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  • 1990-1994  (143)
  • 1985-1989  (133)
  • 1994  (143)
  • 1987  (133)
  • Biochemistry  (276)
  • 101
    Electronic Resource
    Electronic Resource
    Conformation energy around the N(sp3)—O single bond (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1091-1104 
    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 detailed conformational analysis was performed on simple substituted hydroxylamines using either ab initio (from HF/6-31G* to RQCISD/6-311G**) or popular semiempirical (MNDO, AM1, PM3) methods to ascertain the allowed conformations and to establish the influence of the level of theory on the results. All the ab initio results (provision being made for their expected divergences) are similar and show a simple twofold character for the 〉 N—O— rotational energy, without any appreciable populations of the cis conformer. On the other hand, the predictive value of the semiempirical methods for structural and energetical parameters of molecules bearing 〉 N—O— moieties is limited, a situation like that prevailing for peptide bonds. The inversional barriers for the methyl-substituted hydroxylamines were also calculated and compared to the corresponding rotational energy barriers. Rotation is generally favored over inversion for hydroxylamine and its methylated derivatives. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151005
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  • 102
    Electronic Resource
    Electronic Resource
    GEPOL: An improved description of molecular surfaces. III. A new algorithm for the computation of a solvent-excluding surface (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1127-1138 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for computing the Solvent-Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151009
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  • 103
    Electronic Resource
    Electronic Resource
    Stable conformations of CH3CH2OCH2CH2OH: A comparison of theoretical methods (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1176-1185 
    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: This article presents the results of an extensive examination of the stable conformations of CH3CH2OCH2CH2OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151013
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  • 104
    Electronic Resource
    Electronic Resource
    ToBaD: A method for the estimation of torsion barriers from crystal structure data; conformational analysis of N,N-dimethylaniline and derivatives (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1429-1436 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for the estimation of torsion barriers and its application to conformational analysis is presented. This method, the ToBaD method (method of the torsion barrier derivative), makes use of crystal structure data. It is based on the assumption that the conformation of a compound in the crystalline phase must be very close to a (local) minimum energy conformation of this compound in the gas phase. The ToBaD method is demonstrated for the rotation of the phenyl-N bond in N,N-dimethylaniline. Two geometries of this compound are handled separately: one in which the nitrogen substituents are in a pyramidal or sp3 geometry, and the other in which the nitrogen atom and its substituents are coplanar (the sp2 geometry). It is predicted, by means of the ToBaD method, that for both geometries the conformation in which the nitrogen lone pair or p orbital is perpendicular to the aromatic ring is the lowest energy conformation. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151212
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  • 105
    Electronic Resource
    Electronic Resource
    Heats of formation of organic molecules calculated from ab initio theory and a group equivalent scheme: Alkenes (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1437-1445 
    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 bond and group equivalent scheme that allows the calculation of heats of formation of alkenes from ab initio 6-31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 9 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151213
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  • 106
    Electronic Resource
    Electronic Resource
    Molecular mechanics (MM3) calculations on azoxy compounds (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1446-1460 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM3 force field has been extended to include azoxy compounds and also the related amine oxides, both aliphatic and aromatic. The structures of nine molecules were all well fit. The heats of formation for the aliphatic compounds were also well fit, and the vibrational spectra of eight compounds were also fit to the accuracy expected for such calculations. Because many of the experimental data needed to derive the force field were either lacking or were inadequate, ab initio calculations on structures, optimized at the MP2/6-31G* level, were used as needed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151214
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  • 107
    Electronic Resource
    Electronic Resource
    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    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.540150101
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  • 108
    Electronic Resource
    Electronic Resource
    Updated Hessian matrix and the restricted step method for locating transition structures (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1-11 
    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 family of the updated Hessian matrices for locating transition structures is presented. An analysis and improvement of the restricted step algorithm described by Culot et al. is proposed. The efficiency of the latter method is compared with other well-established methods for locating transition structures. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 13 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150102
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  • 109
    Electronic Resource
    Electronic Resource
    Display of the flow of energy in molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 80-89 
    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: In this article, we develop a method to graphically display the flow of energy within molecules. An energy continuity equation is derived leading to a molecular energy flux vector field. Computation of the flux calls for the intramolecular potential, any external interactions, and the phase space trajectories of the molecular motion. The flux provides a means to display energy flow in still frames and as a tool to visualize hitherto undiscovered dynamic pathways in molecules. Examples are presented that show energy flow in three molecular systems and illustrate the point that depiction of energy flux patterns has increasing utility and meaning as one moves to larger molecules. Simple extensions to this work would also allow visualization of the flux of such quantities as linear and angular momentum. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150110
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  • 110
    Electronic Resource
    Electronic Resource
    Applicability of the WKB method in asymmetric double wells with degenerate and nondegenerate minima (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 125-131 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To test the applicability of the WKB semiclassical approximation to correctly describe the tunneling frequencies and energy levels in asymmetric double wells, we have considered the cases where the asymmetry comes from the nondegeneracy of the two minima and when it comes from the asymmetry in the shape of the barrier between both minima. To do this, we compare the tunneling frequencies and energy levels obtained through the WKB method for symmetric and asymmetric cases with exact results obtained by a basis set procedure. Our results show that the semiclassical WKB approximation has to be used with caution for asymmetric double wells. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150202
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  • 111
    Electronic Resource
    Electronic Resource
    Rationalizing nuclear overhauser effect data for compounds adopting multiple-solution conformations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 155-161 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is described for refining the populations of a set of multiple-solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1-O-methyl-α-L-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150206
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  • 112
    Electronic Resource
    Electronic Resource
    Utilization of shape data in molecular mechanics using a potential based on spherical harmonic surfaces (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 190-199 
    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: This article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron-microscopy-based three-dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150209
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  • 113
    Electronic Resource
    Electronic Resource
    Announcement (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 249-249 
    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.540150215
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  • 114
    Electronic Resource
    Electronic Resource
    Molecular mechanics (MM3) calculations on alkyl radicals (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 283-299 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150304
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  • 115
    Electronic Resource
    Electronic Resource
    Quantum mechanical computations on very large molecular systems: The local self-consistent field method (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 269-282 
    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: Quantum chemical computations on a subset of a large molecule can be performed, at the neglect of diatomic differential overlap (NDDO) level, without further approximation provided that the atomic orbitals of the frontier atoms are replaced by parametrized orthogonal hybrid orbitals. The electrostatic interaction with the rest of the molecule, treated classically by the usual molecular mechanical approximations, is included into the self-consistent field (SCF) equations. The first and second derivatives of energy are obtained analytically, allowing the search for energy minima and transition states as well as the resolution of Newton equations in molecular dynamics simulations. The local self-consistent field (LSCF) method based on these approximations is tested by studying the intramolecular proton transfer in a Gly-Arg-Glu-Gly model tetrapeptide, which reveals an excellent agreement between a computation performed on the whole molecule and the results obtained by the present method, especially if the quantum subsystem includes the side chains and the peptidic unit in between. The merits of the LSCF method are examplified by a study of proton transfer in the Asp69 - Arg71 salt bridge in dihydrofolate reductase. Simulations of large systems, involving local changes of electronic structure, are therefore possible at a good degree of approximation by introducing a quantum chemical part in molecular dynamics studies. This methodology is expected to be very useful for reactivity studies in biomolecules or at the surface of covalent solids. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150303
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  • 116
    Electronic Resource
    Electronic Resource
    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    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.540150301
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  • 117
    Electronic Resource
    Electronic Resource
    Computational study of the hydrolysis of degradable polysaccharide biomaterials: Substituent effects on the hydrolytic mechanism (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 241-248 
    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: Hyaluronic acid and its derivatives are absorbable polysaccharides which are used extensively in cosmetics and as biomaterials. Two possible mechanisms of degradation, involving an oxocarbenium ion and the corresponding radical cation, are examined by modeling of the saccharide ring and the effects of various ring substituents on the two possible mechanisms. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150214
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  • 118
    Electronic Resource
    Electronic Resource
    Finite-state and reduced-parameter representations of protein backbone conformations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 300-312 
    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: This article studies the representation of protein backbone conformations using a finite number of values for the backbone dihedral angles. We develop a combinatorial search algorithm that guarantees finding the global minima of functions over the configuration space of discrete protein conformations, and use this procedure to fit finite-state models to the backbones of globular proteins. It is demonstrated that a finite-state representation with a reasonably small number of states yields either a small root-mean-square error or a small dihedral angle deviation from the native structure, but not both at the same time. The problem can be resolved by introducing limited local optimization in each step of the combinatorial search. In addition, it is shown that acceptable approximation is achieved using a single dihedral angle as an independent variable in local optimization. Results for 11 proteins demonstrate the advantages and shortcomings of both the finite-state and reduced-parameter approximations of protein backbone conformations. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150305
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  • 119
    Electronic Resource
    Electronic Resource
    The structures of LiNC, NaNC, and KNC: Potential energy surface for the orbiting motion of the metal cation around the CN group (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 322-332 
    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: Sets of XNC (X = Li, Na, and K) structures have been investigated using a variety of theoretical methods and basis sets. Two linear and a bridged structure correspond to an energy minimum for LiCN. For NaCN and KCN, the linear isocyanide is a minimum at most levels of theory but becomes a second-order stationary point when correlated levels and large basis sets are used. Two transition structures are involved in the interconversion of the bridged form and each linear isomer. The isomerization of the bridged minimum to the linear XCN involves a substantial barrier in each case, so that the satellite motion of the metal is facile at one end but not at the other. Calculations with large basis sets and with electron correlation, fourth-order Møller-Plesset theory for KNC, and quadratic configuration interaction [QCISD(T)] for LiNC and NaNC give qualitative and quantitative agreement with this experiment. The sodium and potassium cyanide prefer bridged forms, in contrast to the linear isocyanide LiNC. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150307
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  • 120
    Electronic Resource
    Electronic Resource
    Announcement (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 374-374 
    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.540150311
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  • 121
    Electronic Resource
    Electronic Resource
    Normal coordinates-finite elements calculation of 3D vibrational energy levels: Henon - Heiles and Eckart potentials, H3+ molecule (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 377-384 
    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: Theoretical and numerical results related to the calculation of multidimensional vibrational levels are presented. A description of the methodological details of a very general method (normal coordinates-finite elements, NC-FEM) is provided. Several representative three-dimensional (3D) systems (Henon-Heiles and Eckart potentials, and the H3+ molecule) are studied, and NC-FEM results are compared with those published by other authors. For the H3+, a vibrational Hamiltonian expressed in terms of the three internuclear distances is integrated, and the results obtained are compared with the experimental ones. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150402
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  • 122
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    Electronic Resource
    Optimization of solute cavities and van der Waals parameters in ab initio MST-SCRF calculations of neutral molecules (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 446-454 
    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 cavity used to represent the solute/water interface in Miertus-Scrocco-Tomasi self-consistent reaction field (MST-SCRF) calculations of neutral molecules has been optimized by fitting to experimental data. The study is focused on the refinement of the van der Waals radii of polar and apolar hydrogens and of the van der Waals parameters used to compute the dispersion/repulsion contribution to the total free energy of hydration. When a scaling coefficient of 1.25 is used to build the solute cavity, comparison of 6-31G*/MST results with experimental data demonstrates that the optimum van der Waals radii for hydrogens are around 1.2 Å (apolar) and 0.9 Å (polar). The optimization of the solute cavity and the refinement of the van der Waals parameters lead to root mean square deviations in the computed free energy of hydration of only 0.9 kcal/mol for the 23 molecules considered in this study. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150408
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  • 123
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    Electronic Resource
    Monte Carlo simulations on short single-stranded oligonucleotides. I. Application to RNA trimers (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 433-445 
    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: Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers - r(AAA) and r(AAG) - obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse-stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse-stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150407
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    Theoretical analysis of the role of the solvent on the reaction mechanisms: One-step versus two-step ketene-imine cycloaddition (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 479-487 
    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 effect of correlation energy, basis set size, zero-point energy (ZPE) correction, and solvation on the reaction mechanism of the ketene-imine cycloaddition reaction has been investigated. The electrostatic solvent effect was studied with a self-consistent reaction field method in which the solvation energy is obtained using a multipole expansion of the molecular charge distribution. The ab initio results have been analyzed by means of a theoretical method based on the expansion of the MOs of the supermolecule in terms of those of the reactants and the performance of the configuration analysis. In gas phase, due to the correlation energy and/or the ZPE corrections, the reaction is predicted to be a one-step process. In solution, the stabilization of the charge-transferred configurations results in the occurrence of a very stable, Zwitterionic intermediate giving a two-step mechanism. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150502
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    Variation of atomic charges during proton transfer in hydrogen bonds (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 553-560 
    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 point atomic charges in a number of ionic H-bonded systems are studied by ab initio calculations as functions of the proton transfer coordinate. In the proton-bound complexes of water-water, ammonia-ammonia, formamide-water, formamide-ammonia, and dimethylether-ammonia, the net atomic charges were obtained using Mulliken population analysis and from the diagonal elements of the atomic polar tensors calculated at the HF/4-31G and MP2/6-31 + G** levels. The dependence of the atomic charges upon the coordinate of the transferring proton was found to be close (within an error of 0.02 e) to a linear function for intermolecular distances in the 2.5-2.8 Å range. The obtained charge and charge flux dependencies highlight the electron redistribution during the proton transfer process and provide insights into the source of the high infrared (IR) intensities of stretching modes of N—H and O—H bonds undergoing hydrogen bonding. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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    Announcement (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 571-571 
    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.540150509
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    Hash codes for the identification and classification of molecular structure elements (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 793-813 
    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 set of algorithms is presented which establish the topological identity of atoms, bonds, molecules, and ensembles of molecules from a basic connection table. The computationally inexpensive result is a fixed-length hash code which is suited for database applications and structure manipulation programs. The degree of differentiation between structural entities is adjusted easily for stereocenters, isotope labeling, atomic charges, and ionization locations or other properties. Special algorithms are presented which deal with problematic cases of uniform atomic environments. A number of practical applications demonstrate the usefulness of these hash codes. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 23 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150802
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    Study of localized molecular orbitals using group theory methods and its approach to the many-electron correlation problem. IV. The symmetry-adaptation of many-center integrals and hamiltonian matrix elements in MCSCF calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 858-865 
    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: Group theoretic methods are presented for the transformations of integrals and the evaluation of matrix elements encountered in multiconfigurational self-consistent field (MCSCF) and configuration interaction (CI) calculations. The method has the advantages of needing only to deal with a symmetry unique set of atomic orbitals (AO) integrals and transformation from unique atomic integrals to unique molecular integrals rather than with all of them. Hamiltonian matrix element is expressed by a linear combination of product terms of many-center unique integrals and geometric factors. The group symmetry localized orbitals as atomic and molecular orbitals are a key feature of this algorithm. The method provides an alternative to traditional method that requires a table of coupling coefficients for products of the irreducible representations of the molecular point group. Geometric factors effectively eliminate these coupling coefficients. The saving of time and space in integral computations and transformations is analyzed. © 1994 by John Wiley & Sons, Inc.
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    Announcement (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 917-917 
    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.540150812
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    Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 820-837 
    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 method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C2 symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540150804
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    Thermodynamic integration calculations on the relative free energies of complex ions in aqueous solution: Application to ligands of dihydrofolate reductase (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 704-718 
    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 (MD) simulation and thermodynamic integration (TI) techniques have been used to study the relative free energies of the 8-methyl-N5-deazapterin and 8-methyl-pterin cations (N3 protonated) in aqueous solution. The MD simulations were performed at constant temperature and volume, and the mutations between the cations were carried out by changing the coupling parameter continuously and linearly with the MD simulation time (continuous coupling or slow growth method). The free energy changes have been calculated using both linear and nonlinear couplings of the potential energy functions. Free energy changes have also been computed using the perturbation method for comparison. After separation into electrostatic and van der Waals mutations, most (ca. 80%) of the total free energy change is found to be due to mutation of the electrostatic terms. The free energy change is found to be sensitive to the cutoff radii for interactions between solvent molecules, but rather insensitive to the cutoff radii for interactions between cation and solvent. The free energy changes have also been calculated using various cation and solvent models. Atomic charges for the cations were derived from the molecular electrostatic potential at the semiempirical AM1 and ab initio self-consistent field (SCF) (3-21G, 6-31G, 6-31G*, 6-311G**) levels using AM1 and 3-21G optimized geometries. The TIP3P and SPC models were adopted for the solvent. For the TIP3P solvent model, the order of the free energy change is 6-31G 〉 3-21G 〉 6-31G* ≈ 6-311G** 〉 AM1, where the difference between 6-31G and AM1 is approximately 1 kcal/mol. The free energies obtained using 3-21G optimized geometries are approximately 0.7 kcal/mol larger than those obtained using AM1 geometries for the cations. The free energy change computed using the TIP3P/6-311G* model is 0.3 kcal/mol larger than that obtained for the SPC/6-311G* model. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150704
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    A computational study of azine, azoethene, and diimine linkages in the poly/oligoazine system (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1163-1175 
    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: Hartree-Fock (HF) and molecular mechanics calculations were performed on linear azine oligomers and model compounds. The rotational energy curves for the model compounds formaldazine, H2C = N—N = CH2, ethenyl diazene, H2C = CH—N = NH, and ethanediimine, HN = CH—CH = NH were calculated for a variety of basis sets at the HF and MP2 level. In all of these cases the rotational energy barriers are quite different from butadienes or aza-substituted butadienes because of the lone pair-lone pair interaction of the adjacent nitrogen atoms. The results on the model compounds were used to generate a set of molecular mechanics (MM) parameters that are appropriate for linear oligo- and polyazines. Comparison of the geometries of the HF results and MM results for the oligoazines showed that the two methods gave comparable results. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151012
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    Thermodynamic molecular mechanics force field: Modified QCFF program (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1254-1265 
    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 QCFF program originated by Warshel and Karplus4a was modified to compute accurate thermodynamic properties So, Cpo, (HTo - H0o)/T, and ΔHfo for various acyclic and cyclic alkenes and alkadienes. Modifications consisted of adjusted bond angle, dihedral angle, bond stretch, and bond energy parameters that improved calculated vibrational frequencies, zero point energies, and thermodynamic functions. Supplemental torsional potential energy functions that were added to existing torsional functions led to greatly improved relative conformer energies and ΔHf0 values. It was shown that inclusion of hindered internal rotation leads to significantly better agreement of calculated thermodynamic functions with observed values for acyclic alkenes at high temperatures. The calculated thermodynamic properties of the alkenes and alkadienes were deemed sufficiently accurate for calculation of standard enthalpies and Gibbs free energies of gas phase chemical reactions at various temperatures. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151107
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    The natural atomic orbital point charge model for PM3: Multipole moments and molecular electrostatic potentials (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1064-1073 
    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 natural atomic orbital/point (NAO-PC) model originally developed to calculate molecular electrostatic potentials (MEPs) and multiple moments based on the AM1 wave function has been extended to PM3. As for AM1, NAO-PC/PM3 reproduces dipole moments calculated by the standard PM3 method very well. There is also a surprisingly good correlation between experimental and calculated quadrupole moments. The MEPs calculated using PM3/NAO-PC are found to be in better agreement with those given by RHF/6-31G* than those obtained from the PM3 wave function using Coulson charges. On the other hand, the NAO-PC model is often slightly worse then the method implemented in MOPAC-ESP. The MEPs calculated using our model based on the PM3 wave function are often in better agreement with those given by RHF/6-31G* than those obtain with AM1. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151003
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    On the calculation of ab initio quantum molecular similarities for large systems: Fitting the electron density (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1113-1120 
    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 set of procedures for rapid calculation of quantum molecular similarities from ab initio wave functions is discussed. In all cases a density fitting is carried out to eliminate the need of calculating costly four-centered integrals. It is proved that this methodology can be applied to large systems to reproduce exact quantum molecular similarity measures at an extremely low computational cost. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540151007
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    The valence isomers of (CH)8 and (SiH)8: An ab initio MO study (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1151-1162 
    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 22 possible valence isomers of the (CH)8 and (SiH)8 systems have been studied by ab initio molecular orbital calculations at the MP2/6-31G*//6-31G* + ZPE level. Optimized geometries, relative energies, and, for some selected compounds, vibrational frequencies are reported. The systematic differences between the carbon and silicon compounds are analyzed. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 6 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540151011
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    Molecular mechanics (MM3) parameterization of hydroxylamine and methyl derivatives (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 866-874 
    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: Based on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6-31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp3) - O(sp3) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150808
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    On the functional representation of bond energy functions (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 919-924 
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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 are used to test the ability of various representations to reproduce bond energies. It is found that expansion in 1/R, where R is the bond length, is remarkably efficient and is consistently better than the usual R expansion. A quadratic form in 1/R is better than a cubic representation in R and sometimes even as good as a quartic representation. A cubic function in 1/R is, in all cases studied, better performing than the quartic expansion in R. It is also found that parameters derived with the 1/R expansion are defined more sharply than those derived for the R expansion. It is suggested that the 1/R expansion may be computationally more efficient for simulations of large biomolecules and for constructions of reactive force fields than the standard bond functions. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150902
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    Conformational study of dipeptides: A sensitivity analysis approach (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 947-962 
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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 studies the backbone influence on the side chains of N-methyl N′-acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein φ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone φ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in φ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in φ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150905
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    Structural and electronic property changes of the nucleic acid bases upon base pair formation (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 981-996 
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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 systematic study of structures and electronic properties has been carried out for the nucleic acid bases adenine, guanine, thymine, and cytosine and for the base pairs adenine-thymine and guanine-cytosine. We focus our attention on these properties, which experience significant changes when single nucleic bases join to form base pairs. Such properties are expected to play an important role during the formation of the DNA molecule in its B conformation. All-electron calculations with inclusion of correlation effects were performed according to the local and nonlocal density functional approaches. We compare our results with previous ab initio and semiempirical values and with available experimental data. Advantages and disadvantages for these density functional-based methods are discussed. We conclude that applications of such models to investigate larger compounds of a similar nature are promising. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540150907
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    Masthead (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994) 
    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.540151001
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    Potential energy surfaces for Rh—CO from DFT calculations (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1053-1063 
    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 potential energy surfaces for Rh—CO obtained from density functional theory for two electronic states of Rh—CO. We have performed local spin-density calculations including relativistic as well as gradient corrections. The construction of a reasonably accurate atom-atom potential for Rh—CO is not possible. We were much more successful in constructing the potential energy surfaces by representing the potential as a spherical expansion. The expansion coefficients, which are functions of the distance between the rhodium atom and the carbon monoxide center of mass, can be represented by Lennard-Jones, Buckingham, or Morse functions, with an error of the fit within 10 kJ/mol. The potential energy surfaces, using Morse functions, predict that the electronic ground state of Rh—CO is 2Σ+ or 2Δ. This is a linear structure with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.253 nm. The bonding energy is -184 kJ/mol. Further, Morse functions predict that the first exicted state is 4A′. This is a bent structure (∠Rh—CO = 14°) with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.298 nm. The bonding energy of this state is -60 kJ/mol. Both these predictions are in good agreement with the actual density functional calculations. We found 0.250 nm with -205 kJ/mol for 2Σ+ and 0.253 nm with -199 kJ/mol for 2Δ. For 4A′, we found 0.271 nm, ∠Rh—CO = 30°, with -63 kJ/mol. The larger deviation for 4A′ than for 2Σ+ or 2Δ is a consequence of the fact that the minimum for 4A′ is a very shallow well. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151002
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    Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1105-1112 
    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 efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
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    URL: http://dx.doi.org/10.1002/jcc.540151006
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  • 144
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    Experimental toxicology of formaldehyde (1987)
    Springer
    Journal of cancer research and clinical oncology 113 (1987), S. 305-309 
    Details
    ISSN: 1432-1335
    Keywords: Formaldehyde ; Mutagenicity ; Metabolism ; Biochemistry ; Carcinogenicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary Formaldehyde is a reactive chemical which undergoes spontaneous reactions with various cellular constituents. Mutagenicity data may be interpreted on the background of this behavior. Mice are better able to reduce the irritating effect of formaldehyde than rats and to reduce their ventilation rate when formaldehyde acts on the respiratory tract. Subacute exposure of rats to concentrations higher than 2 ppm inhibits mucociliary clearance of the nasal epithelium and leads to progressive histological and ultrastructural lesions at this site. The occurrence of squamous cell carcinomas of the nasal epithelium of rats after 2 years inhalation of 14.3 ppm formaldehyde (CIIT study) is probably the result of chronic and recurrent local toxicity; this is supported by species differences in susceptibility to the tissue damaging and carcinogenic effect of formaldehyde (rat, mouse, hamster). Data on formaldehyde-DNA interaction further support the argument that a direct risk extrapolation from the formaldehyde effects in rats to those expected for man is not possible.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00397713
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  • 145
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    Myoadenylate deaminase deficiency: absence of correlation with exercise intolerance in 452 muscle biopsies (1987)
    Springer
    Journal of neurology 234 (1987), S. 385-389 
    Details
    ISSN: 1432-1459
    Keywords: Myoadenylate deaminase ; Histochemistry ; Biochemistry ; Neuromuscular diseases ; Exertional myalgia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary A histochemical assay was routinely performed of myoadenylate deaminase (MAD) in muscle biopsy specimens. MAD was absent in 13 cases, i.e. 2.9% of the specimens. In 10 cases the deficiency was confirmed biochemically. The diagnoses in the 13 patients were: polyneuropathy (n=5), infantile spinal muscular atrophy (n=3), congenital myopathy with type 2 fibre atrophy, facioscapulohumeral myopathy, polymyositis, myotonic dystrophy and hyperornithinaemia with gyrate atrophy of the retina. In contrast, 35 unrelated patients presenting with exercise-related muscle cramps or pains showed normal histochemical MAD activity. The biopsy specimens in all of these patients were essentially normal and in none of them was the diagnosis of a neuromuscular disease made. The results failed to confirm the association of MAD deficiency with aches, cramps and pains or exertional myalgia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00314082
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  • 146
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    Computer enumeration and generation of physical trees (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 549-554 
    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 computer-oriented method for the enumeration and generation of physical trees is presented. Physical trees depict acyclic chemical structures, but the term physical is used to stress the process by which the structures are produced.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080435
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  • 147
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    Announcement (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 562-562 
    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.540080437
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  • 148
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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.540080501
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  • 149
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    Towards a quantum chemical software package utilizing transferable fragments as molecular building blocks (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 555-561 
    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: Computer programs have been developed or are under development for the IBM personal computer that enable their users to get information on atomic charges, electrostatic potentials, conformational and other properties of molecular systems containing H, C, N, O, F, Si, P, S, or Cl atoms. The zero-order wavefunction is constructed of strictly localized molecular orbitals with fixed atomic orbital coefficients. The wave function can be refined by optimizing these coefficients, i.e., considering inductive effects via a coupled set of 2 × 2 secular equations within the CNDO/2 approximation. Delocalization and exchange effects are accounted for by expanding the wavefunction on a basis of the aforementioned strictly localized orbitals, instead of conventional atomic orbitals, and solving the corresponding SCF equations. Our method has been applied to the study of large systems. We calculated the electrostatic field of the complex of β-trypsin and basic pancreatic trypsin inhibitor and it has been found that strong field regions more or less coincide with hydration sites. A further potential application of protein electrostatic fields is in NMR spectroscopy. We found a linear correlation between CαH or backbone NH proton chemical shifts and the protein field at the site of the corresponding proton. At last, we propose a simple method to mimic the bulk around atomic clusters modeling crystalline and amorphous silicon. Based on this method we found a linear correlation between atomic net charges and bond angle distortions in silicon clusters with 35 atoms.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080436
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  • 150
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    Strain energy minimization study of the mechanism of, and the barrier to, conformational interconversion in five-membered diamine chelate rings (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 651-657 
    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 method of Lagrangian multipliers is used to constrain torsion angles during molecular mechanics refinement for the purpose of plotting strain energy against a reaction coordinate. A complete two-dimensional analysis of the conformational interconversion from δ- to λ-[Co(ethane-1,2-diamine) (NH3)4]3+ reveals a mechanism in which the transition state geometry has an envelope conformation and an inversion barrier of 15.7 kJ mol-1. Substitution at the carbon atoms, variation of the metal-nitrogen distance, and replacement of the amine ligands with bidentate amines only slightly alters the inversion barrier. Substitution at the nitrogen atoms of the bidentate ligand increases the inversion barrier significantly to 24.6 kJ mol-1 for (N,N,N′,N′-tetramethylethane-1,2-diamine) [(NH3)4]3+.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080510
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  • 151
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    Two approaches to the calculation of molecular resonance states: Solution of scattering equations and matrix diagonalizationPresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 683-699 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have analyzed two approaches to reproduce the resonance expansion of the scattering matrix appropriate for the calculation of molecular resonance states. The first is based on the resonance theory of Siegert-Humblet-Rosenfeld (SHR) and the second on the Fano-Feshbach formalism. The direct method of calculating the resonance expansion characteristics, devised on the basis of the SHR theory, makes it possible to obtain the energies and partial widths (detailed decay rate constants) of resonances. The Fano-Feshbach formalism, on the other hand, elucidates the resonance state as a concept and facilitates the interpretation of calculation results. The use of computational methods is illustrated by the study of the decay of a model triatomic system and of gas-phase nucleophilic substitution reactions. Used in the latter case is the division of all degrees of freedom of the reacting system into the adiabatic and dynamic ones along with an algorithm of inclusion of the restricted dynamical treatment in the calculation of reaction rate constants.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080514
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  • 152
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    The inverse problem of isomer enumerationPresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 700-717 
    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 present article addresses the problem of identifying the structure of a parent compound through its chemical fingerprints such as the various numbers of isomeric substitution patterns, along the lines of Kekulé when he arrived at his benzene formula. In a pioneering paper (1929), Lunn and Senior laid out the conceptual framework for the permutation group description of substitution isomerism. It remained, however, for Pólya's celebrated contribution (1937) to initiate the actual mathematical realization of their vision. Pólya supplied the tools for solving the isomer enumeration problem: given a (symmetrical) parent compound, enumerate its spectrum of substitution patterns. The converse problem, though ranked the more interesting one by Lunn & Senior, hardly received any mathematical attention. The present article offers a complete and effective solution.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080515
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  • 153
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    Molecular graphs as topological objects in spacePresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 718-726 
    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: Stereochemistry deals primarily with distinctions based on rigid geometry, e.g., bond angles and lengths. But some chemical species have molecular graphs (such as knots, catenanes, and nonplanar graphs K5 and K3.3) that reside in space in a topologically nontrivial way. For such molecules there is hope of using topological methods to gain chemical information. Viewing a molecular graph as a topological object in space makes it unrealistically flexible; but if one proves that a certain graph is “topologically chiral” or that two graphs are “topological diastereomers,” then one has ruled out interconversion under any physical conditions for which the molecular graph still makes sense. In this paper, we consider several kinds of topological questions one might ask about graphs in space, methology and results available, and specific topological properties of various molecules.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080516
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  • 154
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    Hartree Fock instabilities of sulfur-nitrogen ring systems: S2N2Presented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986 (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 727-735 
    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 Hartree-Fock instablities of S2N2 are reported and compared with those of S3N3- and S4N42+. These unsaturated sulfur nitrogen planar rings are π electron rich and although the symmetry adapted HF solutions are singlet stable at the experimental bond lengths they become unstable with only a very modest increase in bond length. The broken symmetry solutions for S2N3, S3N3-, and S4N42+ are of planar C2v type with one of the nitrogens stripped of its π electrons, producing a π hole.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080517
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  • 155
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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.540080601
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  • 156
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    Ab-initioMRD-CI calculations on a C—NO2 decomposition pathway of nitrobenzenePresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 736-743 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To study molecular decomposition pathways it is necessary to use ab initio multireference determinant-configuration interaction or MCSCF (multiconfiguration SCF) calculations. The MRD-CI (multireference double excitation-configuration interaction technique of Buenker and Peyerimhoff) calculations on the decomposition pathway of nitrobenzene were carried out using all of the occupied molecular orbitals in the region of the bond being dissociated, plus all of the virtual orbitals. An effective CI Hamiltonian was used into which were folded the effects of all of the occupied molecular orbitals from which excitations were not allowed. So far we have investigated the lowest 1A1, 3A1, 1A2, 3A2, 1B1, 3B1, 1B2, 3B2 states and are investigating the higher states. Our results show a wealth of structure in the potential energy surfaces for the various electronic states of nitrobenzene as a function of distance. A number of the states are predissociative and change dominant configuration one or more times along these potential energy surfaces.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080518
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  • 157
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    Hamiltonian dynamics of chemical reactions. Consecutive first-order reactions and reactions possessing one autocatalytic intermediatePresented at the Symposium on Computation and Mathematical Chemistry, Saskatoon, Canada, June 1-4, 1986. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 744-751 
    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 recently proposed Hamiltonian approach to phenomenological chemical kinetics [T. Georgian and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 10, 331 (1983); T. Georgian, J.M. Halpin, and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 11, 347 (1984)] is applied to all consecutive first-order, single-step reactions, and to all reactions possessing one autocatalytic intermediate. The reaction Hamiltonians presented are shown to be consistent with the phenomenological rate equations and the relationship between reaction form and the form of the reaction potential is discussed. In particular, we show: (1) that the interaction between consecutive reactions manifests itself as a coupling term in the reaction potential, a term which may be eliminated via transition to “normal reaction coordinates” for the chemical system; and (2) that coupled sets of autocatalytic reactions give rise to coupling terms in the reaction Hamiltonian which are characteristic of the reaction mechanism.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080519
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  • 158
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    Column design. 3. Theoretical studies of a chiral stationary phase used in column chromatography (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 753-760 
    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: Conformational features of a chiral stationary phase used in column chromatography are discussed. The syn forms invoked in chiral recognition models are consistent with MNDO and MM2 calculations. It is speculated that the inherent flexibility of the syn form makes these phases effective templates for analyte binding.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080602
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  • 159
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    Ab initio study of the He(1S)-Li2(X̃, 1∑g+) interaction by the SCF and MP2 methods (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 761-771 
    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 electronic structure calculations have been carried out for the He(1S)-Li2 (X̃, 1∑g+) interaction both by the single-configuration SCF and correlated second-order MP2 methods using an extended basis set. From these calculations, an estimate of the isotropic (V0) and first two anisotropic (V2 and V4) terms of the He-Li2 potential surface has been obtained. An assessment of the leading induced-dipole-induced-dipole dispersion energy is presented from the MP2 energies. Where possible, a comparison is made with previous unpublished ab initio calculations by Staemmler and Stahl using the CEPA method.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080603
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  • 160
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    CNDO Force constants for glucose (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 772-777 
    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: Force constants for both anomers of glucose are evaluated using CNDO/Force method.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080604
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  • 161
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    Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 778-787 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms for a finer description of cavities in continuous media and for a more efficient selection of sampling points on the cavity surface are described. Applications to the evaluation of solute surface and volume and to the calculation of the solute-solvent electrostatic interaction energy, as well as of the cavitation energy are shown as examples.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080605
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  • 162
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    A study of basis set effects on structures and electronic structures of phosphine oxide and fluorophosphine oxide (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 788-793 
    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 variety of basis sets have been used for geometric and electronic structure studies. Electronic effects were measured using integrated spatial electron populations (ISEP). The two largest basis sets used, 6-31G* and DZ+P, give significantly different results. Use of two d-orbital sets (6-31G*[dd]) or decontraction of the 2sp shell on phosphorus has little further effect. d-Orbitals on oxygen are required for consistent electronic structure results, and d-orbitals on fluorine have a small but significant effect. Use of diffuse functions, required for anions, is not recommended with small basis sets on neutral molecules. Large negative charges (≈-1.5) on oxygen are given by all of the larger basis sets by the ISEP procedure and indicate that the PO bond in these compounds is largely semi-polar. The best simple symbolic representation of phosphine oxide is H3P+—0-, rather than H3P=0.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080606
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  • 163
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    Basis set and correlation effects on computed positive ion hydrogen bond energies of the complexes AHn · AHn + 1+1: AHn = NH3, OH2, and FH (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 810-815 
    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: Basis set expansion and correlation effects on computed hydrogen bond energies of the positive ion complexes AHn · AHn + 1+1, for AHn = NH3, OH2 and FH, have been evaluated. The addition of diffuse functions on nonhydrogen atoms is the single most important enhancement of split-valence plus polarization basis sets for computing hydrogen bond energies. Basis set enhancement effects appear to be additive in these systems. The correlation energy contribution to the stabilization energies of these complexes is significant, with the second order term being the largest term and having a stabilizing effect. The third order term is smaller and of opposite sign, while the fourth order term is smaller yet and stabilizing. As a result, computed MP4 stabilization energies are bracketed by the MP2 and MP3 energies. The overall effect of basis set enhancement is to decrease hydrogen bond energies, whereas the addition of electron correlation increases stabilization energies.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080609
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  • 164
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    A powerful truncated Newton method for potential energy minimizationThis work would not have been possible without the expert contibutions of Charles Peskin and Suse Broyde. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1025-1039 
    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: With advances in computer architecture and software, Newton methods are becoming not only feasible for large-scale nonlinear optimization problems, but also reliable, fast and efficient. Truncated Newton methods, in particular, are emerging as a versatile subclass. In this article we present a truncated Newton algorithm specifically developed for potential energy minimization. The method is globally convergent with local quadratic convergence. Its key ingredients are: (1) approximation of the Newton direction far away from local minima, (2) solution of the Newton equation iteratively by the linear Conjugate Gradient method, and (3) preconditioning of the Newton equation by the analytic second-derivative components of the “local” chemical interactions: bond length, bond angle and torsional potentials. Relaxation of the required accuracy of the Newton search direction diverts the minimization search away from regions where the function is nonconvex and towards physically interesting regions. The preconditioning strategy significantly accelerates the iterative solution for the Newton search direction, and therefore reduces the computation time for each iteration. With algorithmic variations, the truncated Newton method can be formulated so that storage and computational requirements are comparable to those of the nonlinear Conjugate Gradient method. As the convergence rate of nonlinear Conjugate Gradient methods is linear and performance less predictable, the application of the truncated Newton code to potential energy functions is promising.
    Additional Material: 3 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080711
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  • 165
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    An efficient newton-like method for molecular mechanics energy minimization of large molecules (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1016-1024 
    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: Techniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O(N2)) and computer time of O(N3). Our suggested implementation of the Truncated Newton technique requires storage of less than O(N1.5) and CPU time of less than O(N2) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10-6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080710
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  • 166
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    On the out-of-plane deformation of aromatic rings, and its representation by molecular mechanics (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1051-1056 
    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 has been found that the previous MM2 (or MMP2) description of out-of-plane deformation of aromatic rings sometimes yields distortions which are much too large. As a result, rotational barriers involving distortions of such rings may be calculated to have values which are too low. Examples are collected and discussed. An alternative formulation, which appears to significantly reduce the calculational error, is presented.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080713
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    Scientific and engineering applications with personal computer, r. annino and r.d. driver. wiley, new york, 1986, $45.00, 577 pp. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1066-1067 
    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.540080715
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  • 168
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    Molecular orbital calculations on solvents and other small molecules: Correlation between electronic and molecular properties ν, αMOL, π*, and β. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1084-1089 
    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 orbital calculation by the MINDO/3 method are reported for 50 compounds used as solvents in chemical reactions. Relationships between various parameters of electronic structure and molecular properties such as dipole moment, polarizability and Taft solvent parameters are presented. Comparison between experimental values of π* and calculated values is given.
    Additional Material: 5 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540080803
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  • 169
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    Systematic drug receptor mapping: A new approach to the analysis of conformational energy calculations of flexible molecules with application to dopaminergic and adrenergic agonists (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1075-1083 
    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 computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n-dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080802
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  • 170
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    On the use of constraints in molecular mechanics. II. The Lagrange multiplier method and non-full-matrix Newton-Raphson minimization (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1099-1103 
    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 shown how the Lagrange Multiplier method for constrained minimization can be implemented in a molecular mechanics program using the common approximations to the full-matrix Newton-Raphson minimization. The method reduces the number of cycles to achieve convergence, and also stabilizes the refinement process. Increases in computer memory requirements are small. As an application, the conformational surface of cycloheptane is calculated.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080805
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  • 171
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    Molecular mechanics study of myelin basic protein (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1104-1108 
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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: Myelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. We have examined the predicted structure of segments of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and coworkers as modified by Chuman, Momany, and Schafer. We have focused upon segments containing the Pro-Pro-Pro sequence (residues 100-102), which have been predicted from standard algorithms to exist in a hairpin loop connecting anti-parallel beta-strands. Both the shorter (98-105, 99-105, and 100-105) and longer segments (87-109, 87-118, and 87-120) have been examined. These results indicate potential for a chain reversal in this region. The shorter segments have been studied by others using NMR techniques and the results are compared.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080806
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  • 172
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    An evaluation of the performance of diffuse function-augmented basis sets for second row elements, Na-ClPart IV of a series on Efficient Diffuse Function-Augmented Basis Sets for Anion Calculation. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1109-1116 
    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 energetic effects of the addition of diffuse functions to molecules with second-row elements are much less dramatic than those for their first-row counterparts. Although diffuse functions on second-row elements have little effect on the geometries and vibrational frequencies of neutral molecules, significant changes are found for anions. While the largest basis set, 6-31 + G*, generally performs best, the results at 3-21 + G* are comparable, and this basis can be recommended for practical applications.
    Additional Material: 10 Tab.
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  • 173
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    Semi-empirical calculations of molecular trajectories: Method and applications to some simple molecular systems (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1117-1123 
    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 MNDO Hamiltonian as incorporated within MOPAC has been utilized to predict dynamics for some simple reactions. In one option, the intrinsic reaction coordinate has been followed along the path of steepest descent from the transition state backward to reactants and forward to products. In a second option, dynamics of isolated molecular systems have been calculated. In each case, the potential surface (as predicted by the MNDO Hamiltonian) is calculated in situ as the atomic trajectories are calculated from Newton's Laws of Motion. Several specific examples are given and discussed.
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  • 174
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    Cooperative effects in extended hydrogen bonded systems involving O—H groups. Ab initio studies of the cyclic S4 water tetramer (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1090-1098 
    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 additional energy stabilization due to cooperative effects was calculated in extended hydrogen bonded systems O—H⃛O—H⃛O—H with unidirectional (homodromic) orientation of the O—H groups. Ab initio restricted Hartree Fock, MP2 and MP3 calculations with geometry optimization and BSSE correction have been performed using the GAUSSIAN 83 program package for the ground states of the linear water dimer with Cs symmetry and the cyclic water tetramer with S4 symmetry. The latter represents the smallest possible, experimentally observed cooperative structure. A new definition for a cooperativity parameter is proposed. The definition is based on the two-body, non-neighbour interaction energy, plus three- and four-body contributions, including one-body deformation terms in relation to the total interaction energy of the water tetramer. The advantage of this definition is its independence of the reference system, which is necessary in complicated molecular systems with an undefined number of hydrogen bonds, such as disordered or flip-flop systems. According to this definition the energy gain based on cooperativity in the S4 water tetramer is 29% with the MP3/6-31G** approximation, (30% with HF/4-31G* and 46% with HF/3-21G). The largest contribution of 18% is due to the three-body term on the MP3/6-31G** level, followed by the two-body, non-neighbour term with 11%. The four-body term and the deformation term are in the order of 1% and cancel each other because they have opposite sign.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080804
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  • 175
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    Nonbonded interactions. 1. Anisotropic hydrogen-hydrogen interactions (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1124-1130 
    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 hydrogen-hydrogen nonbonded potential which may be derived from the calculated interactions between hydrogen molecules has been obtained. The best three-parameter Buckingham function gave an RMS error of 0.18 kcal/mol in fitting Price and Stone's ab initio data for 130 pairs of hydrogen molecules, which may be compared with an RMS error of 0.74 kcal/mol using the parameters in the MM2 force field. Burton's basis set is also considered. A better fit to these data requires that the angular relationship between the bonds be included. The data for hydrogen as well as experimental data for chlorine show that these atoms appear “larger” normal to the bond axis than along the axis, and this is probably also the case for other atoms. When simple angular terms are added it is possible to fit the Price and Stone data set with an RMS error of less than 0.06 kcal/mol. The preferred function was: V = [a0 + a1(sin θ1 + sin θ2)4 + a2r]e-3r - [c0 + c1(1 + sinθ1sinθ2)]/r5. Deficiencies in the current ab initio data are discussed.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080809
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  • 176
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    An analysis of the structural and energetic properties of deoxyribose by potential energy methods (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1199-1224 
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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 discuss the three fundamental issues of a computational approach in structure prediction by potential energy minimization, and analyze them for the nucleic acid component deoxyribose. Predicting the conformation of deoxyribose is important not only because of the molecule's central conformational role in the nucleotide backbone, but also because energetic and geometric discrepancies from experimental data have exposed some underlying uncertainties in potential energy calculations. The three fundamental issues examined here are: (i) choice of coordinate system to represent the molecular conformation; (ii) construction of the potential energy function; and (iii) choice of the minimization technique. For our study, we use the following combination. First, the molecular conformation is represented in cartesian coordinate space with the full set of degrees of freedom. This provides an opportunity for comparison with the pseudorotation approximation. Second, the potential energy function is constructed so that all the interactions other than the nonbonded terms are represented by polynomials of the coordinate variables. Third, two powerful Newton methods that are globally and quadratically convergent are implemented: Gill and Murray's Modified Newton method and a Truncated Newton method, specifically developed for potential energy minimization. These strategies have produced the two experimentally-observed structures of deoxyribose with geometric data (bond angles and dihedral angles) in very good agreement with experiment. More generally, the application of these modeling and minimization techniques to potential energy investigations is promising. The use of cartesian variables and polynomial representation of bond length, bond angle and torsional potentials promotes efficient second-derivative computation and, hence, application of Newton methods. The truncated Newton, in particular, is ideally suited for potential energy minimization not only because the storage and computational requirements of Newton methods are made manageable, but also because it contains an important algorithmic adaptive feature: the minimization search is diverted from regions where the function is nonconvex and is directed quickly toward physically interesting regions.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080817
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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.540080101
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  • 178
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    Recursion formulae for calculation of overlap integrals (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 1-5 
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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: Multi-ζ Slater-type orbitals are frequently used in molecular orbital calculations. Master formulae and numerical tables are available in literature for overlap integrals between s, p, and d atomic orbitals up to principal quantum number (n) = 3 and for some other selected quantum numbers. However, no master formula or numerical table is available for quantum numbers n = 5 and above and involving ƒ orbitals. In this article recursion formulae have been presented for the calculation of the overlap integral between any two s, p, d, and ƒ atomic orbitals formed by a linear combination of Slater-type orbitals. These formulae, when expanded, would give rise to all the master formulae reported in the literature as well as formulae hitherto unreported.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080102
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  • 179
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    Molecular modeling of polymers: I. Correct and efficient enumeration of intrachain conformational energetics (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 28-38 
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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: Polymer conformational analyses can require being able to model the intramolecular energetics of a very long (infinite) chain employing calculations carried out on a relatively short chain sequence. A method to meet this need, based upon symmetry considerations and molecular mechanics energetics, has been developed. Given N equivalent degrees of freedom in a linear polymer chain, N unique molecular groups are determined within the chain. A molecular unit is defined as a group of atoms containing backbone rotational degrees of conformational freedom on each of its ends. The interaction of these N molecular groups, each with a finite number of nearest neighbors, properly describe the intramolecular energetics of a long (infinite) polymer chain. Thus, conformational energetics arising from arbitrarily distant neighbor interactions can be included in the estimation of statistical and thermodynamic properties of a linear polymeric system. This approach is called the polymer reduced interaction matrix method (PRIMM) and the results of applying it to isotactic polystyrene (I-PS) are presented by way of example.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080104
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  • 180
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    Recent advances in multireference second order perturbation CI: The CIPSI method revisited (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 39-47 
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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 evolution of the CIPSI method, with the latest modifications recently implemented in our laboratory, is described. A new version, based on a diagrammatic technique, is presented. Test calculations which have been run on water, ethylene, and transacrolein, show that the new method is a powerful tool for the study of medium-size molecular systems.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080105
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  • 181
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    The role of d functions in ab initio calculations. II. The deformation densities of SO2, NO2, and their ions (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 6-27 
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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: Comparison of the optimized geometries and SCF energies for the series XO2+, XO2, XO2-, XO2-, with X = S,N shows that d(S) functions cause larger bond shortening and energy drop than d functions centered on first-row atoms. This is further emphasized on comparing the separate effects of d(central atom) and d(O) functions for SO2 and NO2-, which are similar only for the first-row molecule. The d(S) functions are also essential for proper prediction of the OSO angles. The deformation densities calculated for each series and the corresponding X-O shared populations, change as expected on adding electrons first into σ* then into π* molecular orbitals. In the regions around nuclei the deformation densities express the behavior of the atomic s and p valence orbitals or of their product inside their radial nodes. Introduction of d functions causes substantial polarization effects. For X = N these are mostly local except in the bonding regions where d(N) and d(O) functions are somewhat interchangeable. However, d(S) functions induce also unique changes in the deformation density near O. They cause π and π′ charge migration from O to S and a σ flow in the opposite direction. These effects are largest for the hypervalent species. The unique populations of the d(S) functions are much larger than those of d(N) and d(O) functions. The contribution of d(S) functions to bonding is related to the larger amplitude at small radii of the atomic 3d(S) orbital as compared with that of 3d(N). The difference in amplitudes is related to penetration effects. Diffuse p functions affect geometries and SCF energies of doubly, but not singly negative ions. However, they mostly describe the diffuse nonbonding clouds and do not affect bonding patterns.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080103
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    On the importance of size-consistency corrections in semiempirical MNDOC calculations (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 48-50 
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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: Energies obtained by configuration interaction calculations including all double excitations with regard to the Hartree-Fock reference determinant can empirically be corrected to size consistency using either the Langhoff-Davidson (LD) formula or a formula suggested by Pople, Seeger, and Krishnan (PSK). Semiempirical MNDOC calculations suggest that for molecular systems with a large number of electrons and important correlation effects the PSK correction is superior to the LD correction.
    Additional Material: 1 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540080106
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  • 183
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    Ab initio studies on van der Waals molecules. A comparative study with several basis sets of the C2v HeLi2 systemThis work was financially supported by the CAICYT No. 0637/81. (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 51-56 
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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 potential energy surface of the van der Waals system HeLi2 is computed for the case in which the system has C2v symmetry and at the Li-Li distance (5.005 bohrs). A comparative study of the results for the two methods used, ab initio Hartree-Fock and second-order Møller-Plesset, and several basis sets, ranging from minimal to near Hartree-Fock quality, is also done. The results show the importance of correcting the basis set superposition error, and the need, in order to obtain a good description of the potential, of basis sets with polarization functions on all the atoms, when the Møller-Plesset method is used. At the Hartree-Fock level, the MINI-1 basis gives results almost of the same quality as the near Hartree-Fock basis.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080107
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    Theoretical study of water-pyridine complexes using intermolecular potentials (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 67-80 
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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: Intermolecular potential functions have been used to determine the equilibrium structures of the water-pyridine complexes. The dimer and symmetrical 2:1 water pyridine systems have been studied. Three water models, ST2, TIPS2, and EMPWI have been combined with two different Lennard Jones nonbonded parameters and various charge distributions for the pyridine molecule to describe the systems. For the dimer, results show two distinguishable classes of preferential hydration sites, which are specific sites corresponding to hydrogen-bonded dimer and nonspecific sites located near the hydrophobic regions. Calculations performed on hydrogen-bonded symmetrical complexes show that the planar complex is generally less stable than the complex with water molecules perpendicular to the pyridine plane. For these complexes, the major factor that influences the hydrogen-bonded configurations is the choice of the water model. The importance of atomic charge distributions for the solute over the choice of potential parameters is pointed out. Finally, the effective lone pair representation on the aromatic nitrogen atom is shown to improve the hydrogen bond geometry and the stability of the complexes.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/jcc.540080109
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    Polarization counterpoise corrections to correlated hydrogen bond interaction energies (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 81-83 
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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: Basis set superposition error in hydrogen-bonded systems can exaggerate attraction calculated from self-consistent field energies as well as from electron correlation energies. One cause of this error is the basis set deficiency in describing the charge polarization of one constituent molecule when its bonding partner approaches. That constituent molecule's description is improved partly because of the proximity of the partner's basis functions, independent of real attraction. That polarization-related error is shown to occur primarily at the SCF level and not at correlated levels.
    Additional Material: 1 Tab.
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    URL: http://dx.doi.org/10.1002/jcc.540080110
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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.540080201
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  • 187
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    Ab initio calculations on the effect of polarization functions on disiloxane (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 84-93 
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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 polarization functions for ab initio molecular orbital calculations at the 3-21G* level has been studied for disiloxane. Calculated molecular geometry, dipole moment, and the linearization barrier variation were analyzed for different uncontracted polarization functions. It was concluded that variation of the polarization function on oxygen has only a minor influence on the molecular properties of disiloxane, but its presence is required to obtain a bent geometry for the disiloxane bond. The calculated molecular properties of disiloxane are greatly influenced when the polarization function on silicon is varied. Two different values (0.3 and 0.9) for the exponent of the silicon polarization function provide results comparable to the experimental values for disiloxane. The only significant differences between the results obtained from ab initio calculations using the two polarization functions are in net atomic charges. The uncontracted polarization function of silicon with a value of 0.3 for its exponent is transferable to other organosilicon compounds. Calculated molecular geometries of flexible or rigid structures are in very good agreement with the experimental values.
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    URL: http://dx.doi.org/10.1002/jcc.540080111
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    Optimized method for the evaluation of the convolutionally distorted decay curves (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 95-106 
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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 nonlinear least squares procedure based on the Meiron method is described for the evaluation of the convolutionally distorted decay curves consisting of exponentials. Most of the special procedures are well known and the selected ones proved to be the most effective. Some new procedures are introduced to facilitate the evaluation work and literature data are analyzed as an example.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080202
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  • 189
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    Combination of MOMM and VEH methods to calculate electronic properties of polymers (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 107-116 
    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 Molecular-Orbital-Based Molecular Mechanics method (MOMM) has been employed to calculate the structures of cyclopentadiene, pyrrole, furan, thiophene, dibenzocyclopentadiene (fluorene), dibenzopyrrole, dibenzofuran, and dibenzothiophene. The dimer structures of the above compounds have also been calculated using the same method to derive the unit cells of polycyclopentadiene, polypyrrole, polyfuran, polythiophene, polydibenzocyclopentadiene, polydibenzopyrrole, polydibenzofuran, and polydibenzothiophene. The band structures, densities of states, ionization potentials, band gaps, reduction potentials, and oxidation potentials of these polymers then have been calculated by using the Valence Effective Hamiltonian method (VEH). The structural effects on electronic properties are discussed.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080203
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  • 190
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    Electronic Resource
    Reliable Gaussian basis sets for closed-shell atoms (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 117-131 
    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: Medium size Gaussian basis sets for inert-gas atoms (from neon to xenon) have been constructed using the energy optimization method which maintains reliable description of the long-range valence atomic region. These basis sets have been tested in SCF calculations on homonuclear inert-gas dimers. For Ne2, Ar2, and Kr2, the present results have been analyzed carefully and compared with those obtained using extended basis sets (for Kr2 extended benchmark calculations are also reported). Our interation energies agree well with accurate values and are compared with experimental data. For Ne2 and Ar2, detailed studies of basis set superposition error also are presented.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080204
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  • 191
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    Hydration structures and energetics of phospholipid (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 57-66 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using previously reported ab initio potentials of the intermolecular interaction energies of phospholipid (PL), Lysophosphatidyl Ethanolamine, with one Na+ ion and one water molecule, we performed Monte Carlo simulations for PL-water and PL-Na+-water systems. Water-water and PL-water interaction energetics of PL hydration sites are analyzed to understand, in a qualitative way, why the PL head part shows hydrophilicity and the tail part shows hydrophobicity. The interaction of Na+ with PL, as well as the interaction of water with PL, is visualized from the analysis of the hydration structures near PL, and the radial distribution functions are analyzed for selected hydration sites. The PL molecule shows much stronger interaction with Na+ than with water. The Na+ ion is likely to be strongly bound to PO4-, even to the extent of being trapped, whereas, for water, there exist two strong binding regions near NH3+ and PO4-. Three water molecules near NH3+ are much more strongly bound than four water molecules near the double-bonded oxygens of PO4-. The hydrogens of CH2 adjacent to NH3+ show somewhat strong hydrophilicity, while the hydrogens of CH2 adjacent to PO4- does not show such characteristics. The CH2 groups at the PL tail part give repulsive interactions with water molecules, showing hydrophobicity. Water molecules near the PL tail are stabilized only by water-water interactions.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080108
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  • 192
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    The ellipsoid algorithm as a method for the determination of polypeptide conformations from experimental distance constraints and energy minimization (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 132-141 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for constrained nonlinear optimization known as the ellipsoid algorithm is evaluated as a means of determining and refining the conformations of peptides. Advantages of the ellipsoid algorithm over conventional optimization methods include that it avoids many local minima that other methods would be trapped by, and that it is sometimes able to find optimum solutions in which the constraints are satisfied exactly. The dihedral angles about single bonds were used as variables to keep the dimensionality low (the rate of convergence decreases rapidly with increasing dimensionality of the problem). The method is evaluated on problems involving distance constraints, and for minimization of conformational energy functions. In an initial application, conformations consistent with an experimental set of NMR distance constraints were obtained in a problem involving 48 variable dihedral angles.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080205
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  • 193
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    Quantum mechanical modeling of a transannular interaction in a bicyclic amidinium ion (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 149-157 
    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 transannular donor-acceptor interaction in a bicyclic azaamidinium salt was modeled by quantum mechanical calculations using a supermolecule complex consisting of a formamidinium cation and an ammonia molecule. Molecular properties are reported at various geometries. These results are compared with the results of similar calculations on the bicyclic cation itself. The model calculations and the bicyclic cation calculations are in good agreement, but both fail to reproduce the experimentally known structure. Results from ab initio calculations on the model system are discussed, as are results from calculations which included iodide as counterion.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080207
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  • 194
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    Comparison of the use of the MNDO and MINDO/3 methods with ab initio methods to study tautomerism in histamine, 2- and 4-methylhistamine (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 142-148 
    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 semiempirical MNDO and MINDO/3 methods are used to study the various tautomeric forms of histamine, 2-methylhistamine, and 4-methylhistamine. Comparisons of the optimized structures and tautomerization energies are made with values obtained from ab initio Hartree-Fock calculations using the 3-21G and STO-3G basis sets. Based on these results and previous comparisons of STO-3G results with x-ray structures, the present results indicate that while there are some differences in the values of the structural parameters, the changes in structure upon tautomerization and/or protonation are very similar. Further analysis of the MNDO and MINDO/3 structures by means of their utilization in 3-21G and STO-3G calculations indicates that either of these semiempirical methods provides reliable values for the structural parameters. Both methods give good qualitative agreement with the ab initio calculations for the relative energies of the various tautomers in the three compounds. In these studies the MNDO method appears to give better quantitative agreement with the 3-21G and STO-3G results than the MINDO/3 method.
    Additional Material: 4 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080206
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  • 195
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    Electronic Resource
    An algorithm for construction of the molecular distance matrix (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 170-173 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A simple computer-oriented method is presented for constructing the (molecular) distance matrix. The distance matrix considered is the graph-theoretical (topological) distance matrix.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080209
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  • 196
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    Announcement (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 186-186 
    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.540080212
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  • 197
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    Electronic Resource
    Macromolecular structure and specificity: Computer-assisted modeling and applications, Edited by Babu Venkataraghavan and Richard J. Feldmann, Annals of the New York Academy of Sciences, New York, 209 pp. Price: $48.00 (1985). (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 185-185 
    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.540080211
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  • 198
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    Electronic Resource
    Molecular mechanics and the deformation of macromolecules: The use of a very short cutoff combined with a quadratic approximation (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 174-184 
    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 approximation to the molecular mechanical treatment of structural deformations of macromolecules is presented. The method is based on a partitioning of the conformational energy into three parts. The first part is covered by the condensed potential functions which absorb many short-range nonbonding interactions. The second part consists of a few nonbonded interactions below a very short cutoff radius of 4 Å. The third part, consisting of the vast majority of pairwise interactions, is approximated by a quadratic expression confined to a subspace of the conformational space. A detailed computational example on LH-RH, including an analysis of the errors resulting from other conventional approximation methods, is given. A comparison to the conventional cutoff approximation used in x-ray refinement delivers a speedup factor of at least two orders of magnitude.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080210
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  • 199
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    Masthead (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987) 
    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.540080401
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  • 200
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    Introduction (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 281-281 
    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.540080402
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