomic mean-squared displacement and melting point.     

Molecular dynamics studies of ionically conducting glasses and ionic liquids: wave number dependence of intermediate scattering function

Dynamical heterogeneity is a key feature to characterize both acceleration and slowing down of the dynamics in interacting disordered materials. In the present work, the heterogeneous ion dynamics in both ionically conducting glass and in room temperature ionic liquids are characterized by the combination of the concepts of Lévy distribution and multifractality. Molecular dynamics simulation data of both systems are analyzed to obtain the fractional power law of the k-dependence of the dynamics, which implies the Lévy distribution of length scale. The multifractality of the motion and structures makes the system more complex. Both contributions in the dynamics become separable by using g(k,t) derived from the intermediate scattering function, F(s)(k,t). When the Lévy index obtained from F(s)(k,t) is combined with fractal dimension analysis of random walks and multifractal analysis, all the spatial exponent controlling both fast and slow dynamics are clarified. This analysis is generally applicable to other complex interacting systems and is deemed beneficial for understanding their dynamics.     

Temperature dependence of dimerization and dewetting of large-scale hydrophobes: a molecular dynamics study

We studied by molecular dynamics simulations the temperature dependence of hydrophobic association and drying transition of large-scale solutes. Similar to the behavior of small solutes, we found the association process to be characterized by a large negative heat capacity change. The origin of this large change in heat capacity is the high fragility of hydrogen bonds between water molecules at the interface with hydrophobic solutes; an increase in temperature breaks more hydrogen bonds at the interface than in the bulk. With increasing temperature, both entropy and enthalpy changes for association strongly decrease, while the change in free energy weakly varies, exhibiting a small minimum at high temperatures. At around T=Ts=360 K, the change in entropy is zero, a behavior similar to the solvation of small nonpolar solutes. Unexpectedly, we find that at Ts, there is still a substantial orientational ordering of the interfacial water molecules relative to the bulk. Nevertheless, at this point, the change in entropy vanishes due to a compensating contribution of translational entropy. Thus, at Ts, there is rotational order and translational disorder of the interfacial water relative to bulk water. In addition, we studied the temperature dependence of the drying-wetting transition. By calculating the contact angle of water on the hydrophobic surface at different temperatures, we compared the critical distance observed in the simulations with the critical distance predicted by macroscopic theory. Although the deviations of the predicted from the observed values are very small (8-23%), there seems to be an increase in the deviations with an increase in temperature. We suggest that these deviations emerge due to increased fluctuations, characterizing finite systems, as the temperature increases.     

Anarchy in the solid state: structural dependence on glass-forming ability in triazine-based molecular glasses

We have recently shown that molecular glasses, small molecules capable of readily forming glassy solids as opposed to crystals, can be designed by exploiting molecular association through strong and directional intermolecular interactions, as exemplified by several members of the bis(mexylamino)triazine family. Herein, 43 new bis(mexylamino)triazine derivatives were synthesized, 31 of which have been found to spontaneously form glassy phases and did not crystallize upon heating.     

Role of hydrogen bonds in the fast dynamics of binary glasses of trehalose and glycerol: a molecular dynamics simulation study

Trehalose-glycerol mixtures are known to be effective in the long time preservation of proteins. However, the microscopic mechanism of their effective preservation abilities remains unclear. In this article we present a molecular dynamics simulation study of the short time, less than 1 ns, dynamics of four trehalose-glycerol mixtures at temperatures below the glass transition temperature. We found that a mixture of 5% glycerol and 95% trehalose has the most suppressed short time dynamics (fast dynamics). This result agrees with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured via neutron scattering, and correlates with the experimentally observed enhancement of the stability of some enzymes at this particular concentration. Our microscopic analysis suggests that the formation of a robust intermolecular hydrogen bonding network is most effective at this concentration and is the main mechanism for the suppression of the fast dynamics.     

A molecular dynamics study and molecular level explanation of pressure dependence of ionic conductivity of potassium chloride in water

Experimental ionic conductivity of different alkali ions in water shows markedly different dependences on pressure. Existing theories such as that of Hubbard-Onsager are unable to explain these dependences on pressure of the ionic conductivity for all ions. We report molecular dynamics investigation of potassium chloride solution at low dilution in water at several pressures between 1 bar and 2 kbar. Two different potential models have been employed. One of the models successfully reproduces the experimentally observed trend in ionic conductivity of K(+) ions in water over the 0.001-2 kbar range. We also propose a theoretical explanation, albeit at a qualitative level, to account for the dependence of ionic conductivity on pressure in terms of the previously studied Levitation Effect. It also provides a microscopic picture in terms of the pore network in liquid water.