arXiv subjects

Lawrence R. Pratt

Publications and source records attributed to Lawrence R. Pratt.

At least 19 recordsLinked to original sources

arXiv2022

Hydrated anions: From clusters to bulk solution with quasi-chemical theory

The interactions of hydrated ions with solution and interface partners are strong on a chemical energy scale. Here, we test the foremost \textit{ab initio theory} for evaluation of hydration free energies of ions, namely, \textit{quasi-chemical theory} (QCT). We focus on halide anions, but also the hydroxide anion, since they have been outstanding challenges for all theories. QCT is built by identification of inner-shell clusters, separate treatment of those clusters, then integration of those results into the broader-scale solution environment. We exploit a close comparison with mass-spectrometric measurements of ion-hydration equilibria. That theory-experiment comparison is excellent with moderate computational effort here. This agreement reinforces both theory and experiment, and provides a numerically accurate inner-shell contribution to QCT. The inner-shell complexes involving heavier halides display strikingly asymmetric hydration clusters. QCT provides a favorable setting for exploitation of the polarizable continuum model (PCM) when the inner-shell material shields the ion from the outer solution environment. For the asymmetrically hydrated, and less effectively shielded, heavier halide ions, we investigate an inverse procedure in which the inner-shell structures are sampled from readily available AIMD calculations on the bulk solutions. This inverse procedure is a remarkable improvement and our final results are in close agreement with a standard tabulation of hydration free energies. Comparison of anion hydration cluster structures with bulk solutions from AIMD simulations emphasize slight differences: the asymmetries of bulk solution inner-shell structures are moderated, but still present; and inner shells fill to slightly higher average coordination numbers in bulk solution than in clusters.

physics.chem-ph↗

arXiv2021

Thermodynamics of Hydration from the Perspective of the Molecular Quasi-Chemical Theory of Solutions

The quasi-chemical organization of the potential distribution theorem -- molecular quasi-chemical theory (QCT) -- enables practical calculations and also provides a conceptual framework for molecular hydration phenomena. QCT can be viewed from multiple perspectives: (a) As a way to regularize an ill-conditioned statistical thermodynamic problem; (b) As an introduction of and emphasis on the neighborship characteristics of a solute of interest; (c) Or as a way to include accurate electronic structure descriptions of near-neighbor interactions in defensible statistical thermodynamics by clearly defining neighborship clusters. The theory has been applied to solutes of a wide range of chemical complexity, ranging from ions that interact with water with both long-ranged and chemically intricate short-ranged interactions, to solutes that interact with water solely through traditional van~der~Waals interations, and including water itself. The solutes range in variety from monoatomic ions to chemically heterogeneous macromolecules. A notable feature of QCT is that in applying the theory to this range of solutes, the theory itself provides guidance on the necessary approximations and simplifications that can facilitate the calculations. In this Perspective, we develop these ideas and document them with examples that reveal the insights that can be extracted using the QCT formulation.

physics.chem-ph↗

arXiv2019

Long-Range Interactions Dominate the Inverse-Temperature Dependence of Polypeptide Hydration Free Energies

Direct, all-atom calculations of the free energy of hydration of aqueous deca-alanine structures --- holistically including backbone and side-chain interactions together --- show that attractive interactions and the thermal expansion of the solvent explain the inverse temperature signatures that have been interpreted traditionally in favor of hydrophobic mechanisms for stabilizing the structure and function of soluble proteins.

physics.chem-ph↗

arXiv2018

Molecular Dynamics of Lithium Ion Transport in a Model Solid Electrolyte Interphase

Li+ transport within a solid electrolyte interphase (SEI) in lithium ion batteries has challenged molecular dynamics (MD) studies due to limited compositional control of that layer. In recent years, experiments and ab initio simulations have identified dilithium ethylene dicarbonate (Li2EDC) as the dominant component of SEI layers. Here, we adopt a parameterized, non-polarizable MD force field for Li2EDC to study transport characteristics of Li+ in this model SEI layer at moderate temperatures. The observed correlations are consistent with recent MD results using a polarizable force field, suggesting that this non-polarizable model is effective for our purposes of investigating Li+ dynamics over long time scales. Mean-squared displacements distinguish three distinct Li+ transport regimes in EDC ballistic, trapping, and diffusive. Compared to liquid ethylene carbonate (EC), the nanosecond trapping times in EDC are significantly longer and naturally decrease at higher temperatures. New materials developed for fast-charging Li-ion batteries should have smaller trapping regions. The analyses implemented in this paper can be used for testing transport of Li+ ion in novel battery materials. Non-Gaussian features of van Hove self -correlation functions for Li+ in EDC, along with the mean-squared displacements, are consistent in describing EDC as a glassy material compared with liquid EC. Vibrational modes of Li+ ion, identified by MD, characterize the trapping and are further validated by electronic structure calculations.

physics.chem-ph↗

arXiv2015

Interfaces of Propylene Carbonate

Propylene carbonate (PC) wets graphite with a contact angle of 31 deg at ambient conditions. Molecular dynamics simulations agree with this contact angle after 40% reduction of the strength of graphite-C atom Lennard-Jones interactions with the solvent, relative to the models used initially. A simulated nano-scale PC droplet on graphite displays a pronounced layering tendency and an Aztex pyramid structure for the droplet. Extrapolation of the computed tensions of PC liquid-vapor interface estimates the critical temperature of PC accurately to about 3%. PC molecules lie flat on the PC liquid-vapor surface, and tend to project the propyl carbon toward the vapor phase. For close PC neighbors in liquid PC, an important packing motif stacks carbonate planes with the outer oxygen of one molecule snuggled into the positively charged propyl end of another molecule so that neighboring molecule dipole moments are approximately antiparallel. The calculated thermal expansion coefficient and the dielectric constants for liquid PC agree well with experiment. The distribution of PC molecule binding energies is closely Gaussian. Evaluation of the density of the coexisting vapor then permits estimation of the packing contribution to the PC chemical potential, and that contribution is about 2/3rds of the magnitude of the contributions due to attractive interactions, with opposite sign.

physics.chem-ph↗

arXiv2012

Microstructures of capped ethylene oxide oligomers in water and n-hexane

This report documents microstructural features of CH3(CH2-O-CH2)mCH3 dissolved in water and n-hexane for m = 11, 21, and 31. Probability densities for end-to-end distance, and the associated potential-of-mean-force (pmf), are more revealing of chain microstructures than are the corresponding results for the radii of gyration. For water, the pmf identifies three distinct regions: loop-closure, globule, and high-extension regions. The globule region affirms a water-swollen chain, and is not evident in the n-hexane results. Chain C-atom density profiles from the chain centroid are also different in the water and n-hexane cases. For n-hexane (but not water), the density profiles are similar for the different chain lengths when the distances are scaled by the observed ^{1/2}. For water (but not n-hexane) and the smaller chains considered, the carbon material exhibits a distinctive enhanced concentration, or internal condensation, at the centroid core of the structure.

physics.chem-ph↗

arXiv2010

Direct observation of a hydrophobic bond in loop-closure of a capped (-OCH2CH2-)n oligomer in water

The small r variation of the probability density P(r) for end-to-end separations of a -CH2CH3 capped (-OCH2CH2-)n oligomer in water is computed to be closely similar to the CH4 ... CH4 potential of mean force under the same circumstances. Since the aqueous solution CH4 ... CH4 potential of mean force is the natural physical definition of a primitive hydrophobic bond, the present result identifies an experimentally accessible circumstance for direct observation of a hydrophobic bond which has not been observed previously because of the low solubility of CH4 in water. The physical picture is that the soluble chain molecule carries the capping groups into aqueous solution, and permits them to find one another with reasonable frequency. Comparison with the corresponding results without the solvent shows that hydration of the solute oxygen atoms swells the chain molecule globule. This supports the view that the chain molecule globule might have a secondary effect on the hydrophobic interaction which is of first interest here. The volume of the chain molecule globule is important for comparing the probabilities with and without solvent because it characterizes the local concentration of capping groups. Study of other capping groups to enable X-ray and neutron diffraction measurements of P(r) is discussed.

physics.chem-ph↗

arXiv2008

Quasi-chemical theory with a soft cutoff

In view of the wide success of molecular quasi-chemical theory of liquids, this paper develops the soft-cutoff version of that theory. This development has important practical consequences in the common cases that the packing contribution dominates the solvation free energy of realistically-modeled molecules because treatment of hard-core interactions usually requires special purpose simulation methods. In contrast, treatment of smooth repulsive interactions is typically straightforward on the basis of widely available software. This development also shows how fluids composed of molecules with smooth repulsive interactions can be treated analogously to the molecular-field theory of the hard-sphere fluid. In the treatment of liquid water, quasi-chemical theory with soft-cutoff conditioning doesn't change the fundamental convergence characteristics of the theory using hard-cutoff conditioning. In fact, hard cutoffs are found here to work better than softer ones.

physics.chem-ph↗

arXiv2008

Role of attractive methane-water interactions in the potential of mean force between methane molecules in water

On the basis of a gaussian quasi-chemical model of hydration, a model of non van der Waals character, we explore the role of attractive methane-water interactions in the hydration of methane and in the potential of mean force between two methane molecules in water. We find that the hydration of methane is dominated by packing and a mean-field energetic contribution. Contributions beyond the mean-field term are unimportant in the hydration phenomena for a hydrophobic solute such as methane. Attractive solute-water interactions make a net repulsive contribution to these pair potentials of mean force. With no conditioning, the observed distributions of binding energies are super-gaussian and can be effectively modeled by a Gumbel (extreme value) distribution. This further supports the view that the characteristic form of the unconditioned distribution in the high-e tail is due to energetic interactions with a small number of molecules. Generalized extreme value distributions also effectively model the results with minimal conditioning, but in those cases the distributions are sufficiently narrow that details of their shape aren't significant.

physics.bio-ph↗

arXiv2007

What is special about water as a matrix of life?

Water offers a large temperature domain of stable liquid, and the characteristic hydrophobic effects are first a consequence of the temperature insensitivity of equation-of-state features of the aqueous medium, compared to other liquids. On this basis, the known aqueous media and conditions offer low risk compared to alternatives as a matrix to which familiar molecular biological structures and processes have adapted. The current molecular-scale understanding of hydrophobic hydration is not conformant in detail with a standard structural entropy rationalization. That classic pictorial explanation may serve as a mnemonic, but isn't necessary. A more defensible view is that peculiar hydrophobic effects can be comprehended by examination of engineering parameters characterizing liquid water.

physics.bio-ph↗

arXiv2007

Water adsorption and dissociation on BeO (001) and (100) surfaces

Plateaus in water adsorption isotherms on hydroxylated BeO surfaces suggest significant differences between the hydroxylated (100) and (001) surface structures and reactivities. Density functional theory structures and energies clarify these differences. Using relaxed surface energies, a Wulff construction yields a prism crystal shape exposing long (100) sides and much smaller (001) faces. This is consistent with the BeO prisms observed when beryllium metal is oxidized. A water oxygen atom binds to a single surface beryllium ion in the preferred adsorption geometry on either surface. The water oxygen/beryllium bonding is stronger on the surface with greater beryllium atom exposure, namely the less-stable (001) surface. Water/beryllium coordination facilitates water dissociation. On the (001) surface, the dissociation products are a hydroxide bridging two beryllium ions and a metal coordinated hydride with some surface charge depletion. On the (100) surface, water dissociates into a hydroxide ligating a Be atom and a proton coordinated to a surface oxygen but the lowest energy water state on the (100) surface is the undissociated metal-coordinated water. The (100) fully hydroxylated surface structure has a hydrogen bonding network which facilitates rapid proton shuffling within the network. The corresponding (001) hydroxylated surface is fairly open and lacks internal hydrogen bonding. This supports previous experimental interpretations of the step in water adsorption isotherms. Further, when the (100) surface is heated to 1000 K, hydroxides and protons associate and water desorbs. The more open (001) hydroxylated surface is stable at 1000 K. This is consistent with the experimental disappearance of the isotherm step when heating to 973 K.

physics.chem-ph↗

arXiv2005

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

The KcsA potassium channel belongs to a class of K+ channels that is selective for K+ over Na+ at rates of K+ transport approaching the diffusion limit. This selectivity is explained thermodynamically in terms of favorable partitioning of K+ relative to Na+ in a narrow selectivity filter in the channel. One mechanism for selectivity based on the atomic structure of the KcsA channel invokes the size difference between K+ and Na+, and the molecular complementarity of the selectivity filter with the larger K+ ion. An alternative view holds that size-based selectivity is precluded because atomic structural fluctuations are greater than the size difference between these two ions. We examine these hypotheses by calculating the distribution of binding energies for Na+ and K+ in a simplified model of the selectivity filter of the KcsA channel. We find that Na+ binds strongly to the selectivity filter with a mean binding energy substantially lower than that for K+. The difference is comparable to the difference in hydration free energies of Na+ and K+ in bulk aqueous solution. Thus, the average filter binding energies do not discriminate Na+ from K+ when measured from the baseline of the difference in bulk hydration free energies. Instead, Na+/K+ discrimination can be attributed to scarcity of good binding configurations for Na+ compared to K+. That relative scarcity is quantified as enhanced binding energy fluctuations, and is consistent with predicted relative constriction of the filter by Na+.

physics.bio-ph↗

arXiv2005

Scaled-Particle Theory and the Length-scales Involved in Hydrophobic Hydration of Aqueous Biomolecular Assemblies

Hydrophobic hydration plays a crucial role in self-assembly processes over multiple length-scales, but the extrapolation of molecular-scale models to larger length-scale hydration phenomena is sometimes not warranted. Scaled-particle theories are based upon an interpolative view of that issue. We revisit the scaled-particle theory proposed thirty years ago by Stillinger, adopt a practical generalization, and consider the implications for hydrophobic hydration in light of our current understanding. The generalization is based upon identifying a molecular length, implicit in previous applications of scaled-particle models, that provides an effective radius for joining microscopic and macroscopic descriptions. We demonstrate that the generalized theory correctly reproduces many of the anomalous thermodynamic properties of hydrophobic hydration for molecularly sized solutes, including solubility minima and entropy convergence, successfully interpolates between the microscopic and macroscopic extremes, and provides new insights into the underlying molecular mechanisms. The results are discussed in terms of length-scales associated with component phenomena; in particular we first discuss the micro-macroscopic joining radius identified by the theory, then we discuss in turn the Tolman length that leads to an analogous length describing curvature corrections of a surface area model of hydrophobic hydration free energies, and the length-scales on which entropy convergence of hydration free energies are expected.

physics.bio-ph↗

arXiv2003

Inner Shell Definition and Absolute Hydration Free Energy of K+(aq) on the Basis of Quasi-chemical Theory and Ab Initio Molecular Dynamics

K+(aq) ion is an integral component of many cellular processes, amongst which the most important, perhaps, is its role in transmitting electrical impulses along the nerve. Understanding its hydration structure and thermodynamics is crucial in dissecting its role in such processes. Her we address these questions using both the statistical mechanical quasi-chemical theory of solutions and ab initio molecular dynamics simulations. Simulations predict an interesting hydration structure for K+(aq): the population of about six (6) water molecules within the initial minimum of the observed g_{KO}(r) at infinite dilution involves four (4) inner-most molecules that the quasi-chemical theory suggests should be taken as the theoretical inner shell. The contribution of the 5th and 6th closest water molecules is observable as a distinct shoulder on the principal maximum of the g_{KO}(r). The quasi-chemical estimate of solvation free energy for the neutral pair KOH is also in good agreement with experiments.

physics.chem-ph↗

arXiv2003

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 quasi-chemical theory of solutions suggests that HO[H2O]3- is the predominant species in the aqueous phase under standard conditions. This result is in close agreement 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[H_2O]4- is the only dominant aqueous solution species. We apply adiabatic ab initio molecular dynamics simulations, and find good agreement with both the quasi-chemical 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 tri-coordinate species is the prominent case. This conclusion is unaltered with changes in the electronic density functional. No evidence is found for rate-determining activated inter-conversion 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.

physics.chem-ph↗

arXiv2003

Free energy of liquid water on the basis of quasi-chemical theory and ab initio molecular dynamics

We use ab initio molecular dynamics as a basis for quasi-chemical theory evaluation of the free energy of water near conventional liquid thermodynamic states. The PW91, PBE, and revised PBE (rPBE) functionals are employed. The oxygen radial density distribution, gOO(r), using the rPBE functional is in reasonable agreement with current experiments, whereas the PW91 and PBE functionals predict a more structured gOO(r). The diffusion coefficient with the rPBE functional is in reasonable accord with experiments. Using a maximum entropy procedure, we obtain x_0 from the coordination number distribution x_n for oxygen atoms having n neighbors. Likewise, we obtain p_0 from p_n, the probability of observing cavities of specified radius containing n water molecules. The probability x_0 is a measure of the local chemical interactions and is central to the quasi-chemical theory of solutions. The probability p_0, 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 314K is calculated to be -5.1kcal/mole with the rPBE functional, in encouraging agreement with the experimental value of -6.1kcal/mole.

physics.chem-ph↗

arXiv2003

The hydration state of HO$^-$(aq)

The HO$^-$(aq) ion participates in myriad aqueous phase chemical processes of biological and chemical interest. A molecularly valid description of its hydration state, currently poorly understood, is a natural prerequisite to modeling chemical transformations involving HO$^-$(aq). Here it is shown that the statistical mechanical quasi-chemical theory of solutions predicts that $\mathrm{HO\cdot[H_2O]_3{}^-}$ is the dominant inner shell coordination structure for HO$^-$(aq) under standard conditions. Experimental observations and other theoretical calculations are adduced to support this conclusion. Hydration free energies of neutral combinations of simple cations with HO$^-$(aq) are evaluated and agree well with experimental values.

physics.chem-ph↗

arXiv2003

Self Consistent Molecular Field Theory for Packing in Classical Liquids

Building on a quasi-chemical 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 as accurate as the most accurate prior theories, particularly the scaled particle (Percus-Yevick compressibility) theory. It is argued that the present approach is particularly simple, and should provide a basis for a molecular-scale description of more complex solutions.

physics.chem-ph↗