Lead hopping using SVM and 3D pharmacophore fingerprints

The combination of 3D pharmacophore fingerprints and the support vector machine classification algorithm has been used to generate robust models that are able to classify compounds as active or inactive in a number of G-protein-coupled receptor assays. The models have been tested against progressively more challenging validation sets where steps are taken to ensure that compounds in the validation set are chemically and structurally distinct from the training set. In the most challenging example, we simulate a lead-hopping experiment by excluding an entire class of compounds (defined by a core substructure) from the training set. The left-out active compounds comprised approximately 40% of the actives. The model trained on the remaining compounds is able to recall 75% of the actives from the "new" lead series while correctly classifying >99% of the 5000 inactives included in the validation set.     

Theory of the two step enantiomeric purification of 1,3 dimethylallene

An application of a recently proposed [P. Kral et al., Phys. Rev. Lett. 90, 033001 (2003)] two step optical control scenario to the purification of a racemic mixture of 1,3 dimethylallene is presented. Both steps combine adiabatic and diabatic passage phenomena. In the first step, three laser pulses of mutually perpendicular linear polarizations, applied in a "cyclic adiabatic passage" scheme, are shown to be able to distinguish between the L and D enantiomers due to their difference in matter-radiation phase. In the second step, which immediately follows the first, a sequence of pulses is used to convert one enantiomer to its mirror-imaged form. This scenario, which only negligibly populates the first excited electronic state, proves extremely useful for systems such as dimethylallene, which can suffer losses from dissociation and internal conversion upon electronic excitation. We computationally observe conversion of a racemic mixture of dimethylallene to a sample containing approximately 95% of the enantiomer of choice.     

Versatile reactions of a para-bromophenylacetylide iron(II) derivative and X-ray structure of the fluoro analogue. Synthesis of new redox-active organoiron(II) synthons

The synthesis of the new (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,3-(C₆H₄X) (m-2a/2b; X=F/Br) and (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,4-(C₆H₄I) (2c) complexes, as well as the solid-state structure of the known (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,4-(C₆H₄F) (2a) complex are described. The catalytic coupling reactions of the bromo complexes with various alkynes were next investigated. Starting from the known (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,4-(C₆H₄Br) complex (2b), the synthesis of the (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,4-(C₆H₄)---CC---H complex (6d) and of the corresponding silyl-protected precursors (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,4-(C₆H₄)CC---SiR₃ (6b/6c; R=ⁱPr/Me) are reported. By use of lithium---bromine exchange reactions on 2b, the silyl- (7a; E=Si; R=Me) and tin- (7b–7d; E=Sn; R=Me, Bu, Ph) substituted analogues (η²-dppe)(η⁵-C₅Me₅)Fe---CC---1,4-(C₆H₄)ER₃ are also isolated. The spectroscopic and electrochemical characterisations of all these new Fe(II)/Fe(III) redox-active building blocks are presented and the electronic substituent parameters for the “(η²-dppe)(η⁵-C₅Me₅)Fe---CC” group are determined by means of ¹⁹F-NMR.     

Determination of ochratoxin A in currants, raisins, sultanas, mixed dried fruit, and dried figs by immunoaffinity column cleanup with liquid chromatography: interlaboratory study

An interlaboratory study was performed on behalf of the Food Standards Agency to evaluate the effectiveness of an affinity column cleanup liquid chromatographic (LC) method for the determination of ochratoxin A in a variety of dried fruit at European regulatory limits. To ensure homogeneity before analysis, laboratory samples are normally slurried with water in the ratio of 5 parts fruit to 4 parts water, and test materials in this form were used in the study. The test portion was extracted with acidified methanol. The extract was filtered, diluted with phosphate-buffered saline, and applied to an affinity column. The column was washed and ochratoxin A was eluted with methanol. Ochratoxin A was quantified by reversed-phase LC. The use of post-column pH shift to enhance the fluorescence of ochratoxin A by the addition of 1.1 M ammonia solution to the column eluant is optional. Determination was by fluorescence. Currants, sultanas, raisins, figs, and mixed fruit (comprising dried pineapple, papaya, sultanas, prunes, dates, and banana chips), both naturally contaminated and blank (very low level), were sent to 24 collaborators in 7 European countries. Participants were asked to spike test portions of all test samples at a level equivalent to 5 ng/g ochratoxin A. Average recoveries ranged from 69 to 74%. Based on results for 5 naturally contaminated test samples (blind duplicates) the relative standard deviation for repeatability (RSDr) ranged from 4.9 to 8.7%, and the relative standard deviation for reproducibility (RSDR) ranged from 14 to 28%. The method showed acceptable within- and between-laboratory precision for all 5 matrixes, as evidenced by HORRAT values <1.3.     

Controlled structural variations in templated uranium sulfates

A series of experiments in the UO(2)(CH(3)CO(2))(2).2H(2)O/H(2)SO(4)/1-(2-aminoethyl)piperazine/H(2)O system were conducted to determine the effects of variation in initial reactant concentrations on the reaction products. Several reaction gels were produced, in which the composition varied from 16:80:4:500 UO(2)(CH(3)CO(2))(2).2H(2)O/H(2)SO(4)/1-(2-aminoethyl)piperazine/H(2)O to 4:92:4:500 UO(2)(CH(3)CO(2))(2).2H(2)O/H(2)SO(4)/1-(2-aminoethyl)piperazine/H(2)O. Single crystals of two new organically templated uranium sulfates, [N(3)C(6)H(18)](2)[(UO(2))(5)(H(2)O)(SO(4))(8)].5H(2)O and [N(3)C(6)H(18)][(UO(2))(2)(H(2)O)(SO(4))(3)(HSO(4))].4.5H(2)O, were isolated. Both compounds exhibit structures in which the inorganic frameworks are two-dimensional and the protonated amines reside between layers, participating in extensive hydrogen bonding. The composition and structure of each compound is dependent on the nature of the starting concentrations. Crystal data: for [N(3)C(6)H(18)](2)[(UO(2))(5)(H(2)O)(SO(4))(8)].5H(2)O, monoclinic, space group P2(1)/n (No. 14), a = 21.5597(3) A, b = 10.2901(2) A, c = 22.8403(3) A, beta = 96.7436(7) degrees, and Z = 4; for [N(3)C(6)H(18)][(UO(2))(2)(H(2)O)(SO(4))(3)(HSO(4))].4.5H(2)O, monoclinic, space group P2(1)/a (No. 14), a = 15.7673(4) A, b = 10.5813(3) A, c = 16.7710(5) A, beta = 99.9216(9) degrees, and Z = 4.     

Synthesis of a Tetracyclo [4.4.0.02,4.03,8]decanone via Intramolecular Reductive Coupling

The reduction of cis-4 a-methyl-1,2,4a,7,8,8 a-hexahydronaphthalene-2,7-dione ( 1 ) was studied by cyclic voltammetry and product analysis. On a preparative scale, 6-hydroxy-3-methyltetracyclo[4.4.0.0^2,4.0^3,8]decan-10-one ( 2 ) was obtained in 22% yield via an intramolecular hydrodimerization/aldol reaction sequence. The CV. results (Hg, DMF) suggest that the cyclopropane ring is formed after the first electron transfer by coupling of the anion radical with the second C. C-double bond.     

Elektronische effekte in cyclopentadienyl-chrom-komplexen,die mehrere akzeptorliganden enthalten

The coordinative properties of the acceptor ligand CS are discussed on the basis of the new thiocarbonyl complexes CpCr(CO)(CS)(NO) (I), [CpCr(CS)(NO)₂]PF₆ (II), CpCr(CS)(L)(NO) (L = pyridine (III) or trimethylphosphane (IV) and related carbonyl complexes. The IR and NMR spectra (¹H, ¹³C, ³¹P) of the complexes indicate ligand—ligand interactions between CS and both the nitrosyl group and the cyclopentadienyl ring. An attempt is made to compare CS with other sulphur-containing acceptor ligands such as NS (in CpCr(CO)₂(NS)) and CS₂ (in CpCr(CS₂)(PMe₃)(NO)).     

Expedient protocol for solid-phase synthesis of secondary and tertiary amines

[reaction: see text] An expedient solid-phase synthetic approach to secondary and tertiary amines was developed. The protocol employs conversion of resin-bound amino alcohols to the corresponding iodides, followed by iodide displacement with primary or secondary amines or with unprotected amino alcohols. This two-step procedure, affording products in good to excellent yields, is suitable for solid-phase synthesis of polyamines.     

Electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry in the electron energy range 0-50 eV

Electron capture dissociation (ECD) of polypeptide cations was obtained with pencil and hollow electron beams for both sidekick and gas-assisted dynamic ion trapping (GADT) using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with an electrostatic ion transfer line. Increasing the number of trapped ions by multiple ICR trap loads using GADT improved the ECD sensitivity in comparison with sidekick ion trapping and ECD efficiency in comparison with single ion trap load by GADT. Furthermore, enhanced sensitivity made it possible to observe ECD in a wide range of electron energies (0-50 eV). The degree, rate and fragmentation characteristics of ECD FTICR-MS were investigated as functions of electron energy, electron irradiation time, electron flux and ion trapping parameters for this broad energy range. The results obtained show that the rate of ECD is higher for more energetic (>1 eV) electrons. Long electron irradiation time with energetic electrons reduces average fragment ion mass and decreases efficiency of formation of c- and z-type ions. The obtained dependencies suggest that the average fragment ion mass and the ECD efficiency are functions of the total fluence of the electron beam (electron energy multiplied by irradiation time). The measured electron energy distributions in low-energy ECD and hot ECD regimes are about 1 eV at full width half maximum in employed experimental configurations.     

Synthesis of the C1-side chain of zaragozic acid D and progress towards a total synthesis

A synthesis of a 1,3-dithiane corresponding to the C1-side chain of zaragozic acid D is described. An aldol reaction using an Evans oxazolidinone is the key step in controlling stereochemistry. Metallation of the derived dithiane monosulfoxide and coupling to an aldehyde effected construction of the C1-C7 bond. Subsequent steps are also reported, including acid-mediated ketalization resulting in formation of an advanced synthetic intermediate containing the bicyclic ketal core of the natural product.