OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

The biosynthesis of quadrone and terrecyclic acid

Feedings of [1-¹³C]- and [1,2-¹³C₂]acetate Aspergillus terreus gave quadrone and terrecyclic acid which were analyzed by ¹³C NMR. The pattern of ¹³C-enrichments and couplings is consistent with the formation of 1 and 2 by cyclization of farnesyl pyrophosphate.     

Use of U-shaped donor-bridge-acceptor molecules to study electron tunneling through nonbonded contacts

A systematic determination of electronic coupling matrix elements in U-shaped molecules is demonstrated. The unique architecture of these systems allows for the determination of the electronic coupling through a pendant molecular moiety that resides between the donor and acceptor groups; this moiety quantifies the efficiency of electron tunneling through nonbonded contacts. Experimental electron-transfer rate constants and reaction free energies are used to calibrate a molecular-based model that describes the solvation energy. This approach makes it possible to experimentally determine electronic couplings and compare them with computational values.     

Synthesis of the β-lactam antibiotic (+)- thienamycin via an intermediate π-allyltricarbonyliron lactone complex

The π-allyltricarbonyliron lactone complex (7), formed by reaction of E-1,2-epoxy-2-methyl-6,6-dimethoxyhex-3-ene(5) with co-ordinatively unsaturated iron carbonyl species, was reacted with benzylamine to give a lactam complex (8) by an S_N'-like mechanism. This complex upon oxidation with Ce(IV) afforded cis-3-isopropenyl-4-[(2',2'-dim (9) which was chemically modified into trans-3-(1'-hydroxyethyl)-4-[(2',2-dimethoxy)ethyl] azetidin-2-one (13), a key intermediate previously used in the synthesis of the antibiotic thienamycin. Similar reaction with (S)-(-)--methylbenzylamine afforded a separable mixture of diastereoisomeric iron lactam complexes (16 and 17). These complexes could be individually converted to the corresponding optically active β-lactam derivatives (27 and 28) and, hence, are precursors for the synthesis of either natural (+)-thienamycin or unnatural (-)-thienamycin.     

The infrared spectra (600-140 cm−1 of the imidazole,pyrazine and pyrimidine adducts of cobalt(II), nickel(II) and zinc(II) acetylacetonates

Summary The complexes M(acac)₂(imidazole)₂ (M = Co or NO and [M(acac)₂B]_n (M = Co, Ni or Zn; B = pyrazine or pyrimidine) have been prepared and their i.r. spectra determined over the 600–140 cm^–1. range. The metal-oxygen and metal-nitrogen stretching frequencies, (M-O) and v(M-N), are assigned on the basis of the band shifts induced by deuteriation of the adducted base and by substitution of the metal ion. Three or fourv(M-O) bands are observed within the 600-200 cm^–1 range. The twov(M-O) bands of higher frequency are considered to the coupled with internal ligand modes. TwovM-N) bands are observed within the 280–170 cm^–1. range. The metal-ligand stretching frequencies are in good agreement with the values previously established for these vibrations in the [M(imidazole)₆]²⁺ and Ni(acac)₂(pyridine)₂ complexes.     

Vibrational population distribution of ground state BaO formed by the reaction Ba + O2

The vibrational population distribution of X ¹Σ(υ′' = 0 through ν′' = 7) BaO formed in the reaction Ba + O₂ at 0.3 torr has been measured by laser induced photoluminescence intensities. On the basis of the assumed similarity between the Ba + O₂ and Ba + N₂O reactions, these data suggest that a population inversion may exist between A ¹Σ(ν′ = 1) and X ¹Σ(υⁿ = 7) BaO formed in the latter reaction at ≈ 16 torr.     

Muonium chemistry: kinetics of the gas phase reaction Mu + F2 → MuF + F from 300 to 400 K

The MSR (muonium spin rotation) technique was used to measure the chemical reaction rate for Mu + F₂ → MuF + F in N₂ moderator at ≈ 1 atm from 295 to 383 K giving the Arrhenius expression: log₁₀k (?/mole s) = (10.83 ± 0.20) - (200 ± 50)/T, with k = (1.46 ± 0.11) × 10¹⁰ ?/mole s at 300 K. This is at least 6.8 times the room temperature rate constant for the analogous H atom reaction. The measured activation energy and enhancement over the H reaction rate are indicative of significant tunnelling in the Mu reaction, in agreement with the recent collinear quantum mechanical calculations of Connor et al.     

Multi-residue method for rapid screening and confirmation of pesticides in crude extracts of fruits and vegetables using isocratic liquid chromatography with electrospray tandem mass spectrometry

A LC-MS-MS method capable of the quantitative determination of a range of pesticide residues present in crude extracts from a variety of fruit and vegetables has been developed. Isocratic LC conditions have been used in conjunction with electrospray ionisation tandem mass spectrometry to detect and identify up to 38 pesticides presented as various mixtures in different matrices. The utility of the method is demonstrated by the analysis of crude extracts, with no sample clean up, from grape, kiwi fruit, strawberry, spinach, lemon, peach and nectarine. Mean recoveries ranging from 63 to 96% with relative standard deviations < 20% were obtained for 30 of the 38 pesticides following analysis of organic produce fortified at concentrations between 0.01 and 0.8 mg/kg. Detected residues were quantified from interpolation against calibration data generated using matrix-matched standards that covered analyte concentration ranges between 0.005 and 0.8 microg/ml. Conditions suitable for the qualitative and quantitative confirmation of residues detected in samples are specified.     

Phosphorescence of thermally oxidised poly(butadiene) and model enones: temperature dependence

The temperature dependence of phosphorescence of model enone compounds in poly (methyl methacrylate) matrix and glassy methylcyclohexane/isopentane solution and of enones formed from thermal oxidation of poly (butadiene) has been studied over the temperature range 77–220°K. The single discontinuity in the plot for the model enone-glassy solvent is due to the freezing of a (solvent perturbed) barrier to rotation in the enone, and an analogous transition is also observed in the model enone poly (methyl methacrylate) samples and in thermally oxidised poly (butadiene). In the polymer matrices, a second transition corresponding to the γ-transition in poly (methyl methacrylate) and the glass transition temperature T_g in poly (butadiene) are also revealed in the Arrhenius plots. The results demonstrate that care must be taken in ascribing such discontinuities solely to polymer properties since intrinsic properties of the luminescence probe itself may exhibit similar features.