@article {2397, title = {Simulation of Water Adsorption on Kaolinite under Atmospheric Conditions}, journal = {Journal of Physical Chemistry A}, volume = {113}, number = {27}, year = {2009}, note = {ISI Document Delivery No.: 466WNTimes Cited: 5Cited Reference Count: 61Croteau, T. Bertram, A. K. Patey, G. N.}, month = {Jul}, pages = {7826-7833}, type = {Article}, abstract = {Grand canonical Monte Carlo calculations are employed to investigate water adsorption on kaolinite at 298 and 235 K. Both basal planes (the Al and Si surfaces) as well as two edge-like surfaces are considered. The general force field CLAYFF is used together with the SPCIE and TIP5P-E models for water. Problems that occur in single slab simulations due to arbitrary truncation of the point charge lattice are identified, and a working remedy is discussed. The edges and the Al surface adsorb water at subsaturation in the atmospherically relevant pressure range. The Si surface remains dry up to saturation. Both edges have a very strong affinity for water and adsorb continuously up to monolayer coverage. The Al surface has a weaker affinity for water but forms a subsaturation monolayer. On the Al surface, the monolayer is formed in an essentially sharp transition, and strong hysteresis is observed upon desorption. This indicates collective behavior among the water molecules which is not present for the edges. Binding energies of singly adsorbed water molecules at 10 K were determined to understand the differences in water uptake by the four kaolinite surfaces. Binding energies (SPC/E) of -21.6, -46.4, -73.5, and -94.1 kJ/mol, were determined for the Si surface, Al surface, unprotonated edge, and protonated edge, respectively. The water monolayer on the Al surface, particularly at 235 K, exhibits hexagonal patterns. However, the associated lattice parameters are not compatible with ice 1h. Water density and hydrogen bonding in the monolayers at both 298 and 235 K were also determined to better understand the structure of the adsorbed water.}, keywords = {ADSORBED, CLAY-MINERALS, COMPUTER-SIMULATION, DYNAMICS, HYDROGEN-BOND, ICE FORMATION, INITIO MOLECULAR-DYNAMICS, LIQUID WATER, MINERAL DUST, MONTE-CARLO SIMULATIONS, NITRIC-ACID, WATER}, isbn = {1089-5639}, url = {://000267694800018}, author = {Croteau, T. and Bertram, A. K. and Patey, G. N.} } @article {1466, title = {Ozonization at the vacancy defect site of the single-walled carbon nanotube}, journal = {J. Phys. Chem. B}, volume = {110}, number = {26}, year = {2006}, note = {ISI Document Delivery No.: 058DSTimes Cited: 11Cited Reference Count: 52}, month = {Jul}, pages = {13037-13044}, type = {Article}, abstract = {

The ozonization at the vacancy defect site of the single-walled carbon nanotube has been studied by static quantum mechanics and atom-centered density matrix propagation based ab initio molecular dynamics within a two-layered ONIOM approach. Among five different reaction pathways at the vacancy defect, the reaction involving the unsaturated active carbon atom is the most probable pathway, where ozone undergoes fast dissociation at the active carbon atom at 300 K. Complementary to the experiments, our work provides a microscopic understanding of the ozonization at the vacancy defect site of the single-walled carbon nanotube.

}, keywords = {AB-INITIO, DENSITY-MATRIX, ETHYLENE, FULLERENE, GAUSSIAN-ORBITALS, INITIO MOLECULAR-DYNAMICS, MECHANICS, OXYGEN, OZONE ADSORPTION, SIDEWALLS}, isbn = {1520-6106}, url = {://000238645700035}, author = {Liu, L. V. and Tian, W. Q. and Y. A. Wang*} } @article {1288, title = {Dynamics of the Staudinger reaction}, journal = {J. Chem. Theory Comput.}, volume = {1}, number = {3}, year = {2005}, note = {ISI Document Delivery No.: 961TUTimes Cited: 6Cited Reference Count: 51}, month = {May-Jun}, pages = {353-362}, type = {Article}, abstract = {

The Staudinger reaction of phosphane and azide has been investigated by Atom-centered Density Matrix Propagation (ADMP) approach to ab initio molecular dynamics (AlMD) in combination with molecular orbital analysis within density functional theory. At room temperature, the reaction pathway with the cis initial attack dominates the Staudinger reaction. Electrostatic interaction, charge transfer, and covalent overlap are responsible for the initial attack and for the system to overcome the initial reaction barrier. The rotation Of PH3 and PH vibrations facilitate the isomerization of the system from cis intermediate to the last transition state, which indicates that small substituent groups on phosphane can facilitate the last stage of the Staudinger reaction. During the course of the reaction, the change of the average polarizability correlates positively to the change of the potential energy of the system, which clearly suggests that polar solvents can facilitate the overall reaction by stabilizing all transition states and reducing all reaction barriers.

}, keywords = {BORN-OPPENHEIMER DYNAMICS, CAR-PARRINELLO, DENSITY-FUNCTIONAL SCHEME, FORCE-FIELD, GAUSSIAN-ORBITALS, INITIO MOLECULAR-DYNAMICS, MATRIX, PATH, PHOSPHAZIDE, X-RAY CRYSTAL}, isbn = {1549-9618}, url = {://000231685500002}, author = {Tian, W. Q. and Y. A. Wang*} } @article {1051, title = {Transferable local pseudopotentials derived via inversion of the Kohn-Sham equations in a bulk environment}, journal = {Phys. Rev. B}, volume = {69}, number = {12}, year = {2004}, note = {ISI Document Delivery No.: 818QGTimes Cited: 22Cited Reference Count: 142}, month = {Mar}, pages = {125109}, type = {Review}, abstract = {

The lack, of accurate transferable local pseudopotentials represents one of the remaining, barriers to the. general application of orbital-free density functional theory (OF-DFT, a linear scaling technique). Here we report a method to generate high quality ab initio local pseudopotentials (LPS\’s) for use in condensed matter DFT calculations. We exploit the first Hohenberg-Kohn theorem, which states that the external potential is, one-to-one mapped to the ground-state electron density. By employing a scheme for inverting the Kohn-Sham (KS) equations due to Wang and Parr, we iteratively solve for the KS effective potential v(eff)(KS)(r) until it reproduces a target density. From v(eff)(KS)(r) we derive a global LPS for the entire system. This global LPS is then further decomposed to obtain an atom-centered LPS. We show that LPS\’s,derived from bulk environments are substantially more transferable than those derived from atoms alone. In KS-DFT tests on Si, we show that this bulk-derived LPS can reproduce accurately phase orderings predicted by nonlocal pseudopotentials for both metallic and semiconducting phases. We then tested this LPS in OF-DFT calculations on Si crystals, where we demonstrate that this bulk-derived LPS (BLPS), combined with a linear-response-based kinetic energy density functional with a density-dependent kernel, correctly predicts a diamond structure ground state for Si in an OF-DFT calculation. Other bulk properties, such as defect formation energies and transition pressures are also presented as tests of this BLPS. This approach for deriving LPS\’s isolates much of the remaining error in OF-DFT to the kinetic energy density functional, providing means to test new functionals as they become available.

}, keywords = {CORRECT ASYMPTOTIC-BEHAVIOR, ELECTRONIC-STRUCTURE CALCULATIONS, ENERGY-DENSITY FUNCTIONALS, EXCHANGE-CORRELATION POTENTIALS, GROUND-STATE GEOMETRIES, INITIO MOLECULAR-DYNAMICS, KINETIC-ENERGY, NORM-CONSERVING PSEUDOPOTENTIALS, THOMAS-FERMI APPROXIMATION, WAVE-FUNCTIONS}, isbn = {1098-0121}, url = {://000221259000035}, author = {Zhou, B. J. and Wang, Y. A. and E. A. Carter*} } @article {533, title = {Structure determination of Cu(410)-O using X-ray diffraction and DFT calculations}, journal = {Surface Science}, volume = {516}, number = {1-2}, year = {2002}, note = {ISI Document Delivery No.: 594AQTimes Cited: 12Cited Reference Count: 52}, month = {Sep}, pages = {16-32}, type = {Article}, abstract = {The Cu(4 1 0)-O surface, involving a 0.5 monolayer (ML) coverage of oxygen, is known to be extremely stable and a range of Cu(1 0 0) vicinal. surfaces facet to (4 1 0) in the presence of adsorbed oxygen. A new surface X-ray diffraction investigation of this surface has been conducted to determine its structure, and the detailed structural parameter values obtained are compared with the results of a density functional theory (DFT) calculation. The results show that the metal structure is unreconstructed, with the oxygen forming an overlayer with 0.25 ML O atoms at near-colinear step-edge sites and 0.25 NIL O atoms at mid-terrace hollow sites, approximately 0.6 Angstrom above the terraces. The large number of independent structural parameters potentially relevant to this vicinal surface presents a significant challenge for unique structural optimisation, but various missing row reconstruction models can be clearly excluded. Two detailed structural solutions are identified which give equally acceptable fits to the X-ray diffraction data after imposition of a Lennard-Jones penalty factor. These models differ especially in the O positions, but one is found to be more favoured by comparison with the results of the DFT calculations, and by considerations based on bond lengths and valence. Substantial relaxations from the bulk metal positions occur for the outermost Cu atoms; the ability of the vicinal surface to relax in this way may help to account for its stability compared with the missing row reconstruction induced by oxygen chemisorption on the Cu(1 0 0) surface. (C) 2002 Elsevier Science B.V. All rights reserved.}, keywords = {ADSORPTION, and, and topography, chemisorption, copper, CU(100), DETERMINATION, DIFFRACTION, ENERGY ION-SCATTERING, INITIO MOLECULAR-DYNAMICS, MISSING-ROW, MORPHOLOGY, OXYGEN, OXYGEN-INDUCED RECONSTRUCTION, RECONSTRUCTION, reflection, relaxation and reconstruction, roughness, SCANNING-TUNNELING-MICROSCOPY, SURFACE, surface structure, SURFACE-STRUCTURE, SURFACES, VICINAL COPPER SURFACES, vicinal single crystal, WAVE BASIS-SET, X-ray scattering}, isbn = {0039-6028}, url = {://000178027000003}, author = {Vlieg, E. and Driver, S. M. and Goedtkindt, P. and Knight, P. J. and Liu, W. and Ludecke, J. and Mitchell, K. A. R. and Murashov, V. and Robinson, I. K. and de Vries, S. A. and Woodruff, D. P.} }