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Journal ArticleDOI

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.
Citations
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Journal ArticleDOI
TL;DR: The analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity, which can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
Abstract: Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα−1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα−0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.

11 citations

Journal ArticleDOI
TL;DR: In this article, the in-plane structure of the water molecules at ambient temperature and pressure is strongly dependent on the water model: all the 3-point water models considered here show square ice formation, whereas no such structural ordering is observed for the 4-Point water models.
Abstract: A monolayer of water confined between two parallel graphene sheets exists in many different phases and exhibits fascinating dielectric properties that have been studied in experiments. In this work, we use molecular dynamics simulations to study how the dielectric properties of a confined monolayer of water is affected by its structure. We consider six of the popular nonpolarizable water models-SPC/E, SPC/Fw, TIP3P, TIP3P_M (modified), TIP4P-2005, and TIP4P-2005f-and find that the in-plane structure of the water molecules at ambient temperature and pressure is strongly dependent on the water model: all the 3-point water models considered here show square ice formation, whereas no such structural ordering is observed for the 4-point water models. This allows us to investigate the role of the in-plane structure of the water monolayer on its dielectric profile. Our simulations show an anomalous perpendicular dielectric constant compared to the bulk, and the models that do not exhibit ice formation show very different dielectric response along the channel width compared to models that exhibit square ice formation. We also demonstrate the occurrence of electromelting of the in-plane ordered water under the application of a perpendicular electric field and find that the critical field for electromelting strongly depends on the water model. Together, we have shown the dependence of confined water properties on the different water structures that it may take when sandwiched between bilayer graphene. These remarkable properties of confined water can be exploited in various nanofluidic devices, artificial ion channels, and molecular sieving.

10 citations

Journal ArticleDOI
TL;DR: In this paper, the authors provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules.
Abstract: Water drives the spontaneous self-assembly of lipids and proteins into quasi two-dimensional biological membranes that act as catalytic scaffolds for numerous processes central to life. However, the functional relevance of hydration in membrane biology is only beginning to be addressed, predominantly because of challenges associated with direct measurements of hydration microstructure and dynamics in a biological milieu. Our recent work on the novel interplay of membrane electrostatics and crowding in shaping membrane hydration dynamics utilizing terahertz (THz) spectroscopy represents an important step in this context. In this Perspective, we provide a glimpse into the ever-broadening functional landscape of hydration dynamics in biological membranes in the backdrop of the unique physical chemistry of water molecules. We further highlight the immense (and largely untapped) potential of the THz toolbox in addressing contemporary problems in membrane biology, while emphasizing the adaptability of the analytical framework reported recently by us to such studies.

10 citations

Journal ArticleDOI
TL;DR: In this article, the authors proposed a mechanism for decomposition of hydrogen peroxide on amino-phospholipids surface model based in Dmol3/DFT calculations, which was built using periodic boundary conditions.
Abstract: Hydrogen peroxide molecules play a significant role in controlling certain cellular functions, and its excess causes significant damage to biological systems. There is experimental evidence that its decomposition is accelerated above phospholipids membranes surface. We propose a mechanism for decomposition of hydrogen peroxide on amino-phospholipids surface model based in Dmol3/DFT calculations. The model was built using periodic boundary conditions. Each unit cell contained two phospholipids molecules, two hydrogen peroxide molecules, and nine water molecules. In the studied reaction, two hydrogen peroxide molecules react in a bimolecular reaction to yield an oxygen molecule and two waters. The reaction proceeds by two steps. In the first step, an intermediate hydrogen trioxide from two H2O2 molecules is formed. In the second step, this intermediate is cleaved in O2 and H2O. There are proton exchanges along the interface between water and amine-phospholipids monolayer in all parts of the pathway. A paral...

10 citations

Journal ArticleDOI
TL;DR: The analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes and the heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts.
Abstract: A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.

10 citations

References
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Journal ArticleDOI
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

25,256 citations

Journal ArticleDOI
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.

8,195 citations

Journal ArticleDOI
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.

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Book ChapterDOI
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

Journal ArticleDOI
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