A molecular dynamics simulation of a sodium–decanoate/decanol/water system is reported. The system is treated in full atomic detail, with the exception of CH2 and CH3 groups that are considered to be ‘‘united atoms,’’ and is a refinement of a previous model membrane [Mol. Phys. 11, 1 (1983)]. The long‐range Coulomb interactions were included specifically. The order parameters of the chain units of the lipids and diffusion constants of components in the system calculated from the simulation agree well with those reported in experiments on this model membrane. The overall structure of the membrane shows considerable disorder, with a broad lipid–water interface, extending over approximately 1 nm. The distribution of the components is such that an almost complete charge cancellation occurs throughout the system, which is in contradiction with the generally assumed electrical double layer structure for membranes. A counterion condensation of 70% is observed. Both the translational and the rotational motions of water are slowed down compared to bulk water. The penetration of water into the hydrocarbon region of the membrane is substantial. Pair correlations of various atom pairs, and dihedral statistics and transition rates of the dihedrals in the lipids are reported. The distributions of chain segments of the lipids, of water molecules, and of sodium ions are compared with theoretical predictions.

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Molecular dynamics simulation of a smectic liquid crystal with atomic detail

A molecular dynamics simulation was carried out for a bilayer of 2 × 64 decane molecules as a model for a biological membrane. Two dimensional periodic conditions were used and head groups were subjected to a simple mean force interaction. Four runs at two different temperatures and head group densities were executed, each over 80 ps. Molecular order parameters were analysed and compared with experiment. A fluctuating tilt of the molecules occurs with respect to the bilayer normal with a spatial correlation of about 1 nm and a temporal correlation of 8 ps. The molecules do not rotate isotropically around their long axes, and a different behaviour of odd and even numbered bonds is apparent. The density profile shows a dip near the middle of the bilayer and the lateral pressure profile shows a negative region near the head groups compensated by a positive region near the tails. Translational diffusion is inhibited by a long negative tail of the velocity autocorrelation function, but still exceeds experiment...

Molecular-dynamics of a bilayer-membrane

The interface between the (110) crystal face of cellulose Iβ and water was studied by molecular dynamics simulation with cellulose coordinates refined from electron diffraction data as a starting point. Potential energies, pucker parameters, torsion angles, and hydrogen bonding have been used for the characterization. Only the topmost layer in the cellulose differs in terms of structure and dynamics from the crystal bulk, but even these difference are small. At the surface approximately half of the cellulose intermolecular hydrogen bonding is lost, but this is compensated by hydrogen bonds with water molecules. Much of the difference between even and odd (200) planes disappears at the interface, except for the orientation of the glucose ring plane. Water dynamics is retarded by a factor of 2−3 close to the surface. The potential energy of water molecules in the first hydration layer is lower by 2 kJ/mol. The cellulose surface contains about five exposed hydroxyl groups per square nanometer, which accounts...

Interface between Monoclinic Crystalline Cellulose and Water: Breakdown of the Odd/Even Duplicity

Simulations generating a statistical ensemble of configurations of a molecular system provide information to derive entropy. For cases where the spatial distribution is bounded, the entropy can be derived from the average of the logarithm of the spatial probability density, but will be subject to systematic errors due to statistical fluctuations. A method is given to eliminate these errors by using different interval sizes and fitting the results to a simple theoretical expression. The method is feasible when the multidimensional case can be broken up into a sum of low dimensional contributions. The validity of the latter approximation and ways to correct for correlations are discussed.

Entropy estimation from simulations of non-diffusive systems

https://pubs.acs.org/doi/pdf/10.1021/cr030440j

Modeling Kinetics of Subcellular Disposition of Chemicals

The conformational entropy of the disordered hydrocarbon chains in a bilayer membrane is calculated from a molecular dynamics simulation. We find that one chain in the mean field of the others is very well described by a trans-gauche model with adjacent gauches of opposite sign forbidden. The effective gauche energy depends, however, on the density of chains and may for realistic densities be between 4·5 and 5·7 kJ mol-1. This gives a conformational entropy of the disordered phase close to the gel-liquid crystalline phase transition temperature that is in rough agreement with the experimental phase transition entropy.

Conformational entropy of a bilayer-membrane derived from a molecular-dynamics simulation

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Conformational entropy of a bilayer-membrane derived from a molecular-dynamics simulation