Accurate ab initio potential energy surfaces for the (3)A '' and (3)A ' electronic states of the O(P-3) plus HBr system

In this work, we report the construction of potential energy surfaces for the (3)A '' and (3)A' states of the system O(P-3) + HBr. These surfaces are based on extensive ab initio calculations employing the MRCI+Q/CBS+SO level of theory. The complete basis set energies were estimated from extrapolation of MRCI+Q/aug-cc-VnZ(-PP) (n = Q, 5) results and corrections due to spin-orbit effects obtained at the CASSCF/aug-cc-pVTZ(-PP) level of theory. These energies, calculated over a region of the configuration space relevant to the study of the reaction O(P-3) + HBr -> OH + Br, were used to generate functions based on the many-body expansion. The three-body potentials were interpolated using the reproducing kernel Hilbert space method. The resulting surface for the (3)A '' electronic state contains van der Waals minima on the entrance and exit channels and a transition state 6.55 kcal/mol higher than the reactants. This barrier height was then scaled to reproduce the value of 5.01 kcal/mol, which was estimated from coupled cluster benchmark calculations performed to include high-order and core-valence correlation, as well as scalar relativistic effects. The (3)A' surface was also scaled, based on the fact that in the collinear saddle point geometry these two electronic states are degenerate. The vibrationally adiabatic barrier heights are 3.44 kcal/mol for the (3)A '' and 4.16 kcal/mol for the (3)A' state. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4705428]

The Structural and Electronic Properties of Tin Oxide Nanowires: An Ab Initio Investigation

We performed an ab initio investigation on the properties of rutile tin oxide (SnOx) nanowires. We computed the wire properties determining the equilibrium geometries, binding energies, and electronic band structures for several wire dimensions and surface facet configurations. The results allowed us to establish scaling laws for the structural properties, in terms of the nanowire perimeters. The results also showed that the surface states control most of the electronic properties of the nanowires. Oxygen incorporation in the nanowire surfaces passivated the surface-related electronic states, and the resulting quantum properties and scaling laws were fully consistent with electrons confined inside the nanowire. Additionally, oxygen incorporation in the wire surfaces generated an unbalanced concentration of spin up and down electrons, leading to magnetic states for the nanowires.

Ab-initio calculations for a realistic sensor: A study of CO sensors based on nitrogen-rich carbon nanotubes

The use of nanoscale low-dimensional systems could boost the sensitivity of gas sensors. In this work we simulate a nanoscopic sensor based on carbon nanotubes with a large number of binding sites using ab initio density functional electronic structure calculations coupled to the Non-Equilibrium Green's Function formalism. We present a recipe where the adsorption process is studied followed by conductance calculations of a single defect system and of more realistic disordered system considering different coverages of molecules as one would expect experimentally. We found that the sensitivity of the disordered system is enhanced by a factor of 5 when compared to the single defect one. Finally, our results from the atomistic electronic transport are used as input to a simple model that connects them to experimental parameters such as temperature and partial gas pressure, providing a procedure for simulating a realistic nanoscopic gas sensor. Using this methodology we show that nitrogen-rich carbon nanotubes could work at room temperature with extremely high sensitivity. Copyright 2012 Author(s). This article is distributed under a Creative Commons Attribution 3.0 Unported License. [http://dx.doi.org/10.1063/1.4739280]

The T-2 phase in the Nb-Si-B system studied by ab initio calculations and synchrotron X-ray diffraction

The solid solution based on Nb5Si3 (Cr5B3 structure type, D8(l), tl32, 14/mcm, No140, a=6.5767 angstrom, c=11.8967 angstrom) in the Nb-Si-B system was studied from the structural and thermodynamic point of view both experimentally and by ab initio calculations. Rietveld refinement of powder X-ray synchrotron data allowed to determine the boron to silicon substitution mechanism and the structural parameters. Ab initio calculations of different ordered compounds and selected disordered alloys allowed to obtain in addition to the enthalpy of formation of the solution, substitution mechanism and structural parameters which are in excellent agreement with the experimental data. The stability of the phase is discussed. (C) 2012 Elsevier Inc. All rights reserved.

Molecular and Electronic Structure of the Peptide Subunit of Geobacter sulfurreducens Conductive Phi from First Principles

The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved a-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pain was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's alpha-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction.

New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination

Crown ethers have the ability of solubilizing inorganic salts in apolar solvents and to promote chemical reactions by phase-transfer catalysis. However, details on how crown ethers catalyze ionic S(N)2 reactions and control selectivity are not well understood. In this work, we have used high level theoretical calculations to shed light on the details of phase-transfer catalysis mechanism of KF reaction with alkyl halides promoted by 18-crown-6. A complete analysis of the of the model reaction between KF(18-crown-6) and ethyl bromide reveals that the calculations can accurately predict the product ratio and the overall kinetics. Our results point out the importance of the K* ion and of the crown ether ring in determining product selectivity. While the K* ion favors the S(N)2 over the E2 anti pathway, the crown ether ring favors the S(N)2 over E2 syn route. The combination effects lead to a predicted 94% for the S(N)2 pathway in excellent agreement with the experimental value of 92%. A detailed analysis of the overall mechanism of the reaction under phase-transfer conditions also reveals that the KBr product generated in the nucleophilic fluorination acts as an inhibitor of the 18-crown-6 catalyst and it is responsible for the observed slow reaction rate. (C) 2012 Elsevier B.V. All rights reserved.

Ab initio studies of pristine and oxidized Cu3Au(100) and (111) surfaces

We review the previous literature and our recent work on first-principles studies of Cu3Au(100) and (111) surfaces, with focus on the segregation of atomic species to the surface at pristine conditions and in the presence of oxygen. In particular, the combined use of experimental and theoretical tools to achieve chemical identification at an atomic level of the surface species is emphasized and discussed.

ESTIMATING REACTION CONSTANTS BY AB INITIO MOLECULAR MODELING: A STUDY ON THE OXIDATION OF PHENOL TO CATECHOL AND HYDROQUINONE IN ADVANCED OXIDATION PROCESSES

Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

In-plane mapping of buried InGaAs quantum rings and hybridization effects on the electronic structure

This work reports the investigation on the structural differences between InAs quantum rings and their precursor quantum dots species as well as on the presence of piezoelectric fields and asymmetries in these nanostructures. The experimental results show significant reduction in the ring dimensions when the sizes of capped and uncapped ring and dot samples are compared. The iso-lattice parameter mapped by grazing-incidence x-ray diffraction has revealed the lateral extent of strained regions in the buried rings. A comparison between strain and composition of dot and ring structures allows inferring on how the ring formation and its final configuration may affect optical response parameters. Based on the experimental observations, a discussion has been introduced on the effective potential profile to emulate theoretically the ring-shape confinement. The effects of confinement and strain field modulation on electron and hole band structures are simulated by a multiband k.p calculation. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4733964]

The influence of different indium-composition profiles on the electronic structure of lens-shaped InxGa1-xAs quantum dots

We present effective-mass calculations of the bound-state energy levels of electrons confined inside lens-shaped InxGa1-xAs quantum dots (QDs) embedded in a GaAs matrix, taking into account the strain as well as the In gradient inside the QDs due to the strong In segregation and In-Ga intermixing present in the InxGa1-xAs/GaAs system. In order to perform the calculations, we used a continuum model for the strain, and the QDs and wetting layer were divided into their constituting monolayers, each one with a different In concentration, to be able to produce a specific composition profile. Our results clearly show that the introduction of such effects is very important if one desires to correctly reproduce or predict the optoelectronic properties of these nanostructures.

Local order and electronic structure of Pb1-xLaxZr0.40Ti0.60O3 materials and its relation with ferroelectric properties

The knowledge of electronic and local structures is a fundamental step towards understanding the properties of ferroelectric ceramics. X-ray absorption near-edge structure (XANES) of Pb1-xLaxZr0.40Ti0.60O3 ferroelectric samples was measured in order to know how the local order and electronic structure are related to their ferroelectric property, which was tailored by the substitution of lead by lanthanum atoms. The analysis of XANES spectra collected at Ti K- and L-edges XANES showed that the substitution of Pb by La leads to a decrement of local distortion around Ti atoms on the TiO6 octahedron. The analysis of O K-edge XANES spectra showed that the hybridization between O 2p and Pb 6sp states is related to the displacement of Ti atoms in the TiO6 octahedra. Based on these results, it is possible to determine that the degree of ferroelectricity in these samples and the manifestation of relaxor behavior are directly related to the weakening of O 2p and Pb 6sp hybridization. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4720472]

Estimating reaction constants by ab initio molecular modeling: a study on the oxidation of phenol to catechol and hydroquinone in advanced oxidation processes

Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

Electronic Structure Calculations in a 2D SixGe1-x Alloy Under an Applied Electric Field.

The recent advances and promises in nanoscience and nanotechnology have been focused on hexagonal materials, mainly on carbon-based nanostructures. Recently, new candidates have been raised, where the greatest efforts are devoted to a new hexagonal and buckled material made of silicon, named Silicene. This new material presents an energy gap due to spin-orbit interaction of approximately 1.5 meV, where the measurement of quantum spin Hall effect(QSHE) can be made experimentally. Some investigations also show that the QSHE in 2D low-buckled hexagonal structures of germanium is present. Since the similarities, and at the same time the differences, between Si and Ge, over the years, have motivated a lot of investigations in these materials. In this work we performed systematic investigations on the electronic structure and band topology in both ordered and disordered SixGe1-x alloys monolayer with 2D honeycomb geometry by first-principles calculations. We show that an applied electric field can tune the gap size for both alloys. However, as a function of electric field, the disordered alloy presents a W-shaped behavior, similarly to the pure Si or Ge, whereas for the ordered alloy a V-shaped behavior is observed.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).

Theoretical and experimental studies on the electronic, optical, and structural properties of poly-pyrrole-2-carboxylic acid films

A theoretical approach is used here to explain experimental results obtained from the electrosynthesis of polypyrrole-2-carboxylic acid (PPY-2-COOH) films in nonaqueous medium. An analysis of the Fukui function (reactivity index) indicates that the monomer (pyrrole-2-carboxylic acid, PY-2-COOH), and dimers and trimers are oxidized in the C4 or C5 positions of the heterocyclic ring of the PY-2-COOH structure. After calculating the heat of formation using semiempirical Austin Model 1 post-Hartree-Fock parameterization for dimer species, both C4 and C5 positions adjacent to the aromatic rings of PPY-2-COOH were considered the most susceptible ones to oxidative coupling reactions. The ZINDO-S/CI semiempirical method was used to simulate the electronic transitions typically seen in the UV-VIS-NIR range in monomer and oligomers with different conjugation lengths. The use of an electrochemical quartz crystal microbalance provides sufficient information to propose a polymerization mechanism of PY-2-COOH based on molecular modeling and experimental results.