Calculating the knowledge-based similarity of functional groups using crystallographic data

A knowledge-based method for calculating the similarity of functional groups is described and validated. The method is based on experimental information derived from small molecule crystal structures. These data are used in the form of scatterplots that show the likelihood of a non-bonded interaction being formed between functional group A (the `central group') and functional group B (the `contact group' or `probe'). The scatterplots are converted into three-dimensional maps that show the propensity of the probe at different positions around the central group. Here we describe how to calculate the similarity of a pair of central groups based on these maps. The similarity method is validated using bioisosteric functional group pairs identified in the Bioster database and Relibase. The Bioster database is a critical compilation of thousands of bioisosteric molecule pairs, including drugs, enzyme inhibitors and agrochemicals. Relibase is an object-oriented database containing structural data about protein-ligand interactions. The distributions of the similarities of the bioisosteric functional group pairs are compared with similarities for all the possible pairs in IsoStar, and are found to be significantly different. Enrichment factors are also calculated showing the similarity method is statistically significantly better than random in predicting bioisosteric functional group pairs.     

Über die Temperaturabhängigkeit der 13C-NMR.-Spektren von Tetracarbonyl (η-(Z)-cycloocten)eisen und (Z)-cycloocten

On the Temperature Dependence of the ¹³C-NMR.-Spectra of Tetracarbonyl (η-( Z )-cyclooctene)iron and of ( Z )-Cyclooctene Reaction of (Z)-cyclooctene (1) with Fe₂(CO)₉ in pentane at 0° yielded tetracarbonyl(η-(Z)-cyclooctene)iron (2) as a yellow oil which can be stored over a longer period only at ?78°. It is shown that the title compounds ( 1 and 2 , respectively) are fluxional. The activation parameters for the conformational C-atom site exchange of (Z)-cyclooctene (1) and tetracarbonyl (η-(Z)-cyclooctene)iron (2) (in CCl₂F₂) have been determined between 113 K and 151 K for 1 and between 151 K and 205 K for 2 , respectively, by a complete line shape analysis of the temperature dependent proton noise-decoupled ¹³C-NMR. signals of the olefinic C-atom. The kinetic data and activation parameters are given in Tables 1 and 2.     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

(Z)-1-[2-(Triarylstannyl)vinyl]-1-cycloheptanols: Synthesis, characterization, halodemetallation and crystal structures

The synthesis and characterization by ¹H, ¹³C, ¹¹⁹Sn NMR and ¹¹⁹Sn Mössbauer spectroscopy of (Z)-1-[2-(triphenylstannyl)vinyl]-1-cycloheptanol,

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(1), and (Z)-1-[2-tri-p-tolylstannyl)vinyl-1-cycloheptanol,

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(2), are described, together with their halodemetallation by I₂, Br₂ and ICIl to yield derivatives of the types

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(Ar = phenyl or p-tolyl, N = 1, 2; X = I, Br, Cl, respectively). The solid-state structures of four compounds have been determined by X-ray diffraction analysis. In the crystals of

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(1) and

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(2) the Sn atom has a tetrahedral geometry distorted towards trigonal bipyramid as a consequence of a close intramolecular contact with the hydroxyl O(1) atom of 2.742(3) Å and 2.768(3) Å, respectively. A trigonal bipyramidal geometry is found in

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(12) and

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(4), in which significant Sn---O(1) interactions are noted [2.437(8) Å and 2.407(8) Å, respectively].     

Tensor products of contexts and complete lattices

Although the categoryCLC of complete lattices and complete homomorphisms does not possess arbitrary coproducts, we show that the tensor product introduced by Wille has the universal property of coproducts for so-called distributing families of morphisms (and only for these). As every family of morphisms into a completely distributive lattice is distributing, this includes the known fact that in the category of completely distributive lattices, arbitrary coproducts exist and coincide with the tensor products. Since the definition of tensor products is based on the notion of contexts and their concept lattices, many results on tensor products extend from complete lattices to contexts. Thus we introduce two kinds of tensor products for arbitrary families of contexts, a partial and a complete one, and establish universal properties of these tensor products.Presented by B. Jonsson.     

Hyperfine interactions in icosahedral quasicrystals: a Mössbauer study

Icosahedral Al₆₅Cu₂₀Fe₁₅ and Al₄₀Cu_9.9Ge₂₅Mn₂₅ ⁵⁷Fe_0.1 quasicrystals are studied using⁵⁷Fe transmission Mössbauer experiments. The spectra are analyzed by distributions of electric-quadrupole interaction accounting for line asymmetries. Temperature dependences of the hyperfine parameters derived comprising average values ofP() distributions, corresponding standard deviations and center shifts are presented in a whole range from 8 to 300 K.     

Local order of icosahedral quasicrystals studied by Mössbauer spectroscopy

Thermodynamically stable Al-Cu-Fe and Fe-doped ferromagnetic Al-Cu-Ge-Mn icosahedral quasicrystals are studied by⁵⁷Fe transmission Mössbauer spectroscopy and X-ray diffraction experiments. Al₆₅Cu₂₀Fe₁₅ quasicrystalline alloy was subjected to a mechanical grinding (MG) for up to 800 hours in a ball mill. Presence of the amorphous phase which co-exists with the quasicrystalline one is revealed in the early stage of MG. Mössbauer measurements were performed on icosahedral Al₄₀Cu_10–x Ge₂₅Mn₂₅Fe _x quasicrystal (x0.1; 3) in a temperature range from 10 K to 548 K. It was found that a magnetic transition occurs at about 30 K which is far belowT _c reported in the literature. It is concluded that AlGeMn ferromagnet which is present in the samples does not affect the magnetic transition observed and the transition is an intrinsic property of the Al-Cu-Ge-Mn host alloy.Samples of icosahedral quasicrystals were kindly provided by Profs. A. Inoue, T. Masumoto and P. H. Shingu. Ball milling was performed in Kyoto University by a courtesy of Prof. P. H. Shingu. This work was supported by the project for priority areas on properties of quasicrystals (No. 01630003) from the Japanese Ministry of Education, Science and Culture.     

Sur de nouvelles phases séléniées ternaires du molybdène

The synthesis and the crystal properties of new selenides of formula M_xMo₃Se₄ are described. If M = Zn, Ag, Cd, Sn and Pb, they are stoichiometric with x = 0.6; if M = Fe, Mn, Cr, V, Ti, triclinic solid solutions are observed with 0.5 < x < 0.7; if M = Cu, Co, Ni, rhombohedral solid solutions are obtained with 0 < x < 1.4 for M = Cu, 0 < x < 0.7 for M = Co and 0 < x < 0.8 for M = Ni All these phases can be deduced from the Mo₃Se₄ structure by introducing metal atoms into the tunnels between the “Mo₆Se₈” metal atom cluster configuration.     

Chemical and thermal stability of alkanethiol and sulfur passivated InP(100)

InP(100) surfaces treated with Na2Sx9H20 and CnH(2n+1)SH are examined by contact angle measurement, X-ray photoelectron spectroscopy, and atomic force microscopy to determine the chemical and thermal behavior of these passivated surfaces. The surfaces coated by octadecanethiol (n = 18) self-assembled monolayers (SAMs) are found to be more stable toward oxidation than the S-passivated surface. The chemical stability of octadecanethiol SAMs in various environments is examined. The thiol monolayer is found to be stable in 0.1 M HCl but degrades in 0.1 M NaOH, boiling chloroform, and water. The behavior of these surfaces at elevated temperatures under a vacuum is also investigated. The octadecanethiol-coated InP(100) is stable up to 473 K, above which the films begin to degrade. Unlike other substrates on which the entire molecule including the sulfur headgroup desorbs together, on InP, the sulfur headgroup remains on the surface even after annealing to 673 K. These observations suggest that the desorption occurs by S-C bond cleavage as well as In-S bond cleavage. The sulfur of S-passivated InP is found to be more thermally stable than that of the octadecanethiol monolayer, perhaps due to their different bonding geometries and hence energies.     

Some applications of silica aerogels

Silica aerogels are very highly divided materials which are synthesised through the association of a chemical step, the so-called sol–gel chemistry, with a physical step which is a particular way of drying the wet gel, namely under supercritical conditions with respect to the liquid phase filling its porosity. This drying process preserves the texture of the dry material: in practice it strongly reduces the pore collapse. The resulting hyperporous solids that have bulk densities of the same magnitude as air develop new and very interesting physical and even chemical properties. Owing to their poor chemical reactivity, very large surface areas (of the order of 1,000 m ²/g), unusual porous volumes (greater than 95%), morphologies (monoliths or powders), optical properties (transparent, opaque or translucent), and very low thermal conductivity, they find high added-value applications in the physics of high-energy particles (Cherenkov emitters), transparent and superinsulating double windows, life and space science as well.