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  • 1
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Comparative molecular field analysis (CoMFA) is a three-dimensional quantitative structure-activity relationship (3D-QSAR) method which correlates precalculated fields surrounding a set of molecules with some target property. Among others, the electrostatic fields are commonly used. These are usually generated by calculating the Coulomb potential between a probe and the molecules bearing atom-centered point charges. The present study was performed in order to investigate up to which extent different methods to calculate electrostatic potentials can influence the results of a CoMFA. Therefore, a variety of charge calculation methods was applied to a data set consisting of 37 ligands of the benzodiazepine receptor inverse agonist-antagonist active site. These methods included Gasteiger-Marsili, semiempirical (MNDO, AM1, and PM3), and ab initio (HF/STO-3G, HF/3-21G*, and HF/6-31G*) charges. Semiempirical as well as ab initio electron populations were derived both from the Mulliken population analysis (MPA) or from fitting the charges to the molecular electrostatic potential (ESPFIT charges). In addition, the molecular electrostatic potentials (MEPs) resulting from ab initio calculations were mapped directly onto the CoMFA grid. With regard to the cross-validated r2 values (r2cv) of the resulting QSAR models, the ESPFIT-derived potentials yielded generally higher r2cv values than those resulting from MPA charges. For example, at the HF/3-21G* level the r2cv rose from 0.61 (MPA-derived potentials) to 0.76 (ESPFIT fields). The MEPs mapped directly onto the CoMFA grid were not superior to the corresponding ESPFIT-derived potentials. Semiempirical ESPFIT charges appeared to be of similar quality compared with ab initio ESPFIT electron populations in the CoMFAs. When no scaling between the steric and electrostatic descriptor matrices was applied, the electrostatic contributions were influenced to a high degree by the magnitude of the corresponding field values. © 1996 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 2
    ISSN: 0192-8651
    Keywords: molecular alignment ; molecular similarity ; Monte Carlo ; QSAR ; CBG steroids ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: 3D-QSAR uses statistical techniques to correlate calculated structural properties with target properties like biological activity. The comparison of calculated structural properties is dependent upon the relative orientations of molecules in a given data set. Typically molecules are aligned by performing an overlap of common structural units. This “alignment rule” is adequate for a data set, that is closely related structurally, but is far more difficult to apply to either a diverse data set or on the basis of some structural property other than shape, even for sterically similar molecules. In this work we describe a new algorithm for molecular alignment based upon optimization of molecular similarity indices. We show that this Monte Carlo based algorithm is more effective and robust than other optimizers applied previously to the similarity based alignment problem. We show that QSARs derived using the alignments generated by our algorithm are superior to QSARs derived using the more common alignment of fitting of common structural units.   © 1997 by John Wiley & Sons, Inc.   J Comput Chem 18: 1344-1353, 1997
    Additional Material: 6 Ill.
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  • 3
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Alternating copolymers of butadiene and propylene (BPR) made by a solution polymerization technique with a modified catalyst of the Furukawa type have highly regular structures. The constitutional repeating unit consists of one propylene and one 1,4-trans-butadiene unit. No chain imperfections were detected, except for ≦2% 1,4-cis-butadiene units. The configurations of the chiral tertiary carbon atoms in the propylene units could not be directly determined by spectroscopic methods. The intrinsic viscosities of the samples studied lie between 1.1 and 1.8 dL/g. The high molecular weight fractions (M 〉 2 × 105) show long-chain branching. Crystallization effects, namely, a decrease in specific volume with time, and melting are observed after annealing unoriented samples at temperatures between -30 and -50°C. X-ray diffraction shows that the structure of the ordered phase depends on polymerization conditions, varying between a liquid crystal-like close packing of parallel chain segments and imperfect crystalline, three-dimensionally periodic arrangements of chains. Both in the noncrystalline and crystalline ordered phases, the molecules are arranged in layers with a spacing of 0.47 nm. The crystalline chains have nonplanar and not fully extended conformations with a repeat distance of 0.72 nm. The rate of crystallization and the relative decrease in volume (≦1.3%) are small compared to stereoregular polymers like natural rubber and high-cis polybutadiene. In crosslinked specimens, stretched 1:6 to 1:10, the crystalline or liquid crystal-like structure persists up to +60°C. The imperfect nature of the crystallization of BPR is caused by stereoisomerism of the chiral carbon atoms. The chains are probably composed of short tactic sequences separated by tactic arrangements.
    Additional Material: 9 Ill.
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  • 4
    ISSN: 0952-3499
    Keywords: automated docking ; simulated annealing ; multispecific IgEs ; allergic cross-reactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A mouse monoclonal anti-2,4,6-trinitrophenyl IgE (clone Lb4) was screened with a random set of over 2000 compounds, and several ligands were found to bind with affinities comparable to that of the immunizing hapten (KD in the μM range). An automated docking algorithm was used for the prediction of complex structures formed by 2,4-dinitrophenyl (DNP) and non-DNP ligands in the fragment variable region of IgE(Lb4). All ligands were found to dock in an L-shaped cavity of 15 × 16 × 10 Å, surrounded by complementary-determining regions L1, L3, H2 and H3. The ligands were found to occupy the same binding site in different orientations. For rigid ligands the most stable orientation could be predicted with high probability, based on the calculated energy of binding and the occurrence frequencies of identical complexes obtained by repeated simulations. The localization of a flexible ligand (cycrimine-R) was more ambiguous, but it still docked in the same site. The results support a model for heteroligating antibody (Ab) binding sites, where different ligands utilize the total set of available contacts in different combinations. It is suggested that although pseudoenergies calculated by the docking algorithm do not correlate with experimentally measured binding energies, the screening-and-docking procedure can be useful for the mapping of Ab and other receptor binding sites ligating small molecules.
    Additional Material: 5 Ill.
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  • 5
    ISSN: 0003-3146
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Description / Table of Contents: Low density polyethylenes (LDPE) synthesized under variable polymerization conditions, e.g. in a tube reactor (type R), have molecular structures considerably different from those of LDPE-samples with similar melt indices and densities which were polymerized under constant conditions, e.g. in a stirred autoclave reactor (type A). Thus, R-type products have narrower molecular weight distributions and wider distributions of short- and long-chain branching than A-type samples and show decreasing branching with increasing molecular weight. Moreover, there are differences in the structure of long-chain branching and in the molecular shape between R- and A-products.The results of measurements may be interpreted assuming that the A-type molecules have tree-like branched structures and approximately globular shapes whereas R-type molecules show comb-like branching and elongated rod-like shapes. The differences in the molecular structure lead to different supramolecular structures - e.g. narrower distributions of densities in spite of wider short-chain branching distributions with R products as compared with A-products-and to different physical and technological properties of the two LDPE-types synthesized in different ways. The results may be interpreted in terms of reaction kinetics. By a new modified autoclave process the molecular structures and the physical and technological properties of low density polyethylenes may be varied within wide limits.
    Notes: Hochdruckpolyäthylene (LDPE), die unter veränderlichen Polymerisationsbedingungen  -  z. B. mit einem Röhrenreaktor (Präparat R)  -  hergestellt wurden, unterscheiden sich in der molekularen Struktur erheblich von Hochdruckpolyäthylenen mit gleichem Schmelzindex und gleicher Dichte, die unter konstanten Polymerisationsbedingungen  -  z. B. mit einem Rührautoklavenreaktor (Präparat A)  -  hergestellt wurden. So haben die Präparate R nicht nur engere Verteilungen der Molekulargewichte und breitere der Kurz- und Langkettenverzweigung sowie einen mit wachsendem Molekulargewicht abnehmenden Verzweigungsgrad, sondern sie unterscheiden sich auch in der Art der Langkettenverzweigung und in der Molekülform von den Präparaten A.Man kann die Meßergebnisse interpretieren, wenn man annimmt, daß die Moleküle des Präparates A eine strauchförmige Verzweigung mit mehr kugeligen Molekülformen besitzen, während die Moleküle des Präparates R eine kammartige Verzweigung und eine gestrecktere (stäbchenförmige) Konformation zeigen. Diese Unterschiede der molekularen Struktur bedingen auch Unterschiede der übermolekularen Struktur  -  z. B. eine engere Verteilung der Dichten trotz breiterer Verteilung der Kurzkettenverzweigungen bei dem Präparat R im Vergleich zum Präparat A  -  und der physikalischen und technologischen Eigenschaften der unterschiedlich hergestellten Hochdruckpolyäthylene. Die Ergebnisse können reaktionskinetisch gedeutet werden. Mit einem neuen modifizierten Àutoklavenverfahren lassen sich die molekularen Strukturen der LDPE und daher auch ihre physikalischen und technologischen Eigenschaften in weiten Grenzen variieren.
    Additional Material: 17 Ill.
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  • 6
    ISSN: 0009-286X
    Keywords: Massensuspensionskultur ; tierische Zellen ; Blasensäule ; Schlaufenreaktor ; Fließbild ; Begasungsleistung ; Scale up ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Additional Material: 1 Ill.
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  • 7
    ISSN: 0947-3440
    Keywords: Bicyclo[4.2.0]octa-1,3,5-triene ; Chromium complexes ; [4+2] Cycloadditions ; Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The syntheses of the tricarbonylchromium complexes 2 and 3 of 1-oxobenzocyclobutene and 1-hydroxybenzocyclobutene are described. Alcoholate 6 of 3 undergoes a ring opening to the corresponding ortho-quinodimethane intermediate between -30 and -20°C, which is trapped by dienophiles with high diastereoselectivity. While with most dienophiles products with a 1,2-cis configuration (7, 8, 10) are formed, vinyl sulfones react in an exo-selective cycloaddition with formation of 1,2-trans-configurated cycloadducts (12, 13). The configuration of the cycloadduct with phenyl vinyl sulfone is confirmed by an X-ray crystal structure analysis. As one of the important aspects of the chemistry of benzocyclobutene complexes is the chirality of compounds like 2 and 3, the enantiomeric resolution has been achieved via the semioxamazones of ketone 2.
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  • 8
    ISSN: 0006-3592
    Keywords: expression ; membrane protein ; glycophorin ; neomycin resistance ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The gene for the integral membrane protein glycophorin A (GPA) was cloned in frame to the 5′ end of the antibiotic resistance gene, neomycin phosphotransferase II (NPT). Protein expression was achieved in Escherichia coli as well as in mammalian cells. In case of Chinese hamster ovary cells (CHO) the resistant populations were analyzed 2 weeks after transfection; the amount of GPA-NPT fusion protein produced was constant from experiment to experiment. Neomycin resistance was directly correlated with GPA expression, thus allowing the direct selection for a stable GPA-expressing cell population without the need of a cloning step. The amount of GPA-NPT produced was further increased by weakening the specific NPT enzymatic activity via site-directed mutagenesis. Detection was simplified by the fact that all different fusion proteins could be detected by the same anti-NPT antibody. This approach may be also applicable to other membrane proteins. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 238-244, 1998.
    Additional Material: 6 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    ISSN: 0365-9496
    Keywords: Chemistry ; Inorganic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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