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  • 201
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 369-377 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Equilibrium twist angles, rotational barriers around essential single bonds, and preferred conformations for over 60 conjugated organic molecules were calculated using the semiempirical AM1 (Austin model 1) method. Comparison with ab initio and experimental data shows that AM1 can be applied quite successfully to conformational problems of this type. Relatively large errors are, however, found for compounds in which lone pair-hydrogen and especially lone pair-lone pair interactions are decisive for their conformational behavior. AM1-calculated rotational barriers in conjugated molecules, however, are found to be much too low. Moreover, AM1 does not seem to even correctly reproduce the trend of rotational barriers within a series of structurally related compounds. E/Z energy differences obtained by AM1 are also frequently considerably too low. In contrast to rotational barriers, their trends and thus conformational preferences, however, are quite satisfactorily calculated by this method. Ionization potentials obtained by AM1 are too high by about 0.5 eV. However, trends are quite well predicted.
    Additional Material: 1 Ill.
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  • 202
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 343-355 
    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 general algorithm is described which exhaustively searches conformational space using an internal coordinate tree search. Using only geometrical operations and a set of criteria for eliminating chemically unreasonable structures, the algorithm generates starting geometries for optimization by molecular mechanics. An implementation of this algorithm is exceedingly fast and finds all known minima, as well as several new ones, for four test alkanes. This method makes feasible global conformational searches for molecules with up to 109 conformational possibilities.
    Additional Material: 3 Ill.
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  • 203
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 378-386 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article describes the use of the ICL Distributed Array Processor (DAP) for the automatic classification of chemical structure databases using the Jarvis-Patrick clustering method. This method is based upon the calculation of a table containing the nearest neighbors for each of the molecules in the database which is to be clustered. These nearest neighbors can be identified very efficiently using the DAP since it allows up to 4096 molecules to be compared with a specified molecule in parallel. Experiments with files of 4096 and 8192 structures from the Fine Chemicals Database show that clustering with the DAP is up to 6.7 times as fast as using a highly efficient, inverted file algorithm on an IBM 3083 mainframe.
    Additional Material: 2 Tab.
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  • 204
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 399-405 
    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 simple electronegativity method is used to calculate atomic charges for molecules of interest to biochemistry. These include purines, pyrimidines, and amino acids. Results are compared to those obtained from other theoretical methods (ab initio and semiempirical) as well as to nuclear magnetic resonance (NMR) data. Correlation is fair with CNDO results but very good for ab initio, DelRe, and other electronegativity methods. Good correlation was also achieved with NMR data. It is shown that a correction factor may be required in some cases and that important resonance effects need to be taken into account. Because of the small amount of calculational effort involved, these results suggest that this method could be quite useful in this field.
    Additional Material: 2 Ill.
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  • 205
    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 monocyclic β-lactam [[4(S)-methyl-2-oxo-1-azetidinyl]thia]acetic acid was studied by the semiempirical molecular orbital methods AM1, MNDO, and MINDO/3. Using the reaction coordinate option in the program MOPAC on VAX and Cray X-MP computers, the potential energy curve was calculated for rotation of the C2-N1-S-C torsional angle in the conformationally flexible side chain while optimizing all other geometrical variables in the molecule. The trajectory taken during geometry optimization was found to be sensitive to the computer, the program version, the convergence criteria, and the degree of code optimization used in the calculation. In order to reduce the likelihood of spurious results, conformational or reaction energy hypersurfaces need to be calculated with the more precise SCF convergence and minimization criteria available in programs for MINDO/3, MNDO, and AM1 calculations. The nitrogen in the model β-lactam antibiotic is predicted to invert periodically as the dihedral angle to the exocyclic N-substituent sweeps through 360°.
    Additional Material: 6 Ill.
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  • 206
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 416-423 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of 13C chemical shifts in some simple hydrocarbons have been carried out using the GIAO approach in the MINDO/3 semiempirical formalism. In order to achieve reasonable agreement with experiment it is necessary to modify (increase) the vacant orbital energies in the MINDO/3 calculation in order to reduce the magnitude of the paramagnetic contribution, and to also modify this dominant term by generally reducing it as a function of the number of hydrogen and carbon atoms bonded to the resonant nucleus in question. For a set of 34 resonant nuclei of the simpler hydrocarbons, agreement with experiment of the order of 7.8 ppm is attained; however, pathological cases such as cyclopropane and some simple allenes continue to cause problems, increasing the standard deviation of the full set to 12.5 ppm. Our results indicate that the MINDO/3 approach is as viable for 13C chemical shift calculations as other semiempirical approaches, all of which seem currently to be limited to a standard deviation of the order of 10 ppm.
    Additional Material: 2 Ill.
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  • 207
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 620-626 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In the multiplicative integral approximation (MIA), two-electron integrals are evaluated using an expansion of a product of two Gaussians in terms of auxiliary functions. An estimator of the error introduced by the approximation is incorporated in the self-consistent field (SCF) calculations and the integrals for which the error estimate is larger than a preset value are systematically corrected. In this way the results of a MIA-assisted calculation have the same accuracy as a conventional calculation. The full exploitation of the expansion technique while constructing the Fock-matrix allows important time savings. Results are presented for a number of test cases.
    Additional Material: 2 Ill.
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  • 208
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structure-taste relationships for 25 acyclic and 20 cyclic carbosulfamates were investigated by means of pattern recognition using different graph theoretical invariants as molecular substituent descriptors. The SIMCA method was used to classify the compounds into sweet and nonsweet classes. All selected graph theoretical invariants that are related to the “rooted” vertex were found to give promising results. Using the weighted path numbers and self-returning walks for the rooted atom as descriptors of substituents, we found 87% of acyclic compounds were correctly classified. Using the atomic path numbers for the rooted atom as descriptors of substituents, we found 81% of cyclic compounds were correctly classified. These results are better than previously used shape and size substituent descriptors. It may be concluded that the graph theoretical descriptors have great potential in encoding structure components in structure-activity studies (SAR) studies.
    Additional Material: 3 Ill.
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  • 209
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 803-809 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Small Sin and Aln clusters (n = 3-10) were studied with the semiempirical molecular orbital method (MO) method SINDO1. For each n, various structures were optimized to determine the most stable structure. To obtain good qualitative agreement with available ab initio calculations d orbitals had to be omitted from the basis set. Both silicon and aluminum tend to build three-dimensional structures rather than two- or one-dimensional structures, except for n = 3 or 4. The structure growth was studied by approaching various sites of stable structures with one or more atoms. It was found that silicon and aluminum exhibit different structure growth, and consequently, different most-stable structures. Ionization potentials, HOMO-LUMO energy differences, binding energies per atom, and average atomic valencies are presented.
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  • 210
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 819-826 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo statistical thermodynamic computer simulations are reported for several clusters Fe+ (H2O)n at different temperatures and for a dilute aqueous solution of Fe+ at 298 K. The energy of each configuration has been calculated in the pairwise additivity approximation using the MCY potential for the water-water interaction and an ab initio analytical potential built by us for the Fe+-H2O interaction. Energy and structural analysis of the generated configurations lead to the prediction of a coordination number of six for the first hydration shell of the Fe+ ion, both in clusters and in dilute solution. Finally, the variation in the distance to the Fe+ ion of the energy and orientation of water molecules in the solution are discussed.
    Additional Material: 5 Ill.
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  • 211
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 851-860 
    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 force field has been developed for use in MM2 calculations of geometric and energy data for linear peroxides R1—O—O—R2 and tested in some of them (R1, R2 = H, Me, Et, Pri, But). The field obtained yield results that agree considerably better with experimental and ab initio data than those afforded by the only set of estimated parameters hitherto available.
    Additional Material: 2 Ill.
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  • 212
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 844-850 
    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 determination of the vibration-rotation eigenvalues (for an electronic state of a diatomic molecule) is done using various algorithms, where the differential equation y″ + f(r)y = 0 (with given initial values yo and y′o at an origin ro) is to be integrated, that is, to be replaced by a “convenient” difference equation (DE). The best known are those of: Numerov (N), Runge-Kutta (RK), and the Taylor series expansion (TS). Each algorithm is commonly associated with an “appropriate” DE, and the conventional comparisons of algorithms and/or DE are often misleading. This work compares different DE used in the same algorithm for the same potential and with the same tests. It considers the mentioned conventional DE, and three nonconventional ones: Hajj et al. (HKN) [J. Comp. Phys., 16, 150 (1974)], Cash and Raptis (CR) [Comput. Phys. Commun., 32, 299 (1984)], and Kobeissi “integrals superposition” (IS) [J. Phys. B, 15, 693 (1982)]. A convenient test of these DE is presented and applied. It is shown that: (i) if ∊ is the average error by using Numerov DE, it is of 4∊ for RK, 2∊ for TS, ∊ × 10-3 for HKN, 4∊ × 10-4 for CR and ∊ × 10-6 for IS; (ii) if τ is the average computing time by using Numerov DE, it is of 2.9τ for RK, 3.4τ for TS, 1.5τ for HKN, 2.7τ for CR and 0.9τ for IS.
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  • 213
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 836-843 
    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 possible Cs, C2v, and C∞v structures of AlO2 corresponding to the two lowest electronic states which dissociate into the neutral Al(2P) and O2(3Σg-) fragments have been investigated at the ab initio self-consistent field (SCF) and CI levels using nonempirical pseudopotentials. The most stable structure corresponds to a C2v symmetry in the 2A2 electronic state. However, this structure presents the three-center three-electron Hartree-Fock instability and CASSCF calculations were necessary to unequivocally characterize it as true minimum. Moreover, only another stable structure, of C2v geometry, was found to be a minimum, corresponding to a low-lying excited state of 2A1 symmetry. The optimized C∞v structures were not minima on the corresponding potential energy surfaces and no evidence of any stable Cs structure was found. Calculating values are compared with the different experimental data obtained from the reaction of Al and O2 in frozen gas inert matrices.
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  • 214
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 827-835 
    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 accuracy and applicability of the finite-element method of the higher order interpolation functions to the one-dimensional Schrödinger equation were examined. When the fifth-order Lagrange and Hermite interpolation functions were used as the basis functions, practically exact solutions were obtained for all eigenvalues of several model potential energy functions. It was demonstrated that the appropriate analytical integration over the potential energy function within each element is important in the matrix element evaluation. The accuracy of the method was examined for the potential functions with a double minimum, which has a large classically forbidden region. The method was also applied to evaluate the Franck-Condon factors of the transitions between the 1 1Σg+ and 2 1Σu+ states of Na2; the latter state having a double minimum in its potential energy function.
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  • 215
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 9 (1988), S. 890-892 
    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 multiple scattering Xα(R) method with the scaling parameter α expressed as a function of the internuclear distance is applied to the Li2, N2, and F2 molecules. Compared with the results obtained by the Xα method, the calculated Xα(R) equilibrium distances are smaller, the total energies are lower, and the dissociation energies are larger.
    Additional Material: 1 Ill.
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  • 216
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    Hoboken, NJ [u.a.] : Wiley-Blackwell
    Journal of Orthopaedic Research 6 (1988), S. 196-204 
    ISSN: 0736-0266
    Keywords: Meniscus ; Exercise ; Proteoglycan ; Collagen ; Biochemistry ; Life and Medical Sciences
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Male white Leghorn chickens were exercised on a treadmill at 70-80% of their maximal oxygen consumption starting at 4 weeks and continuing up to 20 weeks of age. The effect of the strenuous exercise regime on the extracellular matrix of menisci was followed through studies of proteoglycans and collagen. Avian menisci contain type I collagen, chondroitin sulfate proteoglycans, which increase with age in amount and degree of aggregation, and dermatan sulfate proteoglycans, which decrease with age. Five weeks of exercise cause a premature decrease of dermatan sulfate proteoglycans, while the chondroitin sulfate-containing molecules become significantly more aggregrated than those of the tissue of age-matched controls. Strenuous exercise also causes a significant decrease in the number of pyridinoline crosslinks per mole of collagen in the menisci of young runners. The exercise-induced changes of proteoglycan and collagen occur only during the period of active growth, and all parameters return to normal when the animals reach skeletal maturity. The early proteoglycan aggregation and dermatan sulfate decrease induced by exercise are probably an adaption to the increased loading. Although the mechanism by which strenuous exercise reduces or delays the formation of collagen pyridinoline crosslinks in menisci of skeletally immature animals is unknown, their decrease could negatively affect the mechanical properties of the tissue during the period of active growth.
    Additional Material: 2 Ill.
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  • 217
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    Springer
    Journal of cancer research and clinical oncology 113 (1987), S. 305-309 
    ISSN: 1432-1335
    Keywords: Formaldehyde ; Mutagenicity ; Metabolism ; Biochemistry ; Carcinogenicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Formaldehyde is a reactive chemical which undergoes spontaneous reactions with various cellular constituents. Mutagenicity data may be interpreted on the background of this behavior. Mice are better able to reduce the irritating effect of formaldehyde than rats and to reduce their ventilation rate when formaldehyde acts on the respiratory tract. Subacute exposure of rats to concentrations higher than 2 ppm inhibits mucociliary clearance of the nasal epithelium and leads to progressive histological and ultrastructural lesions at this site. The occurrence of squamous cell carcinomas of the nasal epithelium of rats after 2 years inhalation of 14.3 ppm formaldehyde (CIIT study) is probably the result of chronic and recurrent local toxicity; this is supported by species differences in susceptibility to the tissue damaging and carcinogenic effect of formaldehyde (rat, mouse, hamster). Data on formaldehyde-DNA interaction further support the argument that a direct risk extrapolation from the formaldehyde effects in rats to those expected for man is not possible.
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  • 218
    ISSN: 1432-1459
    Keywords: Myoadenylate deaminase ; Histochemistry ; Biochemistry ; Neuromuscular diseases ; Exertional myalgia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A histochemical assay was routinely performed of myoadenylate deaminase (MAD) in muscle biopsy specimens. MAD was absent in 13 cases, i.e. 2.9% of the specimens. In 10 cases the deficiency was confirmed biochemically. The diagnoses in the 13 patients were: polyneuropathy (n=5), infantile spinal muscular atrophy (n=3), congenital myopathy with type 2 fibre atrophy, facioscapulohumeral myopathy, polymyositis, myotonic dystrophy and hyperornithinaemia with gyrate atrophy of the retina. In contrast, 35 unrelated patients presenting with exercise-related muscle cramps or pains showed normal histochemical MAD activity. The biopsy specimens in all of these patients were essentially normal and in none of them was the diagnosis of a neuromuscular disease made. The results failed to confirm the association of MAD deficiency with aches, cramps and pains or exertional myalgia.
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  • 219
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 549-554 
    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-oriented method for the enumeration and generation of physical trees is presented. Physical trees depict acyclic chemical structures, but the term physical is used to stress the process by which the structures are produced.
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  • 220
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    Journal of Computational Chemistry 8 (1987), S. 562-562 
    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
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  • 221
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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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  • 222
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    Journal of Computational Chemistry 8 (1987), S. 555-561 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Computer programs have been developed or are under development for the IBM personal computer that enable their users to get information on atomic charges, electrostatic potentials, conformational and other properties of molecular systems containing H, C, N, O, F, Si, P, S, or Cl atoms. The zero-order wavefunction is constructed of strictly localized molecular orbitals with fixed atomic orbital coefficients. The wave function can be refined by optimizing these coefficients, i.e., considering inductive effects via a coupled set of 2 × 2 secular equations within the CNDO/2 approximation. Delocalization and exchange effects are accounted for by expanding the wavefunction on a basis of the aforementioned strictly localized orbitals, instead of conventional atomic orbitals, and solving the corresponding SCF equations. Our method has been applied to the study of large systems. We calculated the electrostatic field of the complex of β-trypsin and basic pancreatic trypsin inhibitor and it has been found that strong field regions more or less coincide with hydration sites. A further potential application of protein electrostatic fields is in NMR spectroscopy. We found a linear correlation between CαH or backbone NH proton chemical shifts and the protein field at the site of the corresponding proton. At last, we propose a simple method to mimic the bulk around atomic clusters modeling crystalline and amorphous silicon. Based on this method we found a linear correlation between atomic net charges and bond angle distortions in silicon clusters with 35 atoms.
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  • 223
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 651-657 
    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 method of Lagrangian multipliers is used to constrain torsion angles during molecular mechanics refinement for the purpose of plotting strain energy against a reaction coordinate. A complete two-dimensional analysis of the conformational interconversion from δ- to λ-[Co(ethane-1,2-diamine) (NH3)4]3+ reveals a mechanism in which the transition state geometry has an envelope conformation and an inversion barrier of 15.7 kJ mol-1. Substitution at the carbon atoms, variation of the metal-nitrogen distance, and replacement of the amine ligands with bidentate amines only slightly alters the inversion barrier. Substitution at the nitrogen atoms of the bidentate ligand increases the inversion barrier significantly to 24.6 kJ mol-1 for (N,N,N′,N′-tetramethylethane-1,2-diamine) [(NH3)4]3+.
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  • 224
    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 have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert-Humblet-Rosenfeld (SHR) and the second on the Fano-Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano-Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas-phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.
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  • 225
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 700-717 
    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 present article addresses the problem of identifying the structure of a parent compound through its chemical fingerprints such as the various numbers of isomeric substitution patterns, along the lines of Kekulé when he arrived at his benzene formula. In a pioneering paper (1929), Lunn and Senior laid out the conceptual framework for the permutation group description of substitution isomerism. It remained, however, for Pólya's celebrated contribution (1937) to initiate the actual mathematical realization of their vision. Pólya supplied the tools for solving the isomer enumeration problem: given a (symmetrical) parent compound, enumerate its spectrum of substitution patterns. The converse problem, though ranked the more interesting one by Lunn & Senior, hardly received any mathematical attention. The present article offers a complete and effective solution.
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  • 226
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 718-726 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Stereochemistry deals primarily with distinctions based on rigid geometry, e.g., bond angles and lengths. But some chemical species have molecular graphs (such as knots, catenanes, and nonplanar graphs K5 and K3.3) that reside in space in a topologically nontrivial way. For such molecules there is hope of using topological methods to gain chemical information. Viewing a molecular graph as a topological object in space makes it unrealistically flexible; but if one proves that a certain graph is “topologically chiral” or that two graphs are “topological diastereomers,” then one has ruled out interconversion under any physical conditions for which the molecular graph still makes sense. In this paper, we consider several kinds of topological questions one might ask about graphs in space, methology and results available, and specific topological properties of various molecules.
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  • 227
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 727-735 
    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 Hartree-Fock instablities of S2N2 are reported and compared with those of S3N3- and S4N42+. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S2N3, S3N3-, and S4N42+ are of planar C2v type with one of the nitrogens stripped of its π electrons, producing a π hole.
    Additional Material: 13 Ill.
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  • 228
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    Journal of Computational Chemistry 8 (1987) 
    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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  • 229
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: To study molecular decomposition pathways it is necessary to use ab initio multireference determinant-configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD-CI (multireference double excitation-configuration interaction technique of Buenker and Peyerimhoff) calculations on the decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
    Additional Material: 3 Ill.
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  • 230
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A recently proposed Hamiltonian approach to phenomenological chemical kinetics [T. Georgian and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 10, 331 (1983); T. Georgian, J.M. Halpin, and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 11, 347 (1984)] is applied to all consecutive first-order, single-step reactions, and to all reactions possessing one autocatalytic intermediate. The reaction Hamiltonians presented are shown to be consistent with the phenomenological rate equations and the relationship between reaction form and the form of the reaction potential is discussed. In particular, we show: (1) that the interaction between consecutive reactions manifests itself as a coupling term in the reaction potential, a term which may be eliminated via transition to “normal reaction coordinates” for the chemical system; and (2) that coupled sets of autocatalytic reactions give rise to coupling terms in the reaction Hamiltonian which are characteristic of the reaction mechanism.
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  • 231
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    Journal of Computational Chemistry 8 (1987), S. 753-760 
    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 features of a chiral stationary phase used in column chromatography are discussed. The syn forms invoked in chiral recognition models are consistent with MNDO and MM2 calculations. It is speculated that the inherent flexibility of the syn form makes these phases effective templates for analyte binding.
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  • 232
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    Journal of Computational Chemistry 8 (1987), S. 761-771 
    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 electronic structure calculations have been carried out for the He(1S)-Li2 (X̃, 1∑g+) interaction both by the single-configuration SCF and correlated second-order MP2 methods using an extended basis set. From these calculations, an estimate of the isotropic (V0) and first two anisotropic (V2 and V4) terms of the He-Li2 potential surface has been obtained. An assessment of the leading induced-dipole-induced-dipole dispersion energy is presented from the MP2 energies. Where possible, a comparison is made with previous unpublished ab initio calculations by Staemmler and Stahl using the CEPA method.
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  • 233
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    Journal of Computational Chemistry 8 (1987), S. 772-777 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force constants for both anomers of glucose are evaluated using CNDO/Force method.
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  • 234
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    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.
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  • 235
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    Journal of Computational Chemistry 8 (1987), S. 788-793 
    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 variety of basis sets have been used for geometric and electronic structure studies. Electronic effects were measured using integrated spatial electron populations (ISEP). The two largest basis sets used, 6-31G* and DZ+P, give significantly different results. Use of two d-orbital sets (6-31G*[dd]) or decontraction of the 2sp shell on phosphorus has little further effect. d-Orbitals on oxygen are required for consistent electronic structure results, and d-orbitals on fluorine have a small but significant effect. Use of diffuse functions, required for anions, is not recommended with small basis sets on neutral molecules. Large negative charges (≈-1.5) on oxygen are given by all of the larger basis sets by the ISEP procedure and indicate that the PO bond in these compounds is largely semi-polar. The best simple symbolic representation of phosphine oxide is H3P+—0-, rather than H3P=0.
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  • 236
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    Journal of Computational Chemistry 8 (1987), S. 810-815 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis set expansion and correlation effects on computed hydrogen bond energies of the positive ion complexes AHn · AHn + 1+1, for AHn = NH3, OH2 and FH, have been evaluated. The addition of diffuse functions on nonhydrogen atoms is the single most important enhancement of split-valence plus polarization basis sets for computing hydrogen bond energies. Basis set enhancement effects appear to be additive in these systems. The correlation energy contribution to the stabilization energies of these complexes is significant, with the second order term being the largest term and having a stabilizing effect. The third order term is smaller and of opposite sign, while the fourth order term is smaller yet and stabilizing. As a result, computed MP4 stabilization energies are bracketed by the MP2 and MP3 energies. The overall effect of basis set enhancement is to decrease hydrogen bond energies, whereas the addition of electron correlation increases stabilization energies.
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  • 237
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    Journal of Computational Chemistry 8 (1987), S. 1025-1039 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: With advances in computer architecture and software, Newton methods are becoming not only feasible for large-scale nonlinear optimization problems, but also reliable, fast and efficient. Truncated Newton methods, in particular, are emerging as a versatile subclass. In this article we present a truncated Newton algorithm specifically developed for potential energy minimization. The method is globally convergent with local quadratic convergence. Its key ingredients are: (1) approximation of the Newton direction far away from local minima, (2) solution of the Newton equation iteratively by the linear Conjugate Gradient method, and (3) preconditioning of the Newton equation by the analytic second-derivative components of the “local” chemical interactions: bond length, bond angle and torsional potentials. Relaxation of the required accuracy of the Newton search direction diverts the minimization search away from regions where the function is nonconvex and towards physically interesting regions. The preconditioning strategy significantly accelerates the iterative solution for the Newton search direction, and therefore reduces the computation time for each iteration. With algorithmic variations, the truncated Newton method can be formulated so that storage and computational requirements are comparable to those of the nonlinear Conjugate Gradient method. As the convergence rate of nonlinear Conjugate Gradient methods is linear and performance less predictable, the application of the truncated Newton code to potential energy functions is promising.
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  • 238
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    Journal of Computational Chemistry 8 (1987), S. 1016-1024 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Techniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O(N2)) and computer time of O(N3). Our suggested implementation of the Truncated Newton technique requires storage of less than O(N1.5) and CPU time of less than O(N2) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10-6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
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  • 239
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    Journal of Computational Chemistry 8 (1987), S. 1051-1056 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It has been found that the previous MM2 (or MMP2) description of out-of-plane deformation of aromatic rings sometimes yields distortions which are much too large. As a result, rotational barriers involving distortions of such rings may be calculated to have values which are too low. Examples are collected and discussed. An alternative formulation, which appears to significantly reduce the calculational error, is presented.
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    Journal of Computational Chemistry 8 (1987), S. 1066-1067 
    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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  • 241
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    Journal of Computational Chemistry 8 (1987), S. 1084-1089 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular orbital calculation by the MINDO/3 method are reported for 50 compounds used as solvents in chemical reactions. Relationships between various parameters of electronic structure and molecular properties such as dipole moment, polarizability and Taft solvent parameters are presented. Comparison between experimental values of π* and calculated values is given.
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  • 242
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    Notes: The computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n-dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.
    Additional Material: 6 Ill.
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  • 243
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    Journal of Computational Chemistry 8 (1987), S. 1099-1103 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown how the Lagrange Multiplier method for constrained minimization can be implemented in a molecular mechanics program using the common approximations to the full-matrix Newton-Raphson minimization. The method reduces the number of cycles to achieve convergence, and also stabilizes the refinement process. Increases in computer memory requirements are small. As an application, the conformational surface of cycloheptane is calculated.
    Additional Material: 2 Ill.
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    Journal of Computational Chemistry 8 (1987), S. 1104-1108 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Myelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. We have examined the predicted structure of segments of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and coworkers as modified by Chuman, Momany, and Schafer. We have focused upon segments containing the Pro-Pro-Pro sequence (residues 100-102), which have been predicted from standard algorithms to exist in a hairpin loop connecting anti-parallel beta-strands. Both the shorter (98-105, 99-105, and 100-105) and longer segments (87-109, 87-118, and 87-120) have been examined. These results indicate potential for a chain reversal in this region. The shorter segments have been studied by others using NMR techniques and the results are compared.
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  • 245
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
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    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.
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  • 246
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    Journal of Computational Chemistry 8 (1987), S. 1117-1123 
    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 MNDO Hamiltonian as incorporated within MOPAC has been utilized to predict dynamics for some simple reactions. In one option, the intrinsic reaction coordinate has been followed along the path of steepest descent from the transition state backward to reactants and forward to products. In a second option, dynamics of isolated molecular systems have been calculated. In each case, the potential surface (as predicted by the MNDO Hamiltonian) is calculated in situ as the atomic trajectories are calculated from Newton's Laws of Motion. Several specific examples are given and discussed.
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  • 247
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    Journal of Computational Chemistry 8 (1987), S. 1090-1098 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The additional energy stabilization due to cooperative effects was calculated in extended hydrogen bonded systems O—H⃛O—H⃛O—H with unidirectional (homodromic) orientation of the O—H groups. Ab initio restricted Hartree Fock, MP2 and MP3 calculations with geometry optimization and BSSE correction have been performed using the GAUSSIAN 83 program package for the ground states of the linear water dimer with Cs symmetry and the cyclic water tetramer with S4 symmetry. The latter represents the smallest possible, experimentally observed cooperative structure. A new definition for a cooperativity parameter is proposed. The definition is based on the two-body, non-neighbour interaction energy, plus three- and four-body contributions, including one-body deformation terms in relation to the total interaction energy of the water tetramer. The advantage of this definition is its independence of the reference system, which is necessary in complicated molecular systems with an undefined number of hydrogen bonds, such as disordered or flip-flop systems. According to this definition the energy gain based on cooperativity in the S4 water tetramer is 29% with the MP3/6-31G** approximation, (30% with HF/4-31G* and 46% with HF/3-21G). The largest contribution of 18% is due to the three-body term on the MP3/6-31G** level, followed by the two-body, non-neighbour term with 11%. The four-body term and the deformation term are in the order of 1% and cancel each other because they have opposite sign.
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  • 248
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    Journal of Computational Chemistry 8 (1987), S. 1124-1130 
    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 hydrogen-hydrogen nonbonded potential which may be derived from the calculated interactions between hydrogen molecules has been obtained. The best three-parameter Buckingham function gave an RMS error of 0.18 kcal/mol in fitting Price and Stone's ab initio data for 130 pairs of hydrogen molecules, which may be compared with an RMS error of 0.74 kcal/mol using the parameters in the MM2 force field. Burton's basis set is also considered. A better fit to these data requires that the angular relationship between the bonds be included. The data for hydrogen as well as experimental data for chlorine show that these atoms appear “larger” normal to the bond axis than along the axis, and this is probably also the case for other atoms. When simple angular terms are added it is possible to fit the Price and Stone data set with an RMS error of less than 0.06 kcal/mol. The preferred function was: V = [a0 + a1(sin θ1 + sin θ2)4 + a2r]e-3r - [c0 + c1(1 + sinθ1sinθ2)]/r5. Deficiencies in the current ab initio data are discussed.
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    Journal of Computational Chemistry 8 (1987), S. 1199-1224 
    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 discuss the three fundamental issues of a computational approach in structure prediction by potential energy minimization, and analyze them for the nucleic acid component deoxyribose. Predicting the conformation of deoxyribose is important not only because of the molecule's central conformational role in the nucleotide backbone, but also because energetic and geometric discrepancies from experimental data have exposed some underlying uncertainties in potential energy calculations. The three fundamental issues examined here are: (i) choice of coordinate system to represent the molecular conformation; (ii) construction of the potential energy function; and (iii) choice of the minimization technique. For our study, we use the following combination. First, the molecular conformation is represented in cartesian coordinate space with the full set of degrees of freedom. This provides an opportunity for comparison with the pseudorotation approximation. Second, the potential energy function is constructed so that all the interactions other than the nonbonded terms are represented by polynomials of the coordinate variables. Third, two powerful Newton methods that are globally and quadratically convergent are implemented: Gill and Murray's Modified Newton method and a Truncated Newton method, specifically developed for potential energy minimization. These strategies have produced the two experimentally-observed structures of deoxyribose with geometric data (bond angles and dihedral angles) in very good agreement with experiment. More generally, the application of these modeling and minimization techniques to potential energy investigations is promising. The use of cartesian variables and polynomial representation of bond length, bond angle and torsional potentials promotes efficient second-derivative computation and, hence, application of Newton methods. The truncated Newton, in particular, is ideally suited for potential energy minimization not only because the storage and computational requirements of Newton methods are made manageable, but also because it contains an important algorithmic adaptive feature: the minimization search is diverted from regions where the function is nonconvex and is directed quickly toward physically interesting regions.
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  • 250
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    Journal of Computational Chemistry 8 (1987) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 251
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    Journal of Computational Chemistry 8 (1987), S. 1-5 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Multi-ζ Slater-type orbitals are frequently used in molecular orbital calculations. Master formulae and numerical tables are available in literature for overlap integrals between s, p, and d atomic orbitals up to principal quantum number (n) = 3 and for some other selected quantum numbers. However, no master formula or numerical table is available for quantum numbers n = 5 and above and involving ƒ orbitals. In this article recursion formulae have been presented for the calculation of the overlap integral between any two s, p, d, and ƒ atomic orbitals formed by a linear combination of Slater-type orbitals. These formulae, when expanded, would give rise to all the master formulae reported in the literature as well as formulae hitherto unreported.
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    Journal of Computational Chemistry 8 (1987), S. 28-38 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Polymer conformational analyses can require being able to model the intramolecular energetics of a very long (infinite) chain employing calculations carried out on a relatively short chain sequence. A method to meet this need, based upon symmetry considerations and molecular mechanics energetics, has been developed. Given N equivalent degrees of freedom in a linear polymer chain, N unique molecular groups are determined within the chain. A molecular unit is defined as a group of atoms containing backbone rotational degrees of conformational freedom on each of its ends. The interaction of these N molecular groups, each with a finite number of nearest neighbors, properly describe the intramolecular energetics of a long (infinite) polymer chain. Thus, conformational energetics arising from arbitrarily distant neighbor interactions can be included in the estimation of statistical and thermodynamic properties of a linear polymeric system. This approach is called the polymer reduced interaction matrix method (PRIMM) and the results of applying it to isotactic polystyrene (I-PS) are presented by way of example.
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    Journal of Computational Chemistry 8 (1987), S. 39-47 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The evolution of the CIPSI method, with the latest modifications recently implemented in our laboratory, is described. A new version, based on a diagrammatic technique, is presented. Test calculations which have been run on water, ethylene, and transacrolein, show that the new method is a powerful tool for the study of medium-size molecular systems.
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  • 254
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    Journal of Computational Chemistry 8 (1987), S. 6-27 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Comparison of the optimized geometries and SCF energies for the series XO2+, XO2, XO2-, XO2-, with X = S,N shows that d(S) functions cause larger bond shortening and energy drop than d functions centered on first-row atoms. This is further emphasized on comparing the separate effects of d(central atom) and d(O) functions for SO2 and NO2-, which are similar only for the first-row molecule. The d(S) functions are also essential for proper prediction of the OSO angles. The deformation densities calculated for each series and the corresponding X-O shared populations, change as expected on adding electrons first into σ* then into π* molecular orbitals. In the regions around nuclei the deformation densities express the behavior of the atomic s and p valence orbitals or of their product inside their radial nodes. Introduction of d functions causes substantial polarization effects. For X = N these are mostly local except in the bonding regions where d(N) and d(O) functions are somewhat interchangeable. However, d(S) functions induce also unique changes in the deformation density near O. They cause π and π′ charge migration from O to S and a σ flow in the opposite direction. These effects are largest for the hypervalent species. The unique populations of the d(S) functions are much larger than those of d(N) and d(O) functions. The contribution of d(S) functions to bonding is related to the larger amplitude at small radii of the atomic 3d(S) orbital as compared with that of 3d(N). The difference in amplitudes is related to penetration effects. Diffuse p functions affect geometries and SCF energies of doubly, but not singly negative ions. However, they mostly describe the diffuse nonbonding clouds and do not affect bonding patterns.
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  • 255
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    Journal of Computational Chemistry 8 (1987), S. 48-50 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Energies obtained by configuration interaction calculations including all double excitations with regard to the Hartree-Fock reference determinant can empirically be corrected to size consistency using either the Langhoff-Davidson (LD) formula or a formula suggested by Pople, Seeger, and Krishnan (PSK). Semiempirical MNDOC calculations suggest that for molecular systems with a large number of electrons and important correlation effects the PSK correction is superior to the LD correction.
    Additional Material: 1 Tab.
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  • 256
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surface of the van der Waals system HeLi2 is computed for the case in which the system has C2v symmetry and at the Li-Li distance (5.005 bohrs). A comparative study of the results for the two methods used, ab initio Hartree-Fock and second-order Møller-Plesset, and several basis sets, ranging from minimal to near Hartree-Fock quality, is also done. The results show the importance of correcting the basis set superposition error, and the need, in order to obtain a good description of the potential, of basis sets with polarization functions on all the atoms, when the Møller-Plesset method is used. At the Hartree-Fock level, the MINI-1 basis gives results almost of the same quality as the near Hartree-Fock basis.
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  • 257
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    Journal of Computational Chemistry 8 (1987), S. 67-80 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Intermolecular potential functions have been used to determine the equilibrium structures of the water-pyridine complexes. The dimer and symmetrical 2:1 water pyridine systems have been studied. Three water models, ST2, TIPS2, and EMPWI have been combined with two different Lennard Jones nonbonded parameters and various charge distributions for the pyridine molecule to describe the systems. For the dimer, results show two distinguishable classes of preferential hydration sites, which are specific sites corresponding to hydrogen-bonded dimer and nonspecific sites located near the hydrophobic regions. Calculations performed on hydrogen-bonded symmetrical complexes show that the planar complex is generally less stable than the complex with water molecules perpendicular to the pyridine plane. For these complexes, the major factor that influences the hydrogen-bonded configurations is the choice of the water model. The importance of atomic charge distributions for the solute over the choice of potential parameters is pointed out. Finally, the effective lone pair representation on the aromatic nitrogen atom is shown to improve the hydrogen bond geometry and the stability of the complexes.
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  • 258
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    Journal of Computational Chemistry 8 (1987), S. 81-83 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Basis set superposition error in hydrogen-bonded systems can exaggerate attraction calculated from self-consistent field energies as well as from electron correlation energies. One cause of this error is the basis set deficiency in describing the charge polarization of one constituent molecule when its bonding partner approaches. That constituent molecule's description is improved partly because of the proximity of the partner's basis functions, independent of real attraction. That polarization-related error is shown to occur primarily at the SCF level and not at correlated levels.
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  • 259
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    Journal of Computational Chemistry 8 (1987) 
    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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  • 260
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    Journal of Computational Chemistry 8 (1987), S. 84-93 
    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 effect of polarization functions for ab initio molecular orbital calculations at the 3-21G* level has been studied for disiloxane. Calculated molecular geometry, dipole moment, and the linearization barrier variation were analyzed for different uncontracted polarization functions. It was concluded that variation of the polarization function on oxygen has only a minor influence on the molecular properties of disiloxane, but its presence is required to obtain a bent geometry for the disiloxane bond. The calculated molecular properties of disiloxane are greatly influenced when the polarization function on silicon is varied. Two different values (0.3 and 0.9) for the exponent of the silicon polarization function provide results comparable to the experimental values for disiloxane. The only significant differences between the results obtained from ab initio calculations using the two polarization functions are in net atomic charges. The uncontracted polarization function of silicon with a value of 0.3 for its exponent is transferable to other organosilicon compounds. Calculated molecular geometries of flexible or rigid structures are in very good agreement with the experimental values.
    Additional Material: 10 Ill.
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  • 261
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    Journal of Computational Chemistry 8 (1987), S. 95-106 
    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 nonlinear least squares procedure based on the Meiron method is described for the evaluation of the convolutionally distorted decay curves consisting of exponentials. Most of the special procedures are well known and the selected ones proved to be the most effective. Some new procedures are introduced to facilitate the evaluation work and literature data are analyzed as an example.
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  • 262
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    Journal of Computational Chemistry 8 (1987), S. 107-116 
    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 Molecular-Orbital-Based Molecular Mechanics method (MOMM) has been employed to calculate the structures of cyclopentadiene, pyrrole, furan, thiophene, dibenzocyclopentadiene (fluorene), dibenzopyrrole, dibenzofuran, and dibenzothiophene. The dimer structures of the above compounds have also been calculated using the same method to derive the unit cells of polycyclopentadiene, polypyrrole, polyfuran, polythiophene, polydibenzocyclopentadiene, polydibenzopyrrole, polydibenzofuran, and polydibenzothiophene. The band structures, densities of states, ionization potentials, band gaps, reduction potentials, and oxidation potentials of these polymers then have been calculated by using the Valence Effective Hamiltonian method (VEH). The structural effects on electronic properties are discussed.
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  • 263
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    Journal of Computational Chemistry 8 (1987), S. 117-131 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Medium size Gaussian basis sets for inert-gas atoms (from neon to xenon) have been constructed using the energy optimization method which maintains reliable description of the long-range valence atomic region. These basis sets have been tested in SCF calculations on homonuclear inert-gas dimers. For Ne2, Ar2, and Kr2, the present results have been analyzed carefully and compared with those obtained using extended basis sets (for Kr2 extended benchmark calculations are also reported). Our interation energies agree well with accurate values and are compared with experimental data. For Ne2 and Ar2, detailed studies of basis set superposition error also are presented.
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  • 264
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    Journal of Computational Chemistry 8 (1987), S. 57-66 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using previously reported ab initio potentials of the intermolecular interaction energies of phospholipid (PL), Lysophosphatidyl Ethanolamine, with one Na+ ion and one water molecule, we performed Monte Carlo simulations for PL-water and PL-Na+-water systems. Water-water and PL-water interaction energetics of PL hydration sites are analyzed to understand, in a qualitative way, why the PL head part shows hydrophilicity and the tail part shows hydrophobicity. The interaction of Na+ with PL, as well as the interaction of water with PL, is visualized from the analysis of the hydration structures near PL, and the radial distribution functions are analyzed for selected hydration sites. The PL molecule shows much stronger interaction with Na+ than with water. The Na+ ion is likely to be strongly bound to PO4-, even to the extent of being trapped, whereas, for water, there exist two strong binding regions near NH3+ and PO4-. Three water molecules near NH3+ are much more strongly bound than four water molecules near the double-bonded oxygens of PO4-. The hydrogens of CH2 adjacent to NH3+ show somewhat strong hydrophilicity, while the hydrogens of CH2 adjacent to PO4- does not show such characteristics. The CH2 groups at the PL tail part give repulsive interactions with water molecules, showing hydrophobicity. Water molecules near the PL tail are stabilized only by water-water interactions.
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  • 265
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    Journal of Computational Chemistry 8 (1987), S. 132-141 
    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 new method for constrained nonlinear optimization known as the ellipsoid algorithm is evaluated as a means of determining and refining the conformations of peptides. Advantages of the ellipsoid algorithm over conventional optimization methods include that it avoids many local minima that other methods would be trapped by, and that it is sometimes able to find optimum solutions in which the constraints are satisfied exactly. The dihedral angles about single bonds were used as variables to keep the dimensionality low (the rate of convergence decreases rapidly with increasing dimensionality of the problem). The method is evaluated on problems involving distance constraints, and for minimization of conformational energy functions. In an initial application, conformations consistent with an experimental set of NMR distance constraints were obtained in a problem involving 48 variable dihedral angles.
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    Journal of Computational Chemistry 8 (1987), S. 149-157 
    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 transannular donor-acceptor interaction in a bicyclic azaamidinium salt was modeled by quantum mechanical calculations using a supermolecule complex consisting of a formamidinium cation and an ammonia molecule. Molecular properties are reported at various geometries. These results are compared with the results of similar calculations on the bicyclic cation itself. The model calculations and the bicyclic cation calculations are in good agreement, but both fail to reproduce the experimentally known structure. Results from ab initio calculations on the model system are discussed, as are results from calculations which included iodide as counterion.
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  • 267
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    Journal of Computational Chemistry 8 (1987), S. 142-148 
    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 semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2-methylhistamine, and 4-methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree-Fock calculations using the 3-21G and STO-3G basis sets. Based on these results and previous comparisons of STO-3G results with x-ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3-21G and STO-3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3-21G and STO-3G results than the MINDO/3 method.
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  • 268
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    Journal of Computational Chemistry 8 (1987), S. 170-173 
    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 simple computer-oriented method is presented for constructing the (molecular) distance matrix. The distance matrix considered is the graph-theoretical (topological) distance matrix.
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  • 269
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    Journal of Computational Chemistry 8 (1987), S. 186-186 
    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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  • 270
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 271
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    Journal of Computational Chemistry 8 (1987), S. 174-184 
    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 approximation to the molecular mechanical treatment of structural deformations of macromolecules is presented. The method is based on a partitioning of the conformational energy into three parts. The first part is covered by the condensed potential functions which absorb many short-range nonbonding interactions. The second part consists of a few nonbonded interactions below a very short cutoff radius of 4 Å. The third part, consisting of the vast majority of pairwise interactions, is approximated by a quadratic expression confined to a subspace of the conformational space. A detailed computational example on LH-RH, including an analysis of the errors resulting from other conventional approximation methods, is given. A comparison to the conventional cutoff approximation used in x-ray refinement delivers a speedup factor of at least two orders of magnitude.
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    Journal of Computational Chemistry 8 (1987) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 273
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    Journal of Computational Chemistry 8 (1987), S. 281-281 
    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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  • 274
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    Journal of Computational Chemistry 8 (1987), S. 282-290 
    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 have performed large-scale close coupling calculations of rotational-to-rotational energy transfer in HF—HF collisions for the realistic potential energy surface of Brobjer and Murrell. We employ up to 525 angular terms in the expansion of the potential and up to 440 coupled channels in the rotational-orbital basis set. The results for zero total angular momentum are well converged for relative translational energies up to over 0.6 eV, and they show extensive rotational excitation.
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    Journal of Computational Chemistry 8 (1987), S. 158-169 
    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 mechanism of acrylic and benzoic acid decarboxylation in aqueous solution has been investigated by ab initio methods using the STO-3G and 3-21G basis sets. In those reactions, the solvent is represented successively by one and two water molecules. Their active participation as a proton relay in the chemical process is demonstrated by the large decrease in the activation energy with respect to the reaction studied in the absence of water. In the absence of any intermediate found along the reaction pathway, the proposed mechanism is the concerted process; the free acid being the species that undergoes decarboxylation via a pseudounimolecular mechanism by interaction with a chain of water molecules. At the transition state, the carboxylic hydrogen transfer to one water molecule, the reorganization of the chain of water molecules through which the proton is transferred and the cleavage of the C—C bond are much more advanced than the proton transfer from the last water molecule to the α-carbon atom of the carboxyl group.
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    Journal of Computational Chemistry 8 (1987), S. 291-295 
    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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  • 277
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    Journal of Computational Chemistry 8 (1987), S. 296-306 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The theory of an implementation of the diabatic surface model within the Heitler-London valence bond approach is described. It is shown that the HL-VB wave function can be obtained from a Van-Vleck transformation of an MC-SCF wave function which has been built from atom-localized orbitals. This wave function is built from a superposition of two diabatic components, reactantlike and productlike. The transition structure is then obtained as the minimum of the seam of intersection of the diabatic surfaces and the algorithm for performing this constrained optimization is described. Several areas of application are also discussed.
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    Journal of Computational Chemistry 8 (1987), S. 307-312 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our procedure for employing analytical gradients of ab initio potential energy hypersurfaces in the description of centrifugally distorted molecules is applied for the first time to an asymmetric top, namely ozone. Both single determinantal (HF/6-31G*) and analytically fitted multiconfigurational self-consistent field surfaces were utilized. The focus of the HF/6-31G* study is upon the centrifugal distortion pathway. Quartic centrifugal spectroscopic coefficients are obtained in both cases and are in reasonable agreement with experiment.
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    Journal of Computational Chemistry 8 (1987), S. 333-340 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo simulation results are presented for lattice models of uniform stars (one branch point of functionality f = 3), combs (two branch points, ƒ = 3,3) and brushes (two branch points ƒ = 3,4 and ƒ = 3,5). We estimate the critical exponent γ(ƒ), the ratio g(ƒ) = 〈SN2(ƒ)〉/〈SN2(1)〉 (where 〈SN2(ƒ)〉 is the mean-square radius of gyration of a structure having ƒ branches and N monomers), and the meansquare end-to-end branch lengths, as a function of the number and arrangement of branches. Comparisons with theoretical predictions and experimental data are made where possible, leading to a test of some predictions, and a suggestion concerning future experiments.
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  • 280
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    Journal of Computational Chemistry 8 (1987), S. 313-323 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using the dressed molecule picture of molecule radiation interactions (A.D. Bandrauk et al., J. Chem. Phys., 79, 3256; 80, 4926; 83, 2840) one can deduce multiphoton processes (absorption, scattering, nonlinear optical properties, etc.) amplitudes from coupled second-order differential equations with electronic surfaces and transition moments as input data obtainable from quantum chemical calculations. The present approach enables one to include in the calculation bound and continuum states simultaneously by the use of appropriate boundary conditions for the numerical solutions of these coupled equations. In the case of weak radiative couplings, one recovers the usual Fermi-Golden rule expressions for electronic absorption, raman scattering, etc. The method is thus quite general, bridging the weak field (traditional photochemistry) and the strong field (laser chemistry) regimes which are attainable with today's lasers. The numerical solutions of the coupled equations give us the stationary states of the molecule + radiation system, called dressed molecule. Preparation of the initial state can be mimicked in the coupled equations by an artificial channel method for processes involving a final-state dissociation. Examples of such calculations will be presented in the diatomic Cl2 for which several ab initio electronic states and transition moments were available.
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    Journal of Computational Chemistry 8 (1987), S. 324-332 
    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 implementation of the GAUSSIAN 82 system of quantum chemistry codes on the CDC Cyber 205 supercomputer required approximately 1 1/2 man years of effort. Idiosyncracies of the Cyber 205 architecture, operating system, and compiler in so far as they affect the conversion and operation of large quantum chemistry codes on the machine are described. While advantage has not been taken of the powerful vector processor, the high intrinsic speed of the scalar processor and the large virtual storage capacity of the Cyber 205 make it a very powerful research tool for computational chemistry. The impact of the GAUSSIAN 82/Cyber 205 combination on computational chemistry research at the University of Calgary is illustrated by brief descriptions of a range of applications from highly accurate calculations on small systems to semiempirical studies of large molecular aggregates. Complete geometry optimizations and harmonic frequency analyses, for the most part, have become routine.
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    Journal of Computational Chemistry 8 (1987), S. 350-357 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for the solution of the vibronic Schrödinger equation is presented. The proposed approach allows the preservation of the concept of potential surfaces under inclusion of nuclear motion. The dynamical interaction of electrons and nuclei is partially included in the equation determining the potential surfaces. The corresponding electronic wave functions can be used as a basis for a generalized representation. Since the variation principle is involved for the determination of the potential surfaces, the proposed representation may be considered as a generalization of the adiabatic one. As a consequence the vibrational wave equation and the calculation of radiationless transition probabilities is simplified.
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  • 283
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    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The graph-theory derived model for the bonding topology in the globally delocalized polyhedral boranes B6H62- and B12H122- is evaluated by comparison of the energies of the core molecular orbitals with those obtained by the 1962 LCAO-MO extended Hückel calculations of Hoffmann and Lipscomb. Of particular interest is how well the complete graphs K6 and K12 used in the graph-theory derived model approximate the bonding topologies of the unique internal orbitals (radial orbitals) of the octahedron and icosahedron, respectively. In the case of the B6H62- octahedron the single positive eigenvalue of the K6 graph corresponds to the results from the extended Hückel calculations. In addition, the parameters from the latter calculations indicate a ratio of 0.625 for the overlap of the unique internal orbitals of the trans atom pairs relative to cis atom pairs as compared with unity implied by an unweighted K6 graph. In the case of the B12H122- icosahedron the graph-theory derived model is far less satisfactory since the single positive eigenvalue of the K12 graph disagrees with the four bonding core molecular orbitals (an A1g and three triply degenerate T1u molecular orbitals) found by the extended Hückel calculations after removing the effect of the mixing of core and surface bonding orbitals corresponding to the same irreducible representations. However, this core-surface orbital mixing raises the energy of the triply degenerate T1u core molecular orbitals to antibonding levels so that the graph-theory derived model fortuitiously gives correct skeletal electron counts for the regular icosahedron despite this fundamental error.
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  • 284
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: General expressions of the characteristic polynomials of various series of cyclic and linear polymers of polycyclic aromatic hydrocarbons are presented, i.e., polyacene, zigzag-polyacene, 1,4-dimethylbenzene polymer, polyperylene, etc. The densities of states of cyclic and linear polymers with the same repetitive units are shown. In some cases the allowed region of the energy levels of these polymers is found not to be the same. Several related problems are discussed.
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  • 285
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    Journal of Computational Chemistry 8 (1987), S. 367-374 
    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 simple linear notation systems are suggested to encode molecular structure including stereochemical elements. Both systems give rise to a unique numbering of the molecular graph, and thus also lead to a unique linear notation. Both linear notation systems are extremely compact and require only standard chemical symbols. A string comparison technique is developed to measure the similarity of two molecular linear notations. This procedure allows one to define a molecular similarity index with values that range from zero to unity, the zero value characterizing complete dissimilarity and the value of unity denoting identity. The notation and similarity index procedures are applied to several small molecular structures.
    Additional Material: 1 Ill.
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  • 286
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    Journal of Computational Chemistry 8 (1987), S. 375-379 
    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 square root of the density ρ½ satisfies a Schrödinger equation with an effective local potential V(r). The form of this potential is obtained for (a) the ground state of the Be atom, (b) neutral atoms in the limit of very large atomic number from the statistical theory, and (c) almost spherical molecules XH4, again in the limit of many electrons. Some comments are made on the possibility of relativistic generalization of this method.
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  • 287
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    Journal of Computational Chemistry 8 (1987), S. 380-388 
    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 character tables of the Altmann groups for the double internal rotation of C3v rotor molecules of different symmetries were determined. These symmetries were those of para-xylene, trans-1,2-dimethylcyclopropane, cis-N-methylethylidenimine, dimethylamine, and a dimethylated asymmetrical molecule. From these character tables, the symmetry eigenvectors, which block diagonalize the Hamiltonian matrix, were deduced. The symmetry eigenvectors were derived with the help of a small computer.
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  • 288
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    Journal of Computational Chemistry 8 (1987), S. 389-396 
    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 calculations are reported on the energies, geometries, vibrational frequencies, and ionization potentials of the H2C2S2 isomers: 1,2-dithiete, cis-dithioglyoxal, and trans-dithioglyoxal. In contrast to most earlier computations, the results of this work indicate that 1,2-dithiete and cis-dithioglyoxal lie close in energy (within 3 kcal/mol) with the dithial more stable. Trans-dithioglyoxal is found to be 4.1 kcal/mol more stable than the cis isomer and faces a barrier to internal rotation of 5.5 kcal/mol. The predicted rotational constants for 1,2-dithiete agree within ∼0.05 GHz with the experimentally observed values thus lending credence to the predictions for cis-dithioglyoxal (Ae 14.30683, Be 2.46324, Ce 2.10143 GHz). Vibrational frequencies are given as potential aids to the identification of these molecules. 6-31G* ΔSCF calculations predict that at low energies (8 to 13 eV) the photoelectron spectra of 1,2-dithiete, cis-dithioglyoxal and trans-dithioglyoxal should be similar.
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  • 289
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    Journal of Computational Chemistry 8 (1987), S. 397-411 
    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 perturbation theory provides a particularly promising route to EBK quantization of nonseparable systems. However, the number of terms generated when implementing perturbation theory for systems with more than two degrees of freedom can prove too large for general purpose symbolic manipulators to handle. We describe PERTURB, a specialized algebraic manipulation program written in C for quantization of multidimensional systems. A review of operator based classical perturbation theory is given, and the relationship between this type of perturbation theory and quantum mechanical Van Vleck perturbation theory discussed. The relative performance of the Dragt-Finn and Lie transform algorithms is assessed.
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  • 290
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    Journal of Computational Chemistry 8 (1987), S. 412-419 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Diffusion Monte Carlo (DMC) is a random walk computational method for solving the ground-state Schrödinger equation for atoms or molecules. One obtains a biased simulated energy which is used to estimate the exact energy, where the bias increases with the time step used in the simulation. We present six new DMC algorithms, all of which have the same theoretical justification. Yet, when applied to the LiH and H2 molecules, the algorithms give results with markedly different error. Furthermore, algorithms which exhibit a small error when applied to one molecule show significantly greater error for the other. The explanation for these results relates to sampling of configuration space in the neighborhood of the nuclei. We investigate this issue hoping that our results will aid in the design of more efficient DMC algorithms.
    Additional Material: 10 Ill.
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  • 291
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    Journal of Computational Chemistry 8 (1987), S. 420-427 
    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 master equation describing the temporal evolution of a gaseous system in contact with a heat bath can be transformed into a system of linear, constant-coefficient, first-order differential equations of moments of the population distribution. While it has the advantage that populations are obtained directly from observables (moments), this system of equations is not too well-conditioned and unless precautions are taken, unsurmountable numerical problems appear. These are principally associated with manipulations (inversion and taking the exponential of a matrix) involving slightly modified Vandermonde matrices whose elements span a very wide range of orders of magnitude. This article discusses ways to avoid these pitfalls which consist principally of a suitable matrix normalization.
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  • 292
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    Journal of Computational Chemistry 8 (1987), S. 428-435 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Space-time lattice (cellular automaton) models of pattern formation and growth are described. Suitable local rules for automation evolution represent the spreading of wave fronts of activity in an excitable medium. A random distribution of seeds produces expanding rings that fuse and are annihilated. The seeding density, pA, is used as a scaling parameter to give unique, reduced dynamics in an arbitrary dimension d. For d = 2, in this (continuum) picture, the rings fuse globally (percolate) at a critical instant, t̂c = 0.45. For the unscaled time evolution, dynamical percolation is examined in the pA × t plane. A swath of these percolating states is found. On the “explosion” boundary of this swath the percolation cluster just forms; on the “implosion” boundary it breaks up. Using a small-sample method the fractal dimension of the critical (boundary) cluster is estimated to be 1.9 (±0.01). Also percolation for continuously emitting seeds, which produce “discs” of activity, is related to ring evolution.
    Additional Material: 3 Ill.
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  • 293
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    Journal of Computational Chemistry 8 (1987), S. 448-453 
    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 open-shell coupled-cluster method and the diagrams needed for its implementation are described. The method is applied to the electron affinities of Li and Na, which are calculated in two ways: as the ionization potential of the anions or as the energy of adding the second electron to the cations. The two schemes give essentially the same results, in very good agreement (〈0.02 eV) with experiment. Three-body effects are negligible.
    Additional Material: 4 Ill.
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  • 294
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    Journal of Computational Chemistry 8 (1987), S. 436-441 
    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 theory is developed in which closed-shell molecules are viewed as systems of weakly interacting chemical bonds. Composite-particle creation operators obtained by an appropriate quasiparticle transformation are used to create the wave function of two-electron bonds. These quasiparticles are bosons, since they are composed of two electrons, but the total many-electron wave function is properly antisymmetric. The internal structure of the quasi-Bose-particles is affected by inductive interbond interactions. Delocalization and dispersion interactions between different bonds are neglected, thus the approach corresponds to a first-order many-body PT (Perturbation Theory) with a correlated, but fully localized, reference state. The whole formalism is developed ab initio. The nonorthogonality problem is handled by a biorthogonal formulation. To illustrate the effectiveness of the model, numerical calculations are reported.
    Additional Material: 2 Ill.
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  • 295
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    Journal of Computational Chemistry 8 (1987), S. 581-603 
    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 molecular mechanics (MMP2) program and procedures for the treatment of conjugated hydrocarbons, and some of the results which they can achieve are described. The program is an updated version of the similar MMP1 program, but contains some differences. It is based on an SCF π system calculation, rather than on the VESCF method used earlier. All parameters are compatible with those in the MM2 program. Hence it is possible to calculate heats of formation, resonance energies, and structures for conjugated hydrocarbons in a way that is consistent with the calculations on non-conjugated molecules. The overall results as far as structure and energy are somewhat better than they were with the MMP1 program.
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  • 296
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    Journal of Computational Chemistry 8 (1987), S. 618-624 
    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 describe a set of simple VAX assembly language, Fortran-callable subroutines for performing vectorscalar-multiply-and-add operations which can increase processing speed by more than 10%. The routines are simple enough that they may be translated readily for use on other machines.
    Additional Material: 2 Ill.
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  • 297
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    Journal of Computational Chemistry 8 (1987), S. 625-635 
    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 improved algorithm is presented for rapid calculation of the hessian matrix for the conformational energy of a protein as a function of only dihedral angles. The speed of the calculation, which is about one order faster than by the previous method, is achieved by two considerations. First, the algorithm is designed to take advantage of the supercomputer pipeline architecture. Second, long-range, nonbonded interactions are cut off and long-range electrostatic interactions are approximated by dipole-dipole interactions in order to reduce the number of pairwise interactions that have to be computed. The results of benchmark tests of the program are given as applied for four globular proteins of different sizes.
    Additional Material: 3 Ill.
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  • 298
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    Journal of Computational Chemistry 8 (1987), S. 636-644 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Large randomly sparse matrix vector products are important in a number of applications in computational chemistry, such as matrix diagonalization and the solution of simultaneous equations. Vectorization of this process is considered for the CRAY XMP, CRAY 2, and CYBER 205, using a matrix of dimension of 20 000 with from 1% to 6% nonzeros. Efficient SCATTER/GATHER capabilities add coding flexibility and yield significant improvements in performance. For the CYBER 205, it is shown that minor changes in the IO can reduce the CPU time by a factor of 50. Similar changes in the CRAY codes make a far smaller improvement.
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  • 299
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    Journal of Computational Chemistry 8 (1987), S. 645-650 
    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 27-picosecond (ps) molecular dynamics calculation has been carried out for the 1:2 enzyme-ligand complex between porcine pancreatic elastase (PPE) and acetyl-alanine-proline-alanine (APA). A data analysis has been carried out using a total of 450 structures. During the simulation, the root-mean-square fluctuations (RMSF) increased compared with the x-ray data. Some differences of the hydrogen bond arrangement in the MD average structures are found especially for SER 195, suggesting the fluctuations of the ligand molecules. The radius of gyration decreased a little during the simulation. Although intermolecular hydrogen bonds between two substrates (APA1 and APA2) has not been found by a 1.65-Å high-resolution x-ray diffraction study, the MD calculation showed the intermolecular hydrogen bond between them to be 3.2 Å. The extended active site of PPE is so wide compared with the size of a tripeptide that such a hydrogen-bound hexapeptide can be more specific than tripeptides, which is consistent with the kinetic data previously reported.
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  • 300
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    Journal of Computational Chemistry 8 (1987), S. 658-662 
    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 theoretical study of homocyclic sulfur species S6, S7, and S8 was carried out using a molecular valence method involving stepwise approximations for orthogonality and core-valence interactions. The valence shell orbitals are described at the minimal basis level. The geometries of the molecules are predicted well as compared with other theoretical studies and the experimental values. The slight overestimation of the SS bond length is typical to the nonpolarized basis sets. The energies of the valence orbitals are well in accord with the conventional all-electron ab initio results. The trend in the stabilities of the three molecules is discussed. The present method provides an attractive possibility to study homocyclic and heterocyclic systems involving heavier chalcogens with no increase of the computing time.
    Additional Material: 2 Ill.
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