Structural, electronic, and magnetic properties of heterofullerene C(58)Si with odd number of atoms and a near planar tetracoordinate Si atom.

Density functional calculations and minimization techniques have been employed to characterize the structural and electronic properties of [5,6]-heterofullerene-C(58)Si-C(2v). Since it has odd number of atoms and a near planar tetracoordinate Si atom on the skeleton of the cage, it has odd number of atoms assembling a cage and is a novel molecule. Vibrational frequencies of the molecule have been calculated at the B3LYP/6-31G* level of theory. The absence of imaginary vibrational frequency confirms that the molecule corresponds to a true minimum on the potential energy hypersurface. Sixteen (13)C nuclear magnetic resonance (NMR) spectral signals of C(58)Si are characterized, and its heat of formation was estimated in this work.

Toward prediction of binding affinities between the MHC protein and its peptide ligands using quantitative structure-affinity relationship approach.

It is important but challenging to determine the binding specificity of MHC-peptide interactions accurately and to predict their binding affinity quantitatively. In this paper, we discuss the application of an effective amino acid descriptor to model and predict the binding affinities between the MHC protein and its peptide ligands. This amino acid descriptor was derived from 23 electronic properties, 37 steric properties, 54 hydrophobic properties and 5 hydrogen bond properties of coded amino acids using principal component analysis (PCA), called the divided physicochemical property scores (DPPS). The DPPS descriptor was used to characterize a set of mouse MHC (H-2K(K)) binding peptides, and genetic algorithm-partial least square (GA-PLS) models were then constructed. In analyses, these models were statistically consistent with previous reports and molecular graphics exhibition. Hydrophobic interactions and hydrogen bonds were important to antigen recognition and presentation, especially exerting effects on anchor residues of peptides.

Thermodynamic and kinetic approach in density functional theory studies of microscopic structure of GaN(0001) surface in ammonia-rich conditions.

GaN (0001) surface in an ammonia-rich vapor ambient, typical for ammonia annealing, metalo-organic vapor phase epitaxy (MOVPE) or hydride vapor phase epitaxy (HVPE) was considered. It was shown that, in these three cases, the stationary state of the surface corresponds to condition far from equilibrium. The chemical potential of nitrogen and hydrogen at the surface was determined using kinetic arguments, i.e., derived form the magnitude of flux of ammonia. For HVPE and MOVPE growth, the chemical potential of gallium depends on the distance from the steps. Thus, only far distance from the step value of the gallium chemical potential at the GaN(0001) surface could be determined in similar way. In the alternative case of GaN annealing in ammonia atmosphere, gallium chemical potential at the surface remains undetermined (the surface is in a metastable state). Additionally, using thermodynamic arguments, the limits for the chemical potential of gallium (upper) and nitrogen (lower) were formulated for the case of vapor growth, and expressed as functions of temperature and pressure. The results, regarding the atomic processes on the GaN(0001) surface, were obtained using the SIESTA, density functional theory based code, and consequently employed in the comparable thermodynamic and kinetic analysis of the state of GaN(0001) surface.

Sugar synthesis from a gas-phase formose reaction.

Prebiotic possibilities for the synthesis of interstellar ribose through a protic variant of the formose reaction under gas-phase conditions were studied in the absence of any known catalyst. The ion-molecule reaction products, diose and triose, were sought by mass spectrometry, and relevant masses were observed. Ab initio calculations were used to evaluate protic formose mechanism possibilities. A bilateral theoretical and experimental effort yielded a physical model for glycoaldehyde generation whereby a hydronium cation can mediate formaldehyde dimerization followed by covalent bond formation leading to diose and water. These results advance the possibility that ion-molecule reactions between formaldehyde (CH(2)O) and H(3)O(+) lead to formose reaction products and inform us about potential sugar formation processes in interstellar space.

On the 1,3-dipolar cycloaddition reactions of indenone with N-N-C dipoles: density functional theory calculations.

Density functional theory (DFT) calculations at the B3LYP/6-311G* theoretical level have been performed to study the 1,3-dipolar cycloaddition (1,3-DC) reactions between indenone (1) and different 1,3-dipoles (diazomethane and N-methyl C-methoxy carbonyl nitrilimine, compounds 2 and 3, respectively). The geometrical and energetic properties were analysed for the different reactives, transition states and cycloadducts formed (compounds 4-11). The reactions proceed in the gas-phase by an asynchronous concerted mechanism, yielding different regiochemistry dependent on the 1,3-dipole chosen, although with dipole 3 some degree of synchrony was found in the formation of cycloadduct 5. The 1,3-DC between 1 and 3 was regioselective, being the cycloadduct 11 favoured against 9. The NMR chemical shift parameters (GIAO method) were also calculated for the reactives and cycloadducts.

Dynamic mechanical analysis of the SAN co-polymer and the SBR latex co-mixture.

Useful experimental data based on the dynamic effects of the SAN/SBR mixture at higher temperatures were acquired. This data can allow us to gather information about the molecular motion and any interesting behavior of this mixture at elevated temperatures and increases in the SAN to SBR weight proportion. The importance of dynamic mechanical experiments of multi-phase polymer systems is presented. A series of (SAN/SBR) co-mixed samples were prepared with varying weight proportions over a temperature interval. TBA equipment (a type of torsional braid set of equipment) was used to make the dynamic mechanical analysis of the SAN/SBR co-mixture.

Quantitative analysis of (styrene/acrylonitrile/methyl methacrylate) co-polymer systems by infrared resonance spectroscopy.

A detailed careful analysis of the infrared resonance (IR) spectra of polystyrene (PSt), polymethyl methacrylate (PMMA), polyacrylonitrile (PAN) and their co-mixtures were performed. Through this study the absorption peak area to weight ratios as well as working curves were obtained to test for their reliability as well as their suitability. Satisfactory results were achieved and these working curves were then used to measure the polymerized components of binary and ternary co-polymers. By investigating the acquired data we conclude that the monomer preferential polymeric sequence is St > MMA > AN. A quantitative method to measure P (St/AN/MMA) concentrations by IR spectroscopy is proposed in this work.

Prebiotic synthesis of simple sugars by an interstellar formose reaction.

The prebiotic possibilities for the synthesis of interstellar carbohydrates through a protic variant of the formose reaction under gas phase conditions were studied. Ab initio calculations were used to evaluate potential mechanisms. Based on considerations of barrier heights and temperature variations in the Interstellar Medium the plausibility of extended sugar synthesis will be discussed.

Possibility of the nonenzymatic browning (Maillard) reaction in the ISM.

The possibility of the occurrence of the nonenzymatic browning reaction in the gaseous phase in the interstellar medium has been investigated by using Density Functional Theory computations. Mechanisms for the reactions between formaldehyde (Fald) + glycine (Gly), Fald + NH(3) and Fald + methylamine (MeAm) have been proposed, and the possibility of the formation of different compounds in the proposed mechanisms has been evaluated through calculating the Gibb's free energy changes for different steps of the reaction, by following the total mass balance. The Fald + Gly reaction under basic conditions is found as the most favorable for producing 1-methyl-amino methene or 1-methyl-amino methelene (MAM). The reaction under acidic conditions is found to be the least favorable for producing MAM. The Fald + NH(3) reaction is found to be plausible for the production of MeAm, which can participate by reaction with Fald, resulting in the formation of MAM.

Low-symmetry structures of Au32Z (Z = +1, 0, -1) clusters.

In this work, we have explored new stable structures of the Au32Z (Z = +1, 0, -1) clusters. Theoretical calculations using density functional theory within the generalized-gradient approximation were performed. Our results show that, in the anion state (Au32-), low-symmetry (disordered) structures are preferred over the caged fullerene-like isomer. In addition, the cationic cluster (Au32+) also exhibits a disordered low-symmetry structure as its lowest energy configuration, but it is much closer in energy to the fullerene-like isomer. These results, obtained at T = 0 K, indicate that disordered structures for the Au32- and Au32+ clusters may be detected not only at room temperature, as was experimentally verified for the Au32- one, but also at much lower temperatures.

Electron-conformational study for the structure-hallucinogenic activity relationships of phenylalkylamines.

The structure-hallucinogenic activity relationships of a series of phenylethylamine and phenylisopropylamine derivatives have been investigated in the frameworks of electron-conformational method. The calculated geometry and electronic structure parameters accompanying to each atom and bond of each molecule in view were arranged as a matrix called electron-conformational matrix of contiguity (ECMC). The features that are responsible for strong and weak activity demonstrations have been found as submatrices of ECMCs belonging to some template compounds. Two electron-conformational features present in nonhallucinogenic compounds have been revealed. A quantitative model has been improved for predicting hallucinogenic activity numerically. A test series was used to verify the results obtained.