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  • 1985-1989  (1,638)
  • 1920-1924
  • Computational Chemistry and Molecular Modeling  (1,638)
  • 201
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 1016-1030 
    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 analytical representation of atom valence state energy (E(nj), j = 1,…4; E(nj) is a nonlinear function of orbital occupancy numbers nj) is proposed and explicitly derived for H—Ar; the values of electronegativity calculated based on E(nj) agree within truncation error with those of Hinze and Jaffe. However, in our representation, orbital electronegativity χ and hardness parameters η of a given orbital always include nonlinear contributions from other orbitals, hence accounting for their influence on χ and η. An atomic charge calculation procedure based on E(nj) is also described and shown to perform well.
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  • 202
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 1038-1052 
    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 molecular mechanics is used to investigate the structural and electrostatic features of molecular recognition by β-cyclodextrin and capped β-cyclodextrin models of α-chymotrypsin. Since capped β-cyclodextrin has been shown to be the more effective biomimetic catalyst, these features of molecular recognition can be interpreted in terms of the relationship between molecular structure and catalytic function. Calculations in vacuo show that the addition of an N-methylformamide “cap” substituent to each glucose unit appears to change the relative orientation of some glucose fragments from that found in the X-ray structure of the β-cyclodextrin macrocycle. These results indicate that certain structural components of molecular recognition, such as the orientation of the secondary hydroxyls and the related orientation of the caps, may be implicated in the catalysis. In addition, the electrostatic component of molecular recognition was investigated by the analysis of molecular electrostatic potential maps calculated in planes parallel to the average plane of the glycosidic oxygen atoms. The results indicate that the addition of the caps to the β-cyclodextrin macrocycle subtly alters the pattern of the maps in each plane. However, the general qualitative features of electrostatic recognition by β-cyclodextrin and capped β-cyclodextrin are similar.
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  • 203
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 514-519 
    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 charge on oxygen for a series of compounds was obtained using Mulliken population, natural population analysis (NPA), integrated projected electron population (IPP) analysis, and Bader's topological density analysis, “integrated Bader populations” (IBP). The orbital-based methods (Mulliken and NPA) predict oxygen charges of about -0.6 whereas the spatial-based methods (IPP and IBP) predict charges of about - 1.2 to - 1.3. The differences are ascribed primarily to the nuclear-centered basis sets used in the orbital methods that minimize local atomic polarization effects. Accordingly, such population analyses should be used for electronic structure considerations only with due circumspection. The IPP method as an approximation to IBP shows gross similarities; small but significant differences vary in a nonsystematic manner and IPP values must also be used with care.
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  • 204
    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 SCF calculation has been performed on C63H113N11O12, a derivative of the immuno-suppressive drug cyclosporin, using a 3-21G basis set and a Direct SCF method. A distributed multipole analysis has been performed on the resulting charge density to give a set of multipoles at each atomic site, which are used to calculate the electrostatic potential around the molecule. The potential maxima and minima on the accessible surface of the molecule are compared with those predicted using the corresponding Mulliken charges, and also using a potential-derived point-charge model based on the force-field of Kollman et al. The Mulliken charges give a misleading picture of the electrostatic potential around this peptide. The potential-derived charges give results which are in far better agreement with the ab initio distributed multipole model, despite being derived from calculations on smaller molecules with different basis sets and geometries. The limitations of point-charge models for describing the electrostatic interactions of polypeptides are discussed.
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  • 205
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    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 10 (1989), S. 616-627 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a simple computational method for the evaluation of solute-solvent dispersion energy contributions in dilute isotropic solutions, supplementing the method with an analysis of its sensitivity with respect to several parameters (or features of the solvation model) which are left free in the general formulation. The method is a natural complement of the electrostatic solvation procedure described in preceding articles.
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  • 206
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    Journal of Computational Chemistry 10 (1989), S. 648-659 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Calculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6-311G(d) triply split valence set with polarization on the resonant atom and 3-21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
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  • 207
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    Journal of Computational Chemistry 10 (1989), S. 711-717 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical intermolecular force field parameters for the fluorine atom of the 4-fluorophenyl group have been generated for use in molecular mechanics programs. Partial charges on the ring system were obtained by Mulliken population analysis of wave functions generated by molecular orbital calculations in the STO-3G approximation. Fluorine van der Waals parameters were obtained by non-linear least-squares fitting of crystallographic data following the procedure of Hagler and Lifson. The parameters developed are compared to fluorine parameters reported previously.
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  • 208
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    Journal of Computational Chemistry 10 (1989), S. 628-634 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm for the computation and representation of van der Waals surfaces and volumes of supermolecules (several overlapping molecules) by a set of grid points originating from an equidistant lattice is described in detail. The grid points in this set belong either to the “outer” surface of the van der Waals body or to a layer just below that outer surface. By means of this double layer (outer and inner) it is possible to represent the volume via the surface without referring to grid points lying inside the body. The algorithm is based on the octree concept, which means that the final relevant lattice points are derived by the successive refinement of an initial coarse lattice. The main features of the algorithm are the automatic elimination of inner atoms irrelevant for the surface definition and the association of any surface point with only those atoms which define the surface in the vicinity of these points. The most remarkable consequence of these features is that the amount of computation is almost independent of the number of atoms in the supermolecule. The algorithm can be used in solving problems arising in drug design, protein folding, molecular graphics, etc.
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  • 209
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    Journal of Computational Chemistry 10 (1989), S. 660-672 
    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 complete set of second-order Gaussian functions (6D) includes a totally symmetric second-order Gaussian function (3s-type) in addition to the five d-type functions. This 3s-type function in the 3-21G(*) basis set for the sulfur atom is described (1) in terms of its geometric and electronic effects observed in the sulfur atom and in four sulfur-containing molecules and (2) by the ability of a single zero-order 1s-type Gaussian function (with various exponents) to replace it in ab initio Hartree-Fock calculations. The geometry of the molecules (dihydrogen sulfide, dihydrogen thioketone, dihydrogen disulfide, and methanesulfonamide) were obtained using various semiempirical and ab initio methods. It is found that the 3s-type function lowers the energy relative to that calculated with the 3-21G(*) basis set with only five second-order Gaussian functions by ca. 46-48 kcal/mol per sulfur atom. Only small changes in geometry are observed when the latter basis set is augmented with a 3s or 1s function. When the exponent of the 1s replacement function is chosen so that the resulting function has a location similar to that of the 3s function as measured by the degree of overlap or the coincidence of radial distribution maxima, the corresponding drop in energy is less than 8 kcal/mol per sulfur atom. However, when the shape of the radial distribution of the 1s function is similar to that of the 3s, i.e., when the value of the 1s exponent is ca. equal to that of the 3s function (a local maximum in the 1s energy profile), the energy lowering is similar to that produced with the 3s function. The electronic effects observed in the molecules differ from those in the atom, the largest deviations being found in the methanesulfonamide calculations.
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  • 210
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    Journal of Computational Chemistry 10 (1989), S. 733-747 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Several general procedures for the derivation and analysis of a Fourier-series expansion V(φ) over computed torsional energies E(φi) are formulated. STO-3G energy values in n-butane, 1-chloropropane, and 1,2-dichloroethane are used as test data for deriving V(φ) with the numerical methods of interpolation and least squares. The accuracy of each derived V(φ) is assessed on the basis of calculated conformational properties, mean and rms deviations, and an error curve, V(φ)-V(φ)ref, where V(φ)ref represents a reference set of E(φi). Results indicate that given the same number of expansion terms, interpolation and least squares yield functions of comparable accuracy; however, interpolation is a more efficient procedure for monitoring the accuracy of a function in regions of interest. In cases where there are too few input energies to achieve the desired accuracy, energy derivatives can be employed effectively for expanding the input set. In designing special-purpose functions, the error curve can be used meaningfully as a guide; an example for producing functions that are especially well behaved in regions for gauche conformations is provided. The present study continues to add systematics and rigor to the fitting of an internal rotation potential function from energy data.
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  • 211
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    Journal of Computational Chemistry 10 (1989), S. 753-769 
    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 well-tempered Gaussian basis sets (14s 10p) for atoms from lithium to neon were contracted and used in restricted Hartree-Fock calculations on 13 systems: Li2(Σ), B2(Σ), C2(Σ), N2(Σ), O2(Σ), F2(Σ), Ne2(Σ), LiF(Σ), BeO(Σ), BF(Σ), CN-(Σ), CO(Σ), and NO+(Σ). Spectroscopic constants (Re, ωe, ωexe, Be, αe, and ke) and one-electron properties (dipole, quadrupole, and octupole moments at the center of mass and electric field, electric field gradient, potential, and electron density at the nuclei) were evaluated and compared with the Hartree-Fock results. The largest contracted basis set (7s6p3d) gives results very close to the Hartree-Fock values; the remaining differences are attributed to the absence of the f functions in the present basis sets. For Ne2, the interaction energy was calculated; the magnitude of the basis-set superposition error was found to be very small (less than 3 μEh at 2.8 a0 and less than 2 μEh at 5.0 a0).
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  • 212
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    Journal of Computational Chemistry 10 (1989), S. 832-849 
    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 geometries, relative conformational energies, and dipole moments of mono and polychlorosilanes have been calculated using ab initio molecular orbital (MO) theory. Calculations at the HF/3-21G(*) level, with the exception of dipole moments, give reasonable agreement with experimental data. A new MM2 force field for chlorosilanes, which includes terms for bond length shortening and bond angle compression due to the attachment of electronegative Cl atoms, has been developed on the basis of experimental and ab initio results. The new force field is generally successful in predicting structural parameters, but is unable to reproduce the dipole moments of several model systems. While dipole moment predictions are not the authors' main interest, this failure defines a shortcoming in the MM2 method. The new parameters have been applied to problems in the prediction of stereochemistries of cyclic systems, and compared with experimental results where data are available.
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  • 213
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    Journal of Computational Chemistry 10 (1989), S. 850-855 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics simulations out to 100 ps have been carried out at 300 K in vacuo on the repeating pentapeptide, (VPGVG), of the elastin fiber. The structure employed in the simulation is a β-spiral (helical structure) with 2.7 pentamers per turn and with a 9.45 Å rise per turn and 21.6 Å rise per turn in the relaxed and extended states, respectively. Large amplitude backbone torsion angle fluctuations are observed in the relaxed state, and significant damping is observed upon extension, particularly in the suspended segments of the β-spiral structure. Accordingly the entropy change an extension was computed and found to be a substantial -1.1 entropy units per residue. The various energy components are compared for relaxed and extended states and the relevance of the results to the molecular mechanism of entropic elasticity is discussed.
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  • 214
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    Journal of Computational Chemistry 10 (1989), S. 869-874 
    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 a previous article (J. Fernández Rico, R. López and G. Ramírez, J. Comp. Chem., 9, 790 (1988)) we have proposed the calculation of molecular integrals involving STOs by means of some recurrence relations which use two sets (h and H) of overlap integrals (basic matrices). In the present paper, we derive explicit expressions of these integrals employing the two-range expansion of the 0s-function. This approach yields equations for the elements of the two basic matrices in terms of two further matrices, k(x,y) and i(x,y), and some auxiliary functions. Relations between the elements of these matrices and the functions are thoroughly explored and numerical tests are included for illustrating the behavior of the method.
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  • 215
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    Journal of Computational Chemistry 10 (1989) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 216
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    Journal of Computational Chemistry 10 (1989), S. 1-13 
    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 code and nonnumerical algorithm are developed to construct the edge group of a graph and to enumerate the edge colorings of graphs of chemical interest. The edge colorings of graphs have many applications in nuclear magnetic resonance (NMR), multiple quantum NMR, enumeration of structural isomers of unsaturated organic compounds, and in the construction of configurational integral expansion series in statistical mechanics. The code developed is applied to many NMR graphs, complete graphs containing up to 10 vertices, and the Petersen graph.
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  • 217
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    Journal of Computational Chemistry 10 (1989), S. 14-16 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We report the geometry-optimized total energies and bond distances for the closo-carborane isomers 3,5-C2B6H8, 1,7-C2B7H9, and 1,2-C2B7H9 calculated by the ab initio SCF MO method using the STO-3G basis set. Relative energies are compared with those of the other carborane isomers in the 8- and 9- atom classes. These results complete the set of calculations at the same level of theory for all deltahedral carborane isomers except for those of the 11-atom class.
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  • 218
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    Journal of Computational Chemistry 10 (1989), S. 35-54 
    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 unusual type of π-electron delocalization in Y-shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO-3G and 3-21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen-substituted guanidine series (urea, carbamic, and carbonic acids); “extended-guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended-guanidine group is incorporated (3-amino-1,2,4-triazole, 2,4-diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π-bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended-guanidinium group resemble those of the group when incorporated within 6-membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.
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  • 219
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    Journal of Computational Chemistry 10 (1989), S. 55-62 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The determination of minima and saddle points on the potential energy surfaces of the hydrogen bonded species O2-HF and O2-H2O is performed with unrestricted Hartree-Fock calculations. Geometries, electron density distributions, and relative energies for every stationary point are reported. Only one true minimum is found for O2-HF and for O2-H2O, and this approximately corresponds to a structure where the partially positive hydrogen atom is located along one of the superoxide ion electron lone-pair directions. Calculated ΔH, ΔS, and ΔG values for the reaction between O2- and H2O are in good agreement with experimental data.
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  • 220
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    Journal of Computational Chemistry 10 (1989), S. 17-34 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The procedure for deorthogonalization (D) of atomic orbitals in the semiempirical CNDO approach is reviewed. For comparative studies, CNDO/2, CNDO/2D, and STO-3G calculations of molecular dipole moments and Mulliken populations are carried out on 35 prototype molecules containing H, C, N, O, and F atoms. The calculated values are assessed on the basis of how well they agree with experimental trends, chemical bonding theories, and ab initio molecular orbital (MO) values. Results of analyses indicate that the CNDO/2D values for dipole moments are in reasonable agreement with experimental values, and those for net atomic charges and electron populations bear greater resemblance to the ab initio (STO-3G and 6-31G**) values than the original CNDO/2 values. These findings, together with those of previous investigators, demonstrate unequivocally the advantages of incorporating deorthogonalization into routine CNDO/2 or INDO calculations as a means to obtain reasonable estimates of charge distributions.
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  • 221
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    Journal of Computational Chemistry 10 (1989), S. 63-76 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Matrix elements for the first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for stretching, linear, nonlinear, and out-of-plane bending and torsional motion. Derivatives of the energy with respect to the Cartesian coordinates are calculated with the chain rule. Derivatives of the energy with respect to the internal coordinates are straightforward, but the calculation of the derivatives of the internal coordinates with respect to the Cartesian coordinates can be simplified by the following two steps outlined in this article. First, the number of terms in the analytical functions can be reduced or will vanish when the derivatives of the bond length, bond angle, and torsion angle are reported in a local coordinate system in which one bond lies on an axis and an adjacent bond lies in the plane of two axes or is projected onto perpendicular planes for linear and out-of-plane bending motion. Second, a simple rotation transforms these derivatives to the appropriate orientation in the space-fixed molecular coordinate system. Functions of the internal coordinates are invariant with respect to translation and rotation. The translational invariance and the symmetry of the second derivatives for a system with L atoms are used to select L-1- and L(L-1)/2-independent first and second derivatives, respectively, of which approximately half of the latter vanish in the local coordinate system. The rotational invariance permits the transformation of the simplified derivatives in the local coordinate system to any orientation in space. The approach outlined in this article simplifies the formulas by expressing them in a local coordinate system, identifies the most convenient independent elements to compute, from which the dependent ones are calculated, and defines a transformation to the space-fixed molecular coordinate system.
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  • 222
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    Journal of Computational Chemistry 10 (1989), S. 77-93 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Radial dielectric constant (permittivity) functions for ionic solute, polar solvent systems of the type obtainable from the Lorentz-Debye continuum field formulations are reexamined. Major interest is focused on the assumptions underlying these formulations and their expression in limiting field behavior. The analysis is extended to dipolar solutes and the importance of two types of corrections are evaluated. The first draws connections with the concept of the reaction field as employed by Onsager. This correction is shown to be significant as regards range of predicted saturation effects and for dipole moment self-consistency, for the same type molecule serving as solute and solvent. The second type correction involves the phenomenon of electrostriction whose effects appear much more limited both in range and on the intensity of the fields necessary for its observation. Application of the permittivity functions developed to compute modified Born model hydration energies for a variety of ions is illustrated. Excellent asymptotic approximations for all radial permittivity equations of interest are also presented which should enhance their future utility.
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  • 223
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    Journal of Computational Chemistry 10 (1989), S. 94-98 
    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 analysis of the electronic effect of aromatic substituents was done with the use of the AM1 computational procedure. The gas-phase acidity of substituted benzoic acids was linear with the difference in the heat of formation between corresponding benzoic acids and benzoate anions, the energy of the highest occupied molecular orbital, and the net charge on the acidic oxygen atoms of the corresponding benzoate anions. The Hammett σ constant was linearly correlated with the net charge on the atoms of the acid moiety of substituted benzoic acids. The AM1 computational procedure satisfactorily reproduced the electronic properties of a wide variety of substituents.
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  • 224
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    Journal of Computational Chemistry 10 (1989), S. 99-103 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: For a series of simple alkyldisilanes, 3-21G (*) full gradient geometry optimizations have been performed to yield both structural and conformational energy data which was suitable for calibrating the MM2 force field for disilanes. We have examined several model structures which yielded sufficient information about the rotational potential around the Si-Si bond to enable us to revise and augment those reported by Frierson. These parameters were questioned by us in the course of MM2 studies of 1,2-disilacyclobutanes. We report new Si-Si torsion parameters as well as pertinent structural data from 3-21G(*) geometry optimizations and relative conformational energies derived from Møller-Plesset (MP2/MP3) calculations at the 6-31(*)/3-21G(*) level. The new parameters were applied to the 1,2-dimethyl-1,2-disilacyclohexane system and those results are also reported.
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  • 225
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    Journal of Computational Chemistry 10 (1989), S. 104-111 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three improvements on the direct self-consistent field method are proposed and tested which together increase CPU-efficiency by about 50%: (i) selective storage of costly integral batches; (ii) improved integral bond for prescreening; (iii) decomposition of the current density matrix into a linear combination of previous density matrices - for which the two-electron contributions to the Fock matrix are available - and a remainder ΔD, which is minimized; construction of the current Fock matrix only requires processing of the small ΔD which enhances prescreening.
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  • 226
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    Journal of Computational Chemistry 10 (1989), S. 112-117 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Practical methods of generating reliable and economic basis sets for relativistic self-consistent fields (RSCF) calculations are developed. Large component basis sets are generated from constrained optimizations of exponents in the nonrelativistic atomic calculations for light atoms. For heavy atoms, large component basis sets for inner core orbitals are generated by fitting numerical atomic spinors of Dirac-Hartree-Fock calculations with appropriate number of Slater-type functions. Small component basis sets are obtained by using the kinetic balance condition and other computational criteria. With judicious selections of the basis sets, virtual orbitals in RSCF calculations become very similar to those in nonrelativistic calculations, implying that relativistic virtual orbitals can be used in electron correlation calculations in the same manner as the conventional nonrelativistic virtual orbitals. It is also evident that the Koopmans' theorem is also valid in RSCF results.
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  • 227
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    Journal of Computational Chemistry 10 (1989), S. 137-137 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 228
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    Journal of Computational Chemistry 10 (1989), S. 136-136 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 229
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    Journal of Computational Chemistry 10 (1989), S. 138-138 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 230
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    Journal of Computational Chemistry 10 (1989) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 231
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    Journal of Computational Chemistry 10 (1989), S. 118-135 
    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 theory of atoms in molecules defines an unambiguous partitioning of the three-dimensional electron density into atomic basins based on the zero-flux surfaces of the gradient of the electron density, ∇(r). Integrations of the electron density within such basins yield integrated Bader populations (IBP) that have a rigorous foundation in quantum mechanics. In the density integration technique based on the two-dimensional electron density projection function, P(x,z), integrated projection populations (IPP) are obtained by integration within regions demarked by steepest descent lines Dp of P(x,z). These density integration techniques are compared by an analysis of the electron density of diatomic molecules that is based on the properties of the zero-flux surface that partitions the electron density between the atoms. The conventional method for the partitioning of regions of P(x,z) approximates the virial partitioning. Differences between IPP and IBP can be quantitatively described by two terms. One term reflects the error intrinsic to projection populations as a result of the loss of all information about the electron distribution in the third dimension in the calculation of P(x,z). The second term accounts for the effects of the displacement of the demarcation lines Dp toward the less polarizable atom compared with the cross-section of the density with the plane of projection, Dd. The analysis suggests the definition of a projection population IPP2 that is based on the cross-section Dd instead of the demarcation lines Dp. Relations between the populations IPP, IPP2, and IBP are derived for diatomic molecules and numerical results are presented for a series of diatomic molecules. Several polyatomic anions are also discussed. The values of IPP are found to be good approximations of IBP in highly polar diatomic molecules. In cases where the bonding involves comparatively little intramolecular charge transfer IPP2 is the better and equally satisfactory projection population. In the intermediate semipolar bonding situations projection populations provide qualitatively correct descriptions of the charge distributions but the numerical agreement with the IBP values is less satisfactory.
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  • 232
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    Journal of Computational Chemistry 10 (1989), S. 145-151 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Results of molecular orbital (MO) calculations by the complete neglect of differential overlap (CNDO/2) method on 50 small molecules are reported. The summation of calculated atomic polarizabilities are equated with molecular polarizabilities, and these are compared with experimentally determined values. It is found that there is very good agreement between calculated and experimental molecular polarizability. This provides a reliable method for the determination of molecular polarizabilities for compounds for which experimental values are not known. The relationship between log P and polarizability is discussed and analyzed in terms of contributions from electronic components to the partitioning energy.
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  • 233
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    Journal of Computational Chemistry 10 (1989), S. 163-175 
    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 surfaces for the proton transfer processes in H+(H2O)n with n=2 ∼ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H+ (H2O)n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.
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  • 234
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    Journal of Computational Chemistry 10 (1989), S. 152-162 
    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 alternative route toward developing basis sets for post-Hartree-Fock calculations, the hybrid bond polarization function method, is investigated. Two new basis sets, denoted 6-31G(d, p)+ B and 6-31 + G(d,p)+B, are defined for the first-row hydrides. The dissociation energies of the first-row hydride species in their respective ground states are computed using full fourth-order Møller-Plesset theory, and compared with results obtained with large polarized basis sets containing no bond functions. It is shown that results are competitive even with basis sets as large as 6-311++G(3df,3pd), while computation times are reduced by a factor of 4 to 20. On empirical grounds, the basis set superposition error should be neglected entirely.
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  • 235
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    Journal of Computational Chemistry 10 (1989), S. 176-185 
    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 of eliminating the finite-time-step error inherent in diffusion quantum Monte Carlo is presented, utilizing an improved version of the existing differential techniques. An implementation is described and results of several small but representative calculations are discussed. The pertinent computation requirements on these systems were reduced by up to a factor of five by the new algorithm. It is speculated that this method may be easily applied to other quantum Monte Carlo and discretized path integral Monte Carlo techniques having related finite step-size errors with a possibility of obtaining similar good results.
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  • 236
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    Journal of Computational Chemistry 10 (1989), S. 209-220 
    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 obtaining optimized parameters for semiempirical methods has been developed and applied to the modified neglect of diatomic overlap (MNDO) method. The method uses derivatives of calculated values for properties with respect to adjustable parameters to obtain the optimized values of parameters. The large increase in speed is a result of using a simple series expression for calculated values of properties rather than employing full semiempirical calculations. With this optimization procedure, the rate-determining step for parameterizing elements changes from the mechanics of parameterization to the assembling of experimental reference data.
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  • 237
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    Journal of Computational Chemistry 10 (1989), S. 203-208 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The stochastic search method was used to seek all of the conformations for 32 bicyclic hydrocarbons. Since the size of the random kick used is sufficient to invert the configurations of carbon atoms, the out, out, in, out, and in, in conformations were all found in a single stochastic run for each hydrocarbon. The lowest energy conformer obtained in each category is reported. A modification of the program to prevent inversion of configuration was developed. It was found, in some cases, that in, in and out, out isomers for some bicyclic hydrocarbons were interconverted by this modified program, presumably through the “homeomorphic isomerization” process described by Park and Simmons. A statistical formula for estimating the approximate chances of finding (or missing) any conformer as a function of the number of random kicks given is derived and presented.
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  • 238
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    Journal of Computational Chemistry 10 (1989), S. 221-264 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MNDO/AM1-type parameters for twelve elements have been optimized using a newly developed method for optimizing parameters for semiempirical methods. With the new method, MNDO-PM3, the average difference between the predicted heats of formation and experimental values for 657 compounds is 7.8 kcal/mol, and for 106 hypervalent compounds, 13.6 kcal/mol. For MNDO the equivalent differences are 13.9 and 75.8 kcal/mol, while those for AM1, in which MNDO parameters are used for aluminum, phosphorus, and sulfur, are 12.7 and 83.1 kcal/mol, respectively. Average errors for ionization potentials, bond angles, and dipole moments are intermediate between those for MNDO and AM1, while errors in bond lengths are slightly reduced.
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  • 239
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    Journal of Computational Chemistry 10 (1989), S. 186-202 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: π-Electron delocalization in neutral and protonated “doubly-extended-guanidine,” (H2N)2C=N—CH=N - CH=NH, has been studied by ab initio methods at the self-consistent field (SCF) STO-3G and 3-21G levels for a large number of tautomeric, rotameric, pseudocyclic, and monocyclic (disubstituted triazine) forms. These π systems have been characterized in terms of a number of structural and energetic parameters: degree of single/bond character from bond lengths and π bond orders, electron distributions, and tautomer, rotamer, and protonation energies. The acyclic neutral forms exhibit largely alternant single-double bond patterns as predicted by classical bonding structures but with, however, significant deviations due to conjugation. The acyclic protonated forms exhibit bond patterns consistent with resonance delocalized structures extending over the whole molecule (“doubly-extended guanidinium”) or part of the molecule (“extended-guanidinium”) or guanidinium . All systems showed alternant charge distributions with electron-deficient carbons. The energy results have been analyzed in terms of possible contributions from steric interactions, lone-pair repulsions, purportive electrostatic interactions in pseudocyclic forms, overall π-system conformation (extended, kinked, or folded), and specific through-space π-overlap interactions in some pseudocyclic forms. It was found that these other interactions usually dominate the specifically π effects so that the general concept of preferential π delocalization in straight lines does not hold for the acyclic systems. Some interesting examples of pseudocyclic forms exhibiting strongly stabilizing intramolecular interactions attributed to π through-space coupling are identified. These systems with incipient-ring characteristics present intermediate bonding models between the acyclic and closed-ring π systems. The extent of stabilization of the guanidinium-type cations by resonance delocalization in cyclic systems depended on whether it reinforced or interfered with the overall ring delocalization.
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  • 240
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    Journal of Computational Chemistry 10 (1989) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 241
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    Journal of Computational Chemistry 10 (1989), S. 265-283 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A study of systems containing the title moiety is described, with special reference to the anomeric effect. We have calculated ab initio, using Gaussian-80 with the 3-21G basis set, all basic conformations of methylene-diamine (H2N—CH2—NH2) and its N-methyl derivative with full geometry optimization of energy minima and barriers. The structural data thus obtained, were then employed to parameterize Allinger's MM2-80 force field in a procedure similar to that described for oxygen derivatives, including hydrogen-bonding effects and C—N bond shortening in tertiary amines. This modification, termed MM2-AE was then used to calculate larger molecules, including N,N′-di- and N,N,N′,N′-tetramethyl-methylenediamine, various 1,3-diazane systems, and 1,4,5,8-tetraazadecalin derivatives of established (x-ray) structures. The results are discussed in light of their verificative and predictive power and appear to validate MM2-AE as a useful computational procedure.
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  • 242
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    Journal of Computational Chemistry 10 (1989), S. 295-301 
    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 case of appearance of multiple unrestricted Hartree-Fock (UHF) solutions in the SNH+ (2A') radical is reported. This kind of solution does not arise from different electron configurations or symmetry breaking effects and seem to be exclusive of the UHF method. Three solutions are found and studied on the basis of wave function stability tests and several conclusions about their origin are given.
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  • 243
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    Journal of Computational Chemistry 10 (1989), S. 287-294 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The method presented earlier [T. Kikuchi, G. Némethy, and H.A. Scheraga, (1986) J. Comput. Chem. 7, 67] for the classification of patterns of the three-dimensional folding of a covalently crosslinked polypeptide chain has been extended to nonplanar proteins. The procedure described earlier was applicable only to proteins termed planar, i.e., with a connexity of the crosslinks (e.g., disulfide bonds) that can be represented in a planar diagram. The procedure described in the present work is applicable to any (planar or nonplanar) pattern of crosslinking. The classification is based on a systematic and objective method of enumeration of spatial geometric arrangements of loops (SGAL) using no information other than the location of the disulfide bonds in the amino acid sequence. Various SGAL classes correspond to the presence of different ways of mutual penetration of loops, called thrustings and entanglements. Information on SGAL classes can be of use in structural predictions of folding patterns of proteins.
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  • 244
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    Journal of Computational Chemistry 10 (1989), S. 302-308 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular structure of haloperidol as free base in its C(13) - C(14) trans form is optimized using Pulay's gradient method and a 4-21G basis set without any geometrical constraints. The resulting structure is compared with the experimental structure of the free base in the C(13) - C(14) gauche form and with the experimental structure of the HBr salt of haloperidol in the C(13) - C(14) trans form. Apart from the obvious differences, the two rotameric forms of the free base show many similarities. This, together with the manner in which the differences of the two experimental structures are distributed over the haloperidol molecule, leads to the conclusion that the conspicuous differences between the experimental structures are caused by inaccuracies in the X-ray determination of the HBr salt. Deviations of phenyl ring geometries from D6h symmetry and the asymmetry of the conformation around C(1) - C(9) could be rationalized by intramolecular effects.
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  • 245
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    Journal of Computational Chemistry 10 (1989), S. 309-328 
    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 lowest singlet along with selected high spin states of three isomers of Si4H4 have been investigated, using highly correlated wave functions in conjunction with a local pseudopotential approach. Tetrasilabicyclo[1.1.0]but-1(3)-ene 1 and tetrasilatetrahedrane 3a are established as true minima by means of the harmonic vibrational frequencies. The local minimum for tetrasilacyclobutadiene is not a planar 2a but a puckered conformer 2b. Isomer 1 was found to be the most stable of the investigated isomers lying 1.96 eV below 3a and 1.04 eV below 2b. A previously examined bond stretch isomer of tetrasilatetrahedrane 3b lies only 0.2 eV above isomer 1. The Si—Si bond energies of 2b, 3a, and 3b are determined as 208, 124, and 228 kJ/mol, respectively. An explanation of the bonding situation in 1 is given.
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  • 246
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    Journal of Computational Chemistry 10 (1989), S. 344-345 
    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 self-consistent field (SCF) calculations the construction of the Fock matrix is most time-consuming step. The Fock matrix construction may formally be seen as a matrix-vector multiplication, where the matrix is the supermatrix,Pijkl, and the vector is the first-order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the P matrix, typically in the order of 106-108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.
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  • 247
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    Journal of Computational Chemistry 10 (1989), S. 346-357 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The proton affinity, dipole moment, and first vertical ionization potential of a number of ortho-mono-substituted pyridines are computed at the restricted Hartree-Fock level, using a number of different basis sets. Some approximations concerning the geometry, the force constants, and the basis set superposition error are introduced. The effect of both the basis set and the approximations is investigated systematically. Two nonstandard basis sets, 4-31G(*) and 4-31+G(*), in which polarization functions are only applied to heteroatoms, are defined. A qualitative explanation for the effects of electron correlation on the proton affinity is given and underbuilt with the results of some MP2 calculations. While accuracy is maintained, computational cost is reduced very substantially.
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  • 248
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Different highly accurate experimental determinations of molecular structures (ED: rg and r0α, MW: r0, rs, and rz, and X-ray distances) of 14 unstrained hydrocarbons have been linearly correlated with corresponding self-consistent field Hartree Fock (SCF HF) ab initio full gradient-optimized structures. From the eight applied basis sets (STO-3G, STO-6G; 3-21G, 4-31G, 6-31G, 6-311G; 6-31G*, and 6-31G**) the 6-31G basis set, although not best regarding total energies, yields statistically the most precise regression equation, which allows the prediction of ED rg CC distances as reliable as the best experimental determinations. Surprisingly the accuracy of all calculated CC distances (measured as difference Δ between calculated CC distances and experimental ED rg values) depends linearly on bond distances, with the largest deviations being observed for triple bonds. This seems to be a clear indication of different influences of correlation effects on calculated geometries which are neglected in the applied HF treatment. The linear regression equations presented here allow the prediction of any kind of experimental CC distance parameters for each of the eight basis sets considered. Even experimentally unknown re CC distances may be predicted from these single determinantal HF optimizations.
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  • 249
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    Journal of Computational Chemistry 10 (1989), S. 358-366 
    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 problem of the computation of the matrix elements \documentclass{article}\pagestyle{empty}\begin{document}$$ I(v,v';k) = \int_0^x {\Psi _v (r)(r - r_e )} ^k \Psi _{v'} (r)dr, $$\end{document} is considered when Ψv(r) and Ψv(r) are eigenfunctions related to a diatomic potential of the RKR type (defined by the coordinates of its turning points Pi with polynomial interpolations). The eigenfunction Ψ(r) is computed by the canonical functions method making use of the abscissas ri of Pi uniquely. This limited number of points allows the storage of ψv(ri) for all the required levels v, and reduces greatly the computational effort when v, ν′, and k are varying. The present method maintains all the advantages of a highly accurate numerical method (even for levels near the dissociation), and reduces greatly the computing time. Furthermore, it is shown that it may be extended to analytical potentials like Morse and Lennard-Jones functions, to vibrational-rotational eigenfunctions and to matrix elements between eigenfunctions related to two different potentials. Numerical applications are presented and discussed.
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  • 250
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    Journal of Computational Chemistry 10 (1989), S. 376-379 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is described for rapid calculation of excluded volume of large molecules. The excluded volume is defined based on coordinates of constituent atoms as the volume of overlapping spheres, each standing for a space around an atom inaccessible for a solvent molecule. A computer program based on the algorithm has been tested on a protein, ovomucoid. The accuracy of the numerical calculation is discussed.
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    Journal of Computational Chemistry 10 (1989), S. 380-385 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Prolog is applied to calculate the zero- through the sixth-order molecular connectivity indexes. A description of the program is given. Enumeration of substructure fragments, which is the most time-consuming part for this calculation, can be executed quite compactly by Prolog. For this execution, molecular structures and substructures are represented by Prolog facts and rules. An example of calculation is presented for a polycyclic structure. In addition, the method to increase the calculation speed is demonstrated.
    Additional Material: 6 Ill.
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  • 252
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    Journal of Computational Chemistry 10 (1989), S. 367-375 
    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 topological properties of the electron density and the properties of an atom in a molecule are calculated by means of second-order Møller-Plesset perturbation theory (MP2) and compared with the results of configuration interaction calculations (C12) which include all single and double substitutions from the Hartree-Fock reference configuration. A software package for analyzing the effects of electron correlation on the topological properties of the electron density of molecules is described. H2CO is used to provide a numerical example and to indicate that the number of bond critical points is unaffected by the inclusion of electron correlation. Correlation leads to only a small shift in the positions of bond critical points and a small change in the electron density at bond critical points. It is further shown that the energy of an atom in a molecule can be calculated to an accuracy of 1 kcal/mol and the electron population of an atom to about 0.001e. A statistical method is used to show that the deviation of the MP2 correlation correction relative to the CI2 correlation correction for a variety of atomic properties is about 25%.
    Additional Material: 1 Ill.
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  • 253
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    Journal of Computational Chemistry 10 (1989), S. 386-391 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Comparisons have been made between relaxation methods and certain preconditioned conjugate gradient techniques for solving the system of linear equations arising from the finite-difference form of the linearized Poisson-Boltzmann equation. The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.
    Additional Material: 5 Ill.
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  • 254
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    Journal of Computational Chemistry 10 (1989), S. 392-406 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A general survey of the topological properties of various phospines, phosphaalkenes, and phosphaalkynes is presented. Fifteen compounds containing carbon-phosphorus single, aromatic, double, and triple bonds were optimized at the Hartree-Fock-self-consistent field (HF-SCF) level using the 3-21G, 3-21G(*) and 6-31G* basis sets. Inclusion of d-orbitals was necessary to obtain reasonable structures. The electron densities of these compounds were analyzed using the topological method of Bader, revealing a number of trends. The value of the electron density at the P—C bond critical point correlates strongly with the bond distance and bond order. Integrated electron populations correlate with coordination number. The integrated charge indicates a strongly polarized C—P bond in all compounds. Comparisons with five C—N compounds are made.
    Additional Material: 7 Ill.
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  • 255
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    Journal of Computational Chemistry 10 (1989), S. 417-425 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Algorithms and codes based on the method of Schur functions and Frobenius' theorem are used to generate the character tables of the symmetric groups (Sn) containing n! elements. The codes developed can generate characters of Sn up to n = 20.
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  • 256
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    Journal of Computational Chemistry 10 (1989), S. 413-416 
    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 convergence of the S matrix for the renormalized Numerov method, the original log-derivative method, and one recent version of this method is studied. A single- and a two-channel problem are analyzed and the percent relative errors for the S matrix and transition probabilities are calculated.
    Additional Material: 2 Ill.
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  • 257
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational equilibria of mono-, di-, and trimethylisochromanes substituted in the heterocyclic ring are calculated by the MMP2(85) force field program. The results are in generally good agreement with the experimental findings of Pihlaja et al. The accuracy of experimental studies based on vicinal coupling constants is examined.
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  • 258
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    Journal of Computational Chemistry 10 (1989), S. 426-433 
    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 annular tautomerism of 1,2,3-triazole and 3(5)-methylpyrazole is discussed by means of a combination of theoretical calculations and experimental (ICR) gas-phase basicities and acidities. In the gas phase 1,2,3-triazole exists as the 2H-tautomer, whereas both tautomers of 3(5)-methylpyrazole are of similar energy. The solvent effects on these prototropic equilibria are discussed taking into account solvent properties as polarity/polarizability, acidity, and basicity. In nonhydrogen bonding solvents, the difference in dipole moments between both tautomers plays a role that has usually been underestimated.
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  • 259
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    Journal of Computational Chemistry 10 (1989), S. 434-434 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 260
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    Journal of Computational Chemistry 10 (1989) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 261
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Hydrogen exchange reactions between lithium and sodium compounds, MX (M=Li: X=H, CH3, NH2, OH, F; M=Na: X=CH3), and the corresponding hydrides, HX, have been modelled by means of ab initio calculations including electron correlation and zero point energy (ZPE) corrections. Small or no activation barriers (from the initial complexes) are encountered in systems involving lone pairs (10.8, 2.4, 0.0 kcal/mol for X=NH2, OH, F, respectively). Since the association energies of the initial complexes are much larger (21.0, 20.4, 23.5 kcal/mol, respectively; MP2/6-31+G*/6-31+G* + ZPE), such exchange reactions should occur spontaneously in the gas phase. The methyl systems (X=CH3) have the largest barriers: 26.7 (M=Li) and 31.7 (M=Na) kcal/mol (MP2/6-31+G*/6-31G* + ZPE), and the initial complexes are only weakly bound. The significance of these systems as models for hydrogen exchange reactions in complexes of electropositive transition metals is discussed. However, the gegenion-free exchange of hydrogen between CH3 and CH4 has a much lower, 11.8 kcal/mol barrier (MP2/6-31+G*/6-31+G* + ZPE). All the transition structures are highly ionic (charges on the metals 〉 +0.8). The effect of aggregation has been considered by examining the hydrogen exchange between (LiX)2 and HX(X=H, CH3, NH2, OH). Although these dimer reactions formally involve six, instead of four electrons, no “aromatic” preference is observed.
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  • 262
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    Journal of Computational Chemistry 10 (1989), S. 468-478 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Polarization and correlation effects on the nitrogen inversion barrier of some three-membered rings have been investigated. The characteristics of the barrier have been analyzed in terms of perturbation theory arguments. This analysis shows that the HOMO is the orbital that changes more dramatically along the inversion barrier. As a consequence, there is a good linear correlation between the destabilization undergone by the HOMO along the pyramidalization process and the barrier height. To obtain quantitatively meaningful barriers it is necessary to use polarized basis sets. Although polarization effects at the inverting center are dominant, a proper polarization of the remaining atoms of the ring seems also necessary. In general, with the only exception of 1H-diazirine, correlation effects on the barrier height are small if a polarized basis set is used.
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  • 263
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    Source: Wiley InterScience Backfile Collection 1832-2000
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    Notes: Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted pyridines in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: F, Cl, CN, CH3, CF3, CHO, NO2, NH2, N(CH3)2, OCH3, and SCH3. The results are compared with experimental values. It is found that all MINDO/3 PAs are ca. 6% too high (mean value) compared to the experimental results; on the other hand, the MNDO values are ca. 7% too low (mean value). However, a much better agreement has been observed for the AM1 method where the theoretical values are only ca. 2.4% too low (mean value). Correlations between the calculated proton affinities on one hand and the charges on the acid H atom and Hammett constants on the other hand are studied. Particularly good linear relationships are found for the 4-monosubstituted compounds within the AM1 formalism.
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  • 264
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    International Journal of Quantum Chemistry 33 (1988) 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 265
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    International Journal of Quantum Chemistry 33 (1988), S. 19-26 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A completely analytic method for evaluating three-center nuclear attraction integrals for STOS is presented. The method exploits a separation of the STO into an ‘evenly loaded’ solid harmonic and a OS STO. The harmonics are translated to the molecular center of mass in closed finite terms. The OS STO is translated using the Gegenbauer addition theorem; 1s STOS are translated using a single parametric differentiation of the OS formula. Explicit formulas for the integrals are presented for arbitrarily located atoms. A numerical example is given to illustrate the method.
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  • 266
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 267
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    International Journal of Quantum Chemistry 33 (1988), S. 87-113 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two three-dimensional numerical schemes are presented for molecular integrands such as matrix alements of one-electron operators occuring in the Fock operator and expectation values of one-electron operators describing molecular properties. The schemes are based on a judicious partitioning of space so that product-Gauss integration rules can be used in each region. Convergence with the number of integration points is such that very high accuracy (8-10 digits) may be obtained with obtained with a modest number of points. The use of point group symmetry to reduce the required number of points is discussed. Examples are given for overlap, nuclear potential, and electric field gradient integrals.
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  • 268
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    Topics: Chemistry and Pharmacology
    Notes: A new definition of a canonical set of bonded functions has been introduced. For a given configuration with r singly occupied orbitals and given multiplicity, the set exhibits symmetry properties of a group of order r. It simplifies the evaluation of the energy matrix H as well as the orthogonalization procedure.
    Additional Material: 2 Ill.
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  • 269
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    International Journal of Quantum Chemistry 33 (1988), S. 369-369 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 270
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    International Journal of Quantum Chemistry 33 (1988) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 271
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    International Journal of Quantum Chemistry 33 (1988), S. 373-394 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We examine various perturbation-variational approximations for molecular electronic energy when the fifth-order perturbational energies are available. Such theories require very little additional computation once the sequence of perturbation energies are known yet supply a bound even when the peturbation sequence is poorly convergent. We choose for computational examples results obtained very rapidly from a zeroth order wave function consisting of doubly occupied localized bonds and examine polarization within these bonds, delocalization, and bond breaking. In general, we find that the fifth-order energy itself, and especially the [2, 1] Padé approximant on this sequence, are especially accurate in estimating the total energy and more accurate than any variational scheme when the zeroth order localized wave function is a good description of the electronic structure. The variational results, however, are nearly as accurate, and a [1, 0] Padé on the sequence of variational results is remarkably robust, even in those cases where the perturbation sequence is poorly defined.We also examine several scaling techniques, or partitionings of the Hamiltonian. Although these scaling techniques do accelerate convergence of the perturbation sequence, none that we examine give better results, than the [2, 1] padé, which is independent of any scaling.
    Additional Material: 2 Ill.
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  • 272
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 273
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    International Journal of Quantum Chemistry 34 (1988), S. 1-8 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new MO-LCAO description of the nephelauxetic effect is proposed based on the concept of the topological atom and on the method of reduced density matrices. This approach allows one to overcome some conceptual difficulties of ligand-field theory and to derive effective parameters of d-d electron repulsion of a bound transition-metal in a proper way. The two ligand-field mechanisms of the nephelauxetic effect - the central field covalency and the symmetry-restricted covalency - are clarified and generalized. In addition, a new factor, important for the nephelauxetic effect is found: its size-dependence on the region of the topological atom.
    Additional Material: 1 Ill.
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  • 274
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    International Journal of Quantum Chemistry 34 (1988), S. 47-71 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A Hartree-Fock (HF) self-consistent field (SCF) crystal orbital (CO) formalism for two- and three-dimensional (2D/3D) solids on the basis of semiempirical CNDO/INDO (complete neglect of differential overlap; intermediate neglect of differential overlap) Hamiltonians is presented. The employed SCF variants allow for the treatment of atomic species up to bromine under the inclusion of the first (i.e., 3d) transition metal series. Band structure investigations of 2D and 3D materials containing more than 30 atoms per unit cell are feasible by the present SCF HF CO formalism. The theoretical background of the computational scheme is given in this contribution. Special emphasis is placed on physically reliable truncation criteria for the lattice sums, the adaptation of the crystal symmetry in k space, as well as the suitable choice of domains in Brillouin zone (BZ) integrations required in the determination of charge-density matrices. The capability and limitations of the semiempirical SCF HF CO approach is demonstrated for some simpler solids by comparing the present computational results with those of ab initio CO schemes as well as conventional numerical methods in soid-state theory. The employed model solids are graphite and BN (2D and 3D networks for both solids) as well as diamond, silicon, germanium, and TiS2.
    Additional Material: 4 Ill.
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  • 275
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    International Journal of Quantum Chemistry 34 (1988), S. 143-160 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The dynamics of a model triatomic hydrogen bond are analyzed through classical mechanics. The approximate separability of the equations of motion induces the existence of an adiabatic invariant for the intramolecular mode motion. This mode is governed by a Mathieu equation, a feature already present for the antisymmetric mode in symmetric triatomics. The corresponding spectrum readily obtained as the Fourier transform of a classical trajectory shows that the fundamental frequency is shifted to lower values owing to the anharmonicity of the potential. We observe also a substructure of combination lines generated by a nonlinear resonance with the intermolecular mode. These properties are consistent with experimental observation. In a four-atoms model, the lines are split when intramolecular Fermi resonance occurs. When the intermolecular mode becomes chaotic there is no vibrational heating of the intramolecular neighboring mode which tends to behave like a local isolated oscillator.
    Additional Material: 6 Ill.
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  • 276
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    International Journal of Quantum Chemistry 34 (1988), S. 85-86 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
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  • 277
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    International Journal of Quantum Chemistry 34 (1988), S. 87-87 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 278
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 279
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    International Journal of Quantum Chemistry 34 (1988), S. 121-131 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A new and very simple one-range expansion of the 0s function is derived and employed as the starting point of three recurrence relations which allow the expansion of arbitrary Slater functions over displaced centers. Convergence of the expansions, both pointwise and in norm, are analyzed, and three-center nuclear attraction integrals are chosen for a further test of the formal developments and the numerical behavior of these expansions.
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    International Journal of Quantum Chemistry 34 (1988), S. 193-193 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 281
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    International Journal of Quantum Chemistry 34 (1988), S. 207-216 
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    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Two molecular charge similarity index (CSI) methods are further evaluated for practical application: one method based on a simple CNDO-type approximation to the electron density function and the other based on an ab initio pseudo total charge density function. The test system consists of isosteric analogues of dimethyl ether and methoxy acetic acid. The effects of differences in skeletal structure on the CSI measure of electron density similarity about corresponding atoms is estimated, and two new developments are presented for application of the ab initio-based method: (1) an INDO-type approximation which improves the efficiency of the CSI calculation; and (2) a FOCUS feature which enables comparisons of local molecule regions.
    Additional Material: 2 Ill.
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  • 282
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    International Journal of Quantum Chemistry 34 (1988), S. 247-266 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The distribution of energy levels of an N-identical-particle system among the irreducible representations of the permutation group is examined for a “spin-free” problem. There are calculated the sums of powers of the eigenenergies obtained from the original N!-fold degenerate energy level when the interaction between the particles is switched on. The first-order perturbation theory is applied. Some results of the present approach are shown to be equivalent to the results of the Weyl's theory of the permutation group. The distribution of energy levels is found to be symmetric with respect to the average energy level belonging to a self-conjugate representation. For a special case of the Coulomb interaction the wave function of the highest level is fully symmetric, whereas that of the lowest level is fully antisymmetric with respect to the interchange of the coordinates of any two particles. The average energy and the dispersion of the levels belonging to a given representation are calculated for some N.
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  • 283
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    International Journal of Quantum Chemistry 34 (1988), S. 289-300 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: It is shown how the properties of the one-particle Green's function lead naturally to the definition of the so-called natural energy orbitals. These orbitals allow the fully correlated total energy of a system to be written in Hartree-Fock-like fashion and might therefore provide a bridge between sophisticated correlated wave functions and approximate theories of chemical structure and reactivity based on a Hartree-Fock-like energy expression. Moreover these orbitals form the basis for a self-consistent scheme to calculate the one-particle Green's function. The relation between these natural energy orbitals and the extended Koopmans' theorem is considered. Finally it is shown that the exactness of the lowest extended Koopmans' ionization potential implies the linear independence of the corresponding Dyson orbital from all other Dyson orbitals.
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    International Journal of Quantum Chemistry 34 (1988), S. 309-323 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The shape wave u(r) is defined in such a way that the square of its absolute value gives the shape of the electron charge density for a nonrelativistic many-electron system: |u(r)|2 = ρ(r)/∫ρ(r) dr, where ρ(r) is the total electron charge density. The u(r) is treated as the probability amplitude for the shape of the electron charge density in the real three-dimensional space. The secular equation of the u(r) is given as L(r)u(r) = λu(r), where L(r) and λ are a real Hermitean operator and the eigenvalue, respectively. This equation has the form of the spinless one-particle Schrödinger equation. The potential is local and is a functional of ρ(r), and so we need a self-consistent field procedure to solve it. For equilibrium state shape wave u = ueq, which is temperature-dependent, and for stationary state shape wave u = u0, respectively, Leq(r)ueq(r) = λequeq(r) and L0(r)u0(r) = λ0u0(r). For one-electron systems, the latter equation reduces to the Schrödinger equation for a stationary state, with the usual eigenvalue λ0 = E0. In general, λ is identified with the Gibbs chemical potential μG. Boundary conditions such as the cusp condition at a nucleus and exponential decay at an infinitely large distance from the nucleus are easily implemented. In case L(r) allows complex eigenfunctions, u(r) = A(r)eiS(r), the hydrodynamical potential appears in the secular equation for the real amplitude A(r). The real phase S(r) satisfies the equation of continuity. By introducing «apparatus» operators [16], the excited state shape wave is also obtained. Comparisons are made with a recent discussion of Levy, Perdew, and Sahni [3].
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  • 285
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    International Journal of Quantum Chemistry 34 (1988), S. 401-406 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 286
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    International Journal of Quantum Chemistry 34 (1988), S. 67-84 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A class of thromboxane antagonists exists where the prostaglandin side chain containing the C16 hydroxyl moiety is replaced by a phenyl ring, and the bridged six-membered pyranose moiety by cyclohexane, pyranose and dioxane ring systems. Analysis of antagonist potency data in terms of a binding constant model previously used for membrane bound receptor-drug interactions shows that the major patterns of antagonist potency are governed as much by axial/equatorial conformer preference of the phenyl moiety and its orientation as by electrostatic effects of the aliphatic ring oxygen atoms. The conformational restriction of the two substituted side chains of the σ-bonded 6-membered ring is shown to be a primary requirement for binding to thromboxane receptors, and a quantitative separation of electrostatic and conformational components in the potency data is attempted.
    Additional Material: 10 Ill.
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  • 287
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    International Journal of Quantum Chemistry 34 (1988), S. 119-135 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Ab initio calculations have been performed to investigate hydrogen bonding and ion-molecule association in complexes of H2O with the neutral, protonated, and Li+ complexes of N-formylformaldehyde and N-formylformamidine. In the complexes with the neutral bases, H2O assumes an in-plane bridging position in the amide and amidine regions. The most stable complex is the bridging N-formylformamidine-H2O complex in the amidine region, which has an MP2/6-31 + G(d,p) binding energy of -9 kcal/mol. Hydrogen bonded complexes of H2O with the oxygen-protonated bases have open structures with the protonated bases as proton donors, and binding energies ranging from -16 to -24 kcal/mol. Nitrogen protonation of N-formylformamidine leads to an equilibrium chelated hydrogen bonded structure with a stabilization energy of -21 kcal/mol. When Li+ associates with these bases at a carbonyl oxygen, hydrogen-bonded bridging structures with H2O reappear, and wobble complexes exist in the amide and amidine regions of N-formylformaldehyde and N-formylformamidine. These complexes have binding energies of -13 to -14 kcal/mol. However, the most stable comples has H2O directly bonded to Li+, with an MP2 binding energy of -30 kcal/mol. No hydrogen bonded structures of H2O with N-formylformamidine exist in the amide region when Li+ associates with this base at the C=N group. Hydrogen bond energies computed at the single-determinant Hartree-Fock level with the 6-31G(d) basis set approximate correlated MP2/6-31 + G(d, p) energies to within 1 kcal/mol for all of the neutral and charged complexes. However, when H2O is bonded to Li+, HF6-31G(d) association energies overestimate MP2/6-31 + G(d, p) energies by 3 kcal/mol.
    Additional Material: 8 Ill.
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  • 288
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    International Journal of Quantum Chemistry 34 (1988), S. 301-304 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The role of the boundary conditions is emphasized in determining the relation between the counting problem, posed by Coulson and solved by the number theorists, and the physical problem from which it arises. The surface energy term, which Coulson sought, does exist, but only when the periodic boundary conditions, which he used, are replaced by the finite box conditions.
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  • 289
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    International Journal of Quantum Chemistry 34 (1988), S. 325-332 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The graph theory of molecular orbitals including second neighbor interactions (η) is considered here. Graphical methods of getting the characteristic polynomial for the π system of a conjugated molecule are given. It is shown that the characteristic polynomial can be factorized if there are symmetries in the molecule.
    Additional Material: 5 Ill.
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  • 290
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    International Journal of Quantum Chemistry 34 (1988), S. 375-383 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Calculations have been made at the minima of the X1A1 ground state of the ozone molecule. The equilibrium geometries have been obtained by means of CID calculations. The criterion adopted for the choice of configurations gives realistic results. CIPSI calculations at the two minima lead to an estimated gap of 0.92 eV between them.Our results agree with the analysis of previous theoretical works on the relative stability of open and cyclic zone structures, showing that the D3h minimum is stable relative to the ground state dissociation limit.
    Additional Material: 2 Ill.
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  • 291
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    International Journal of Quantum Chemistry 34 (1988), S. 407-415 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ground state energies of finite Hubbard molecules are calculated by numerically solving the Lieb-Wu equations for a complex Hubbard repulsion parameter U. From the positions of the singular points located in the complex plane, the radii of convergence of the perturbation expansions for the ground state energies are determined.
    Additional Material: 3 Ill.
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  • 292
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    International Journal of Quantum Chemistry 34 (1988), S. 445-455 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple procedure has been created for indexing the spin-free configurations of an N-electron system in spin state S. This indexing has been linked to a procedure for generating the matrix representations of the generators of the unitary group U(n) to enable a direct configuration study to be undertaken.
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  • 293
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    International Journal of Quantum Chemistry 34 (1988), S. 485-486 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 294
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    International Journal of Quantum Chemistry 34 (1988), S. 509-515 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A perturbation expansion which connects the hydrogenic limit energy density functional to the Thomas-Fermi functional is discussed. This perturbation series, where the Coulomb energy density functional is treated as the perturbation to the hydrogenic limit functional, is, in fact, the q = (N/Z) expansion of Thomas-Fermi theory. A truncated form of the first-order correction to the functional provides further insight into the model which treats the ground state energy as a local functional of the electron density.
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  • 295
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    International Journal of Quantum Chemistry 34 (1988), S. 103-118 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A formalism for a computational treatment of the polarization of a solvent and polar solutes immersed in it is presented. The solvent is modeled as a continuum dielectric. Polarization effects are represented by a polarization charge density at the dielectric boundaries and by induced dipoles at the polarizable atoms. Applications of this formalism with nonpolarizable atoms have led to excellent agreement between the calculated and experimental hydration enthalpies of a variety of polar molecules. A problem of the choice of the charge distribution of the solute is addressed in calculations of the solution dipole moment and hydration enthalpy of polarizable molecule of water in solution. Experimental values of these properties were well reproduced in calculations starting with point charges fitted to the vacuum dipole moment of the water molecule. Tests calculations for spherical models and for a 13-residue peptide show good convergence of the computational method. It is shown in calculations on simplified models that a change in the exposure of a charged side chain can lead to large changes in the potential inside protein measured at a fixed distance from the charge and at the same depth from the protein surface. Calculations performed for the C-peptide of the ribonuclease suggest that the differential screening of partial charges can reverse the sign of the vacuum potential of the helix dipole.
    Additional Material: 3 Ill.
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  • 296
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    International Journal of Quantum Chemistry 34 (1988), S. 167-178 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present models for the interaction of glucocorticoids: dexamethasone (DEX), dexamethasone-21-mesylate (DEXM) and deacylcortivazol (DAC) with the hexanucleotide sequence d(TGTTCT)2 (CORE sequence) found in the long terminal repeat of MMTV. These models are obtained by computer-aided geometry simulation with energy minimization technique, making use of the empirical potential energy functions. We have considered both intercalative and nonintercalative binding. Differences in the glucocorticoid activity of these steroids are explained on the basis of stereochemical and energetic differences. A model is proposed for interaction of the steroid-receptor complex with the hormone-responsive element (HRE).
    Additional Material: 6 Ill.
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  • 297
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    International Journal of Quantum Chemistry 34 (1988), S. 191-199 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Recently, one of the members of this group (Fritz) has observed some unusual properties of rouleaugenic polymer solutions. It was found that the diffusion coefficient of polystyrene spheres in these solutions displayed an expected fall followed by an unexpected rise in values when the radii of these particles are changed. In this paper we present some of these experiments and provide a thermodynamic interpretation of the rise in the values of the diffusion coefficient.
    Additional Material: 2 Ill.
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  • 298
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    International Journal of Quantum Chemistry 34 (1988), S. 235-245 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Data and analyses are presented on the first synthetic polypeptide system to exhibit mechanochemical coupling; the mechanochemical coupling can also be demonstrated to be both polymer-based and solvent-based with respect to where the result of the change in the chemical potential is focused. Both polymer-based and solvent-based processes are the result of chemomechanical transduction in which the change in chemical potential results in a change in the temperature at which an inverse temperature transition occurs. In the polymer-based process, the contraction/relaxation occurs due to a change in the chemical nature of the polypeptide; in the solvent-based process there is no change in the chemical nature of the polypeptide on contraction or relaxation, but rather the change in chemical potential changes the state of hydration of the polypeptide. The new mechanochemical system provides an experimental system with which to clarify and to quantitate what may be called aqueous mediated apolar-polar interaction energies in polypeptides and proteins with hydrophobic groups that may be variously exposed to the aqueous solution or buried within the folded polypeptide or protein. Furthermore, it is noted that any conformational change exhibited by a polypeptide or protein that is the result of a binding of a chemical moiety, the change in chemical nature of a bound moiety or the change in chemical potential of the medium can be viewed in terms of mechanochemical coupling or chemomechanical transduction.
    Additional Material: 5 Ill.
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  • 299
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    International Journal of Quantum Chemistry 34 (1988), S. 275-285 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A modified cluster approach for modeling local chemisorption phenomena is suggested on the basis of the linear combination of Gaussian-type orbitals (LCGTO) Xα method. Contractions of the fitting bases are employed to take into account the reduced polarizability of a surface cluster and to access larger cluster sizes. Furthermore, embedding of a cluster in the surface is mimicked by Gaussian broadening of the one-electron levels leading to fractional occupation numbers via a self-consistently determined Fermi energy of the cluster. As a first application results are presented for the clusters NinNa (n = 5, 9, 17) modeling the low coverage limit of the chemisorption system Ni(100)/Na. Calculated bond length, binding energy, and induced “surface” dipole moment show fair agreement with experimental values, indicating a substantial covalent character of alkali bonding on transition metal surfaces even in the zero coverage limit.
    Additional Material: 3 Ill.
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  • 300
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    International Journal of Quantum Chemistry 34 (1988), S. 319-328 
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The spectra and characteristic polynomials of polyhedral cluster graphs containing 4-120 vertices are obtained. Some of the polyhedral graphs considered such as icosahedron, Archimedene etc., are models for some interesting clusters such as C120. For the Archimedene the spectra and delocalization energies are obtained with and without bond alternations. The characteristic polynomials and spectra of all the polyhedral clusters considered in this investigation are unique.
    Additional Material: 1 Ill.
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