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  • Theoretical, Physical and Computational Chemistry  (13)
  • Wiley-Blackwell  (13)
  • Oxford University Press
  • 1
    Electronic Resource
    Electronic Resource
    GROMOS-MD simulations on the coenzyme thiamin diphosphate in apoenzyme environment (1998)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 70 (1998), S. 407-413 
    Details
    ISSN: 0020-7608
    Keywords: molecular dynamics ; hydrogen bonding ; conformational studies ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Thiamin diphosphate (ThDP) is an essential cofactor for a number of enzymes, especially of pyruvate decarboxylase (PDC) which catalyzes the decarboxylation of α-keto acids. Recently, the crystal structure of PDC-bound ThDP has been determined. Based on these X-ray data molecular dynamics (MD) simulations of the isolated coenzyme as well as of ThDP in its enzymatic environment were performed, using the GROMOS87 software package. In the ThDP-apoenzyme model all significant amino acid residues with a cut-off radius less than 8.5 Å from the cofactor were considered. The conformational behavior and the formation of specific structures of both ThDP and enzyme-bound ThDP were investigated in order to get hints on the activity and the mechanism of the coenzyme. Therefore, trajectories of significant structural parameters were analyzed by our graphics tool. Moreover, Ramachandran-like plots with respect to significant torsion angles were used for the illustration. Finally, MD simulations on ThDP analogs with less or none catalytic activity and apoenzyme mutants were included, in order to study the cofactor-apoenzyme binding.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 407-413, 1998
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  • 2
    Electronic Resource
    Electronic Resource
    Aromaticity of pericyclic reaction transition structures: magnetic evidence (1998)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 11 (1998), S. 655-662 
    Details
    ISSN: 0894-3230
    Keywords: pericyclic reaction transition structures ; aromaticity ; magnetic susceptibility ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The transition states of thermally allowed pericyclic reactions are aromatic. They not only have highly delocalized structures and large resonance stabilizations (energies of concert), but also strongly enhanced magnetic susceptibilities (Λ) and appreciable NICS (nucleus-independent chemical shifts) values arising from the diatropic ring currents. Aromaticity is the consequence of cyclic electron delocalization, which can have σ and hybrid, and not just π character. © 1998 John Wiley & Sons, Ltd.
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  • 3
    Electronic Resource
    Electronic Resource
    Ab initio study of the formation of C3H3+ from the reaction of CH3+ with acetylene (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 905-909 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio molecular orbital theory has been used to study the mechanism of the formation of C3H3+ from the reaction of CH3+ with acetylene. The highest level geometry optimizations and frequencies were computed at MP2-FC/6-31G**; single point energies of all the critical structures were computed to the MP4-FC/6-31G**//MP2-FC/6-31G** theory level. One of the three alternative transition structures leading to the formation of C3H3+ gives the cyclopropenyl cation and the other two the propargyl cation. The proportions of C3H2D+ and C3HD2+ obtained when CD3+ reacts with acetylene, and the composite nature of the metastable peak observed for the[C3H5]+→[C3H3]++ H2 fragmentation are explained by assuming a different degree of deuterium scrambling depending on the energy of the system. © 1996 by John Wiley & Sons, Inc.
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  • 4
    Electronic Resource
    Electronic Resource
    Editorial (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 489-489 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540170502
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  • 5
    Electronic Resource
    Electronic Resource
    Empirical force-field and ab initio calculations on delocalized open chain cations (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 28-44 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force-field calculations are reported for large delocalized cations. The results for the geometries, heats of formation, and π-electron densities agree well with MP2(full)/6-31G* ab initio calculations. Both methods give similar results for the distortion of the carbon skeletons of unsubstituted cations by hyperconjugating methyl groups. Because of the SCF treatment of π-interactions, the MMP2 force-field technique enables calculations of resonance energies in delocalized cations. The additional resonance stabilization produced by extending conjugation is directly related to the π-charge on the carbon at which a vinyl group is substituted. The good agreement of MMP2 results for nonbonded resonance effects in large delocalized cationic π-systems with ab initio data suggests that MMP2 can be used to study the influence of these interactions in cationic π-systems too large to be calculated by correlated ab initio methods. © 1997 by John Wiley & Sons, Inc.
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  • 6
    Electronic Resource
    Electronic Resource
    NMR chemical shielding surface of N-Acetyl-N′-Methylalaninamide: A density functional study (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 126-138 
    Details
    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 five energetically lowest minima on the potential energy surface of N-acetyl-N′-methylalaninamide were optimized at the Becke3LYP/DZd level of theory to compare these density functional theory results with the literature findings at restricted Hartree-Fock/3-21G. While the relative energies are very similar, the amide moiety is predicted to be much more flexible at Becke3LYP/DZd. As a consequence, the three minima that favor a nonplanar amide group differ by up to 14° in their φ and ψ values between the two levels. To compare the change in the density functional NMR chemical shifts with respect to φ and ψ with experimental results, Becke3LYP/DZd was employed to optimize a structure for N-acetyl-N′-methylalaninamide at each 30° interval on the (φ, ψ) surface in the regions that correspond to the α helix and the β-pleated sheet and at each 60° interval elsewhere. The corresponding NMR chemical shielding surface was computed with the density functional program deMon. The resultant NMR chemical shielding surfaces for N and Cβ are in good agreement with the experiment, while the change in the NMR chemical shielding of C′ and Cα cannot be described only in terms of φ and ψ. The chemical shifts for those atoms also depend on the nonplanarity of the amide moiety. We evaluated this dependence for N-methylacetamide as a model system. Estimates of the parameters derived from N-methyl-acetamide allowed the NMR-shielding surfaces of C′ and Cα to be corrected for the nonplanar nitrogen influence. Although the effect is less pronounced with lower level theoretical geometries, due to the smaller degree of pyramidalization of the amide nitrogen, the (φ, ψ) NMR chemical shielding surfaces will need to be corrected. The agreement with the experiment was much better for the corrected surface of C′ when the nitrogen in the α helix had a nonplanar environment. © 1997 by John Wiley & Sons, Inc.
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  • 7
    Electronic Resource
    Electronic Resource
    Internal conrotation and disrotation in H2BCH2BH2 and diborylmethane 1,3 H exchangeThis work is dedicated to Professor Ronald Hoffmann on the occasion of his 60th birthday. (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1792-1803 
    Details
    ISSN: 0192-8651
    Keywords: diborylmethane ; conrotation and disrotation ; 1,3 H exchange ; orbital deletion procedure ; gradient line reaction path ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The paths of correlated internal disrotation (barrier less than 0.4 kcal/mol) and conrotation (barrier around 1.9 kcal/mol) of the two BH2 groups in H2BCH2BH2 have been computed employing ab initio [MP2(full)/6-31G**] and density functional theory (Becke3LYP/6-311+G**) methods. Two B(SINGLE BOND)C(DOTTED BOND)B(p) hyperconjugative interactions stabilize the Cs symmetric H2BCH2BH2 isomer (1). The B(SINGLE BOND)C(DOTTED BOND)B(p) hyperconjugative stabilization, evaluated by homodesmotic reactions and using the orbital deletion procedure (which “deactivates” the “vacant” born p orbital), is less than 6 kcal/mol in diborylmethane. The B(SINGLE BOND)C(DOTTED BOND)B(p) stabilization is shown to be remarkably large in C4B6H10 (Td). At MP2(fu)/6-31G**, disproportionation into 1 and methane is only 5.6 kcal/mol exothermic. The 1,3 H exchange in diborylmethane is an asynchronous process and proceeds via a doubly bridged cyclic intermediate with 9.3 kcal/mol barrier. Structures with “planar tetracoordinate” carbon are stabilized considerably by BH2 substituents, but they are still high in energy.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1792-1803, 1997
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  • 8
    Electronic Resource
    Electronic Resource
    Structure and stability of B+13 clusters (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 203-214 
    Details
    ISSN: 0192-8651
    Keywords: structure ; stability ; B+13 clusters ; B3LYP/6-31G* density functional theory ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The structures and energies of B+13, observed experimentally to be an unusually abundant species among cationic boron clusters, have been studied systematically with B3LYP/6-31G* density functional theory. The most thermodynamically stable B+12 and B+13 clusters are confirmed to have planar or quasiplanar rather than globular structures. However, the computed dissociation energies of the 3-dimensional B+13 clusters are much closer to the experimental values than those of the planar or quasiplanar structures. Hence, planar and 3-dimensional B+13 may both exist.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 203-214, 1998
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  • 9
    Electronic Resource
    Electronic Resource
    A critical analysis of electronic density functionals for structural, energetic, dynamic, and magnetic properties of hydrogen fluoride clusters (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1695-1719 
    Details
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present extensive computational results on density functional calculations for hydrogen fluoride species (HF)n (with 1≤n≤6) and compare them to results from other approaches and experiments, where available. Among the calculated properties we discuss equilibrium structural parameters, vibrational frequencies, electric dipole moments, IR intensities, dissociation energies, barriers for rearrangement by proton tunneling, NMR chemical shifts and spin couplings for 1H and 19F, and magnetic susceptibilities. It is found that density functional (particularly BLYP) and even more so hybrid approaches (particularly B3LYP) provide useful results. However, we show that due to some characteristic deficiencies, these are in general not competitive with more quantitative results from large basis set MP2 calculations. The calculated magnetic properties do not indicate any “aromaticity” connected to a hypothetical electronic ring current.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1695-1719, 1997
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  • 10
    Electronic Resource
    Electronic Resource
    Performance of parallel TURBOMOLE for density functional calculations (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 19 (1998), S. 1746-1757 
    Details
    ISSN: 0192-8651
    Keywords: ab initio ; density functional ; parallelization ; quantum chemistry ; message passing ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The parallelization of density functional treatments of molecular electronic energy and first-order gradients is described, and the performance is documented. The quadrature required for exchange correlation terms and the treatment of exact Coulomb interaction scales virtually linearly up to 100 nodes. The RI-J technique to approximate Coulomb interactions (by means of an auxiliary basis set approximation for the electron density) even shows superlinear speedup on distributed memory architectures. The bottleneck is then linear algebra. Demonstrative application examples include molecules with up to 300 atoms and 3000 basis functions that can now be treated in a few hours per geometry optimization cycle in C1 symmetry.   © 1998 John Wiley & Sons, Inc.   J Comput Chem 19: 1746-1757, 1998
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