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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Molecular engineering 5 (1995), S. 89-105 
    ISSN: 1572-8951
    Keywords: Molecular modelling ; protein side-chains ; hydrogen bonding ; electrostatic energy ; distributed multipole analysis ; amino/aromatic interactions ; intermolecular perturbation theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The study of small model molecules containing the relevant functional groups can help us to understand the interactions between side-chains in proteins.Ab initio quantum chemical techniques allow the interactions between the model molecules to be studied with much greater accuracy than is possible for an entire protein, where the use of simple empirical potentials is the norm. In particular, the use ofab initio methods on model molecules permits us to incorporate the atom-atom anisotropic directionality of these interactions. We survey various methods of obtaining the components of theab initio interaction energy. These are then applied to three systems of biological interest. The first of these is the arginine/aspartate pair found in salt bridges, which involves hydrogen bonding between two charged species. Secondly, we look at the arginine/phosphotyrosine interaction found in complexes between SH2 domains and peptide ligands: here we find that the arginine/phosphate part of the interaction is energetically far more important than the arginine/aromatic part. Finally, we describe a detailed study of amino/aromatic interactions in proteins: ‘unconventional hydrogen bonds’ are found to be remarkably uncommon relative to stacked geometries, and the reasons for this are examined.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1573-4951
    Keywords: DMA ; Multipoles ; Electrostatic potentials ; Molecular similarity ; Agonists ; Antagonists ; Adenosine receptor ; Binding site
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The electrostatic properties of adenosine-based agonists and xanthine-based antagonists for the adenosine A1 receptor were used to assess various proposals for their relative orientation in the unknown binding site. The electrostatic properties were calculated from distributed multipole representations of SCF wavefunctions. A range of methods of assessing the electrostatic similarity of the ligands were used in the comparison. One of the methods, comparing the sign of the potential around the two molecules, gave inconclusive results. The other approaches, however, provided a mutually complementary and consistent picture of the electrostatic similarity and dissimilarity of the molecules in the three proposed relative orientations. This was significantly different from the results obtained previously with MOPAC AM1 point charges. In the standard model overlay, where the aromatic nitrogen atoms of both agonists and antagonists are in the same position relative to the binding site, the electrostatic potentials are so dissimilar that binding to the same receptor site is highly unlikely. Overlaying the N6-region of adenosine with that near C8 of theophylline (the N6-C8 model) produces the greatest similarity in electrostatic properties for these ligands. However, N6-cyclopentyladenosine (CPA) and 1,3-dipropyl-8-cyclopentylxanthine (DPCPX) show greater electrostatic similarity when the aromatic rings are superimposed according to the flipped model, in which the xanthine ring is rotated around its horizontal axis. This difference is mainly attributed to the change in conformation of N6-substituted adenosines and could result in a different orientation for theophylline and DPCPX within the receptor binding site. However, it is more likely that DPCPX also binds according to the N6-C8 model, as this model gives the best steric overlay and would be favoured by the lipophilic forces, provided that the binding site residues could accommodate the different electrostatic properties in the N6/N7-region. Finally, we have shown that Distributed Multipole Analysis (DMA) offers a new, feasible tool for the medicinal chemist, because it provides the use of reliable electrostatic models to determine plausible relative binding orientations.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 757-774 
    ISSN: 0192-8651
    Keywords: O(SINGLE BOND)H ··· O hydrogen bond ; intermolecular perturbation theory ; crystal structures ; directionality ; esters ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An attractive way to study intermolecular hydrogen bonding is to combine analysis of experimental crystallographic data with ab initio - based energy calculations. Using the Cambridge Structural Database (CSD), a distributed multipole analysis (DMA)-based description of the electrostatic energy, and intermolecular perturbation theory (IMPT) calculations, hydrogen bonding between donor alkanol hydroxyl groups and oxygen acceptor atoms in ketone, ether, and ester functional groups is characterized. The presence and absence of lone pair directionality to carbonyl and ether or ester oxygens, respectively, can be explained in terms of favored electrostatic energies, the major attractive contribution in hydrogen bonding. A hydrogen bond in its optimum geometry is only slightly stronger when formed to a ketone group than to an ether group. Hydrogen bonds formed to carbonyl groups have similar properties in a ketone or ester, but the ester O2 differs from an ether oxygen due to various environmental effects rather than a change in its intrinsic properties. For (E)-ester oxygens, there are few hydrogen bonds found in the CSD because of the competition with the adjacent carbonyl group, but the interaction energies are similar to an ether. Hydrogen bonds to O2 of (Z)-esters are destabilized by the repulsive electrostatic interaction with the carbonyl group. The relative abundance of nonlinear hydrogen bonds found in the CSD can be explained by geometrical factors, and is also due to environmental effects producing slightly stronger intermolecular interaction energies for an off-linear geometry. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 757-774, 1997
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
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