Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Åqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4PEW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells

Geometrical and Electronic Characteristics of AunO2- (n=2-7)

Most density functionals do not properly describe the characteristics of superoxide (O2-) (i.e., first two vertical electron detachment energies and the excitation energies of neutralized singlet state) of small even-numbered AunO2- clusters. However, the second-order M??ller-Plesset theory (MP2) shows significant charge transfer from Au cluster anions to oxygen molecule and so provides proper electronic characteristics of superoxide of small even-numbered AunO2- clusters. This has allowed us to properly describe the properties of even-numbered AunO2- clusters. Even in the case of odd-numbered AunO2- clusters, we find that Au5- is a chemically O2-adsorbed singlet state at 0 K, against a commonly accepted physisorbed triplet state. This is further evidenced by our extensive coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] calculations, including the relativistic effect. However, the entropy effect makes the physisorbed triplet state more stable than the chemisorbed singlet state at higher temperatures, consistent with the experiment. The weak O2 binding by odd-numbered cluster anions (n = 3, 5, and 7) could be further weakened by the entropic effect, which results in van der Waals complexes at high temperatures. The present study reports the geometrical and electronic characteristics of small AunO2- (n = 2-7) clusters including isomers, which match the corresponding photoelectron spectra (PES). 2015 American Chemical Society.close0