The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

Enzymatic kinetic of cellulose hydrolysis

The ethanol effect on the Trichoderma reesei cellulases was studied to quantify and clarify this inhibition type. To determine inhibition parameters of crude cellulase and purified exoglucanase Cel7A, integrated Michaelis-Menten equations were used assuming the presence of two inhibitors: cellobiose as the reaction product and ethanol as a possible bioproduct of cellulose fermentation. It was found that hydrolysis of cellulose by crude enzyme follows a model that considers noncompetitive inhibition by ethanol, whereas Cel7A is very slightly competitively inhibited. Crude cellulase is much more inhibited (K _iul=K _icl=151.9 mM) than exoglucanase Cel7A (K _icl=1.6 × 10¹⁵ mM). Also, calculated inhibition constants showed that cellobiose inhibition is more potent than ethanol inhibition both for the crude enzyme as well as exoglucanase Cel7A.     

Mass spectra of bile acid methyl ester acetate derivatives

Deuterium labeling in the acetate derivatives of cholic acid demonstrates that electron impact induced consecutive loss of HOAc from the molecular ion occurs in the following order of decreasing preference: 12α-OAc > 7α-OAc > 3α-OAc. Numerous examples are presented showing that consecutive loss of HOAc from a common ion generally increases progressively with relative intensity. In the acetate pregnan-20-one derivatives of cholic acid, loss of 43 mass units from the molecular ion comes from the 12α-OAc and not the 17β-acetyl sidechain. Ketene is ejected from an acetoxy group located in an α position to a carbonyl on which an ion-radical charge is localized.     

A formula periodic table for benzenoid hydrocarbons and the aufbau and excised internal structure concepts in benzenoid enumerations

The genesis of the aufbau and excised internal structure concepts is traced. These concepts were pivotal to the first published enumerations of the strictly peri-condensed, non-Kekuléan, and essentially strain-free total resonant sextet benzenoid groups. Aperiodic table set is defined as a partially ordered set forming a two-dimensional array which complies with thetriad principle where a central element has a metric property that is the arithmetic mean of two adjacent surrounding member elements.     

Mass spectral fragmentation of functionalized lanostanes-I

Mass spectra of various functionalized lanostanes and their deuterated analogs are compared. It is proposed that the transfer of a hydrogen from the 18-methyl group to the 11-oxo group via a McLafferty rearrangement is made geometrically possible by prior ionization of the 13,14 bond which allows an optimum interatomic distance between the oxygen and hydrogen to be acquired; the 8,9 double bond is a requisite for electronic induction of this specific process. Transfer of the hydrogen from the 7β-hydroxy group to position 14 is implicated in the mass spectrum of 3β-acetoxy-7β-hydroxy-5α-lanostan-11-one.     

A theoretical study of π-hydrocarbon-iron tricarbonyl complexes

The molecular orbital parameters for tricarbonyl(tetrahapto-unsaturated-hydrocarbon)iron complexes are computed using graph-theoretical methods. The results are in agreement with their experimental properties.     

A systematic density functional theory study of the electronic structure of bulk and (001) surface of transition-metals carbides

A systematic study of the bulk and surface geometrical and electronic properties of a series of transition-metal carbides (TMC with TM = Ti, V, Zr, Nb, Mo, Hf, Ta, and W) by first-principles methods is presented. It is shown that in these materials the chemical bonding is strongly covalent, the cohesive energies being directly related to the bonding-antibonding gap although the shift of the center of the C(2s) band related peak in the density of states with respect to diamond indicates that some metal to carbon charge transfer does also take place. The (001) face of these metal carbides exhibits a noticeable surface rumpling which grows along the series. It is shown that neglecting surface relaxation results in very large errors on the surface energy and work function. The surface formation induces a significant shift of electronic energy levels with respect to the corresponding values in the bulk. The extent and nature of the shift can be understood from simple bonding-antibonding arguments and is enhanced by the structural rippling of this surface.     

Solution conformation of a nitrobenzoxadiazole derivative of the polyene antibiotic nystatin: a FRET study

Nystatin is a polyene antibiotic frequently applied in the treatment of topical fungal infections. In this work, a 7-nitrobenz-2-oxa-1,3-diazole (NBD) hexanoyl amide derivative of nystatin was synthesized and its detailed photophysical characterization is presented. The average conformation of the labelled antibiotic in tetrahydrofuran, ethanol and methanol was determined by intramolecular (tetraene to NBD) fluorescence resonance energy transfer measurements. At variance with the literature [Can. J. Chem. 63 (1985) 77-85], it was concluded that there is no need to invoke a solvent-dependent conformational equilibrium between extended and closed conformers of the antibiotic, because the mean tetraene-to-NBD separating distance was found to remain constant (approximately 18 A) in all the solvents studied. In addition, the large solvent dependence of the fluorescence anisotropy observed for the non-derivatized nystatin, was rationalized on the basis of the prolate ellipsoidal geometry of the molecule. It was concluded that the rod shaped and amphipathic antibiotic remains monomeric in different solvents within the concentration range studied (2-20 microM).