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  • Computational Chemistry and Molecular Modeling  (16)
  • 1990-1994  (16)
  • 1
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 46 (1993), S. 119-125 
    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 lowest-energy N4 is computed ab initio to be the planar C2h(3Bu) open-chain structure 13. The open-chain N4 singlet-state structures dissociate on geometry optimization. The tetraazatetrahedrane Td structure 1 and the tetrazete D2h structure 2 are minima at MP2/6-31G*. However, both are higher in energy than 13 (24.1 and 21.2 Kcal/mol [UQCISD) (T)(full)/6-311+G*//MP2/6-31G* + ZPE(MP2/6-31G)*, respectively]. The energy of 13 is 157.5 kcal/mol higher than that of two N2(1∑g+ molecules [UQCISD(T)(Full)/6-311+G*//MP2/6-31G*] © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1065-1076 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below -10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below -10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.
    Additional Material: 16 Ill.
    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 14 (1993), S. 510-521 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present analytical expressions to calculate the gradient of the water-accessible surface area of proteins with respect to Cartesian coordinates and dihedral angles. A detailed mathematical analysis leads to corrected equations for the gradient calculation used previously in the ANAREA program. To study the hydrophobic effect of solvent-protein interactions, our expressions have been implemented to further improve the program package FANTOM. We used this version of FANTOM to minimize the ECEPP/2 and the hydrophobic energy of tendamistat. © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 46 (1993), S. 137-144 
    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: Silicon analogs of aromatic monocyclic ions, (SiH)3+ (4), (SiH)42+ (5), and (SiH)5- (6) have been studied ab initio at MP2(full)/6-31G*. The D3h structure of Si3H3+ is the global minimum, whereas other two ions are nonplanar. The D2d structure of (SiH)42+ is less folded than the carbon analog and possesses a higher stabilization energy. Stabilization energies for the monocharged ions are diminished with respect to the corresponding carbons © 1993 John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 13-18 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The principles of an efficient, fast algorithm for the calculation of diagrams appearing in Green function and many-body perturbation methods are discussed and timing examples are given. Within the suggested algorithm, the third order-diagrams required in the Green function approach are evaluated by arranging computations in such a way that the most inner loops contain only simple scalar products and multiplication of vector by scalar operations. The molecular symmetry is taken into account for abelian groups. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1149-1163 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: High-level ab initio calculations {QCISD(T)/6-311 +G**//MP2(fu)/6-31 +G**, with corrections for higher polarization [evaluated at MP2/6-311 +G(3df,2p)] and ΔZPE//MP2(fu)/6-31 +G**, i.e., comparable to Gaussian-2 theory} indicate concerted mechanisms for double- and triple-hydrogen exchange reactions in HF and HCl dimers and trimers, in mixed dimers and trimers containing one NH3, and in mixed dimers of HF, HCl, and NH3 with formic acid. All these reactions proceed via cyclic four- or six-center transition structures, the latter being generally more favorable. Calculated activation barriers (ΔHd̊ at 0 K, kcal/mol) are 42.3 for (HF)2, 20.3 for (HF)3, 41.2 for (HCl)2, 25.6 for (HCl)3, 36.0 for NH3-HF, 10.6 for NH3(HF)2, 19.9 for NH3-HCl, 2.3 for NH3(HCl)2, 9.7 for HCO2H-HF, 7.0 for HCO2H-HCl, and 11.3, for HCO2H-NH3. The barriers are lower for the more ionic systems and when more ion pair character is present. © John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1164-1171 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: One task in the interpretation of the 2-D nuclear magnetic resonance (NMR) spectrum is to assign its signal patterns to their corresponding amino acids in proteins or polypeptides. To carry out this task of interpretation, one requires sufficient chemical knowledge and expertise to reason from a set of highly noisy data. We present a system called RUBIDIUM (a Rule-Based Identification in 2-D NMR Spectrum) to formulate the expertise and automate the process of interpretation. Given a protein or polypeptide with a known amino acid sequence and the 2-D NMR spectra (both COSY and NOESY), RUBIDIUM yields plausible assignments of lines that account for most signals observed in the spectrum and conform to prior chemical knowledge. Rules of pattern matching are used to detect plausible signal patterns. The expertise of the sequence-specific assignment task is formulated to assign a signal pattern to amino acids. To cope with ambiguities and noise, RUBIDIUM adopts various low-level data preprocessing techniques, the strategy of divide and conquer, and the relaxation technique to decrease the complexity and recover from overconstrained conditions. The polypeptides oxytocin and vasopressin are used to illustrate the performance of RUBIDIUM. © John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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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: Vinyloxyboranes, CH2=CH—;O—;BR2, are shown by ab initio molecular orbital theory to be more stable than the isomeric β-aldoboranes, R2B—CH2—CH=O, by ca. 19 kcal/mol. The MP2/6-31G*/6-31G* + ZPE barrier for the [1,3] boron shift is only 10.9 kcal/mol (R = Me) relative to the aldoborane. Other C2H5BO isomers (β-ketoboranes, boraepoxides and organoboron oxides), which are related to the proposed stages in the carbonylation reaction of boranes, are shown to be plausible intermediates. However, some of the computed barriers for methyl group migrations are unrealistically large, up to ca. 63 kcal/mol.
    Additional Material: 3 Ill.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 997-1003 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The closely related Cs (1) and C2v (3) structures of CH5+ have been reinvestigated at many ab initio levels using MP2/6-31G** and MP2/6-311 + + G(2df, 2pd) geometries. The largest basis sets employed were 6-311G(3df, 2p), 6-311 + + G(3df, 3pd), and the Dunning “correlation consistent” polarized triple-split valence basis set (cc-pVTZ). Electron correlation was probed at the MP4 level, but the QCISD method was also used with the largest basis sets. While electron correlation favors 3 over 1 by about 2 kcal/mol, the correlated relative energies with all basis sets employed range from 0.36-1.03 kcal/mol in favor of 1. The best estimate of this difference, 0.86 kcal/mol, is essentially identical with the (scaled) zero-point energy difference, 0.84 kcal/mol, favoring 3 over 1. These results indicate that 1 and 3 have almost exactly the same energy at 0 K. Our best value for the dissociation energy of CH5+ is 42.0 kcal/mol [QCISD(T)/6-311 + + G(3df, 3pd)//MP2(fu)/6-311 + + G(2df, 2pd), corrected to 298 K], which agrees very well with the experimental value. © 1992 by John Wiley & Sons, Inc.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1-1 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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