Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems

A Genetic Algorithm for Geometry Optimizations (GALGO) program has been developed to study the efficiency of this method of finding global minimum structures. Using a semiempirical tight-binding potential, the behavior of different genetic algorithm (GA) operators has been tested for the linear chain isomer of a C₈ cluster. An optimum set of parameters for the GA operators is proposed for this problem and afterward is used to obtain the global minimum structure of rare-gas atomic clusters of up to 13 atoms using the 12–6 Lennard-Jones interatomic pair potential. © 1995 by John Wiley & Sons, Inc.     

A complete shape characterization for molecular charge densities represented by Gaussian-type functions

An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented, tested and applied for a family of AB₂ molecules. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend continuously on two parameters: a density value defining the density contour, and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is modeled by means of Gaussian-type functions. The method employs an explicit form of the charge density function in order to compute the curvature properties for the molecular surfaces analytically, from which the shape groups are derived by the algorithm. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visual inspection of the results of the shape analysis is a possible option. For a given molecule, in a given nuclear configuration, the technique provides a two-dimensional shape map, displaying the distribution of shape groups as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis of shape maps automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, several two-dimensional shape maps for simple systems are discussed. The changes induced in these maps by a change in the nuclear geometry, as well as by the changes of the nuclear charge, are also analyzed. The method is applicable to large biomolecules of interest if charge density information is available.     

Catalytic oxidation of thiols to disulfides using iodine and CeCl3·7H2O in graphite

A very simple procedure for the efficient oxidation of thiols to disulfides catalyzed by I₂/CeCl₃·7H₂O in graphite and ethyl acetate as the solvent, in an open system at room temperature is described. The reaction proceeds cleanly under mild conditions and was performed with aromatic, aliphatic, and heterocyclic thiols.     

Chalcogenide Exchange Reaction of [RGa(μ3-Te)]4 with Elemental Sulfur and Selenium: A Density Functional Theory Study

Thermodynamic and mechanistic features of the chalcogen exchange reaction between [RGa( ₃-Te)]₄ and elemental sulfur or selenium have been studied employing density functional theory (DFT) calculations using the BL3YP basis set and Stuttgart pseudopotentials. For [MeGa( ₃-E)]₄ (E=S, Se, Te) the correlation between the calculated parameters and diffraction data for their isolable analogs is greater than 98%. Each step of the conversion of [MeGa( ₃-Te)]₄ to [MeGa( ₃-E)]₄ via [Me₄Ga₄( ₃-Te)_4–x ( ₃-E) _x ] (E=S, Se) is predicted to occur as a series of isolated reactions. The entropy change for each chalcogen exchange is small in magnitude and corresponds to the degree of cage distortion within the cubane molecules. Calculations performed on [MeGa( ₃-Te)]₄...S₈ and [MeGa( ₃-Te)]₄-S suggest that an increase in electrophilicity of the gallium next to a surface bound tellurium may result in nucleophilic cage opening for which intermediate structures are calculated.     

Mass spectrometric characterization of two novel inflammatory peptides from the venom of the social wasp Polybia paulista

The social wasp P. paulista is relatively common in southeast Brazil causing many medically important stinging incidents. The seriousness of these incidents is dependent on the amount of venom inoculated by the wasps into the victims, and the characteristic envenomation symptoms are strongly dependent on the types of peptides present in the venom. In order to identify some of these naturally occurring peptides available in very low amounts, an analytical protocol was developed that uses a combination of reversed-phase and normal-phase high-performance liquid chromatography (HPLC) of wasp venom for peptide purification, with matrix-assisted laser desorption/ionization time-of-flight post-source decay mass spectrometry (MALDI-Tof-PSD-MS) and low-energy collision-induced dissociation (CID) in a quadrupole time-of-flight tandem mass spectrometry (QTof-MS/MS) instrument for peptide sequencing at the sub-picomole level. The distinction between Leu and Ile was achieved both by observing d-type fragment ions obtained under CID conditions and by comparison of retention times of the natural peptides and their synthetic counterparts (with different combinations of I and/or L at N- and C-terminal positions). To distinguish the isobaric residues K and Q, acetylation of peptides was followed by Q-Tof-MS analysis. The primary sequences obtained were INWLKLGKMVIDAL-NH(2) (MW 1611.98 Da) and IDWLKLGKMVMDVL-NH(2) (MW 1658.98 Da). Micro-scale bioassay protocols characterized both peptides as presenting potent hemolytic action, mast cell degranulation, and chemotaxis of polymorphonucleated leukocyte (PMNL) cells. The primary sequences and the bioassay results suggest that these toxins constitute members of a new sub-class of mastoparan toxins, directly involved in the occurrence of inflammatory processes after wasp stinging.     

Gold(III) complexes with imidazole,benzoxazole, purine and pyrimidine derivatives

Summary The synthesis and characterization of Au^III complexes with several heterocyclic ligands are reported. The compounds have general formula [AuX₃(L)], where L =N-methylimidazole (N-MeIz),N-ethylimidazole (N-EtIz),N-propylimidazole (N-PrIz), benzoxazole (BO), 2-methylbenzoxazole (2-MeBO), 2,5-dimethylbenzoxazole (2,5-diMeBO), 2-amino-pyrimidine (2-APm), 4(6) -hydroxy-pyrimidine [4(6)-hydrPm] or hypoxanthine (Hypox) and X = Cl or Br. Elemental analysis, conductivity measurements and spectral studies were used for the characterization of the complexes. A square-planar geometry withN-bonded heterocyclic ligands is suggested.     

Single wall carbon nanotubes density of states: comparison of experiment and theory

We study the electronic structure of a variety of single wall carbon nanotubes and report density of states obtained with the Perdew–Burke–Ernzerhof (PBE) generalized gradient approximation and hybrid PBE0 approximation of density functional theory using Gaussian orbitals and periodic boundary conditions. PBE gives very good results for metallic tubes but the addition of a portion of exact exchange in the hybrid PBE0 functional worsens the agreement between experiment and theory. On the other hand, the PBE0 hybrid significantly improves the theoretical predictions (compared to PBE) for semiconducting tubes.     

A catalyst-free synthesis of asymmetric diaryl ketones from aryltins

A series of diaryl ketones have been synthesized in good yields (40-78%) through the catalyst-free reaction of trimethylarylstannanes with aroyl chlorides in chlorobenzene as solvent. In addition, an attractive feature is that these reactions are completely regioselective making possible the synthesis of diarylketones which are not usually available under the influence of the directing forces of the substituents present in the aromatic ring. Also, the reaction conditions are mild enough to be applied to acid sensitive molecules.     

A new steroidal saponin from Agave attenuata

A new steroidal saponin was isolated from the leaves of Agave attenuata. Its structure was established as (3beta,beta,25S)-spirostan-3-yl O-beta-D-glucopyranosyl-(1 --> 2)-beta-D-glucopyranosyl-(1 --> 2)-O-[beta-D-glucopyranosyl-(1 --> 3)]-beta-D-glucopyranosyl-(1 --> 4)-beta-D-galactopyranoside. The structural identification was performed using detailed analyses of 1H- and 13C-NMR spectra including 2D NMR spectroscopic techniques (COSY, HETCOR, and COLOC) and chemical conversions. The hemolytic activity of the steroidal saponin was evaluated using an in vitro assay.