Unit cell structure of water-filled monoolein into inverted hexagonal (H(II)) mesophase modeled by molecular dynamics.

The study investigates the unit cell structure of inverted hexagonal (H(II)) mesophase composed of monoolein (1-monoolein, GMO) and water using atomistic molecular dynamics methods without imposing any restraints on lipid and water molecules. Statistically meaningful and very contrast images of the radial mass density distribution, scrutinizing also the separate components water, monoolein, the polar headgroups of the lipids, the double bond, and the termini of the hydrocarbon chain (the tail), are obtained. The lipid/water interface structure is analyzed based on the obtained water density distribution, on the estimated number of hydrogen bonds per monoolein headgroup, and on the headgroup-water radial distribution functions. The headgroup mass density distribution demonstrates hexagonal shape of the monoolein/water interface that is well-defined at higher water/monoolein ratios. Water interacts with the headgroups by forming a three-layer diffusive mass density distribution, and each layer's shape is close to hexagonal, which is an indication of long-range structural interactions. It is found that the monoolein headgroups form a constant number of hydrogen bonds leaving an excessive amount of water molecules outside the first lipid coordination sphere. Furthermore, the quantity of water at the monoolein/water interface increases steadily upon extension of the unit cell, so the interface should have a very dynamic structure. Investigation of the hydrocarbon residues reveals high compression and well-expressed structuring of the tails. The tails form a very compressed and constrained structure of defined layers across the unit cell with properties corresponding to a more densely packed nonpolar liquid (oil). Due to the hexagonal shape the 2D packing frustration is constant and does not depend on the water content. All reported structural features are based on averaging of the atomic coordinates over the time-length of the simulation trajectories. That kind of processing allows the observation of the water/GMO interface shape and its stability and mobility at a time scale close to the ones of the intermolecular interactions.

Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation.

Fully atomistic molecular dynamics simulations were performed on liquid n-pentane, n-hexane, and n-heptane to derive an atomistic model for middle-chain-length alkanes. All simulations were based on existing molecular-mechanical parameters for alkanes. The computational protocol was optimized, for example, in terms of thermo- and barostat, to reproduce properly the properties of the liquids. The model was validated by comparison of thermal, structural, and dynamic properties of the normal alkane liquids to experimental data. Two different combinations of temperature and pressure coupling algorithms were tested. A simple differential approach was applied to evaluate fluctuation-related properties with sufficient accuracy. Analysis of the data reveals a satisfactory representation of the hydrophobic systems behavior. Thermodynamic parameters are close to the experimental values and exhibit correct temperature dependence. The observed intramolecular geometry corresponds to extended conformations domination, whereas the intermolecular structure demonstrates all characteristics of liquid systems. Cavity size distribution function was calculated from coordinates analysis and was applied to study the solubility of gases in hexane and heptane oils. This study provides a platform for further in-depth research on hydrophobic solutions and multicomponent systems.

Fully doped oligomers of emeraldine salt: polaronic versus bipolaronic configuration.

Calculations for model oligomers of the emeraldine salt with UBLYP/6-31G*/PCM are performed. The models differ in number of monomers, in the position of the counterions (Cl(-)), and in multiplicity. The molecular features affected most prominently by the protonation, namely, structure, energetics, and electron and spin density partitioning are analyzed. The results show unequivocally that the studied molecular characteristics are essentially size independent. The octamer profiles of all parameters are repeated in the dodecamer and the hexadecamer. The bipolaronic forms are energetically more favorable than the polaronic ones within the chosen protocol. The electronic structure in the intermediate multiplicities differs from the bipolaronic and polaronic periodicity. The geometrical changes and electron density redistribution upon increase of multiplicity illustrate the pathway of intramolecular bipolaron-polaron conversion. The orbital analysis rationalizes the observed behavior of the oligomers.

Dielectric properties tangential to the interface in model insoluble monolayers: theoretical assessment.

Studies of insoluble monolayers built of phospholipids and various long-chained fatty acids or their glycerin esters are the major source for what is currently known about the relationship between monolayer composition and physicochemical properties. The surface pressure, dipole moment, dielectric permittivity, polarizability, refractivity, and other electrical and optical features are governed by the surfactant structural specificity and solvent organization at the microscopic level. To provide insight into the atomistic details of the interfacial structure, model monolayers at the air/water interface of two distinctly different in composition and isotherm profile surfactants are investigated by means of molecular dynamics all-atom simulations. Analysis of the computational results allows the estimation of empirically unattainable quantities such as tangential (di)electric properties, their decomposition to surfactant and water contributions, and their relationship with the changes in interfacial molecular organization at different surface concentrations. The employed theoretical approach provides a comprehensive description of interfacial phenomena at the molecular level where the traditional phenomenological investigations are ineffective.

Theoretical study of the influence of monomer excess on the structure and properties of polyaniline oligomers.

Polyaniline is among the most intensely investigated polymers because of its exceptional properties affording its current and potential applications. The structure and energy spectra of isolated oligomers and infinite chains in different oxidation states and degrees of protonation have been discussed at length from experimental and theoretical perspectives. The reaction environment effect, however, has received less attention and, particularly, the influence of monomer excess has been completely neglected in theoretical studies. Experimental measurements show that residual aniline is always detected in emeraldine samples obtained at low pH. Upon addition of oxidant to emeraldine PANI samples, post-polymerization due to the presence of excess monomers occurs. This is an indication of the formation of aniline-PANI complexes in the reaction medium. The presence of aniline monomers should affect the PANI chain arrangement and optical/conducting characteristics. Therefore, model clusters of aniline with neutral or singly protonated emeraldine tetramers in explicit water medium and periodic boundary conditions are addressed in this paper using a Monte Carlo/AMBER96/AM1 computational protocol to simulate the absorption spectra. The monomer impact on the structure, energy characteristics, and UV/vis spectra of the polymer are discussed.