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.     

Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909

Analysis of large, flexible molecules, such as the dopamine reuptake inhibitor GBR 12909 (1), is complicated by the fact that they can take on a wide range of closely related conformations. The first step in the analysis is to classify the conformers into groups. Here, Singular Value Decomposition (SVD) was used to group conformations of GBR 12909 analogs by the similarity of their nonring torsional angles. The significance of the present work, the first application of SVD to the analysis of very flexible molecules, lies in the development of a novel scaling technique for circular data and in the grouping of molecular conformations using a technique that is independent of molecular alignment. Over 700 conformers each of a piperazine (2) and piperidine (3) analog of 1 were studied. Analysis of the score and loading plots showed that the conformers of 2 separate into three large groups due to torsional angles on the naphthalene side of the molecule, whereas those of 3 separate into nine groups due to torsional angles on the bisphenyl side of the molecule. These differences are due to nitrogen inversion at the unprotonated piperazinyl nitrogen of 2, which results in a different ensemble of conformers than those of 3, where no inversion is possible at the corresponding piperidinyl carbon.     

Pd-catalyzed cross-coupling reactions of alkyl halides

Cross-coupling reactions have become indispensable tools for creating carbon-carbon (or heteroatom) bonds in organic synthesis. Like in other important transition metal catalyzed reactions, such as metathesis, addition, and polymerization, unsaturated compounds are usually employed as substrates for cross-coupling reactions. However during the past decade, a great deal of effort has been devoted to the use of alkyl halides as saturated compounds in cross-coupling reactions, which has resulted in significant progress in this undeveloped area by introducing new effective ligands. Many useful catalytic systems are now available for synthetic transformations based on C(sp(3))-C(sp(3)), C(sp(3))-C(sp(2)) and C(sp(3))-C(sp) bond formation as complementary methods to conventional C(sp(2))-C(sp(2)), C(sp(2))-C(sp) and C(sp)-C(sp) coupling. This tutorial review summarizes recent advances in cross-coupling reactions of alkyl halides and pseudohalides catalyzed by a palladium complex.     

Hierarchical clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs

Pharmacophore modeling of large, drug-like molecules, such as the dopamine reuptake inhibitor GBR 12909, is complicated by their flexibility. A comprehensive hierarchical clustering study of two GBR 12909 analogs was performed to identify representative conformers for input to three-dimensional quantitative structure–activity relationship studies of closely-related analogs. Two data sets of more than 700 conformers each produced by random search conformational analysis of a piperazine and a piperidine GBR 12909 analog were studied. Several clustering studies were carried out based on different feature sets that include the important pharmacophore elements. The distance maps, the plot of the effective number of clusters versus actual number of clusters, and the novel derived clustering statistic, percentage change in the effective number of clusters, were shown to be useful in determining the appropriate clustering level.Six clusters were chosen for each analog, each representing a different region of the torsional angle space that determines the relative orientation of the pharmacophore elements. Conformers of each cluster that are representative of these regions were identified and compared for each analog. This study illustrates the utility of using hierarchical clustering for the classification of conformers of highly flexible molecules in terms of the three-dimensional spatial orientation of key pharmacophore elements.     

Scandium arene inverted-sandwich complexes supported by a ferrocene diamide ligand

The synthesis and characterization of the first scandium arene inverted-sandwich complexes supported by a ferrocene diamide ligand (NN(fc)) are reported. Through the use of (NN(fc))ScI(THF)(2) as a precursor and potassium graphite (KC(8)) as a reducing agent, the naphthalene and anthracene complexes [(NN(fc))Sc](2)(μ-C(10)H(8)) and [(NN(fc))Sc](2)(μ-C(14)H(10)), respectively, were synthesized and isolated in moderate to high yields. Both molecular structures feature an inverted-sandwich geometry and exhibit short Fe-Sc distances. DFT calculations were employed to gain understanding of the electronic structures of these new scandium arene complexes. A variable-temperature NMR spectroscopic study of [(NN(fc))Sc](2)(μ-C(14)H(10)) indicated that two different structures are accessible in solution. Reactivity studies showed that the naphthalene complex [(NN(fc))Sc](2)(μ-C(10)H(8)) can be converted to the corresponding anthracene species [(NN(fc))Sc](2)(μ-C(14)H(10)) and that [(NN(fc))Sc](2)(μ-C(10)H(8)) can act as either a reductant or a proton acceptor. The reaction of [(NN(fc))Sc](2)(μ-C(10)H(8)) with excess pyridine led to a rare example of C-C bond formation between two pyridine rings at the para position.     

Directed heterodimerization: stereocontrolled assembly via solvent-caged unsymmetrical diazene fragmentation

A general strategy for the directed and stereocontrolled assembly of carbon-carbon linked heterodimeric hexahydropyrroloindoles is described. The stepwise union of complex amines in the form of mixed diazenes followed by photoexpulsion of dinitrogen in a solvent cage provides completely guided assembly at challenging C(sp(3))-C(sp(3)) and C(sp(3))-C(sp(2)) connections.     

Phenyliodine bis(trifluoroacetate)-mediated oxidative C-C bond formation: synthesis of 3-hydroxy-2-oxindoles and spirooxindoles from anilides

The reaction of phenyliodine bis(trifluoroacetate) (PIFA) with a series of anilides 1 (E = CO(2)Et) in CF(3)CH(2)OH was found to give 3-hydroxy-2-oxindole derivatives 2, while that with various anilides 1' (E = CON(R(4))Ar) afforded the C(2)-symmetric or unsymmetric spirooxindoles 3. These processes feature a metal-free oxidative C(sp(2))-C(sp(3)) bond formation, followed by oxidative hydroxylation or spirocyclization.     

Access to C(sp3)-C(sp2) and C(sp2)-C(sp2) bond formation via sequential intermolecular carbopalladation of multiple carbon-carbon bonds

A synthetic strategy of 4-benzyl-substituted 1,3-butadiene derivatives through Pd-catalyzed three-component coupling reaction of benzyl chlorides, alkynes, and monosubstituted alkenes is described. This tandem coupling reaction forms a C(sp(3))-C(sp(2)) bond and a C(sp(2))-C(sp(2)) bond sequentially in a single-step operation.     

A nonsymmetric pincer-catalyzed Suzuki-Miyaura arylation of benzyl halides and other nonactivated unusual coupling partners

The catalytic activity of a PCN-type palladium pincer complex is evaluated in the construction of C(sp(2))-C(sp(2)) and C(sp(2))-C(sp(3)) bonds by Suzuki-Miyaura cross-couplings employing nontypical substrates such as benzyl halides, alpha-haloenones, or alkylboronic acids as coupling partners. Most of the reported reactions are achieved in aqueous media, with all of the advantages implied.     

Crystal structure of N,N,N',N'-tetrakis(methyldiphenylphosphino)-bis(2'-phenoxy)-3,6-dioxaoctane.

The title molecule, [C70H68N2O4P4], is a polydentate podand consisting of four etheral oxygens, two tertiary amine nitrogens and four diphenylphosphin groups. It crystallizes in the triclinic space group P1, and there is only one half a molecule in the asymmetric unit. The coordinations around the N and P atoms are pyramidal. The conformations about C20-C21, O2-C21 and O2-C22 are gauche, anti and anti, respectively.     

Group 14 Metal Terminal Phosphides: Correlating Structure with |J(MP)|

A series of heavier group 14 element, terminal phosphide complexes, M(BDI)(PR(2)) (M = Ge, Sn, Pb; BDI = CH{(CH(3))CN-2,6-iPr(2)C(6)H(3)}(2); R = Ph, Cy, SiMe(3)) have been synthesized. Two different conformations (endo and exo) are observed in the solid-state; the complexes with an endo conformation have a planar coordination geometry at phosphorus (M = Ge, Sn; R = SiMe(3)) whereas the complexes possessing an exo conformation have a pyramidal geometry at phosphorus. Solution-state NMR studies reveal through-space scalar coupling between the tin and the isopropyl groups on the N-aryl moiety of the BDI ligand, with endo and exo exhibiting different J(SnC) values. The magnitudes of the tin-phosphorus and lead-phosphorus coupling constants, |J(SnP)| and |J(PbP)|, differ significantly depending upon the hybridization of the phosphorus atom. For Sn(BDI)(P{SiMe(3)}(2)), |J(SnP)| is the largest reported in the literature, surpassing values attributed to compounds with tin-phosphorus multiple-bonds. Low temperature NMR studies of Pb(BDI)(P{SiMe(3)}(2)) show two species with vastly different |J(PbP)| values, interpreted as belonging to the endo and exo conformations, with sp(2)- and sp(3)-hybridized phosphorus, respectively.     

Syntheses of functionalized ferratricarbadecaboranyl complexes

The reactions of nitriles (RCN) with arachno-4,6-C(2)B(7)H(12)(-) provide a general route to functionalized tricarbadecaboranyl anions, 6-R-nido-5,6,9-C(3)B(7)H(9)(-), R = C(6)H(5) (2(-)), NC(CH(2))(4) (4(-)), (p-BrC(6)H(4))(Me(3)SiO)CH (6(-)), C(14)H(11) (8(-)), and H(3)BNMe(2)(CH(2))(2) (10(-)). Further reaction of these anions with (eta(5)-C(5)H(5))Fe(CO)(2)I yields the functionalized ferratricarbadecaboranyl complexes 1-(eta(5)-C(5)H(5))-2-C(6)H(5)-closo-1,2,3,4-FeC(3)B(7)H(9) (3), 1-(eta(5)-C(5)H(5))-2-NC(CH(2))(4)-closo-1,2,3,4-FeC(3)B(7)H(9) (5), 1-(eta(5)-C(5)H(5))-2-[(p-BrC(6)H(4))(Me(3)SiO)CH]-closo-1,2,3,4-FeC(3)B(7)H(9) (7), 1-(eta(5)-C(5)H(5))-2-C(14)H(11)-closo-1,2,3,4-FeC(3)B(7)H(9) (9), and 1-(eta(5)-C(5)H(5))-2-H(3)BNMe(2)(CH(2))(2)-closo-1,2,3,4-FeC(3)B(7)H(9) (11). Reaction of 11 with DABCO (triethylenediamine) resulted in removal of the BH(3) group coordinated to the nitrogen of the side chain, giving 1-(eta(5)-C(5)H(5))-2-NMe(2)(CH(2))(2)-closo-1,2,3,4-FeC(3)B(7)H(9) (12). Crystallographic studies of complexes 3, 5, 7, 9, and 11 confirmed that these complexes are ferrocene analogues in which a formal Fe(2+) ion is sandwiched between the cyclopentadienyl and tricarbadecaboranyl monoanionic ligands. The metals are eta(6)-coordinated to the puckered six-membered face of the tricarbadecaboranyl cage, with the exopolyhedral substituents bonded to the low-coordinate carbon adjacent to the iron.     

Synthesis,lipophilicity and structure of 2,5‐disubstituted 1, 3, 5‐dithiazine derivatives

A series of 2,5‐disubstituted 1,3,5‐dithiazine derivatives were synthesized as potential analogues of the potent dopamine uptake inhibitor GBR 12909. The lipophilic character of the 1,3,5‐dithiazine derivatives were experimentally (log P) and computationally (clog P) determined. The in vitro binding affinities of the 2,5‐disubstituted 1,3,5‐dithiazine derivatives at the dopamine transporter were determined to be much less potent than the binding affinity of GBR 12909 due to steric and electronic effects inherent to the 1,3,5‐dithiazine ring system. The X‐ray crystal structure of 2‐(2‐[bis(4‐fluorophenyl)methoxy]ethyl)‐5‐(3‐phenylpropyl)‐1,3,5‐dithiazine (7) revealed that the 5‐(3‐phenylpropyl) group is in a pseudo‐axial orientation and syn to the 2‐ethoxybenzhydryl moiety.     

Synthesis and Structure of 6-(4- Fluorobenzylamino)-3-methylthio-1,5- diphenyl-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-one

1 INTRODUCTION It was reported that the pyrazolopyrimidinone derivatives play a very important role in the bio- chemistry of living cell. Many potential drugs[1～3] and agrochemicals[4, 5] have been modeled on the compound, and the study on derivatives …     

Silver-catalyzed decarboxylative alkynylation of aliphatic carboxylic acids in aqueous solution

C(sp(3))-C(sp) bond formations are of immense interest in chemistry and material sciences. We report herein a convenient, radical-mediated and catalytic method for C(sp(3))-C(sp) cross-coupling. Thus, with AgNO(3) as the catalyst and K(2)S(2)O(8) as the oxidant, various aliphatic carboxylic acids underwent decarboxylative alkynylation with commercially available ethynylbenziodoxolones in aqueous solution under mild conditions. This site-specific alkynylation is not only general and efficient but also functional group compatible. In addition, it exhibits remarkable chemo- and stereoselectivity.     

Bayesian model based clustering analysis: application to a molecular dynamics trajectory of the HIV-1 integrase catalytic core

This work describes the application of a Bayesian method for clustering protein conformations sampled during a molecular dynamics simulation of the HIV-1 integrase catalytic core. A clustering analysis is carried out under the assumption of normal distribution without fixing the number of clusters in advance. Some performance measures, such as posterior probability and class cross entropy, are used to determine the most probable set of clusters. The Bayesian clustering method results in meaningful groups identifying transitions between conformational ensembles. The dihedral angles involved in such transitions are also examined in detail. The conformations in high dimensional space are projected into 3D space employing a multidimensional scaling technique to provide a visual inspection.     

Synthesis, structure and conformation of partially-modified retro- and retro-inverso psi[NHCH(CF3)]Gly peptides

Partially modified retro- (PMR) and retro-inverso (PMRI) psi[NHCH(CF(3))]Gly peptides, a conceptually new class of peptidomimetics, have been synthesized in wide structural diversity and variable length by aza-Michael reaction of enantiomerically pure alpha-amino esters and peptides with enantiomerically and geometrically pure N-4,4,4-trifluorocrotonoyl-oxazolidin-2-ones. The factors underlying the observed moderate to good diastereocontrol have been investigated. The conformations of model PMR-psi[NHCH(CF(3))]Gly tripeptides have been studied in solution by (1)H NMR spectroscopy supported by MD calculations, as well as in the solid-state by X-ray diffraction. Remarkable stability of turn-like conformations, comparable to that of parent malonyl-based retropeptides, was evidenced, as a likely consequence of two main factors: 1) severe torsional restrictions about sp(3) bonds in the [CO-CH(2)-CH(CF(3))-NH-CH(R)-CO] module, which is biased by the stereoelectronically demanding CF(3) group and the R side chain; 2) formation of nine-membered intramolecularly hydrogen-bonded rings, which have been clearly detected both in CHCl(3) solution and in some crystal structures. The former factor seems to be more important, as turn-like conformations were found in the solid-state even in the absence of intramolecular hydrogen bonding. The relative configuration of the -C*H(CF(3))NHC*H(R)- stereogenic centers has a major effect on the stability of the turn-like conformation, which seems to require a syn stereochemistry. X-ray diffraction and ab initio computational studies showed that the [-CH(CF(3))NH-] group can be seen as a sort of hybrid between a peptide bond mimic and a proteolytic transition state analogue, as it combines some of the properties of a peptidyl -CONH- group (low NH basicity, CH(CF(3))-NH-CH backbone angle close to 120 degrees, C-CF(3) bond substantially isopolar with the C=O) with some others of the tetrahedral intermediate [-C(OX)(O(-))NH-] involved in the protease-mediated hydrolysis reaction of a peptide bond (high electron density on the CF(3) group, tetrahedral backbone carbon).     

Novel method for constructing a large-scale design space in lubrication process by using bayesian estimation based on the reliability of a scale-up rule

A reliable large-scale design space was constructed by integrating the reliability of a scale-up rule into the Bayesian estimation without enforcing a large-scale design of experiments (DoE). A small-scale DoE was conducted using various Froude numbers (X(1)) and blending times (X(2)) in the lubricant blending process for theophylline tablets. The response surfaces, design space, and their reliability of the compression rate of the powder mixture (Y(1)), tablet hardness (Y(2)), and dissolution rate (Y(3)) on a small scale were calculated using multivariate spline interpolation, a bootstrap resampling technique, and self-organizing map clustering. A constant Froude number was applied as a scale-up rule. Experiments were conducted at four different small scales with the same Froude number and blending time in order to determine the discrepancies in the response variables between the scales so as to indicate the reliability of the scale-up rule. Three experiments under an optimal condition and two experiments under other conditions were performed on a large scale. The response surfaces on the small scale were corrected to those on the large scale by Bayesian estimation using the large-scale results and the reliability of the scale-up rule. Large-scale experiments performed under three additional sets of conditions showed that the corrected design space was more reliable than the small-scale design space even when there was some discrepancy in the pharmaceutical quality between the manufacturing scales. This approach is useful for setting up a design space in pharmaceutical development when a DoE cannot be performed at a commercial large manufacturing scale.     

Carbon-based leaving group in substitution reactions: functionalization of sp3-hybridized quaternary and tertiary benzylic carbon centers

Lewis acid promoted substitution reactions employing Meldrum's acid and 5-methyl Meldrum's acid as carbon-based leaving groups are described which transform unstrained quaternary and tertiary benzylic C(sp(3))-C(sp(3)) bonds into C(sp(3))-X bonds (X = C, H, N). Importantly, this reaction has a broad scope in terms of both suitable substrates and nucleophiles with good to excellent yields obtained (typically >90%).     

Perfluoroalkyl-substituted triazapentadienes and their metal complexes

Triazapentadienides, C(3)F(7)-C(=NR)-N=C(NHR)-C(3)F(7), result from the reaction of primary amines RNH(2) with the fluorinated imine C(3)F(7)-CF=N-C(4)F(9). The aniline derivative (R = Ph) is a weak monoprotic acid in dmso. Its conjugate base exhibits an extensive coordination chemistry. It acts as a bidentate ligand toward the molecular fragments Pd(C(3)H(5)), Rh(c-C(8)H(12)), Ir(c-C(8)H(12)), and Rh(CO)(2). The chelates [C(3)F(7)-C(NPh)-N-C(NPh)-C(3)F(7)](2)M, M = Mg, Mn, Fe, Co, Ni, Cu, Zn, and Pd, were prepared. In the crystallographically characterized Co complex, the metal is 3d(7), S = (3)/(2) and tetrahedrally coordinated. Spin densities at carbon in the C(6)H(5) and C(3)F(7) groups were estimated from the (1)H and (19)F contact shifts. Spin delocalization onto phenyl sp(2) carbons is approximately 10 times greater than onto the fluorinated sp(3) carbons.