Thermodynamics of water modeled using ab initio simulations

We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal energy and hence also the excess entropy are not. Our work emphasizes the importance of thermodynamic characterization in assessing the quality of electron density functionals in describing liquid water and hydration phenomena

Quasichemical theory and the description of associating fluids relative to a reference: Multiple bonding of a single site solute

We derive an expression for the chemical potential of an associating solute in a solvent relative to the value in a reference fluid using the quasichemical organization of the potential distribution theorem. The fraction of times the solute is not associated with the solvent, the monomer fraction, is expressed in terms of (a) the statistics of occupancy of the solvent around the solute in the reference fluid and (b) the Widom factors that arise because of turning on solute-solvent association. Assuming pair-additivity, we expand the Widom factor into a product of Mayer f-functions and the resulting expression is rearranged to reveal a form of the monomer fraction that is analogous to that used within the statistical associating fluid theory (SAFT). The present formulation avoids all graph-theoretic arguments and provides a fresh, more intuitive, perspective on Wertheim's theory and SAFT. Importantly, multi-body effects are transparently incorporated into the very foundations of the theory. We illustrate the generality of the present approach by considering examples of multiple solvent association to a colloid solute with bonding domains that range from a small patch on the sphere, a Janus particle, and a solute whose entire surface is available for association

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+.Comment: 8 pages, 6 figure

Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptides

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell. The cavity contribution is obtained for two different envelopes, $\Sigma_{SE}$ which theory identifies as the solvent excluded volume and a larger envelope ($\Sigma_G$) beyond which solute-solvent interactions are Gaussian. For both envelopes, the cavity contribution in water is proportional to the surface area of the envelope. The same does not hold for GdmCl(aq), revealing limitations of using molecular area to assess solvation energetics, especially in mixed solvents. The $\Sigma_G$-cavity contribution predicts that GdmCl(aq) should favor the more compact state, contrary to the role of GdmCl in unfolding proteins. The chemistry contribution attenuates this effect, but still the net local (chemistry plus $\Sigma_G$-packing) contribution is inadequate in capturing the role of GdmCl. With the inclusion of the long-range contribution, which is dominated by van~der~Waals interaction, aqueous GdmCl favors the extended conformation over the compact conformation. Our finding emphasizes the importance of weak, but attractive, long-range dispersion interactions in protein solution thermodynamics

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.Comment: 7 pages, 5 figures, additional results include