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Journal ArticleDOI

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

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.

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Journal ArticleDOI

Structural Changes of Interfacial Water upon Fluid-Ripple-Gel Phase Transitions of Bilayers

TL;DR: In this paper , all atom molecular dynamics simulations of fully hydrated dimyristoylphosphatidylcholine lipid bilayers are performed for total 9.45 μs showing a fluid to a ripple to a gel phase transition.
Journal ArticleDOI

Spectrally Resolved Estimation of Water Entropy in the Active Site of Human Carbonic Anhydrase II.

TL;DR: In this paper, the authors used atomistic molecular dynamics simulations to compute the absolute entropy of the individual water molecules confined in the active site of hCAII using a spectrally resolved estimation (SRE) approach.
Dissertation

Ion binding landscapes and molecular dynamics of phospholipid membranes

Jing Yang
TL;DR: This work provides a general methodology to explore the free energy landscapes for ions at complex biological interfaces which can be extended to study other interactions of interest between ions and charged headgroups in colloidal chemistry and biology.
Journal ArticleDOI

Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study.

TL;DR: In this paper , the effects of aqueous arginine solution on the conformational stability of the secondary structural segments of a globular protein, ubiquitin, and the structure and dynamics of the surrounding water and arginines were examined by performing atomistic molecular dynamics (MD) simulations.
Journal ArticleDOI

Comparative vibrational study of two N-isopropylacrylamide-based co-polymers: Influence of the polymer hydrophobicity on the phase transition

TL;DR: In this article, the temperature induced phase transition in solutions of two random co-polymers based on N-isopropylacrylamide (NIPA) was investigated by FTIR spectroscopy in ATR geometry.
References
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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.
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