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Lawrence R Pratt

Publications and source records attributed to Lawrence R Pratt.

10 recordsLinked to original sources
PubMed2006

Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity.

The thermodynamic exclusion of Na+ relative to K+ in potassium channels is examined by calculating the distribution of binding energies for Na+ and K+ in a model of the selectivity filter of the KcsA potassium channel. These distributions are observed to take a surprisingly simple form: Gaussian with a slight positive skewness that is insignificant in the present context. Complications that might be anticipated from these distributions are not problematic here. Na+ occupies the filter with a mean binding energy substantially lower than that of K+. The difference is comparable to the difference in hydration free energies of Na+ and K+ in bulk aqueous solution. Thus, the average energies of binding to the filter do not discriminate Na+ from K+ when measured from a baseline of the difference in bulk hydration free energies. The strong binding of Na+ constricts the filter, consistent with a negative partial molar volume of Na+ in water in contrast with a positive partial molar volume of K+ in water. Discrimination in favor of K+)can be attributed to the scarcity of favorable binding configurations for Na+ compared to K+. That relative scarcity is quantified as enhanced binding energy fluctuations, which reflects both the energetically stronger binding of Na+ and the constriction of the filter induced by Na+ binding.

Journal Article↗
PubMed2005

Deblurred observation of the molecular structure of an oil-water interface.

We simulated the interface between liquid water and a stationary phase of tethered n-C18 alkyl chains at a thermodynamic state of low pressure and water vapor-liquid coexistence. The interfacial water (oxygen atom) density profile so obtained is compared with a precisely defined proximal density of water molecules (oxygen atoms) conditional on the alkyl chain configurations. Though the conventional interfacial density profile takes a traditional monotonic form, the proximal radial distribution of oxygen atoms around a specific methyl (methylene) group closely resembles that for a solitary methane solute in liquid water. Moreover, this proximal radial distribution function is sufficient to accurately reconstruct the water oxygen density profile of the oil-water interface. These observations provide an alternative interpretation to collective drying or vaporization interpretations of commonly observed oil-water interfacial profiles for which water penetration into the interfacial region plays a role.

Carbon↗
PubMed2004

Hydration and mobility of HO-(aq).

The hydroxide anion plays an essential role in many chemical and biochemical reactions. But a molecular-scale description of its hydration state, and hence also its transport, in water is currently controversial. The statistical mechanical quasichemical theory of solutions suggests that HO.[H2O]3(-) is the predominant species in the aqueous phase under standard conditions. This result agrees with recent spectroscopic studies on hydroxide water clusters and with the available thermodynamic hydration free energies. In contrast, a recent ab initio molecular dynamics simulation has suggested that HO.[H2O]4(-) is the only dominant aqueous solution species. We apply adiabatic ab initio molecular dynamics simulations and find good agreement with both the quasichemical theoretical predictions and experimental results. The present results suggest a picture that is simpler, more traditional, but with additional subtlety. These coordination structures are labile but the tricoordinate species is the prominent case. This conclusion is unaltered with changes in the electronic density functional. No evidence is found for rate-determining activated interconversion of a HO.[H2O]4(-) trap structure to HO.[H2O]3(-) mediating hydroxide transport. The view of HO- diffusion as the hopping of a proton hole has substantial validity, the rate depending largely on the dynamic disorder of the water hydrogen-bond network.

Journal Article↗
PubMed2004

Hydration structure and free energy of biomolecularly specific aqueous dications, including Zn2+ and first transition row metals.

The hydration of some of the alkaline earth divalent metal cations and first row transition metal cations is considered within the quasi-chemical theory of solutions. Quantum chemical calculations provide information on the chemically important interactions between the ion and its first-shell water molecules. A dielectric continuum model supplies the outer-shell contribution. The theory then provides the framework to mesh these quantities together. The agreement between the calculated and experimental quantities is good. For the transition metal cations, it is seen that the ligand field contributions play an important role in the physics of hydration. Removing these bonding contributions from the computed hydration free energy results in a linear decrease in the hydration free energy along the period. It is precisely such effects that molecular mechanics force fields have not captured. The implications and extensions of this study to metal atoms in proteins are suggested.

Calcium↗
PubMed2003

Free energy of liquid water on the basis of quasichemical theory and ab initio molecular dynamics.

We use ab initio molecular dynamics as a basis for quasichemical theory evaluation of the free energy of water near conventional liquid thermodynamic states. The Perdew-Wang-91 (PW91), Perdew-Burke-Ernzerhof (PBE), and revised PBE (rPBE) functionals are employed. The oxygen radial density distribution using the rPBE functional is in reasonable agreement with current experiments, whereas the PW91 and PBE functionals predict a more structured oxygen radial density distribution. The diffusion coefficient with the rPBE functional is in reasonable accord with experiments. Using a maximum entropy procedure, we obtain x0 from the coordination number distribution xn for oxygen atoms having n neighbors. Likewise, we obtain p0 from pn, the probability of observing cavities of specified radius containing n water molecules. The probability x0 is a measure of the local chemical interactions and is central to the quasichemical theory of solutions. The probability p0, central to the theory of liquids, is a measure of the free energy required to open cavities of defined sizes in the solvent. Using these values and a reasonable model for electrostatic and dispersion effects, the hydration free energy of water in water at 314 K is calculated to be -5.1 kcal/mole with the rPBE functional, in encouraging agreement with the experimental value of -6.1 kcal/mole.

Computer Simulation↗
PubMed2003

Self-consistent molecular field theory for packing in classical liquids.

Building on a quasichemical formulation of solution theory, this paper proposes a self-consistent molecular field theory for packing problems in classical liquids, and tests the theoretical predictions for the excess chemical potential of the hard sphere fluid. Results are given for the self-consistent molecular fields obtained, and for the probabilities of occupancy of a molecular observation volume. For this system, the excess chemical potential predicted is nearly as accurate as the most accurate prior theories, specifically the scaled particle (Percus-Yevick compressibility) theory. A compact formula is obtained to throw light on the variation of the chemical potential with the radius of a distinguished hard sphere solute in general solvents. It is argued that the present approach is particularly simple, permits a natural description of possibilities for multiphasic behavior of the solution, and should provide a basis for a molecular-scale description of more complex solutions.

Journal Article↗
PubMed2003

Hydration of krypton and consideration of clathrate models of hydrophobic effects from the perspective of quasi-chemical theory.

Ab initio molecular dynamics (AIMD) results on a krypton-water liquid solution are presented and compared to recent XAFS results for the radial hydration structure for a Kr atom in liquid water solution. Though these AIMD calculations have important limitations of scale, the comparisons with the liquid solution results are satisfactory and significantly different from the radial distributions extracted from the data on the solid Kr/H(2)O clathrate hydrate phase. The calculations also produce the coordination number distribution that can be examined for metastable coordination structures suggesting possibilities for clathrate-like organization; none are seen in these results. Clathrate pictures of hydrophobic hydration are discussed, as is the quasi-chemical theory that should provide a basis for clathrate pictures. Outer shell contributions are discussed and estimated; they are positive and larger than the positive experimental hydration free energy of Kr(aq), implying that inner shell contributions must be negative and of comparable size. Clathrate-like inner shell hydration structures on a Kr atom solute are obtained for some, but not all, of the coordination number cases observed in the simulation. The structures found have a delicate stability. Inner shell coordination structures extracted from the simulation of the liquid, and then subjected to quantum chemical optimization, always decomposed. Interactions with the outer shell material are decisive in stabilizing coordination structures observed in liquid solution and in clathrate phases. The primitive quasi-chemical estimate that uses a dielectric model for the influence of the outer shell material on the inner shell equilibria gives a contribution to hydration free energy that is positive and larger than the experimental hydration free energy. The 'what are we to tell students' question about hydrophobic hydration, often answered with structural clathrate pictures, is then considered; we propose an alternative answer that is consistent with successful molecular theories of hydrophobic effects and based upon distinctive observable properties of liquid water. Considerations of parsimony, for instance Ockham's razor, then suggest that additional structural hypotheses in response to 'what are we to tell students' are not required at this stage.

Hydrophobic and Hydrophilic Interactions↗
PubMed2002

Molecular theory of hydrophobic effects: "She is too mean to have her name repeated.".

This paper reviews the molecular theory of hydrophobic effects relevant to biomolecular structure and assembly in aqueous solution. Recent progress has resulted in simple, validated molecular statistical thermodynamic theories and clarification of confusing theories of decades ago. Current work is resolving effects of wider variations of thermodynamic state, e.g., pressure denaturation of soluble proteins, and more exotic questions such as effects of surface chemistry in treating stability of macromolecular structures in aqueous solution.

Journal Article↗