Spin contamination in XOO radicals X = F, Cl, Br, HO: How is the investigation of the HOOO radical affected

We have analysed the effect of spin contamination in the wavefunction of HOOO. At least, two solutions can be found for the HF wavefunction. One, lower in energy, presents a high spin contamination and gives qualitatively incorrect structural parameters. On the other hand, the less contaminated HF reference gives structural parameters that are in better agreement with experiment, and positive spin densities on all atoms. Some of the problems described during previous investigations of HOOO can now be traced to problems in the HF reference. For the first time we report a CCSD(T) estimation of the structure of HOOO cis employing a HF reference with small spin contamination. (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.

Low-lying singlet and triplet electronic states of RhB

The low-lying X-1 Sigma(+), a(3)Delta, A(1)Delta, b(3)Sigma(+), B-1 Pi, c(3)Pi, C-1 Phi, D-1 Sigma(+), E-1 Pi, d(1)Phi, and e(3)Pi electronic states of RhB have been investigated at the ab initio level, using the multistate multiconfigurational second-order perturbation (MS-CASPT2) theory, with extended atomic basis sets and inclusion of scalar relativistic effects. Among the eleven electronic states included in this work, only three (the X-1 Sigma(+), D-1 Sigma(+), and E-1 Pi states) have been investigated experimentally. Potential energy curves, spectroscopic constants, dipole moments, binding energies, and chemical bonding aspects are presented for all electronic states.

On the Relaxation Mechanisms of 6-Azauracil

The nonadiabatic photochemistry of 6-azauracil has been studied by means of the CASPT2//CASSCF protocol and double-zeta plus polarization ANO basis sets. Minimum energy states, transition states, minimum energy paths, and surface intersections have been computed in order to obtain an accurate description of several potential energy hypersurfaces. It is concluded that, after absorption of ultraviolet radiation (248 nm), two main relaxation mechanisms may occur, via which the lowest (3)(pi pi*) state can be populated. The first one takes place via a conical intersection involving the bright (1)(pi pi*) and the lowest (1)(n pi*) states, ((1)pi pi*/(1)n pi*)(CI), from which a low energy singlet-triplet crossing, ((1)n pi*/(3)pi pi*)(STC), connecting the (1)(n pi*) state to the lowest (3)(pi pi*) triplet state is accessible. The second mechanism arises via a singlet-triplet crossing, ((1)pi pi*/(3)n pi*)(STC), leading to a conical intersection in the triplet manifold, ((3)n pi*/(3)pi pi*)(CI), evolving to the lowest (3)(pi pi*) state. Further radiationless decay to the ground state is possible through a (gs/(3)pi pi*)(STC).

A three-state model for the photophysics of guanine

The nonadiabatic photochemistry of the guanine molecule (2-amino-6-oxopurine) and some of its tautomers has been studied by means of the high-level theoretical ab initio quantum chemistry methods CASSCF and CASPT2. Accurate computations, based by the first time on minimum energy reaction paths, states minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of the molecules lead to interpret the photochemistry of guanine and derivatives within a three-state model. As in the other purine DNA nucleobase, adenine, the ultrafast subpicosecond fluorescence decay measured in guanine is attributed to the barrierless character of the path leading from the initially populated (1)(pi pi* L-a) spectroscopic state of the molecule toward the low-lying methanamine-like conical intersection (gs/pi pi* L-a)(CI). On the contrary, other tautomers are shown to have a reaction energy barrier along the main relaxation profile. A second, slower decay is attributed to a path involving switches toward two other states, (1)(pi pi* L-b) and, in particular, (1)(n(o)pi*), ultimately leading to conical intersections with the ground state. A common framework for the ultrafast relaxation of the natural nucleobases is obtained in which the predominant role of a pi pi*-type state is confirmed.

Thiothionyl bromide (S=SBr2): The elusive isomer of dibromodisulfane (BrSSBr)

CCSD(T) with a series of correlation consistent basis up to quadruple-zeta is used to investigate the structures, vibrational spectra, relative stability, heats of formation, and barrier to isomerization of S=SBr2 and BrSSBr. It represents the most accurate and detailed characterization of these molecules to date. We show that the frequency mode at 302 cm(-1), detected in various studies and assigned to impurities by some authors, and to the anti-symmetric SBr stretch in BrSSBr by others, thus in fact corresponds to the anti-symmetric SBr stretch in the elusive S=SBr2 species; it thus corroborates and complements an earlier partial IR spectra study attributable to S=SBr2. Including corrections for relativistic and core-valence correlation effects, we also predict 26.33 (12.74) kcal/mol for Delta H-f (298.15 K) of S=SBr2 (BrSSBr). For the S=SBr2 -> BrSSBr reaction, our best estimates for the Gibbs free energy and the enthalpy of the reaction at 298.15 K are -13.71 and -13.44 kcal/mol, respectively. For a value of Delta G(#) equal to 23.52 kcal/mol, we estimate a TST rate constant, at 298.15 K, of 3.57 x 10(-5) s(-1). (c) 2007 Elsevier B.V. All rights reserved.

Sequential IRMPD of XGe(OEt)(4)(-) ions: Gas-phase synthesis of novel oxy-germanium anions

The gas-phase ion/molecule reactions of F(-) and EtO(-) with Ge(OEt)(4) yield readily and exclusively pentacoordinated complexes XGe(OEt)(4)(-) (X = F, EtO) at pressures in the 10(-8) T range as observed by FT-ICR techniques. These hypervalent species are prone to undergo sequential fragmentations induced by infrared multiphoton excitation that lead to a variety of germyl and germanate anions. In the case of FGe(OEt)(4)(-), three primary competitive channels are observed in the IRMPD process that can be identified as (EtO)(3)GeO(-), F(EtO)(2)GeO(-) and (EtO)(3)Ge(-). Ab initio calculations have been carried out to characterize the primary fragmentation paths induced by IRMPD and the most favorable structure of the resulting anions. The gas-phase acidity of a number of these germanium-containing ions have been estimated by bracketing experiments and by theoretical calculations. Germanate anions such as (EtO)(3)GeO(-) undergo some interesting reactions with H(2)S to give rise to anions such as (EtO)(3)GeS(-) and (EtO)(2)Ge(OH)S(-). (C) 2010 Elsevier B.V. All rights reserved.

Spectroscopic and theoretical studies of some N,N-diethyl-2-[(4 `-substituted)phenylsulfonyl]acetamides

The analysis of the IR carbonyl band of the N,N-diethyl-2-[(4`-substituted)phenylsulfonyl]acetamides Et(2)NC(O)CH(2)S(O)(2)-C(6)H(4)-Y (Y = OMe 1, Me 2,1-13, Cl 4, Br 5, NO(2) 6) supported by B3LYP/6-31G(d,p) calculations for 3, indicated the existence of three pairs (anti and syn) of cis (c) and gauche (g(1) and g(2)) conformers in the gas phase, being the gauche conformers significantly more stable than the cis ones. The anti geometry is more stable than the syn one, for each pair of cis and gauche conformers. The summing up of the orbital (NBO analysis) and electrostatic interactions justifies quite well the populations and the v(CO) frequencies of the anti and syn pairs of c, g(1) and g(2) conformers. The IR higher carbonyl frequency component whose population is ca. 10%, in CCl(4), may be ascribed to the least stable and most polar cis conformer pair (in the gas phase) and the lower frequency component whose population is ca. 90%, to the summing up of the populations of the two most stable and least polar gauche conformer pairs (g(1) and g(2)) (in the gas phase). The reversal of the cis(c)/gauche (g(1) + g(2)) population ratio observed in chloroform ca. 60% (cis)/40% (gauche) and the occurrence of the most polar cis(c) conformer only, in acetonitrile, strongly suggests the coalescence of the two gauche components in a unique carbonyl band in solution. A further support to this rationalization is given by the single point PCM solvation model performed by HF/6-31G(d,p) method, which showed a progressive increase of the c/(g(1) + g(2)) ratio going from gas to CCl(4), to CHCl(3) and to CH(3)CN. X-ray single crystal analysis of 4 indicates that this compound assumes, in the solid state, the syn-clinal (gauche) conformation with respect to the [O=C-CH(2)-S] moiety, and the most stable anti geometry relative to the [C(O)N(CH(2)CH(3))(2)] fragment. In order to obtain larger energy gain from the crystal packing the molecules of 4 are linked in centrosymmetric dimers through two C-H center dot center dot center dot O interactions (C-H([O-Ph])center dot center dot center dot O([SO2])) forming a step ladder. (C) 2011 Elsevier B.V. All rights reserved.

Spectroscopic and theoretical studies of some 2-ethylsulfinyl-(4 `-substituted)-phenylthioacetates

The analysis of the IR nu(co) bands of the 2-ethylsulfinyl-(4`-substituted)-phenylthioacetates 4`-Y-C(6)H(4)SC(O)CH(2)S(O)Et (Y = NO(2) 1, Cl 2, Br 3, H 4, Me 5, OMe 6) supported by B3LY/6-31G(d,p) calculations along with the NBO analysis for 1.4 and 6 and X-ray analysis for 3, indicated the existence of four gauche (q-g-syn, g(3)-syn. g(1)-atin and q-g(2)-syn) conformers for 1-6 The calculations reproduce quite well the experimental results, i e the computed q-g-syn and g3-syn conformers correspond in the IR spectrum (in solution), to the nu(co) doublet higher frequency component of larger intensity, while the computed grant, conformer correspond to the nu(co) doublet lower frequency component (in solution) NBO analysis showed that the n(s) -> pi(center dot)(c1=o2), no(co) -> sigma(c1-s3), no(co) -> sigma(c1-c4) orbital interactions are the main factors which stabilize the q-g-syn, g(3)-syn, g(1)-anti and q-g(2)-syn conformers for 1, 4 and 6 The no(co) -> sigma(c1-s3) interaction which stabilizes the q-g-syn, g(3)-syn and q-g(2)-syn conformers into a larger extent than the granti conformer, is responsible for the larger tto frequencies of the former conformers relative to the latter one. The q-g-syn, g(3)-syn and q-g(2)-syn conformers are further stabilized sigma(c4-s5) -> pi(co)center dot (strong). pi(co)/sigma(c1-c4,) no(co) -> sigma(c6-H17[Et]) (weak) and pi(co)/sigma(c4-c5) pi(co) (strong) orbital interactions. The q-g-syn conformer is also stabilized by sigma(c4-s5) -> pi(center dot)(co) (strong), pi(co)/sigma(c4-c5).no(co) -> sigma(c6-H17[Et]), pi(C9=C11[ph]) -> sigma(c4-H6x-CH2]) (weak). no((SO)) -> sigma(C11-H23[ph]) (medium) pi(co)/sigma(c4-c5)(strong) orbital interactions. The q-g-syn conformei is further stabilized by the n(S5) O((C))(8-) S((SO))(8+) attractive Coulornbic interaction while the q-g(2)-syn conformer is destabilized by the n55 0,8c-0) repulsive Coulombic interaction. This analysis indicates the following conformer stabilization order. q-g-syn, g(3)-syn > g(1)-anti >> q-g(2)-syn X-ray single crystal analysis of 3 indicates that it assumes in the solid a distorted q-g(2)-syn geometry which is stabilized through almost the same orbital and Coulombic interaction which takes place for the q-g(2)-syn conformer, in the gas, along with dipole moment coupling and a series intermolecular C-HO0 interactions. (C) 2010 Elsevier B V All rights reserved

Oxindole-Schiff base copper(II) complexes interactions with human serum albumin: Spectroscopic, oxidative damage, and computational studies

CD and EPR were used to characterize interactions of oxindole-Schiff base copper(II) complexes with human serum albumin (HSA). These imine ligands form very stable complexes with copper, and can efficiently compete for this metal ion towards the specific N-terminal binding site of the protein, consisting of the amino acid sequence Asp-Ala-His. Relative stability constants for the corresponding complexes were estimated from CD data, using the protein as competitive ligand, with values of log K(CuL) in the range 15.7-18.1, very close to that of [Cu(HSA)] itself, with log K(CuHSA) 16.2. Some of the complexes are also able to interfere in the a-helix structure of the protein, while others seem not to affect it. EPR spectra corroborate those results, indicating at least two different metal species in solution, depending on the imine ligand. Oxidative damage to the protein after incubation with these copper(II) complexes, particularly in the presence of hydrogen peroxide, was monitored by carbonyl groups formation, and was observed to be more severe when conformational features of the protein were modified. Complementary EPR spin-trapping data indicated significant formation of hydroxyl and carbon centered radicals, consistent with an oxidative mechanism. Theoretical calculations at density functional theory (DFT) level were employed to evaluate Cu(II)-L binding energies, L -> Cu(II) donation, and Cu(II) -> L back-donation, by considering the Schiff bases and the N-terminal site of HSA as ligands. These results complement previous studies on cytotoxicity, nuclease and pro-apoptotic properties of this kind of copper(II) complexes, providing additional information about their possibilities of transport and disposition in blood plasma. (C) 2009 Elsevier Inc. All rights reserved.

Human regulatory protein Ki-1/57 has characteristics of an intrinsically unstructured protein

The human protein Ki-1/57 was first identified through the cross reactivity of the anti-CD30 monoclonal antibody Ki-1; in Hodgkin lymphoma cells. The expression of Ki-1/57 in diverse cancer cells and its phosphorylation in peripheral blood leukocytes after mitogenic activation suggested its possible role in cell signaling. Ki-1/57 interacts with several other regulatory proteins involved in cellular signaling, transcriptional regulation and RNA metabolism, suggesting it may have pleiotropic functions. In a previous spectroscopic analysis, we observed a low content of secondary structure for Ki-1/57 constructs. Here, Circular dichroism experiments, in vitro RNA binding analysis, and limited proteolysis assays of recombinant Ki-1/57(122-413) and proteolysis assays of endogenous full length protein from human HEK293 cells suggested that Ki-1/57 has characteristics of an intrinsically unstructured protein. Small-angle X-ray scattering (SAXS) experiments were performed with the C-terminal fragment Ki-1/57(122-413). These results indicated an elongated shape and a partially unstructured conformation of the molecule in solution, confirming the characteristics of an intrinsically unstructured protein. Experimental curves together with ab initio modeling approaches revealed an extended and flexible molecule in solution. An elongated shape was also observed by analytical gel filtration. Furthermore, sedimentation velocity analysis suggested that Ki-1/57 is a highly asymmetric protein. These findings may explain the functional plasticity of Ki-1/57, as suggested by the wide array of proteins with which it is capable of interacting in yeast two-hybrid interaction assays.

A theoretical study on the XeF(2) molecule

A relativistic four-component study was performed for the XeF(2) molecule by using the Dirac-Coulomb (DC) Hamiltonian and the relativistic adapted Gaussian basis sets (RAGBSs). The comparison of bond lengths obtained showed that relativistic effects on this property are small (increase of only 0.01 angstrom) while the contribution of electron correlation, obtained at CCSD(T) or CCSD-T levels, is more important (increase of 0.05 angstrom). Electron correlation is also dominant over relativistic effects for dissociation energies. Moreover, the correlation-relativity interaction is shown to be negligible for these properties. The electron affinity, the first ionization potential and the double ionization potential are obtained by means of the Fock-space coupled cluster (FSCC) method, resulting in DC-CCSD-T values of 0.3 eV, 12.5 eV and 32.3 eV, respectively. Vibrational frequencies and some anharmonicity constants were also calculated under the four-component formalism by means of standard perturbation equations. All these molecular properties are, in general, ill satisfactory agreement with available experimental results. Finally, a partition in terms of charge-charge flux-dipole flux (CCFDF) contributions derived by means of the quantum theory of atoms in molecules (QTAIM) in non-relativistic QCISD(FC)/3-21G* calculations was carried out for XeF(2) and KrF(2). This analysis showed that the most remarkable difference between both molecules lies on the charge flux contribution to the asymmetric stretching mode, which is negligible in KrF(2) but important in XeF(2). (c) 2008 Elsevier B.V. All rights reserved.

A quantum chemical study on the formation of phosphorus mononitride

The chemical mechanism of the (1)PN formation was successfully studied by using the CCSD(T)/6-311++G(3df,3pd) level of theory. The (1)NH(3) + (3)PH and (4)P + NH(3) reaction paths are not energetically favorable to form the (1)PN molecule. However, the (3)NH + (3)PH, (4)N + (3)PH(3), (4)N + (3)PH, (4)P + (3)NH, and (4)P + (2)NH(2) reaction paths to form the (1)PN molecule are only energetically favorable by taking place through specific transition states to form the (1)PN molecule. The NH(3) + (3)PH, (4)N + (1)PH(3), NH(3) + (4)P, and (4)N + (2)PH(2) reactions are spin-forbidden and the probability of hopping for these reactions was estimated to be 0 by the Landau-Zener theory. This is the first detailed study on the chemical mechanism for the (1)PN formation. (C) 2009 Elsevier B.V. All rights reserved.

Síntese e enriquecimento enantiomérico via catálise enzimática do sistema 5-bromo-12-oxa-pentaciclo[6.2.16,9.12,7.12,10]dodeca-4-eno-3-endo-ol e derivados. RMN de 1H e 13C: correlação de parâmetros teóricos e experimentais

Partindo de ciclopentadieno, ciclohexadieno, p-benzoquinona e 2,5-dibromo-pbenzoquinona, os adutos 1, 5, 30 e 31 foram sintetizados. Os adutos 1, 5 e 30 foram utilizados como produtos de partida para a síntese de 13 (treze) novos compostos, em sua maioria com potenciais características para apresentarem atividade biológica inibidora de glicosidases e reguladora da liberação de Insulina no sangue. O aduto 31 é inédito na literatura até o momento. Cinco novas propostas de mecanismos são apresentadas. Os álcoois racêmicos 6 e 29 foram submetidos a reações de transesterificação catalisadas por lipase de Pseudomonas cepacia em diferentes preparações e seus enantiômeros separados com enantiosseletividade (E) maior que 100 em todos os casos. Este processo resultou, também, na obtenção dos respectivos acetatos 43 e 44 enantiomericamente puros e com excelentes rendimentos químicos. Os compostos 6, 29 e 34 depois de terem suas estruturas moleculares resolvidas através dos métodos espectroscópicos de rotina, tiveram suas estruturas moleculares calculadas pelo método ab initio e por Funcionais de Densidade. As geometrias otimizadas foram submetidas ao método GIAO para o cálculo dos tensores de blindagem magnética isotrópica. Estes cálculos mostraram-se eficazes na descrição dos deslocamentos químicos da maioria dos átomos, incluindo os dos anéis ciclopropanos presentes nas estruturas moleculares de cada composto. Algumas dificuldades foram encontradas para a descrição do sistema vinílico halogenado dos álcoois 6 e 29. Foram utilizadas moléculas modelo para verificar a extensão de tais dificuldades.

Estudo computacional de líquidos iônicos do tipo dialquilimidazólio

Neste trabalho foram desenvolvidos parâmetros de campo de força dos ânions tetrafenilborato (BPh4 -) e hexafluorfosfato (PF6 -) dentro da metodologia AMBER para a simulação computacional por dinâmica molecular de Líquidos Iônicos formados por estes ânions e cátions do tipo dialquilimidazólio, o 1-n-butil-3-metilimidazólio (BMI+), o 1-etil-3-metilimidazólio (EMI+) e o 1,3-dimetilimidazólio (MMI+). A validação destes parâmetros foi realizada por comparação entre as freqüências dos modos normais obtido por cálculo ab initio com aquelas obtidas por mecânica molecular, juntamente com uma comparação entre as estruturas moleculares e momentos multipolares obtidos pelas duas metodologias. Seguiu-se então a validação por comparação dos resultados dos cálculos de dinâmica molecular com dados experimentais, como densidades, entalpias de vaporização, condutividade elétrica, estrutura radial e espacial e também dados de difração de nêutrons. Foi atingida uma concordância bastante grande entre dados experimentais e cálculo teórico principalmente no que diz respeito à estrutura dos Líquidos Iônicos e foi possível racionalizar em termos de tamanho do grupo alquila do cátion (n-butil, metil ou etil) e do tamanho do ânion tanto propriedades estruturais deste líquidos quanto características dinâmicas dos mesmos.