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  • Biochemistry  (14)
  • SOLAR PHYSICS  (13)
  • 1990-1994  (27)
  • 1
    Electronic Resource
    Electronic Resource
    Efficient search for all low energy conformations of polypeptides by Monte Carlo methods (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1065-1076 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540120904
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  • 2
    Electronic Resource
    Electronic Resource
    Minimization of empirical energy functions in proteins including hydrophobic surface area effects (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 510-521 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140503
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  • 3
    Electronic Resource
    Electronic Resource
    Vectorizable algorithm for green function and many-body perturbation methods (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 13-18 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140105
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  • 4
    Electronic Resource
    Electronic Resource
    Ab initio models for multiple-hydrogen exchange: Comparison of cyclic four- and six-center systems (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1149-1163 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540141005
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  • 5
    Electronic Resource
    Electronic Resource
    Divide-and-conquer, pattern matching, and relaxation methods in interpretation of 2-D NMR spectra of polypeptides (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1164-1171 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540141006
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  • 6
    Electronic Resource
    Electronic Resource
    Vinyloxyborane and its isomers. An ab initio study of the C2H5BO potential energy surface, the barrier to 1,3-shifts in β-ketoboranes, and the mechanism of the carbonylation reaction of boranes (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 423-428 
    Details
    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.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130405
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  • 7
    Electronic Resource
    Electronic Resource
    Does CH5+ prefer a C2v rather than a Cs structure? (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 997-1003 
    Details
    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.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130810
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  • 8
    Electronic Resource
    Electronic Resource
    Editorial (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1-1 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140102
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  • 9
    Electronic Resource
    Electronic Resource
    Is tetrahedral H42+ a minimum? Anomalous behavior of popular basis sets with the standard p exponents on hydrogen (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 285-294 
    Details
    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 nature of the tetrahedral H42+ stationary point (minimum or triply degenerate saddle) depends remarkably upon the theoretical level employed. Harmonic vibrational analyses with, e.g., the 6-31G** (and 6-31 + +G**) and Dunning's [4s2p1d;2s1p] [D95(d,p)] basis sets using the standard p exponent suggest (erroneously) that the Td geometry is a minimum at both the HF and MP2 levels. This is not the case at definitive higher levels. The C3H42+ structure with an apical H is another example of the failure of the calculations with the 6-31G**, 6-311G**, and D95(d,p) basis sets. Even at MP2/6-31G** and MP2/ cc-pVDZ levels, the C3v structure has no negative eigenvalues of the Hessian. Actually, this form is a second-order saddle point as shown by the MP2/6-31G** calculation with the optimized exponent. The D4h methane dication structure is also an example of the misleading performance of the 6-31G** basis set. In all these cases, energy-optimized hydrogen p exponents give the correct results, i.e., those found with more extended treatments. Optimized values of the hydrogen polarization function exponents eliminate these defects in 6-31G** calculations. Species with higher coordinate hydrogens may also be calculated reliably by using more than one set of p functions on hydrogen [e.g., the 6-31G(d,2p) basis set]. Not all cases are critical. A survey of examples, also including some boron compounds, provides calibration. © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140305
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular orbital studies of enzyme mechanisms. II. Catalytic oxidation of alcohols by liver alcohol dehydrogenase (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 392-400 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Semiempirical (AM1) molecular orbital theory has been used to investigate the oxidation of alcohols at the active site of liver alcohol dehydrogenase (LADH). The model active site consists of a zinc dication coordinated to two methyl-mercaptans (Cys-46, Cys-176), an imidazole (His-67), and a water. An imidazole (His-51) hydrogen bonded to a hydroxy-acetate (Ser-48) forms the remote base. AM1 calculations that address the two distinct steps in the catalytic mechanism of ethanol oxidation by LADH are reported. These two steps are: (1) the deprotonation of ethanol by imidazole (His-51) via hydrogen-bonded hydroxy-acetate (Ser-48), creating a proton relay system; and (2) the rate-limiting hydride transfer step from ethanol C1 to nicotinamide adenine dinucleotide (NAD+), leading to product formation. Detailed calculations have been used to resolve the unsolved problems of mechanisms that have been suggested on the basis of kinetic data and crystal structures of several LADH complexes. We investigated two possible mechanisms for the deprotonation of ethanol, by zinc-bound OH- and by direct deprotonation of zinc-bound ethanol by imidazole via hydroxyacetate (Ser-48). Our calculations show that there is no need for LADH to activate a water molecule at the active site as in many other zinc enzymes. This result agrees with experimental evidence. Our calculations also indicate that substrates are bound in an inner-sphere-pentacoordinated complex to the active site zincion. In this case, spectroscopic investigations agree with our results but crystallographic data do not. The highest activation energy is found for the hydride transfer, in agreement with the experiment. Finally, we proposed an alternative mechanism for the mode of action of LADH based upon our results. © 1993 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140403
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