Polarizable potential models for the interaction of Li + , Na + , K + , and NH 4 + ions with benzene are parametrized based on ab initio quantum mechanical calculations. The models reproduce the ab initio complexation energies and potential energy surfaces of the cationÀπ dimers. They also reproduce the cooperative behavior of "stacked", cationÀπÀπ trimers and the anticooperative behavior of "sandwiched", πÀcationÀπ trimers. The NH 4 + model is calibrated to reproduce the energy of the NH 4+ ÀH 2 O dimer and yields correct free energy of hydration and hydration structure without further adjustments. The models are used to investigate cationÀπ interactions in aqueous solution by calculating the potential of mean force between each of the four cations and a benzene molecule and by analyzing the organization of the solvent as a function of the cationÀbenzene separation. The results show that Li + and Na + ions are preferentially solvated by water and do not associate with benzene, while K + and NH 4 + ions bind benzene with 1.2 and 1.4 kcal/mol affinities, respectively. Molecular dynamics simulations of NH 4 + and of K + in presence of two benzene molecules in water show that cationÀπ and πÀπ affinities are mutually enhanced compared to the pairwise affinities, confirming that the cooperativity of cationÀπ and πÀπ interactions persists in aqueous solution.

Proteins of the Amt/MEP family facilitate ammonium transport across the membranes of plants, fungi, and bacteria and are essential for growth in nitrogen-poor environments. Some are known to facilitate the diffusion of the neutral NH(3), while others, notably in plants, transport the positively charged NH(4)(+). On the basis of the structural data for AmtB from Escherichia coli , we illustrate the mechanism by which proteins from the Amt family can sustain electrogenic transport. Free energy calculations show that NH(4)(+) is stable in the AmtB pore, reaching a binding site from which it can spontaneously transfer a proton to a pore-lining histidine residue (His168). The substrate diffuses down the pore in the form of NH(3), while the excess proton is cotransported through a highly conserved hydrogen-bonded His168-His318 pair. This constitutes a novel permeation mechanism that confers to the histidine dyad an essential mechanistic role that was so far unknown.

A polarizable model for ammonia is optimized based on the ab initio properties of the NH3 molecule and the NH3-NH3 and NH3-H2O dimers calculated at the MP2 level. For larger (NH3)m, NH3(H2O)n, and H2O(NH3)n clusters (m = 2-7 and n = 1-4), the model yields structural and binding energies in good agreement with ab initio calculations without further adjustments. It also reproduces the structure, density, heat of vaporization, self-diffusion coefficient, heat capacity, and isothermal compressibility of liquid ammonia at the boiling point. The model is further validated by calculating some of these properties at various temperatures and pressures spanning the liquid and supercritical phases of the fluid (up to 700 K and 200 MPa). The excellent transferability of the model suggests that it can be used to investigate properties of fluid ammonia under conditions for which experiments are not easy to perform. For aqueous ammonia solutions, the model yields liquid structures and densities in good agreement with experimental data and allows the nonlinearity in the density-composition plot to be interpreted in terms of structural changes with composition. Finally, the model is used to investigate the solvation structure of ammonia in liquid water and of water in liquid ammonia and to calculate the solvation free energy of NH3 and H2O in aqueous ammonia as a function of solution composition and temperature. The simulation results suggest the presence of a transition around 50% molar NH3/H2O compositions, above which water molecules are preferably solvated by ammonia.

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Hydrogen peroxide (HO) has numerous industrial, environmental, medical, cosmetic, and biological applications. Given its importance, we provide a simple model as an alternative to experiment for studying the properties of pure liquid HO and its concentrated aqueous solutions, which are hazardous, and for understanding the biological roles of HO at the molecular level. A four-site additive model is calibrated for HO based on the ab initio and experimental properties of the gaseous monomer and the density and heat of vaporization of liquid HO at 0 °C. Our model together with the TIP3P water model reproduce the ab initio binding energies of (HO) , HO· nHO, and nHO·HO clusters ( m = 2, 3 and n = 1, 2) calculated at the MP2 level using the 6-311++G(d,p) or the 6-311++G(3df,3pd) basis set. It yields structure, the self-diffusion coefficient, heat capacity, and densities at temperatures up to 200 °C of the pure liquid in good agreement with experiment. The model correctly predicts the hydration free energy of HO and reproduces the experimental density of aqueous HO solutions at 0-96 °C. Investigation of the solvation of HO and HO in aqueous HO solutions reveals that, as in the gas phase, HO is a better H-bond donor but poorer acceptor than HO and the bonding stability follows the order O-H···O > O-H···O ≥ O-H···O > O-H···O. Stronger H-bonding in HO/HO mixtures than in the pure liquids is consistent with exothermic heats of mixing and explains why the observed density and vapor pressure of the aqueous solutions are higher and lower, respectively, than expected from ideal mixing. Results also show that HO adopts a skewed equilibrium geometry in gas and liquid phases but more polar cis and nonpolar trans conformations also are accessible and will stabilize HO in environments of different polarity. In sum, our simple model presents a reliable tool for simulating HO in chemistry and biology.