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: A suitably scaled dimensionless self-diffusivity shows an exponential dependence on the excess entropy of the adsorbed phase, analogous to excess entropy scaling rules seen in many bulk and confined fluids.
Abstract: Molecular dynamics simulations have been performed on monatomic sorbates confined within zeolite NaY to obtain the dependence of entropy and self-diffusivity on the sorbate diameter. Previously, molecular dynamics simulations by Santikary and Yashonath J. Phys. Chem. 98, 6368 (1994)], theoretical analysis by Derouane J. Catal. 110, 58 (1988)] as well as experiments by Kemball Adv. Catal. 2, 233 (1950)] found that certain sorbates in certain adsorbents exhibit unusually high self-diffusivity. Experiments showed that the loss of entropy for certain sorbates in specific adsorbents was minimum. Kemball suggested that such sorbates will have high self-diffusivity in these adsorbents. Entropy of the adsorbed phase has been evaluated from the trajectory information by two alternative methods: two-phase and multiparticle expansion. The results show that anomalous maximum in entropy is also seen as a function of the sorbate diameter. Further, the experimental observation of Kemball that minimum loss of entropy is associated with maximum in self-diffusivity is found to be true for the system studied here. A suitably scaled dimensionless self-diffusivity shows an exponential dependence on the excess entropy of the adsorbed phase, analogous to excess entropy scaling rules seen in many bulk and confined fluids. The two trajectory-based estimators for the entropy show good semiquantitative agreement and provide some interesting microscopic insights into entropy changes associated with confinement.
28 citations
TL;DR: The results indicate that there is no intermediate exchange of slow moving water molecules from the solutes to the lipid atoms and vice versa, and the exchange relies on the reservoir of unbounded ("free") water molecules in the interfacial bilayer region.
28 citations
TL;DR: In this paper, the authors investigated the dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer using an all atom molecular dynamics simulation.
Abstract: Dynamics of hydration layers of a dimyristoylphosphatidylcholine (DMPC) bilayer are investigated using an all atom molecular dynamics simulation. Based upon the geometric criteria, continuously residing interface water molecules which form hydrogen bonds solely among themselves and then concertedly hydrogen bonded to carbonyl, phosphate, and glycerol head groups of DMPC are identified. The interface water hydrogen bonded to lipids shows slower relaxation rates for translational and rotational dynamics compared to that of the bulk water and is found to follow sub-diffusive and non-diffusive behaviors, respectively. The mean square displacements and the reorientational auto-correlation functions are slowest for the interfacial waters hydrogen bonded to the carbonyl oxygen since these are buried deep in the hydrophobic core among all interfacial water studied. The intermittent hydrogen bond auto-correlation functions are calculated, which allows breaking and reformations of the hydrogen bonds. The auto-correlation functions for interfacial hydrogen bonded networks develop humps during a transition from cage-like motion to eventual power law behavior of t−3/2. The asymptotic t−3/2 behavior indicates translational diffusion dictated dynamics during hydrogen bond breaking and formation irrespective of the nature of the chemical confinement. Employing reactive flux correlation analysis, the forward rate constant of hydrogen bond breaking and formation is calculated which is used to obtain Gibbs energy of activation of the hydrogen bond breaking. The relaxation rates of the networks buried in the hydrophobic core are slower than the networks near the lipid-water interface which is again slower than bulk due to the higher Gibbs energy of activation. Since hydrogen bond breakage follows a translational diffusion dictated mechanism, chemically confined hydrogen bond networks need an activation energy to diffuse through water depleted hydrophobic environments. Our calculations reveal that the slow relaxation rates of interfacial waters in the vicinity of lipids are originated from the chemical confinement of concerted hydrogen bond networks. The analysis suggests that the networks in the hydration layer of membranes dynamically facilitate the water mediated lipid-lipid associations which can provide insights on the thermodynamic stability of soft interfaces relevant to biological systems in the future.
28 citations
TL;DR: The results reveal that the spontaneous filling and entry of water into the pore in AQPs are driven by an entropic gain, and water molecules exhibit an elevated degree of rotational motion inside the pores, while their translational motion is slow compared with bulk.
Abstract: We report here a detailed thermodynamic description of water molecules inside a biological water channel. Taking advantage of high-resolution molecular dynamics trajectories calculated for an aquaporin (AQP) channel, we compute the spatial translational and rotational components of water diffusion and entropy in AQP. Our results reveal that the spontaneous filling and entry of water into the pore in AQPs are driven by an entropic gain. Specifically, water molecules exhibit an elevated degree of rotational motion inside the pore, while their translational motion is slow compared with bulk. The partial charges of the lining asparagine residues at the conserved signature Asn-Pro-Ala motifs play a key role in enhancing rotational diffusion and facilitating dipole flipping of water inside the pore. The frequencies of the translational and rotational motions in the power spectra overlap indicating a strong coupling of these motions in AQPs. A shooting mechanism with diffusive behavior is observed in the extracellular region which might be a key factor in the fast conduction of water in AQPs.
27 citations
TL;DR: The Janus interface appears to provide the optimal environment for water transport, providing a design strategy while assembling graphene oxide-based membrane stacks for water purification.
Abstract: Graphene oxide membranes have been widely studied for their potential applications in water desalination applications. To understand the influence of surface oxidation and the inherent heterogeneit...
26 citations
References
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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.
Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath
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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.
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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.
Abstract: GROMACS 3.0 is the latest release of a versatile and very well optimized package for molecular simulation. Much effort has been devoted to achieving extremely high performance on both workstations and parallel computers. 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. Inner loops are generated automatically in C or Fortran at compile time, with optimizations adapted to each architecture. Assembly loops using SSE and 3DNow! Multimedia instructions are provided for x86 processors, resulting in exceptional performance on inexpensive PC workstations. The interface is simple and easy to use (no scripting language), based on standard command line arguments with self-explanatory functionality and integrated documentation. All binary files are independent of hardware endian and can be read by versions of GROMACS compiled using different floating-point precision. A large collection of flexible tools for trajectory analysis is included, with output in the form of finished Xmgr/Grace graphs. A basic trajectory viewer is included, and several external visualization tools can read the GROMACS trajectory format. Starting with version 3.0, GROMACS is available under the GNU General Public License from http://www.gromacs.org.
6,375 citations
01 Jan 1981
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.
Abstract: For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.
5,336 citations
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.
Abstract: The ideas of 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. These equations are tested against data obtained by various authors on mixtures of normal liquids, and on solutions of non‐polar gases in normal solvents. Good general agreement is found, and it is concluded that in such solutions the physical picture of molecules moving in a ``normal'' manner in each others' force fields is adequate. As would be expected, permanent gases, when dissolved in normal liquids, loosen the forces on neighboring solvent molecules producing a solvent reaction which increases the partial molal entropy of the solute.Entropies of vaporization from aqueous solutions diverge strikingly from the normal behavior established for non‐aqueous solutions. The nature of the deviations found for non‐polar solutes in water, together with the large effect of temperature upon them, leads to the idea that the water forms frozen patches or microscopic icebergs around such solute molecules, the extent of the iceberg increasing with the size of the solute molecule. Such icebergs are apparently formed also about the non‐polar parts of the molecules of polar substances such as alcohols and amines dissolved in water, in agreement with Butler's observation that the increasing insolubility of large non‐polar molecules is an entropy effect. The entropies of hydration of ions are discussed from the same point of view, and the conclusion is reached that ions, to an extent which depends on their sizes and charges, may cause a breaking down of water structure as well as a freezing or saturation of the water nearest them. Various phenomena recorded in the literature are interpreted in these terms. The influence of temperature on certain salting‐out coefficients is interpreted in terms of entropy changes. It appears that the salting‐out phenomenon is at least partly a structural effect. It is suggested that structural influences modify the distribution of ions in an electrolytesolution, and reasons are given for postulating the existence of a super‐lattice structure in solutions of LaCl3 and of EuCl3. An example is given of a possible additional influence of structural factors upon reacting tendencies in aqueous solutions.
2,572 citations