The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations

Time-resolved kinetic studies of the reactions of silylene, SiH2, and dideutero-silylene, SiD2, generated by laser. ash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH3C CCH3. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(-1)/RTln10 log(k(D)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTln10 Additionally, pressure-dependent rate coefficients for the reaction of SiH2 with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC4H8 reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH2C(CH3)=C(CH3)-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH3CH=C(CH3)SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H - D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei

Blumeria graminis is an economically important obligate plant-pathogenic fungus, whose entire genome was recently sequenced and manually annotated using ab initio in silico predictions [7]. Employing large scale proteogenomic analysis we are now able to verify independently the existence of proteins predicted by 24% of open reading frame models. We compared the haustoria and sporulating hyphae proteomes and identified 71 proteins exclusively in haustoria, the feeding and effector-delivery organs of the pathogen. These proteins are ‘significantly smaller than the rest of the protein pool and predicted to be secreted. Most do not share any similarities with Swiss–Prot or Trembl entries nor possess any identifiable Pfam domains. We used a novel automated prediction pipeline to model the 3D structures of the proteins, identify putative ligand binding sites and predict regions of intrinsic disorder. This revealed that the protein set found exclusively in haustoria is significantly less disordered than the rest of the identified Blumeria proteins or random (and representative) protein sets generated from the yeast proteome. For most of the haustorial proteins with unknown functions no good templates could be found, from which to generate high quality models. Thus, these unknown proteins present potentially new protein folds that can be specific to the interaction of the pathogen with its host.

Band gap control via tuning of inversion degree in CdIn2S4 spinel

Based on theoretical arguments we propose a possible route for controlling the band-gap in the promising photovoltaic material CdIn2S4. Our ab initio calculations show that the experimental degree of inversion in this spinel (fraction of tetrahedral sites occupied by In) corresponds approximately to the equilibrium value given by the minimum of the theoretical inversion free energy at a typical synthesis temperature. Modification of this temperature, or of the cooling rate after synthesis, is then expected to change the inversion degree, which in turn sensitively tunes the electronic band-gap of the solid, as shown here by Heyd-Scuseria-Ernzerhof screened hybrid functional calculations.

Many-body energy decomposition of hydrogen-bonded glycine clusters in gas-phase

A detailed analysis of the many-body contribution to the interaction energies of the gas-phase hydrogen-bonded glycine clusters, (Gly)(N), N = 1-4 is presented. The energetics of the hydrogen-bonded dimer, trimer and tetramer complexes have been analyzed using density-functional theory. The magnitude of the two-through four-body energy terms have been calculated and compared. The relaxation energy and the two-body energy terms are the principal contributors to the total binding energy. Four-body contribution is negligible. However, the three-body contribution is found to be sizable and the formation of the cyclic glycine trimer presents geometric strains that make it less favorable. (C) 2010 Elsevier B.V. All rights reserved.

Calculations of vibrational frequencies, Raman activities and degrees of depolarization for complexes involving water, methanol and ethanol

Raman activities and degrees of depolarization are reported for 14 complexes involving methanol, ethanol and water using the MP2/aug-cc-pVDZ model. For ethanol both trans and gauche isomers are considered. The red-shifts of the OH stretching and the blue shifts of the bending tau(CO-OH) mode were analyzed for the proton-donor molecules upon hydrogen bond. The shift of the nu(CO) stretching mode of the alcohol molecules are also analyzed and found to be specific giving characterization of the amphoteric relation, being positive for the proton-acceptor and negative for the proton-donor molecule. (c) 2008 Elsevier B.V. All rights reserved.

Electronic transport properties of ascorbic acid and nicotinamide adsorbed on single-walled carbon nanotubes

Ab initio simulations of carbon nanotubes interacting with ascorbic acid and nicotinamide are reported. The electronic transport properties of these systems are studied using a combination of density functional theory and non-equilibrium Green`s functions methods. The adsorptions of both molecules are observed to depend strongly on their functionalization. The interaction through the appropriate functionalized species modifies the structural and electronic properties of the original system, resulting in a chemisorption regime. Changes in the electronic transport properties are also observed, with reductions on the total electronic transmission probabilities. Nevertheless, when the molecules interact through the pristine form, a physisorption interaction is observed with insignificant structural and electronic transport changes. (c) 2011 Elsevier B.V. All rights reserved.

On the Nucleophilicity of Boryllithium Compounds. A Theoretical Study

Boron compounds are widely used in synthetic chemistry. The synthesis of the compounds is relatively easy, presenting thermodynamic stability and synthetic versatility. Almost all of them show electrophilic reactivity. Recently, some boryllithium species have been reported as a base or a nucleophile in reaction with organic electrophiles in S(N)2 reactions. In the present work, the proton affinity (PA) of boryllithium compounds was calculated. These values can be useful as theoretical reference values and to provide valuable complementary information for the interpretation and discussion of the basicity of these compounds. The proton affinity was calculated using a theoretical method based on density functional theory and high-level theoretical methods through MP2 and G2MP2 levels of theory. In addition, some global and local reactivity indexes based on density functional theory (DFT) on boryllithium compounds were studied. In order to compare and discuss the chemical reactivity of these compounds, some analogues and electrophilic boron compounds were also studied. Our results showed a local and global nucleophilic reactivity of the boryllithium molecules in agreement with the experimental. reactivity. The boryllithium compounds revealed to be strong bases in comparison to other analogue compounds studied in this work.

Degenerate Two-Photon Absorption in All-Trans Retinal: Nonlinear Spectrum and Theoretical Calculations

In this work we investigate the degenerate two-photon absorption spectrum of all-trans retinal ill ethanol employing the Z-scan technique with femtosecond pulses, The two-photon absorption (2PA) spectrum presents a monotonous increase as the excitation wavelength approaches the one-photon absorption band and it peak at 790 nm. We attribute the 2PA hand to the mixing of states (1)B(u)+-like and vertical bar S(1)>, which are strongly allowed by one- and two-photon, respectively. We modeled the 2PA spectrum by using the sum-over-states approach and obtained spectroscopic parameters of the electronic transitions to vertical bar S >, vertical bar S(2)> (""(1)Bu(+)""), vertical bar S(3)>, and vertical bar S(4)> singlet-excited states. The results were compared with theoretical predictions of one- and two-photon transition calculations using the response Functions formalism within the density functional theory framework with the aid of the CAM-B3LYP functional.

Intense violet-blue photoluminescence in BaZrO3 powders: A theoretical and experimental investigation of structural order-disorder

Intense violet-blue photoluminescence (PL) emission at room temperature was verified in BaZrO3 (BZO) powders with structural order-disorder. Ab-initio calculations, ultraviolet-visible absorption spectroscopy and PL were performed. Theoretical results showed that the local disorder in the network-formed Zr clusters present an important role in the formation of hole-electron pair. The experimental data and theoretical results are in agreement, indicating that the PL emission in BZO powders can be related to the structural order-disorder degree in the lattice. (C) 2008 Elsevier B.V. All rights reserved.

Experimental and theoretical investigation of molecular structure and conformation of the 4-isopropylthioxanthone

In this study, the molecular structure and conformational analyses of the 4-isopropylthioxanthone (4-ITX) are reported according to experimental and theoretical results. The compound crystallizes in the centrosymmetric P (1) over bar space group with only one molecule in the asymmetric unit, presenting the most stable conformation, in which the three fused-rings adopt a planar geometry, and the isopropyl group assumes a torsional angle with less sterical hindrance. The structural and conformational analyses were performed using theoretical calculations such as Hartree-Fock (HF), DFT method in combination with 6-311G(d,p) and 6-31++G(d,p) and the results were compared with infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). The supramolecular assembly of 4-ITX is kept by non-classical C-H center dot center dot center dot O hydrogen bonds and weak interactions such as pi-pi stacking. 4-ITX was also studied by (1)H and (13)C NMR spectroscopy. UV-Vis absorption spectroscopic properties of the 4-ITX showed the long-wavelength maximum shifts towards high energy when the solvent polarity increases. (C) 2011 Elsevier B.V. All rights reserved.

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.

The electronic delocalization in para-substituted beta-nitrostyrenes probed by resonance Raman spectroscopy and quantum-chemical calculations

The electronic (UV-vis) and resonance Raman (RR) spectra of a series of para-substituted trans-beta-nitrostyrenes were investigated to determine the influence of the electron donating properties of the substituent (X = H, NO2, COOH, Cl, OCH3, OH, N(CH3)(2), and O-) on the extent of the charge transfer to the electron-withdrawing NO2 group directly linked to the ethylenic (C=C) unit. The Raman spectra and quantum chemical calculations show clearly the correlation of the electron donating power of the X group with the wavenumbers of the nu(s)(NO2) and nu (C=C)(sty) normal modes. In conditions of resonance with the lowest excited electronic state, one observes for X = OH and N(CH3)2 that the symmetric stretching of the NO2. nu(s)(NO2), is the most substantially enhanced mode, whereas for X = O-, the chromophore is extended over the whole molecule, with substantial enhancement of several carbon backbone modes. Copyright (c) 2008 John Wiley & Sons, Ltd.

New insights on surface-enhanced Raman scattering based on controlled aggregation and spectroscopic studies, DFT calculations and symmetry analysis for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine adsorbed onto citrate-stabilized gold nanoparticles

Asystematic study on the surface-enhanced Raman scattering (SERS) for 3,6-bi-2-pyridyl-1,2,4,5-tetrazine (bptz) adsorbed onto citrate-modified gold nanoparticles (cit-AuNps) was carried out based on electronic and vibrational spectroscopy and density functional methods. The citrate/bptz exchange was carefully controlled by the stepwise addition of bptz to the cit-AuNps, inducing flocculation and leading to the rise of a characteristic plasmon coupling band in the visible region. Such stepwise procedure led to a uniform decrease of the citrate SERS signals and to the rise of characteristic peaks of bptz, consistent with surface binding via the N heterocyclic atoms. In contrast, single addition of a large amount of bptz promoted complete aggregation of the nanoparticles, leading to a strong enhancement of the SERS signals. In this case, from the distinct Raman profiles involved, the formation of a new SERS environment became apparent, conjugating the influence of the local hot spots and charge-transfer (CT) effects. The most strongly enhanced vibrations belong to a(1) and b(2) representations, and were interpreted in terms of the electromagnetic and the CT mechanisms: the latter involving significant contribution of vibronic coupling in the system. Copyright (C) 2010 John Wiley & Sons, Ltd.

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.

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.