Ab initio Molecular Dynamics Study of Glycine Intramolecular Proton Transfer in Water

We use ab initio molecular dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number Nw of glycine is not constant along the reaction coordinate, but rather progresses from Nw=5 in the neutral molecule to Nw=8 for the zwitterion. We report the free energy difference between the neutral and charged glycine molecules, and the free energy barrier to proton transfer. Finally, we identify approximations inherent in our method and estimate corresponding corrections to our reported thermodynamic predictions.Comment: 14 pages, 10 figures, to appear in J. Chem. Phy

Quasi-Chemical Theory and Implicit Solvent Models for Simulations

A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent model is based upon the quasi-chemical approach, distinct from the common integral equation trunk of the theory of liquid solutions. The physical content of this theory is the hypothesis that a small set of solvent molecules are decisive for these solvation problems. A detailed derivation of the quasi-chemical theory escorts the development of this proposal. The numerical application of the quasi-chemical treatment to Li$^+$ ion hydration in liquid water is used to motivate and exemplify the quasi-chemical theory. Those results underscore the fact that the quasi-chemical approach refines the path for utilization of ion-water cluster results for the statistical thermodynamics of solutions.Comment: 30 pages, contribution to Santa Fe Workshop on Treatment of Electrostatic Interactions in Computer Simulation of Condensed Medi

Ab initio molecular dynamics calculations of ion hydration free energies

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD Delta G(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+-> Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of Delta G(hyd) for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.Comment: 18 pages, 8 figures. This version is essentially the one published in J. Chem. Phy

Density functional theory and DFT+U study of transition metal porphines adsorbed on Au(111) surfaces and effects of applied electric fields

We apply Density Functional Theory (DFT) and the DFT+U technique to study the adsorption of transition metal porphine molecules on atomistically flat Au(111) surfaces. DFT calculations using the Perdew-Burke-Ernzerhof (PBE) exchange correlation functional correctly predict the palladium porphine (PdP) low-spin ground state. PdP is found to adsorb preferentially on gold in a flat geometry, not in an edgewise geometry, in qualitative agreement with experiments on substituted porphyrins. It exhibits no covalent bonding to Au(111), and the binding energy is a small fraction of an eV. The DFT+U technique, parameterized to B3LYP predicted spin state ordering of the Mn d-electrons, is found to be crucial for reproducing the correct magnetic moment and geometry of the isolated manganese porphine (MnP) molecule. Adsorption of Mn(II)P on Au(111) substantially alters the Mn ion spin state. Its interaction with the gold substrate is stronger and more site-specific than PdP. The binding can be partially reversed by applying an electric potential, which leads to significant changes in the electronic and magnetic properties of adsorbed MnP, and ~ 0.1 Angstrom, changes in the Mn-nitrogen distances within the porphine macrocycle. We conjecture that this DFT+U approach may be a useful general method for modeling first row transition metal ion complexes in a condensed-matter setting.Comment: 14 pages, 6 figure

Computational and experimental platform for understanding and optimizing water flux and salt rejection in nanoporous membranes.

Affordable clean water is both a global and a national security issue as lack of it can cause death, disease, and international tension. Furthermore, efficient water filtration reduces the demand for energy, another national issue. The best current solution to clean water lies in reverse osmosis (RO) membranes that remove salts from water with applied pressure, but widely used polymeric membrane technology is energy intensive and produces water depleted in useful electrolytes. Furthermore incremental improvements, based on engineering solutions rather than new materials, have yielded only modest gains in performance over the last 25 years. We have pursued a creative and innovative new approach to membrane design and development for cheap desalination membranes by approaching the problem at the molecular level of pore design. Our inspiration comes from natural biological channels, which permit faster water transport than current reverse osmosis membranes and selectively pass healthy ions. Aiming for an order-of-magnitude improvement over mature polymer technology carries significant inherent risks. The success of our fundamental research effort lies in our exploiting, extending, and integrating recent advances by our team in theory, modeling, nano-fabrication and platform development. A combined theoretical and experimental platform has been developed to understand the interplay between water flux and ion rejection in precisely-defined nano-channels. Our innovative functionalization of solid state nanoporous membranes with organic protein-mimetic polymers achieves 3-fold improvement in water flux over commercial RO membranes and has yielded a pending patent and industrial interest. Our success has generated useful contributions to energy storage, nanoscience, and membrane technology research and development important for national health and prosperity