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  • Biochemistry  (12)
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  • 1
    Electronic Resource
    Electronic Resource
    Three-Electron bonds. II. SS and SCL three-electron bonds (1982)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 112-116 
    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: Ab initio molecular orbital calculations are reported for the H2SSH· and H2SCl· radicals and for the H2SClH+· radical cation. The two neutral species are found to be very weakly bound van der Waals' complexes, whereas the H2SClH+· radical cation is bound by 11.9 kcal mol-1 at MP2/4-31G. The importance of charge in σ* radicals is discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540030116
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  • 2
    Electronic Resource
    Electronic Resource
    An evaluation of the performance of diffuse function-augmented basis sets for second row elements, Na-ClPart IV of a series on Efficient Diffuse Function-Augmented Basis Sets for Anion Calculation. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1109-1116 
    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 energetic effects of the addition of diffuse functions to molecules with second-row elements are much less dramatic than those for their first-row counterparts. Although diffuse functions on second-row elements have little effect on the geometries and vibrational frequencies of neutral molecules, significant changes are found for anions. While the largest basis set, 6-31 + G*, generally performs best, the results at 3-21 + G* are comparable, and this basis can be recommended for practical applications.
    Additional Material: 10 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080807
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  • 3
    Electronic Resource
    Electronic Resource
    Three electron bonds. I. The H2SSH2+ radical cation (1981)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 261-265 
    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: Ab initio molecular orbital calculations are reported for H2S, its radical cation, and the H2SSH2+ radical cation. At the MP2/4-31G level the S—S three-electron bond is 2.85 Å long, and has a dissociation energy of 31.2 kcal mole-1. The performance of MNDO semiempirical molecular orbital theory is compared with the ab initio results.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540020307
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  • 4
    Electronic Resource
    Electronic Resource
    Stabilization of methyl anions by first-row substituents. The superiority of diffuse function-augmented basis sets for anion calculations (1982)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 3 (1982), S. 363-371 
    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 entire set of methyl anions, XCH2-, substituted by first-row substituents, Li, BeH, BH2, CH3, NH2, OH, and F, was examined at various ab initio levels. Diffuse orbital-augmented basis sets, such as 4-31+G and 6-31+G*, are needed to describe the energies of these anions adequately. Estimates of proton affinities are further improved by second-order Møller-Plesset (MP2) electron correlation corrections, but relative energies are less affected. The methyl group in the ethyl anion is destabilizing, the amino substituent is borderline, but all other groups are stabilizing. Very large π effects are exhibited by BH2 and BeH groups; inductive stabilization by the electronegative F and OH groups is less effective. Lithium also is stabilizing, but the best singlet geometry of CH2Li- is not planar. A planar CH2Li- triplet with a π1 configuration may be lower in energy.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540030311
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  • 5
    Electronic Resource
    Electronic Resource
    A cautionary note on the use of the frozen-core approximation for correlation energy calculations involving alkali metals (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1147-1150 
    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: Test calculations have shown that correlation energies calculated using the frozen-core approximation in programs, such as the Gaussian series, that assume the lowest MOs to be the core orbitals may be significantly in error. Some valence orbitals in systems involving the heavier alkali metals and electronegative elements have lower energies than the highest core orbitals of the metal and are therefore erroneously omitted from the correlation energy calculation. Some examples are discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111005
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  • 6
    Electronic Resource
    Electronic Resource
    The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1064-1073 
    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 natural atomic orbital/point (NAO-PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO-PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO-PC are found to be in better agreement with those given by RHF/6-31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO-PC model is often slightly worse then the method implemented in MOPAC-ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6-31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151003
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  • 7
    Electronic Resource
    Electronic Resource
    Conformational preferences of 34 valence electron A2X4 molecules: An ab initio Study of B2F4, B2Cl4, N2O4, and C2O42- (1981)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 2 (1981), S. 20-29 
    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: Ab initio molecular orbital structures and energies of B2F4, B2Cl4, N2O4, and C2O42- have been calculated for both perpendicular D2d and planar D2h rotamers. The experimental trend toward greater preference for the D2d forms in going from B2F4 to B2Cl4 is reproduced. N2O4 favors the planar conformation, although the rotation barrier is overestimated at the theoretical levels used. The oxalate dianion is calculated to be more stable in the D2d conformation; the experimental planar arrangement in the solid may be due to crystal packing forces. The preferences for one conformation over another are small; analysis indicates that different effects may predominate in each case: π stabilization for B2F4, hyperconjugation for B2Cl4, lone-pair interactions for N2O4, and electrostatic repulsions for C2O42-.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540020106
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  • 8
    Electronic Resource
    Electronic Resource
    Efficient diffuse function-augmented basis sets for anion calculations. III.For parts I and II, and other applications of the 4-31+G basis set, see ref. 1. The 3-21+G basis set for first-row elements, Li-F (1983)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 4 (1983), S. 294-301 
    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 relatively small diffuse function-augmented basis set, 3-21+G, is shown to describe anion geometries and proton affinities adequately. The diffuse sp orbital exponents are recommended for general use to augment larger basis sets.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540040303
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  • 9
    Electronic Resource
    Electronic Resource
    Three-electron bonds. III. Phosphorus and chlorine σ* radical cations (1983)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 4 (1983), S. 404-409 
    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 radical cations H3PPH3+⋅, H3PSH2+⋅, H3PClH+·, and HClClH+· have been studied by ab initio molecular-orbital theory. An increasing tendency to adopt trigonal bipyramidal (TBP) gemoetries is observed for the phosphorus radicals with sulfur and chlorine ligands. The three-electron bond dissociation energies are calculated to be between 7 and 31 kcal mol-1. The dependence of these bond energies on the ionization potentials for the neutral hydrides is illustrated, and the deformation of phosphorus σ* radicals towards TBP structures is discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540040316
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  • 10
    Electronic Resource
    Electronic Resource
    MO-Studies of enzyme reaction mechanisms. I. Model molecular orbital study of the cleavage of peptides by carboxypeptidase A (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 704-717 
    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: Ab initio and semiempiridal (AM1) molecular orbital theory has been used to model the cleavage of formamide at the active site of carboxypeptidase A. The model active site consists of a zinc dication coordinated to two imidazoles, an acetate, a water with a hydrogen-bonded formate, and a formamide molecule as model substrate. AM1 has been compared with ab initio theory for the coordination of water and formamide to Zn++ and found to give excellent energetic results. The course of the amide cleavage was therefore calculated with AM1. The first step of the reaction is the dissociation of the zinc-coordinated water to give an active ZnOH+ species. The remote formate acts as proton acceptor. This process has an activation energy of only 4.6 kcal mol-1. The next and rate-determining step is the concerted addition of the ZnOH+ moiety to the formamide C=O bond. The Zn—O distance in the transition state is more than 3 Å. In four further steps, the amide nitrogen is protonated and the C—N bond cleaved. The net activation energy for the entire process is 15.5 kcal mol-1 relative to the active site model and 19.6 kcal mol-1 relative to the most stable point on the calculated reaction profile.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130605
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