Dominic R. Alfonso

A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods

A driver program for carrying out nudged elastic band optimizations of minimum energy reaction pathways is described. This approach allows for the determination of minimum energy pathways using only energies and gradient information. The driver code has been interfaced with the GAUSSIAN 98 program. Applications to two isomerization reactions and to a cluster model for H2 desorption from the Si(100)‐2x1 surface are presented.

Rearrangement pathways of the water trimer and tetramer anions

Minimum energy pathways for the rearrangement of the anions of the water trimer and tetramer anions between their cyclic and chain structures were investigated by means of ab initio electronic structure calculations, coupled with nudged elastic band optimizations. The rearrangements of both anions are found to proceed by opening of the cyclic structure and reorientation of the water molecules as the excess electron migrates to the terminal water fragment with the dangling hydrogens. The activation energies for the cyclic→chain rearrangements are calculated to be 0.11 and 0.32 eV for (H2O)3− and (H2O)4−, respectively.

First-Principles Studies of Hydrogenated Si(111)-7×7

The relaxed geometries and electronic properties of the hydrogenated phases of the Si(111)-7

Structure of diamond(100) stepped surfaces from ab initio calculations

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Active sites of ligand-protected Au25 nanoparticle catalysts for CO2 electroreduction to CO

7 surface are studied using first-principles molecular dynamics. A monohydride phase, with one H per dangling bond adsorbed on the bare surface is found to be energetically favorable. Another phase where 43 hydrogens saturate the dangling bonds created by the removal of the adatoms from the clean surface is found to be nearly equivalent energetically. Experimental STM and differential reflectance characteristics of the hydrogenated surfaces agree well with the calculated features.

First-principles studies of adsorption of CO on the Na(100) surface

We present theoretical studies of relaxations of monoatomic SA; SB (b) and SB (n) steps on the diamond(100)-(21) surface employing an ab initio molecular dynamics simulation method that is based on density functional theory. Stable dimer structures are found in the upper and lower planes of the step surfaces in agreement with experiment. Significant atomic relaxations occur near the step edges of SB (b) and SB (n) stepped surfaces induced by the creation of the steps. Atomic H adsorption on these step surfaces to form monohydride structures is energetically favourable. We also simulate the presence of radical sites near the step edges of SA ,S B(n) and SB (b) and local reconstruction involving the dimer containing the radical sites is found. Electronic charge density profiles of the filled states near the Fermi level show features associated with the dimer structures.

Simulation of hyperthermal deposition of Si and C on SiC surfaces

Recent experimental studies have reported the electrochemical reduction of carbon dioxide (CO2) into CO at atomically precise negatively charged Au25 (-) nanoclusters. The studies showed CO2 conversion at remarkably low overpotentials, but the exact mechanisms and nature of the active sites remain unclear. We used first-principles density functional theory and continuum solvation models to examine the role of the cluster during electrochemical CO2 reduction and analyze the free energies of proposed intermediate species. Contrary to previous assumptions, our results show that the fully ligand protected cluster is not an active CO2 reduction catalyst because formation of the crucial carboxyl intermediate required very high electrochemical potentials. Instead, our calculations suggest that the reduction process likely occurs on a dethiolated gold site, and adsorbed carboxyl intermediate formation was significantly stabilized at dethiolated gold sites. These findings point to the crucial role of exposed metal sites during electrochemical CO2 reduction at gold nanocluster catalysts.

Characterization of silicon-silicon bonds on the Si(100) surfaces

We have investigated the interaction of CO with the Na(100) substrate in the framework of density functional theory formulated for periodic systems. We established that there is an attractive but weak chemisorption bond between CO and Na(100). The binding energy of the CO molecule at an on-top site and adsorbed normal to the surface with the carbon end down is ∼0.25 eV for the Perdew–Burke–Enzerhof (PBE96) exchange correlation functional. The structural, electronic and vibrational properties indicate weakening of the intramolecular CO bond by adsorption on Na(100). The occupied orbitals of CO are generally shifted up in energy upon adsorption, with exception of the highest occupied orbital 5σ. The adsorbate–surface interaction is primarily characterized by: (i) partial charge transfer from the occupied 3sp band of Na to the CO antibonding 2π∗ orbital and (ii) the interaction between the 5σ orbital of CO and the metal states.

Optical Signature of the GaN (1010) Surface

We describe the adsorption dynamics of Si and C atoms at supersonic velocities on Si- and C-terminated 6H–SiC(0001) substrates using molecular dynamics simulations. The sticking probabilities of adatoms are found to be very high and not to change substantially with increasing incident kinetic energy. We identify two mechanisms responsible for the high sticking probabilities of the adatoms: (a) efficient transfer of adatom energy to the substrate and (b) strong attractive forces experienced by the impinging adatom over the entire surface. The calculated potential energy surfaces reveal possible binding sites of the adatoms on the substrates.

Structural, electronic, and vibrational properties of diamond (100), (111), and (110) surfaces from ab initio calculations.

The bonding nature of the surface atoms in the (2×1) and c(4×2) reconstruction of the Si(100) surface has been characterized using local analysis technique in the context of nonorthogonal tight binding approximation. We demonstrate the capability of this method to yield a real-space picture of the bonding character of the surface atoms for these systems. We also report our analysis of the surface atom bonds on the Si(100) substrate with single-dimer vacancy.