Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics,thrombin and thermolysin inhibitors

Summary A relative comparison of the binding properties of different drug molecules requires their mutual superposition with respect to various alignment criteria. In order to validate the results of different alignment methods, the crystallographically observed binding geometries of ligands in the pocket of a common protein receptor have been used. The alignment function in the program SEAL that calculates the mutual superposition of molecules has been optimized with respect to these references. Across the reference data set, alignments could be produced that show mean rms deviations of approximately 1 Å compared to the experimental situation. For structures with obvious skeletal similarities a multiple-flexible fit, linking common pharmacophoric groups by virtual springs, has been incorporated into the molecular mechanics program MOMO. In order to combine conformational searching with comparative alignments, the optimized SEAL approach has been applied to sets of conformers generated by MIMUMBA, a program for conformational analysis. Multiple-flexible fits have been calculated for inhibitors of ergosterol biosynthesis. Sets of different thrombin and thermolysin inhibitors have been conformationally analyzed and subsequently aligned by a combined MIMUMBA/SEAL approach. Since for these examples crystallographic data on their mutual alignment are available, an objective assessment of the computed results could be performed. Among the generated conformers, one geometry could be selected for the thrombin and thermolysin inhibitors that approached reasonably well the experimentally observed alignment.     

Synthese und Kristallstrukturen der Phosphanimin-Komplexe MCl2(Me3SiNPMe3)2 mit M = Zn und Co,und CoCl2(HNPMe3)2

Syntheses and Crystal Structures of the Phosphaneimine Complexes MCl₂(Me₃SiNPMe₃)₂ with M = Zn and Co, and CoCl₂(HNPMe₃)₂ The molecular complexes MCl₂(Me₃SiNPMe₃)₂ (M = Zn, Co) have been prepared by the reaction of the dichlorides of zinc and cobalt with Me₃SiNPMe₃ in CH₃CN and CH₂Cl₂, respectively, whereas the complex CoCl₂(HNPMe₃)₂ has been prepared by the reaction of CoCl₂ with NaF in boiling acetonitrile in the presence of Me₃SiNPMe₃. All complexes were characterized by IR spectroscopy and by crystal structure determinations. The complexes MCl₂(Me₃SiNPMe₃)₂ crystallize isotypically. ZnCl₂(Me₃SiNPMe₃)₂: Space group P2₁2₁2₁, Z = 4, 2677 observed unique reflections, R = 0.024. Lattice dimensions at ?70°C: a = 1243.6; b = 1319.0; c = 1464.7 pm. CoCl₂(Me₃SiNPMe₃)₂: Space group P2₁2₁2₁, Z = 4, 3963 observed unique reflections, R = 0,071. Lattice dimensions at ?80°C: a = 1236.3; b = 1317.4; c = 1457.6 pm. CoCl₂(HNPMe₃)₂ · CH₂Cl₂: Space group Pbca, Z = 8, 1354 observed unique reflections, R = 0.055. Lattice dimensions at ?80°C: a = 1247.3; b = 998.4; c = 2882.4 pm. All complexes have monomeric molecular structures, in which the metal atoms are coordinated in a distorted tetrahedral fashion by the two chlorine atoms and by the nitrogen atoms of the phosphaneimine molecules.     

取代基对α-氨基乙腈热解反应影响的研究

用MINDO/3方法洋细研究了取代基对α-氨基乙腈热消除反应的影响. 研究表明, 对于孤立分子的气相反应, 给电子基使活化势垒降低, 吸电子基使活化势垒上升; 而对OH~-催化下的反应, 给电子基和吸电子基均使活化势垒上升.     

Comparison of pre-reducing agents for antimony determination by hydride generation atomic fluorescence spectrometry

A systematic study of antimony reduction prior to its determination by hydride generation atomic fluorescence spectrometry (HG-AFS) was carried out. The efficiency of l-cysteine, potassium iodide and potassium iodide/ascorbic acid was studied for this purpose. The hydride generation step was optimised in the presence of those pre-reductors. From the results, l-cysteine was found to be the most suitable pre-reducing agent. Methodology was validated, obtaining detection limits lower than 90 ng l⁻¹ and repeatability and reproducibility better than 3% R.S.D. and 5% R.S.D., respectively, in all cases. In order to evaluate the methodology developed and the influence of the matrix, recovery from waters from different sources was tested by HG-AFS and also by inductively coupled plasma mass spectrometry (ICP-MS). Accuracy was assessed by analysing three water reference materials at different antimony concentration levels. The high sensitivity of the developed methodology enables it to be applied for monitoring drinking waters according to the maximum admissible concentration of antimony established by the EU Directives.     

Tricarbonyl complexes of rhenium(I) and technetium(I) with thiourea derivatives

fac-[M(CO)₃X₃]²⁻ complexes (M=Re, X=Br; M=Tc, X=Cl) react with thiourea derivatives under formation of stable rhenium(I) and technetium(I) complexes. The composition of the products can be controlled by the steric requirements of the ligands and their ability to form chelates.The products of reactions with tetramethylthiourea, Me₄tu (I), N,N-diethylthiocarbamoylbenzamidine, H₂Et₂tcb (II), and morpholinylthiocarbamoylbenzamidine, H₂morphtcb (III), have been studied by X-ray crystallography showing that the products belong to three different structural types. A mononuclear complex of the composition fac-[Re(CO)₃Br(Me₄tu)₂] has been isolated with tetramethylthiourea, whereas the thiocarbamoylbenzamidines deprotonate and act as N,S-chelating ligands. This results in the formation of a dimeric [Tc(CO)₃(HEt₂tcb-N,S)]₂ complex with a central, almost square Tc₂S₂ unit and a monomeric compound of the composition [Tc(CO)₃(Hmorphtcb-N,S)(H₂morphtcb-S)]. The latter compound contains a neutral, S-bonded morpholinylthiocarbamoylbenzamidine in the unusual imine form in addition to a chelate-bonded Hmorphtcb⁻ ligand.     

Synthesis, band structure, and optical properties of Ba2ZnV2O8

A novel compound Ba₂ZnV₂O₈ has been synthesized in high temperature solution reaction and its crystal structure has been characterized by means of single crystal X-ray diffraction analysis. It crystallizes in monoclinic system and belongs to space group P2₁/c with a=7.9050(16), b=16.149(3), , β=90.49(3). It builds up from 1-D branchy chains of [ZnV₂O₈⁴⁻]_∞, and the Ba²⁺ cations are located in the space among these chains. The IR spectrum, ultraviolet-visible diffuse reflection integral spectrum and fluorescent spectra of this compound have been investigated. The calculated results of energy band structure by the density functional theory method show that the solid-state compound of Ba₂ZnV₂O₈ is an insulator with direct band gap of 3.48 eV. The calculated total and partial density of states indicate that the top valence bands are contributions from the mixings of O-2p, V-3d, and Zn-3d states and low conduction bands mostly originate from unoccupied antibonding states between the V-3d and O-2p states. The V-O bonds are mostly covalence characters and Zn-O bonds are mostly ionic interactions, and the ionic interaction strength is stronger between the Ba-O than between the Zn-O. The refractive index of n_x, n_y, and n_z is estimated to be 1.7453, 1.7469, and 1.7126, respectively, at wavelength of 1060 nm for Ba₂ZnV₂O₈ crystal.     

Enzymatic synthesis of optically active α-chloro-δ-hydroxy-β-ketoalkanephosphonates and reactions thereof

A novel and enzymatic approach to α-chloro-δ-hydroxy-β-ketoalkanephosphonates was developed via enantioselective CALB-catalyzed acetylation and CRL-catalyzed hydrolysis. The resultant optically active compounds provide, via Horner-Wadsworth-Emmons (HWE) reaction, chiral α,β-unsaturated ketones that are building block with potential application in organic synthesis.     

Asymmetric 1,4-addition of alkenylzirconium reagents to α,β-unsaturated ketones catalyzed by chiral rhodium complexes

Highly enantioselective 1,4-addition of alkenylzirconocene chlorides to α,β-enones was found to be catalyzed by a chiral rhodium complex generated from [Rh(cod)(MeCN)₂]BF₄ and (S)-BINAP. The reaction can be applied to either cyclic or acyclic enones and the optical yield was up to 99% ee. The reaction mechanism would involve the transmetalation between the alkenylzirconocene chloride and the rhodium complex to give the alkenylrhodium species as a key intermediate.     

Trace elemental determination in alcohol automotive fuel by electrothermal atomic absorption spectrometry

Suitable analytical methodologies were developed allowing direct determination of As, Cu, Fe, Pb, Sb and Sn in alcohol fuel samples by electrothermal atomic absorption spectrometry. Different chemical modification approaches were tested and compared in terms of analytical performance and in practical terms. Experimental conditions were optimized allowing little sample dilution and use of calibration curves prepared with aqueous inorganic analyte standards. Methodologies were tested with analyte spiked alcohol samples. Good analyte recoveries from spiked alcohol samples, precision better than 10% and limits of detection in the sub μg l⁻¹ range were achieved.     

Anomalies in the Structural Chemistry of Silicon

In contrast to carbon, silicon fails to form multiple bonds that are stable at room temperature. Consequently molecules in which silicon exhibits coordination numbers (CN) of 1, 2, and 3 may only be obtained at very high or low temperatures. Under these conditions their structural features, including multiple bonds, resemble those of carbon. On the other hand, silicon is capable of forming various hexacoordinated compounds making use of its d orbitals. Nitrogen and oxygen bonded to silicon develop an unusual stereochemistry: planar nitrogen, nearly or completely linear oxygen, and considerable shortening of SiN, SiO, and SiF bonds are specific examples. N(SiR₃)₂ and CH₂SiR₃ ligands permit stabilization of unusually low CNs of many metals and give rise to amino and alkyl derivatives of unexpectedly high stability due to the particular electronic, the R₃Si group.