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  • 1
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 2
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-2234
    Keywords: Key words: Gas phase proton transfer reactions ; H-bonding effects ; Dissociation effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Recently, the proton affinity (PA) of ozone was experimentally determined by Cacace and Speranza [Science (1994) 265: 208] using a bracketing technique that involved the proton transfer (PT) reactions: O3H++B⇒O3+BH+; for different Brönsted bases B. These authors showed that the simple collision model is not adequate to describe PT. We now present a theoretical model reflecting this bracketing procedure by explicitly introducing H-bonding complexing, dissociation and PT contributions, to discuss the kinetic model that assumes that PT occurs through one elementary step. The methods used include semiempirical density functional theory and ab initio Hartree-Fock methods. The procedure is gauged by using estimated PA of ozone obtained from deprotonation reactions including the Brönsted bases B NH3, H2O, HOCl, SO2, CH3F and Kr. The PA-obtained range was from 145.3 to 160.3 kcal/mol, in fair agreement with the experimental value of 148.0±3 kcal/mol. The model seems to be fairly independent of the reference bases used to evaluate the PA. H-bonding effects appear to be a determining factor to explain collision efficiencies.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 101 (1999), S. 234-240 
    ISSN: 1432-2234
    Keywords: Key words: Rubisco mechanism ; Transition-state structures ; Ab initio calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The carboxylation and oxygenation processes of a model substrate, 3,4-dihydroxy-2-pentanone, have been theoreticaly characterized as a set of steps, mimicking the corresponding reactions of D-ribulose-1,5-bisphosphate catalyzed by rubisco. A theoretical characterization is carried out of transition-state structures and possible molecular intermediates represented as saddle points of index 1 and minimum energy structures, respectively. The quantum chemical characterization, at the HF/3-21G calculation level, of these stationary points is used to rationalize and to discuss both catalyzed sequences. The reported set of these stationary points maps out most experimental aspects of the reaction pathways for the real system.
    Type of Medium: Electronic Resource
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  • 5
    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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  • 6
    ISSN: 1432-2234
    Keywords: Molecular mechanism ; N-Chloro-α-glycine ; Potential energy surface ; Post Hartree-Fock procedures
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Stationary points were localized and characterized on potential energy surfaces for the unimolecular decomposition of the anionic form of N-chloro-α-glycine in its singlet and triplet electronic states by means of QCISD(T), DFT and MCSCF methods. The present study predicts that the unimolecular decomposition mechanism takes place in the singlet electronic state through a concerted and slightly asynchronous process and the transition structure has an antiperiplanar conformation. A comparison of the structures for stationary points calculated with different methods yields similar geometries and the components of transition vector are weakly dependent on the computing method.
    Type of Medium: Electronic Resource
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  • 7
    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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  • 8
    ISSN: 0020-7608
    Keywords: keto/enol and imine/enamine tautomerizations ; intramolecular hydrogen shift ; transition structures ; comparison of several calculation methods ; asynchronous process ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The transition structures associated with the possible intramolecular tautomerization for acetaldehyde/vinyl alcohol and acetaldimine/vinylamine systems as models of keto/enol and imine/enamine interconversion processes, respectively, were characterized. The relative stabilities of the tautomers and the associated barrier heights were calculated. Ab initio analytical gradients and second derivatives at the HF level of theory and 3-21G, 6-31G, 6-31G**, 6-31++G**, and 6-311++G** basis-set, DFT (BP86/6-311++G** and BLYP/6-311++G**), and semiempirical (AM1 and PM3) procedures were used to identify the stationary points. Correlation effects were estimated using the perturbational approach at MP2/6-31G**, MP2/6-311++G**, and MP2/6-311++G (3df,2p) levels. The geometry, electronic structure, harmonic vibrational frequencies, and transition vector associated with the transition structures as well as the relative stabilities of different isomers and barrier heights were analyzed. The dependence of these properties upon theoretical methods is analyzed and discussed. The transition structures are four-membered rings and the corresponding transition vectors are associated to collective fluctuations. The 1,3 intramolecular hydrogen migration is much more advanced than are the hybridization changes on donor and acceptor centers at the transition structure. The corresponding barrier heights can be related to the change of bond orders and acid/base properties of these centers. A comparison of the results obtained with different methods renders that the nature of the transition structure seems to be a rather robust entity.   © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66: 9-24, 1998
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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  • 9
    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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  • 10
    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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