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  • Articles  (87)
  • Biochemistry  (87)
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  • 1984  (87)
  • 11
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 261-262 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Additional Material: 2 Tab.
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  • 12
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 241-247 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Previous investigators have shown that statistical mechanical averages for configuration-dependent physical properties of long unperturbed polyoxyethylene chains are sensitive to the gauche-trans energy difference for rotation about C—C bonds. Agreement between theory and experiment could be obtained only by significant adjustment of this energy away from values predicted by semiempirical conformational energy computations. The present work examines the success of MM2 in evaluating conformational properties of long unperturbed polyoxyethylene chains. Calculations are performed which identify the rotational isomers, and their energies, for the indicated bonds in CH3OCH2CH2O—CH2—CH2—OCH2CH2OCH3. These energies are used to assign statistical weights utilized in the configuration partition function for a rotational isomeric state chain with symmetric threefold interdependent rotations. The customary generator matrix scheme is employed to evaluate the mean-square unperturbed end-to-end distance, mean-square unperturbed dipole moment, and their temperature coefficients. Contrary to computational schemes employed previously, MM2 is found to provide an estimate of the gauche-trans energy difference for rotation about C—C which is in harmony with the known dimensions and dipole moments of the unperturbed polymer. MM2 also provides good estimates for most of the other parameters required in the rotational isomeric state treatment. A notable exception is provided by the gauche-trans energy difference for rotation about the C—O bond. This energy difference is overestimated by MM2.
    Additional Material: 1 Ill.
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  • 13
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 272-279 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Various algorithms for evaluating nonbonded interactions in molecular dynamics (MD) simulations of macromolecular systems are considered, and a combination of two techniques using a space grid for finding neighbor atoms is proposed. The application of grid search techniques to nonrectangular periodic systems is discussed. Finally, the computing time required by different algorithms is compared on a Cray-1 vector processing computer as well as on a CDC Cyber 170/760 sequential computer. Neighbor list techniques turn out to be faster than the grid search techniques for the systems considered here. However, storage requirements may exclude the use of neighbor list techniques for large systems. Finally, MD of complex macromolecular systems turned out to be about 4-14 times faster on a Cray-1 than on a Cyber 170/760.
    Additional Material: 2 Ill.
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  • 14
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 280-287 
    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 computer program is described which evaluates the second-order Møller-Plesset energy using the integral list formed by HONDO 5. In this program use may be made of full molecular symmetry for most common point groups, even if they contain two-dimensional representations. The algorithm for the integral transformation may also be applied to other methods beyond Hartree-Fock. Some numerical results and timings are presented.
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  • 15
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 571-575 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Classical conformational analysis was applied to the study of the variation of heats of formation (HOF) and geometrical parameters of small-ring propellanes. As expected, the calculated HOF is the smallest for [4,4,4] propellane I and the largest for [2,2,2]propellane X. In spite of the different trends exhibited by the strain energy components, the calculated HOF values may be reproduced within a simple additivity scheme. The calculated bridgehead-bridgehead bond length is the longest for [2,2,2]propellane (1.655 Å), lowers with increasing molecular size, and is equal to 1.558 Å for [4,4,4]propellane. In agreement with experimental findings the latter value is significantly larger than the standard value of 1.54 Å typical for unstrained hydrocarbons. Other calculated geometrical parameters as well as HOF values cannot be compared with experimental and/or theoretical results since there is a lack of reliable experimental data. Surprisingly, [2,2,2]propellane was found to be more flexible than the less strained bicyclo[2,2,2]octane.
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  • 16
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 581-588 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three newly defined information theoretic topological indices, namely “degree complexity (Id),” “graph vertex complexity (HV),” and “graph distance complexity (HD)” along with three other information indices have been used to study their discriminating power of 45 trees and 19 monocyclic graphs. It is found that the newly defined indices have satisfactory discriminating power while HD has been found to be the only index to discriminate all the graphs studied.
    Additional Material: 4 Ill.
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  • 17
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 589-597 
    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 formula for the first derivative of the MCSCF energy with respect to a nuclear coordinate is reviewed. The efficient utilization of symmetry in programs employing symmetry-adapted basis functions is described: Advantages that are also obtained for higher derivatives and for gradients of nonself-consistent wave functions are briefly discussed. Using CASSCF wave functions, the method is applied to the question of nonlinearity in the heavy atom chain of propadienone (CH2CCO).
    Additional Material: 3 Ill.
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  • 18
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 606-611 
    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 transition states involved in the hetero-Diels-Alder reactions of acrylaldehyde-ethylene and butadiene-formaldehyde systems were characterized using an efficient method of locating a saddle point on the energy surface of two coordinates calculated with MINDO/3 method. It has been shown that parallel transition and rotation of the conjugate coordinate frame lead to the reaction and orthogonal coordinate system on the hyperbolic paraboloid energy surface. It was concluded that the method we adopted is similar to the “X-method” but is much simpler to apply to real reaction systems.
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  • 19
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984) 
    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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  • 20
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 5 (1984), S. 24-34 
    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 consider the problem of predicting the mode of binding of a small molecule to a receptor site on a protein. One plausible approach, given a rigid molecule and its geometry, is to search directly for the orientation in space that maximizes the degree of contact. The computation time required for such a naive procedure is proportional to n3m3, where n is the number of points in the site where binding can occur, and m is the number of atoms in the ligand. We give an alternative, combinatorial approach, in which only “contact-no-contact” criteria are considered. We relate this problem to the well-known combinatorial problem of finding cliques in a graph and show that we can use a solution to the clique problem not only to solve our original problem, but also the problem of avoiding energetically unfavorable matches. Our experience with this method indicates that the computation time required is proportional to nm2.8, with a lower constant of proportionality than that of the naive procedure.
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