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  • 1
    ISSN: 1432-2234
    Keywords: SCF interaction energies ; Dispersion terms ; Variationperturbation approach
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A variation-perturbation procedure for the evaluation of dispersion interaction, originally proposed by Jeziorski and van Hemert, has been reformulated to include basis set extension effects on an equal footing with the SCF interaction energy, corrected for basis set superposition error (BSSE). This approach has been tested for He2, (H2)2, (H2O)2, and (C2H4)2 complexes.
    Type of Medium: Electronic Resource
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  • 2
    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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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 87 (1987), S. 526-534 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular charge distributions for several neutral and charged molecules (LiH, HF, H2O, NH3, CH3, CH4, OH−, H3O+, N2, CO, HCN, H2CO, C2H2, and N2O) have been decomposed into the sets of correlated cumulative atomic multipole moments (CCAMM). These segmental moments sum up to the corresponding correlated molecular multipole moments (CMMM) and match closely the available experimental values. The corresponding correlation contributions have been compared with basis set extension effects for a number of 6-311G(nd/mp) basis sets with multiple polarization functions. The uncorrelated moments have been presented too, allowing the correction of intramolecular correlation and basis set truncation effects in the electrostatic multipole interaction energies, molecular electrostatic potentials, etc.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The detailed mechanism of thermal cis–trans inversion of protonated diazenes and azobenzenes has been investigated for the first time using ab initio Hartree–Fock (HF), density functional theory (DFT), second order Møller–Plesset (MP2), and complete active space self consistent field (CASSCF) approaches. Protonation of one of the nitrogens at the N(Double Bond)N bond leads to a considerable (5–20 kcal/mol) reduction of the activation barrier. The magnitude of this effect depends on the electron withdrawing nature of the substituents and the differential stabilization of the transition state by positively charged functional groups. In the case of 4-phenylazopirydine protonated at pyridine nitrogen, the barrier is dramatically reduced to just 7 kcal/mol. This result establishes the lowest (close to an experimental estimate) ab initio value for the cis–trans isomerization for a substituted azobenzene. The structures of neutral and protonated transition states are similar, and the correlation effects for molecular parameters as well as the energy are negligible for extended basis set calculations. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 5
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    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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  • 7
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atom-atom potentials representing separate contributions to the nonempirical interaction energy have been derived in the SCF decomposition scheme corrected for basis set superposition error by the counterpoise method. The nontransferable long-range electrostatic multipole and classical induction terms have been evaluated directly from cumulative atomic multipole expansions, whereas the short-range exchange, charge-transfer, and electrostatic penetration contributions have been represented by simplified potentials of the form (β + δR-1) exp(-δR) fitted to the corresponding ab initio results for 336 dimer configurations formed by HF, H2O, NH3, CH4, CO, and CO2. The dominant anisotropic character of electrostatic multipole atom-atom potentials and much more isotropic nature of the potentials representing short-range terms is illustrated in the Appendix for head-on interactions in CO ‥ OC and HF ‥ FH dimers.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 8
    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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  • 9
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General guidelines for development of small but efficient basis sets for intermolecular interaction calculations have been proposed and tested for simple model systems. It has been demonstrated that the use of overlap matched atomic orbitals (OMAO) leads to significant improvement in the first-order exchange and electrostatic penetration contributions. Basis sets assuring proper charge distribution lead to a better description of the electrostatic multipole component. The ab-initio effective-core-model potential technique permits a considerable reduction of basis size while having little effect on the selfconsistent field (SCF) interaction energy if basis-set superposition error is corrected properly.
    Additional Material: 1 Ill.
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  • 10
    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.
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