Automated NMR structure determination and disulfide bond identification of the myotoxin crotamine from Crotalus durissus terrificus

Crotamine is one of four major components of the venom of the South American rattlesnake Crotalus durissus terrificus. Similar to its counterparts in the family of the myotoxins, it induces myonecrosis of skeletal muscle cells. This paper describes a new NMR structure determination of crotamine in aqueous solution at pH 5.8 and 20 degrees C, using standard homonuclear (1)H NMR spectroscopy at 900 MHz and the automated structure calculation software ATNOS/CANDID/DYANA. The automatic NOESY spectral analysis included the identification of a most likely combination of the six cysteines into three disulfide bonds, i.e. Cys4-Cys36, Cys11-Cys30 and Cys18-Cys37; thereby a generally applicable new computational protocol is introduced to determine unknown disulfide bond connectivities in globular proteins. A previous NMR structure determination was thus confirmed and the structure refined. Crotamine contains an alpha-helix with residues 1-7 and a two-stranded anti-parallel beta-sheet with residues 9-13 and 34-38 as the only regular secondary structures. These are connected with each other and the remainder of the polypeptide chain by the three disulfide bonds, which also form part of a central hydrophobic core. A single conformation was observed, with Pro13 and Pro21 in the trans and Pro20 in the cis-form. The global fold and the cysteine-pairing pattern of crotamine are similar to the beta-defensin fold, although the two proteins have low sequence homology, and display different biological activities. (c) 2005 Elsevier Ltd. All rights reserved.

Structure characterization of molecular complexes for non-linear optical materials. II. 1 : 1 complexes of 4-methyl-morpholine-N-oxide (1) and 3-picoline-N-oxide (2) with 2,4,6-trinitrophenol, studied by X-ray, AM1 and DFT calculations

(1) C6H2N3O7- center dot C5H12NO2+, Mr = 346.26, P2(1)/c, a = 7.2356(6), b = 10.5765(9), c = 19.593(2) angstrom, 3 beta=95.101(6)degrees, V = 1493.5(2) angstrom(3), Z = 4, R-1 = 0.0414; (2) C6H2N3O7- center dot C6H8NO+, Mr = 38.24, P2(1)/n, a = 7.8713(5), b = 6.1979(7), c = 28.697(3) angstrom, beta = 90.028(7)degrees, V = 1400.0(2) angstrom(3), Z = 4, R-1 = 0.0416. The packing units in both compounds consist of hydrogen bonded cation-anion pairs. The (hyper)polarizabilities have been calculated for the crystallographic and optimized molecules, by AM1 and at the DFT/B3LYP(6-31G**) level.

Conductivity and F-19 NMR in PbGeO3-PbF2-CdF2 glasses and glass-ceramics

The temperature dependence of the electrical conductivity and the F-19 nuclear magnetic resonance (NMR) of PbGeO3-PbF2CdF, glasses and glass ceramics are investigated. The measured conductivity values of the glasses are above 10(-5) Skin at 500 K, and increase with increasing lead fluoride content. Activation energies extracted from the conductivity data are in the range 0.59-0.73 eV. Results are consistent with the hypothesis that in these oxyfluoride glasses lead fluoride rich clusters are dispersed in a metagermanate based matrix providing increasing mobility pathways for conducting ions. The conductivity of a sample of the glass ceramic of composition (mol%) 60PbGeO(3-)20PbF(2)-20CdF(2) was found to be smaller than that in the corresponding glass, suggesting that there are poor ionic conducting regions in the interface between the nanometer sized crystals. The temperature dependence of the F-19 relaxation times, measured in the range 100-800 K, exhibit the qualitative features associated with high fluorine mobility in both, glass and glass ceramics materials. We suggest that de-convolution of the spin-lattice relaxation rates observed in the glass ceramics shows that the observed high temperature rate maximum is associated with the diffusional motions of the fluorine ions in beta-PbF2 crystals. (c) 2005 Elsevier B.V. All rights reserved.

DFT study of the reaction between VO2+ and C2H6

The molecular mechanisms of the reaction VO2+ ((1)A(1)/(3)A'') + C2H6 ((1)A(g)) to yield V(OH)(2)(+) ((1)Sigma(+)/(3)Sigma(-)) + C2H4 ((1)A(g)) and/or VO+ ((1)Delta/(3)Sigma) + H2O ((1)A(1)) + C2H4 (Ag-1) have been investigated with density functional theory (DFT) at the B3LYP/6-311G(2d,p) level. Calculations including geometry optimization, vibrational analysis, and Gibbs free energy for the stationary points on the reactive potential energy surfaces at both the singlet (s) and first excited triplet (t) electronic states have been carried out. The most thermodynamically and kinetically favorable pathway is the formation of t-V(OH)(2)(+) + C2H4 along a four-step molecular mechanism (insertion, two consecutive hydrogen transfers, and elimination). A crossing point between s and t electronic states has been characterized. A comparison with previous works on VO2+ + C2H4 (Gracia et al. J. Phys. Chem. A 2003, 107, 3107-3120) and VO2+ + C3H8 (Engeser et al. Organometallics 2003, 22, 3933-3943) reactions allows us a rationalization of the different reactivity patterns. The catalytic role of water molecules in the tautomerization process between hydrated oxide cation, VO(H2O)(+,) and dihydroxide cation, V(OH)(2)(+), is achieved by a water-assisted mechanism.

Experimental and theoretical study of the compound [Pd(dmba)(NCO)(imz)]

The compound [Pd(dmba)(NCO)(imz)] (dmba = N,N-dimethylbenzilamine; NCO = cyanate; imz = imidazole) was studied through experimental and theoretical methods. The complex was synthesized and characterized by IR and NMR spectroscopy. To an appropriate representation of the molecular environment, Gaussian basis sets for the constituent atoms of the compound were built and, after adequate supplementation with polarization and diffuse functions, they were used to study the molecule. Calculations of electronic and vibrational structure of two possible isomers were carried out, showing that the compound, which contains the NCO GROUP trans to the Pd-C bond, is 4.29 kcal/mol more stable than the analogous one, where the imz ligand is trans to the Pd-C bond. The calculated molecular parameters, bond distances, and bond angles showed that the geometry around the metallic center is square-planar with the cyanate being linear. The theoretical infrared spectrum of C(1) symmetry (electronic state (1)A) is in accordance with the experimental one. It also verified the contribution of Pd (4d(xz) + 4d(yz)) and Pd (4d(xy)) in the HOMO and LUMO orbitals, respectively. (c) 2006 Elsevier B.V. All rights reserved.

H-1-N-15 NMR studies of the complex bis(S-allyl-L-cysteinate)palladium(II)

H-1-N-15 2D NMR data for S-allyl-L-cysteine (deoxyalliin) and for bis(S-allyl-L-cysteinate)palladium(II) complex are presented in this manuscript. Large upfield N-15 NMR shift of the amine nitrogen in the spectrum of the complex when compared to the spectrum of the ligand shows clearly coordination of S-allyl-L-cysteine, in the anion form, to palladium(II) through the NH2 group. (c) 2005 Elsevier B.V. All rights reserved.