Molecular Science Computing

By scanning tunneling microscopy and spectroscopy, we study nearly free electron band formation of the σ*lowest unoccupied molecular orbital of C₆F₆ on a Cu(111) surface. In fractal islands, the lowest unoccupied molecular orbital energy systematically stabilizes with the number of interacting near-neighbor C₆F₆ molecules. Density functional theory calculations reveal the origin of effective intermo- lecular orbital overlap in the previously unrecognized superatom character of the σ*orbital of ₆F₆ molecules. The discovery of superatom orbitals in planar molecules offers a new universal principle for effective band formation, which can be exploited in designing organic semiconductors with nearly free electron properties

The structure, stability, and catalytic activity of a number of single- and double-wall platinum (n,m) nanotubes ranging in diameter from 0.3 to 2.0 nm were studied using plane-wave based density functional theory in the gas phase and water environment. The change in the catalytic activity toward the oxygen reduction reaction (ORR) with the size and chirality of the nanotube was studied by calculating equilibrium adsorption potentials for ORR intermediates and by constructing free energy diagrams in the ORR dissociative mechanism network. In addition, the stability of the platinum nanotubes is investigated in terms of electrochemical dissolution potentials and by determining the most stable state of the material as a function of pH and
potential, as represented in Pourbaix diagrams. Our results show that the catalytic activity and the stability toward electrochemical dissolution depend greatly on the diameter and chirality of the nanotube. On the basis of the estimated overpotentials for ORR, we conclude that smaller, approximately 0.5 nm in diameter single-wall platinum nanotubes consistently show a huge, up to 400 mV larger overpotential than platinum, indicating very poor catalytic activity toward ORR. This is the
result of substantial structural changes induced by the adsorption of any chemical species on these tubes. Single-wall n = m platinum nanotubes with a diameter larger than 1 nm have smaller ORR overpotentials than bulk platinum for up to 180 mV and
thus show improved catalytic activity relative to bulk. We also predict that these nanotubes can endure the highest cell potentials but dissolution potentials are still for 110 mV lower than for the bulk, indicating a possible corrosion problem.

We demonstrate that the electronic structure of mesoporous silicon is affected by adsorption of nitrobased explosive molecules in a compound-selective manner. This selective response is demonstrated by probing the adsorption of two nitro-based molecular explosives (trinitrotoluene and cyclotrimethylenetrinitramine) and a
nonexplosive nitro-based aromatic molecule (nitrotoluene) on mesoporous silicon using soft X-ray spectroscopy. The Si atoms strongly interact with adsorbed molecules to form Si-O and Si-N bonds, as evident from the large shifts in emission energy present in the Si L2,3 X-ray emission spectroscopy (XES) measurements. Furthermore, we find that the energy gap (band gap) of mesoporous silicon changes depending on the adsorbant, as estimated from the Si L2,3 XES and 2p X-ray absorption spectroscopy (XAS) measurements. Our ab initio molecular dynamics calculations of model compounds suggest that these changes are due to
spontaneous breaking of the nitro groups upon contacting surface Si atoms. This compound-selective change in electronic structure may provide a powerful tool for the detection and identification of trace quantities of airborne explosive molecules.

The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structure of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.

Uranophane is a rare U(VI) secondary silicate mineral formed in nature by the oxidation of the primary mineral uraninite. It is also relevant to the long-term geochemistry of nuclear waste repositories, where it can be formed under oxidizing conditions and has the potential to act as a secondary barrier to the migration of radionuclides through mineral sorption reactions. A combination of classical molecular dynamics and ab-initio density functional theory (DFT) has been employed to investigate the uranophane|water interface as well as the interfacial reactivity of the U(VI) silicate toward acidic conditions and radionuclide ion sorption. The sorption simulations have been complemented by experimental sorption studies and laser induced fluorescence spectroscopy to help identify the molecular structure of the surface sorbed species. Experimental distances and essential coordination numbers are properly captured by the simulation results within bulk uranophane, while interfacial water is found to orient primarily with the hydrogen-atoms directed towards the negatively charged surface. Sorption sites for water are observed to belong to 3 different groups: (1) those involving uranyl oxygen, (2) involving uranyl and silica hydroxyl oxygen atoms, and (3) involving hydroxyl hydrogen. The pKa of the surface -OH groups have been calculated using a variety of models, including a bond valence approach and utilization of the energetics of deprotonation within DFT. Under basic conditions, deprotonation of the Si-OH groups is likely responsible for uranophane dissolution. Finally, the stability and structure of surface sorbed Eu3+ has been examined, with a stable inner-sphere species being observed.