scispace - formally typeset
Journal ArticleDOI

Entropy and dynamics of water in hydration layers of a bilayer.

Reads0
Chats0
TLDR
The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface, supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water.
Abstract
We compute the entropy and transport properties of water in the hydration layer of dipalmitoylphosphatidylcholine bilayer by using a recently developed theoretical scheme [two-phase thermodynamic model, termed as 2PT method; S.-T. Lin et al., J. Chem. Phys. 119, 11792 (2003)] based on the translational and rotational velocity autocorrelation functions and their power spectra. The weights of translational and rotational power spectra shift from higher to lower frequency as one goes from the bilayer interface to the bulk. Water molecules near the bilayer head groups have substantially lower entropy (48.36 J/mol/K) than water molecules in the intermediate region (51.36 J/mol/K), which have again lower entropy than the molecules (60.52 J/mol/K) in bulk. Thus, the entropic contribution to the free energy change (TΔS) of transferring an interface water molecule to the bulk is 3.65 kJ/mol and of transferring intermediate water to the bulk is 2.75 kJ/mol at 300 K, which is to be compared with 6.03 kJ/mol for melting of ice at 273 K. The translational diffusion of water in the vicinity of the head groups is found to be in a subdiffusive regime and the rotational diffusion constant increases going away from the interface. This behavior is supported by the slower reorientational relaxation of the dipole vector and OH bond vector of interfacial water. The ratio of reorientational relaxation time for Legendre polynomials of order 1 and 2 is approximately 2 for interface, intermediate, and bulk water, indicating the presence of jump dynamics in these water molecules.

read more

Citations
More filters
Journal ArticleDOI

Absolute thermodynamic properties of molten salts using the two-phase thermodynamic (2PT) superpositioning method

TL;DR: It is shown that the absolute thermodynamic properties of molten salts can be accurately determined from the two-phase thermodynamic (2PT) method that is based on superpositioning of solid-like and gas-like (hard-sphere) vibrational density of states (DoS).
Journal ArticleDOI

Single Mutations Reshape the Structural Correlation Network of the DMXAA-Human STING Complex.

TL;DR: In this article, structural correlations in the interaction of STINGAQ with DMXAA are analyzed and two key interactions are identified that mediate the strong cross-protomer correlation in the DM-XAA-STING-AQ interaction network, which are partially and totally interrupted by the S162A and E260I mutations.
Book ChapterDOI

Long-Range Lipid-Water Interaction as Observed by ATR-FTIR Spectroscopy

TL;DR: Modification of interlamellar water properties may clarify the role of water-mediated effects in biological processes and in confined membrane environments nearly all water molecules can be perturbed.
Journal ArticleDOI

Accurate calculation of zero point energy from molecular dynamics simulations of liquids and their mixtures

TL;DR: The obtained results demonstrate that the 2PT model is a powerful method for efficient ZPE calculations, in particular, to account for solvent effects and polarization.
Journal ArticleDOI

Diffusive and quantum effects of water properties in different states of matter

TL;DR: The two-phase thermodynamic (2PT) model is demonstrated as a unified approach to obtain the properties of water over the whole phase region of water from short (∼20 ps) classical molecular dynamics trajectories and is found to be consistent with those obtained from more sophisticated calculations.
References
More filters
Journal ArticleDOI

Molecular dynamics with coupling to an external bath.

TL;DR: In this paper, a method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling, which can be easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints.
Journal ArticleDOI

GROMACS: A message-passing parallel molecular dynamics implementation

TL;DR: A parallel message-passing implementation of a molecular dynamics program that is useful for bio(macro)molecules in aqueous environment is described and can handle rectangular periodic boundary conditions with temperature and pressure scaling.
Journal ArticleDOI

GROMACS 3.0: a package for molecular simulation and trajectory analysis

TL;DR: The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2.
Book ChapterDOI

Interaction Models for Water in Relation to Protein Hydration

TL;DR: In this article, a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6-12 potential on the oxygen positions only was developed, and parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion.
Journal ArticleDOI

Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes

TL;DR: The first and second papers in this series, which make it possible to interpret entropy data in terms of a physical picture, are applied to binary solutions, and equations are derived relating energy and volume changes when a solution is formed to the entropy change for the process as discussed by the authors.
Related Papers (5)