Bacterial Reduction of Chromium

A mixed culture was enriched from surface soil obtained from an eastern United States site highly contaminated with chromate. Growth of the culture was inhibited by a chromium concentration of 12 mg/L. Another mixed culture was enriched from subsurface soil obtained from the Hanford reservation, at the fringe of a chromate plume. The enrichment medium was minimal salts solution augmented with acetate as the carbon source, nitrate as the terminal electron acceptor, and various levels of chromate. This mixed culture exhibited chromate tolerance, but not chromate reduction capability, when growing anaerobically on this medium. However, this culture did exhibit chromate reduction capability when growing anaerobically on TSB. Growth of this culture was not inhibited by a chromium concentration of 12 mg/L. Mixed cultures exhibited decreasing diversity with increasing levels of chromate in the enrichment medium. An in situ bioremediation strategy is suggested for chromate contaminated soil and groundwater.

     

Construction of diverse peptide structural architectures via chemoselective peptide ligation

Herein, we report the development of a facile synthetic strategy for constructing diverse peptide structural architectures via chemoselective peptide ligation. The key advancement involved is to utilize the benzofuran moiety as the peptide salicylaldehyde ester surrogate, and Dap–Ser/Lys–Ser dipeptide as the hydroxyl amino functionality, which could be successfully introduced at the side chain of peptides enabling peptide ligation. With this method, the side chain-to-side chain cyclic peptide, branched/bridged peptides, tailed cyclic peptides and multi-cyclic peptides have been designed and successfully synthesized with native peptidic linkages at the ligation sites. This strategy has provided an alternative strategic opportunity for synthetic peptide development. It also serves as an inspiration for the structural design of PPI inhibitors with new modalities.

Methods of introducing peptide salicylaldehyde esters and hydroxyl amine functionality into the peptide side chain have been developed. Diverse peptide structural motifs were constructed via ligation with native amide linkages at the ligation sites.     

DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

The rate of O2 and CO binding to a copper complex, determined by a "flash-and-trap" technique, exceeds that for hemes

The observation and fast time-scale kinetic determination of a primary dioxygen-copper interaction have been studied. The ability to photorelease carbon monoxide from [Cu(I)(tmpa)(CO)](+) in mixtures of CO and O(2) in tetrahydrofuran (THF) between 188 and 218 K results in the observable formation of a copper-superoxide species, [Cu(II)(tmpa)(O(2)(-))](+) lambda(max) = 425 nm. Via this "flash-and-trap" technique, temperature-dependent kinetic studies on the forward reaction between dioxygen and [Cu(I)(tmpa)(thf)](+) afford activation parameters DeltaH = 7.62 kJ/mol and DeltaS = -45.1 J/mol K. The corresponding reverse reaction proceeds with DeltaH = 58.0 kJ/mol and DeltaS = 105 J/mol K. Overall thermodynamic parameters are DeltaH degrees = -48.5 kJ/mol and DeltaS degrees = -140 J/mol K. The temperature-dependent data allowed us to determine the room-temperature second-order rate constant, k(O2) = 1.3 x 10(9) M(-1) s(-1). Comparisons to copper and heme proteins and synthetic complexes are discussed.     

Mechanism of the glutathione transferase-catalyzed conversion of antitumor 2-crotonyloxymethyl-2-cycloalkenones to GSH adducts

Human glutathione (GSH) transferase (hGSTP1-1) processes with similar kinetic efficiencies the antitumor agents 2-crotonyloxymethyl-2-cyclohexenone (COMC-6), 2-crotonyloxymethyl-2-cycloheptenone (COMC-7), and 2-crotonyloxymethyl-2-cyclopentenone (COMC-5) to 2-glutathionylmethyl-2-cyclohexenone, 2-glutathionylmethyl-3-glutathionyl-2-cycloheptenone, and 2-glutathionylmethyl-2-cyclopentenone, respectively. This process likely involves initial enzyme-catalyzed Michael addition of GSH to the COMC derivative to give a glutathionylated enol(ate), which undergoes nonstereospecific ketonization, either while bound to the active site or free in solution, to a glutathionylated exocyclic enone. Free in solution, GSH reacts at the exomethylene carbon of the exocyclic enone, displacing the first GSH to give the final product. This mechanism is supported by the observation of multiphasic kinetics in the presence of high concentrations of hGSTP1-1 and the ability to trap kinetically competent exocyclic enones in aqueous acid using COMC-6 and COMC-7 as substrates. That the exocyclic enone is formed by nonstereospecific ketonization of an enol(ate) species is indicated by the observation that COMC-6 (chirally labeled with deuterium at the exomethylene carbon) gives stereorandomly labeled exocyclic enone. The isozymes hGSTP1-1, hGSTA1-1, hGSTA4-4, and hGSTM2-2 catalyze the conversion of COMC-6 to final product with similar efficiencies (K(m) = 0.08-0.34 mM, k(cat) = 1.5-6.1 s(-)(1)); no activity was detected with the rat rGSTT2-2 isozyme. Molecular docking studies indicate that in hGSTP1-1, the hydroxyl group of Tyr108 might serve as a general acid catalyst during substrate turnover. The possible significance of these observations with respect to the metabolism of COMC derivatives in multidrug resistant tumors is discussed.     

A direct injection high-throughput liquid chromatography tandem mass spectrometry method for the determination of a new orally active alphavbeta3 antagonist in human urine and dialysate

A generic high-throughput liquid chromatography (HTLC) tandem mass spectrometry (MS/MS) assay for the determination of compound I in human urine and dialysate (hemodialysis) was developed and validated. By using the HTLC on-line extraction technique, sample pretreatment was not necessary. The sample was directly injected onto a narrow bore large particle size extraction column (50 x 1.0 mm, 60 microm) where the sample matrix was rapidly washed away using a high flow rate (5 mL/min) aqueous mobile phase while analytes were retained. The analytes were subsequently eluted from the extraction column onto an analytical column using an organic-enriched mobile phase prior to mass spectrometric detection. The analytes were then eluted from the analytical column to the mass spectrometer for the determination. The linear dynamic range was 2.0-6000 ng/mL for the urine assay and 0.1-300 ng/mL for the dialysate assay. Intraday accuracy and precision were evaluated by analyzing five replicates of calibration standards at all concentrations used to construct the standard curve. For the urine assay, the precision (RSD%, n=5) ranged from 1.9 to 8.0% and the accuracy ranged from 87.8 to 105.2% of nominal value. For the dialysate assay, the precision (RSD%, n=5) ranged from 1.1 to 10.0% and the accuracy from 94.5 to 105.2% of nominal value. In-source fragmentation of the acyl glucuronide metabolite (compound III) did not interfere with the determination of parent compound I. The developed HTLC/MS/MS methodology was specific for compound I in the presence of compound III. Column life-time is increased and sample analysis time is decreased over traditional reversed-phase methods when direct injection assays for urine and dialysate are coupled with the technology of HTLC.     

Structure and reactivity of bis(silyl) dihydride complexes (PMe(3))(3)Ru(SiR(3))(2)(H)(2): model compounds and real intermediates in a dehydrogenative C-Si bond forming reaction

A series of stable complexes, (PMe(3))(3)Ru(SiR(3))(2)(H)(2) ((SiR(3))(2) = (SiH(2)Ph)(2), 3a; (SiHPh(2))(2), 3b; (SiMe(2)CH(2)CH(2)SiMe(2)), 3c), has been synthesized by the reaction of hydridosilanes with (PMe(3))(3)Ru(SiMe(3))H(3) or (PMe(3))(4)Ru(SiMe(3))H. Compounds 3a and 3c adopt overall pentagonal bipyramidal geometries in solution and the solid state, with phosphine and silyl ligands defining trigonal bipyramids and ruthenium hydrides arranged in the equatorial plane. Compound 3a exhibits meridional phosphines, with both silyl ligands equatorial, whereas the constraints of the chelate in 3c result in both axial and equatorial silyl environments and facial phosphines. Although there is no evidence for agostic Si-H interactions in 3a and 3b, the equatorial silyl group in 3c is in close contact with one hydride (1.81(4) A) and is moderately close to the other hydride (2.15(3) A) in the solid state and solution (nu(Ru.H.Si) = 1740 cm(-)(1) and nu(RuH) = 1940 cm(-)(1)). The analogous bis(silyl) dihydride, (PMe(3))(3)Ru(SiMe(3))(2)(H)(2) (3d), is not stable at room temperature, but can be generated in situ at low temperature from the 16e(-) complex (PMe(3))(3)Ru(SiMe(3))H (1) and HSiMe(3). Complexes 3b and 3d have been characterized by multinuclear, variable temperature NMR and appear to be isostructural with 3a. All four complexes exhibit dynamic NMR spectra, but the slow exchange limit could not be observed for 3c. Treatment of 1 with HSiMe(3) at room temperature leads to formation of (PMe(3))(3)Ru(SiMe(2)CH(2)SiMe(3))H(3) (4b) via a CH functionalization process critical to catalytic dehydrocoupling of HSiMe(3) at higher temperatures. Closer inspection of this reaction between -110 and -10 degrees C by NMR reveals a plethora of silyl hydride phosphine complexes formed by ligand redistribution prior to CH activation. Above ca. 0 degrees C this mixture converts cleanly via silane dehydrogenation to the very stable tris(phosphine) trihydride carbosilyl complex 4b. The structure of 4b was determined crystallographically and exhibits a tetrahedral P(3)Si environment around the metal with the three hydrides adjacent to silicon and capping the P(2)Si faces. Although strong Si.HRu interactions are not indicated in the structure or by IR, the HSi distances (2.00(4) - 2.09(4) A) and average coupling constant (J(SiH) = 25 Hz) suggest some degree of nonclassical SiH bonding in the RuH(3)Si moiety. The least hindered complex, 3a, reacts with carbon monoxide principally via an H(2) elimination pathway to yield mer-(PMe(3))(3)(CO)Ru(SiH(2)Ph)(2), with SiH elimination as a minor process. However, only SiH elimination and formation of (PMe(3))(3)(CO)Ru(SiR(3))H is observed for 3b-d. The most hindered bis(silyl) complex, 3d, is extremely labile and even in the absence of CO undergoes SiH reductive elimination to generate the 16e(-) species 1 (DeltaH(SiH)(-)(elim) = 11.0 +/- 0.6 kcal x mol(-)(1) and DeltaS(SiH)(-)(elim) = 40 +/- 2 cal x mol(-)(1) x K(-)(1); Delta = 9.2 +/- 0.8 kcal x mol(-)(1) and Delta = 9 +/- 3 cal x mol(-)(1).K(-)(1)). The minimum barrier for the H(2) reductive elimination can be estimated, and is higher than that for silane elimination at temperatures above ca. -50 degrees C. The thermodynamic preferences for oxidative additions to 1 are dominated by entropy contributions and steric effects. Addition of H(2) is by far most favorable, whereas the relative aptitudes for intramolecular silyl CH activation and intermolecular SiH addition are strongly dependent on temperature (DeltaH(SiH)(-)(add) = -11.0 +/- 0.6 kcal x mol(-)(1) and DeltaS(SiH)(-)(add) = -40 +/- 2 cal.mol(-)(1) x K(-)(1); DeltaH(beta)(-CH)(-)(add) = -2.7 +/- 0.3 kcal x mol(-)(1) and DeltaS(beta)(-CH)(-)(add) = -6 +/- 1 cal x mol(-)(1) x K(-)(1)). Kinetic preferences for oxidative additions to 1 - intermolecular SiH and intramolecular CH - have been also quantified: Delta = -1.8 +/- 0.8 kcal x mol(-)(1) and Delta = -31 +/- 3 cal x mol(-)(1).K(-)(1); Delta = 16.4 +/- 0.6 kcal x mol(-)(1) and Delta = -13 +/- 6 cal x mol(-)(1).K(-)(1). The relative enthalpies of activation (-)(1) x K(-)(1)). Kinetic preferences for oxidative additions to 1 - intermolecular SiH and intramolecular CH - have been also quantified: Delta (H)SiH(add) = 1.8 +/- 0.8 kcal x mol(-)(1) and Delta S((SiH-add) =31+/- 3 cal x mol(-)(1) x K(-)(1); Delta S (SiH -add) = 16.4 +/- 0.6 kcal x mol(-)(1) and =Delta S (SiH -CH -add) =13+/- 6 cal x mol(-)(1) x K(-)(1). The relative enthalpies of activation are interpreted in terms of strong SiH sigma-complex formation - and much weaker CH coordination - in the transition state for oxidative addition.     

Polymer phase separation in composite latex particles. 1. Considerations for the nucleation and growth mechanism

This study addresses the question of how polymer phase separation takes place during polymerization reactions within composite latex particles. Experiments resulted in acrylic/styrene latices with two-phase structures that were analyzed via TEM. Those that resulted from the use of semi-batch reactions allowed us to observe domains that likely did not undergo phase rearrangement after they were formed within the particles. We computed the critical size of the phase-separated domains by assuming that the nucleation and growth mechanism applied to such experiments. We also computed how much these domains would increase in size by subsequent polymerization within those domains. Comparisons of predicted and experimental domain sizes and distributions showed quite reasonable agreement. The domains formed in latex particles of about 350 nm were in the 30–50-nm range. Despite the close agreement between theory and experiment, we are not convinced that phase separation occurs by nucleation and growth, as it appears to us that given the relative rates of reaction and polymer diffusion, phase separation events will often be forced to occur within the spinodal region of the phase diagram. To cite this article: J.M. Stubbs, C. R. Chimie 6 (2003).     

Investigation of the enzymatic and nonenzymatic cope rearrangement of carbaprephenate to carbachorismate

The dimethyl esters of carbaprephenate and 4-epi-carbaprephenate were prepared by modification of published procedures. In methanol these compounds are converted quantitatively to isomeric 6-hydroxytricyclo[3.3.1.0(2,7)]non-3-en-1,3-dimethyl esters via a two-step sequence involving an initial Cope rearrangement, followed by intramolecular Diels-Alder reaction of the dimethyl carbachorismate or 4-epi-carbachorismate intermediates. Carbaprephenate and its epimer were obtained by alkaline hydrolysis of the corresponding dimethyl esters. These compounds, in contrast to their ester precursors, undergo spontaneous acid-catalyzed decarboxylation in aqueous solution. Only at high pH does the Cope rearrangement compete with decarboxylation. At pH 12 and 90 degrees C, carbaprephenate slowly rearranges to carbachorismate, which rapidly loses water to give 3-(2-carboxyallyl)benzoic acid as the major product. A small amount of the intramolecular Diels-Alder adduct derived from carbachorismate is also observed by NMR as a minor product. Carbaprephenate is not a substrate for the enzyme chorismate mutase from Bacillus subtilis (BsCM), nor does carbaprephenate inhibit the normal chorismate mutase activity of this enzyme, even when present in 200-fold excess over chorismate. Its low affinity for the enzyme-active site is presumably a consequence of placing a methylene group rather than an oxygen atom proximal to the essential cationic residue Arg90. Nevertheless, BsCM variants that lack this cation (R90G and R90A) do not accelerate the Cope rearrangement of carbaprephenate either, and a catalytic antibody 1F7, which exhibits modest chorismate mutase activity, is similarly inactive. Poor substrate binding and the relatively high barrier for the Cope compared to the Claisen rearrangement presumably account for the lack of detectable catalysis. Acceleration of this sigmatropic rearrangement apparently requires more than an active site that is complementary in shape to the reactive substrate conformer.     

Kinetic separation methodology for the stereoselective synthesis of (E)- and (Z)-alpha-fluoro-alpha,beta-unsaturated esters via the palladium-catalyzed carboalkoxylation of 1-bromo-1-fluoroalkenes

[reaction: see text] Methodology for the stereoselective preparation of both (E)- and (Z)-alpha-fluoro-alpha,beta-unsaturated esters is described. 1-Bromo-1-fluoroalkenes (E/Z approximate 1:1) can be isomerized to high E/Z ratio mixtures, which participate in palladium-catalyzed carboalkoxylation and lead to (Z)-alpha-fluoro-alpha,beta-unsaturated esters in high stereoselectivity. The same starting material can also be kinetically reduced to get an E/Z ratio of 0:100; similar carboalkoxylation reaction at 70 degrees C affords (E)-alpha-fluoro-alpha,beta-unsaturated esters stereospecifically.