MTD-PLS: a PLS variant of the minimal topologic difference method. III. Mapping interactions between estradiol derivatives and the alpha estrogenic receptor

A homogeneous collection of 45 estrogen agonist derivatives with relative binding affinities measured to the estrogen receptor from Ratus norvegicus was used. The quantitative structure-activity relationships were derived using an improved minimal topologic difference (MTD) method in a partial least-squares (PLS) variant. The spatially assigned analysis of fragment properties can provide receptor site maps, within the limits of the existing series. A steric misfit was found for the steroidal position 2; benefic hydrophobic and van der Waals (enhanced by high polarizability) interactions were found for the 17alpha-CH=CH-X group. MTD-PLS mapping results are confirmed by the experimentally derived estradiol-estrogen receptor binding site contacts (based on X-ray crystallography). Our results suggest that this MTD-PLS method can yield useful results for interactions with receptors of unknown 3D structure and, generally, for the steric rigidity of receptor sites.     

Steric vs. electrostatic effects in the nucleophilic addition to a hindered cyclohexanone

The relative importance of steric vs. electrostatic effects in the nucleophilic addition to (4R,6S)-4-(tert-butyldimethylsiloxy)-2,2,6-trimethylcyclohexanone (1), a well-known chiral building block, is investigated.     

Comparison of Reliability of log P Values Calculated from a Group Contribution Approach and from the Autocorrelation Method

Abstract

The values of log P (n-octanol/water partition coefficient) for 1449 chemicals were calculated from the fragmental/regression model of Klopman and co-workers (J. Chem. Inf. Comput. Sci. 1994, 34, 752-781) and from the autocorrelation/backpropagation neural network model implemented in AUTOLOGP_TM (Version 4.0). Both models provided good simulation results but the superiority of the latter was demonstrated.     

Data‐independent liquid chromatography/mass spectrometry (LC/MSE) detection and quantification of the secreted Apium graveolens pathogen defense protein mannitol dehydrogenase

Plant cells secrete a wide variety of defense‐related proteins into the extracellular space or apoplast in response to pathogen attack. One of these, mannitol dehydrogenase (MTD), is normally a cytoplasmic enzyme whose primary role is the regulation of intracellular levels of the sugar alcohol mannitol in plants. Recent immunological and biochemical evidence, however, suggests that MTD is also secreted into the apoplast in response to pathogen attack, despite lacking a known peptide signal sequence for Golgi‐mediated secretion. Because many plant pathogenic fungi secrete mannitol to overcome pathogen‐induced generation of reactive oxygen species (ROS) by the plant, extracellular localization of MTD is hypothesized to have a defensive role of catabolizing pathogen‐secreted mannitol. In the current study, LC/MS^E was used to analyze proteins in the secretome of Apium graveolens (celery) following treatment with salicylic acid (SA), an endogenous elicitor of defense responses in plants. Levels of MTD in the secretome of SA‐treated celery cell cultures were found to be induced at least 18‐fold over secretome samples from cell cultures not exposed to SA. This value is in close agreement with published immunological and biochemical observations. Overall, this report provides the first mass spectrometry identification and quantification measurements supporting the hypothesis that MTD is secreted in response to simulated pathogen attack via a non‐classical secretion mechanism. As demonstrated with MTD secretion, LC/MS^E can be implemented as a discovery‐driven MRM‐based quantitative approach which can be used to reveal potential post‐translational modifications, thus providing a new method in the area of gel‐free and label‐free proteomic analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

SYNTHESIS AND STRUCTURE OF A POLYMERIC 1,3-BENZENEDICARBOXYLATO COMPLEX OF Mn(II) WITH PHENANTHROLINE

Abstract

A novel Mn(II) complex bridged by 1,3-benzenedicarboxylate (BDC) has been synthesized by the diffusion method. The complex crystallizes in space group P2₁/c with a = 8.345(2), b = 10.427(1), c = 18.756(2) Å, β = 100.19(1)°. Each BDC bridges three Mn(II) atoms through two carboxyl groups with different coordination modes to form a complex polymeric chain. The coordination geometry around the Mn(II) atom is seriously distorted from the normal octahedron. Large deviations of the donor atoms out of the coordination planes and unexpected bond angles around Mn(II) and donor O atoms suggest the existence of an electrostatic interaction between Mn(II) and donor atoms in the complex. Close stacking of aromatic rings is observed in the complex, the distance between the neighboring phen planes being 3.2085 Å.     

Vanadatesulfuric Acid: A Novel,Recyclable, and Heterogeneous Catalyst for the One-Pot Synthesis of Dihydropyrimidinones and Dihydropyrimidinthiones Under Solvent-Free Conditions

Abstract

Vanadatesulfuric acid (VSA), as a novel and heterogeneous catalyst, was used for an efficient synthesis of 3,4-dihydropyrimidin-2(1H)-ones (thiones) using an aldehyde, urea, or thiourea and an acyclic β-dicarbonyl compound under solvent-free conditions. VSA is prepared via the reaction of sodium metavanadate and chlorosulfonic acid in high purity. The catalyst was characterized by FTIR, X-ray diffraction (XRD), and transmission electron microscopy (TEM) analysis. Compared to the classical Biginelli reactions, this method consistently has the advantage of high yields, simple workup, short reaction times, and reusability of the catalyst.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.     

Modeling of interaction properties of surfaces of phyllosilicates: A theoretical forecast of adsorption isotherms of noble gases at the talc surface

The electrostatic potential and the intensity of the electric field above the isolated layer of the phyllosilicate mineral talc (layer group symmetry C2/m) were computed using the semiempirical INDO /2 method. The electrostatic potential V_c and the intensity of electric field (OVERBAR)E_c, above the surface of semi-infinite crystal were obtained as the sum of the contributions of the infinite number of individual layers. The interaction energy U_int between a noble gas atom and the talc crystal was computed as (a) a pure Lennard-Jones energy U_LJ and (b) the sum of U_LJ and interaction energy with induced dipole moment: U_ind = α|(OVERBAR)E|², where α is the dipole polarizability of the noble gas atom. The one-particle configurational integral was calculated within the classical mechanics limit. Both the free and adsorbed gas phases were assumed to be ideal. The obtained results demonstrate that in the case of uncharged and nonpolar adsorbate and an uncharged surface the electrostatic part of the interaction energy should be included in the total interaction energy. © 1996 John Wiley & Sons, Inc.     

Three double- or triple-stranded chains constructed from different cobalt(II) salts and a flexible bis-triazole ligand

Three coordination compounds, {[Co(btrp)₂(H₂O)₂]?·?NO₃?·?H₂O} _n (1), {[Co(btrp)₂(H₂O)₂]?·?H₂O?·?2H₂btc} _n (2), and {[Co(btrp)₃]?·?2ClO₄} _n (3) (btrp?=?1,3-bis(1,2,4-triazol-1-yl)propane; H₃btc?=?benzene-1,3,5-tricarboxylic acid), have been prepared via solvothermal method and characterized by single-crystal X-ray diffraction and elemental analyses. Compound 1 possesses a 1-D double-stranded chain composed of ribbons of 20-membered cycles. Binuclear water clusters link adjacent nitrate anions to form a 1-D supramolecular helix in the structure. Compound 2 has a 1-D double-stranded chain wherein free H₂btc ligands constitute 1-D negative chains through classical hydrogen-bonding interactions (O–H?···?O). Compound 3 exhibits a triple-stranded 1-D chain. For 1–3, 3-D supramolecular structures are consolidated by interchain weak hydrogen-bonding interactions as well as electrostatic interactions.     

Crystal and Molecular Structures of (E)-(2-Phenylethenyl)cyclooctatetraene and (E)-(2-(4-Nitrophenyl)ethenyl)cyclooctatetraene. Conformations of Substituted Cyclooctatetraenes

The single crystal x-ray structures of (E)-(2-arylethenyl)cyclooctatetraenes 1 and 2 have been determined. The nitro group in 2 does not influence the geometry of the COT ring relative to that of 1. The influence of various substituents on several structural parameters of the COT ring are analyzed in terms of steric/electrostatic and electronegativity effects of the substituent.     

A crystallographic and DFT study on a NHC complex of niobium oxide trifluoride

The complex [NbOF₃(Ipr)]₂, 1, was afforded in crystalline form by reaction of NbF₅ with the bulky NHC ligand 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr) in toluene by slow contact with moisture air. The molecular structure of 1 was ascertained by X-ray diffraction, providing the first example of a dinuclear NbOF₃ derivative and also a rare case of niobium compound with a monodentate NHC. A DFT investigation has shown that the Nb–C bond consists of a weak NHC to Nb σ donation, reinforced by an electrostatic contribution presumably favored by the presence of the ancillary fluoride ligands. The computed enthalpy for the dissociation of one Ipr from 1 is ca. 36 kcal mol^?1. The presence of bulky 2,6-diisopropylphenyl substituents on the carbene ligand has negligible influence on the Nb–C bond, as highlighted by DFT analyses on simplified models.     

Comparison of multi-recognition molecularly imprinted polymers for recognition of melamine,cyromazine, triamterene,and trimethoprim

Three fragmental templates, including 2,4-diamino-6-methyl-1,3,5-triazine (DMT), cyromazine (CYR), and trimethoprim (TME), were used to prepare the fragment molecularly imprinted polymers (FMIPs), respectively, in polar ternary porogen which was composed of ionic liquid ([BMIM]BF₄), methanol, and water. The morphology, specific surface areas, and selectivity of the obtained FMIPs for fragmental analogues were systematically characterized. The experimental results showed that the FMIPs possessed the best specific recognition ability to the relative template and the greatest imprinting factor (IF) was 5.25, 6.69, and 7.11 of DMT on DMT-MIPs, CYR on CYR-MIPs, and TME on TME-MIPs, respectively. In addition, DMT-MIPs also showed excellent recognition capability for fragmental analogues including CYR, melamine (MEL), triamterene (TAT), and TME, and the IFs were 2.08, 3.89, 2.18, and 2.60, respectively. The effects of pH and temperature on the retention of the fragmental and structural analogues were studied in detail. Van’t Hoff analysis indicated that the retention and selectivity on FMIPs were an entropy-driven process, i.e., steric interaction. The resulting DMT-MIPs were used as a solid-phase extraction material to enrich CYR, MEL, TAT, and TME in different bio-matrix samples for high-performance liquid chromatography analysis. The developed method had acceptable recoveries (86.8–98.6 %, n?=?3) and precision (2.7–4.6 %) at three spiked levels (0.05–0.5 μg g^?1).     

Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations

Ab initio MP2/6-31G* interaction energies were calculated for more than 80 geometries of stacked cytosine dimer. Diffuse polarization functions were used to properly cover the dispersion energy. The results of ab initio calculations were compared with those obtained from three electrostatic empirical potential models, constructed as the sum of a Lennard-Jones potential (covering dispersion and repulsion contributions) and the electrostatic term. Point charges and point multipoles of the electrostatic term were also obtained at the MP2/6-31G* level of theory. The point charge MEP model (atomic charges derived from molecular electrostatic potential) satisfactorily reproduced the ab initio data. Addition of π-charges localized below and above the cytosine plane did not affect the calculated energies. The model employing the distributed multipole analysis gave worse agreement with the ab initio data than the MEP approach. The MP2 MEP charges were also derived using larger sets of atomic orbitals: cc-pVDZ, 6-311 + G(2d, p), and aug-cc-pVDZ. Differences between interaction energies calculated using these three sets of point charges and the MP2/6-31G* charges were smaller than 0.8 kcal/mol. The correlated ab initio calculations were also compared with the density functional theory (DFT) method. DFT calculations well reproduced the electrostatic part of interaction energy. They also covered some nonelectrostatic short-range effects which were not reproduced by the empirical potentials. The DFT method does not include the dispersion energy. This energy, approximated by an empirical term, was therefore added to the DFT interaction energy. The resulting interaction energy exhibited an artifact secondary minimum for a 3.9-4.0 vertical separation of bases. This defect is inherent in the DFT functionals, because it is not observed for the Hartree-Fock + dispersion interaction energy.© 1996 John Wiley & Sons, Inc.     

Dioxin-Type Activity for Polyhalogenated Arylic Derivatives. A QSAR Model Based on MTD-Method

Abstract

QSARs by the Minimal Steric/Topologic Difference (MTD)-method were performed for general toxicity, hepatic cytosol receptor binding and aryl hydrocarbon hydroxylase induction on polychlorinated and polybrominated derivatives of dibenzo-p-dioxin, dibenzofuran and biphenyl. Low energy conformations selected by molecular mechanics calculations and superpositions of the considered structures for the construction of the hypermolecule were performed using the COSMIC molecular modelling package. The multiconformational-MTD-method was used. Correlation coefficients of r = 0.8 to 0.9 were obtained as well as good cross-validation results, for series of up to 70 compounds. Conformational analysis of flexible molecules suggests their accommodation in the receptor site also in non planar conformations corresponding to the first stable one (minimum energy costs) above the global minimum. A common optimised receptor site can be attributed for all series of compounds, with a rather high symmetry, which suggests that these compounds produce gene activation by dimerization of their receptor protein. The high toxicity of dioxin-type compounds could be explained by their high stability that produce long lasting, abnormally high levels of some detoxification enzymes—without toxic effects at their low and normal levels.