9,581 research outputs found
Quasi-Chemical and Structural Analysis of Polarizable Anion Hydration
Quasi-chemical theory is utilized to analyze the roles of solute polarization
and size in determining the structure and thermodynamics of bulk anion
hydration for the Hofmeister series Cl, Br, and I. Excellent
agreement with experiment is obtained for whole salt hydration free energies
using the polarizable AMOEBA force field. The quasi-chemical approach exactly
partitions the solvation free energy into inner-shell, outer-shell packing, and
outer-shell long-ranged contributions by means of a hard-sphere condition.
Small conditioning radii, even well inside the first maximum of the
ion-water(oxygen) radial distribution function, result in Gaussian behavior for
the long-ranged contribution that dominates the ion hydration free energy. The
spatial partitioning allows for a mean-field treatment of the long-ranged
contribution, leading to a natural division into first-order electrostatic,
induction, and van der Waals terms. The induction piece exhibits the strongest
ion polarizability dependence, while the larger-magnitude first-order
electrostatic piece yields an opposing but weaker polarizability dependence. In
addition, a structural analysis is performed to examine the solvation
anisotropy around the anions. As opposed to the hydration free energies, the
solvation anisotropy depends more on ion polarizability than on ion size:
increased polarizability leads to increased anisotropy. The water dipole
moments near the ion are similar in magnitude to bulk water, while the ion
dipole moments are found to be significantly larger than those observed in
quantum mechanical studies. Possible impacts of the observed over-polarization
of the ions on simulated anion surface segregation are discussed.Comment: slight revision, in press at J. Chem. Phy
Polarization and Charge Transfer in the Hydration of Chloride Ions
A theoretical study of the structural and electronic properties of the
chloride ion and water molecules in the first hydration shell is presented. The
calculations are performed on an ensemble of configurations obtained from
molecular dynamics simulations of a single chloride ion in bulk water. The
simulations utilize the polarizable AMOEBA force field for trajectory
generation, and MP2-level calculations are performed to examine the electronic
structure properties of the ions and surrounding waters in the external field
of more distant waters. The ChelpG method is employed to explore the effective
charges and dipoles on the chloride ions and first-shell waters. The Quantum
Theory of Atoms in Molecules (QTAIM) is further utilized to examine charge
transfer from the anion to surrounding water molecules.
From the QTAIM analysis, 0.2 elementary charges are transferred from the ion
to the first-shell water molecules. The default AMOEBA model overestimates the
average dipole moment magnitude of the ion compared with the estimated quantum
mechanical value. The average magnitude of the dipole moment of the water
molecules in the first shell treated at the MP2 level, with the more distant
waters handled with an AMOEBA effective charge model, is 2.67 D. This value is
close to the AMOEBA result for first-shell waters (2.72 D) and is slightly
reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment
of the water molecules in the first solvation shell is most strongly affected
by the local water-water interactions and hydrogen bonds with the second
solvation shell, rather than by interactions with the ion.Comment: Slight revision, in press at J. Chem. Phy
Bilayer polarity and its thermal dependency in the e(o) and e(d) phases of binary phosphatidylcholine/cholesterol mixtures
Diverse variations in membrane properties are observed in binary phosphatidylcholine/cholesterol mixtures. These mixtures are nonideal, displaying single or phase coexistence, depending on chemical composition and other thermodynamic parameters. When compared with pure phospholipid bilayers, there are changes in water permeability, bilayer thickness and thermomechanical properties, molecular packing and conformational freedom of phospholipid acyl chains, in internal dipolar potential and in lipid lateral diffusion. Based on the phase diagrams for DMPC/cholesterol and DPPC/cholesterol, we compare the equivalent polarity of pure bilayers with specific compositions of these mixtures, by using the Py empirical scale of polarity. Besides the contrast between pure and mixed lipid bilayers, we find that liquid-ordered and liquid-disordered (e(d)) phases display significantly different polarities. Moreover, in the e(o) phase, the polarities of bilayers and their thermal dependences vary with the chemical composition, showing noteworthy differences for cholesterol proportions at 35, 40, and 45 mol%. At 20 degrees C, for DMPC/ cholesterol at 35 and 45 mol%, the equivalent dielectric constants are 21.8 and 23.8, respectively. Additionally, we illustrate potential implications of polarity in various membrane-based processes and reactions, proposing that for cholesterol containing bilayers, it may also go along with the occurrence of lateral heterogeneity in biological membranes. (c) 2007 Elsevier B.V. All rights reserved.info:eu-repo/semantics/publishedVersio
Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive
Atomistic molecular simulations are a powerful way to make quantitative
predictions, but the accuracy of these predictions depends entirely on the
quality of the forcefield employed. While experimental measurements of
fundamental physical properties offer a straightforward approach for evaluating
forcefield quality, the bulk of this information has been tied up in formats
that are not machine-readable. Compiling benchmark datasets of physical
properties from non-machine-readable sources require substantial human effort
and is prone to accumulation of human errors, hindering the development of
reproducible benchmarks of forcefield accuracy. Here, we examine the
feasibility of benchmarking atomistic forcefields against the NIST ThermoML
data archive of physicochemical measurements, which aggregates thousands of
experimental measurements in a portable, machine-readable, self-annotating
format. As a proof of concept, we present a detailed benchmark of the
generalized Amber small molecule forcefield (GAFF) using the AM1-BCC charge
model against measurements (specifically bulk liquid densities and static
dielectric constants at ambient pressure) automatically extracted from the
archive, and discuss the extent of available data. The results of this
benchmark highlight a general problem with fixed-charge forcefields in the
representation low dielectric environments such as those seen in binding
cavities or biological membranes
Spectrum of slow and super-slow (picosecond to nanosecond) water dynamics around organic and biological solutes
Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ~50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins
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