Entropy and dynamics of water in hydration layers of a bilayer.

Abstract: Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are 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. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes.

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.

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.

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.

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.

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

Abstract: A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro)molecules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can run on any parallel system onto which a a ring of processors can be mapped and which supports PVM-like block send and receive calls. The GROMACS software consists of a preprocessor, a parallel MD and energy minimization program that can use an arbitrary number of processors (including one), an optional monitor, and several analysis tools. The programs are written in ANSI C and available by ftp (information: gromacs@chem.rug.nl). The functionality is based on the GROMOS (GROningen MOlecular Simulation) package (van Gunsteren and Berendsen, 1987; BIOMOS B.V., Nijenborgh 4, 9747 AG Groningen). Conversion programs between GROMOS and GROMACS formats are included. The MD program can handle rectangular periodic boundary conditions with temperature and pressure scaling. The interactions that can be handled without modification are variable non-bonded pair interactions with Coulomb and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based on charge groups, and fixed bonded interactions of either harmonic or constraint type for bonds and bond angles and either periodic or cosine power series interactions for dihedral angles. Special forces can be added to groups of particles (for non-equilibrium dynamics or for position restraining) or between particles (for distance restraints). The parallelism is based on particle decomposition. Interprocessor communication is largely limited to position and force distribution over the ring once per time step.

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.

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.

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.