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  • Biochemistry  (103)
  • Wiley-Blackwell  (103)
  • American Chemical Society
  • Elsevier
  • International Union of Crystallography
  • Springer
  • 2000-2004
  • 1985-1989  (103)
Collection
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  • Wiley-Blackwell  (103)
  • American Chemical Society
  • Elsevier
  • International Union of Crystallography
  • Springer
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  • 1
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted pyridines in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: F, Cl, CN, CH3, CF3, CHO, NO2, NH2, N(CH3)2, OCH3, and SCH3. The results are compared with experimental values. It is found that all MINDO/3 PAs are ca. 6% too high (mean value) compared to the experimental results; on the other hand, the MNDO values are ca. 7% too low (mean value). However, a much better agreement has been observed for the AM1 method where the theoretical values are only ca. 2.4% too low (mean value). Correlations between the calculated proton affinities on one hand and the charges on the acid H atom and Hammett constants on the other hand are studied. Particularly good linear relationships are found for the 4-monosubstituted compounds within the AM1 formalism.
    Additional Material: 11 Ill.
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  • 2
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energy profiles were calculated for τ1, the C—C—C=O torsion, and τ2, the C—C—C—C torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4-21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ1, τ2) = (0, -60), (0, 180), (120, 180), (120, -60), and the maxima (0, 0), (180, 180), and (60, -60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a C—H bond trans to a C—C bond (C—Hs) is consistently shorter than a C—H bond (C—Ha) trans to another C—H bond. Specifically, for X—C(α) (= O)—C(β)—C(γ)—C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2-pentanone: (1) C(δ)—Hs 〈 C(δ)—Ha in all the conformers in which the δ-methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)-methyl and the ester groups, the bonding pattern is affected by a C—H⃛O=C interaction. (2) In the most stable conformers, (0, 60), C(β)—Ha 〈 C(β)—Hs, and C(γ)—Ha 〈 C(γ)—Hs, regardless of X. (3) The average C—C bonds in the τ2 = 180° conformers are consistently shorter than those with τ2 = 60° (compared at τ1 constant). In the most stable conformations (τ1 = 0°, τ2 = 60° or 180°), the bonding sequence is consistently C(α)—C(β) 〈 C(β)—C(γ) 〈 C(γ)—C(δ); whereas, when τ1 = 120°, C(α)—C(β) 〈 C(β)—C(γ) 〉 C(γ)—C(δ).
    Additional Material: 5 Ill.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 201-207 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A direct minimization method previously presented by the authors is applied here to biconfigurational wave functions. A very moderate increasing in the time by iteration with respect to the one-determinant calculation and good convergence properties have been found. So qualitatively correct studies on singlet systems with strong biradical character can be performed with a cost similar to that required by Hartree-Fock calculations.
    Additional Material: 3 Ill.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 778-787 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms for a finer description of cavities in continuous media and for a more efficient selection of sampling points on the cavity surface are described. Applications to the evaluation of solute surface and volume and to the calculation of the solute-solvent electrostatic interaction energy, as well as of the cavitation energy are shown as examples.
    Additional Material: 8 Ill.
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 133-147 
    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 here a protocol for the determination of oligosaccharide solution conformation from a combination of molecular mechanics calculations and NMR distance constraints treated as pseudoenergies. As an illustration of our methodology we have chosen the determination of the solution conformation of the tetrasaccharide headgroup of the glycolipid globoside. In order to test the ability of our methodology to avoid becoming trapped in local minima, we have chosen three starting structures, well displaced from one another in conformational space. The structures obtained upon convergence of the calculations with distance constraint pseudoenergies were quite similar to one another. For two of the three glycosidic linkages in globoside, the results from the calculations were virtually identical for each of the three starting structures. We also apply our protocol to a model which allows for the existence of multiple conformers in an effort to explore the possibility of conformational flexibility in the oligosaccharide headgroup of globoside.
    Additional Material: 3 Ill.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 63-76 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.
    Additional Material: 2 Ill.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 152-162 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An alternative route toward developing basis sets for post-Hartree-Fock calculations, the hybrid bond polarization function method, is investigated. Two new basis sets, denoted 6-31G(d, p)+ B and 6-31 + G(d,p)+B, are defined for the first-row hydrides. The dissociation energies of the first-row hydride species in their respective ground states are computed using full fourth-order Møller-Plesset theory, and compared with results obtained with large polarized basis sets containing no bond functions. It is shown that results are competitive even with basis sets as large as 6-311++G(3df,3pd), while computation times are reduced by a factor of 4 to 20. On empirical grounds, the basis set superposition error should be neglected entirely.
    Additional Material: 12 Tab.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 429-431 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Timings are reported for 6-31G*/UMP2 calculations on planar allene, twisted ethylene, cyclopropenyl anion, allyl, ethyl, isopropyl and CF3 radicals performed by means of the programs GAUSSIAN 80 and HONDO UMP2. The comparison of the two programs is used for pointing out several factors affecting the speed of MP2 calculations.
    Additional Material: 2 Tab.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 693-700 
    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.
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  • 10
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: From a suitable reorganisation of the sum-over-states (SOS) equations of the usual time-independent perturbation theory, recurrent expressions for static polarizability (α) and second- (beta;) and third-(γ) order hyperpolarizabilities are obtained. These expressions are given in a well-adapted way for computer implementation and lead to an efficient algorithm reducing the computing time by a factor of 50 with respect to a “brute-force” translation of the standard SOS equations.
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