Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

Six rigid-body parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are commonly used to describe the relative displacement and orientation of successive base pairs in a nucleic acid structure. The present work adapts this approach to describe the relative displacement and orientation of any two planes in an arbitrary molecule-specifically, planes which contain important pharmacophore elements. Relevant code from the 3DNA software package (Nucleic Acids Res. 2003, 31, 5108-5121) was generalized to treat molecular fragments other than DNA bases as input for the calculation of the corresponding rigid-body (or "planes") parameters. These parameters were used to construct feature vectors for a fuzzy relational clustering study of over 700 conformations of a flexible analogue of the dopamine reuptake inhibitor, GBR 12909. Several cluster validity measures were used to determine the optimal number of clusters. Translational (Shift, Slide, Rise) rather than rotational (Tilt, Roll, Twist) features dominate clustering based on planes that are relatively far apart, whereas both types of features are important to clustering when the pair of planes are close by. This approach was able to classify the data set of molecular conformations into groups and to identify representative conformers for use as template conformers in future Comparative Molecular Field Analysis studies of GBR 12909 analogues. The advantage of using the planes parameters, rather than the combination of atomic coordinates and angles between molecular planes used in our previous fuzzy relational clustering of the same data set (J. Chem. Inf. Model. 2005, 45, 610-623), is that the present clustering results are independent of molecular superposition and the technique is able to identify clusters in the molecule considered as a whole. This approach is easily generalizable to any two planes in any molecule.     

Transition Metal Complexes with Bidentate Ligands Spanning trans-Positions. VII. The preparation of the five-coordinate complexes [M(CO)3(1)] (M = Fe,Ru; (1) = 2,11-bis(diphenylphosphinomethyl)benzo[c]phenanthrene)

The five-coordinate mononuclear complexes [M(CO)₃( 1 )] (M = Fe, Ru; ( 1 ) = 2,11-bis(diphenylphosphinomethyl)benzo[c]phenanthrene) have been prepared and assigned trigonal bipyramidal structures with apical phosphorus atoms from IR. and NMR. data.     

Computational analysis of binding affinity and neural response at the l-alanine receptor

Summary A model of analogue-receptor binding is developed for the l-alanine receptor in the channel catfish using the AM1-SM2 and ab initio SCRF computational methods. Besides interactions involving the zwitterionic moiety of the amino acid analogue and complementary subsites on the receptor, the model suggests the presence of a hydrophobic pocket with dispersion interactions between the receptor and the residue on the amino acid analogue. Conformational analysis suggests not only a small compact active site on the receptor, but also that the analogues with the highest affinity occupy nearly identical regions of space. Although the binding interaction is dominated by the ionic terms, AM1-SM2 calculations indicate that free energy terms associated with cavity formation, solvent reorganization, and dispersion interactions can be correlated to activation and neural response. From a consideration of this model, molecular features of the analogues that are important for binding and neural response were deduced and other analogues or ligands were developed and tested.     

Book reviews

Please forward books for review to the Book Review Editor: Magdolna Hargittai, Structural Chemistry Research Group of the Hungarian Academy of Sciences, Eötvös University, H-1431 Budapest, Pf. 117, Hungary.     

1，3-双(二烷基膦甲基)苯(烷基=Et,Me)和铂(Ⅱ)钯(Ⅱ)、镍(Ⅱ)配合物的合成及表征

本文首次报道了双膦配体：1，3-双(二乙基膦甲基)苯(1)-a和1，3-双(二甲基膦甲基)苯(1)-b的合成及表征，通过配位体与Pt(Ⅱ)、Pd(Ⅱ)、Ni(Ⅱ)的金属环化反应，合成了五个新配合物并对它们进行了表征。     

The Protonation of [Pt3(m̈-CO)3(PCy3)3]

The cluster [Pt₃(m?-CO)₃(PCy₃)₃] can be protonated with HBF₄ · OEt₂ to form the cluster [Pt₃(m?-CO)₃(PCy₃)₃](m?₃-H) ⁺BF ( 2 ). This unstable compound was isolated and characterised by NMR and IR spectroscopy.     

Transition metal complexes with bidentate ligands spanning trans-positions. IV. Preparation and properties of some rhodium and iridium complexes of 2,11-bis(diphenylphosphinomethyl)benzo [c]phenanthrene

The bidentate phosphine 2,11-bis(diphenylphosphinomethyl)benzo [c]phenanthrene ( 1 ) has been used to prepare the mononuclear, square planar complexes trans-[MX(CO)( 1 )] and trans-[M(CO)(CH₃CN)( 1 )][BF₄] (M = Rh, Ir; X = Cl, Br, I, NCS). It is found that the tendency of these complexes to form adducts with CO, O₂ and SO₂ is significantly lower than that of the corresponding Ph₃P complexes. The oxidative-addition reactions of complexes trans-[IrX (CO) ( 1 )] with hydrogen halides give the six-coordinate species [IrHX₂(CO) ( 1 )]. The complexes [IrH₂I (CO) ( 1 )] and [IrH₂L (CO) ( 1 )] [BF₄] (L = CO and CH₃CN) have been obtained from hydrogen and the corresponding substrates. The model compounds trans-[MCl (CO) (Ph₂PCH₂Ph)₂] (M = Rh, Ir), trans-[Ir (CO) (CH₃CN) (Ph₂PCH₂Ph)₂] [BF₄], [IrHCl₂(CO)(Ph₂PCH₂Ph)₂] and [IrH₂(CO)₂(Ph₂PCH₂Ph)₂] [BF₄] have been prepared and their special parameters are compared with those of the corresponding complexes of ligand 1 . The influence of the static requirements of this ligand on the chemistry of its rhodium and iridium complexes is discussed.     

Transition-Metal Complexes with Bidentate Ligands Spanning trans-Positions. I. The synthesis of 2,11-bis(diphenylphosphinomethyl)benzo[c]-phenanthrene,a ligand promoting the formation of square planar complexes

The bidentate ligand 2,11-bis(diphenylphosphinomethyl)benzo[c]phenanthrene ( 1 ) was synthesized from 2,11-dimethyl-benzo[c]phenanthrene ( 3 ) via the corresponding bromomethyl derivative 9. 3 was obtained from the cyclization with boron trifluoride etherate of 1,1-di-(p-methylphenethyl)-epoxyethane ( 7 ), which was prepared from 1,5-di(p-tolyl)-pentan-3-one ( 6 ).     

A combined spectroscopic and theoretical study of a series of conformationally restricted hexapeptides carrying a rigid binaphthyl-nitroxide donor-acceptor pair

The structural features of a series of linear hexapeptides of general formula Boc‐B‐A_r‐T‐A_m‐OtBu, where A is L ‐Ala or Aib (α‐aminoisobutyric acid), B is (R)‐Bin, a binaphthyl‐based C^α,α‐disubstituted Gly residue, T is Toac, a nitroxide spin‐labeled C^α,α‐disubstituted Gly, and r+m=4, were investigated in methanol solution by fluorescence, transient absorption, IR and CD spectroscopic studies, and by molecular mechanics calculations. These peptides are denoted as B‐T/r‐m, to emphasize the different position of Toac with respect to that of the Bin fluorophore in the amino acid sequence. The rigidity of the B‐T donor–acceptor pair and of the Aib‐rich backbone allowed us to investigate the influence of the interchromophoric distance and orientation on the photophysics of the peptides examined. The excited state relaxation processes of binaphthyl were investigated by time‐resolved fluorescence and transient absorption experiments. Dynamic quenching of the excited singlet state of binaphthyl by Toac was successfully interpreted by the Förster energy transfer model, provided that the mutual orientation of the chromophores is taken into account. This implies that interconversion among conformational substates, which involves puckering of the Toac piperidine ring, is slow on the time scale of the transfer process, that is slower than 5 ns. By comparison of the experimental and theoretical data, the type of secondary structure (right‐handed 3₁₀ helix) from the B‐T/r‐m peptides in solution was determined; this would not have been achievable by using the CD and NMR data only, as the data are not diagnostic in this case. Static quenching was observed in all peptides examined but B‐T/1‐3, where the effect can be ascribed to a non‐fluorescent complex. Among the computed low‐energy conformers of these peptides, there is one structure exhibiting a NO ^. –naphthalene center‐to‐center distance <6 Å, which might be assigned to this complex. The overall results emphasize the versatility of fluorescence experiments in 3D‐structural studies in solution.     

Transition-Metal Complexes with Bidentate Ligands Spanning trans-Positions. III. Preparation and solution studies of complexes [MX(1)] (M = Cu,Ag and Au; X = anionic ligand; 1 = 2, 11-bis(diphenylphosphinomethyl)benzo[c]phenanthrene)

The preparation of monomeric complexes [MX( 1 )] is reported where M = Cu, Ag, Au; X = I, Cl, NO₃, BF₄ and 1 = 2,11-bis(diphenylphosphinomethyl)benzo[c]phenanthrene. The solution structure of the complexes is discussed on the basis of molecular weight, conductivity and NMR. measurements. In acetonitrile and nitromethane, the nitrate and fluoroborate complexes exist as ionic species [M( 1 )]⁺X^? whereas the halo-complexes are present as equilibrium mixtures of ‘covalent’ and ‘ionic’ forms. All the complexes are associated in CH₂Cl₂-solutions. The values of ¹J show that this association in [Ag(NO₃) ( 1 )] and [Ag(BF₄) ( 1 )] is best described in terms of ion-pairing while that for species [AgX( 1 )] (X = Cl, Br and I) is mainly ‘covalent’ in nature. Evidence is presented for the formation of the complex ion [Ag(CH₃CN)_n( 1 )]⁺ in acetonitrile solution.