Kuehne TD, Pascal TA, Kaxiras E, Jung Y. New Insights into the Structure of the Vapor/Water Interface from Large-Scale First-Principles Simulations. Journal of Physical Chemistry Letters. 2011;2 :105-113.Abstract

We present extensive ab initio simulations of the molecular arrangements at the vapor/water interface, which provide valuable insights into the interface structure. In particular, the simulations address the controversy of whether there is a significant amount of nondonor configurations at this prototypical interface, using a novel Car-Parrinello-like ab initio molecular dynamics approach. The interface is modeled by a system of 384 water molecules for 125 ps in a two-dimensional periodic slab, the most extensive ab initio molecular dynamics simulation to date. In contrast to previous theoretical simulations and X-ray absorption spectroscopy, but consistent with sum-frequency generation experiments, we observe no evidence for a significant occurrence of acceptoronly species at the vapor/water interface. Besides a distinct surface relaxation effect, we find that only the topmost layers of the interface obey structural order.

Ren J, Meng S, Wang Y-L, Ma X-C, Xue Q-K, Kaxiras E. Properties of copper (fluoro-)phthalocyanine layers deposited on epitaxial graphene. Journal of Chemical Physics. 2011;134 :194706.Abstract

We investigate the atomic structure and electronic properties of monolayers of copper phthalocyanines (CuPc) deposited on epitaxial graphene substrate. We focus in particular on hexadecafluorophthalocyanine (F16CuPc), using both theoretical and experimental (scanning tunneling microscopy – STM) studies. For the individual CuPc and F16CuPc molecules, we calculated the electronic and optical properties using density functional theory (DFT) and time-dependent DFT and found a red-shift in the absorption peaks of F16CuPc relative to those of CuPc. In F16CuPc, the electronic wavefunctions are more polarized toward the electronegative fluorine atoms and away from the Cu atom at the center of the molecule. When adsorbed on graphene, the molecules lie flat and form closely packed patterns: F16CuPc forms a hexagonal pattern with two well-ordered alternating α and β stripes while CuPc arranges into a square lattice. The competition between molecule-substrate and intermolecular van der Waals interactions plays a crucial role in establishing the molecular patterns leading to tunable electron transfer from graphene to the molecules. This transfer is controlled by the layer thickness of, or the applied voltage on, epitaxial graphene resulting in selective F16CuPc adsorption, as observed in STM experiments. In addition, phthalocyanine adsorption modifies the electronic structure of the underlying graphene substrate introducing intensity smoothing in the range of 2–3 eV below the Dirac point (ED) and a small peak in the density of states at ∼0.4 eV above ED.

Maze JR, Gali A, Togan E, Chu Y, Trifonov A, Kaxiras E, Lukin MD. Properties of nitrogen-vacancy centers in diamond: the group theoretic approach. New Journal of Physics. 2011;13 :025025.Abstract

We present a procedure that makes use of group theory to analyze and predict the main properties of the negatively charged nitrogen-vacancy (NV) center in diamond. We focus on the relatively low temperature limit where both the spin–spin and spin–orbit effects are important to consider. We demonstrate that group theory may be used to clarify several aspects of the NV structure, such as ordering of the singlets in the (e 2 ) electronic configuration and the spin–spin and spin–orbit interactions in the (ae) electronic configuration. We also discuss how the optical selection rules and the response of the center to electric field can be used for spin–photon entanglement schemes. Our general formalism is applicable to a broad class of local defects in solids. The present results have important implications for applications in quantum information science and nanomagnetometry.

Baker TA, Xu B, Jensen SC, Friend CM, Kaxiras E. Role of defects in propene adsorption and reaction on a partially O-covered Au(111) surface. Catalysis Science & Technology. 2011;1 :1166-1174.Abstract

We investigate the role of defects—adatoms, vacancies, and steps—in the bonding and reaction of propene on Au(111) containing atomic oxygen, using density functional theory (DFT) calculations. The adsorption of propene is stronger on a surface containing defects compared to the flat, bulk-terminated surface, with the largest gain in binding (~0.7 eV) on a surface with a 1/9 monolayer (ML) of Au adatoms. Charge-density difference plots reveal that the difference between defective surfaces and the bulk-terminated surface is a more pronounced depletion of electron density from the carbon–carbon p bond and a charge accumulation between the double bond and the gold atom to which the propene is bound. We calculate the energy barriers for two competing reactions that are important in determining the selectivity for propene oxidation. Allylic H abstraction by adsorbed O leads to combustion, whereas O addition to form an oxymetallacycle is the first step in propene epoxide formation. A comparison of the energetics of these two pathways on flat and defect-containing Au surfaces indicates that the reactivity depends on the nature and prevalence of surface defects. Both electronic and geometric factors, such as the path and the distance the oxygen must travel to meet the allylic hydrogen for abstraction, are important in explaining the reaction trends.

Haubrich J, Kaxiras E, Friend CM. The Role of Surface and Subsurface Point Defects for Chemical Model Studies on TiO2: A First-Principles Theoretical Study of Formaldehyde Bonding on Rutile TiO2(110). Chemistry - a European Journal. 2011;17 :4496-4506.Abstract

We report a systematic investigation of the effects of different surface and subsurface point defects on the adsorption of formaldehyde on rutile TiO2(110) surfaces using density functional theory (DFT). All point defects investigated—including surface bridging oxygen vacancies, titanium interstitials, and subsurface oxygen vacancies—stabilize the adsorption significantly by up to 56 kJ mol-1 at a coverage of 0.1 monolayer (ML). The stabilization is due to a decrease of the coordination (covalent saturation) of the surface Ti adsorption sites adjacent to the defects, which leads to a stronger molecule–surface interaction. This change in the Ti is caused by the removal of a neighboring atom (oxygen vacancies) or substantial lattice relaxations induced by the subsurface defects. On the stoichiometric reference surface, the most stable adsorption geometry of formaldehyde is a tilted η2 -dioxymethylene (with an adsorption energy Eads=-125 kJ mol-1 ), in which a bond forms to a nearby bridging O atom and the carbonyl-O atom in the formaldehyde binds to a Ti atom in the adjacent fivefold coordinated lattice site. The η1 -top configuration on fivecoordinate Ti4+ is much less favorable (Eads=-69 kJ mol-1 ). The largest stabilization is exerted by subsurface Ti interstitials between the first and second layers. These defects stabilize the η2 -dioxymethylene structure by nearly 40 kJ mol-1 to an adsorption energy of 164 kJ mol-1 . Contrary to popular belief, adsorption in a bridging oxygen vacancy (Eads=-86 kJ mol-1 ) is much less favorable for formaldehyde compared to the η2 - dioxymethylene structures. From these results we conclude that formaldehyde will bind in the η2 - dioxymethylene structure on the stoichiometric surface as well as in the presence of Ti interstitials and bridging oxygen vacancies. In the light of these substantial effects, we conclude that it is essential to include all the types of point defects present in typical, reduced rutile samples used for model studies, at realistic concentrations to obtain correct adsorption sites, structures, energetic, and chemi-physical properties. 

Li H, Knaup JM, Kaxiras E, Vlassak JJ. Stiffening of organosilicate glasses by organic cross-linking. Acta Materialia. 2011;59 :44-52.Abstract

Atomistic simulations show that organosilicates, used as low permittivity dielectric materials in advanced integrated circuits, can be made substantially stiffer than amorphous silica, while maintaining a lower mass density. The enhanced stiffness is achieved by incorporating organic cross-links to replace bridging oxygen atoms in the silica network. To elucidate the mechanism responsible for the enhanced stiffness, the conformational changes in the network upon hydrostatic and shear loading are examined. The structural and mechanical impact of terminal methyl groups is also assessed quantitatively and compared with continuous random network theory.

Xu B, Haubrich J, Baker TA, Kaxiras E, Friend CM. Theoretical Study of O-Assisted Selective Coupling of Methanol on Au(111). Journal of Physical Chemistry C. 2011;115 :3703-3708.Abstract

We report the first systematic theoretical study of the oxidative self-coupling of methanol to form the ester, methylformate, on atomic-oxygen-covered Au(111) using density functional theory calculations. The first step in the process —dissociation of the O-H bond in methanol—has a lower barrier for transfer of the proton to adsorbed oxygen than for transfer of H to gold, consistent with experimental observations that O is necessary to initiate the reaction. The computed barrier for formation of methoxy (CH3O) and OH is 0.41 eV, compared with 1.58 eV calculated for the transfer of H to the clean Au surface. Several different pathways for the ensuing β-H elimination in CH3O(ads) to form formaldehyde have been considered, namely, attack by adsorbed O, OH, or a second CH3O, and transfer to the Au metal. Methoxy attacked by surface oxygen has the lowest calculated barrier, 0.49 eV, and leads to adsorbed H2C=O and OH. Subsequent coupling of methoxy and formaldehyde has no apparent barrier in the calculation, consistent with the experimental conclusion that β-H elimination is the rate-limiting step for the overall reaction. With the exception of surface oxygen, all other surface species have low diffusion barriers, suggesting that rearrangement and movement of these species from the preferred adsorption sites to configurations necessary for reactions occur readily, thus contributing to the activity for coupling on gold.

Lin M-W, Ling C, Agapito LA, Kioussis N, Zhang Y, Cheng MM-C, Wang WL, Kaxiras E, Zhou Z. Approaching the intrinsic band gap in suspended high-mobility graphene nanoribbons. Physical Review B. 2011;84 :125411.Abstract

We report electrical transport measurements on a suspended ultra-low-disorder graphene nanoribbon (GNR) with nearly atomically smooth edges that reveal a high mobility exceeding 3000 cm2 V−1 s−1 and an intrinsic band gap. The experimentally derived band gap is in quantitative agreement with the results of our electronic structure calculations on chiral GNRs with comparable width taking into account the electron-electron interactions, indicating that the origin of the band gap in nonarmchair GNRs is partially due to the magnetic zigzag edges

Gali A, Kaxiras E, Zimanyi GT, Meng S. Effect of symmetry breaking on the optical absorption of semiconductor nanoparticles. Physical Review B. 2011;84 :035325.Abstract

The shape of semiconductor nanoparticles (NPs) can have an important influence on their optical absorption spectra with enhanced absorption resulting from breaking their symmetries. To illustrate this effect, we present broad energy optical excitation spectra of ∼2 nm Si and PbSe nanoparticles, obtained from extensive timedependent density functional theory calculations. We considered both highly symmetric spherical shapes and low-symmetry rodlike and disklike shapes. The low-symmetry shapes exhibit an increase in absorption at low and relatively high energies compared to the absorption of spherical NPs of similar volume, independent of their chemical compositions and surface structures. Our results elucidate the mechanism of enhanced multiexciton generation in semiconductor NPs, which is important in the quest to improve their photovoltaic applications.

Chang CL, Sankaranarayanan SKRS, Ruzmetov D, Engelhard MH, Kaxiras E, Ramanathan S. Compositional tuning of ultrathin surface oxides on metal and alloysubstrates using photons: Dynamic simulations and experiments. Phys. Rev. B. 2010;81 :085406.
Meng S, Kaxiras E. Electron and Hole Dynamics in Dye-Sensitized Solar Cells:Influencing Factors and Systematic Trends. NanoLett. 2010;10 :1238.
Chen HP, Kalia RK, Kaxiras E, Lu G, Nakano A, Nomura K, van Duin ACT, Vashishta P, Yuan ZS. Embrittlement of Metal by Solute Segregation-Induced Amorphization. Phys. Rev. Lett. 2010;104 :155502.
Bernaschi M, Fatica M, Melchionna S, Succi S, Kaxiras E. A flexible high-performance Lattice Boltzmann GPU code for thesimulations of fluid flows in complex geometries. Concurrency Computat.: Pract. Exper. 2010;22 :1.
Melchionna S, Bernaschi M, Succi S, Kaxiras E, Rybicki FJ, Mitsouras D, Coskun AU, Feldman CL. Hydrokinetic approach to large-scale cardiovascular blood flow. Comp. Phys. Comm. 2010;181 :462.
Baker TA, Friend CM, Kaxiras E. Local Bonding Effects in the Oxidation of CO on Oxygen-CoveredAu(111) from Ab Initio Molecular Dynamics Simulations. J. Chem. Theory Comput. 2010;6 :279.
Manousakis E, Ren J, Meng S, Kaxiras E. Is the nature of magnetic order in copper-oxides and iron-pnictides different?. Sol. St. Comm. 2010;150 :62.
Agapito LA, Kioussis N, Kaxiras E. Electric-field control of magnetism in graphene quantum dots: Ab initio calculations. Phys. Rev. B. 2010;82 :201411.
Wang WL, Kaxiras E. Graphene hydrate: theoretical prediction of a new insulating form of graphene. New J. Phys. 2010;12 :125012.
Baker TA, Kaxiras E, Friend CM. Insights from Theory on the Relationship Between Surface Reactivityand Gold Atom Release. Top. Catal. 2010;53 :365.
Peters A, Melchionna S, Kaxiras E, Latt J, Sircar J, Bernaschi M, Bisson M, Succi S. Multiscale simulation of cardiovascular flows on the IBM Bluegene : full heart-circulation system at near red-blood cell resolution. 2010 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis. 2010;doi: 10.1109/SC.2010.33.