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  • 11
    Electronic Resource
    Electronic Resource
    An MNDO treatment of sigma values (1985)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 6 (1985), S. 437-440 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Hammett σ and Taft σ0 constants have been examined using the MNDO computational procedure. They are both best explained by using computed properties based upon the benzoate ion, especially the reciprocal of the energy of the highest occupied molecular orbital.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540060511
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  • 12
    Electronic Resource
    Electronic Resource
    Reactions involving CO2, H2O, and NH3: The formation of (i) carbamic acid, (ii) urea, and (iii) carbonic acid (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 283-293 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A complete understanding of the synthesis of urea, (NH2)2CO, from NH3, CO2, and H2O remains an unsolved problem. It is considered that the formation of the intermediate ammonium carbamate (or the equivalent carbamic acid) takes place through the interaction of neutral species, and that this part of the synthesis is open to ab initio computations. Such calculations are reported on the formation of carbamic acid from NH3, CO2, and H2O. We have also investigated the formation of carbonic acid from CO2 and H2O showing that the six-membered ring transition state is non-planar, in contradiction with earlier reported calculations.
    Additional Material: 13 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070306
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  • 13
    Electronic Resource
    Electronic Resource
    Conformational stability and flexibility of the ala dipeptide in free space and water: Monte Carlo computer simulation studiesDedicated to Professor J. A. Pople on the occasion of his 60th birthday. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 345-348 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Monte Carlo determinations of the intramolecular thermodynamics of the Ala dipeptide in the C7, C5, αR, and PII conformations are reported. The calculations are carried out in the quasiharmonic approximation, with intramolecular entropies determined from the covariance matrix of the atomic displacements. The free energy of transition from C7 to C5, αR, and PII are found to be endergonic and dominated by the intrinsic energy of disrupting the intramolecular hydrogen bond in the C7 conformation. These results are combined with previous estimates of the free energy of hydration of the Ala dipeptide in water computed from liquid state Monte Carlo simulations using the probability ratio method. The net free energy of C7, αR, and PII are found to be similar, and it is thus reasonable to expect that all three forms are thermally populated at ambient temperature. The intermolecular carbonyl-water hydrogen bond in C5, αR, and PII competes successfully with the intramolecular N—H…O—C interaction in C7.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070311
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  • 14
    Electronic Resource
    Electronic Resource
    Molecular orbital theory of the properties of inorganic and organometallic compounds 4. Extended basis sets for third-and fourth-row, main-group elementsDedicated to john pople on the occasion of his 60th birthday. (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 359-378 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two new series of efficient basis sets for third- and fourth-row, main-group elements have been developed. Split-valence 3-21G basis sets have been formulated from the minimal expansions by Huzinaga, in which each atomic orbital has been represented by a sum of three Gaussians. The original expansions for s- and p-type orbitals (except those for 1s) have been replaced by new combinations in which the two sets of orbitals (of the same n quantum number) share Gaussian exponents. The Huzinaga expansions for 1s, 3d and 4d (fourth-row elements only) have been employed without further alteration. The valence atomic functions 4s, 4p for third-row elements; 5s, 5p for fourth-row elements have been split into two and one Gaussian parts. Supplemented 3-21G(*) representations have been formed from the 3-21G basis sets by the addition of a set of single d-type Gaussian functions.The performance of 3-21G and 3-21G(*) basis sets is examined with regard to the calculation of equilibrium geometries, normal mode vibrational frequencies, reaction energies, and electric dipole moments involving a variety of normal and hypervalent compounds containing third- and fourth-row, main-group elements. The supplementary functions incorporated into the 3-21G(*) basis sets are generally found to be important, especially for the proper description of equilibrium bond lengths and electric dipole moments. 3-21G(*) representations are recommended for general use in lieu of the unsupplemented 3-21G basis sets.
    Additional Material: 12 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070313
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  • 15
    Electronic Resource
    Electronic Resource
    An empirical potential function for metal centers: Application to molecular mechanics calculations on metalloproteins (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 701-710 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: At present, most molecular mechanics programs that model metalloproteins do not allow for specific geometric requirements at metal centers. An analysis of small-molecule crystal structures containing four-, five-, and six-coordinated zinc, retrieved from the Cambridge Structural Database (CSD), leads to a new metal-center potential function for use in molecular mechanisc programs. This potential function includes as variables the metal-ligand separations and the angles subtended at the metal and allows specifically for distortions from frequently occurring types of coordination geometries (e.g. tetrahedron square pyramid, trigonal bipyramid, and octahedron). The combination of such a metal-center potential function and one for hydrogen bonds allowing for Ione-pair directionality makes monopole electrostatic contributions to the force-field energy superfluous, thus circumventing many problems associated with the assignment to the force-field energy superfluous, thus circumventing many problems associated with the assignment of atomic apartial charges and a dielectric constant. The molecular mechanics program ‘YETI’, containing both types of potential functions, has been used to refine details of substrate binding of 16 complexes of human carbonic anhydrase II with small molecules. The stereochemistry of the refined complexes is in good agreement with data retrived from the CSD and hence allows realistic structure activity relationships.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070602
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  • 16
    Electronic Resource
    Electronic Resource
    Improving the flexible molecular fitting technique using distance matrices (1986)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 7 (1986), S. 739-744 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program for the molecular superposition of flexible molecules, IFMFIT (Improved or Interactive Flexible Molecular Fit), is presented. The essential new feature involves a complete revision of the representation of molecular structures making use of the briefly discussed Distance Matrix algorithm. A comparison is given between the input mode required by the original FMFIT program and that of our version as exemplified by the superposition of (R)-chrysanthemic acid and (S)-3-methyl-2-(parachlorophenyl)-butyric acid. This example demonstrates the superiority and the user-interactive character made possible by our IFMFIT version.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540070606
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  • 17
    Electronic Resource
    Electronic Resource
    The role of d functions in ab initio calculations. II. The deformation densities of SO2, NO2, and their ions (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 6-27 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Comparison of the optimized geometries and SCF energies for the series XO2+, XO2, XO2-, XO2-, with X = S,N shows that d(S) functions cause larger bond shortening and energy drop than d functions centered on first-row atoms. This is further emphasized on comparing the separate effects of d(central atom) and d(O) functions for SO2 and NO2-, which are similar only for the first-row molecule. The d(S) functions are also essential for proper prediction of the OSO angles. The deformation densities calculated for each series and the corresponding X-O shared populations, change as expected on adding electrons first into σ* then into π* molecular orbitals. In the regions around nuclei the deformation densities express the behavior of the atomic s and p valence orbitals or of their product inside their radial nodes. Introduction of d functions causes substantial polarization effects. For X = N these are mostly local except in the bonding regions where d(N) and d(O) functions are somewhat interchangeable. However, d(S) functions induce also unique changes in the deformation density near O. They cause π and π′ charge migration from O to S and a σ flow in the opposite direction. These effects are largest for the hypervalent species. The unique populations of the d(S) functions are much larger than those of d(N) and d(O) functions. The contribution of d(S) functions to bonding is related to the larger amplitude at small radii of the atomic 3d(S) orbital as compared with that of 3d(N). The difference in amplitudes is related to penetration effects. Diffuse p functions affect geometries and SCF energies of doubly, but not singly negative ions. However, they mostly describe the diffuse nonbonding clouds and do not affect bonding patterns.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080103
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  • 18
    Electronic Resource
    Electronic Resource
    Coupled equations approach to multiphoton molecular processes (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 313-323 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Using the dressed molecule picture of molecule radiation interactions (A.D. Bandrauk et al., J. Chem. Phys., 79, 3256; 80, 4926; 83, 2840) one can deduce multiphoton processes (absorption, scattering, nonlinear optical properties, etc.) amplitudes from coupled second-order differential equations with electronic surfaces and transition moments as input data obtainable from quantum chemical calculations. The present approach enables one to include in the calculation bound and continuum states simultaneously by the use of appropriate boundary conditions for the numerical solutions of these coupled equations. In the case of weak radiative couplings, one recovers the usual Fermi-Golden rule expressions for electronic absorption, raman scattering, etc. The method is thus quite general, bridging the weak field (traditional photochemistry) and the strong field (laser chemistry) regimes which are attainable with today's lasers. The numerical solutions of the coupled equations give us the stationary states of the molecule + radiation system, called dressed molecule. Preparation of the initial state can be mimicked in the coupled equations by an artificial channel method for processes involving a final-state dissociation. Examples of such calculations will be presented in the diatomic Cl2 for which several ab initio electronic states and transition moments were available.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080407
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  • 19
    Electronic Resource
    Electronic Resource
    Computational studies of 1,2-dithiete and dithioglyoxal (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 389-396 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations are reported on the energies, geometries, vibrational frequencies, and ionization potentials of the H2C2S2 isomers: 1,2-dithiete, cis-dithioglyoxal, and trans-dithioglyoxal. In contrast to most earlier computations, the results of this work indicate that 1,2-dithiete and cis-dithioglyoxal lie close in energy (within 3 kcal/mol) with the dithial more stable. Trans-dithioglyoxal is found to be 4.1 kcal/mol more stable than the cis isomer and faces a barrier to internal rotation of 5.5 kcal/mol. The predicted rotational constants for 1,2-dithiete agree within ∼0.05 GHz with the experimentally observed values thus lending credence to the predictions for cis-dithioglyoxal (Ae 14.30683, Be 2.46324, Ce 2.10143 GHz). Vibrational frequencies are given as potential aids to the identification of these molecules. 6-31G* ΔSCF calculations predict that at low energies (8 to 13 eV) the photoelectron spectra of 1,2-dithiete, cis-dithioglyoxal and trans-dithioglyoxal should be similar.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080416
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  • 20
    Electronic Resource
    Electronic Resource
    Molecular orbital theory of the properties of inorganic and organometallic compounds 5. Extended basis sets for first-row transition metals (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 8 (1987), S. 861-879 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A series of efficient split-valence basis sets for first-row transition metals, termed 3-21G, has been constructed based on previously-formulated minimal expansions of Huzinaga, in which each atomic orbital has been represented by a sum of three gaussians. The original Huzinaga expansions for s- and p-type orbitals (except those for 1s) have been fit by least squares to new three-gaussian combinations in which the two sets of orbitals (of the same n quantum number) share gaussian exponents. The Huzinaga three-gaussian expansions for ls and 3d atomic orbitals have been employed without alteration. The valence description of the 3-21G basis sets comprises 3d-, 4s- and 4p-type functions, each of which has been split into two- and one-gaussian parts. 4p functions, while not populated in the ground state of the free atoms, are believed to be important to the description of the bonding in molecules. The performance of the 3-21G basis sets is examined with regard to the calculation of equilibrium geometries and normalmode vibrational frequencies for a variety of inorganic and organometallic compounds containing first-row transition metals. Calculated equilibrium structures, while generally superior to those obtained at STO-3G, are not as good as those for compounds containing main-group elements only. The calculations generally underestimate the lengths of double bonds between transition metals and main-group elements, and overestimate the lengths of single linkages. Calculated normal-mode vibrational frequencies for metal-containing systems are less uniform than in those for main-group compounds.
    Additional Material: 10 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540080614
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