Identification of species formed after pyridine adsorption on iron, cobalt, nickel and silver electrodes by SERS and theoretical calculations

The adsorption of pyridine (py) on Fe, Co, Ni and Ag electrodes was studied using surface-enhanced Raman scattering (SERS) to gain insight into the nature of the adsorbed species. The wavenumber values and relative intensities of the SERS bands were compared to the normal Raman spectrum of the chemically prepared transition metal complexes. Raman spectra of model clusters M(4)(py) (four metal atoms bonded to one py moiety) and M(4)(alpha-pyridil) where M = Ag, Fe, Co or Ni were calculated by density functional theory (DFT) and used to interpret the experimental SERS results. The similarity of the calculated M(4)(py) spectra with the experimental SERS spectra confirm the molecular adsorption of py on the surface of the metallic electrodes. All these results exclude the formation of adsorbed alpha-pyridil species, as suggested previously. Copyright (C) 2009 John Wiley & Sons, Ltd.

Exploring new molecular species on the (1)[H, Se, F] singlet potential energy surface: Energetics, structures, IR spectra, and heats of formation

Structural, energetic, and vibrational properties of new molecular species, HSeF and HFSe, the associated transition state, and dissociation fragments are investigated using a state-of-the-art theoretical approach, CCSD(T)/CBS. HSeF is a normal covalently bonded molecule 38.98 kcal mol (1) more stable than the complex HF-Se, which shows an unusual structure with a central fluorine atom and a bond angle of 101.8 degrees.A barrier (Delta G(#)) of 49.01 kcal mol (1) separates the two species. Vibrational frequencies are also quite distinct. Heats of formation are evaluated for the diatomic fragments and HSeF. Final Delta(f)H values depend on the experimental accuracy of those of Se(g) and H(2)Se. (c) 2009 Elsevier B.V. All rights reserved.

The intramolecular charge transfer in a donor-pi-acceptor dianion probed by resonance Raman spectroscopy and quantum chemical calculations

The dideprotonation of 4-(4-nitrophenylazo)resorcinol generates an anionic species with substantial electronic pi delocalization. As compared to the parent neutral species, the anionic first excited electronic transition, characterized as an intramolecular charge transfer (ICT) from the CO(-) groups to the NO(2) moiety, shows a drastic red shift of ca. 200 nm in the lambda(max) in the UV-vis spectrum, leading to one of the lowest ICT energies observed (lambda(max) = 630 nm in dimethyl sulfoxide (DMSO)) in this class of push-pull molecular systems. Concomitantly, a threefold increase in the molar absorptivity (epsilon(max)) in comparison to the neutral species is observed. The resonance Raman enhancement profiles reveal that in the neutral species the chromophore involves several modes, as nu(C-N), nu(N=N), nu(C=C) and nu(s)(NO(2)), whereas in the dianion, there is a selective enhancement of the NO(2) vibrational modes. The quantum chemical calculations of the electronic transitions and vibrational wavenumbers led to a consistent analysis of the enhancement patterns observed in the resonance Raman spectra. Copyright (C) 2009 John Wiley & Sons, Ltd.

Predicting new molecular species of potential interest to atmospheric chemistry: The isomers HSI and HIS

Structural, vibrational, and energetic properties of new molecular species, HSI and HIS are investigated for the first time using a state-of-the-art theoretical approach. These molecules can be easily differentiated by their geometric parameters and vibrational spectra. HSI is much more stable, and a direct unimolecular isomerization is very unlikely. Kinetics estimates predict that only at low temperatures there is a possibility of isolating HIS. For HS-I, we estimate a bond dissociation energy of 46.25 kcal/mol, and a heat of formation at 298.15 K of 12.84 kcal/mol. For the H(2)S + I(2) -> HSI + HI reaction enthalpy, we found 8.40 kcal/ mol. (C) 2008 Elsevier B.V. All rights reserved.

Azo-hydrazone tautomerism in protonated aminoazobenzenes: Resonance Raman spectroscopy and quantum-chemical calculations

The protonation effect on the vibrational and electronic spectra of 4-aminoazobenzene and 4-(dimethylamino)azobenzene was investigated by resonance Raman spectroscopy, and the results were discussed on the basis of quantum-chemical calculations. Although this class of molecular systems has been investigated in the past concerning the azo-hydrazone tautomerism, the present work is the first to use CASSCF/CASPT2 calculations to unveil the structure of both tautomers as well the nature of the molecular orbitals involved in chromophoric moieties responsible for the resonance Raman enhancement patterns. More specifically both the resonance Raman and theoretical results show clearly that in the neutral species, the charge transfer transition involves mainly the azo moiety, whereas in the protonated forms there is a great difference, depending on the tautomer. In fact, for the azo tautomer the transition is similar to that observed in the corresponding neutral species, whereas in the hydrazone tautomer such a transition is much more delocalized due to the contribution of the quinoid structure. The characterization of protonated species and the understanding of the tautomerization mechanism are crucial for controlling molecular properties depending on the polarity and pH of the medium.

The interaction between atoms of Au and Cu with clean Si(111) surface: A study combining synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations

In order to evaluate the interactions between Au/Cu atoms and clean Si(l 11) surface, we used synchrotron radiation grazing incidence X-ray fluorescence analysis and theoretical calculations. Optimized geometries and energies on different adsorption sites indicate that the binding energies at different adsorption sites are high, suggesting a strong interaction between metal atom and silicon surface. The Au atom showed higher interaction than Cu atom. The theoretical and experimental data showed good agreement. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.

Crystal structure and theoretical calculations of Julocrotine, a natural product with antileishmanial activity

Julocrotine, N-(2,6-dioxo-l-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data. (C) 2007 Wiley Periodicals, Inc.

Defeitos pontuais nos compostos intermetálicos ZrNi e Zr/sub 2/Ni estudados por dinâmica molecular

Empregamos a técnica de Dinâmica Molecular para estudar propriedades de defeitos pontuais nos compostos intermetálicos ZrNi e Zr2Ni. Descrevemos as configurações estáveis de defeitos e mecanismos de migração, assim como as energias envolvidas. Os potenciais interatômicos foram derivados do Embedded Atom Model. No intuito de levar em conta a variação de estequiometria causada pela presença de alguns tipos de defeitos em intermetálicos, apresentamos um método numérico que fornece a energia efetiva de formação de defeitos e aplicamos o método ao ZrNi e Zr2Ni. Os resultados mostraram que vacâncias são mais estáveis na sub—rede do Ni, com energia de formação de 0,83 e-0,61 eV em ZrNi e Zr2Ni, respectivamente. Vacâncias de Zr são instáveis em ambos compostos; elas decaem espontaneamente em pares anti—sítio e vacância de Ni. Configurações e energias de formação de intersticiais também foram calculadas e mostraram comportamentos similares. Em ZrNi, a migração de vacâncias ocorre preferencialmente nas direções [025] e [100], com as respectivas energias de migração 0,67 e 0,73 eV, e é um processo essencialmente bidimensional no plano (001). Em Zr,Ni, a migração de vacâncias é unidimensional, ocorrendo na direção [001], com energia de migração de 0,67 eV. Em ambos compostos a presença de defeitos de anti—sítio de Ni diminui a energia de migração da vacância de Ni em até 3 vezes e facilita a movimentação em três dimensões. Mecanismos de anel não são energeticamente eficientes em comparação com saltos diretos. As configurações estáveis de intersticiais em ambos compostos consistem em um átomo de Ni sobre o plano (001) entre dois vizinhos de Zr fora do plano. Intersticiais de Zr são instáveis e tendem a deslocar um átomo de Ni, ocupando seu sítio. Energias de deslocamento foram estudadas através de simulações de irradiação de ambos compostos. Durante o processo de colisão binária, um potencial universal ZBL foi usado para colisões a curta distância. Para distâncias intermediárias usamos um potencial de união arbitrário. Zr mostrou—se mais difícil de ser arrancado de seu sítio do que Ni. Encontramos valores de energia de deslocamento no intervalo de aproximadamente 29 eV até 546 eV. Alguns resultados experimentais são mostrados e apresentam boa concordância com os cálculos.

Modelagem molecular na caracterização eletrônica de oligopeptídeos e na descrição quântica da interação fármaco-receptor

In this dissertation, the theoretical principles governing the molecular modeling were applied for electronic characterization of oligopeptide α3 and its variants (5Q, 7Q)-α3, as well as in the quantum description of the interaction of the aminoglycoside hygromycin B and the 30S subunit of bacterial ribosome. In the first study, the linear and neutral dipeptides which make up the mentioned oligopeptides were modeled and then optimized for a structure of lower potential energy and appropriate dihedral angles. In this case, three subsequent geometric optimization processes, based on classical Newtonian theory, the semi-empirical and density functional theory (DFT), explore the energy landscape of each dipeptide during the search of ideal minimum energy structures. Finally, great conformers were described about its electrostatic potential, ionization energy (amino acids), and frontier molecular orbitals and hopping term. From the hopping terms described in this study, it was possible in subsequent studies to characterize the charge transport propertie of these peptides models. It envisioned a new biosensor technology capable of diagnosing amyloid diseases, related to an accumulation of misshapen proteins, based on the conductivity displayed by proteins of the patient. In a second step of this dissertation, a study carried out by quantum molecular modeling of the interaction energy of an antibiotic ribosomal aminoglicosídico on your receiver. It is known that the hygromycin B (hygB) is an aminoglycoside antibiotic that affects ribosomal translocation by direct interaction with the small subunit of the bacterial ribosome (30S), specifically with nucleotides in helix 44 of the 16S ribosomal RNA (16S rRNA). Due to strong electrostatic character of this connection, it was proposed an energetic investigation of the binding mechanism of this complex using different values of dielectric constants (ε = 0, 4, 10, 20 and 40), which have been widely used to study the electrostatic properties of biomolecules. For this, increasing radii centered on the hygB centroid were measured from the 30S-hygB crystal structure (1HNZ.pdb), and only the individual interaction energy of each enclosed nucleotide was determined for quantum calculations using molecular fractionation with conjugate caps (MFCC) strategy. It was noticed that the dielectric constants underestimated the energies of individual interactions, allowing the convergence state is achieved quickly. But only for ε = 40, the total binding energy of drug-receptor interaction is stabilized at r = 18A, which provided an appropriate binding pocket because it encompassed the main residues that interact more strongly with the hygB - C1403, C1404, G1405, A1493, G1494, U1495, U1498 and C1496. Thus, the dielectric constant ≈ 40 is ideal for the treatment of systems with many electrical charges. By comparing the individual binding energies of 16S rRNA nucleotides with the experimental tests that determine the minimum inhibitory concentration (MIC) of hygB, it is believed that those residues with high binding values generated bacterial resistance to the drug when mutated. With the same reasoning, since those with low interaction energy do not influence effectively the affinity of the hygB in its binding site, there is no loss of effectiveness if they were replaced.

Investigation of the two-photon absorption cross-section in perylene tetracarboxylic derivatives: Nonlinear spectra and molecular structure

We investigated the 2PA absorption spectrum of a family of perylene tetracarboxylic derivatives ( PTCDs): bis( benzimidazo) perylene ( AzoPTCD), bis( benzimidazo) thioperylene ( Monothio BZP), n-pentylimidobenzimidazoperylene ( PazoPTCD), and bis( n-butylimido) perylene ( BuPTCD). These compounds present extremely high two-photon absorption, which makes them attractive for applications in photonics devices. The two-photon absorption cross-section spectra of perylene derivatives obtained via Z-scan technique were fitted by means of a sum-over-states ( SOS) model, which described with accuracy the different regions of the 2PA cross-section spectra. Frontier molecular orbital calculations show that all molecules present similar features, indicating that nonlinear optical properties in PTCDs are mainly determined by the central portion of the molecule, with minimal effect from the lateral side groups. In general, our results pointed out that the differences in the 2PA cross-sections among the compounds are mainly due to the nonlinearity resonance enhancement.

Molecular and morphological characterization of bis benzimidazo perylene films and surface-enhanced phenomena

Thin solid films of bis benzimidazo perylene (AzoPTCD) were fabricated using physical vapor deposition (PVD) technique. Thermal stability and integrity of the AzoPTCD PVD films during the fabrication (similar to 400 degrees C at 10(-6) Torr) were monitored by Raman scattering. Complementary thermogravimetric results showed that thermal degradation of AzoPTCD occurs at 675 degrees C. The growth of the PVD films was established through UV-vis absorption spectroscopy, and the surface morphology was surveyed by atomic force microscopy (AFM) as a function of the mass thickness. The AzoPTCD molecular organization in these PVD films was determined using the selection rules of infrared absorption spectroscopy (transmission and reflection-absorption modes). Despite the molecular packing, X-ray diffraction revealed that the PVD films are amorphous. Theoretical calculations (density functional theory, B3LYP) were used to assign the vibrational modes in the infrared and Raman spectra. Metallic nanostructures, able to sustain localized surface plasmons (LSP) were used to achieve surface-enhanced resonance Raman scattering (SERRS) and surface-enhanced fluorescence (SEF).

Theoretical study on the molecular mechanism for the reaction of VO2+ with C2H4

The complex reaction between VO2+ ((1)A(1)/(3)A) and C2H4 (Ag-1(g)/(3)A(1)) to yield VO+ ((1)Delta/(3)Sigma) and CH3CHO ('A'/(3)A) has been studied by means of B3LYP/6-31G* and B3LYP/6-311G(2d,p) calculations. The structures of all reactants, products, intermediates, and transition structures of this reaction have been optimized and characterized at the fundamental singlet and first excited triplet electronic states. Crossing points are localized, and possible spin inversion processes are discussed by means of the intrinsic reaction coordinate approach. Relevant stationary points along the most favorable reaction pathways have been studied at the CCSD/6-311G(2d,p)//B3LYP/6-311G(2d,p) calculation level. The theoretical results allow the development of thermodynamic and kinetic arguments about the reaction pathways of the title process. In the singlet state, the first step is the barrierless obtention of a reactant complex associated with the formation of a V-C bond, while in the triplet state a three-membered ring addition complex with the V bonded to the two C atoms is obtained. Similar behavior is found in the exit channels: the product complexes can be formed from isolated products without barriers. The reactant and product complexes are the most stable stationary points in the singlet and triplet electronic states. From the singlet state reactant complex, two reaction pathways are posssible to reach the triplet state product complex. (i) A mechanism in which a hydrogen transfer process is the first and rate limiting step and the second step is an oxygen transfer between vanadium and carbon atoms with a concomitant change in the spin state. The crossing point between singlet and triplet spin states is not kinetically relevant because it takes place at a later stage occurring in the exit channel. (ii) A mechanism in which the first stage renders a four-membered ring between vanadyl cation and the ethylene fragment and an oxygencarbon bond is formed; on going from this minimum to the second transition structure, associated with a carbon-vanadium bond breaking process, the crossing point between singlet and triplet spin states is reached. The final step is the hydrogen transfer between both carbon atoms to yield the product complex. In this case the spin change opens a lower barrier pathway. The transition structures with larger values of relative energies for both reactive channels of VO2+ ((1)A(1)) + C2H4 (Ag-1) --> VO+ ((3)Sigma) + CH3CHO ((1)A') present similar energies, and the two reaction pathways can be considered as competitive.

NH3+N2O3 reaction. High level calculations

We have undertaken a comprehensive study of the NH3 + N2O3 reaction in gas phase. Total energies of reactants, intermediates, transition states, and products have been calculated at CBS-QB3 level of theory. The corresponding BSSE analysis were performed at the highest level of theory, i.e. MP2 using the complete basis set (CBS) extrapolation at CBS-QB3 optimized geometries. A detailed mechanism was proposed for 2NH(3) - N2O3 -> 2N(2) - 3H(2)O with Delta H-r= - 170.08 kcal/mol N-2. (c) 2005 Elsevier B.V. All rights reserved.

Close-coupling calculations of positronium formation in positron-helium scattering

Positronium (Ps) formation in positron-helium scattering has been investigated in different partial waves at medium energies including the Ore gap region using the close-coupling approximation with realistic wavefunctions for the following states: He(1s1s), He(1s2s), He(1s2p), He(1s3s), He(1s3p), Ps(ls), Ps(2s), Ps(2p). Calculations are reported of rearrangement cross sections to Ps(ls), Ps(2s) and Ps(2p) states for incident positron energies up to 200 eV. The present partial cross sections are in good agreement with experimental results and a variational calculation in the Ore gap region.

Close-coupling calculations of elastic and inelastic positron-helium scattering

Elastic and inelastic positron-helium scattering have been investigated in different partial waves at medium energies using the close-coupling approximation with realistic wavefunctions employing the following states: He(1s1s), He(1s2s), He(1s2p), He(1s3s), He(1s3p), Ps(1s), Ps(2s) and Ps(2p). All excitations of the helium atom are in the spin-singlet electronic state. Calculations are reported of cross sections to He(1s1s), He(1s2s), and He(1s2p) transitions for incident positron energies up to 200 eV. These cross sections are in good agreement with experimental results.