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  • Theoretical, Physical and Computational Chemistry  (4)
  • Hybrid theoretical calculations  (1)
  • 1
    ISSN: 1432-2234
    Keywords: Key words: Rubisco ; Carboxylation step ; QM/MM ; Hybrid theoretical calculations ; Transition state structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The present study elucidates structural features related to the molecular mechanism in the carboxylation step of the reaction catalyzed by Rubisco. Starting from the initial X-ray Protein Data Bank structure of a Rubisco monomer, the reactive subsystem in vacuo is subjected to quantum chemical semiempirical and ab initio studies, while the effects of the protein environments are included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. The QM/MM is used to characterize the transition structure for carboxylation inside the protein. The calculations were made with the AM1/CHARMM/GRACE scheme. Comparisons between the in vacuo and in situ transition structures show remarkable invariance with respect to geometric parameters, index and transition vector amplitudes. The transition state couples the carbon dioxide attack to the C2 center of the substrate in its dienol form with a simultaneous intramolecular hydrogen transfer from the C2 atom to the hydroxyl group linked to the C3 center. This study suggests that carboxylation may be simultaneously coupled to the activation of the C3 center in the enzyme.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 11 (1998), S. 670-677 
    ISSN: 0894-3230
    Keywords: abnormal Reimer-Tiemann reaction ; theoretical study ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The molecular mechanism for the pyrrole ring expansion to yield 3-chloropyridine, as a model of the abnormal Reimer-Tiemann rearrangement, was characterized theoretically in vacuo by means of the HF/6-31G* computational method. The electron correlation was estimated at the MP2/6-31G* level and by calculations based on density functional theory, B3LYP/6- 31G* and B3LYP/6- 31+G*. Solvent effects of the diethyl ether and ethanol media were analyzed by using a polarizable continuum model. The stationary points were characterized with analytical gradient techniques in the gas phase and insolvents. The topology of the potential energy surfaces calculated at the MP2/6-31G* and B3LYP/6-31G* levels shows that the molecular mechanism corresponds to an inverted energy profile along one intermediate, associated with the addition of dichlorocarbene at the β-position of the pyrrole anion, and only one transition structure related to the ring expansion associated with the breaking and forming of Cα - Cβ and C - Cα bonds, respectively, and the Cl- leaving process. © 1998 John Wiley & Sons, Ltd.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 0894-3230
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: A theoretical study of the catalytic mechanism of lactate dehydrogenase enzyme on different model systems was carried out with the help of the PM3 semi-empirical procedure and an ab initio method at the 4-31G and 6-31G** basis sets at a Hartree-Fock (HF) level of theory.The geometry, transition vector (TV) and electronic structure of the transition structure (TS) for the acid-catalysed hydride reduction were obtained. The dependence of these properties on the computing method and model system is analysed and discussed. Proton transfer is much more advanced than hydride transfer occurring in roughly perpendicular planes. All the TSs render very similar structural features, the control of the chemical reaction being associated with the hydride transfer process. A comparison among simple and sophisticated molecular models shows that the TS seems to be structurally a rather robust entity. There is a minimal molecular model with a TS which describes the essentials of the chemical interconversion step in a given enzyme mechanism and the corresponding TV is an invariant feature.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The molecular mechanisms for the ring openings of cyclopropanone, 2,2-dimethylcyclopropanone, trans-2,3-di-tert-butylcyclopropanone, and spiro(bicyclo[2.2.1]heptane-2.1′-cyclopropan)-2′-one systems were studied at the PM3 semiempirical level in the gas phase and including solvent effects. The behavior of the solvent polarity was considered by using the SCRF polarizable continuum method. Six solvents were selected: hexane, ether, tetrahydrofuran, pyridine, acetone, and acetonitrile. An extensive exploration of the potential energy surface using analytical gradient techniques allows the characterization of stationary points associated to the stereomutation conversion. Along a disrotatory ring-opening mechanism, cyclopropanone, 2,2-dimethylcyclopropanone and trans-2,3-di-tert-butylcyclopropanone are intraconverted via an oxyallyl intermediate. The epimeric forms of the spiro(bicyclo[2.2.1]heptane-2.1′-cyclopropan)-2′-one intraconvert along two competitive pathways correspond to two-step processes by a disrotatory ring-opening mechanism. Two oxyallyl intermediates and four transition structures were obtained and the corresponding transition vectors are associated to the carbon-carbon bond-breaking process and the dihedral angle measuring the conrotatory movement of the plane defined by the three carbon atoms of the cyclopropanone ring. The oxyallyl intermediates and the transition structures for the four model systems present similar structures and energies and they are located on a rather flat region. The analysis of the theoretical results shows that the solvent reaction field decreases the energy barriers for the ring-opening processes and a stabilization of the oxyallyl intermediates takes place. The calculated relative barrier heights are in good agreement with the experimental data available, and the trends in the kinetics can be explained primarily by steric interactions. Nevertheless, for the spiro(bicyclo[2.2.1]heptane-2.1′-cyclopropan)-2′-one system, it is necessary to include a specific interaction of a discrete molecule of the nucleophilic solvent on the quantum mechanical representation to explain the experimental behavior.   © 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 729-738, 1997
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 63 (1997), S. 373-391 
    ISSN: 0020-7608
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A quantum approach to chemical processes is developed. The chemical interconversion is described as an electronic process. The reaction corresponds to histories involving quantum states belonging to different stationary molecular Hamiltonians. The system may be embedded in a weak (thermal) and/or external electromagnetic field. The electromagnetic transverse fields lead to transition moments yielding finite probability amplitudes for the system to change from one quantum state to another. Bottleneck subspaces (transition states) are defined; they mediate the interconversions in generic unimolecular and bimolecular processes. Active precursor and successor complexes are introduced to help bridge reactant and product electronic states. The stationary states are modeled with Born-Oppenheimer Hamiltonians. At a qualitative level, the theory is general. The rate, measured as a time derivative of product concentration, is expressed in terms of concentrations of active precursor and successor complexes. The kinetic coefficients are given in terms of quantum processes involving electronic bottleneck states. Stationary structures and vibrational zero-point energies characterizing the reactive CH3++H2 system are determined at a Hartree-Fock level of theory with 6-31++G** basis set. The vibrational levels are corrected with anharmonicity effects. The saddle point of index one for hydrogen scrambling reactions has been obtained and shown to be related to the CH5+ molecular complex together with the precursor and successor complexes geometries. The unusual properties of the system with respect to standard transition-state theory are fairly well described within this approach, in particular, isotope scrambling as well as photon emission during formation of the carbocation. The theory suggests that these types of reactions, which are found in outer space, may contribute to the scattering of the cosmic microwave background. © 1997 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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