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As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable. 相似文献
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Wallace IM Urbanus ML Luciani GM Burns AR Han MK Wang H Arora K Heisler LE Proctor M St Onge RP Roemer T Roy PJ Cummins CL Bader GD Nislow C Giaever G 《Chemistry & biology》2011,18(10):1273-1283
Preselection of compounds that are more likely to induce a phenotype can increase the efficiency and reduce the costs for model organism screening. To identify such molecules, we screened ~81,000 compounds in Saccharomyces cerevisiae and identified ~7500 that inhibit cell growth. Screening these growth-inhibitory molecules across a diverse panel of model organisms resulted in an increased phenotypic hit-rate. These data were used to build a model to predict compounds that inhibit yeast growth. Empirical and in silico application of the model enriched the discovery of bioactive compounds in diverse model organisms. To demonstrate the potential of these molecules as lead chemical probes, we used chemogenomic profiling in yeast and identified specific inhibitors of lanosterol synthase and of stearoyl-CoA 9-desaturase. As community resources, the ~7500 growth-inhibitory molecules have been made commercially available and the computational model and filter used are provided. 相似文献
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Stephens FH Johnson MJ Cummins CC Kryatova OP Kryatov SV Rybak-Akimova EV McDonough JE Hoff CD 《Journal of the American Chemical Society》2005,127(43):15191-15200
White phosphorus (P(4)) reacts with three-coordinate molybdenum(III) trisamides or molybdaziridine hydride complexes to produce either bridging or terminal phosphide (P(3)(-)) species, depending upon the ancillary ligand steric demands. Thermochemical measurements have been made that place the MoP triple bond dissociation enthalpy at 92.2 kcal.mol(-)(1). Thermochemical measurements together with computational analysis rule out simple P-atom abstraction from P(4) as a step in the phosphorus activation mechanism. Kinetic measurements made by the stopped-flow method show that the reaction between the monomeric molybdenum complexes and P(4) is first-order both in metal complex and in P(4). Cyclo-P(3) complexes can be obtained when ancillary ligand steric demands are small, but kinetic measurements rule them out as monometallic intermediates in the P(4) activation mechanism. Also studied by calorimetric, kinetic, and in one case variable-temperature NMR methods is the process of mu-phosphide bridge formation. Post-rate-determining steps of the P(4) activation process were examined in a search for minima on the reaction's potential energy surface, leading to the proposal of two plausible, parallel, bimetallic reaction channels. 相似文献
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The nitridotungsten(vi) complex NW(N[i-Pr]Ar)(3) (-N, Ar = 3,5-Me(2)C(6)H(3)) reacts with (CF(3)C(O))(2)O followed by ClSiMe(3) to give the isolable trifluoroacetylimido-chloride complex -(NC(O)CF(3))Cl, with oxalyl chloride to give cyanate-dichloride -(OCN)(Cl)(2), and with PCl(5) to give trichlorophosphinimide-dichloride -(NPCl(3))(Cl)(2). The oxo-chloride complex -(O)Cl, obtained from -N upon treatment with pivaloyl chloride, reacts with PCl(5) to give trichloride -(Cl)(3). Synthetic and structural details are reported for the new tungsten trisanilide derivatives. 相似文献
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The diphosphaazide complex (Mes*NPP)Nb(N[Np]Ar)3 (Mes* = 2,4,6-tri-tert-butylphenyl, Np = neopentyl, Ar = 3,5-Me2C6H3), 1, has previously been reported to lose the P2 unit upon gentle heating, to form (Mes*N)Nb(N[Np]Ar)3, 2. The first-order activation parameters for this process have been estimated here using an Eyring analysis to have the values Delta H(double dagger) = 19.6(2) kcal/mol and Delta S(double dagger) = -14.2(5) eu. The eliminated P2 unit can be transferred to the terminal phosphide complexes P[triple bond]M(N[(i)Pr]Ar)3, 3-M (M = Mo, W), and [P[triple bond]Nb(N[Np]Ar)3](-), 3-Nb, to give the cyclo-P3 complexes (P3)M(N[(i)Pr]Ar)3 and [(P3)Nb(N[Np]Ar)3](-). These reactions represent the formal addition of a P[triple bond]P triple bond across a M[triple bond]P triple bond and are the first efficient transfers of the P2 unit to substrates present in stoichiometric quantities. The related complex (OC)5W(Mes*NPP)Nb(N[Np]Ar)3, 1-W(CO)5, was used to transfer the (P2)W(CO)5 unit in an analogous manner to the substrates 3-M (M = Mo, W, Nb) as well as to [(OC)5WP[triple bond]Nb(N[Np]Ar)3](-). The rate constants for the fragmentation of 1 and 1-W(CO)5 were unchanged in the presence of the terminal phosphide 3-Mo, supporting the hypothesis that molecular P2 and (P2)W(CO)5, respectively, are reactive intermediates. In a reaction related to the combination of P[triple bond]P and M[triple bond]P triple bonds, the phosphaalkyne AdC[triple bond]P (Ad = 1-adamantyl) was observed to react with 3-Mo to generate the cyclo-CP2 complex (AdCP2)Mo(N[(i)Pr]Ar)3. Reactions of the electrophiles Ph3SnCl, Mes*NPCl, and AdC(O)Cl with the anionic, nucleophilic complexes [(OC)5W(P3)Nb(N[Np]Ar)3](-) and [{(OC)5W}2(P3)Nb(N[Np]Ar)3](-) yielded coordinated eta(2)-triphosphirene ligands. The Mes*NPW(CO)5 group of one such product engages in a fluxional ring-migration process, according to NMR spectroscopic data. The structures of (OC)5W(P3)W(N[(i)Pr]Ar)3, [(Et2O)Na][{(OC)5W}2(P3)Nb(N[Np]Ar)3], (AdCP2)Mo(N[(i)Pr]Ar)3, (OC)5W(Ph3SnP3)Nb(N[Np]Ar)3, Mes*NP(W(CO)5)P3Nb(N[Np]Ar)3, and {(OC)5W}2AdC(O)P3Nb(N[Np]Ar)3, as determined by X-ray crystallography, are discussed in detail. 相似文献