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: This study reveals that the effect of the aqueous interface on the first solvation shell of the ion pair and thus on the ion pairing thermodynamics becomes more pronounced in the polarizable model, and that the free energy profile along the interionic distance cannot capture the difference in the degree of solvent participation in ion pairing at the water/membrane interface.
Abstract: The anomalous properties of interfacial water at the surface of a lipid membrane and their implications on nearby chemical processes are well recognized. However, we have found that ion pairing thermodynamics may not be significantly affected by interfacial water in a classical, nonpolarizable force field. To trace the root cause of such a counterintuitive finding, we performed atomistic molecular dynamics simulations to explore the impact of polarizable interactions and characterize the hydration structure of a sodium chloride (NaCl) ion pair at the surface of a model lipid membrane and in a bulk phase. Our study reveals that the effect of the aqueous interface on the first solvation shell of the ion pair and thus on the ion pairing thermodynamics becomes more pronounced in the polarizable model, and that the free energy profile along the interionic distance cannot capture the difference in the degree of solvent participation in ion pairing at the water/membrane interface. This study also forms the basis for the future design of a reaction coordinate that takes the behavior of the interfacial water into account.
9 citations
TL;DR: The combined findings from this study suggest that the presence of H3O+ ions affects the properties of interfacial water, accentuates the deviation from bulk properties and extends the long-range effect of these deviations further away from the membrane surface.
Abstract: This study investigates the effect of hydronium ions (H3O+) on the structure and dynamics of water at the interface of a phospholipid bilayer using molecular dynamics simulations of a POPC bilayer in the presence and absence of H3O+ ions. From these simulations, the survival probability, hydrogen bond lifetimes, orientation relaxation, and angular distribution of interfacial water, at increasing distances from the membrane surface, were calculated. Simulations of POPC in the absence of H3O+ ions reproduce previously reported deviations of interfacial water from the properties of bulk water. Our results show that in the presence of H3O+, these deviations are even more pronounced with the strongest effects seen in the survival probability and orientation relaxation. To further investigate the effect of the H3O+-induced reduction of area per lipid on interfacial water, we carried out simulations where H3O+ ions were removed, but the area per lipid was fixed to the values seen in the presence of H3O+. The combined findings from our study suggest that the presence of H3O+ ions affects the properties of interfacial water, accentuates the deviation from bulk properties, and extends the long-range effect of these deviations further away from the membrane surface.
9 citations
01 Oct 2013
TL;DR: In this article, first principles and first principles derived interatomic potential based simulations were used to predict fundamental thermokinetic properties of dissolved actinides and fission products in molten salts.
Abstract: Recovery of actinides is an integral part of a closed nuclear fuel cycle. Pyrometallurgical nuclear fuel recycling processes have been developed in the past for recovering actinides from spent metallic and nitride fuels. The process is essentially to dissolve the spent fuel in a molten salt and then extract just the actinides for reuse in a reactor. Extraction is typically done through electrorefining, which involves electrochemical reduction of the dissolved actinides and plating onto a cathode. Knowledge of a number of basic thermokinetic properties of salts and salt-fuel mixtures is necessary for optimizing present and developing new approaches for pyrometallurgical waste processing. The properties of salt-fuel mixtures are presently being studied, but there are so many solutes and varying concentrations that direct experimental investigation is prohibitively time consuming and expensive (particularly for radioactive elements like Pu). Therefore, there is a need to reduce the number of required experiments through modeling of salt and salt-fuel mixture properties. This project will develop first-principles-based molecular modeling and simulation approaches to predict fundamental thermokinetic properties of dissolved actinides and fission products in molten salts. The focus of the proposed work is on property changes with higher concentrations (up to 5 mol%) of dissolved fuel components, where there is still very limited experimental data. The properties predicted with the modeling will be density, which is used to assess the amount of dissolved material in the salt; diffusion coefficients, which can control rates of material transport during separation; and solute activity, which determines total solubility and reduction potentials used during electrorefining. The work will focus on La, Sr, and U, which are chosen to include the important distinct categories of lanthanides, alkali earths, and actinides, respectively. Studies will be performed using LiCl-KCl salt at the eutectic composition (58 mol% LiCl, 42 mol% KCl), which is used for treating spent EBR-II fuel. The same process being used for EBRII fuel is currently being studied for widespread international implementation. The methods will focus on first-principles and first- principles derived interatomic potential based simulations, primarily using molecular dynamics. Results will be validated against existing literature and parallel ongoing experimental efforts. The simulation results will be of value for interpreting experimental results, validating analytical models, and for optimizing waste separation by potentially developing new salt configurations and operating conditions.
8 citations
Cites background from "Entropy and dynamics of water in hy..."
...Absolute thermodynamic properties [9-15] are needed for optimizing the back-end of the nuclear fuel cycle, which entails the crucial step of separation of actinides from the spent nuclear fuel, followed by the development of new fuel through recycling....
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...Originally developed by Lin, Blanco and Goddard [26], the two-phase thermodynamic (2PT) model has recently gained wide attention and success in predicting absolute thermodynamic properties for several types of fluids [9, 10, 12, 13, 15, 27-30]....
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TL;DR: The collective modes characterised in this work can enable the membrane to dissipate excess energy and thus maintain its structural integrity, e.g., under mechanical stress.
Abstract: The collective behaviour of individual lipid molecules determines the properties of phospholipid membranes. However, the collective molecular motions often remain challenging to characterise at the desired spatial and temporal resolution. Here we study collective vibrational motion on picosecond time scales in dioleoylphosphatidylcholine lipid bilayers with varying cholesterol content using all-atom molecular dynamics simulations. Cholesterol is found to not only laterally compact the lipid bilayer, but also to change the velocity of longitudinal density fluctuations propagating in the plane of the membrane. Cholesterol-induced reduction of the area per lipid alters the collective dynamics of the lipid headgroups, but not of the lipid tails. The introduction of cholesterol reduces the number of water molecules interacting with the lipid headgroups, leading to a decrease in the velocity of the laterally-propagating sound mode. Thus, the stiffening effect of cholesterol is found to be indirect: decreasing the area per lipid weakens the interactions between the lipid headgroups and water. The collective modes characterised in this work can enable the membrane to dissipate excess energy and thus maintain its structural integrity, e.g., under mechanical stress.
7 citations
TL;DR: The results imply that the slowed water dynamics in the interfacial regions of the noncognate complex when the protein chances upon a cognate sequence allow the formation of a stable specific protein-DNA complex leading to catalytic action.
Abstract: Water plays an important role in protein–DNA interactions. Here, we examine using molecular dynamics simulations the differences in the dynamic and thermodynamic properties of water in the interfacial and intercalating regions of EcoRI bound to the cognate and to a minimally mutated noncognate DNA chain. The results show that the noncognate complex is not only more hydrated than the cognate complex, but the interfacial waters in the noncognate complex exhibit a faster dynamics, which in turn reduces the hydrogen-bond lifetimes. Thus, the higher hydration, faster reorientation dynamics and faster hydrogen-bond-relaxation times of water, taken together, indicate that, even with a minimal mutation of the DNA sequence, the interfacial regions of the noncognate complex are more poised to allowing the protein to diffuse away than to promoting the formation of a stable complex. Alternatively, the results imply that the slowed water dynamics in the interfacial regions when the protein chances upon a cognate sequence allow the formation of a stable specific protein–DNA complex leading to catalytic action.
7 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
25,256 citations
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
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