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  • 1990-1994  (136)
  • 1920-1924
  • 1990  (136)
  • Biochemistry  (136)
  • 1
    Electronic Resource
    Electronic Resource
    Histochemical and biochemical plasticity of muscle fibers in the little brown bat (Myotis lucifugus) (1990)
    Springer
    Journal of comparative physiology 160 (1990), S. 183-186 
    Details
    ISSN: 1432-136X
    Keywords: Histology ; Biochemistry ; Muscle physiology ; Hibernations ; Metabolism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Fiber composition, and glycolytic and oxidative capacities of the pectoralis, gastrocnemius, and cardiac muscles from active and hibernating little brown bats (Myotis lucifugus) was studied. The data were used to test two hypotheses: First, since hibernating bats maintain the capability of flight and make use of leg muscles to maintain a roosting position all winter, the fiber composition of the pectoralis and gastrocnemius muscles should not change with season. Second, we tested the hypothesis of Ianuzzo et al. (in press), who propose that the oxidative potential of mammalian cardiac muscle should increase with increasing heart rate while glycolytic potential should not. Our results indicate that the fiber composition of the pectoralis muscle was uniformly fast-twitch oxidative (FO)_ regardless of the time of year, as predicted. However, the gastrocnemius muscle exhibited a change in FO composition from 83% in active to 61% in hibernating animals. Contrary to the variable change in histochemical properties with metabolic state, a trend of reduced maximal oxidative (CS) and glycolytic (PFK) potential during hibernation in both flight and leg muscles was apparent. The oxidative potential of flight and leg muscles decreased by 15.2% and 56.5%, respectively, while the glycolytic potential of the same muscles decreased by 23.5% and 60.5%, respectively. As predicted, the glycolytic potential of cardiac muscle remained constant between active and hibernating bats, although there was a significant decrease (22.0%) in oxidative potential during hibernation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00300951
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  • 2
    Electronic Resource
    Electronic Resource
    SCF, MP2, and CEPA-1 calculations on the OH ‥ O hydrogen bonded complexes (H2O)2 and (H2O-H2CO) (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1-18 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Counterpoise corrected ab initio calculations are reported for (H2O)2 and H2O-H2CO. Geometry searches were done in the moment-optimized basis DZP' at the SCF, MP2, and CEPA-1 levels of theory, followed by more accurate single-point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are -4.7 ±0.3 kcal/mol for a near-linear (H2O)2 structure and -4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA-1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110102
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  • 3
    Electronic Resource
    Electronic Resource
    A data compression method applicable to first-order convergent iterative procedures (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 45-57 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A data compression method is presented that is generally applicable to first-order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110105
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  • 4
    Electronic Resource
    Electronic Resource
    Partial optimization of large molecules and clusters (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 67-75 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By examining the displacement coordinate metric three modes of constrained optimization for large molecules and clusters are suggested. The first method corresponds to a conventional optimization using internal coordinates. The second mode has applications with respect to both internal and cartesian coordinates. The final mode is particularly interesting because it can result in computational savings. A mixture of both internal and cartesian coordinates is specified where these coordinates are usually a subset of the molecules or clusters total coordinate set. In the optimization only a subset of the energy derivatives need be evaluated reducing the computational effort associated with the gradient calculation.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110108
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  • 5
    Electronic Resource
    Electronic Resource
    Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 159-169 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Electrostatic potentials calculated from AM1 wave functions have been compared with ab initio STO-3G values and qualitative agreement has been found. Atomic charges derived from AM1 electrostatic potentials for both experimental and AM1 optimized geometries are of comparable quality with STO-3G potential derived charges. These results suggest that the AM1 electrostatic potential may be useful both in its own right and also for deriving atomic charges for use in molecular dynamics studies.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110202
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  • 6
    Electronic Resource
    Electronic Resource
    The theoretical reaction path for the cation radical vinylcyclobutane rearrangement: A concerted SR path (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 896-898 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio reaction path calculations for the cation radical vinylcyclobutane rearrangement at the MP2/ 6-31G*//3-21G level reveal a concerted, sr reaction path with an activation energy of 9.4 kcal/mol. The vinylcyclobutane cation radical itself, at both the MP2 and MP3 levels of theory has predominant olefin cation radical character but with modest stretching of one of the adjacent ring carbon - carbon bonds.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110710
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  • 7
    Electronic Resource
    Electronic Resource
    On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 909-923 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point-charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO-3G and 6-31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6-31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6-31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6-31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110803
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  • 8
    Electronic Resource
    Electronic Resource
    Molecular mechanics parameterization: Bond lengths and angles for nitrogen and phosphorus containing compounds (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 952-957 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular mechanics provides an excellent means of generating reasonable chemical structures in a short amount of time. Using a classical representation, a molecule can be partitioned into a collection of n-fold atomic interactions, each with an associated force constant. In order for a calculation to proceed, all of the required force constants must be known. This article presents a method of rapidly determining the values for missing parameters using appropriately scaled quantum chemical techniques.
    Additional Material: 7 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110807
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  • 9
    Electronic Resource
    Electronic Resource
    Hydration of superoxide studied by molecular dynamics simulation (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1003-1008 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics was used to study the hydration of superoxide (O2-). The Helmholtz free energy of hydration of O2- was estimated by the thermodynamic integration method. The diffusion of O2- and the water structure around O2- were also studied. Two water models were used in the calculations and the results were compared to experiments.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110812
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  • 10
    Electronic Resource
    Electronic Resource
    Pepto: An expert system for automatic peak assignment of two-dimensional nuclear magnetic resonance spectra of proteins (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 805-818 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two-dimensional Nuclear Magnetic Resonance (2DFTNMR) is presently the most powerful tool to determine protein structures in solution. Peak assignment (an interpretation of the two-dimensional spectra that leads to the individuation of pairs of Hydrogen atoms that are involved in an NOE peak) is a cornerstone of such use of 2DFTNMR. Manual peak assignment of a protein often requires months of work by a specialized equipe. An automation of this task could speed up the protein study process, or alternatively allow to study previously unmanageable proteins. This article describes PEPTO, an expert system for the interpretation of sets of 2DFTNMR spectra on proteins. The present version of the program deals with spectra obtained from NOESY and COSY experiments. Tests of PEPTO on simulated spectra of five proteins with known assignments are also described and dicussed.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110704
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  • 11
    Electronic Resource
    Electronic Resource
    Molecular mechanics. The MM3 force field for alkenes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 848-867 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM3 force field has been extended to include alkenes. Forty-five compounds were examined, and structures, conformational equilibria, heats of formation, and rotational barriers, were calculated. For a smaller representative group, the vibrational spectra and entropies were also calculated. In general, these quantities, except for the vibrational spectra, agree with available data to approximately within experimental error. The vibrational frequencies for a set of eight well-assigned structures were calculated to a root-mean-square error of 47 cm-1.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110708
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  • 12
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110801
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  • 13
    Electronic Resource
    Electronic Resource
    Combinatorial models and algorithms in chemistry. The expanded Wiener number - a novel topological index (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 899-908 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An expanded form of the Wiener number is suggested for characterization of molecular graphs and structure-property correlations. The simple, computer-oriented method for counting of the novel index is briefly discussed.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110802
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  • 14
    Electronic Resource
    Electronic Resource
    ARGOS, a vectorized general molecular dynamics program (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 943-951 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The organization of the highly vectorizable molecular dynamics simulation program ARGOS is described. The specific choice of the data structure and the separation of the calculation of interactions involving solutes and solvent molecules allows a considerable improvement in computation speed. Illustrative results are given for the NEC SX-2/400 supercomputer. For the simulation of a large biological molecule in water a speedup factor of 5 is obtained as a result of vectorization of the code to 87%. The parts of the code used in a simulation of pure water could be vectorized to 98%, leading to an overall speedup factor due to vectorization of 13. The simulation of pure water runs over 300 times faster on the SX-2/400 than on the VAX 8650.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110806
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  • 15
    Electronic Resource
    Electronic Resource
    Correlation of the acidity of substituted phenols, anilines, and benzoic acids calculated by MNDO, AM1, and PM3 with Hammett-type substituent constants (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1009-1016 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation and net atomic charges of some 120 structures involving substituted phenols, anilines, and benzoic acids and the corresponding anions were calculated by MNDO, AM1, and PM3 semiempirical methods. The gas phase acidities of substituted phenols and anilines and the net atomic charges on the anionic heteroatoms of the corresponding anions have been successfully correlated with σ- constants. Moreover, good correlations with σ were found for the charges on the acidic hydrogens of substituted phenols and anilines. In contrast, the gas phase acidities of substituted benzoic acids and the charges on the anionic oxygens of the corresponding anions are better correlated with Taft σ° constants. Comparisons of these results with experimental data and ab initio theoretical calculations indicate that AM1 and PM3 methods are much better than MNDO in predicting the acidity of aromatic compounds.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110902
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  • 16
    Electronic Resource
    Electronic Resource
    Pseudopotential calculations for methyl compounds of zinc and magnesium (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1029-1037 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Pseudopotentials and valence basis sets to be used in calculations for organometallic compounds of zinc and magnesium have been tested in calculations for the M(CH3)n (M = Zn, Mg; n = 1,2) molecules. Valence correlation effects are treated at the SDCI and CEPA levels. The capability of a polarization potential on zinc to account for the valence shell contracting effect of core valence correlation is studied. Properties considered are geometries, force constants, Mulliken populations, ionization potentials, atomization, and binding energies. Differences in bonding between the two dimethyl compounds are discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110905
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  • 17
    Electronic Resource
    Electronic Resource
    AM1 study of acid-catalyzed hydrolysis of maleamic (4-amino-4-oxo-2-butenoic) acids (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1094-1100 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The acid-catalyzed hydrolysis mechanisms of maleamic (4-amino-4-oxo-2-butenoic) acids were studied using AM1 method. The reaction proceeded mainly in two steps: (1) nucleophilic attack of the undissociated carboxyl group on the adjacent aminocarbonyl carbon via a zwitterionic intermediate; and (2) the rate-determining proton transfer to form the zwitterionic tetrahedral intermediate. In each step, the hydration of water and hydronium ion molecules was important in stabilizing the polarized intermediates. The substituent effects at the amide moiety and the 2,3-positions of the maleamic acids were qualitatively estimated for each step.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110913
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  • 18
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540111001
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  • 19
    Electronic Resource
    Electronic Resource
    The application of molecular similarity calculations (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1139-1146 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A prescription for applying the method of molecular similarity calculations based on electrostatic potentials and fields is developed by consideration of a typical structure-activity series. Firm conclusions are drawn about the nature of the grid of points surrounding the molecules and about the choice of geometry, but options for point charges are less clearcut.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111004
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  • 20
    Electronic Resource
    Electronic Resource
    A space-saving modification of Davidson's eigenvector algorithm (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1164-1168 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A modification of Davidson's eigenvalue algorithm, based on the conjugate gradient method, is described. This method needs storage only for a few vectors (five to seven, depending on the implementation), making it practical for very large problems where disk storage is the limiting factor, without the necessity of restarting or discarding some expansion vectors. The convergence characteristics of the modified method are essentially identical with those of the original Davidson method if all expansion vectors are retained in the latter.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111008
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  • 21
    Electronic Resource
    Electronic Resource
    A cautionary note on the use of the frozen-core approximation for correlation energy calculations involving alkali metals (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1147-1150 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Test calculations have shown that correlation energies calculated using the frozen-core approximation in programs, such as the Gaussian series, that assume the lowest MOs to be the core orbitals may be significantly in error. Some valence orbitals in systems involving the heavier alkali metals and electronegative elements have lower energies than the highest core orbitals of the metal and are therefore erroneously omitted from the correlation energy calculation. Some examples are discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111005
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  • 22
    Electronic Resource
    Electronic Resource
    On the evaluation of the characteristic polynomial of a chemical graph (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 217-222 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The evaluation of the characteristic polynomial of a chemical graph is considered. It is shown that the operation count of the Le Verrier-Faddeev-Frame method, which is presently considered to be the most efficient method for the calculation of the characteristic polynomial, is of the order n4. Here n is the order of the adjacency matrix A or equivalently, the number of vertices in the graph G. Two new algorithms are described which both have the operation count of the order n3. These algorithms are stable, fast, and efficient. A related problem of finding a characteristic polynomial from the known eigenvalues λi of the adjacency matrix is also considered. An algorithm is described which requires only n(n - 1)/2 operations for the solution of this problem.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110207
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  • 23
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulations of polymers: Methods for optimal Fortran programming (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 236-241 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structure of the general classical trajectory FORTRAN code is discussed for use in molecular dynamics simulations of polymer processes. Substantial reductions in the number of mathematical operations in the code are achieved by using statement functions, modifying the ususal chain rule derivatives, applying appropriate vector identities, and using closure relationships among the required derivatives of the potential.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110209
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  • 24
    Electronic Resource
    Electronic Resource
    Alternate realities - mathematical models of nature and man, by John L. Casti, Institute for Econometrics, Operations Research, and System Theory, Technical University of Vienna, John Wiley & Sons, New York, 1989, xvii + 493 pp. $34.95 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 266-267 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110213
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  • 25
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110301
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    Electronic Resource
    Ab initio study of substituent effect on the addition of hydrogen fluoride to fluoroethylenes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 170-180 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio 3-21G study of the direct addition of HF to C2HnF(4-n), with n = 0 to 4, has been performed to investigate the effect of the substituent on the reaction. Geometry optimization of all charge-transfer complexes and transition states has been done. Standard analysis of activation energies of addition reactions, vibrational and thermodynamical analysis, as well as Morokuma energy decomposition, BSSE correction, PMO analysis, and Pauling bond orders were used to explain the results. A subset of the reactions, including that of C2H4 as reference one and the two most favorable cases, was also studied at the MP2/6-31G(d,p)//HF/6-31G(d,p) level. The barriers so obtained are in agreement with the indirectly found from experimental data. It was found that the effect of the substituent is not monotonic for the additions. Decomposition of the interaction energy is shown to be adequate to explain this nonmonotonic behavior. The implications for laser chemistry of the addition of hydrogen halides to fluorosubstituted olefins is briefly discussed.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110203
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  • 27
    Electronic Resource
    Electronic Resource
    Numerical solution of a partial differential equation system describing chemical kinetics and diffusion in a cell with the aid of compartmentalization (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 194-204 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To build a kinetic model of a cell with diffusion one has to solve a coupled nonlinear partial differential equation system consisting of several hundred equations. (Several hundred chemical components undergoing several hundred reactions.) To solve this formidable mathematical problem the division of the model cell into compartments (most biochemical reactions take place in a certain part of the cell) was suggested.1 Solving the differential equation system in one compartment, the results can be used as input at other compartments until mutually consistent solutions are achieved.To test this suggestion 10 coupled chemical reactions with diffusion were investigated in a model that contains three compartments. The results in the case of pure diffusion are in excellent agreement with and without compartmentalization. After this the full problem was treated by compartmentalization using for the solution of the differential equation system a discretization of the concentrations as functions of space and time and the Newton-Raphson iterative procedure. The results obtained give reasonable space and time dependence for the concentrations of all 10 components.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110205
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  • 28
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    Relaxed potential energy surfaces of N-linked oligosaccharides: The mannose-α(1 → 3)-mannose case (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 205-216 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report calculations of potential energy surfaces where all the internal coordinates of the disaccharide Man-α(1 → 3)-Man-α-O-Me were relaxed and minimized through an extensive molecular mechanics scheme. Flexibility within the mannopyranose rings plays a crucial role. Introduction of the relaxed principle into the conformational description of the disaccharide does not greatly alter the overall shape of the low-energy domains but it reveals new local minima. However, its principle effect is the lowering of energy barriers in the potential energy surface. New conformational transitions about the glycosidic bonds appear, permiting pathways among the low energy sections. This occurs with only little variation of the classical 4C1 conformation of the mannopyranose residues. All the conformations observed in the solid state, along with those already predicted through the joint use of NMR and modeling techniques, fall into the populations of stable conformers calculated in the present work. Moreover, a satisfactory agreement is reached between previously observed NOE values, and the theoretical one, calculated from the averaging of more than 500 microstates. The present results reconciliate most of the apparently conflicting data previously reported; they provide strong support for the application of the concept of conformational averaging to solution behavior. Some limitations of the proposed methodology are also discussed.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110206
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    Electronic Resource
    Distance geometry and molecular conformation, by G. M. Crippen and T. F. Havel, Research Studies Press, Taunton, England, John Wiley and Sons, New York, 1988. pp. 541 + x pp. Price: $142.00 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 265-266 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110212
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  • 30
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    Announcement (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 268-268 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110214
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  • 31
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    Electronic Resource
    Derivation of net atomic charges from molecular electrostatic potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 297-310 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The dependence of net atomic charges, as derived from least-squares fitting to electrostatic potentials, on molecular orientation and potential site location is critically examined. A unique rotationally invariant algorithm, in which the charges may be constrained to reproduce the molecular dipole moment, is presented and the results for several basis sets compared to previous work. Significant improvements in dipole moments derived from the unconstrained charges are noted.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110304
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  • 32
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    Theoretical study of the proton affinities of 2-, 3-, and 4-monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 269-290 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted phenolates in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: H, F, Cl (only MNDO and AM1), CN, CH3, OH, NO2, OCH3, COOH, and NH2. The results are compared with experimental values (high-pressure mass spectroscopy) at 600 K. The MINDO/3 method overestimates the experimental PAs with a mean percentual error of ca. 4.3%. The MNDO results agree much better with the experimental values and are only ca. 1.3% too high. However, the best agreement is observed for the AM1 method, where the mean percentual error is only ca. 0.69% (in absolute value). The greatest disagreement is found for 2-hydroxyphenolate (ca. +2.0%) and 2-carboxyphenolate (ca. +2.7%). The PA of 2-nitrophenolate is underestimated by ca. 1.6%. Correlations between the calculated proton affinities on the one hand, charge densities on the acid H atom of the phenols, charges on the O atom in the phenolate ions, and substituent parameters on the other hand are studied. Particularly good linear relationships are found for the 3- and 4-monosubstituted compounds within the AM1 formlism. For the 2-substituted phenolates, only the AM1 method is satifactory. As a general conclusion, the AM1 method appears to be distinctly superior to MNDO for the calculation of PAs, and definitely superior to MINDO/3.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110302
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    Electronic Resource
    Use of parallel processing in the study of protein. Ligand binding (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 314-325 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have undertaken an energy minimization study of the binding of a small ligand, water, to amino acid side-chains. These calculations have been performed on a Meiko Computing surface containing a small number of transputers and on a larger transputer array installed at Edinburgh University. The aim of this study is twofold. First, we wished to compare these potential energy maps for a given side-chain as a function of the local secondary structure and also of the neighboring residue types. Secondly, the energy maps are found to be in good agreement with experimental distributions on the binding of water molecules to amino acid side-chains. The use of our in-house Meiko computing surface increases the speed of these calculations by a factor of about 25 over a VAX 11/750. With larger arrays of transputers, such as that at Edinburgh “concurrent” Supercomputer Project, we achieve increases in speed of over 200 such that these energy maps can be calculated at interactive speeds.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110306
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  • 34
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    Electronic Resource
    Calculating electrostatic forces from grid-calculated potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 401-409 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center-to-center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110315
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    Computing the electric potential of biomolecules: Application of a new method of molecular surface triangulation (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 603-622 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method is presented for defining a smooth, triangulated analytic surface for biological molecules. The surface produced by the algorithm is well-suited for use with a recently developed polarizationcharge technique1 for the computation of the electrostatic potential of solvated molecules, and may also be used for calculations of molecular surface areas and volumes. The new method employs Connolly's definitions of contact, reentrant and saddle surface,2 but includes modifications that preclude the presence of self-interesting reentrant surface, and also insure a rigorous decomposition of contact regions into curvilinear finite elements. The triangulation algorithm may be used in conjunction with the electrostatic methods described previously to compute the electric potential of molecules of arbitrary shape in solution. Applications include the estimation of hydration enthalpies, computation of the electrostatic forces associated with solvation, estimation of interactions between separate charged species in solution, and computation of the three-dimensional form of the molecular electric potential. Test calculations are presented for a double-stranded dinucleotide, the polypeptide enkephalin, and the protein ferredoxin.
    Additional Material: 16 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110509
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    Electronic Resource
    Adaptation of D2h ab initio computer code to higher-symmetry point groups (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 636-643 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The imposition of symmetry in electronic structure calculations can be plagued by artifactual symmetry-breaking in orbital or configuration amplitudes. While most ab initio computer code is well-developed to impose symmetry constraints in D2h and its subgroups, the problem is not nearly as tractable in higher-symmetry point groups. This article describes the successful modification of existing D2h ab initio computer code to handle symmetry constraints in higher-symmetry point groups. Prospects for the development of ab initio computer code that runs fully under any point group are also discussed.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110512
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    Electronic Resource
    Electronic Resource
    Extended basis sets for the transition metals yttrium through cadmium (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 518-523 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Extended Slater basis sets were developed for the transition metals yttrium through cadmium. Gaussian expansions of these basis sets are extremely useful for ab initio methods which employ six Cartesian Gaussians for the description of the d orbitals. The s-type function generated from the symmetric combination of the x2, y2, and z2 Cartesian Gaussians is used to describe the 4s region, thereby reducing the overall number of functions for molecular calculations and reducing the redundancy in the basis set.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110410
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    Electronic Resource
    Reply to “Comments on a comparison of AM1 with the recently developed PM3 method” (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 543-544 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110414
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    Electronic Resource
    H/He Molecules in strong electric fields (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 548-559 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Floating spherical Gaussian orbitals are used within a split-shell description to calculate the properties of H, He, He+, H2, H+2, HeH+, and H+3 in a strong uniform electric field. Accurate polarizabilities including their field strength dependence are obtained with two basis functions at most. Critical field strengths for ionization and deprotonation are determined for different orientations of molecules. Electron tunneling is described within the time dependent approach using floating Gaussian orbitals also.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110503
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    A vibrational molecular force field of model compounds with biological interest. I. Harmonic dynamics of crystalline urea at 123 K (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 560-568 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Normal coordinate calculations have been performed for urea and deuterated urea in the crystalline state. We have used the modified Urey-Bradley-Shimanouchi intramolecular potential energy function and a rather sophisticated intermolecular energy function to reproduce I.R. and Raman frequencies with an average error of 2 cm-1. The general agreement between the calculation and experiment suggests that intermolecular interactions must be taken into account to determine reliable intramolecular parameters of the potential energy function, mainly the barrier to internal rotation around the C—N bond. The intermolecular energy function, which consists of the Buckingham function and an explicit harmonic function for hydrogen-bonding, then has the merit to reproduce quite well the observed frequencies of lattice vibrations.
    Additional Material: 11 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110504
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    Electronic Resource
    Design and application of a molecular mechanics force field for alkyl iodides including an electrostatic polarization model (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 734-742 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe a force field extending Boyd and Kesner's molecule mechanics treatment of alkyl chlorides, fluorides and bromides to alkyl iodides: accordingly, as well as parameters for the potential energy of bond stretching and bending and for interactions between nonbonded atoms, the field includes parameters taking into account permanent and induced C-I dipoles, whose values have been estimated by fitting the model to experimental dipole moment data. The results of applying this force field to 22 organic iodides comprising several substitution series are reported, and the structural and energy trends in the various series are discussed. These results agree satisfactorily with available experimental data and with those obtained by A. Y. Meyer using a different kind of force field.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110606
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    On the interaction of palladium with olefinic systems (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 754-763 
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    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 all electron Hartree-Fock gradient calculations and geometry optimizations on systems composed of one to three palladium atoms and: CH3 cation and anion, C2H4, C2H3NH2, C4H4, NH3, and (NH3) + (C2H4). Several basis set considerations are discussed and the binding energies of Pd to these small molecules are reported. We find the counterpoise correction to the binding energies of these systems to be large. We also present MP2 calculations of the palladium binding energy with a large uncontracted palladium spd basis set in the PdC2H4 and PdNH3 systems. The binding interaction between ethylene and palladium results in a mixing of the 4d-π* and 5s-π orbitals, and, is dissociative to the ethylene. The palladium-butadiene and palladium-cyclobutene relative stabilites and structures are interesting since these molecules could form from acetylene on a palladium surface. We find the Pd-butadiene cyclic structure to be 43 kcal/mol more stable than the Pd-cyclobutene product.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110608
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    Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride-ion transfer between the NADH analogue, 1-methyl-dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 791-804 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: As part of a study of factors controlling biological redox reactions of nicotinamide cofactors [nicotinamide adenine dinucleotide (phosphate) NAD(P)H], we have investigated the effect on a model reaction of the conformational state (cis or trans) of the carboxamide side chain, using quantum chemical methods. The reaction is that for the enzyme dihydrofolate reductase between the NADPH analogue, 1-methyl-dihydronicotinamide, and the protonated forms of the folate and dihydrofolate substrate analogues, pyrazine and dihydropyrazine. Some calculations on pterin and dihydropterin substrate analogues were also carried out in order to gauge the effects of inter-ring coupling. The influence of carboxamide side-chain conformation of nicotinamide on the energetics of the hydride-ion transfer, and on the structures of the transition states and stable intermolecular-interaction complexes, are examined as a function of the orientation of approach of the reactants. These approach geometries include those corresponding to the observed binding of cofactor and either substrate or inhibitor in the enzyme active site. Reactant, product, reactants-complex, and transition-state geometries were optimized at the semiempirical AM1 level, while ab initio SCF/STO-3G and SCF/3-21G single-point calculations were carried out at the AM1 optimized geometries for all species, as well as full geometry optimizations for isolated reactants and products. The results show that reactants-complex and transition-state energies are lower for the trans conformer of dihydronicotinamide than for the cis conformer, due to more favorable H-bonding or electrostatic interactions with the protonated substrate. Also, consideration of the structural parameters, including reaction coordinate bond lengths, ring geometries, and charge distributions, indicate that the trans transition states are more product-like than those for the cis. For the (trans) approaches corresponding to the enzymic orientation for substrate, the intermolecular interaction for the folate reaction lacks the stabilizing influence of the formal H-bond which is present for the dihydrofolate reaction, and consequently the reactants-complex and transition state are less stable.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110703
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    The anomeric effect: Ab-initio studies on molecules of the type X—CH2—O—CH3 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 765-790 
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    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 anomeric effect of the functional groups X = C≡N, C≡CH, COOH, COO-, O—CH3, NH2, and NH+3 has been studied with ab initio techniques. Geometry effects upon rotation around the central C—O bond in X—CH2—O—CH3 have been compared in the various compounds. The energy differences between the conformers with a gauche and trans (X—C—O—C) arrangement were calculated at the 6-31G* level in the fully optimized 4-21G geometries. Energy differences calculated at the 4-21G level appeared not to be reliable, especially for the groups X that contain non-sp3 hybridized atoms. The 6-31G* energy differences indicate a normal anomeric effect for X = COO-, O—CH3, and NH2(g+) (ca. 13 kJ/mol) and a small anomeric effect for X = COOH, C≡N, and C≡CH (ca. 6 kJ/mol). For X = NH2(t) and NH+3 a reverse anomeric effect occurs. These observations are in line with experimental results and evidence is given for a competition among various stereoelectronic interactions that occur at the same anomeric center. Geometry variations can be understood in terms of simple rules associated with anomeric orbital interactions. Trends followed when the group X is varied cannot be related in a straightforward way to the energy differences between the trans and the gauche forms in these compounds. Only the variation in the gauche torsion angle X—C—O—C follows roughly the same trend.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110702
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    Electronic Resource
    Computer generation of distance polynomials of graphs (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 829-836 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computer program is developed to compute distance polynomials of graphs containing up to 200 vertices. The code also computes the eigenvalues and the eigenvectors of the distance matrix. It requires as input only the neighborhood information from which the program constructs the distance matrix. The eigenvalues and eigenvectors are computed using the Givens-Householder method while the characteristic polynomials of the distance matrix are constructed using the codes developed by the author before. The newly developed codes are tested out on many graphs containing large numbers of vertices. It is shown that some cyclic isospectral graphs are differentiated by their distance polynomials although distance polynomials themselves are in general not unique structural invariants.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110706
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  • 46
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    Molecular mechanics (MM3) calculations on conjugated hydrocarbons (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 868-895 
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    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 MM3 molecular mechanics program has been extended to conjugated systems. A VESCF method is applied to the pi-system to calculate bond orders, from which various stretching and torsional parameters are obtained. The procedure gives somewhat better results than the analogous MM2 calculations. It has been applied to a study of 81 compounds of aromatic and other conjugated hydrocarbons, as well as 45 alkenes and unconjugated polyenes. The structures calculated are generally in good agreement with experiment, and the heats of formation of these compounds can be calculated with a rms value of 0.62 kcal/mol, which may be compared with the average experimental error of 0.61 kcal/mol. In addition, vibrational frequencies for five representative conjugated model structures are calculated, with an rms value of 46 cm-1, and from these, other properties such as entropy can be calculated.
    Additional Material: 29 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110709
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    Simulations of internal rotation potential energies for substituted ethanes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 743-753 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two approaches to the simulation of internal rotation potential energies in substituted ethanes are formulated for general applications. Called the vicinal Fourier coefficient and vicinal pair energy methods, they differ only in form. The latter procedure has the advantage of yielding energy terms that represent pairwise interactions between vicinal substitutents. As numerical examples, the potential energies of ethane and five of its simple methyl and chloro derivatives are employed to simulate the corresponding energies of two higher derivatives of the series. The initial energy data were calculated by the molecular mechanics method (MM2) with geometry optimizations and the ab initio MO procedure (STO-3G) with standard geometries. Results indicate that simulated energies are reasonably accurate for the flexible-rotor model (MM2) and extremely accurate for the rigid-rotor model (STO-3G). Deviations appear to be systematic and may be rationalized on the basis of molecular structure.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110607
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    Automated conformational analysis: Directed conformational search using the A* algorithm (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1193-1205 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A common requirement in conformational analysis is the identification of a molecule's lowest energy conformations. The application of the A* algorithm to this problem is examined. The algorithm uses heuristic information about the problem domain to direct the search and has been implemented in a system for performing automated conformational analysis. The method is detailed and sample results presented. Some limitations of the approach are identified.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111012
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    Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1169-1180 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (α-helical decaglycine) in vacuo, a protein (Pancreatic Trypsin Inhibitor, PTI) in vacuo, and a fully solvated protein (PTI in water). The equations of motion were integrated using Andersen's velocity version of the Verlet algorithm with internal contraints (the RATTLE algorithm). The accuracy with which the equations of motion are integrated has been analyzed for several different simulation conditions. The effects of various nonbonded interaction truncation schemes on the conservation of energy have been examined, including the use of atomic cutoffs, and (neutral group) residue cutoffs. The use of a smoothing function to eliminate the discontinuities in the potential at the cutoff leads to a significant improvement in the accuracy of the integration for each of the systems studied. The accuracy with which the equations of motion are integrated using the RATTLE algorithm for pure water and for the solvated protein are found to be comparable when the nonbonded interactions are tapered with a smoothing function at the cutoff.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111009
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    Compact contracted basis sets for third-row atoms: Ga-Kr (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1206-1216 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The (14s11p5d) primitive basis set of Dunning for the third-row main group atoms Ga-Kr has been contracted [6s4p1d]. The core functions have been relatively highly contracted while those which represent the valence region have been left uncontracted to maintain flexibility. Calculations with the [6s4p1d] contraction are reported for a variety of molecules involving third-row atoms. This basis set is found to satisfactorily reproduce experimental properties such as geometric configurations, dipole moments, and vibrational frequencies for a range of molecules. Comparisons are made with the performance of the uncontracted basis set. Polarization functions for the contracted basis set are reported and performance of the basis set with and without polarization functions is examined. A relaxation of the [6s4p1d] contraction to [9s6p2d] for higher level evergy calculations is also presented.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111013
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    The effect of diffuse functions on minimal basis set superposition errors for H-bonded dimers (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 930-942 
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    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 the addition of diffuse functions of sp type on the first row atoms (and/or of d type on phosphorus) to a MINI-1 minimal basis set is evaluated by comparing the SCF description of the interaction energy and its decomposition, counterpoise (CP) corrected and uncorrected for basis set superposition errors (BSSEs), with that produced by extended basis sets (6-31G** and 3-21G+) as well as by basis sets (6-31G** + VPS and (2d)S), previously successfully tested, designed to minimize the BSSE. The systems considered are a few anions (F-, HCOO-, H2PO-4) H-bonded to water; the basis set performance on a different geometry (bifurcated instead of linear) of the phosphate-water adduct was also considered. An additional comparison with the interaction energy in a neutral dimer, (HF)2, was carried out. The addition of diffuse functions to the MINI-1 basis set, instead of resorting to extended basis sets, seems to be a sensible choice for anions. The equilibrium distance is shifted towards the reference basis set value at the CP corrected level as well as at the uncorrected one. The spread of the energy due to the basis set is hardly distinguishable when the CP corrected values are plotted. The description of the interaction energy in dimers involving phosphorus is improved using d type diffuse functions.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110805
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    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110901
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    Theoretical analysis of the electronic spectrum of GeH4 from ab initio CI calculations (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1017-1020 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio CI calculations using pseudopotentials to describe germanium inner electrons are carried out on the low-lying excited singlet states (T2) of GeH4. A theoretical analysis of these states in terms of Mulliken population of Rydberg orbitals for each state and oscillator strengths allow us to reinterpret its experimental Vacuum UV electronic spectrum.
    Additional Material: 3 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110903
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    GEPOL: An improved description of molecular surfaces. I. Building the spherical surface set (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1047-1060 
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    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 algorithm used by the program GEPOL to compute the Molecular Surface (MS), as defined by Richards, is presented in detail. GEPOL starts like other algorithms from a set of spheres with van der Waals radii, centered on the atoms or group of atoms of the molecule. GEPOL computes the MS by first searching the spaces inaccessible to the solvent and consequently filling them with a new set of spheres. Here we study the behavior of the method with its parameters, presenting several examples of application.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110907
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    An algorithm for the simultaneous superposition of a structural series (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1187-1192 
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    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 procedure is delineated for finding the optimal superposition of a series of chemical structures. Quaternions are used to represent the absolute orientation of the structures-rotations of the structures need never be carried out explicitly. The Rational Function Optimization method is used to minimize a simultaneous superposition residual similar to the one given by Gerber and Müller. The robustness of the method is illustrated by comparing a series of conformations of a polyene carotenoid.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540111011
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    The nature of the N — H…O=C hydrogen bond: An intermolecular perturbation theory study of the formamide/formaldehyde complex (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1217-1233 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have used Hayes-Stone Intermolecular Perturbation Theory (IMPT) to study the variation with distance and orientation of the various components of the interaction energy of the N — H…O = C hydrogen bonded trans- formamide/formaldehyde complex, a model system for hydrogen bonding in proteins. The directionality of the total interaction energy is similar to that of the electrostatic component alone. We have analysed our data in terms of two model atom-atom intermolecular potentials, using an isotropic functional form and an anisotropic one. The anisotropic form gives an excellent representation of the IMPT potential energy surface, considerably better than the isotropic model, and is comprised entirely of theoretically justified, physically meaningful terms.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540111014
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    High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic “222” cryptand (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 19-31 
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    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 “High Temperature Annealed Molecular Dynamics Simulations” (HTAMDS) on the bicyclic 222 cryptand, and on model M+/222 cryptates with different representations of M+. The analysis of four sets of 500 structures allows assessment of the ability of HTAMDS to: (1) interconvert experimentally known conformers starting from one of them, (2) locate the energy minima, (3) generate new conformers of low energy, and (4) account for the average structure observed on the NMR time scale. In view of the ionophoric behavior of 222, structures are also analyzed in terms of the “in/out” orientation of the binding sites. It is found that simulations on the free molecule, although widely sampling the conformational space, do not give structures adequate for cation inclusion. They generate however the lowest energy structure known experimentally and other new closely related ones. Inclusion of the substrate in the simulation (either as a purely electrostatic “driver,” or as a charged sphere) is required to generate conformations found in several complexes. These results suggest that in the field of drug design, conformation of drugs suitable for binding to a given receptor may not be found when the simulations are performed on the isolated drug or substrate.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110103
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    Hydration free energy calculations by the acceptance ratio method (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 76-81 
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    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 hydration energy difference between the alanine and glycine zwitter ions was calculated by both the free energy perturbation method and the acceptance ratio method. The calculations were carried out by using different increments of the mutation parameter λ, δλ = - 0.05, -0.10, and -0.20. The free energy difference calculated by the acceptance ratio method was found to be approximately the same as an average of the two free energy differences in the forward and the backward directions calculated by the perturbation method. The results by the perturbation method were significantly affected by large δλ as compared with that by the acceptance ratio method. The statistical error caused by decreasing the simulation time for sampling equilibrium configurations is discussed.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110109
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    Hydrocarbon acidities calculated with MINDO/3, MNDO, and AM1 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 94-104 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Acidities of 32 hydrocarbons have been calculated using MINDO/3, MNDO, and AM1. All three semiempirical procedures have systematic errors and reproduce experimental acidities poorly. A linear correlation, however, does exist between the calculated and experimental results. Correction of the AM1 or MNDO acidities leads to good agreement with literature values even for acids, such as methane and ethylene, whose conjugate bases are small localized anions. Predictions for several hydrocarbons are given.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110112
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    Evaluation of a finite multipole expansion technique for the computation of electrostatic potentials of dibenzo-p-dioxins and related systems (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 112-120 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electrostatic potential V(r) that the nuclei and electrons of a molecule create in the surrounding space is well established as a guide in the study of molecular reactivity, and particularly, of biological recognition processes. Its rigorous computation is, however, very demanding of computer time for large molecules, such as those of interest in recognition interactions. We have accordingly investigated the use of an approximate finite multicenter multipole expansion technique to determine its applicability for producing reliable electrostatic potentials of dibenzo-p-dioxins and related molecules, with significantly reduced amounts of computer time, at distances of interest in recognition studies. A comparative analysis of the potentials of three dibenzo-p-dioxins and a substituted naphthalene molecule computed using both the multipole expansion technique and Gaussian 82 at the STO-5G level has been carried out. Overall we find that regions of negative and positive V(r) at 1.75 Å above the molecular plane are very well reproduced by the multipole expansion technique, with up to a 20-fold improvement in computer time.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110114
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    Molecular mechanics criterion for metal complex formation (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 326-335 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical force-field calculations were carried out before and after metal-complex formation for a cobalt(III)-complex system with a series of aliphatic amines. The limit of the strain-energy differences in metal-complex formation is evaluated by comparing the calculated data with experimental results. A criterion for the synthesizability of unknown metal complexes was derived from these findings. The strain energy of the ion pair was also calculated for some of the complexes. The results suggest that the ion-pair formation effectively contributes to their stabilization.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110307
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    Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 346-350 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic partial charges for three model systems that mimic the metal-ligand moiety of the active site in the enzyme Cu, Zn superoxide dismutase (SOD) have been calculated at the ab initio level. The model systems include copper and zinc complexes with imidazole, formate and ammonia ligands. The partial charges thus obtained have been incorporated into force fields for molecular simulations. Simulations carried out with these force fields justify the need for specialized charge assignments for the metals and their ligands.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110309
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    Coordination numbers for biomolecular hydration: A quantitative method based on pattern recognition analysis of Monte Carlo simulations of aqueous solutions (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 374-381 
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    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 coordination number model (CNM) has been developed that reproduces coordination numbers generated by rigorous Monte Carlo simulations of dilute aqueous solutions. The molecular coordination number is calculated by using the volume of the Voronoi polyhedron surrounding each solute atom and a set of linear least squares fitted parameters. Agreement with simulation data is good, with average deviation of less than 5%. Although CNM is presently parameterized against a simulation database founded on the potential functions of Clementi and coworkers, the method is perfectly general and can be applied to simulation data derived from any potential function form. Finally, the method is fast and can predict coordination numbers within minutes on a microcomputer.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110312
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    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110401
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    η5-P- or η4-P-Coordination in apically oxygenated phosphoranes? An ab initio study of PH4O-, PH4O- · E (E = Li+, NH4+, and HF) and related fluorinated oxyphosphoranes (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 249-264 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Structural optimizations of the apically substituted isomer of PH4O- and the diapically substituted isomer of PH3FO- with diffuse-function augmented 3-21G* basis sets and with the 6-31 + G* and 6-31 + + G* basis sets result in P-η4-coordination in these anions. The structures obtained are those of a hydride or fluoride ion “solvated” by or complexed with phosphine oxide, rather than phosphoranes. In contrast, 3-21G* basis sets without diffuse functions on the atom in the trans-apical position with regard to the oxy-substituent yield P-η5-phosphorane structures that appear to be computational artifacts of the small basis set; the formation of the P-η4-geometries is curtailed by the insufficient functional description of the potential trans-apical nucleophilic leaving group. The overall neutral apical isomers of PH4O- · E(E = Li+, NH4+), the diapical isomer of PH3FO-Li+, as well as the model-solvated apical isomer of PH4O- · HF favor P-η5-phosphorane geometries at all of these computational levels. The mechanism by which the E-group alters the electronic structures within PH4Oa- is discussed based on the geometries, the molecular orbitals, and electron density analysis techniques.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110211
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    Theoretical study of adsorption of hydrocarbons on graphite (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 291-296 
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    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 adsorption of methane, ethane, propane, n-butane, ethylene, propene, 1-butene, 1,3-butadiene, acetylene, benzene, toluene, naphthalene, anthracene, and pyrene on the basal plane of graphite has been studied by means of a semiempirical method proposed by Fraga based on a 1/R expansion of atom-atom pair potentials. The energies of interaction obtained agree reasonably well with experimental data and statistical calculations. The orientation of the adsorbed molecules relative to the graphite surface rendered by Fraga's method improves the picture provided by other calculations with empirical potentials. These results display Fraga's method as an economical alternative for the study of physisorption of hydrocarbons on the graphite surface.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110303
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    On the validity of polarization and correlation additivity in ab initio molecular orbital calculations (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 311-313 
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    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 common approximation used in ab initio molecular orbital calculations assumes that the changes in energy due to use of a larger basis set (as in the inclusion of polarization orbitals) and to allowance for electron correlation are additives. Thus, small basis sets may be used for correlated ab initio calculations, resulting in a great savings in time. While this approach has been shown to perform acceptably in some cases, a systematic study has not been published. We examined 35 species and computed the heats of reaction for 15 processes at the 6-31G level of theory using polarization and correlation correction up to the MP4 level. The same items were then treated by an additive procedure to attain the same level of theory. We also examined the conrotrary ring opening of cyclobutene. Our results indicate that the errors do cancel to some extent but that the uncertainty associated with open shell species is significantly larger than closed shell systems. This calls into question the use of the procedure in predicting the properties of transition states.
    Additional Material: 3 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110305
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    First and second derivative matrix elements for linear and out-of-plane bending motion (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 336-345 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simplified formulas for first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for linear and out-of-plane bending motion. They are expressed in a local coordinate system and then rotated to a space-fixed Cartesian coordinate system. For linear motion the important points are: (1) the invariance of the energy with respect to translational and rotational coordinate transformations and (2) the presentation of derivatives of the energy in terms of (α - π)2 rather than (α - π), where α is the bond angle, to avoid indeterminant forms. By factoring the second derivatives of the energy with respect to (α - π) and sinα, analysis in this local coordinate system avoids division by sinα as α → π. The formulas describe linear systems without the need to project the motion onto two perpendicular planes. When the angle is exactly π two degenerate directions arise, and the coordinate axes perpendicular to the axis of the linear sequence of atoms may be chosen arbitrarily. Further refinements and clarifications of methods reported previously to obtain matrix elements for linear and out-of-plane motion are presented.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110308
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    On the use of series to integrate rate equations (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 382-395 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The coefficients in power series, in the variable time, describing coupled nonlinear chemical reactions are easily obtained from a recursion relation. Since these series have a limited radius of convergence they are not very useful as such. If the series are inverted to give time as a function of the appropriate power of a progress variable, the new series converge over the entire time course of the reaction. If, further, the long-time asymptotic behavior, obtained from the linearized kinetic equations, is used, one can obtain a series expansion for a function that describes the correct short-time behavior. This function can be estimated very well using truncated series. The method works well for consecutive nonlinear reactions where the progress variables are monotonic functions of time; this includes many cases where the concentrations of intermediate species go through a maximum as the reaction progresses.
    Additional Material: 19 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110313
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  • 70
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    Force field calculation of equilibrium thermodynamic properties: Diels-Alder reaction of 1,3-butadiene and ethylene and Diels-Alder dimerization of 1,3-butadiene (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 351-360 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: ΔH0, ΔS0, and Kp have been calculated by force field methods for two prototype Diels-Alder reactions, the condensation of 1,3-butadiene and ethylene, and the dimerization of 1,3-butadiene. Three force field programs were employed, Allinger's MMP2, Warshel and Karplus' CFF/PI, and Boyd's MOLBD3 (with Anet and Yavari diene parameters). MMP2 and CFF/PI were combined to calculate reactant and product ΔHf0 (by MMP2) and thermodynamic functions S0, CP0, and (HT0 - HO0) by use of CFF/PI molecular geometry and vibrational frequencies. MOLBD3 was used separately to calculate these properties. The combined MMP2, CFF/PI calculations exhibited excellent agreement with available experimental equilibrium data for both reactions, despite uncertainties in the number and energies of adduct conformers in the dimerization reaction. The MOLBD3 results were less satisfying, particularly for the dimerization reaction, because the entropy of 1,3-butadiene was overestimated by 2.5 cal mol-1 K-1.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110310
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  • 71
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    Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 361-373 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An improved method for computing potential-derived charges is described which is based upon the CHELP program available from QCPE.1 This approach (CHELPG) is shown to be considerably less dependent upon molecular orientation than the original CHELP program. In the second part of this work, the CHELPG point selection algorithm was used to analyze the changes in the potential-derived charges in formamide during rotation about the C—N bond. In order to achieve a level of rotational invariance less than 10% of the magnitude of the electronic effects studied, an equally-spaced array of points 0.3 Å apart was required. Points found to be greater than 2.8 Å from any nucleus were eliminated, along with all points contained within the defined VDW distances from each of the atoms. The results are compared to those obtained by using CHELP. Even when large numbers of points (ca. 3000) were sampled using the CHELP selection routine, the results did not indicate a satisfactory level of rotatational invariance. On the basis of these results, the original CHELP program was found to be inadequate for analyzing internal rotations.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110311
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  • 72
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    Methods in computational chemistry, volume II, edited by Stephen Wilson, Plenum Press, New York, 1988 (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 410-410 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110316
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  • 73
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    Efficient formulation of the large generator matrices required for computation of the higher moments, and mixed moments, of conformation-dependent properties of chain molecules with independent bonds (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 396-400 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Dimensionless ratios of various moments of conformation-dependent physical properties play an important role in the evaluation of the behavior of chain molecules. For example, the correlation coefficient, ρxy, between two conformation-dependent physical properties, denoted here as x and y, is determined by the three dimensionless ratios 〈x2〉/〈x〉2, 〈y2〉/〈y〉2, and 〈xy〉/〈x〉〈y〉. Angle brackets denote the statistical mechanical average of the enclosed property. In the rotational isomeric state approximation, generator matrices of modest size can often be used for calculation of 〈x〉 and 〈y〉. The dimensions of the matrices grow rapidly upon going to higher moments or to mixed moments, such as 〈xy〉. Formulation of these large matrices, while straight-forward, has been extremely tedious for chains with independent bonds, arbitrary rotational potentials, and arbitrary bond angles (which need not be fixed). Here we describe an approach that quickly and accurately solves this problem for all cases in which the generator matrices required for 〈x〉 and 〈y〉 are known. The algorithm is validitated by successful use for the computation of ρr2s2 for r2 and s2 for freely jointed chains of various n, a case for which an exact analytical result in closed form is available in the literature. Here r2 and s2 denote the squared end-to-end distance and squared radius of gyration for a specified conformation, and n denotes the number of bonds.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110314
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  • 74
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    Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 416-430 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO-3G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split-valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6-31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110403
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  • 75
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    Dynamics of peptides with fixed geometry: Kinetic energy terms and potential energy derivatives as functions of dihedral angles (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 487-492 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Expressions are derived for computing the kinetic energy of a peptide with fixed geometry, in terms of dihedral angles as generalized coordinates; other expressions required for the solution of Lagrange's equations are also presented. The peptide is regarded as held stationary at one end. We also outline the computations that are needed in calculating the components of the third derivative of a potential energy function that consists of a sum of pairwise interatomic interactions.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110407
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  • 76
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    Free energy calculation of a soft sphere solid using an adaptive, importance sampling Monte Carlo algorithm (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 511-517 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using an adaptive, importance sampling Monte Carlo algorithm, the free energy and equation of state of a soft sphere solid are calculated. The Monte Carlo integration technique to be described is unlike standard methods in that it can evaluate directly the partition function and consequently the free energy of a solid. The results for a soft sphere solid are compared with data obtained from a thermodynamic integration method due to Hoover et al.7 The equation of state obtained from Monte Carlo integration is in agreement with Hoover's method while the free energy calculations compare favorably only at densities greater than that of the freezing transition.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110409
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  • 77
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    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110501
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  • 78
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    Molecular modeling studies of novel heteroarotinoids (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 531-540 
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    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 structure and conformational properties of structurally related oxo and thio heteroarotinoids have been calculated by employing AM1 molecular orbital and both MM2P and Chem-X “optimize” molecular mechanics methods, and the results have been compared with crystal structure data. For the cis and trans oxo heteroarotinoids, MM2P gives values of the bridge torsion angles φ1 and φ2 in closest agreement with the crystal structure, and all three computational methods yield values of φ1 and φ2 within about 10° of that found in the crystal structures. All three computational methods locate a minimum-energy conformation for the trans isomer corresponding to the two bridged aryl rings being mutually perpendicular, in agreement with the crystal structure and similar to that found for the structurally analogous trans-stilbene. The calculated heteroring geometries also reproduce the twist-sofa conformation observed for the crystal structure. Calculated conformational energies versus φ1 and φ2 indicate broad energy wells about the minimum-energy conformation with barriers to rotation at the planar and perpendicular conformations, and with higher barriers found for the more sterically congested cis isomer. The corresponding cis and trans thio heteroarotinoids exhibit conformational properties similar to their oxo analogues. Both AM1 and MM2P fare poorly in reproducing the crystal structure values of the sulfur-containing bond lengths and bond angles. The C-S bonds found in these thio heteroarotinoids may possess more double-bond character than accounted for in the calculations. Also, the results suggest that the MM2P sulfur-related force-field parameters adopted for these calculations may require further refinement.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110412
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  • 79
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    Electronic structure and hypolipidemic activity of phthalimide and related compounds. A QSAR study (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 569-572 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The hypolipidemic activities of phthalimide and seven related compounds are subjected to a QSAR analysis based on results from AM1 molecular orbital calculations. Least-squares fits show a correlation of the activities with LUMO energies and carbonyl polarities and predict enhanced activities for two new phthalimide derivatives.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110505
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  • 80
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    Electronic Resource
    Computer generation of character tables of generalized wreath product groups (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 589-602 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms and computer codes in FORTRAN 77 are developed for the computation of characters of generalized wreath product groups through generating function methods. Characters of generalized wreath product groups of symmetric groups are computed in terms of the characters of much smaller composing groups using plethysms of S-functions. The developed codes were tested for many generalized wreath product groups. The character tables of generalized wreath products, S2[S3, S2, S2] (NMR group of hexane) and S4[S3] containing 576 and 31,104 elements, respectively, were constructed as examples.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110508
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  • 81
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    Effect of basic set quality and electron correlation on the scale factors of a harmonic force field (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 623-628 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The completely optimized structure and harmonic force field of s-trans-buta-1,3-diene are reported at the MP2/6-31G and MP2/6-31G* levels of computation. Sets of empirical scale factors for the calculated force fields are derived and compared with the corresponding values computed at the RHF/4-31G and RHF/6-31G levels. Changes in the scale factors for this series of force fields are discussed. The vibrational frequencies are also reported for thirteen isotopomers of s-trans-buta-1,3-diene using the MP2/6-31G* force field. Some characteristics of the gauche and cis forms of buta-1,3-diene are also given.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110510
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    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110601
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  • 83
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    The application of Artificial Intelligence to the conformational analysis of strained molecules (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 680-693 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for predicting the conformations of strained molecules using Artificial Intelligence techniques is described and illustrated with some typical examples.
    Additional Material: 21 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110603
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  • 84
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    Electronic structure and photoelectron spectra of Sb2 and Sb4 from local-spin-density calculations. Model potential for Sb (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 924-929 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry, electronic structure, and photoelectron spectra of Sb2 and Sb4 have been investigated employing the LCGTO-MP-LSD method. For both molecules the geometrical and spectroscopic constants computed using the VWN potential are in very good agreement with the available experimental data. The HeI photoelectron spectra were computed with different potentials (Xα, GL, HL, BH, and VWN). The calculated spectra are in excellent agreement with the experimental ones and the use of the VWN potential gives the most accurate results. The reliable results for molecules complement those for the Sb atom and show that the proposed LSD Model Potential is able to give an accurate description of the structural and spectroscopic properties of the title molecules.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540110804
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  • 85
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    Different approaches to conformational analysis: A comparison of completeness, efficiency, and reliability based on the study of a nine-membered lactam (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1021-1028 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different methods such as molecular dynamics, systematic, or stochastic search and a special “generic shape” algorithm have been employed in the conformational analysis of a nine-membered lactam. Furthermore, crystal data were used to generate conformations of the compound under consideration. The various methods are compared in terms of their efficiency and completeness in the search for conformations with an energy content of up to 60 kJ/mol above the global minimum. Additionally, the generated conformations have been optimized by different techniques, molecular mechanics and quantum chemical calculations, to compare the number of existing local minima and their relative energies and geometries.
    Additional Material: 8 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110904
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  • 86
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    Concise, open-ended implementation of Rys polynomial evaluation of two-Electron integrals (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 972-977 
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    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 quadrature-point-driven implementation of the standard Rys polynomial method for computing two-electron repulsion integrals of gaussian basis functions has been found to be both concise and openended with respect to the angular momentum of the gaussian functions (i.e., s,p,d,f,g,…). These are important features in certain applications, such as molecular properties and property gradients.
    Additional Material: 1 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540110809
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  • 87
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    Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 994-1002 
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    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute -9.8 kcal/mol to the free energy of binding, with a 108-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is -11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO-2 group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.
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    URL: http://dx.doi.org/10.1002/jcc.540110811
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  • 88
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    Comparative study of imidazole hydration: Ab initio and electrostatic calculations vs. Cambridge structural database analysis (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1038-1046 
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    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 studied geometries and energies of complexes between water and neutral or protonated imidazole by ab initio molecular orbital calculations using the 4-31G basis set with and without the counterpoise correction. Positions of hydration sites and relative binding energies could be also estimated by using the electrostatic field map of imidazole as calculated by our bond increment method. The reliability of the calculations is confirmed by comparing the geometries of the imidazole-water complex to the experimental ones from the Cambridge Structural Database. These were obtained by X-ray diffraction studies on crystals with water bound to a molecule containing the imidazole fragment.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110906
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  • 89
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    Molecular mechanics calculations of several lanthanide complexes: An application of the random incremental pulse search (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1061-1071 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for the evaluation of metal complexes with molecular mechanics calculations is described. The method has been employed to determine the global minimum energy conformations of three seven-coordinate lanthanide complexes. The method searches the potential energy surface of the metal complexes for the global minimum structure using the recently reported Random Incremental Pulse Search (RIPS). The molecular mechanics calculations were performed using the MM2 metal-extended force field (MM2MX). This force field excludes 1-3 bending terms about the metal center and, instead, explicitly includes 1-3 nonbonded van der Waals interactions. This affords a model based mainly on steric interactions about the ligating atoms, and removes the necessity of specifying ligand-metal-ligand bond angles for seven-coordinate and higher metal complexes in which no preferred bond angle can be proficiently determined. The calculated minimum-energy structures were well known seven-coordinate conformations in all cases, and a comparison with X-ray crystallographic is presented.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110908
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  • 90
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    Electronic Resource
    Construction and molecular modeling of phospholipid surfaces (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1181-1186 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A protocol is given for the construction of phospholipid surfaces that possess variable head groups and thus variable net charge. Ab initio quantum mechanical calculations are performed to establish the necessary force field (AMBER) parameters. The charge distribution is defined by an electrostatic potential method consistent with the ab initio wave function. As a model calculation, a monolayer surface with head groups of phosphatidylserine and phosphatidylcholine derived from the crystal structure of 1,2-dilauroyl-DL-phosphatidylethanolamine (DLPE) is placed in a water bath with two Ca(II) ions present. The resultant surface is energy-optimized followed by 64 ps of molecular dynamics integration. Evaluation of calcium ion coordination environments, characterization of the P-N dipole inclination with respect ot the plane of the monolayer, and calculation of molecular surface area is performed and compared with experimental data.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111010
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  • 91
    Electronic Resource
    Electronic Resource
    A boundary element method for molecular electrostatics with electrolyte effects (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1080-1086 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A boundary element method is developed to compute the electrostatic potential inside and around molecules in an electrolyte solution. A set of boundary integral equations are derived based on the integral formulations of the Poisson equation and the linearized Poisson-Boltzmann equation. The boundary integral equations are then solved numerically after discretizing the molecular surface into a number of flat triangular elements. The method is applied to a spherical molecule for which analytical solutions are available. Use is made of both constant and linearly varying unknowns over the boundary elements, and the method is tested for various values of parameters such as the dielectric constant of the molecule, ionic strength, and the location of the interior point charge. The use of the boundary integral method incorporating the nonlinear Poisson-Boltzmann equation is also briefly discussed.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110911
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  • 92
    Electronic Resource
    Electronic Resource
    An improved empirical force field for saturated hydrocarbons (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1125-1138 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new molecular mechanics force field for alkanes is presented. The force field aims to eliminate some identified failures of the well-known MM2 force field. The new energy function gives an improved prediction of the rotational barriers of highly congested molecules, a better calculation of short nonbonded contacts, and the correct reproduction of bond elongation in small torsion angles. The calculation of sublimation enthalpies is also improved. The standard deviation of the formation enthalpies for a set of 54 compounds is 0.63 kcal/mol; this compares with the reported value of 0.42 calculated with MM2 and MM3 for different sets. The force field parameters were obtained using a least squares method.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111003
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  • 93
    Electronic Resource
    Electronic Resource
    Theoretical studies on the intramolecular cyclization of alkyl halide anions (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1119-1124 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The intramolecular cyclization reactions of alkyl fluoride and chloride anions1 were investigated theoretically using the AM1 method. Formation of five-membered ring was the most reactive and that of three-membered ring was the least reactive process in both series. For the fluoride series the reactivity order of n = 5 〉 6 〉 7 〉 4 〉 3 was dictated by the enthalpy (ΔH≠) effect while for the chloride series the entropy (ΔS≠) effect was found to play somewhat greater role due to the much better leaving ability of the chloride anion leading to the reactivity order of n = 5 〉 6 〉 4 〉 7 〉 3. For both series, BEP principle held and the degree of bond formation was greater with the fluoride series owing to the poor electron acceptor ability of the cleaving bond.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111002
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  • 94
    Electronic Resource
    Electronic Resource
    The bond order - bond length relationship (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 1160-1163 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The difference in length between two bond orders was reported by Pauling to be essentially the same, regardless of the atoms that make up the bond. To a first approximation these differences hold not only for bond orders 1, 2 and 3 but also for six membered aromatic rings containing all carbon, carbon-nitrogen, nitrogen-nitrogen, carbon-phosphorous, carbon-arsenic, and carbon-antimony bonds. An equation was developed (based upon these differences) that relates bond order and bond length. The output of this equation was compared with those of Gordy and Pauling. Our equation as well as the Gordy equation (with revised constants) return a bond length of 1.4 Å for bond order 1.67 which is consistent with theory. (This bond order was not used in developing either the equation or the revised Gordy constants.)
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540111007
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  • 95
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110101
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  • 96
    Electronic Resource
    Electronic Resource
    A comparison of the IGLO and LORG methods for the calculations of nuclear magnetic shieldings (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 32-44 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The individual gauge for localized orbitals (IGLO) and localized orbital/local origin (LORG) methods for the calculation of chemical shieldings are compared from their theoretical and computational viewpoints. A detailed analysis of the fluorine α-substituent effect in a series of fluoromethanes is given in terms of the IGLO and LORG bond contributions. The performance of both methods is discussed for molecular systems of fairly different sizes.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110104
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  • 97
    Electronic Resource
    Electronic Resource
    A stringent formulation of the overall rotational diffusion in molecules and other flexible assemblies (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 64-66 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110107
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  • 98
    Electronic Resource
    Electronic Resource
    An empirically adjusted Newton-Raphson algorithm for finding local minima on molecular potential energy surfaces (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 58-63 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple extension of the Newton-Raphson method is proposed that approximately accounts for anharmonicity in bond-stretching coordinates. By modeling each bonded distance in a polyatomic molecule as a Morse oscillator with no anharmonic stretch-stretch or stretch-bend coupling, a multiplicative correction factor to the Newton-Raphson step is derived. Representative examples suggest that the rate of convergence of the proposed scheme is typically faster than that of the standard Newton-Raphson method.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110106
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  • 99
    Electronic Resource
    Electronic Resource
    Calculation of Langevin-type capture rate constants for rotating molecules with arbitrary interaction potentials (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 88-93 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Approximate classical trajectory calculations of capture rates are performed for collisions occurring under the influence of a combination of angle-dependent and isotropic potentials. Results calculated for a wide range of temperatures are in good accord with existing data for ion-dipole (H3+ + HCN), ionquadrupole (OH- + C2H2), dipole-dipole (BH + NO), and dipole-quadrupole (CN + O2) reactions.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110111
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  • 100
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990) 
    Details
    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
    URL: http://dx.doi.org/10.1002/jcc.540110201
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