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  • 1
    ISSN: 1438-2199
    Keywords: Amino acids ; Atomic multipoles ; Electrostatic effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Contemporary theoretical models used in describing electrostatic properties of amino acids in polypeptides rely usually on atomic point charges. Recently noted defects of such models in reproducing protein folding originate from the inadequate representation of the electrostatic term, in particular inability of atomic charges to account for local anisotropy of molecular charge distribution. Such defects could be corrected by multicenter multipole moments derived directly from any high quality quantum chemical wavefunctions. This is illustrated by comparison of monopole and multipole electrostatic interactions between some amino acids within glutathione S-transferase. High quality Point Charge Models (PCM) can be derived analytically from multipole moment databases. Preliminary results suggest that torsional potentials are controlled by electrostatic interactions of atomic multipoles. Examples illustrating various uses of multicenter multipole moment databases of protein building blocks in modeling various properties of amino acids and polypeptides have been described, including calculation of molecular electrostatic potentials, electric fields, interactions between amino acid residues, estimates of pKa shifts and changes in catalytic activity induced by amino acid substitutions in mutated enzymes.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Compact representation of molecular charge distribution in molecular crystals has been derived from ab-initio crystal orbital wavefunction within the framework of cumulative atomic multipole moment (CAMM) expansion. Results for HF, CO2, and cubane C8H8 crystals have been compared with values calculated for corresponding clusters within conventional LCAO MO SCF approach. CAMM technique has also been used to represent molecular charge distribution in electronic excited states using CI wavefunction obtained from multireference configuration interaction (MRD-CI) calculations. This approach supplements previously introduced uncorrelated and correlated CAMM's and allows accurate nonempirical modeling of electrostatic effects involving molecules in excited states or in crystalline environment. Improved point charge model derived from CAMM has been also described.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Correlated molecular mulitpole moments and compact correlated cumulative atomic multipole moment (CCAMM) representation of molecular charge distribution in ground as well as in excited states have been derived directly from multiple reference double-excitation configuration interaction (MRD-CI) wave functions for BH and H2CO molecules using several extended basis sets with multiple polarization functions. This approach extends previously introduced uncorrelated and correlated CAMMs, and allows obtaining inexpensive modeling of electrostatic effects involving molecules in excited electronic states. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-2234
    Keywords: Point charge model ; Multicenter multipole expansion
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Distributed Point Charge Models (PCM) for CO, (H2O)2, and HS-SH molecules have been computed from analytical expressions using multicenter multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer —S—S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter —O—O— bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1432-1432
    Keywords: Aminoacyl tRNA synthetase ; Catalytic activity ; Transition state stabilization ; Sequence motif ; Quantum chemical study ; Enzyme evolution ; Aminoacyl adenylate formation ; Signature sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The changes in the catalytic activity resulting from amino acid substitutions in the active site region have been theoretically modeled for tyrosyl tRNA synthetase (Tyr-RS). The catalytic activity was calculated as the differential stabilization of the transition state using electrostatic approximation. The results indicate that charged residues His45, His48, Asp78, Asp176, Asp194, Lys225, Lys230, Lys233, Arg265, and Lys268 play essential roles in catalysis of aminoacyl adenylate formation in Tyr-RS, which is in general agreement with previously known experimental data for residues 45, 48, 194, 230, and 233. These catalytic residues have also been used to search for sequence homology patterns among class I aminoacyl RSs of which HIGH and KMSKS conserved sequence motifs are well known. His45 and His48 belong to the HIGH signature sequence of class I aminoacyl tRNA synthetases (aRSs), whereas Arg265 and Lys268 can constitute a part of the KMSKS charge pattern. Lys225, Lys230, and Lys233 may be part of the conservative substitution pattern [HKR]-X(4)-[HKR]-X(2)-[HKR], and Asp 194 is part of the new GSDQ motif. This demonstrates that the three dimensional charge distribution near the active site is an essential feature of the catalytic activity of aRS and that the theoretical technique used in this work can be utilized in searches for the catalytically important residues that may provide a clue for a charge residue pattern conserved in evolution. The appearance of patterns I–IV in Arg-, Gln-, Met-, Ile-, Leu-, Trp-, Val-, Glu-, Cys-, and Tyr-RS indicates that all these enzymes could have the same ancestor.
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