A model for the stabilization of atomic hydrogen centers in borate glasses

A previously proposed model describing the trapping site of the interstitial atomic hydrogen in borate glasses is analyzed. In this model the atomic hydrogen is stabilized at the centers of oxygen polygons belonging to B-O ring structures in the glass network by van der Waals forces. The previously reported atomic hydrogen isothermal decay experimental data are discussed in the light of this microscopic model. A coupled differential equation system of the observed decay kinetics was solved numerically using the Runge Kutta method. The experimental untrapping activation energy of 0.7 x 10(-19) J is in good agreement with the calculated results of dispersion interaction between the stabilized atomic hydrogen and the neighboring oxygen atoms at the vertices of hexagonal ring structures. (C) 2009 Elsevier B.V. All rights reserved.

Prevalence and nonrandom distribution of exonic mutations in interferon regulatory factor 6 in 307 families with Van der Woude syndrome and 37 families with popliteal pterygium syndrome

Purpose: Interferon regulatory factor 6 encodes a member of the IRF family of transcription factors. Mutations in interferon regulatory factor 6 cause Van der Woude and popliteal pterygium syndrome, two related orofacial clefting disorders. Here, we compared and contrasted the frequency and distribution of exonic Mutations in interferon regulatory factor 6 between two large geographically distinct collections of families with Van der Woude and between one collection of families with popliteal pterygium syndrome. Methods: We performed direct sequence analysis of interferon regulatory factor 6 exons oil samples from three collections, two with Van der Woude and one with popliteal pterygium syndrome. Results: We identified mutations in interferon regulatory factor 6 exons in 68% of families in both Van der Woude collections and in 97% of families with popliteal pterygium syndrome. In sum, 106 novel disease-causing variants were found. The distribution of mutations in the interferon regulatory factor 6 exons in each collection was not random; exons 3, 4, 7, and 9 accounted for 80%. In the Van der Woude collections, the mutations were evenly divided between protein truncation and missense, whereas most mutations identified in the popliteal pterygium syndrome collection were missense. Further, the missense mutations associated with popliteal pterygium syndrome were localized significantly to exon 4, at residues that are predicted to bind directly to DNA. Conclusion: The nonrandom distribution of mutations in the interferon regulatory factor 6 exons suggests a two-tier approach for efficient mutation screens for interferon regulatory factor 6. The type and distribution of mutations are consistent with the hypothesis that Van der Woude is caused by haploinsufficiency of interferon regulatory factor 6. Oil the other hand, the distribution of popliteal pterygium syndrome-associated mutations suggests a different, though not mutually exclusive, effect oil interferon regulatory factor 6 function. Genet Med 2009:11(4):241-247.

MODELLING OF HIGH-PRESSURE PHASE EQUILIBRIUM IN SYSTEMS OF INTEREST IN THE FOOD ENGINEERING FIELD USING THE PENG-ROBINSON EQUATION OF STATE WITH TWO DIFFERENT MIXING RULES

In this work, thermodynamic models for fitting the phase equilibrium of binary systems were applied, aiming to predict the high pressure phase equilibrium of multicomponent systems of interest in the food engineering field, comparing the results generated by the models with new experimental data and with those from the literature. Two mixing rules were used with the Peng-Robinson equation of state, one with the mixing rule of van der Waals and the other with the composition-dependent mixing rule of Mathias et al. The systems chosen are of fundamental importance in food industries, such as the binary systems CO(2)-limonene, CO(2)-citral and CO(2)-linalool, and the ternary systems CO(2)-Limonene-Citral and CO(2)-Limonene-Linalool, where high pressure phase equilibrium knowledge is important to extract and fractionate citrus fruit essential oils. For the CO(2)-limonene system, some experimental data were also measured in this work. The results showed the high capability of the model using the composition-dependent mixing rule to model the phase equilibrium behavior of these systems.

Spectroscopic Investigation on the Formation of a Dinuclear Me(2)SO-Ru(2)-Mercaptopyridine Bridged Complex: [Ru(2)Cl(3)(mu-pyS)(mu-dmso)(dmso)(4)]center dot 2H(2)O

A dinuclear ruthenium(II) complex double-bridged by an N-aromatic ligand 2-mercaptopyridine (2-pyridinethiol or 2-pyridyl mercaptan) and a methyl sulfoxide (dmso) have been characterized by X-ray crystallography. The reported compound with formula [Ru(2)Cl(3) (mu-pyS)(mu-dmso)(dmso)(4)] center dot 2H(2)O, [C(15)H(36)Cl(3)NO(7)S(6)Ru(2)] (P2/c, a = 13.8175(2) angstrom, b = 10.5608(2) angstrom, c = 21.3544 (3) angstrom, beta = 106.090(1)degrees, V = 2,994.05(8) angstrom(3), Z = 4) represents a seven-membered ring system with both rutheniums in an octahedral geometry. All the hydrogen bonds (C-H-Cl) and the van der Waals contacts give rise to three-dimensional network in the structure and add stability to the dinuclear compound. To our knowledge, this is the first time that the formation of a dinuclear ruthenium(II) complex double-bridged by an N-aromatic ligand 2-mercaptopyridine and dmso have been reported. The study also provided valuable insight into bioinorganic chemistry as continuing efforts are being made to develop metal-based cancer chemotherapeutics. A major feature of this paper is the resolution of a double bridged ruthenium structure which contributes to a better understanding of ruthenium reactivity.

Analyzing Ru(III)-dmso and Ru(III)-dms motifs in compounds used in the synthesis of the antimetastatic agents

The chemistry of Ru(III) complexes containing dmso as a ligand has become an interesting area in the cancer treatment field. Because of this, structural knowledge and chemistry of the moiety Ru(III)-dmso have become important to cancer research. The crystal structures of the compounds mer-[RuCl(3)(dms)(3)] (1) and mer-[RuCl(3)(dms)(2)(dmso)]:mer-[RuCl(3)(dms)(3)] (2) were determined by X-ray crystallography and a speciation of the presence of intramolecular hydrogen bond in these structures has been studied. Compound (1) crystallizes in the orthorhombic space group, Pna2(1); a = 16.591(8) angstrom, b = 8.724(2) angstrom. c = 10.547(3) angstrom; Z = 12 and (2) crystallizes in the space group, P2(1)/C: a = 11.9930(2) angstrom, b = 7.9390(2) angstrom, c = 15.8700(3) angstrom, beta = 93.266(1)degrees, Z = 2. From the X-ray structures solved in this work, were possible to suggest an interpretation for the broad lines observed in the EPR spectra of the Ru(III) compounds explored here. Also, the exchange interactions detected by EPR spectroscopy in solid state and in solution, confirm the presence of van der Waals interactions such as C-H center dot center dot center dot Cl in the compounds (1), (2) and (3). The use of techniques such as IR, UV-vis, (1)H NMR and EPR Spectroscopy and Cyclic Voltammetry were applied in this work to analyze the behavior of these metallocompounds. (c) 2008 Elsevier B.V. All rights reserved.

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Towards to the trans-bromination of 2-styrylpyridine with a palladacycle intermediary and structure analysis for trans-1,2-dibromo-2-styrylpyridine

The simple halogenation of alkynes in conventional organic reactions gives a blend of cis and trans isomers. It is proposed then, a synthesis of stereospecific halogenation of alkynes in trans position, using palladacycle as intermediaries. The recrystallization of the compound obtained by bromination of 2-Styrylpyridine, with cyclepalladium intermediary results in a single crystal, which is subjected to X-ray diffraction. The crystal packing is established through weak interactions of three types. The first one is of the type pi x pi interactions, from symmetry operation, between the centroids. The second one is of the type C-X center dot center dot center dot pi interactions. And the last type is an anomalous intermolecular interaction between halogens, C-X center dot center dot center dot X-C, with bond distances smaller than the sum of the van der Waals radii. The conformation on the C=C bond is trans and the dihedral angle between the aromatic rings is (with esd approximate) 18.1(3)degrees. (C) 2010 Elsevier B.V. All rights reserved.

Investigating the Nature of Noble Gas-Copper Bonds by the Quantum Theory of Atoms in Molecules

We investigated noble gas copper bonds in linear complexes represented by the NgCuX general formula in which Ng and X stand for a noble gas (neon, argon, krypton, or xenon) and a halogen (fluorine, chlorine or bromine), respectively, by coupled cluster methods and modified cc-pVQZ basis sets. The quantum theory of atoms in molecules (QTAIM) shows a linear relation between the dissociation energy or noble gas-copper bonds and the amount of electronic charge transferred mainly from the noble gas to copper during complexation. Large changes in the QTAIM quadrupole moments of copper and noble gases resulting from this bonding and a comparison between NgCuX and NgNaCl systems indicate that these noble gas-copper bonds should be better interpreted as predominantly covalent. Finally, QTAIM atomic dipoles of noble gases in NgNaCl systems agree satisfactorily with atomic dipoles given by a simple model for these NgNa van der Waals bonds.