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  • Biochemistry  (1,116)
  • Wiley-Blackwell  (1,116)
  • Annual Reviews
  • 2005-2009
  • 1990-1994  (749)
  • 1980-1984  (367)
  • 1
    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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  • 2
    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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  • 3
    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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  • 4
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    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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  • 5
    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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  • 6
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    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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  • 7
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    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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  • 8
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    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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  • 9
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    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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  • 10
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    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 
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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 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.
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    URL: http://dx.doi.org/10.1002/jcc.540110708
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  • 11
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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.540110801
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  • 12
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    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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  • 13
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    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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  • 14
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    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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  • 15
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    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.
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    URL: http://dx.doi.org/10.1002/jcc.540110905
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  • 16
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    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.
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    URL: http://dx.doi.org/10.1002/jcc.540110913
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  • 17
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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.540111001
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  • 18
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    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.
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    URL: http://dx.doi.org/10.1002/jcc.540111004
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  • 19
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    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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  • 20
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    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 
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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: 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.
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    URL: http://dx.doi.org/10.1002/jcc.540111005
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  • 21
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    A critical comparison of MINDO/3, MNDO, AM1, and PM3 for a model problem: Carbon clusters C2-C10. An ad hoc reparametrization of MNDO well suited for the accurate prediction of their spectroscopic constants (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 52-70 
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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: Dissociation energies and potential energy surface features for the carbon clusters C2 to C10 are compared with ab initio or experimental results for the semiempirical methods MINDO/3, MNDO, AM1, and PM3. Quite surprisingly, MINDO/3 gives a rather good account of the various structures and electronic states, unlike the other three methods. MINDO/3 tends towards systematic overestimates of binding energies, the other methods to systematic gross underestimates. Reparametrization of the diatomic parameters α, βs, and βp for exact reproduction of the experimental data for C3 results in much improved values for binding energies, but fails to correct the state splittings. Also reparametrizing Uss, Upp, ζs, and ζp to reproduce the ab initio linear-rhombic energy difference in C4 results in a much improved description of the other states. For the linear structures, computed harmonic frequencies with the latter parameters are in surprisingly good agreement with experimental or correlated ab initio data, where available; experimental values are consistently overestimated by about 40 cm-1. Other results are comparable in quality to good ab initio treatments. The experimental IR bands at 2128 and 1892 cm-1, formerly assigned to C9, should be reassigned to linear C7. The intense 1997 cm-1 feature almost certainly belongs to C9; bands at 1952 and 1197 cm-1 both belong to linear C6. Tentative assignments of bands in the 1600-1850 cm-1 region to various cyclic structures of C6, C8, and C10 have been made. As such, this suggests a new and promising procedure for the theoretical study of large molecules in general, and of large clusters in particular.
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    URL: http://dx.doi.org/10.1002/jcc.540120107
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  • 22
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    Force related atomic multipoles in planar molecules. Derivation of atomic quadrupole and octupole moments (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 91-105 
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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 multipoles as defined by current methods generally do not account for forces in molecules that arise from external electrostatic fields. It is pointed out that such forces and the electrostatic potential that the molecule itself generates are both determined by the molecular multipolar tensors. The latter constitute therefore the fundamental molecular constants that determine the molecular electrostatics apart from polarization. In general the multipolar tensors include contributions from the atomic multipoles and their fluxes. In planar molecules, however, the perpendicular charge flux is zero by symmetry. This gives rise to a (previously introduced) formalism that extracts analytical, force-related, atomic multipoles from the molecular multipolar tensors. This formalism is extended in this work to include force-related (FR) atomic quadrupoles and octupoles in planar molecules. The properties of the FR atomic multipoles, including their perpendicular fluxes, are discussed and some formal theoretical and computational advantages that characterize them are indicated. As an example, the electrostatics of OCS, including the molecular electrostatic potential and the forces on the nuclei due to an external point charge, is discussed.
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    URL: http://dx.doi.org/10.1002/jcc.540120110
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  • 23
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    Masthead (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991) 
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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
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    URL: http://dx.doi.org/10.1002/jcc.540120201
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  • 24
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    Theoretical calculation of the steric effects of ortho substituents by the AM1 method (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 135-138 
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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 AM1 calculation was done for ortho-substituted toluenes (o-X-C6H4-CH3) and ortho-substituted tert-butylbenzenes (o-X-C6H4-t-Bu). The difference in the calculated heat of formation between o-X-C6H4-CH3 and o-X-C6H4-t-Bu was used as a theoretical steric index for ortho-X. The correlation of this theoretical steric index with the empirical steric parameter sets such as our recently defined Es(AMD) and the Taft-Kutter-Hansch (TKH) Es was examined. In spite of the simplicity of the model system, the theoretical index was linear with the Es(AMD) constant with a correlation coefficient of r = 0.972 for 17 substituents of various structures. Including the phenyl group, the correlation with the TKH Es constant was r = 0.948. The theoretically calculated index was shown to serve as a measure of the ortho steric effect.
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    Macromolecular dynamics on a shared-memory multiprocessor (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 175-179 
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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: This is a study of the effect of data structures and algorithms on parallelism and vectorization for the molecular dynamics package GROMOS. About 80% of the computing time (for the GROMOS benchmark) is spent on the nonbonded interactions, and an important issue is the method that is used for finding all pairs of atoms (actually atom groups) which are within a given cutoff radius of each other. Favored by the authors of GROMOS is the use of the (Verlet) neighbor list with direct calculation of all distances. Substantial restructuring of their code for the nonbonded interactions has resulted in a speedup of a factor 6.9 for the eight-processor Alliant FX/8 through the use of concurrent subroutine calls. Vectorization gave a further improvement of 30%. However, the direct calculation of all distances does not scale up linearly with the number of atoms. (Nor would neighbor lists be needed if cutoffs were abandoned in favor of such techniques as the fast multipole method). Therefore an alternative GROMOS subroutine that implements the “gridcell plus linked list” approach without a neighbor list was also rewritten and tested. This resulted in the discovery of an apparent flaw in an early study of the relative merits of the two algorithms. It is observed that actually the neighbor list version of GROMOS is not much faster.
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    A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 200-208 
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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: Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MM2(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MM2(85) gives results which are in best agreement with the experimentally determined values.
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    Towards the truly nonempirical computation of hyperfine interactions: A contribution to the debate on the t-butyl radicalPresented (in part) at the Faraday Symposium 19: Molecular Electronic Structure Calculations - Methods and Applications (Cambridge, December 1984) and (in more detail) at the 22nd Annual Quantum Theory Conference (York, September 1989). (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 231-236 
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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: Carefully calibrated large-scale nonempirical CI computations have been performed for the isotropic hyperfine splittings of the t-butyl radical. The results have been used to interpret the effects of out-of-plane vibration of the radical center, with and without coupling to methyl rotations, on the observed splitting at the radical center. In particular, the value computed under rotation-inversion is 39 G, in good agreement with the ESR result of 45 G.
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    Applications of simulated annealing to the conformational analysis of flexible molecules (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 342-349 
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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 describe in this article our solution to the global minimum problem which uses the simulated annealing algorithm of Kirkpatrick. This method is a Metropolis (e-ΔE/kT) Monte Carlo sampling of conformation space with simultaneous constraint of the search by lowering the temperature T so that the search converges on the global minimum. The Anneal-Conformer program has been extensively tested with peptides and organic molecules using either the Amber or MM2 force fields. A history file of the simulated annealing process allows reconstruction of the random walk in conformation space for subsequent examination. Thus plots of distance and dihedral angle changes during the search for the global minimum can be examined to deduce molecular shape and flexibility. A separate program Conf-Gen reads the history file and extracts all low energy conformations visited during the run.
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    Projection operator method for geometry optimization with constraints (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 376-384 
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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 new approach is presented for performing geometry optimization for stationary points on potential energy hypersurfaces with equality constraints on the internal coordinates of a polyatomic system. The working equations are the same as for unconstrained Newton-Raphson optimization in Cartesian coordinates except that projection operators are applied to the gradient and Hessian to enforce the constraints. Two reactive systems with different kinds of constraints are treated as examples: OH + H2 → OH3≠ → H2O + H with one constrained OH bond distance and CH3 + H2 → CH5≠ → CH4 + H with one constrained H—C—H bond angle in the CH3 group or with one constrained bond distance and one simultaneously constrained bond angle. In each case we optimized all reactants and products as well as the saddle point, all subject to the constraints.
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    Masthead (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991) 
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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
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    URL: http://dx.doi.org/10.1002/jcc.540120401
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    Splicing I: Using mixed basis sets in ab initio calculations (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 421-426 
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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 mixing (or “splicing”) extended and minimal basis sets on molecular properties such as geometries, Mulliken charges, dipoles, and internal rotation barriers was studied for several test molecules. The effect is gauged by comparison with full extended basis set calculations. It is found that splicing improves most properties relative to full minimal basis set calculations, and little accuracy is lost if the splicing is done in a judicious manner.
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    Ab initio calculations on CO4 centers in silicon dioxide (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 446-453 
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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: Ab initio SCF-MO Hartree-Fock calculations were performed using the STO-3G, 6-31G, and 6-31G* basis sets to model hypothetical substitutional carbon impurities in silicon dioxide. We utilized nine-atom clusters, [C(OH)4]qt, with charge number qt = 0 and + 1. The positions of the C and O atoms were varied to achieve minimum total energies, while the fixed protons served to simulate the rigid crystal surroundings. In the optimized configuration of the neutral cluster, the C—O bond lengths are appreciably longer than typical C—O bonds, indicating relatively weak bonds for a carbon impurity at a silicon site. For comparison, the relative positions of all nine atoms in the [C(OH)4]0 model were allowed to vary. This unconstrained model yielded more normal bond lengths and was lower in energy than the fixed-proton model by 6.80 eV with the 6-31G* basis set. The free-H model compared favorably with the x-ray diffraction data for an analogous orthocarbonate. Our results are in concert with the lack of reports of any substitutional carbon impurity in α-quartz. In the fixed-H models, the twofold local symmetry was found to be retained when qt is 0 but not when qt is + 1. For the latter ion, the unrestricted H-F calculations indicate that this paramagnetic center has its spin population almost entirely on one oxygen ion and is high in energy (5.31 eV with 6-31G) compared to the diamagnetic neutral one. Conclusions reached with the nine-atom clusters were confirmed by a series of calculations on the extended model [C(OSiH3)4]0.
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    Searching for conformers of nine- to twelve-ring hydrocarbons on the MM2 and MM3 energy surfaces: Stochastic search for interconversion pathways (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 645-663 
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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 stochastic search method was employed to find as many conformers on the MM2 and MM3 energy surfaces as possible for cyclic saturated hydrocarbons with ring sizes from 9 through 12. The number found was 8 MM2 (8 MM3) for 9 rings, 18 MM2 (16 MM3) for 10 rings, 40 MM2 (29 MM3) for 11 rings, and 111 MM2 (90 MM3) for 12 rings. A measure of similarity between pairs of conformers of a compound, called conformational distance, is described. It was used to correlate similar MM2 and MM3 conformers. It was discovered that some conformers on each energy surface are not close to minima on the other surface in rings larger than 9. On refinement with the other optimizer, they changed considerably - going downhill to other previously found minima on the other energy surface or (in a few cases) going to minima which had not been found by direct searches. Conformational distance was also employed as an indication of which pairs of MM2 (or MM3) conformers are likely to interconvert rapidly. A new stochastic procedure of using small kicks was used to search for the most likely interconversion processes among the conformers. There is fairly good agreement between the most facile pathways located by it and unusually short conformational distances. Several additional 12-ring conformers (not found with previous methods) were located through application of this small kick procedure.
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    MRD-CI potential surfaces using balanced basis sets. VI. Correlation of bond order with bond function composition for first-row diatomic molecules (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 690-696 
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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: This article presents theoretical calculations on bond energies for the first-row diatomics C2, CN, CO, CF, N2, NO, NF, O2, FO, and F2, which vary in bond order from one to three. The atomic-centered basis functions are systematically augmented with bond functions (BFs), which range in composition from (sp) to 2(spd), to determine the basis set which yields a dissociation energy closest to the experimental De. A strong correlation is found to exist between the bond order and the number of BFs required in the optimum basis set. Based on these results, we are able to predict the optimum composition of the BF basis which should be added to a DZP-quality AO basis set for a case in which only the bond order is known. These optimized BF basis sets are shown in the accompanying article to give more accurate potential curves than larger basis sets without bond functions.
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    The use of ultraviolet resonance Raman intensities to test proposed molecular force fields for nucleic acid bases (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 731-741 
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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 harmonic molecular force fields for the nucleic acid bases, cytosine, and guanine, that have been previously published by several investigators are tested by the calculation of the relative intensities of the in-plane modes in the ultraviolet resonance Raman (UVRR) effect from the two lowest lying absorption bands using a theoretical approach devised previously.1-3 Since only a fraction of the 2N - 3 in-plane vibrations of a molecule are active in the UVRR, the two criteria that are taken for the adjustment of the force constant are: (1) the closest possible agreement between the observed and calculated frequencies of the 2N - 3 in-plane vibrations, and (2) the closest possible agreement between the calculated and observed intensities of those few vibrations that are strongly active in the ultraviolet resonance Raman effect. In particular it is necessary that the force constants be adjusted to avoid the calculation of intense Raman lines with frequencies that are not observed in the UVRR spectrum. Using this criteria, a new force field has been developed that appears to give better agreement with the observed UVRR intensities than previously published ones. It is suggested that this calculation of the UVRR intensities can be used to refine molecular force fields in combination with other methods such as isotopic replacement currently in use to refine force constants.
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    Dispersion and repulsion contributions to the solvation energy: Refinements to a simple computational model in the continuum approximation (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 784-791 
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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 computational method for the evaluation of dispersion and repulsion contributions to the solvation energy is here presented in a formulation which makes use of a continuous distribution of the solvent, without introducing additional assumptions (e.g., local isotropy in the solvent distribution). The analysis is addressed to compare the relative importance of the various components of the dispersion energy (n = 6, 8, 10) and of the repulsion term, to compare several molecular indicators (molecular surface and volume, number of electrons) which may be put in relation to the dispersion-repulsion energy, and to define simplified computational strategies. The numerical examples refer to saturated hydrocarbons in water, treated with the homogeneous approximation of the distribution function which for this type of solution appears to be acceptable.
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    Self-consistent, nonorthogonal group function approximation. III. Approaches for modeling intermolecular interactions (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 811-828 
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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 new program has been developed for the implementation of the self-consistent nonorthogonal group function (NOGF) approximation for the calculation of wavefunctions between interacting systems. The NOGF approach is based on the reformulation of a single-determinental, closed shell wavefunction into an antisymmetrized product of nonorthogonal group functions, each of which is a single determinant of doubly occupied orbitals. The group product form of the wavefunction combined with the relaxation of the orthogonality constraints and the structure of the orbital equations allows each group's orbitals to be expanded in a local basis set, and makes it possible to modify the orbital expansions or iterative process to simplify the computation. Three models for approximating the full single-determinental wavefunction are tested: (1) different quality basis sets for orbitals belonging to different groups, (2) variation of the types of intergroup interactions included in the wavefunction, and (3) the use of frozen orbitals which have been predetermined in a subsystem and are subsequently transferred to the system of interest. These approximations are applied to the calculation of protonation energies of formate, ammonia, imidazole, and guanidine with part of the first hydration shell being represented by two water molecules hydrogen bonded to each species. The results from different basis sets are compared. Then interaction potentials between the acid and ammonia are calculated for both neutral and charged forms, again with inclusion of part of the first hydration shell. The results show that these techniques can yield reliable wavefunctions of the same quality as obtained with the standard supermolecule approach. The effect of the basis set superposition error in the NOGF approach is briefly considered, and the reduction in computing effort resulting from the three models is discussed.
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    A vectorized algorithm for calculating the accessible surface area of macromolecules (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 868-871 
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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: An algorithm is presented for calculating the solvent accessible surface area of proteins using a three-dimensional grid. Since it requires only calculations based on single atomic positions, the algorithm is easy to be vectorized. It has been implemented on ST100 and may also be implemented on supercomputers like the CRAY or the CYBER. Results on several proteins indicate that its deviation from that of the Shrake-Rupley algorithm is very small while the computation time is much reduced.
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    The half-projected Hartree-Fock model for computing thermally “forbidden” pericyclic reactionsA contribution from the Grup the Química Quàntica de l'I.E.C. (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 792-802 
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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 possible use of a half-projected Hartree-Fock (HPHF) wavefunction correlating a single pair of electrons is investigated in relation with the computation of potential energy hypersurfaces associated to pericyclic reactions of systems with an even number of electrons, in which the orbital configuration of the lowest-energy singlet state is not conserved during the course of the reaction. The results of calculations, within the framework of the MINDO/3 Hamiltonian, for eleven stationary points on the potential energy hypersurfaces of three prototypical thermally “forbidden” pericyclic reactions indicate that, in general, the HPHF model provides a geometrical and energetical description that is equivalent to that obtained from a conventional two-configuration self-consistent-field approach.
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    Conformational energies and rotational barriers in 3-methyl-1-butene and 1-butene: An ab initio and molecular mechanics study (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 839-843 
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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 calculated result obtained with MM2(87) for the rotation of the isopropyl group in 3-methyl-1-butene is not in agreement with experimental data. In order to reparametrize the Csp2-Csp3-Csp-Csp3 torsional angle, 3-methyl-1-butene and 1-butene have been studied by molecular mechanics (MM2(87)) and ab initio (MP2/6-31G* and MP3/6-31G*) calculations. The reparametrization of the torsional angle gives calculated results from MM2(87) in agreement with experimental data and ab initio calculations for both 3-methyl-1-butene and 1-butene. The calculated barriers for the rotation of alkyl groups in alkylbenzenes are improved with these new parameters.
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    Conformational studies of 2-methylbutyronitrile and 3-methyl-1-pentyne by vibrational spectroscopy and molecular mechanics (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 880-884 
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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: Vibrational spectra were obtained for the structurally similar compounds 2-methylbutyronitrile and 3-methyl-1-pentyne, and vibrational assignments were made with the aid of normal coordinate calculations. Molecular mechanics calculations were also made, and each compound was shown to exist as a mixture of three conformers, with the most stable conformer being the one with the two methyl groups trans to each other. Results of the calculations are given.
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    Quantitative comparison of molecular electrostatic potentials for structure-activity studiesDisclaimer: The research described in this article has been reviewed by the Health Effects Research Laboratory, U.S. Environmental Protection Agency and approved for publication. Approval does not signify that the contents necessarily reflect the views and policies of the agency, nor does mention of trade names or commercial products constitute endorsement or recommendation for use. (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 959-969 
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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: An approach for representing, efficiently calculating and comparing discrete three-dimensional molecular electrostatic potentials using a quantitative similarity index (MEP-SI) based on a Carbo-type formalism is presented. A radial-type (MACRA) grid representation is described that provides more efficient storage of MEP information than a cubic grid of similar range, appropriate emphasis, and a convenient means for restricting the comparison of MEP functions to a local molecule region. The MACRA based MEP-SI formalism was used to evaluate the suitability of a variety of approximate methods for efficiently calculating the MEP for use in MEP-SI comparison of dissimilar molecules. The Mulliken charge method was found inadequate, while the method of potential-derived charges (PDCs), with additional charges for lone electron pairs included on sulfur, provided an efficient and sufficiently accurate representation of the MEP for this purpose. Convergence of the MEP-SI with respect to MACRA grid extent and mesh size was demonstrated; the effect of MEP error and different grid point emphasis in the MACRA versus the cubic grid results was investigated, and MEP-SI results were compared for different forms of the SI equation. The methodology proposed in this study provides an efficient and practical means for comparing MEP functions for two molecules and gives discriminating results for a sample series of molecular analogues consistent with expectations.
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    A computer automated structure evaluation (CASE) approach to calculation of partition coefficient (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1025-1032 
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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 Automated Structure Evaluation (CASE) approach to the calculation of partition coefficient (log P) has been developed. A linear regression equation was obtained linking the log P value of molecules to some of their fragments as identified by a CASE analysis. The relationship was obtained for a database consisting of 935 compounds (r2 = 0.93, s = 0.39, F(39, 895, 0.05) = 316.5). It was found that this approach produced accurate log P estimations even for complex molecules and, in general, gave better results than previously described techniques.
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    Basis sets for geometry optimizations of second-row transition metal inorganic and organometallic complexes (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 923-933 
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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: Modest-sized basis sets for the second-row transition metal atoms are developed for use in geometry optimization calculations. Our method is patterned after previous work on basis sets for first-row transition metal atoms. The basis sets are constructed from the minimal basis sets of Huzinaga and are augmented with a set of diffuse p and d functions. The exponents of these diffuse functions are chosen to minimize both the difference between the calculated and experimental equilibrium geometries and the total molecular energies for several second-row transition metal inorganic and organon etallic complexes. Slightly smaller basis sets, based on the same Huzinaga minimal sets but augmented with a set of diffuse s and p functions rather than diffuse p and d functions, are also presented. The performance of these basis sets is tested on a wide variety of second-row transition metal inorganic and organometallic complexes and is compared to pseudopotential basis sets incorporating effective core potentials.
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    Counterpoise corrected calculations at the correlated level: A simplified method using LMOs (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 953-958 
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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: Ab initio calculations have been performed in order to investigate the counterpoise corrections, especially at the correlated level for molecular interactions. It is pointed out that, when using a localized representation, the calculations using the MBPT/MP2 method can be simplified. The H2O + H2O system was studied, with the use of 6-31 G* basis set. The method allows one to determine the intramolecular correlation components in a simplified way. Boys' localization procedure was applied throughout, both in the occupied as well as in the virtual spaces.
    Additional Material: 5 Tab.
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    New method for the computation of ionic distribution around rod-like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson-Boltzmann equation (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 981-993 
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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: This article is a first step in an attempt to reevaluate the relative role of different contributions to the energetics of DNA in salt solutions. To identify individual terms yielding such contributions a new derivation is given of the generalized Poisson-Boltzmann equation, which includes correlation effects, and explicitly shows terms ignored in the regular Poisson-Boltzmann approach. A general method based on the Boundary Element Technique is discussed, which can be used to evaluate these terms in the next steps of the reevaluation. An implementation of this method for the solution of the nonlinear Poisson-Boltzmann equation is described in detail, and is used to compute the ionic atmosphere around DNAs modeled as cylinders with helical distributions of charges. In the B-type DNA models, it is found that the ion densities in the minor and major grooves near the DNA surface differ by up to threefold. This difference is ca. 10-fold for Z-type DNA models. There are 20-25% differences in the magnitude of the maximum ionic charge density between DNA models of the same type. The addition of excess salt (up to 0.15 M) changes this maximum by only 10-15%. This change is not proportional to the concentration of excess salt. The contributions of different factors to the stabilization of alternative forms of DNA are evaluated. These factors are: (1) interactions between the phosphates, (2) interactions of phosphates with water, (3) interactions of phosphates with the ionic cloud, (4) interactions within the ionic cloud, (5) entropy of the ionic cloud. It is found that regardless of large variations in the counterion distributions around different DNAs, energetic contributions from these distributions are similar (-12.65 ± 0.6 kcal/mol · cell). The calculated change in stabilization per unit cell of models of B and Z-type DNAs due to 0.15 M excess NaCl is only -0.56 ± 0.02 kcal/mol, indicating no tendency toward B-Z transition in this concentration range. Significantly larger variations of the order of 10 kcal/mol per unit cell can result from factors 1-2. Possible effects of the realistic DNA-solvent boundaries on the energetics of DNA solutions are discussed.
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    Simulations of lipid crystals: Characterization of potential energy functions and parameters for lecithin molecules (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1033-1046 
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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 evaluate an empirical potential energy function and associated parameters for classical molecular dynamics simulations of lecithins, a common class of lipid. The physical accuracy of the force field was tested through its application to molecular dynamics simulations of the known crystal structures of lipid molecules. Average atomic positions and molecular conformation are well maintained during the simulations despite considerable thermal motion. Calculated isotropic temperature factors correlate highly with those from experiment.
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    GEPOL: An improved description of molecular surfaces II. Computing the molecular area and volume (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1077-1088 
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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 for a finer description of molecular surface (for a fast calculation of molecular area and volume and for an efficient selection of sampling points) is presented in detail. Different types of surfaces such as van der Waals and Richard's molecular surfaces can be computed. As we described in the first article (J.L. Pascual-Ahuir and E. Silla, J. Comp. Chem., 11, 1047(1990)), GEPOL begins by building a set of spherical surfaces which fill the space which is not solvent accessible. In this second article, a triangular tessellation approach to select the parts of these spherical surfaces which form the molecular surface is described. By using a data coded generic pentakisdodecahedron, each spherical surface is divided in triangular tesserae. A simple method is used to eliminate all triangles found at the intersection volume of the spheres. The center coordinates and the surface of the remaining triangles are used in order to calculate the molecular area and volume and as starting point of the graphic representation of scalar and vector properties. We study the behavior of the method, presenting several examples of application. Special attention is given to the accuracy, spatial invariance and computer efficiency measured by CPU time. Some models of aligned spheres whose area and volume can be found exactly allow us to do a comparative study with a well-known method, analyzing their behavior in line with their respective graining parameters. A fragment of protein is used as an example of the application of the method for characterizing biomolecular surfaces. Aqueous solubility of organic compounds is studied as an example of the experimental property that depends on the molecular area obtaining a good correlation between the logarithm of the solubility and the area calculated using GEPOL.
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    Long range nonbonded attractive constants for some charged atoms (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1125-1128 
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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: Employing the hydrodynamic formulation of time-dependent Kohn-Sham theory, long range dispersion constants are calculated for some metal ions. We show that these quantities, when used in molecular mechanics calculations or molecular dynamics simulations, lead to excellent results.
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    An ab initio study of the proton affinities of some heteroatomic rings: Imidazole, oxazole, and thiazole (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1142-1146 
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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 proton affinities of imidazole, oxazole, and thiazole rings, relevant to the binding of lexitropsins that contain these rings to the minor groove of DNA, are calculated using ab initio (Hartree-Fock) calculations. It is found that the proton affinities decrease in the order imidazole, oxazole, thiazole and that a methyl group substituent increases the proton affinity of imidazole, while a peptidic group decreases it.
    Additional Material: 10 Ill.
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    Announcements (1991)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 1163-1163 
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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
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    URL: http://dx.doi.org/10.1002/jcc.540120916
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    Topological analysis of complex molecular surfaces (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 76-84 
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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: An algorithm for the calculation of local and global curvatures of molecular surfaces is presented. The analysis is based on a surface representation as a set of points in 3-D space (“dotted surface” representation). The surface data are used to subdivide the surfac into domains with different curvatures. All domains are characterized by a reference point with a corresponding curvature profile specifiying the topological properties in its neighborhood. The curvature profiles provide a method for a systematic comparison of the shapes of different molecules. Such a strategy is important for the treatment of molecular recognition problems. The enzyme-inhibitor complex trypsin/BPTI was chosen to demonstrate the scopes of the method.
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    Masthead (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
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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
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    URL: http://dx.doi.org/10.1002/jcc.540130401
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    Floating functions satisfying the hellmann - feynman theorem: Single floating scheme (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 457-467 
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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 electrostatic calculation for molecules using approximated variational wave functions leads to well known difficulties connected with the application of the Hellmann-Feynman (H—F) theorem. This is due to the basis set inadequacies in the underlying calculations. This defect can easily be remedied by floating functions, whose centers are optimized in space. We can keep almost everything of the traditional wave function with a nuclear-fixed basis set, but we apply single floating to ensure the H—F theorem. Then, one can obtain a wave function obeying the H—F theorem. This provides a great conceptual simplification and may lead to practical advantages. The single floating scheme, which retains one expansion center per nucleus, is successfully applied to a series of small molecules using SCF and CASSCF wave functions with sufficiently polarized basis sets.
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    Precision of free energies calculated by molecular dynamics simulations of peptides in solution (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 429-442 
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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: Errors in free energies for molecular replacement and for conformation change of a small model peptide have been determined empirically by repeated simulations from different starting points. All calculations have been done using thermodynamic integration, in which the system's potential energy is coupled to a parameter λ, that is increased or decreased by a small amount at each step of the simulation. The effects of several factors that may alter the precision are evaluated. These factors include: the length of the simulation, the dependence of the potential energy on λ, the use of conformational restraints, and their magnitude and form. The methods used for restraint and conformational forcing are described in detail. The free energy change, calculated as the mean from several successive simulations with alternately increasing and decreasing λ, is found to be independent of the length of the simulations. As expected, longer simulations produce more precise results. The variation of the calculated free energies is found to consist of two parts, a random error and a systematic hysteresis, i.e., a dependence on the direction in which λ changes. The hysteresis varies as the inverse of the length of the simulation and the random error as the inverse square root The advantage of the use of a different (nonlinear) dependence of the attractive and repulsive parts of the nonbonded potential energy on the coupling parameter when “creating” particles in solution is found to be very large. This nonlinear coupling was found to be superior to the use of linear coupling and a nonlinear change of the coupling parameter with the simulation time. The hysteresis in conformational free energy calculations is found to increase markedly if too weak a forcing restraint is chosen. It is shown how to deconvolute the contribution of a torsional restraint from the dependence of the free energy on a torsion angle.
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    A conformational analysis of 3′-azido-3′-deoxythymidine (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 478-491 
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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: An extensive conformational analysis of 3′-azido-3′-deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine - furan, furan - azide, furan - methylene, and methylene - hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2—;HO), which until recently has not been mentioned in the literature, is observed in a few low-energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6—;OH and H6—Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OH—Ofur, which also has not been mentioned for AZT in the literature until recently). The AM1-optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
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    Masthead (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992) 
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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
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130201
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    Alternative expressions for energies and forces due to angle bending and torsional energy (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 585-594 
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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 derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial \cos \phi }}\frac{{\partial \cos \phi }}{{\partial x}} $$\end{document} where φ is a bond or torsion angle, E(φ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, -1/sin φ, when φ is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, φ°, other than 0 or π, such as in E(φ) = κ[1 + cos(nφ - phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial x}} $$\end{document} This form still possesses singularities for the bond angle forces since the last factor is undefined when φ is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.
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    Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 622-632 
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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 monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.
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    Pauli repulsion in the open shell species BeH and Co+Part of this study was carried out during the author's stay at the Dauhousie University, Halifax, Canada. (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 268-274 
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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: Using the natural bond orbital method, one may associate the valence bond configuration and Lewis structure concepts to wave functions consisting of molecular orbitals and thus gain intuitive insight into the molecular potential energy curves. Natural bond orbital analysis of the restricted open shell Hartree-Fock and unrestricted Hartree-Fock wave functions for the BeH ground state provides an intuitive model to help understand the nature of the bonding in this open shell species. The contrasting behavior of the bonding orbitals for different spins can be attributed to differences in the Pauli repulsive interactions with the lonepair orbitals. Such behavior occurs in BeH(2Σ) but does not in CO+(2Π) because the Pauli repulsion depends on the orbital overlap.
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    Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. II. Systematic searches for short loops in proteins: Applications to bovine pancreatic ribonuclease A and human lysozyme (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 329-350 
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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: A rigid-geometry approach to protein conformational searches has been used to calculate stable structures for localized regions of the molecules bovine pancreatic ribonuclease A and human lysozyme. The search method is essentially an application of the local deformation algorithm of Gō and Scheraga [Macromolecules, 3, 178-187 (1970)]. A series of local chain deformations is produced in the polypeptide chain. The deformations are screened to eliminate structures having serious atomic overlaps or energetically unreasonable backbone dihedral angles. The remaining structures are refined by energy minimization and the rms deviations of the energy-minimized structures, relative to the native structures, are calculated. The correlation between low rms deviation and low energy is reasonably good, indicating that this method should be useful in generating a small number of candidate structures for further energy refinement. Further applications to proteins with an unknown structure, such as homology-based modeling applications, should now be amenable to this type of procedure.
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    Ab initio and molecular mechanics study of n-phenyl phthalimide and its crystal structure (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 408-413 
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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: Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N-phenyl phthalimide using 3-21G, 6-31G, and 6-31G** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least-squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.
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    Modeling a reaction path by molecular mechanics: Dimerization of carbon free radicals (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 541-550 
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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 variable force field model for radical dimerization was developed. It uses MM2 force constants for most atoms and new parameters only for the core atoms involved in bonding changes. The change in hybridization from sp2 to sp3 is modeled using distance-dependent switch functions. The validity of the model has been tested by calculating the minimum energy path of the dimerization of di-tert-butylmethyl radicals. The calculated and experimental values for the enthalpy of activation of both dimerization of the radicals and dissociation of the dimer are in excellent agreement. The model has also been successfully applied to the stereoselective dimerization of 1-phenylneopentyl radicals: The form of the potential energy surface yields an explanation for the observed stereoselectivity. Another common feature in radical dimerization seems to be the formation of adsorption complexes prior to dimerization that can lead to increased reactivity. The results suggest that it is important to analyze the whole reaction path and not only the transition state alone.
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    Powerful simulated-annealing algorithm locates global minimum of protein-folding potentials from multiple starting conformations (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 579-584 
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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: Protein-folding potentials, designed with the explicit goal that the global energy minimum correspond to crystallographically observed conformations of protein molecules, may offer great promise toward calculating native protein structures. Achieving this promise, however, depends on finding an effective means of dealing with the multiple-minimum problem inherent in such potentials. In this study, a protein-folding-potential test system has been developed that exhibits the properties of general protein-folding potentials yet has a unique well-defined global energy minimum corresponding to the crystallographically determined conformation of the test molecule. A simulated-annealing algorithm is developed that locates the global minimum of this potential in four of eight test runs from random starting conformations. Exploration of the energy-conformation surface of the potential indicates that it contains the numerous local minima typical of protein-folding potentials and that the global minimum is not easily located by conventional minimization procedures. When the annealing algorithm is applied to a previously developed actual folding potential to analyze the conformation of avian pancreatic polypeptide, a new conformer is located that is lower in energy than any conformer located in previous studies using a variety of minimization techniques.
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    Pathways for ring inversion in 9, 10-dihydroanthracene, 9, 10-dihydrophenanthrene, and 7, 12-dihydropleiadene: Combined molecular orbital and molecular mechanics study (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 633-639 
    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 combined semiempirical AM1 and MM2 study of the ring inversion processes in 9, 10-dihydroanthracene (1), 9, 10-dihydrophenanthrene (2), and 7, 12-dihydropleiadene (3) predicts planar transition states for 1 and 2, in accord with earlier assumptions. In the case of 3, however, a nonplanar, chair-like transition state is located on the potential energy surface in contrast with previous conclusions. Implications of the nonplanar TS on the rationalization of available experimental data are discussed. The calculated barriers for ring inversion in 1-3 are in reasonable agreement with both experiment and previous theoretical results. In general, AM1 is found to slightly underestimate the barriers as compared to the MM2 calculations.
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    An ab initio and molecular mechanical investigation of ureas and amide derivatives (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 657-666 
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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: Ab initio molecular orbital theory with the 6-31G* basis set has been used to investigate the geometries and preferred conformations for urea, derivatives of urea, and a few complicated amide derivatives. The results from the ab initio calculations provide insight into the gas-phase rotational barrier about the C—N bond and have been used to generate parameters for the MM2(87) molecular mechanics program. When applicable, theoretical structures are compared with corresponding previously reported experimental geometries. Urea is predicted to be nonplanar with pyramidal amino groups.
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    Theoretical calculations of β-lactam antibiotics. III. AM1, MNDO, and MINDO/3 calculations of hydrolysis of β-lactam compound (azetidin-2-one ring) (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 681-692 
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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: Semiempirical AM1, MINDO/3, and MNDO methods have been used in the study of the alkaline hydrolysis of β-lactam antibiotics through a base-catalyzed, acyl-cleavage, bimolecular mechanism. In this work, the hydroxyl ion has been chosen as nucleophilic agent and the azetidin-2-one ring like a model of β-lactam antibiotic. The MINDO/3 method does not predict correctly the energies of small rings. This, together with the fact that, like MNDO, it cannot detect the occurrence of hydrogen bonds, gives rise to uncertain estimates of energy barriers. The AM1 method can be considered the most suitable for studying the hydrolysis of β-lactam compounds.
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    Theoretical study of some nitriles: Intramolecular hydrogen bonds and anomeric effect (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 722-729 
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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: An ab initio study of 3-chloro-, 3-hydroxy-, 3-mercapto-, and 3-amino-propanenitrile and 4-chloro-bu- tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.
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    Conformational preferences for hydroxyl groups in substituted tetrahydropyrans (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 772-791 
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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: Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
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    Conformational analysis of carbonyl and thiocarbonyl ethyl esters: The HC(=X) (X, Y = O or S) internal rotation (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 799-809 
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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 internal rotation in the HC(=X)YCH2CH3 (X, Y = O or S) series of molecules was studied by the ab initio SCF-MO method using 3-21G and 3-21G + d(ζ = 0.65S) basis sets. Energies and structures of several conformations of these molecules, determined by gradient geometry refinement, are reported and used to assess the effects of oxygen-by-sulphur substitution on molecular properties. The nature and relative importance of intramolecular interactions involving both the —CH2CH3 and the HC(=X)Y (X, Y = O or S) fragments are also discussed. © 1992 by John Wiley & Sons, Inc.
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    Semiempirical study of compounds with O-H—O intramolecular hydrogen bond (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 860-866 
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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: Application of MNDO, AM1, PM3, MNDO/H, and MNDO/M methods to a set of compounds with intramolecular hydrogen bonds suggested that none of these methods accurately modeled the characteristics of the hydrogen bonds. Since the MNDO/H and MNDO/M methods work well for intermolecular hydrogen bonds, we followed their example and modified MNDO for intramolecular hydrogen bonds by altering the empirical core-core repulsion energy function for all pairs of atoms involved in intramolecular O-H—O bonds. The resulting modified method models the behavior of these bonds quite well, especially as regards their geometry and the barrier to proton transfer. © 1992 by John Wiley & Sons, Inc.
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    Semiempirical study of electronic and bonding properties of cobalt silicide clusters (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 867-873 
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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 electronic structure of cobalt silicide clusters Co7Si7 and Si7Co7 was studied in comparison to that of Co19 and Si17 clusters under the scope of the MINDO/SR method. Clusters Co7Si7 and Si7Co7 represent the environment of a cobalt atom and that of a silicon atom in the cobalt monosilicide bulk, respectively. It is found that the Co—Si bond is essentially sp in character with an indirect participation (by electrostatic interaction) of the cobalt d orbitals. Our calculations show a charge transfer from silicon to the d orbitals of cobalt via sp-sp interaction with an internal sp-d hybridization. The theoretical density of states for cobalt silicide clusters are reported and compared with experimental results of surface spectroscopies. © 1992 by John Wiley & Sons, Inc.
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    Study of hydrogen bonding interactions relevant to biomolecular structure and function (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1151-1169 
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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: Ab initio molecular orbital calculations were used to study hydrogen bonding interactions and interatomic distances of a number of hydrogen bonded complexes that are germane to biomolecular structure and function. The calculations were carried out at the STO-3G, 3-21G, 6-31G*, and MP2/6-31G* levels (geometries were fully optimized at each level). For anionic species, 6-31 + G* and MP2/6-31 + G* were also used. In some cases, more sophisticated calculations were also carried out. Whenever possible, the corresponding enthalpy, entropy, and free energy of complexation were calculated. The agreement with the limited quantity of experimental data is good. For comparison, we also carried out semiempirical molecular orbital calculations. In general, AM1 and PM3 give lower interaction enthalpies than the best ab initio results. With regard to structural results, AM1 tends to favor bifurcated structures for O—H-O and N—HO types of hydrogen bonds, but not for hydrogen bonds involving O-H—S and S-H—O, where the usual hydrogen bond patterns are observed. Overall, AM1 geometries are in general in poor agreement with ab initio structural results. On the other hand, PM3 gives geometries similar to the ab initio ones. Hence, from the structural point of view PM3 does show some improvement over AM1. Finally, insights into the formation of cyclic or open formate-water hydrogen bonded complexes are presented. © 1992 by John Wiley & Sons, Inc.
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    Molecular dynamics simulation of a poly(oxyethylene) chain dissolved in benzene (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1210-1215 
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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: Molecular dynamics simulations of pure benzene and a poly(oxyethylene) chain in benzene are performed. The simulation of pure benzene is found to agree excellently with previous simulations despite using a different force field. A comparison is made between the results of simulations of the poly(oxyethylene) chain in benzene and in water and of stochastic simulations with respect to mean torsional angles, trans/gauche fractions, and transition rates. Characteristic deviations are found for the simulation in water and explained by specific atomic interactions, while there is satisfactory agreement with a stochastic simulation based upon the simple Langevin equation using a friction coefficient of 1 ps-1. The characteristic ratio of poly(oxyethylene) in benzene is calculated on the basis of the rotational isomeric state model. © 1992 by John Wiley & Sons, Inc.
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    PM3-SM3: A general parameterization for including aqueous solvation effects in the PM3 molecular orbital model (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1089-1097 
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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: Our recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.
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    General expression for the density dependence of the mori coefficients (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1119-1124 
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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 particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two- and three-dimensional system. © 1992 by John Wiley & Sons, Inc.
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    Announcement (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1170-1170 
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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
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    URL: http://dx.doi.org/10.1002/jcc.540130917
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    Conformational distribution of heptaalanine: Analysis using a new Monte Carlo chain growth method (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 1216-1233 
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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 distribution of conformations of heptaalanine is obtained using a new Monte Carlo (MC) method that grows the chain atom by atom. Resulting configurations are energy minimized and a detailed analysis is performed of the minimum-energy conformers using a method of classification that partitions φψ space. The MC-generated configurations are compared with those generated from high-temperature molecular dynamics (MD) simulations. It is found that the new method generates a wide distribution of low-energy conformers at least 10 times more quickly than the MD. An analysis of the generated energy minima demonstrates that they can be divided into clusters in the space defined by the five pairs of φ - ψ angles of the inner residues. The space occupied by the minima populating each cluster is restricted. © 1992 by John Wiley & Sons, Inc.
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    Optimal use of the recurrence relations for the evaluation of molecular integrals over Cartesian Gaussian basis functions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 30-36 
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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 consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function-based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.
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    Off-lattice Monte Carlo method with constraints: Long-time dynamics of a protein model without nonbonded interactions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 19-29 
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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 method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 106 scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 103-104 scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.
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    MORMIN: A quasi-Newtonian energy minimizer fitting the nuclear overhauser data (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 226-236 
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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: In this article, we describe the program MORMIN, which can simultaneously minimize the mechanical energy of a given macromolecular structure, together with a weighted quadratic penalty function of the difference between the observed and computed nuclear Overhauser effect (nOe) peaks. The gradient of the nOe penalty function relatively to the proton coordinates is computed from an exact closed formula of a matrix exponential derivative. To cut CPU time, the molecular system is partitioned into nonoverlapping subsets containing the protons involved in the observed peaks. The algorithm is no longer exact, but if a 1% relative error is accepted it can be run, on a scalar computer, in about the same CPU time as needed for the calculation of the mechanical energy. We have successfully run the program in more than 1000 situations, including cases where the hybrid method failed because of the occurrence of negative eigenvalues. In some cases, the optimization of the Cartesian coordinates could be successfully extended to individual atomic diffusion times. © 1993 John Wiley & Sons, Inc.
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    Masthead (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993) 
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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
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    URL: http://dx.doi.org/10.1002/jcc.540140301
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    Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 253-262 
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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 present investigations on the use of dielectric continuum models for the self-consistent description of electrostatic solvent effects on the ground state of a molecule and on excitation energies. The electronic structure calculations have been carried out in the framework of the INDO and INDO/S-CI method, respectively. We compare the performance of three implementations of the cavity model that all allow an arbitrary shape of the solute cavity. The procedures differ in the effort spent on the description of the charge density at the cavity surface. Two procedures in the vein of Miertus̆, Scrocco, and Tomasi (MST) rely upon point charges to model the reaction field and differ in the way the cavity surface is modeled. While one implementation divides the surface into flat triangular patches, the improved version uses curved triangles. Alternatively, we investigate a finite element method (FEM) for the calculation of the surface charge density. Applications to rod-shaped organic molecules (including their charge transfer excitations) illustrate the superiority of the improved MST formalism over the primitive one, as it exhibits faster convergence of the results with increasing node density on the cavity surface. The FEM approach, which also employs curved surface patches, leads to a further improvement as it needs less computational effort, especially in the treatment of excited states. © 1993 John Wiley & Sons, Inc.
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    AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 312-329 
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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 fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed-memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen-containing bonds but also all heavy-atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time-step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.
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    Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 349-352 
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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 report the development of a new approximate method of calculating molecular surface areas. Our technique is based upon the method of Sharake and Rupley but incorporates several major advances. First, we represent the state of surface points as bits in a bit string so we can utilize Boolean operations to simultaneously turn off multiple test points in one Boolean AND operation. Second, we use a series of Boolean mask look-up tables to reduce the time complexity of the calculation of molecular surface area down to the same magnitude as doing a potential energy evaluation. When we use a 256 surface point sphere for all of the atoms in BPTI, a 454 nonhydrogen atom protein, and a 1.4-Å solvent probe, we in general underestimate the total solvent-accessible surface area (SASA) by approximately 1.25% with a correlation coefficient of 0.9990 over a wide range of conformations. The average CPU time required to calculate the SASA of a BPTI conformer is 0.58 s on an SGI 4D/220 workstation. We also describe a method by which we can calculate an approximate finite difference SASA gradient for BPTI in 0.79 of CPU time. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140309
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    Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3-benzazepines for the D1receptor (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 620-626 
    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 computed the free energy of solvation for a series of ions and neutral molecules using two different continuum approaches. First, we used the AM1-SM1 technique, where the AM1 Fock matrix is modified to include a generalized Born contribution. Second, we applied the DelPhi approach, where the electrostatic component of the free energy of solvation is evaluated by resolving the Poisson-Boltzman equation by a finite difference method. Both methods appear equally reliable for ionic systems. For neutral compounds, AM1-SM1 performs better than DelPhi; however, the differences become less pronounced for compounds with larger free energies of solvation. In parallel, both methods were applied to study the influence of the solvation process in the overall drug receptor interaction for a series of closely related ligands for the D1 dopamine receptor. An inverse linear relationship was found between the free energy of solvation and the logarithm of the affinity of the ligands; nevertheless, electrostatic properties are likely to modulate affinity as well. © 1993 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540140514
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    Molecular mechanics calculations (MM3) on sulfones (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 655-666 
    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 structures of several sulfones, including dimethyl sulfone, methyl ethyl sulfone, methyl vinyl sulfone, and diphenyl sulfone, have been fit with the MM3 force field to existing experimental data from electron diffraction and microwave spectroscopy. The vibrational spectra have also been fit for six of these compounds. The torsional parameters for the aliphatic sulfones were fit to ab initio 6-31G data. Heats of formation were also fit. © 1993 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540140605
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    Model calculations for small closed-ring CdS clusters and chemisorption processes by a quantum chemical cluster approach (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 667-672 
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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: Chemisorption on small, closed-ring CdS clusters and the electronic structure of the surface were studied using Hartree-Fock valence calculations based upon stepwise density matrix approximations. Detailed valence calculations gave stabilization energies similar to the all-electron results for the small CdS clusters, verifying our valence method in which the approximations of the density matrices were fitted against the atomic calculations. Chemisorption studies have shown that the 4d shell relaxation on the Cd atom plays a crucial role even though the 4d does not participate directly in the substrate-adsorbate bonds. Thus, the CdCl2 was found unbound to the surface in the case of implicit description of the 4d orbital of the Cd whereas treating the Cd 4d orbital explicitly in the variational calculation the CdCl2 bonds to the surface with the calculated adsorption energy of 107.4 kJ/mol. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140606
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    Calculation of hydrophobic interactions from molecular dynamics, surface areas, and experimental hydrocarbon solubilities (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 741-750 
    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 experimental solubilities and partial pressures for hydrocarbon solution in water and molecular dynamics calculations of hydrocarbon water interaction energies, hydrocarbon-water cavity potentials are obtained and then plotted vs. accessible surface area. The data used is mainly for aliphatic hydrocarbons, but benzene is included. Molecular dynamics calculations of pairs of hydrocarbon molecules together with the cavity potential curve are then used to obtain hydrophobic interaction free energies between the hydrocarbon pairs. While the cavity potential change is related to a change in surface area for hydrocarbon systems, the hydrocarbon-water interaction energy is not, so that the hydrophobic binding energy is not. The results are in agreement with previous results by a different method (R.B. Hermann, In Seventh Jerusalem Symposium on Quantum Pharmacology, E. Bergman and B. Pullman, Eds., D. Reidel, Dordrecht, 1974, p. 441) in that there is little or no solvent-induced binding free energy between small hydrocarbon molecules in a dilute aqueous solution. It is proposed that the cavity potential vs. accessible surface area curve obtained here can be used together with OPLS parameters to calculate both hydrocarbon-water solvation free energies and hydrophobic interactions. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140616
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    Linear combination of Lanczos vectors: A storage-efficient algorithm for sparse matrix eigenvector computations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 769-774 
    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 present a storage-efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight-binding models of ordered and disordered 2-D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10-4 is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140703
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    Beyond the MNDO model: Methodical considerations and numerical results (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 775-789 
    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: It is suggested to improve the MNDO model by the explicit inclusion of valence-shell orthogonalization corrections, penetration integrals, and effective core potentials (ECPs) in the one-center part of the core Hamiltonian matrix. Guided by analytic formulas and numerical ab initio results, the orthogonalization corrections are expressed in terms of the resonance integrals that are represented by a new empirical parametric function. All two-center Coulomb interactions and ECP integrals are evaluated analytically in a Gaussian basis followed by a uniform Klopman-Ohno scaling. One particular implementation of the proposed NDDO SCF approach is described and parameterized for the elements H, C, N, O, and F. In a statistical evaluation of ground-state properties, this implementation shows slight but consistent improvements over MNDO, AM1, and PM3. Significant improvements are found for excited states, transition states, and strong hydrogen bonds. Possible further enhancements of the current implementation are discussed. © 1993 John Wiley & Sons, Inc.
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    Hydrolytic degradation of α-substituted polyglycolic acids: A semiempirical computational study (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 809-817 
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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 two-step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140707
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    Molecular dynamics of 18-crown-6 complexes with alkali-metal cations and urea: Prediction of their conformations and comparison with data from the cambridge structural database (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 899-906 
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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: Complexes of 18-crown-6 with alkali-metal cations (Na+, K+, and Rb+), urea, and the uncomplexed crown ether were studied in vacuo with the molecular dynamics method. Conformational data from these calculations (simulation times in the range from 6-15 ns) was compared with information from the Cambridge Structural Database. Despite the differences in condition between the simulations and the solid state, a number of interesting similarities are observed. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140804
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    Quantitative comparison of molecular electrostatic potential distributions from several semiempirical and ab initio wave functions (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 922-927 
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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 quantitative comparative analysis of molecular electrostatic potential (MEP) distributions generated from different wave functions was carried out. Wave functions were computed by using MNDO, AMl, STO-3G, 3-21G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** methods. Ten different compounds, which include usual atoms and groups of biomolecules, such as hydroxyl, carbonyl, amine, amide, imine, double and triple bonds, and heteroaromatic rings, were studied. For each compound, MEP values in the points of a common 3-D grid were computed; thereafter, the similarity between each pair of MEP distributions generated by different methods was assessed. Similarities were measured using the Spearman rank correlation coefficient. A similarity matrix was obtained for each compound. Similarity matrices were averaged and a hierarchical cluster analysis was carried out to classify the different quantum chemical methods. In the compounds studied, the main conclusion is the negligible difference between the pattern of MEP distributions generated from all split valence basis sets (with and without polarization functions). © 1993 John Wiley & Sons, Inc.
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    Modified MM2 scheme for computation of O—C—N-containing systems (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 944-960 
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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 modification of Allinger's MM2 force field for the anomeric effect in O—C—N systems is presented. For optimal consistency, it was parameterized by alternate use of ab initio (3-21G level) and X-ray results to account for the energetic and structural manifestations of the effect in the gas or condensed phase, respectively. The results obtained with the modified force field are in good agreement with those from both theoretical and experimental methods. The parameterization scheme explicitly treats all structural parameters of the C—O—C—N—C moiety as well as C—N bond lengths in tertiary amines contained within an anomeric unit. In addition, it includes directional H-bond type interactions. A limited number of parameters is put forward, in accord with the general MM2 force-field approach. © 1993 John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540140810
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    Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 977-985 
    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 application of parallel processing techniques to molecular mechanics calculations is evaluated. Using the standard molecular mechanics package, MM2, four different parallel versions of the program are implemented in a four-processor computing environment. A set of 529 test structures is used to compare the efficiency of the parallel versions of MM2 to a standard serial version of the program. Statistics describing execution times and program execution cycles are gathered and analyzed. The effects of parallel processing overhead and computer system load are explored, and the practical utility of parallel processing in molecular mechanics is estimated. The results of these parallelization experiments indicate that for geometry optimizations requiring significant amounts of computing time an improvement in program execution speed approaching 50% is realizable. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140813
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    AMBER force-field parameters for guanosine triphosphate and its imido and methylene analogs (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 995-1005 
    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: Parameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom-atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na4 GTP and Na2 Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140815
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    Ab initio study of hydrogen bonding in the phenol-water system (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1027-1035 
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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: Three hydrogen-bonded minima on the phenol-water, C6H5OH - H2O, potential energy surface were located with 3-21G and 6-31G** basis sets at both Hartree-Fock and MP2 levels of theory. MP2 binding energies were computed using large “correlation consistent” basis sets that included extra diffuse functions on all atoms. An estimate of the effect of expanding the basis set to the triple-zeta level (multiple f functions on carbon and oxygen and multiple d functions on hydrogen) was derived from calculations on a related prototype system. The best estimates of the electronic binding energies for the three minima are -7.8, -5.0, and -2.0 kcal/mol. The consequences of uncertainties in the geometries and limitations in the level of correlation recovery are analyzed. It is suggested that our best estimates will likely underestimate the complete basis set, full CI values by 0.1-0.3 kcal/mol. Vibrational normal modes were determined for all three minima, including an MP2/6-31G** analysis for the most strongly bound complex. Computational strategies for larger phenol-water complexes are discussed. © John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140904
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    Evaluation of one-electron integrals for arbitrary operators V(r) over Cartesian Gaussians: Application to inverse-square distance and Yukawa operators (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 986-994 
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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 general procedure is presented for generating one-electron integrals over any arbitrary potential operator that is a function of radial distance only. The procedure outlines that for a nucleus centered at point C integrals over Cartesian Gaussians can be written as linear combinations of 1-D integrals. These Cartesian Gaussian functions are expressed in a compact form involving easily computed auxiliary functions. It is well known that integrals over the Coulomb operator can be expressed in terms of Fn(T) integrals, where \documentclass{article}\pagestyle{empty}\begin{document}$$ F_n \left(T \right) = \int_0^1 {u^{2n} e^{ - Tu^2 } {\rm d}u} $$\end{document} By means of a substitution for Fn(T) by other simple functions, algorithms that form integrals over an arbitrary function can be generated. Formation of such integrals is accomplished with minor editing of existing code based on the McMurchie-Davidson formalism. Further, the method is applied using the inverse-square distance and Yukawa potential operators V(r) over Cartesian Gaussian functions. Thus, the proposed methodology covers a large class of one-electron integrals necessary for theoretical studies of molecular systems by ab initio calculations. Finally, by virtue of the procedure's recursive nature it provides us with an efficient scheme of computing the proposed class of one-electron integrals. © 1993 John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540140814
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    Assessment of methods used for predicting lipophilicity: Application to nucleosides and nucleoside bases (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 1019-1026 
    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: Estimating log P (logarithm of “1-octanol to water” partition coefficients) as a measure of lipophilicity for organic compounds is of considerable importance in drug discovery. Several methods have been developed for this purpose, each with its own drawbacks and advantages. In this article, a systematic comparison of three well-documented and fully computerized methods has been attempted for a set of nucleosides and bases. The first method (BLOGP) is based on overall molecular properties derived from a molecular orbital calculation to predict log P. The second method (CLOGP) uses fragmental lipophilicity constants with correction factors and treats log P as an additive-constitutive property. The third method (ALOGP) is based on an additivity scheme of atomic lipophilicity constants, with the constitutive factor governed by an elaborate list of atom types. However, none of these methods take into account conformational flexibility or intramolecular hydrogen bonding, which can cause substantial discrepancy between observations and predictions. A comparison of predictions from each of these methods indicates that the atomic contribution method (ALOGP with r = 0.842 and SD = 0.51) is better than other methods (with r = 0.395 and SD = 1.2 for BLOGP and r = 0.713 and SD = 0.93 for CLOGP) for this class of compounds. Our overall assessment is that we do not have, as yet, a highly reliable, fully computerized log P prediction method applicable to flexible heterocycles such as nucleoside analogs. © John Wiley & Sons, Inc.
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