Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism

Herein, we present results from MD simulations of the Michaelis complex formed between the B. cereus zinc-beta-lactamase enzyme and benzylpenicillin. The structural and dynamical effects induced by substrate-binding, the specific role of the conserved residues, and the near attack conformers of the Michaelis complex are discussed. Quantum chemical methods (HF/6-31G* and B3LYP/6-31G*) are also applied to study the hydrolysis reaction of N-methylazetidinone catalyzed by a monozinc system consisting of the side chains of the histidine residues (His86, His88, and His149) complexed with Zn-OH and the side chains of Asp90 and His210. From this model system, we built molecular-mechanics representations of the prereactive complex and transition state configurations docked into the active site. Linear-scaling semiempirical calculations coupled with a continuum solvent model were then performed on these static models. We propose that the experimental rate data for the B. cereus enzyme is compatible with a one-step mechanism for the hydrolysis of beta-lactam substrates in which His210 acts as a proton donor.     

Synthesis of 4,5-bifunctionally substituted imidazolidin-2-ones

It is shown that the reaction of readily available 4,5-dihydroxyimidazolidin-2-ones with hydrazoic or p-toluenesulfinic acid takes place stereo- and regioselectively and leads to the formation of 4,5-diazido- or 4,5-di(p-tolylsulfonyl)imidazolidin-2-ones. The example of 4,5-diazidoimidazolidin-2-one is used to demonstrate the possibility of using compounds of this type for stereoselective introduction of substituents into the 4 and 5 positions of the imidazole ring.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1645–1649, December, 1993.     

Neutron activation for precise nuclear data

Techniques for extracting neutron flux parameters pertaining to the irradiation positions and nuclear data pertaining to the isotopes concemed from measured reaction rates have been developed. An adjustment procedure based on the generalized least squares method with incorporates the, evaluated literature nuclear data, estimates of flux parameters and the experimentally measured reaction rates using high resolution -ray spectrometry is applied. More precise values of the nuclear data, i.e., thermal neutron cross sections, resonance integrals and -ray emission probabilities are thus generated. The irradiation of a multi-element standard (MES) containing 24 elements is carried out in six diffieret positions in two diverse types of reactor in the UK and Russia. It is shown that the improvement in nuclear data is revelaed in moire than 90% of the cases.     

Enzyme catalysis in organic solvents: a promising field for optical biosensing

The ability of enzymes to work in non-aqueous media offers new and almost unexploited possibilities for the development of new optical biosensors. The advantages of performing biocatalytic reactions in non-aqueous media are discussed in relation to their possible application in optical biosensor design. Attention is focused on the factors that influence enzymatic catalysis in organic solvents, including the role of enzyme-associated water, criteria for solvent selection and the alteration of enzyme specificity. Recent examples of relevant applications and future prospects of organic-phase optical biosensing are discussed.     

Use of the hydroxyl radical and gel electrophoresis to study DNA structure

The hydroxyl radical has been used as a chemical probe to study in solution the structure of DNA and DNA-protein complexes. The hydroxyl radical abstracts a deoxyribose hydrogen atom, cleaving one strand of the DNA. The cutting pattern, visualized by separating the cleavage products using gel electrophoresis, shows the reactivity of each backbone position toward the radical. This method has been applied to studies of DNA bending and helical twist. Phased runs of adenines (adenine tracts) cause sequence-directed DNA bending. The hydroxyl radical cleavage of a bent DNA fragment containing short adenine tracts phased with the helix screw gives rise to an unusual cutting pattern. The hydroxyl radical cleavage rate decreases in the 5' to 3' direction along each adenine tract, with a minimum at the 3' end of each adenine tract. The cleavage of the matching thymine tract is similar, but the minimum in the pattern is offset in the 3' direction. This pattern on the autoradiograph of the gel is interpreted to indicate that bending is accompanied by a narrow minor groove in the DNA molecule. Furthermore, hydroxyl radical cleavage results in different cutting patterns for two similar sequences, (CGA4T4)5 and (CGT4A4)5, which have been shown to be bent and relatively straight, respectively. The hydroxyl radical method has also been used to determine the helical repeat of the metallothionein IIA gene to be about 10.5 base pairs per turn. Methods of optimizing the hydroxyl radical reaction for DNA-protein footprinting are discussed. Because individual gel bands give information about cutting frequency at particular positions in the backbone, gel resolution and clear autoradiographs are important to this work.(ABSTRACT TRUNCATED AT 250 WORDS)     

Synthesis and reactions of the transition metal substituted tin hydride HSn[Mo(CO)3C5H5]3

Reaction of HMo(CO)₃C₅H₅ and Sn(C₅H₅)₂ produces the tin hydride HSn[Mo(CO)₃C₅H₅]₃ (I). Reaction of I with CCl₄, CHCl₃, or CH₂Cl₂ gives ClSn[Mo(CO)₃C₅H₅]₃ (II). With hydrogen chloride the hydride I reacts to produce the dichloride Cl₂Sn[Mo(CO)₃C₅H₅]₂. The first step in this reaction is cleavage of the SnH bond to produce the chloride II. The hydride I reacts with acetic acid to produce the diacetate (CH₃COO)₂Sn[Mo(CO)₃C₅H₅]₂.     

Vibrational and high pressure conformational studies of 1,1,2-trichloroethane

The infrared spectra of 1,1,2-trichloroethane were recorded from 4000 to 50 cm^?1 in the vapour and liquid states. Additional spectra above 200 cm^?1 of the low temperature crystal and of two crystalline solids, prepared by compressing the sample in a diamond anvil cell, were obtained. Also, infrared spectra of the liquid and of the compound dissolved in CS₂ were recorded at increased pressures. Raman spectral data of the liquid (including polarization measurements) and of the low temperature crystal were obtained.The fundamental frequencies for each of the two conformers, C₁ and C_s, were assigned and the results checked by normal coordinate analysis. The same diagonal and off-diagonal force constants were employed for the two conformers and the force fields were derived by means of a least squares refinement, including data for chloroethane, 1,1-dichloroethane and various deuterated species. A standard deviation of 3 % was obtained in the final fit.From the changes in relative intensities for infrared bands belonging to the C₁ and C_s conformers with increasing pressure, the volume differences (ΔV¯between the conformers were determined in CS₂ solution and in the pure liquid.     

Reaction of pentachloropyridine N-oxide with potassium hydrogen sulfide

Depending on the conditions, the reaction of pentachloropyridine N-oxide with potassium hydrogen sulfide leads to the N-oxide of the potassium salt of 3,4,5,6-tetrachloropyridin-2-thiol or the dipotassium salt of 3,4,5-trichloropyridine-2,6-dithiol, which are converted by the action of dimethyl sulfate into the corresponding methylthio derivatives. Oxidation of the latter has given sulfones. It has been shown that for these sulfones,reactions with nucleophilic reagents take place at the methylsulfonyl group and not at the chlorine atoms.     

Possibilites et limites de l'analyse par activation neutronique multielementaire d'echantillons biologiques avec ou sans separation de la matrice activable

The possibilities and limits of the multi-elemental determinations in biological samples by neutron activation analysis with and without chemical separation are discussed.