Building on the previously developed multistate empirical valence bond model [U. W. Schmitt and G. A. Voth, J. Chem. Phys 111, 9361 (1999)] for the dynamics and energetics of an excess proton in bulk phase water, a second generation model is described. This model is shown to produce similar dynamic and structural properties to the previous model, while allowing for the use of the full hydronium charge. This characteristic of the model is required for its implementation in a host of realistic applications beyond bulk water. An improved state selection algorithm is also presented, resulting in a significantly reduced energy drift during microcanonical molecular dynamics simulations. The unusually high self diffusion constant of an excess proton in water due to the proton hopping (Grotthuss) process is observed in the simulation data and is found to be quantitatively in the same range as the experimental value if a quantum correction is taken into consideration. Importantly, a more complete analysis of proton transport process is also presented.

The relative energies of H and D bonds are due to differences in zero-point vibrational energy (ZPVE). Ab initio calculations are used to assess the changes in this quantity that accompany all possible substitutions of protium by deuterium in a number of complexes. The ZPVE of the D bond is lower than that of the H bond in the neutral dimer and trimer of water. This difference can be traced to one particular vibrational mode, the one which displaces the bridging atom away from the O···O axis. The heavier mass of D lowers the frequency, and hence the ZPVE associated with it. The situation reverses itself in ionic H bonds. The total ZPVE of the (H2O··H··OH2)+ complex is higher when a D occupies the bridging position, as compared to a terminal site. This difference is attributed to the intramolecular modes. Although replacement of the central H by D reduces the intermolecular ZPVE, the reduction of the intramolecular ZPVE is even larger when the substitution is made at a peripheral atom, so a D would tend to migrate away from a bridging location. This effect is noted also in the larger complex in which two methanol molecules are bound by a proton. The lower energy of a H bond as compared to a D bond is observed as well in the anionic (HOH··OH)- system, although the magnitude of the preference is smaller here. In all cases, raising the temperature, and thus invoking thermal vibrational and entropic effects, tends to preferentially stabilize H over D bonds.

The development and application of a multistate empirical valence bond (MS-EVB) model for a weak acid dissociation and subsequent proton transport in aqueous solution is described. The weak acid dissociation step is modeled by the inclusion of an additional EVB state describing the case when proton is bound to the acid's conjugate base. The model was parametrized for the imidazolium cation deprotonation. Classical molecular dynamics simulation methodology was used to study both equilibrium and dynamic properties of this system. Free energy profiles of the deprotonation reaction, studied using a novel center of excess charge reaction coordinate, reveal the need to include several solvation shells around the weak acid in order to stabilize the hydronium species formed upon the weak acid deprotonation. The solvent atomic density plots examined at selected points along the proton transfer coordinate display a relatively large reorganization of the solvent around the weak acid molecule, caused by the shift in the weak acid molecule atomic point charges caused by the deprotonation. Finally, since the concentration of the weak acid in the system under study is low, its presence has only mimimal effect on the solvent diffusion and on the transfer dynamics of the excess proton in the water solution after the weak acid dissociation step.

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The thermal discrete dipole approximation (T-DDA) is a numerical approach for modeling nearfield radiative heat transfer in complex three-dimensional geometries. In this work, the convergence of the T-DDA is investigated by comparison against the exact results for two spheres separated by a vacuum gap. The error associated with the T-DDA is reported for various sphere sizes, refractive indices and vacuum gap thicknesses. The results reveal that for a fixed number of subvolumes, the accuracy of the T-DDA degrades as the refractive index and the sphere diameter to gap ratio increase. A converging trend is observed as the number of subvolumes increases. The large computational requirements associated with increasing the number of subvolumes, and the shape error induced by large sphere diameter to gap ratios, are mitigated by using a nonuniform discretization scheme. Nonuniform discretization is shown to significantly accelerate the convergence of the T-DDA, and is thus recommended for near-field thermal radiation simulations. Errors less than 5% are obtained in 74% of the cases studied by using up to 82712 subvolumes. Additionally, the convergence analysis demonstrates that the T- † Corresponding authors. Tel.: +1 801 581 5721, Fax: +1 801 585 9825 E-mail addresses: mfrancoeur@mech.utah.edu (M. Francoeur), sheila.edalatpour@utah.edu (S. Edalatpour) 2 DDA is very accurate when dealing with surface polariton resonant modes dominating radiative heat transfer in the near field.

We perform extensive first-principles calculations to simulate the topographical atomic-force-microscope image of an adatom on the Si(111)-(7 x 7) surface, demonstrating the feasibility of imaging not only the atoms but also the atomic orbitals. Our comparative study of tip terminations shows that two subatomic features can appear for a single adatom when it is imaged by a Si(001)-type tip having two dangling bonds on its apex, while only one feature would appear if it were imaged by a Si(111)-type tip having one dangling bond on the apex. The key condition for seeing the atomic orbitals is to bring the tip so close to the surface that the angular-dependent force dominates the tip-surface interaction.