Modeling benzene with single-site potentials fromab initiocalculations: A step toward hybrid models of complex molecules

Rupture mechanism of liquid crystal thin films realized by large-scale molecular simulations

The ability of liquid crystal (LC) molecules to respond to changes in their environment makes them an interesting candidate for thin film applications, particularly in bio-sensing, bio-mimicking devices, and optics. Yet the understanding of the (in)stability of this family of thin films has been limited by the inherent challenges encountered by experiment and continuum models. Using unprecedented large-scale molecular dynamics (MD) simulations, we address the rupture origin of LC thin films wetting a solid substrate at length scales similar to those in experiment. Our simulations show the key signatures of spinodal instability in isotropic and nematic films on top of thermal nucleation, and importantly, for the first time, evidence of a common rupture mechanism independent of initial thickness and LC orientational ordering. We further demonstrate that the primary driving force for rupture is closely related to the tendency of the LC mesogens to recover their local environment in the bulk state. Our study not only provides new insights into the rupture mechanism of liquid crystal films, but also sets the stage for future investigations of thin film systems using peta-scale molecular dynamics simulations.

Molecular dynamics simulations of the liquid-crystal phases of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine and 5-(4-butyloxyphenyl)-2-octyloxypyrimidine

In this paper, molecular dynamics simulations are employed to study the liquid-crystal phases of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine and 5-(4-butyloxyphenyl)-2-octyloxypyrimidine. Both mesogens consist of aromatic phenyl-pyrimidine cores in between two identical alkoxy tails, but they differ in the preferred core conformation. The ab initio-based derivation of suitable molecular models is discussed in detail, with particular emphasis on capturing proper ring-ring interactions. The presence of ring quadrupoles in the molecular model is shown to be essential to the correct reproduction of the experimentally observed phases. Simulations of these fluids at various temperatures are performed and order, for the aromatic core and the flexible tails, is analyzed. To differentiate smectic- A from smectic- C phases, intermolecular structure is divided into contributions parallel and perpendicular to the director and layer normal.

Generalized coarse-grained model based on point multipole and Gay-Berne potentials

This paper presents a general coarse-grained molecular mechanics model based on electric point multipole expansion and Gay-Berne [J. Chem. Phys. 74, 3316 (1981)] potential. Coarse graining of van der Waals potential is achieved by treating molecules as soft uniaxial ellipsoids interacting via a generalized anisotropic Gay-Berne function. The charge distribution is represented by point multipole expansion, including point charge, dipole, and quadrupole moments placed at the center of mass. The Gay-Berne and point multipole potentials are combined in the local reference frame defined by the inertial frame of the all-atom counterpart. The coarse-grained model has been applied to rigid-body molecular dynamics simulations of molecular liquids including benzene and methanol. The computational efficiency is improved by several orders of magnitude, while the results are in reasonable agreement with all-atom models and experimental data. We also discuss the implications of using point multipole for polar molecules capable of hydrogen bonding and the applicability of this model to a broad range of molecular systems including highly charged biopolymers.

Study of the Thermal Diffusion Behavior of Alkane/Benzene Mixtures by Thermal Diffusion Forced Rayleigh Scattering Experiments and Lattice Model Calculations

In this work the thermal diffusion behavior of binary mixtures of linear alkanes (heptane, nonane, undecane, tridecane, pentadecane, heptadecane) in benzene has been investigated by thermal diffusion forced Rayleigh scattering (TDFRS) for a range of concentrations and temperatures. The Soret coefficient ST of the alkane was found to be negative for these n-alkane/benzene mixtures indicating that the alkanes are enriched in the warmer regions of the liquid mixtures. For the compositions investigated in this work, the magnitude of the Soret coefficient decreases with increasing chain length and increasing alkane content of the mixtures. The temperature dependence of the Soret coefficient depends on mixture composition and alkane chain length; the slope of ST versus temperature changes from positive to negative with increasing chain length at intermediate compositions. To study the influence of molecular architecture on the Soret effect, mixtures of branched alkanes (2-methylhexane, 3-methylhexane, 2,3-dimethylpentane, 2,4-dimethylpentane, 2,2,3-trimethylbutane, and 2,2,4-trimethylpentane) in benzene were also investigated. Our results for the Soret coefficients show that the tendency for the alkanes to move to the warmer regions of the fluid decreases with increasing degree of branching. The branching effect is so strong that for 2,2,4-trimethylpentane/benzene mixtures the Soret coefficient changes sign at high alkane content and that equimolar 2,2,3-trimethylbutane/benzene mixtures have positive Soret coefficients in the investigated temperature range. In order to investigate the effect of molecular interactions on thermal diffusion, we adapted a recently developed two-chamber lattice model to n-alkane/benzene mixtures. The model includes the effects of chain-length, compressibility, and orientation dependence of benzene-benzene interactions and yields good qualitative predictions for the Soret effect in n-alkane/benzene mixtures. For the branched isomers, we find some correlations between the moments of inertia of the molecules and the Soret coefficients. PACS numbers: 66.10.Cb, 61.25.Hq.

Anomalous orientation-dependent effective pair interaction among histidine and other amino acid residues in metalloproteins: breakdown of the hydropathy scale index

Hydropathy scale is widely used to obtain a measure of the effective interaction between any two amino acid residues in proteins and is based on the assumption that attraction between two hydrophobic groups and repulsion between hydrophilic groups (in water) can be translated straightforwardly to protein environment. Here we employ a recently developed statistical mechanical approach combined with the Protein Data Bank to obtain both distance- and orientation-dependent potential of mean force (ODPMF). This allowed us to explore effective pair potential among many amino acid residues and to examine the validity of the hydropathy scale in modeling the interaction among amino acid residues. We find that in some cases, like Phe-Phe and Lys-Lys, the hydropathy scale approach is largely obeyed. However, we also observe many unexpected pair interactions which defy the trend given by published hydropathy scales. An example of the former is the arginine-arginine (Arg-Arg) pair interaction which is found to be strongly and surprisingly attractive at short separation, even though it is the most hydrophilic residue. Here the head-to-head (see text) interaction is also stabilized. Tryptophan residues also exhibit strong attractive interaction. Equally important, we find strong influence of metal in determining effective interaction among the amino acid residues. It is the behavior of the histidine (His) which is found to be the most unusual. It exhibits a strong attractive interaction with itself which gets significantly enhanced in metalloproteins. These results highlight the important (sometime hidden) role of metals in protein structure and folding.

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.