Reductive activation of nitrate reductases

Protein film voltammetry of Paracoccus pantotrophus respiratory nitrate reductase (NarGH) and Synechococcus elongatus assimilatory nitrate reductase (NarB) shows that reductive activation of these enzymes may be required before steady state catalysis is observed. For NarGH complementary spectroscopic studies suggest a structural context for the activation. Catalytic protein film voltammetry at a range of temperatures has allowed quantitation of the activation energies for nitrate reduction. For NarGH with an operating potential of ca. 0.05 V the activation energy of ca. 35 kJ mol-1 is over twice that measured for NarB whose operating potential is ca. -0.35 V.     

Identification of reactive dyes in spent dyebaths and wastewater by capillary electrophoresis-mass spectrometry

Capillary electrophoresis with diode array detection and mass spectrometry combined with solid-phase extraction were employed for the identification of reactive vinylsulfone and chlorotriazine dyes and their hydrolysis products in spent dyebaths and raw and treated wastewater. Recoveries of dyes from treated wastewater as their tetrabutylammonium ion-pairs using C18 reversed-phase cartridges ranged from 81 to 121%. Detection limits in sewage effluent of the different dyes and hydrolysis products ranged from 23 to 42 microg/l. The method was successfully applied to the detection of the hydrolysis products of five reactive dyes in influents and effluents of a municipal wastewater treatment plant receiving dyehouse effluents.     

Synthesis and antibacterial activity of 7-ethyl-3-methyl-4,7-dihydro-4-oxoisothiazolo[5,4-b]pyridine-5-carboxylic acid

The synthesis of the quinolone, 7-ethyl-3-methyl-4,7-dihydro-4-oxoisothiazolo[5,4-b]pyridine-5-carboxylic acid 4 was accomplished utilizing the Gould-Jacobs dependent route. The compound had very weak in vitro activity as compared to nalidixic acid versus E. coli, P. aeruginosa, K. pnuemoniae, S. aureus and P. mirabilis.     

The first structural and spectroscopic characterization of a neptunyl polyoxometalate complex

The reaction between PW9O349- and NpO2+ has yielded the first structurally characterized neptunyl(V) polyoxometalate complex, [Na2(NpO2)2(A-PW9O34)2]14-. This complex is isostructural with the uranyl(VI) analogue, and there is also spectroscopic evidence for its existence in solution. The complex is readily extracted into toluene, and this may have significance in the sequestering and/or separation of the neptunyl ion in terms of nuclear waste management.     

Electronic structure, vibrational stability, and predicted infrared-Raman spectra of the As20, As @ Ni12, and As @ Ni12 @ As20 clusters

Recently an inorganic fullerine-like [As@Ni(12)@As(20)](3-) onion with near-perfect icosahedral symmetry in the crystalline phase was reported [M. J. Moses, J. C. Fettinger, and B. W. Eichhorn, Science 300, 778 (2003)]. This paper presents a detailed computational study in the framework of density functional theory on various aspects of this molecule. The electronic structure of the As@Ni(12)@As(20) is investigated in its neutral as well as -3 charged state together with its subunits As(20) and As@Ni(12) by the all electron linear combination of Gaussian-type orbitals method. The bonding is studied by examining the integrated charge within atomic sphere, the electron localization function, changes in the electron density distribution, and from vibrational modes. We find that strong covalent As-As bonds seen in isolated As(20) become weaker in the As@Ni(12)@As(20) and strong covalent As-Ni bonds are formed. The structural stability of all four clusters is examined by analyzing the energetics and by calculating the vibrational frequencies. Further, the infrared and Raman spectra is predicted for both the neutral and charged As@Ni(12)@As(20) clusters. Finally, the energy barrier for removal of a single arsenic atom is calculated for the neutral As@Ni(12)@As(20) cluster.     

The complexity of catalysis: origins of enantio- and diastereocontrol in sulfur ylide mediated epoxidation reactions

The reaction of chiral sulfur ylides with aldehydes and ketones has emerged as a useful asymmetric process for the synthesis of epoxides. Processes employing either catalytic or stoichiometric amounts of sulfides have been developed. Although a large number of chiral sulfur ylides have been tested in the epoxidation process, only a few have delivered high diastereo- and enantio- selectivity. This review examines the factors that influence stereocontrol (steric hindrance of the sulfide, ylide conformation, ylide face selectivity, reversibility of betaine formation, solvent, and metal salts). This analysis leads to the conclusion that high reversibility in betaine formation leads to high diastereoselectivity but low enantioselectivity, and non-reversible betaine formation leads to low diastereoselectivity and high enantioselectivity (provided that other criteria are met). To achieve both high diastereoselectivity and high enantioselectivity simultaneously, requires non-reversible formation of the anti-betaine and reversible formation of the syn-betaine. Thus, factors that influence the degree of reversibility in betaine formation are critically important since with subtle changes in reaction conditions (solvent, temperature, metal ions) both high enantio- and diastereoselectivity can often be achieved.     

Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography/tandem mass spectrometry data

The quantity and variable quality of data that can be generated from liquid chromatography (LC)/mass spectrometry (MS)-based proteomics analyses creates many challenges in interpreting the spectra in terms of the actual proteins in a complex sample. In spite of improvements in algorithms that match putative peptide sequences to MS/MS spectra, the assembly of these lists of possible or probable peptides into a 'correct' set of proteins is still problematic. We have observed a trend in a simple relationship, derived from standard database search outputs, which can be useful in assessing the quality of a MS/MS-based protein identification. Specifically, the ratio of the protein score and number of non-redundant peptides, or average peptide score (APS), can facilitate initial filtering of database search results in addition to providing a useful measure of confidence for the proteins identified. This parameter has been applied to results from the analysis of multi-protein complexes derived from pull-down experiments analyzed using a two-dimensional LC/MS/MS workflow. In particular, the complex list of protein identifications derived from a drug affinity pull-down with immobilized ampicillin and an E. coli lysate was greatly simplified by applying the APS as a filter, allowing for facile identification of the penicillin-binding proteins known to interact with ampicillin. Furthermore, an APS threshold can be used for any data sets derived from electrospray ionization (ESI)- or matrix-assisted laser desorption/ionization (MALDI)-MS/MS experiments and is also not specific to any database search program.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Conformational dependence of the n→π* rotatory strength in dissymmetric carboxylic acid compounds

The conformational dependence of the chiroptical properties associated with electronic transitions in α-hydroxy, α-fluoro, α-chloro, and α-mercapto carboxylic acids is examined with a theoretical model in which rotatory strengths are calculated directly from molecular orbitals calculated using INDO and CNDO semi-empirical molecular orbital models, and excited state wave functions constructed in the virtual orbital-configuration interaction approximation. Binding energies, ground state dipole moments, and vertical ionization potentials (calculated according to Koopman's theorem) are calculated, as well as transition energies, dipole strengths, oscillator strengths, rotatory strengths and dissymmetry factors. Special emphasis is placed on correlating the signs of the rotatory strengths calculated for the lowest energy singlet-singlet transitions with conformational isomerism about the C(α)-COOH band of acyclic α-substituted carboxylic acids. The calculated results for S-lactic acid are in agreement with and strongly support the empirically based spectra-structure relationships previously proposed for S-lactic acid and its derivatives. The calculated results for 2(S)-chloropropionic acid do not agree with previously proposed spectra-structure relationships and this finding is discussed. The results obtained for 2(S)-mercaptopropionic acid are in partial agreement with experiment and spectra-structure relationships in this case involve some uncertainty.