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  • 1
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 767-780 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular geometries of the 1-chloro-, 1-fluoro-, 1-methyl-, and 1-hydrogenosilatranes were fully optimized by the restricted Hartree-Fock (HF) method supplemented with 3-21G, 3-21G(d), 6-31G(d), and CEP-31G(d) basis sets; by MP2 calculations using 6-31G(d) and CEP-31G(d) basis sets; and by GGA-DFT calculations using 6-31G(d5) basis set with the aim of locating the positions of the local minima on the energy hypersurface. The HF/6-31G(d) calculations predict long (〉254 pm) and the MP2/CEP calculations predicted short (∼225 pm) equilibrium Si(SINGLE BOND)N distances. The present GGA-DFT calculations reproduce the available gas phase experimental Si(SINGLE BOND)N distances correctly. The solid phase experimental results predict that the Si(SINGLE BOND)N distance is shorter in 1-chlorosilatrane than in 1-fluorosilatrane. In this respect the HF results show a strong basis set dependence, the MP2/CEP results contradict the experiment, and the GGA-DFT results in electrolytic medium agree with the experiment. The latter calculations predict that 1-chlorosilatrane is more polarizable than 1-fluorosilatrane and also support a general Si(SINGLE BOND)N distance shortening trend for silatranes during the transition from gas phase to polar liquid or solid phase. The calculations predict that the ethoxy links of the silatrane skeleton are flexible. Consequently, it is difficult to measure experimentally the related bond lengths and bond and torsion angles. This is the probable origin of the surprisingly large differences for the experimental structural parameters. On the basis of experimental analogies, ab initio calculations, and density functional theory (DFT) calculations, a gas phase equilibrium (re) geometry is predicted for 1-chlorosilatrane. The semiempirical methods predict a so-called exo minimum (at above 310 pm Si(SINGLE BOND)N distance); however, the ab initio and GGA-DFT calculations suggest that this form is nonexistent. The GGA-DFT geometry optima were characterized by frequency analysis. © 1996 by John Wiley & Sons, Inc.
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  • 2
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 178-184 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A configuration interaction (CI) method in restricted CI (RCI) space obtained by imposing inequality-type restrictions on the occupancies of groups of molecular orbitals (MOs) was studied. The direct CI approach in such space was analyzed, and some recommendations concerning practical implementation of the RCI method are given. The corresponding program has been written in FORTRAN 77 for an IBM 486 DX personal computer and has been used for electronic structure calculations on transition metal complexes using a valence MO basis with the INDO approximation. © 1996 by John Wiley & Sons, Inc.
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  • 3
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 522-532 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon - carbon rather than carbon - nitrogen bonds. © 1997 by John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 308-318 
    ISSN: 0192-8651
    Keywords: tellurium tetrachloride ; ab initio calculations ; density functional theory ; vibrational analysis ; scaled quantum mechanical method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Vibrational analysis of tellurium tetrachloride, TeCl4, was performed with Hartree-Fock (HF), MP2, and generalized gradient approximation density functional theory (DFT) methods supplemented with polarized double-zeta split valence (DZVP) basis sets and relativistic effective core potentials (RECP) of Hay and Wadt. The molecular geometry is best reproduced at the HF and MP2/RECP+DZVP [polarized Hay and Wadt RECP for Te and 6-31G(d) basis set for Cl] levels of theory. The DFT methods gave rise to poorer results, especially those using Becke's 1988 exchange functional. Generally, the vibrational frequencies calculated by the MP2 and B3-type DFT methods with the all electron and RECP+DZVP basis sets as well as at the HF/RECP level were in satisfactory accord with the experimental data. The agreement was good enough to assist the assignment of the measured vibrational spectra. The best agreement with the experimental vibrational frequencies was achieved with the scaled HF/RECP force field. Consistent results were obtained for the unobserved A2 (ν4) fundamental, where the results of the best methods were within 4 cm-1. The best force fields were obtained with the following methods: Becke3-Lee-Yang-Parr and Becke3-Perdew/all electron basis, MP2 and Becke3-Perdew/RECP+DZVP, and HF/RECP. The methods using RECPs are advantageous for large-scale computations. The RECP basis set effectively compensates the errors of the HF method for TeCl4; however, it provides poor results with correlated methods.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 308-318, 1998
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 19-29 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A theoretical model to investigate chemical processes in solution is described. It is based on the use of a coupled density functional/molecular mechanics Hamiltonian. The most interesting feature of the method is that it allows a detailed study of the solute's electronic distribution and of its fluctuations. We present the results for isothermal-isobaric constant-NPT Monte Carlo simulation of a water molecule in liquid water. The quantum subsystem is described using a double-zeta quality basis set with polarization orbitals and nonlocal exchange-correlation corrections. The classical system is constituted by 128 classical TIP3P or Simple Point Charge (SPC) water molecules. The atom-atom radial distribution functions present a good agreement with the experimental curves. Differences with respect to the classical simulation are discussed. The instantaneous and the averaged polarization of the quantum molecule are also analyzed. © 1996 by John Wiley & Sons, Inc.
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  • 6
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 238-249 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Metropolis Monte Carlo method has been developed for studying the effects of dielectric constant and counterion charge density and distribution on the energetics of formation and equilibria of the regular arrays or domain structures formed by bacteria l lipopolysaccharides. The method utilizes a regular triangular prism primitive as a reductive structural representation of each lipopolysaccharide anchor (lipid A molecule). Charges for the two phosphate groups are localized at one apex and midway along the opposite side of the regular triangular top face of each prism. The counterions are not localized but are represented as a fine cloud of charge modeled by distributing the total charge over a fine two-dimensional cubic lattice. The six alkyl chains of the lipid A molecule are aligned along the long axes of the prism and are contained by its faces. All prisms are confined to the same plane but are allowed to translate within the plane and to rotate about axes perpendicular to the plane. The potential energy function contains an electrostatic term and a van der Waals term. A discontinuous dielectric is used to separate the aqueous and hydrophobic areas of the system. Trial moves involve both a rotational and a translational operation. The configurations predicted by this method are consistent with the crystal morphologies which have been observed for lipopolysaccharides. This analysis readily allows the evaluation of thermodynamic properties, such as heat capacity, entropy, and energy. The root mean square average separation of units was also calculated as a function of iteration number. © 1996 by John Wiley & Sons, Inc.
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  • 7
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1757-1770 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773-1073 K and densities in the range 115-659 kg/m3. We present thermodynamic data, pair correlation functions, self-diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self-diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.
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  • 8
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1804-1819 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational behavior of 2-trifluoromethylphenol was investigated by means of theoretical calculations. Four characteristic structures have been found on the potential energy hypersurface of the compound: anti form (local minimum), in which the hydroxy hydrogen points away from the trifluoromethyl group; and three syn forms (the hydrogen points towards the trifluoromethyl group), with different trifluoromethyl torsions (global minimum, one low and another one high lying saddle-point). The geometry of these conformers were optimized by ab initio calculations using 6-31G** basis set. The effects of electron correlation were investigated by MP2 and various DFT methods. To investigate the intramolecular interaction in the syn forms, the electron density distribution was calculated at the MP2 level of theory. In the structure corresponding to the global minimum at the MP2/6-31G** level a bond critical point was found in Bader's sense between the hydroxy hydrogen and a fluorine of the trifluoromethyl group indicating hydrogen bonding interaction. The length of the hydrogen bond, 1.98 Å, corresponds to medium strength interaction. The O(SINGLE BOND)H bond is slightly twisted and the C(SINGLE BOND)F bond, interacting with it, is considerably twisted out of the plane of the benzene ring to the same side of the ring. The most pronounced geometrical consequence of the hydrogen bond is the 0.02-Å lengthening of the C(SINGLE BOND)F bond participating in its formation. All the other geometrical changes in 2-trifluoromethylphenol, as compared with trifluoromethylbenzene and phenol, are also consistent with the phenomenon of resonance-assisted hydrogen bonding. © 1996 by John Wiley & Sons, Inc.
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 330-342 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The conformational space of 1C4 α-L-fucose was searched by the MM2*-SUMM molecular mechanics conformational search technique. The molecular geometries of the first 17 structures of lowest energy were analyzed at the HF/3-21G, 6-31G(d), and generalized gradient approximation (GGA) DFT levels of theory. © 1997 by John Wiley & Sons, Inc.
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1534-1545 
    ISSN: 0192-8651
    Keywords: self-interaction error ; hybrid functionals ; H2, total energy ; equilibrium bond length ; electron density ; KS potential ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The performance of the currently used generalized gradient approximation density functionals is analyzed using several simple, yet critical requirements. We analyze the effects of the self-interaction error, the inclusion of the exact exchange, and the parameter settings used in the popular three-parameter hybrid density functionals. The results show that the elimination of the self-interaction error from the current density functionals lead to very poor results for H2. The inclusion of the exact exchange does not significantly influence the self-interaction corrected results. The variation of the A, B, and C parameters of a hybrid DFT method influences the H(SINGLE BOND)H equilibrium bond length through a very simple linear equation, and it is possible to reproduce the experimental H(SINGLE BOND)H distance with appropriate selection of these parameters, although an infinite number of solutions exists. Similar results were obtained for the total energy and the electron density along the internuclear axis. The analysis of the exact KS potential at the bond critical point of the dissociating H2 molecule shows that, for this property, the second order Moller-Plesset perturbation theory yields a better potential than the density functionals studied in this article.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1534-1545, 1997
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