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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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Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

TL;DR: By using atomistic computer simulations, this work is able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects.
Journal ArticleDOI

Simulation Analysis of the Temperature Dependence of Lignin Structure and Dynamics

TL;DR: The detailed characterization obtained here provides insight at atomic detail into processes relevant to biomass pretreatment for cellulosic ethanol production and general polymer coil-globule transition phenomena.
Journal ArticleDOI

Aqueous Solutions at the Interface with Phospholipid Bilayers

TL;DR: The interaction of pure water, and also of aqueous ionic solutions, with model membranes is described, showing that a symbiosis of experimental and computational work over the past few years has resulted in substantial progress in the field.
Journal ArticleDOI

Critical update on 2-methacryloyloxyethyl phosphorylcholine (MPC) polymer science

TL;DR: This review focuses on three topics that highlight the latest findings on MPC polymers, that is, specific recognition of C-reactive protein (CRP), cell-membrane-penetration abilities, and lubrication properties.
Journal ArticleDOI

Thermodynamics of Water Entry in Hydrophobic Channels of Carbon Nanotubes

TL;DR: The recently developed two phase thermodynamics method is used to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and shows that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy.
References
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Journal ArticleDOI

Water dynamical anomalies evidenced by molecular-dynamics simulations at the solvent-protein interface

TL;DR: In this article, the authors present a computer simulation picture of the dynamical behavior, at room temperature, of water in the region close to a protein surface, showing that the probability distribution of water molecules diffusing near the surface deviates from a Gaussian, which is predicted for Brownian particles.
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Dielectric Relaxation Dynamics of Water in Model Membranes Probed by Terahertz Spectroscopy

TL;DR: This work studies hydrated model membranes, consisting of stacked bilayers of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids, using terahertz time-domain and infrared spectroscopy to elucidate how the interplay between the model membrane and water molecules results in different water dynamics.
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Hydrogen Bonding Structure and Dynamics of Water at the Dimyristoylphosphatidylcholine Lipid Bilayer Surface from a Molecular Dynamics Simulation

TL;DR: In this article, the structural and dynamical hydrogen bonding interactions at the lipid water interface from a 10 ns molecular dynamics simulation of a hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayer is presented.
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Structure and Dynamics of DNA−Dendrimer Complexation: Role of Counterions, Water, and Base Pair Sequence

TL;DR: Simulations reveal formation of a stable complex of sequence-dependent complexation between oligonucleotides and various generation ethylene diamine cored poly amido amide dendrimers through atomistic molecular dynamics simulations accompanied by free energy calculations and inherent structure determination.
Journal ArticleDOI

On the residence time for water in a solute hydration shell: application to aqueous halide solutions.

TL;DR: An alternate, robust determination based on the stable states picture (SSP) of chemical reactions is suggested where recrossing is naturally discarded, and results are in good agreement with the residence times estimated by a separate kinetic analysis, and differ noticeably from those calculated in the conventional fashion.
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