Peter J. Rossky

The structure of liquid water at an extended hydrophobic surface

Molecular dynamics simulations have been carried out for liquid water between flat hydrophobic surfaces. The surfaces produce density oscillations that extend at least 10 A into the liquid, and significant molecular orientational preferences that extend at least 7 A into the liquid. The liquid structure nearest the surface is characterized by ‘‘dangling’’ hydrogen bonds; i.e., a typical water molecule at the surface has one potentially hydrogen‐bonding group oriented toward the hydrophobic surface. This surface arrangement represents a balance between the tendencies of the liquid to maximize the number of hydrogen bonds on the one hand, and to maximize the packing density of the molecules on the other. A detailed analysis shows that the structural properties of the liquid farther from the surface can be understood as effects imposed by this surface structure. These results show that the hydration structure of large hydrophobic surfaces can be very different from that of small hydrophobic molecules.

Alkali halides in water: Ion–solvent correlations and ion–ion potentials of mean force at infinite dilution

Using the specialization of the extended RISM equation to infinitely dilute systems, we have calculated correlation functions and interionic potentials of mean force for a set of models corresponding to the first few alkali halides in water. From the results obtained at infinite dilution we calculate the lowest order corrections to the solution properties of the ions. Higher concentrations are explored by using the interionic potentials of mean force at infinite dilution as effective solvent mediated pair potentials. Our results indicate that certain thermodynamic properties, such as the mean activity coefficients and osmotic pressures, are quite sensitive to the details of both the theory and the potential models.

An extended rism equation for molecular polar fluids

Abstract The RISM integral equation is extended to molecules with charged sites via a renormalization of the Coulomb potentials and the introduction of appropriate closure relations. For a fluid of diatomics with atomic charges of ±0.2 e the equation yields site-site correlation functions in qualitative agreement with those from computer simulation.

A comparison of the structure and dynamics of liquid water at hydrophobic and hydrophilic surfaces—a molecular dynamics simulation study

The structure and dynamics of liquid water at the interface with three solid surfaces has been investigated via molecular dynamics simulation. The three surfaces include a flat hydrophobic surface, an atomically rough hydrophobic surface, and a contrasting, hydrophilic, fully hydroxylated silica surface. The results of analysis show that, as expected, the solvent near each of the two hydrophobic surfaces behaves essentially equivalently, with loss of hydrogen bonding at the interface. For the hydroxylated surface, surface–solvent hydrogen bonding is stronger than interactions in the bulk solvent, with the nearest solvent layer interacting specifically with up to three surface hydroxyl groups. Nevertheless, distinct structural perturbation of the solvent extends in every case no more than about 10 A from the surface, and the perturbation is only strong in the immediate solvation layer. Furthermore, the corresponding dynamical perturbation of the solvent, as measured by the diffusion rates and reorientation...

Nonadiabatic processes in condensed matter: semi-classical theory and implementation

Abstract The description of nonadiabatic processes is important to the understanding of a wide variety of dynamical processes in condensed matter. We describe technical aspects of our “quantum molecular dynamics” algorithm, focusing on: (1) the interaction between a quantum system and classical bath via a “quantum” force, (2) general properties and advantages of such a semiclassical theory, and (3) significant improvement in two numerical techniques developed for implementation of the theory. The successful application to large-scale simulations is briefly described.

From Molecules to Materials: Current Trends and Future Directions

The development, characterization, and exploitation of novel materials based on the assembly of molecular components is an exceptionally active and rapidly expanding field. For this reason, the topic of molecule-based materials (MBMs) was chosen as the subject of a workshop sponsored by the Chemical Sciences Division of the United States Department of Energy. The purpose of the workshop was to review and discuss the diverse research trajectories in the field from a chemical perspective, and to focus on the critical elements that are likely to be essential for rapid progress. The MBMs discussed encompass a diverse set of compositions and structures, including clusters, supramolecular assemblies, and assemblies incorporating biomolecule-based components. A full range of potentially interesting materials properties, including electronic, magnetic, optical, structural, mechanical, and chemical characteristics were considered. Key themes of the workshop included synthesis of novel components, structural control, characterization of structure and properties, and the development of underlying principles and models. MBMs, defined as auseful substances prepared from molecules or molecular ions that maintain aspects of the parent molecular frameworko are of special significance because of the capacity for diversity in composition, structure, and properties, both chemical and physical. Key attributes are the ability in MBMs to access the additional dimension of multiple length scales and available structural complexity via organic chemistry synthetic methodologies and the innovative assembly of such diverse components. The interaction among the assembled components can thus lead to unique behavior. A consequence of the complexity is the need for a multiplicity of both existing and new tools for materials synthesis, assembly, characterization, and

Brownian dynamics as smart Monte Carlo simulation

A new Monte Carlo simulation procedure is developed which is expected to produce more rapid convergence than the standard Metropolis method. The trial particle moves are chosen in accord with a Brownian dynamics algorithm rather than at random. For two model systems, a string of point masses joined by harmonic springs and a cluster of charged soft spheres, the new procedure is compared to the standard one and shown to manifest a more rapid convergence rate for some important energetic and structural properties.

Collapse of stiff conjugated polymers with chemical defects into ordered, cylindrical conformations

The optical, electronic and mechanical properties of synthetic and biological materials consisting of polymer chains depend sensitively on the conformation adopted by these chains. The range of conformations available to such systems has accordingly been of intense fundamental as well as practical interest, and distinct conformational classes have been predicted, depending on the stiffness of the polymer chains and the strength of attractive interactions between segments within a chain. For example, flexible polymers should adopt highly disordered conformations resembling either a random coil or, in the presence of strong intrachain attractions, a so-called ‘molten globule’. Stiff polymers with strong intrachain interactions, in contrast, are expected to collapse into conformations with long-range order, in the shape of toroids or rod-like structures. Here we use computer simulations to show that the anisotropy distribution obtained from polarization spectroscopy measurements on individual poly[2-methoxy-5-(2′-ethylhexyl)oxy-1,4-phenylenevinylene] polymer molecules is consistent with this prototypical stiff conjugated polymer adopting a highly ordered, collapsed conformation that cannot be correlated with ideal toroid or rod structures. We find that the presence of so-called ‘tetrahedral chemical defects’, where conjugated carbon–carbon links are replaced by tetrahedral links, divides the polymer chain into structurally identifiable quasi-straight segments that allow the molecule to adopt cylindrical conformations. Indeed, highly ordered, cylindrical conformations may be a critical factor in dictating the extraordinary photophysical properties of conjugated polymers, including highly efficient intramolecular energy transfer and significant local optical anisotropy in thin films.

Surface topography dependence of biomolecular hydrophobic hydration

Many biomolecules are characterized by surfaces containing extended nonpolar regions, and the aggregation and subsequent removal of such surfaces from water is believed to play a critical role in the biomolecular assembly in cells. A better understanding of the hydrophobic hydration of biomolecules may therefore yield new insights into intracellular assembly. Conventional views hold that the hydration shell of small hydrophobic solutes is clathrate-like, characterized by local cage-like hydrogen-bonding structures and a distinct loss in entropy. The hydration of extended nonpolar planar surfaces, however, appears to involve structures that are orientationally inverted relative to clathrate-like hydration shells,, with unsatisfied hydrogen bonds that are directed towards the hydrophobic surface. Here we present computer simulations of the interaction between the polypeptide melittin and water that demonstrate that the two different hydration structures also exist near a biomolecular surface. We find that the two structures are distinguished by a substantial difference in the water–water interaction enthalpy, and that their relative contributions depend strongly on the surface topography of the melittin molecule: clathrate-like structures dominate near convex surface patches, whereas the hydration shell near flat surfaces fluctuates between clathrate-like and less-ordered or inverted structures. The strong influence of surface topography on the structure and free energy of hydrophobic hydration is likely to hold in general, and will be particularly important for the many biomolecules whose surfaces contain convex patches, deep or shallow concave grooves and roughly planar areas.

Mean-field molecular dynamics with surface hopping

Molecular dynamics simulations of many degree of freedom systems are often comprised of classical evolutions on quantum adiabatic energy surfaces with intermittent instantaneous hops from one surface to another. However, since quantum transitions are inherently nonadiabatic processes, the adiabatic approximation underlying the classical equations of motion does not hold in the regions where quantum transitions take place, and the restriction to classical trajectories for adiabatic quantum states is an approximation. Alternatives which employ classical paths that account more fully for nonadiabaticity can be computationally expensive and algorithmically complicated. Here, we propose a new method, which combines the surface hopping idea with the mean-field approximation for classical paths. Applied to three test systems, the method is shown to outperform the methods based on an adiabatic force without significant extra effort. This makes it an appealing alternative for modeling complex quantum–classical pro...