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  • Biochemistry  (4)
  • conformational analysis  (1)
  • 1
    Electronic Resource
    Electronic Resource
    Torsional energy levels and wave functions (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 874-882 
    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: A numerical method for solving the approximate Schrödinger equation (SE) for a single internal motion is presented. In the SE the reduced moment of inertia I(φ) and potential energy V(φ) are expressed as functions of the torsional angle φ. Molecular examples include ethane, chloroethane, and 1,2-dichloroethane for which I(φ) and V(φ) have been derived from the HF/6-31G* optimized geometries and energies at φ increments of 30°. The resulting potential energy curves, energy levels, and wave functions are shown graphically. The calculated fundamental torsional frequencies are found to fall within 10 cm-1 of the experimental values. Approximations for the off-diagonal energy matrix elements, and numerical accuracy of torsional energy levels, are shown to be satisfactory. Attention is called to the computer programs developed for this work and their applications to torsional studies in relevant areas of spectroscopy, thermodynamics, and reaction rates. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130712
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  • 2
    Electronic Resource
    Electronic Resource
    Deorthogonalization of atomic originals in the CNDO approach (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 17-34 
    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 procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO-3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO-3G and 6-31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100104
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  • 3
    Electronic Resource
    Electronic Resource
    Methods for the Fourier-series expansion of torsional energies (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 733-747 
    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: Several general procedures for the derivation and analysis of a Fourier-series expansion V(φ) over computed torsional energies E(φi) are formulated. STO-3G energy values in n-butane, 1-chloropropane, and 1,2-dichloroethane are used as test data for deriving V(φ) with the numerical methods of interpolation and least squares. The accuracy of each derived V(φ) is assessed on the basis of calculated conformational properties, mean and rms deviations, and an error curve, V(φ)-V(φ)ref, where V(φ)ref represents a reference set of E(φi). Results indicate that given the same number of expansion terms, interpolation and least squares yield functions of comparable accuracy; however, interpolation is a more efficient procedure for monitoring the accuracy of a function in regions of interest. In cases where there are too few input energies to achieve the desired accuracy, energy derivatives can be employed effectively for expanding the input set. In designing special-purpose functions, the error curve can be used meaningfully as a guide; an example for producing functions that are especially well behaved in regions for gauche conformations is provided. The present study continues to add systematics and rigor to the fitting of an internal rotation potential function from energy data.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540100514
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  • 4
    Electronic Resource
    Electronic Resource
    Conformers of gaseous protonated glycine (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1862-1876 
    Details
    ISSN: 0192-8651
    Keywords: protonation of glycine ; ab initio calculations ; conformational analysis ; gas-phase basicity ; amino acids ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller-Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH3+ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)2+. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0-10 and 30-40 kcal mol-1. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1862-1876, 1998
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 5
    Electronic Resource
    Electronic Resource
    Simulations of internal rotation potential energies for substituted ethanes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 743-753 
    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: Two approaches to the simulation of internal rotation potential energies in substituted ethanes are formulated for general applications. Called the vicinal Fourier coefficient and vicinal pair energy methods, they differ only in form. The latter procedure has the advantage of yielding energy terms that represent pairwise interactions between vicinal substitutents. As numerical examples, the potential energies of ethane and five of its simple methyl and chloro derivatives are employed to simulate the corresponding energies of two higher derivatives of the series. The initial energy data were calculated by the molecular mechanics method (MM2) with geometry optimizations and the ab initio MO procedure (STO-3G) with standard geometries. Results indicate that simulated energies are reasonably accurate for the flexible-rotor model (MM2) and extremely accurate for the rigid-rotor model (STO-3G). Deviations appear to be systematic and may be rationalized on the basis of molecular structure.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110607
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