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  • 1
    Digitale Medien
    Digitale Medien
    Springer
    Journal of computer aided molecular design 6 (1992), S. 175-190 
    ISSN: 1573-4951
    Schlagwort(e): Met-enkephalin ; Conformation ; Solvent effects ; Conformational search
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Summary An extensive exploration of the conformational hypersurface of Met-enkephalin has been carried out, in order to characterize different low-energy conformational domains accessible to this pentapeptide. The search strategy used consisted of two steps. First, systematic nested rotations were performed using the ECEPP potential. Ninety-two low-energy structures were found and minimized using the CHARMm potential. High and low-temperature molecular dynamics trajectories were then computed for the lowest energy structures in an iterative fashion until no lower energy conformers could be found. The same search strategy was used in these studies simulating three different environments, a distance-dependent dielectric ɛ=r, and two constant dielectrics ɛ=10 and ɛ=80. The lowest energy structure found in a distance-dependent dielectric is a Gly-Gly β-II′-type turn. All other structures found for ɛ=r within 10 kcal/mol of this lowest energy structure are also bends. In the more polar environments, the density of conformational states is significantly larger compared to the apolar media. Moreover, fewer hydrogen bonds are formed in the more polar environments, which increases the flexibility of the peptide and results in less structured conformers. Comparisons are made with previous calculations and experimental results.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Digitale Medien
    Digitale Medien
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 11 (1976), S. 1158-1167 
    ISSN: 0030-493X
    Schlagwort(e): Chemistry ; Analytical Chemistry and Spectroscopy
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Semi-empirical molecular orbital calculations have been used to study the substituent effect on the intensity of the m/e 43 peak ([COCH3]+) in the mass spectra of a series of 25 substituted acetophenones. The two most relevant molecular properties calculated appear to be the ionization potential and the bond density of the fragmenting bond. A semi-logarithmic plot of relative peak intensities[the ratio of m/e (43/[M]+)] versus the ratio of ionization potential to bond density for these compounds produced a linear relationship with a correlation coefficient of 0.90 from the INDO method and 0.93 from the IEHT method. The use of two different semi-empirical methods to calculate ionization potentials and bond densities, together with the qualitative agreement between the two methods and with available experimental data, substantiates the correlations obtained. In addition, the molecular orbital calculations were used to understand the anomalous behavior of the teritary butyl and para-phenyl substitutes.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 15 (1976), S. 1637-1640 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: An extensive and systematic search strategy to determine the conformational profile of 12 cyclic disulfide-bridged opioid peptides with varying affinities at the δ receptor has been carried out to identify the structure that is recognized by the δ receptor for each analogue. The methods and procedures used here for the conformational search have already been validated for [D-Pen2, D-Pen5] enkephalin (DPDPE), one member of this family. Use of these methods led to a low-energy solution conformation of DPDPE in excellent agreement with all the geometric properties deduced from its solution nmr spectra. Each of the analogue was subjected to the same procedure, involving a combination of molecular dynamics simulations at high and low temperature. The study was repeated in two environmental conditions, an apolar environment, simulated by using a distance-dependent dielectric constant, and a polar environment by embedding the peptides in a high constant dielectric ( ε = 80). An automated comparison of the different conformers based on their backbone rms and average distance between the key aromatic moieties was followed by graphic analysis using maximum structural overlap. The cross-comparison of the conformations for each analogue revealed a unique conformer that may be recognized by the δ receptor for each high-affinity analogue that permitted maintaining the critical elements required for recognition in a simple spatial orientation, while maximizing similarity in other regions. © 1993 John Wiley & Sons, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Digitale Medien
    Digitale Medien
    New York : Wiley-Blackwell
    Biopolymers 38 (1996), S. 759-768 
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The stereochemical requirements for δ-opioid receptor binding of a series of linear peptide antagonists with a novel conformationally restricted Phe analogue (Tic) as a second residue were examined by using a variety of computational chemistry methods. The δ-opioid receptor analogues with significant affinity, Tyr-Tic-NH2 (TI-NH2), Tyr-Tic-Phe-OH (TIP), Tyr-Tic-Phe-NH2(TIP-NH2), Tyr-Tic-Phe-Phe-OH (TIPP), Tyr-Tic-Phe-Phe-NH2) (TIPP-NH2), and the low affinity δ-opioid peptides Tyr-Pro-Phe-Pro-NH2 (morphiceptin) and Tyr-Phe-Phe-Phe-NH2 (TPPP-NH2), were included in this study. The conformational profiles of these peptides were obtained by consecutive cycles of high and low temperature molecular dynamic simulations, coupled to molecular mechanical energy minimization carried out until no new conformational minima were obtained. Comparing the results for TPPP-NH2 and TIPP-NH2, the presence of the conformationally restricted Tic residue did not greatly reduce the number of unique low energy conformations, but did allow low energy conformers involving cis bonds between the first two residues. The conformational libraries of these peptides were examined for their ability to satisfy the three key ligand components for receptor recognition already identified by previous studies of high affinity cyclic (Tyr1-D-Pen2-Gly3-Phe4-D -Pen5) enkephalin (DPDPE) type agonists: a protonated amine group, an aromatic ring, and a lipophilic moiety in a specific geometric arrangement. Two types of conformations common to the five high δ-opioid affinity L-Tic analogues were found that satisfied these requirements, one with a cis and the other with a trans peptide bond between the Tyr1 and Tic2 residues. Moreover, both the Tic2 and Phe3 residues could mimic the hydrophobic interactions with the receptor of the Phe4 moiety in the cyclic DPDPE type agonists, consistent with the appreciable affinity of both di-and tripeptides. The low δ-opioid receptor affinity of morphiceptin can be understood as the result of conformational preferences that prevent the fulfillment of this pharmacophore for recognition. © 1996 John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Digitale Medien
    Digitale Medien
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 7 (1973), S. 1241-1251 
    ISSN: 0030-493X
    Schlagwort(e): Chemistry ; Analytical Chemistry and Spectroscopy
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Semi-empirical molecular orbital calculations have been carried out on the steroidal hormone estrone, both as a neutral molecule and the corresponding positively charge molecular ion. These calculations provide estimates of bond densities and net atomic charges, factors deemed important in past correlations of observed mass spectra with molecular structure. Calculated net charges appear to be unrelated to fragmentation processes. Calculated bond densities of the ground state molecular ion of estrone allow prediction of gross features of fragmentation. Bond densities of excited electronic states of the molecular ion may provide a basis for finer distinction among sites of initial bond cleavage, which is information crucial to rationalization of subsequent fragmentation of the molecular ion.
    Zusätzliches Material: 4 Tab.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 273-288 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam were determined using (1) free energy simulation, (2) AMSOL-SM2 semiempirical methods, and (3) Poisson-Boltzmann methods. The goals of this study were threefold: (1) to compare the results obtained from the three different methods, (2) to investigate the effect of inclusion of intraperturbed group interactions on free energy simulation estimates of solvation free energy differences, and (3) to investigate to what extent differences in free energies of solvation among three of these inhibitors could account for observed differences in their enzyme binding free energies. In general, relative solvation free energies obtained from the free energy simulations and AMSOL-SM2 methods give comparable results (i.e., the same rank ordering and similar quantitative results, differing significantly from results obtained using Poisson-Boltzmann methods). The free energy simulation studies suggest that the neglect of intraperturbed group interactions had little effect on rank order of free energies of solvation of the polar phenylimidazoles. The relative desolvation free energies of the three inhibitors of P450cam - 1-phenylimidazole (1-PI), 2-phenylimidazole (2-PI), and 4-phenylimidazole (4-PI) - with known enzyme bound X-ray structures parallel that of their known binding affinities and could account for most of the differences in the free energies of binding of these three inhibitors to P450cam. The origin of the difference of the free energies of solution of these three inhibitors is primarily the additional interaction between solvent and N(SINGLE BOND)H group in the imidazole ring of 2- and 4-phenylimidazole that is absent in the 1-phenylimidazole isomer. This hypothesis is substantiated by a second comparison of the relative solvation free energies of 4-phenylimidazole with its methylated derivative, 3-methyl-4-phenylimidazole, also lacking an N(SINGLE BOND)H group. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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