Bound Charge Layering Near a Spherical Ion: Moving Beyond Born Theory.

The response of aqueous solvent to a dissolved ion is analyzed in terms of the bound charge, the net charge of the solvent in the vicinity of the solute. The total amount of bound charge is , where is the charge of the ion and ϵ is the solvent dielectric constant, in both continuum and molecular theory. Aqueous solvation involves an inner layer of bound charge way over this value, followed by another layer that almost or over compensates the first layer, and so on.

A New Approach for Estimating the Free Energy Differences among Multiple Thermodynamic States in Statistical Simulations.

In this letter, a new approach to compute free energy differences (FEDs) between multiple thermodynamics states is introduced. The method directly uses energy probability densities, which can be extracted with high accuracy from equilibrium simulations to obtain FEDs. Methods in current use, such as Bennett acceptance ratio (BAR), its multistate generalization (MBAR), or the weighted histogram analysis method (WHAM), require iterative solution of nonlinear equations which are known to be slowly convergent.

Dielectric Behavior near a Spherical Ion.

The dielectric response of a polar solvent to an ion is analyzed in terms of the bound charge, the net charge that accumulates near the ion as a consequence of the inhomogeneous polarization of the surrounding solvent. We demonstrate that the total bound charge arising in a full molecular treatment is identical to the total bound charge from standard continuum theory. In continuum theory, the bound charge resides in an infinitely thin layer, while in a molecular description the bound charge is spread over a region of finite width.

A theoretical study of polymorphism in VQIVYK fibrils.

The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated.

Mechanism of surface freezing of alkanes.

Using molecular dynamics simulation of octane (C) and nonadecane (C), we probe the mechanism of n-alkane surface freezing, the appearance of a crystalline monolayer above the liquid at a temperature T above the bulk freezing point T. Formation of a crystalline monolayer occurs robustly in these systems. When T > T, the surface frozen phase is metastable with respect to the solid but persists for long periods for study in simulations.

Molecular Dynamics Study of the Electric Double Layer and Nonlinear Spectroscopy at the Amorphous Silica-Water Interface.

The electrical double layer (EDL) at the amorphous silica-aqueous electrolyte interface is of long-standing scientific interest and current technological relevance. Using extensive molecular dynamics simulations, we have studied this EDL as a function of salt concentration for a silica surface charge density of -0.82/nm ( = electron charge).

Biomolecules at the amorphous silica/water interface: Binding and fluorescence anisotropy of peptides.

We investigate binding of the tripeptides Lys-Trp-Lys (KWK) and Glu-Trp-Glu (EWE) to the amorphous silica surface using atomistic simulations. These peptides were chosen because they were previously utilized in experiments measuring binding affinity and steady-state fluorescence anisotropy from the indole chromophore of the tryptophan residue. Our simulations were performed using silica with surface change density of -0.

On the determination of the crystal-vapor surface free energy, and why a Gaussian expression can be accurate for a system far from Gaussian.

The crystal-vapor surface free energy γ is an important physical parameter governing physical processes, such as wetting and adhesion. We explore exact and approximate routes to calculate γ based on cleaving an intact crystal into non-interacting sub-systems with crystal-vapor interfaces. We do this by turning off the interactions, ΔV, between the sub-systems.

Polarization charge: Theory and applications to aqueous interfaces.

When an electric field is applied across an interface, a dielectric will acquire a polarization charge layer, assumed infinitely thin in the theory of macroscopic dielectrics and also in most treatments of electrokinetic phenomena in nanoscale structures. In this work we explore the polarization charge layer in molecular detail. Various formal relations and a linear response theory for the polarization charge are presented.

DNA Binding to the Silica Surface.

We investigate the DNA-silica binding mechanism using molecular dynamics simulations. This system is of technological importance, and also of interest to explore how negatively charged DNA can bind to a silica surface, which is also negatively charged at pH values above its isoelectric point near pH 3. We find that the two major binding mechanisms are attractive interactions between DNA phosphate and surface silanol groups and hydrophobic bonding between DNA base and silica hydrophobic region.

Displacements, mean-squared displacements, and codisplacements for the calculation of nonequilibrium properties.

We study two situations in which nonequilibrium phenomena can be efficiently calculated using displacements, mean-squared displacements, or codisplacements instead of accumulating velocities or currents. The flow velocity profile for a fluid confined within a pore can be expressed as a sum of displacements within slabs from a molecular dynamics trajectory. In this form, an accurate flow profile is obtained from very sparse sampling of the trajectory.

Experimental evidence for surface freezing in supercooled n-alkane nanodroplets.

Intermediate chain length (16 ≤i≤ 50) n-alkanes are known to surface freeze at temperatures that are up to three degrees higher than the equilibrium melting point [B. M. Ocko et al.

Analysis of the subcritical carbon dioxide-water interface.

We follow the evolution of the H(2)O/CO(2) interface at 300 K from the low pressure limit to near-critical pressures in molecular dynamics simulations using the SPC water and EPM2 carbon dioxide models. The intrinsic structure of the interface is elucidated by accumulating density profiles relative to the fluctuating capillary wave surface. Our main finding is that a carbon dioxide film of increasing density and thickness grows in two stages at the interface while the structure of the water surface barely changes.

An AIMD study of the CPD repair mechanism in water: reaction free energy surface and mechanistic implications.

In a series of two papers, we report the detailed mechanism of cyclobutane pyrimidine dimer repair in aqueous solvent using ab initio molecular dynamics simulations (AIMD). Umbrella sampling is used to determine the free energy surface for dimer splitting. The two-dimensional free energy surface for splitting of the C5-C5' and C6-C6' bonds on the anion surface is reported.

An AIMD study of CPD repair mechanism in water: role of solvent in ring splitting.

In this paper, we continue to explore the repair mechanisms of the cyclobutane pyrimidine dimer. We find that a full description of both C5-C5' and C6-C6' bond splitting requires a multidimensional treatment involving a solvent coordinate in addition to changes in internal dimer coordinates. Nonequilibrium effects are likely to be important as well, although the initial conditions following forward electron transfer to the dimer, beyond the scope of this study, will ultimately determine the importance of these effects.

The water-amorphous silica interface: analysis of the Stern layer and surface conduction.

To explain why dynamical properties of an aqueous electrolyte near a charged surface seem to be governed by a surface charge less than the actual one, the canonical Stern model supposes an interfacial layer of ions and immobile fluid. However, large ion mobilities within the Stern layer are needed to reconcile the Stern model with surface conduction measurements. Modeling the aqueous electrolyte-amorphous silica interface at typical charge densities, a prototypical double layer system, the flow velocity does not vanish until right at the surface.

The Dissociated Amorphous Silica Surface: Model Development and Evaluation.

At pH 7, amorphous silica has a characteristic negative charge due to the deprotonation of silanol groups on the surface. Electrokinetic phenomena and transport of biomolecules in devices depend sensitively on the surface morphology, distribution of ions and solvent, and adsorption properties of solutes close to the surface in the electrical double layer region. Hence, simulation of these phenomena requires detailed atomistic models of the double layer region.

Site disorder in ice VII arising from hydrogen bond fluctuations.

Recently, multisite models used for the refinement of neutron diffraction data have suggested that the structure of ice VII is quite unlike that of its ordered counterpart, ice VIII. We investigate the oxygen site disorder by modeling the site displacement, obtained from periodic DFT calculations, as a function of the local hydrogen bond network. Then, using graph invariants to describe hydrogen bond fluctuations in the thermodynamic limit, we perform statistical mechanical calculations using the oxygen site displacement model developed here.

Origin of slow relaxation following photoexcitation of W7 in myoglobin and the dynamics of its hydration layer.

Molecular dynamics simulations are used to calculate the time-dependent Stokes shift following photoexcitation of Trp-7 (W7) in myoglobin. In agreement with experiment, a long time (approximately 60 ps) component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of photoexcitation, we firmly establish that protein flexibility is required to observe slow Stokes shift dynamics in this case.

Hydrogen bond ordering in ice V and the transition to ice XIII.

The proton ordered version of ice V, ice XIII, was recently identified using Raman spectroscopy and neutron diffraction techniques. The transformation, between 108 and 117 K, only occurred in the presence of a small amount of dopant, similar to the proton ordering transition of ice Ih/XI. In this work, we investigate the hydrogen bond fluctuations in ice V and XIII with statistical mechanical techniques that use results from periodic electronic density functional theory calculations as input.

Model for the water-amorphous silica interface: the undissociated surface.

The physical and chemical properties of the amorphous silica-water interface are of crucial importance for a fundamental understanding of electrochemical and electrokinetic phenomena, and for various applications including chromatography, sensors, metal ion extraction, and the construction of micro- and nanoscale devices. A model for the undissociated amorphous silica-water interface reported here is a step toward a practical microscopic model of this important system. We have extended the popular BKS and SPC/E models for bulk silica and water to describe the hydrated, hydroxylated amorphous silica surface.

Hydration dynamics and time scales of coupled water-protein fluctuations.

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior.

A reexamination of the ice III/IX hydrogen bond ordering phase transition.

Ice III is a hydrogen bond disordered crystal which when cooled 1 K / min or faster transforms to an antiferroelectric hydrogen bond ordered structure, ice IX. Throughout its region of stability, experiments indicate that the H bonds in ice III are, in fact, partially ordered, i.e.

Prediction of a phase transition to a hydrogen bond ordered form of ice VI.

Ice VI is a hydrogen bond disordered crystal over its known region of stability. In this work, we predict that ice VI will transform into a hydrogen bond ordered phase near 108 K, and have identified the likely low-temperature phase as ferroelectric (space group Cc) with an antiferroelectric structure (space group P2(1)2(1)2(1)) close by in energy. Electronic density functional theory calculations provide input to our calculations, which are extended to cells large enough for statistical simulations by using graph invariants.

Hydrogen bond topology and the ice VII/VIII and Ih/XI proton ordering phase transitions.

Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled under special conditions is believed to transform to ferroelectric proton-ordered ice XI, but this transformation is still subject to controversy. Ice VII, also proton disordered throughout its region of stability, transforms to proton-ordered ice VIII upon cooling. In contrast to the ice Ih/XI transition, the VII/VIII transition and the crystal structure of ice VIII are well characterized.