Entropy and dynamics of water in hydration layers of a bilayer.
07 Nov 2010-Journal of Chemical Physics (American Institute of Physics)-Vol. 133, Iss: 17, pp 174704-174704
TL;DR: 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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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.
169 citations
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...5 kJ/mol at 300 K to move a single water molecule from a DPPC interface to bulk water (48)....
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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.
Abstract: Lignins are hydrophobic, branched polymers that regulate water conduction and provide protection against chemical and biological degradation in plant cell walls. Lignins also form a residual barrier to effective hydrolysis of plant biomass pretreated at elevated temperatures in cellulosic ethanol production. Here, the temperature-dependent structure and dynamics of individual softwood lignin polymers in aqueous solution are examined using extensive (17 μs) molecular dynamics simulations. With decreasing temperature the lignins are found to transition from mobile, extended to glassy, compact states. The polymers are composed of blobs, inside which the radius of gyration of a polymer segment is a power-law function of the number of monomers comprising it. In the low temperature states the blobs are interpermeable, the polymer does not conform to Zimm/Stockmayer theory, and branching does not lead to reduction of the polymer size, the radius of gyration being instead determined by shape anisotropy. At high temperatures the blobs become spatially separated leading to a fractal crumpled globule form. The low-temperature collapse is thermodynamically driven by the increase of the translational entropy and density fluctuations of water molecules removed from the hydration shell, thus distinguishing lignin collapse from enthalpically driven coil-globule polymer transitions and providing a thermodynamic role of hydration water density fluctuations in driving hydrophobic polymer collapse. Although hydrophobic, lignin is wetted, leading to locally enhanced chain dynamics of solvent-exposed monomers. 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.
126 citations
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.
Abstract: In a sense, life is defined by membranes, because they
delineate the barrier between the living cell and its
surroundings. Membranes are also essential for regulating the
machinery of life throughout many interfaces within the cell's
interior. A large number of experimental, computational, and
theoretical studies have demonstrated how the properties of
water and ionic aqueous solutions change due to the vicinity of
membranes and, in turn, how the properties of membranes depend
on the presence of aqueous solutions. Consequently,
understanding the character of aqueous solutions at their
interface with biological membranes is critical to research
progress on many fronts. The importance of incorporating a
molecular-level description of water into the study of
biomembrane surfaces was demonstrated by an examination of the
interaction between phospholipid bilayers that can serve as
model biological membranes. The results showed that, in
addition to well-known forces, such as van der Waals and
screened Coulomb, one has to consider a repulsion force due to
the removal of water between surfaces. It was also known that
physicochemical properties of biological membranes are strongly
influenced by the specific character of the ions in the
surrounding aqueous solutions because of the observation that
different anions produce different effects on muscle twitch
tension. In this Account, we describe the interaction of pure
water, and also of aqueous ionic solutions, with model
membranes. We show that a symbiosis of experimental and
computational work over the past few years has resulted in
substantial progress in the field. We now better understand the
origin of the hydration force, the structural properties of
water at the interface with phospholipid bilayers, and the
influence of phospholipid headgroups on the dynamics of water.
We also improved our knowledge of the ion-specific effect,
which is observed at the interface of the phospholipid bilayer
and aqueous solution, and its connection with the Hofmeister
series.
102 citations
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.
Abstract: 2-Methacryloyloxyethyl phosphorylcholine (MPC) is a custom methacrylate with a zwitterionic phosphorylcholine moiety on the side chain. In the past 25 years, MPC has been used as a building block for a wide range of polymeric biomaterials because of its excellent resistance to nonspecific protein adsorption, cell adhesion, and blood coagulation. Recently, MPC polymers with specific features have been used in bioengineering and nanomedicine. 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. These developments will extend the applications of this biomimetic material from bioinert polymers to biosensing, CRP inhibitors, prodrug carriers, subcellular bioimaging, cell manipulation, and joint replacement. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 41766.
99 citations
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.
Abstract: Experiments and computer simulations demonstrate that water spontaneously fills the hydrophobic cavity of a carbon nanotube. To gain a quantitative thermody- namic understanding of this phenomenon, we use the recently developed Two Phase Thermodynamics (2PT) method to compute translational and rotational entropies of confined water molecules inside single-walled carbon nanotubes and show that the increase in energy of a water molecule inside the nanotube is compensated by the gain in its rotational entropy. The confined water is in equilibrium with the bulk wa- ter and the Helmholtz free energy per water molecule of confined water is the same as that in the bulk within the accuracy of the simulation results. A comparison of translational and rotational spectra of water molecules confined in carbon nanotubes with that of bulk water shows significant shifts in the positions of the spectral peaks that are directly related to the tube radius.
88 citations
References
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TL;DR: The uncertainty in structural results for lipid bilayers is being reduced and best current values are provided for bilayers of five lipids.
2,497 citations
Book•
05 Feb 1976
TL;DR: In this paper, a comprehensive introduction to principles underlying laser light scattering focuses on time dependence of fluctuations in fluid systems and provides an introduction to theory of time correlation functions, with chapters on projection operator techniques in statistical mechanics.
Abstract: This comprehensive introduction to principles underlying laser light scattering focuses on time dependence of fluctuations in fluid systems It also serves as introduction to theory of time correlation functions, with chapters on projection operator techniques in statistical mechanics Over 60 text figures 1976 edition
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TL;DR: In this paper, the effects of velocity rescaling on the self-diffusion coefficient D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data.
Abstract: Molecular dynamics simulations of five water models, the TIP3P (original and modified), SPC (original and refined), and SPC/E (original), were performed using the CHARMM molecular mechanics program. All simulations were carried out in the microcanonical NVE ensemble, using 901 water molecules in a cubic simulation cell furnished with periodic boundary conditions at 298 K. The SHAKE algorithm was used to keep water molecules rigid. Nanosecond trajectories were calculated with all water models for high statistical accuracy. The characteristic self-diffusion coefficients D and radial distribution functions, gOO, gOH, and gHH for all five water models were determined and compared to experimental data. The effects of velocity rescaling on the self-diffusion coefficient D were examined. All these empirical water models used in this study are similar by having three interaction sites, but the small differences in their pair potentials composed of Lennard-Jones (LJ) and Coulombic terms give significant difference...
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TL;DR: A new semi-empirical method for calculating free energies of binding from molecular dynamics simulations is presented, based on standard thermodynamic cycles and on a linear approximation of polar and non-polar free energy contributions from the corresponding MD averages.
Abstract: A new semi-empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non-polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.
1,085 citations
TL;DR: Using numerical simulations, support is found for a pathway in which the rotating water molecule breaks a hydrogen bond with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second- shell neighbor.
Abstract: Despite long study, a molecular picture of the mechanism of water reorientation is still lacking Using numerical simulations, we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor The H-bond cleavage and the molecular reorientation occur concertedly and not successively as usually considered This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive
997 citations