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.     

Aggregate, Polymer and Cluster Formation from Metal-Imino Carboxylate Complexes

Reaction of tris-(2-aminoethyl)amine (tren) andthe sodium salt of an -ketocarboxylic acid, typically sodium pyruvate, affordsin the presence of a lanthanide ion aseries of complexes and aggregates includingmononuclear, cyclic tetranuclear and polymerspecies of [L¹]^3- ([L¹]^3-=N[CH₂CH₂N=C(CH₃)COO^-]³).The aggregation of these and related d-block elementcomplexes with Na⁺ ions leadsto the formation of polymeric materials, and thefactors influencing the formation and controlof these various aggregation states are discussed.Metal cations also template the aggregationof the fragment [Ni(L²)] ([L²]^2- =CH₂[CH₂N = C(CH₃)COO^-]₂)to give, in high yield, the polynuclearaggregates {[Ni(L²)]₆M}^x+(M = Nd, Pr, Ce, La, x = 3; M = Sr, Ba, x = 2). The structures of{[Ni(L²)]₆M}^x+ show aninterstitial twelve co-ordinate, icosahedralcation M^x+ encapsulated by six [Ni(L²)]fragments. In the presence ofNa⁺, aggregation of [Ni(L²)] fragments affords {[Ni(L²)]₉Na₄(H₂O)(MeOH)(ClO₄)}³⁺ thestructure of whichshows four Na⁺ ions templating the formation ofa distorted tricapped trigonal prismatic[Ni(L²)]₉ cage. Thus, control overconstruction of various polynuclear cages viaself-assembly at octahedral junctions can beachieved using main group, transition metaland lanthanide ion templates.     

Beiträge zur Chemie der Alkylverbindungen von Übergangsmetallen. 59. Cyclopentadienyl-2-(dimethylaminomethyl)ferrocenyl-Verbindungen elektronenarmer 3 d-Elemente

Contributions to the Chemistry of Transition Metal Alkyl Compounds. 59. Cyclopentadienyl-2-(dimethylaminomethyl)ferrocenyl Compounds of Early 3 d-Elements Compounds of the type (C₅H₅)₂M(FcN) (M = Sc ( 1 ), Ti ( 2 ), V ( 3 ), Cr ( 4 ); FcN = 2-dimethylaminomethyl)ferrocenyl group), and (C₅H₅)M(FcN)₂ (M = Ti ( 5 ), Cr ( 6 ) were synthesized and investigated. A detailled characterization with respect to the existence of chelate structures was realized by the uv-vis, ¹H-n.m.r. spectroscopic measurements and determination of magnetic moments.     

镍基催化剂上硫醇与异戊二烯硫醚化反应的研究

在上流式气-液-固三相固定床微型反应装置上，对Ni／Al2O3催化剂上硫醇与异戊二烯硫醚化反应进行了研究，并考察了反应温度、压力、空速、临氢条件对催化剂二烯硫醚化反应性能的影响。结果表明，异戊二烯与硫醇在镍基催化剂的作用下，可以发生反应生成高沸点的硫醚化合物，反应温度和空速对催化剂二烯硫醚化活性有明显的影响，提高反应温度和降低空速有利于提高硫醇在二烯硫醚化反应过程中的转化率，在临氢反应条下，可以提高催化剂二烯硫醚化反应的活性和稳定性。     

N-取代苯甲酰基-N'-取代芳基硫脲的合成、晶体结构及生物活性

为了寻找新的高活性农药, 利用工业易得的三氟羧草醚及其中间体为起始原料, 设计合成了9个未见报道的N-取代苯甲酰基-N'-取代芳基硫脲化合物, 结构经IR, ¹H NMR, 元素分析确认. X射线衍射测定了化合物4b的晶体结构, 结果表明: 其分子属于三斜晶系, 空间群P-1, a＝0.51588(19) nm, b＝1.0766(4) nm, c＝2.0596(8) nm, α＝81.113(6)°, β＝89.702(6)°, γ＝78.131(6)°, V＝1.1056(7) nm³, D_c＝1.445 Mg/m³, Z＝2, F(000)＝492, μ＝0.319 mm^－1. 初步生物活性测试结果表明, 部分化合物具有较好的除草活性.     

纳米二氧化锆在甲醇合成催化剂Cu/Ga2O3/ZrO2中的作用

The introduction of mesoporous nanosize zirconia to the catalyst for methanol synthesis dedicates the nanosized catalyst and mesoporous duplicated properties. The catalyst bears the larger surface area, larger mesoporous volume and more uniform diameter, more surface metal atoms and oxygen vacancies than the catalyst prepared with the conventional coprecipitation method. The modification of microstructure and electronic effect could result in the change of the reduced chemical state and decrease of reducuction temperature of copper, donating the higher activity and methanol selectivity to the catalyst. The results of methanol synthesis demonstrate that the Cu^＋ is the optimum active site. Also, the interaction between the copper and zirconia shows the synergistic effect to fulfil the methanol synthesis.     

苯并噻二嗪衍生物电子结构和非线性光学性质的研究

运用量子化学PM3方法，对苯并噻二嗪几种衍生物的几何构型、电子结构和前线分子轨道成分进行了分析，研究了电荷分布规律。同时，基于体系中电子转移的特点，利用有限场FF方法探讨了其非线性光学性质的变化。结果表明，苯并噻二嗪分子具有较好的二阶非线性光学性质，并可能成为一类良好的光学材料。     

An improved nicotinic pharmacophore and a stereoselective CoMFA-model for nicotinic agonists acting at the central nicotinic acetylcholine receptors labelled by [3H]-N-methylcarbamylcholine

A study of a series of compounds with agonistic effect at the alpha4beta2 nicotinic acetylcholine receptors resulted in an improved pharmacophore model as well as a CoMFA model. The pharmacophore was composed of three pharmacophoric elements: (1) a site point (a) corresponding to a protonated nitrogen atom, (2) a site point (b) corresponding to an electronegative atom capable of forming a hydrogen bond, and (3) the centre of a heteroaromatic ring or a C=O bond (c). The pharmacophoric elements were related by the following parameters: (a-b) 7.3-8.0 A, (a-c) 6.5-7.4 A, and the angle between the two distance vectors (delta bac) 30.4-35.8 degrees. In addition to this, a stereoselective CoMFA model was developed, which showed good predictability even for compound classes not present in the training set.     

A density functional theory study of the gas-phase elimination reactions of 4-arylideneimino-1,2,4-triazol-3(2H )-ones and their 3(2H )-thione analogues

Theoretical studies on the thermolysis in the gas phase of 4-arylideneimino-1,2,4-triazol-3(2H)-ones and 4-arylideneimino-1,2,4-triazol-3(2H)-thiones were carried out using density functional theory methods, at the B3LYP/6-31G(d) and B3LYP/6-311+G(2d,p) levels of theory. The proposed reaction mechanism occurs in one step, leading to the formation of 3-hydroxy-(2H)-1,2,4-triazole or 3-mercapto-(2H)-1,2,4-triazole and a 4-substituted benzonitrile, via a six-membered cyclic transition state. The progress of the reactions was followed by means of the Wiberg bond indices. The results indicate that the transition states have character intermediate between reactants and products, and the calculated synchronicities show that the reactions are slightly asynchronous, in the case of triazolones, and show a higher asynchronicity in the case of triazolthiones. The bond-breaking processes are slightly more advanced than the bond-forming ones, indicating a small bond deficiency in the transition states. Kinetic and activation parameters for the reactions studied have been calculated and compared with available experimental data.From the Proceedings of the 28th Congreso deQuímicos Teóricos de Expresión Latina (QUITEL 2002)     

First synthesis of an α-d-Fucp3NAc containing oligosaccharide: a study on d-Fucp3NAc glycosylation

3-Acetamido-3,6-dideoxy-d-galactopyranose (d-Fucp3NAc) is an aminosugar almost exclusively found in phytopathogenic O-antigens. The glycosylation reaction involving d-Fucp3NAc donors was studied with several rhamnosyl acceptors, revealing that the best yields and highest α-stereoselectivity were obtainable by coupling a N-phenyl trifluoroacetimidate glycosyl donor in a ternary mixture (dioxane/DME/toluene 4:1:1) as solvent. For the first time a synthetic access to α-d-Fucp3NAc containing oligorhamnans, that are interesting molecules for studying the effects of O-antigen model oligosaccharides on the modulation of plant response to bacteria, was reported. An example is the pentasaccharide repeating unit of the major O-antigen component from Pseudomonas syringae pv. holci IMV 8300, which was synthesized as its methyl glycoside.