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A Pohorille

Publications and source records attributed to A Pohorille.

At least 37 records · Page 2Linked to original sources
PubMed1996

An information theory model of hydrophobic interactions.

A molecular model of poorly understood hydrophobic effects is heuristically developed using the methods of information theory. Because primitive hydrophobic effects can be tied to the probability of observing a molecular-sized cavity in the solvent, the probability distribution of the number of solvent centers in a cavity volume is modeled on the basis of the two moments available from the density and radial distribution of oxygen atoms in liquid water. The modeled distribution then yields the probability that no solvent centers are found in the cavity volume. This model is shown to account quantitatively for the central hydrophobic phenomena of cavity formation and association of inert gas solutes. The connection of information theory to statistical thermodynamics provides a basis for clarification of hydrophobic effects. The simplicity and flexibility of the approach suggest that it should permit applications to conformational equilibria of nonpolar solutes and hydrophobic residues in biopolymers.

Journal Article↗
PubMed1996

Mechanism of unassisted ion transport across membrane bilayers.

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

Cell Membrane Permeability↗
PubMed1996

Interactions of anesthetics with the membrane-water interface.

Although the potency of conventional anesthetics correlates with lipophilicity, an affinity to water also is essential. It was recently found that compounds with very low affinities to water do not produce anesthesia regardless of their lipophilicity. This finding implies that clinical anesthesia might arise because of interactions at molecular sites near the interface of neuronal membranes with the aqueous environment and, therefore, might require increased concentrations of anesthetic molecules at membrane interfaces. As an initial test of this hypothesis, we calculated in molecular dynamics simulations the free energy profiles for the transfer of anesthetic 1,1,2-trifluoroethane and nonanesthetic perfluoroethane across water-membrane and water-hexane interfaces. Consistent with the hypothesis, it was found that trifluoroethane, but not perfluoroethane, exhibits a free energy minimum and, therefore, increased concentrations at both interfaces. The transfer of trifluoroethane from water to the nonpolar hexane or interior of the membrane is accompanied by a considerable, solvent-induced shift in the conformational equilibrium around the C-C bond.

Anesthetics↗
PubMed1996

Excess chemical potential of small solutes across water--membrane and water--hexane interfaces.

The excess chemical potentials of five small, structurally related solutes, CH4, CH3F, CH2F2, CHF3, and CF4, across the water-glycerol 1-monooleate bilayer and water-hexane interfaces were calculated at 300, 310, and 340 K using the particle insertion method. The excess chemical potentials of nonpolar molecules (CH4 and CF4) decrease monotonically or nearly monotonically from water to a nonpolar phase. In contrast, for molecules that possess permanent dipole moments (CH3F, CH2F, and CHF3), the excess chemical potentials exhibit an interfacial minimum that arises from superposition of two monotonically and oppositely changing contributions: electrostatic and nonelectrostatic. The nonelectrostatic term, dominated by the reversible work of creating a cavity that accommodates the solute, decreases, whereas the electrostatic term increases across the interface from water to the membrane interior. In water, the dependence of this term on the dipole moment is accurately described by second order perturbation theory. To achieve the same accuracy at the interface, third order terms must also be included. In the interfacial region, the molecular structure of the solvent influences both the excess chemical potential and solute orientations. The excess chemical potential across the interface increases with temperature, but this effect is rather small. Our analysis indicates that a broad range of small, moderately polar molecules should be surface active at the water-membrane and water-oil interfaces. The biological and medical significance of this result, especially in relation to the mechanism of anesthetic action, is discussed.

Anesthetics↗
PubMed1996

Molecular modeling of protocellular functions.

The mechanisms of three protocellular functions have been studied using molecular modeling techniques. These functions are (1) the transport of ions across membranes, (2) the formation of photoactivated proton gradient that could drive chemical synthesis in the protocell, and (3) the organization of small peptides necessary for catalytic activity. In all these processes, membranes play an essential role. The transfer of ions across the barrier formed by protocellular walls is facilitated by the formation of deep, thinning defects in the membrane. Membranes also form a barrier to charged species that allows for retaining proton gradients. These gradients can be generated by a simple transmembrane proton pump consisting of a proton source and two acceptors. The directionality of the pump is ensured by a "gate-keeping" mechanism involving a water molecule, conformational change of the primary acceptor or tautomerization of a histidine. The pump can be formed by two transmembrane helices but not one helix. They provide surfaces at which organic molecules concentrate and small peptides can organize into ordered, amphiphilic structures. In general, valuable information about the origins and evolution of protocells can be obtained from the knowledge of physical and chemical principles that govern functioning of contemporary cells.

Amino Acid Sequence↗
PubMed1995

Scattering of water from the glycerol liquid-vacuum interface.

Molecular dynamics calculations of the scattering of D2O from the glycerol surface at different collision energies are reported. The results for the trapping probabilities and energy transfer are in good agreement with experiments. The calculations demonstrate that the strong attractive forces between these two strongly hydrogen bonding molecules have only a minor effect on the initial collision dynamics. The trapping probability is influenced to a significant extent by the repulsive hard sphere-like initial encounter with the corrugated surface and, only at a later stage, by the efficiency of energy flow in the multiple interactions between the water and the surface molecules.

Chemical Phenomena↗
PubMed1995

Probing the structure of cometary ice.

Computer simulations of bulk and vapor deposited amorphous ices are presented. The structure of the bulk low density amorphous ice is in good agreement with experiments on pressure disordered amorphous ice. Both the low density bulk ice and the vapor deposited ices exhibit strong ordering. Vapor deposition of hot (300 K) water molecules onto a cold (77 K) substrate yields less porous ices than deposition of cold (77 K) water molecules onto a cold substrate. Both vapor deposited ices are more porous than the bulk amorphous ice. The structure of bulk high density amorphous ice is only in fair agreement with experimental results. Attempts to simulate high density amorphous ice via vapor deposition were not successful. Electron diffraction results on vapor deposited amorphous ice indicate that the temperature of the nucleation of the cubic phase depends upon the amount of time between the deposition and the onset of crystallization, suggesting that freshly deposited ice layers reconstruct on times of the order of hours. The temperature dependence of the microporosity of the vapor deposited amorphous ices might affect laboratory experiments that are aimed at simulating astrophysical ices in the context of the origin of prebiotic organic material and its transport to the Earth.

Computer Simulation↗
PubMed1995

Molecular dynamics studies of simple membrane-water interfaces: structure and functions in the beginnings of cellular life.

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience "interfacial resistance" to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

Biophysical Phenomena↗
PubMed1994

Molecular dynamics of a water-lipid bilayer interface.

We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5 ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profiles, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

Carbon↗
PubMed1993

Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study.

The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

Carbon↗
PubMed1993

Viewpoint 9--molecular structure of aqueous interfaces.

In this review we summarize recent progress in our understanding of the structure of aqueous interfaces emerging from molecular level computer simulations. It is emphasized that the presence of the interface induces specific structural effects which, in turn, influence a wide variety of phenomena occurring near the phase boundaries. At the liquid-vapor interface, the most probable orientations of a water molecule is such that its dipole moment lies parallel to the interface, one O-H bond points toward the vapor and the other O-H bond is directed toward the liquid. The orientational distributions are broad and slightly asymmetric, resulting in an excess dipole moment pointing toward the liquid. These structural preferences persist at interfaces between water and nonpolar liquids, indicating that the interactions between the two liquids in contact are weak. It was found that liquid-liquid interfaces are locally sharp but broadened by capillary waves. One consequence of anisotropic orientations of interfacial water molecules is asymmetric interactions, with respect to the sign of the charge, of ions with the water surface. It was found that even very close to the surface ions retain their hydration shells. New features of aqueous interfaces have been revealed in studies of water-membrane and water-monolayer systems. In particular, water molecules are strongly oriented by the polar head groups of the amphiphilic phase, and they penetrate the hydrophilic head-group region, but not the hydrophobic core. At infinite dilution near interfaces, amphiphilic molecules exhibit behavior different from that in the gas phase or in bulk water. This result sheds new light on the nature of hydrophobic effect in the interfacial regions. The presence of interfaces was also shown to affect both equilibrium and dynamic components of rates of chemical reactions. Applications of continuum models to interfacial problems have been, so far, unsuccessful. This, again, underscores the importance of molecular-level information about interfaces.

Computer Simulation↗
PubMed1993

Structure and Energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamics study.

A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate. This result underscores the difference between hydrophobic hydration at the surface and in the bulk solvent, when nonpolar molecular fragments adopt compact conformations.

Adsorption↗
PubMed1992

Theory of hydrophobicity: transient cavities in molecular liquids.

Observation of the size distribution of transient cavities in computer simulations of water, n-hexane, and n-dodecane under benchtop conditions shows that the sizes of cavities are more sharply defined in liquid water but the most-probable-size cavities are about the same size in each of these liquids. The calculated solvent atomic density in contact with these cavities shows that water applies more force per unit area of cavity surface than do the hydrocarbon liquids. This contact density, or "squeezing" force, reaches a maximum near cavity diameters of 2.4 angstroms. The results for liquid water are compared to the predictions of simple theories and, in addition, to results for a reference simple liquid. The numerical data for water at a range of temperatures are analyzed to extract a surface free energy contribution to the work of formation of atomic-size cavities. Comparison with the liquid-vapor interfacial tensions of the model liquids studied here indicates that the surface free energies extracted for atomic-size cavities cannot be accurately identified with the macroscopic surface tensions of the systems.

Alkanes↗
PubMed1991

Interaction of monovalent ions with the water liquid-vapor interface: a molecular dynamics study.

Results of molecular dynamics studies on the ions Na+, F-, and Cl- near the water liquid-vapor interface are reported. The free energies required to move the ions to the interface are presented and shown to depend on the sign of the ionic charge, and not the size of the ion. F- and Cl- can approach to within 2 molecular layers of the interface without incurring a significant change in free energy, while it costs about 2.5 kcal/mole to move Na+ this same distance. The free energy differences between the cation and the anions arise from the interaction of the ions with the water molecules in the interfacial region. These water molecules are oriented with a slight preference for their molecular dipoles to point toward the liquid. Thus, the anions approaching the interface disrupt the water structure less than does the cation. The calculated free energy curves are compared with predictions of simple dielectric models. It is shown that these models do not provide a good description of ions at the water surface. The ions are found to retain their first solvation shells at the interface. The anions also retain part of their second solvation shells, while Na+ does not. As a result, a larger bulge in the water surface is observed above the anions than above Na+. The lateral mobilities of the ions increase at the interface, in qualitative agreement with predictions of hydrodynamic models.

Chemical Phenomena↗
PubMed1991

Molecular dynamics of phenol at the liquid-vapor interface of water.

Molecular dynamics results are presented for phenol at the water liquid-vapor interface at 300 K. The calculated excess free energy of phenol at the interface is -2.8 +/- 0.4 kcal/mol, in good agreement with the recent experimental results of Eisenthal and co-workers. The most probable orientation of the phenol molecule at the surface is such that the aromatic ring is perpendicular to the interface and the OH group is fully immersed in water. The hydroxyl substituent has a preferred orientation which is similar to the orientation of OH bonds of water at the pure water liquid-vapor interface. The transition between interfacial and bulk-like behavior of phenol is abrupt and occurs when the center of mass of the solute is located about 6 angstroms from the Gibbs surface of water. In this region the para carbon atom of the hydrophobic benzene ring can reach the interface and become partially dehydrated. This result suggests that the width of the interfacial region in which the behavior of a simple amphiphilic solute in water is influenced by the presence of the surface depends primarily on the size of its hydrophobic part. The role of the OH substituent was investigated by comparing phenol at the interface with two model systems: benzene with and without partial charges on carbon and hydrogen atoms. It is shown that in the absence of the hydrophilic substituent the solute is located further away from the liquid phase and is more likely to be oriented parallel to the interface. However, when the center of mass of the solute is moved into the interfacial region where the density of water approaches that of the bulk solvent, all three molecules become oriented perpendicularly to the surface. In this orientation the work of cavity formation needed to accommodate the hydrophobic ring in aqueous solvent is minimized.

Algorithms↗
PubMed1990

Cavities in molecular liquids and the theory of hydrophobic solubilities.

Thermal configurational data on neat liquids are used to obtain the work of formation of hard spherical cavities of atomic size in six molecular solvents: n-hexane, n-dodecane, n-undecyl alcohol, chloroform, carbon tetrachloride, and water. These results are used to test a recent suggestion that the differences between nonaqueous solvents and liquid water in solvation of inert gases are not principally due to the hydrogen-bonded structure of liquid water but rather to the comparatively small size of the water molecule. The frequencies of occurrence of cavities in liquid water can be meaningfully distinguished from those in the organic solvents. Liquid water has a larger fractional free volume, but that free volume is distributed in smaller packets. With respect to cavity work, water is compared to a solvent of the same molecular density and composed of hard spheres of the same size as the water molecule. That comparison indicates that the hard-sphere liquid finds more ways to configure its free volume in order to accommodate an atomic solute of substantial size and thus, would be more favorable solvent for inert gases. The scaled particle model of inert gas solubility in liquid water predicts cavity works 20% below the numerical data for TIP4P water at 300 K and 1.0 g/cm3 for cavity radii near 2.0 angstroms. It is argued that the sign of this difference is just the sign that ought to be expected and that the magnitude of this difference measures structural differences between water and the directly comparable hard-sphere liquid. In conjunction with previous data, these results indicate that atomic sized cavities should be considered submacroscopic.

Alkanes↗
PubMed1990

DNA dynamics in aqueous solution: opening the double helix.

The opening of a DNA base pair is a simple reaction that is a prerequisite for replication, transcription, and other vital biological functions. Understanding the molecular mechanisms of biological reactions is crucial for predicting and, ultimately, controlling them. Realistic computer simulations of the reactions can provide the needed understanding. To model even the simplest reaction in aqueous solution requires hundreds of hours of supercomputing time. We have used molecular dynamics techniques to simulate fraying of the ends of a six base pair double strand of DNA, [TCGCGA]2, where the four bases of DNA are denoted by T (thymine), C (cytosine), G (guanine), and A (adenine), and to estimate the free energy barrier to this process. The calculations, in which the DNA was surrounded by 2,594 water molecules, required 50 hours of CRAY-2 CPU time for every simulated 100 picoseconds. A free energy barrier to fraying, which is mainly characterized by the movement of adenine away from thymine into aqueous environment, was estimated to be 4 kcal/mol. Another fraying pathway, which leads to stacking between terminal adenine and thymine, was also observed. These detailed pictures of the motions and energetics of DNA base pair opening in water are a first step toward understanding how DNA will interact with any molecule.

Adenine↗