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  • 1
    Electronic Resource
    Electronic Resource
    Hydroxide Ion in Liquid Water: Structure, Energetics, and Proton Transfer Using a Mixed Discrete-Continuum ab Initio Model (1995)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 3798-3805 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100011a056
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  • 2
    Electronic Resource
    Electronic Resource
    Solvent effects on molecular geometries and isomerization processes: a study of push-pull ethylenes in solution (1993)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 115 (1993), S. 3722-3730 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00062a043
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  • 3
    Electronic Resource
    Electronic Resource
    The reaction field of a water molecule in liquid water: Comparison of different quantum/classical models (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 115 (2001), S. 5220-5227 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reaction field of a water molecule in liquid water has been computed with the help of continuum, discrete-continuum, and discrete models, using density functional theory calculations. In the continuum model, the liquid is simply described by a polarizable dielectric medium. The solute is placed in a cavity defined by a scaled van der Waals surface. Two different sets of van der Waals radii have been used for the atomic spheres. The discrete-continuum model consists of a quantum molecule surrounded by four classical molecules, the resulting aggregate being embedded in a dielectric continuum. Finally, in the discrete model, a molecular dynamics simulation is carried out for a quantum molecule in a box containing 215 classical molecules with periodic boundary conditions. The reaction field and the induced dipole moment in the standard continuum model are substantially underestimated. However, the use of optimized van der Waals radii for the atomic spheres produces a notable improvement. The discrete-continuum and discrete models lead to close results that are in good agreement with experimental data and previous theoretical estimations. For instance, the induced dipole moment (0.80 and 0.82 D for discrete-continuum and discrete models, respectively) compares well with the experimental estimate (0.75 D) and with Car–Parrinello simulations (1.08 D). The reaction field potential is analyzed in terms of multipole moment contributions. The role of the first shell and bulk solvent are also examined. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1389094
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  • 4
    Electronic Resource
    Electronic Resource
    A Hybrid Density Functional-Classical Molecular Dynamics Simulation of a Water Molecule in Liquid Water (1995)
    Springer
    Journal of molecular modeling 1 (1995), S. 196-201 
    Details
    ISSN: 0948-5023
    Keywords: Keywords Computer Simulations, QM/MM Potentials, Density Functional Theory, Molecular Dynamics, Liquid Water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A hybrid NVE Molecular Dynamics simulation of liquid water is presented using a coupled Density Functional/Molecular Mechanics hamiltonian. The quantum subsystem is a single water molecule described by means of a triple-zeta quality basis set with polarization orbitals on oxygen and hydrogen atoms. Non-local exchange-correlation corrections are included self-consistently. The classical system is constituted by 128 classical TIP3P water molecules. Results are in reasonable agreement with experimental data and in particular a good description of the solute polarization is obtained. Large fluctuations of the instantaneous value of the dipole moment of the quantum molecule are predicted.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s008940050016
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  • 5
    Electronic Resource
    Electronic Resource
    Effect of Solvation on Ozonolysis Reaction Intermediates and Transition States (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 608-617 
    Details
    ISSN: 0948-5023
    Keywords: Ozonolysis ; Ozone ; Reaction mechanisms ; Solvent effects ; Theoretical calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Electrostatic solvent effects on the ozonolysis of ethylene have been investigated using correlated ab initio and density functional approaches. We use a simple polarizable continuum model for the solvent. It allows us to evaluate the medium effect on both the electronic and nuclear structure of the chemical species involved in the reaction. The computations confirm that basically the reaction proceeds through the Criegee mechanism. However, formation of the van der Waals complexes ethyl-ene/ozone and carbonyl oxide/formaldehyde also appears to play a role. All the calculated species are stabilized with respect to the reactants except the transition state corresponding to the primary ozonide formation. In general, electrostatic solvent effects are relatively small for activation barriers of single reaction steps and more substantial for the corresponding reaction energies. Moreover, the medium significantly modifies the structure of some species for which polarization effects are crucial.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060608
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  • 6
    Electronic Resource
    Electronic Resource
    Insights in the Peptide Hydrolysis Mechanism by Thermolysin: A Theoretical QM/MM study (2000)
    Springer
    Journal of molecular modeling 6 (2000), S. 527-538 
    Details
    ISSN: 0948-5023
    Keywords: Hybrid methods ; QM/MM ; LSCF ; Zinc metalloproteases ; Thermolysin ; Peptide hydrolysis ; Enzymatic mechanism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The hydrolysis by thermolysin of a Gly-Phe-Leu peptide, considered as a model substrate of the enkephalin family, has been studied with a mixed QM/MM method with the AM1/AMBER parameterization. This study is based on the mechanism proposed by Matthews in which the Glu-143 residue plays the role of a proton shuttle in the course of the reaction. The study focused on the description of every step of the process, reaction intermediates and transition states, and on the influence, both energetical and structural, of the whole protein on these stationary points. The overall mechanism appears to be quite realistic, but the study shows that some reaction steps that were assumed to be concerted should occur in two phases. Analysis of the role of the amino-acids surrounding the active site has shown their important participation in the fluctuations of the energy. In particular, the major role of His-231 on the overall mechanism has been confirmed. This study shows that modeling reaction mechanisms for enzymes is quite feasible and opens the way for computer experiments that may be helpful in devising and interpreting detailed experimental investigations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s0089400060527
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  • 7
    Electronic Resource
    Electronic Resource
    The Hydrolysis Mechanism of Formamide Revisited: Comparison Between ab initio, Semiempirical and DFT Results (1997)
    Springer
    Journal of molecular modeling 3 (1997), S. 434-442 
    Details
    ISSN: 0948-5023
    Keywords: Keywords: Amides ; Hydrolysis ; Reaction mechanism ; Peptides ; Theoretical calculations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The hydrolysis of amides is a model reaction to study peptide hydrolysis. This process has been previously considered in the literature at the ab initio level. In this work, we revisit different reaction mechanisms (water-assisted, non-assisted, neutral and acid-catalyzed) with various theoretical methods : semiempirical, ab initio and Density Functional. The ab initio calculations are carried out at a computational level which is substantially higher than in previous studies. We describe the structure of the transition states and discuss the influence of the catalyst. We also compute the activation free energies for these processes at the Density Functional Theory level. Comparison of the methods allows to outline the main trends of these theoretical approaches which may be useful to design new computational strategies for investigating biological reaction mechanisms through the use of combined Quantum Mechanics/Molecular Mechanics methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s008940050061
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  • 8
    Electronic Resource
    Electronic Resource
    Intramolecular proton transfer of serine in aqueous solution. Mechanism and energetics (2000)
    Springer
    Theoretical chemistry accounts 104 (2000), S. 89-95 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Proton transfer – Serine – Continuum solvent model – Nonequilibrium effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Serine amino acid in aqueous solution is theoretically studied at the B3PW91/6-31+G** level using a dielectric continuum solvent model. Neutral and zwitterionic structures in the gas phase and in solution are described and the proton-transfer mechanism is discussed. A neutral conformation in which the carboxyl hydrogen atom is already oriented toward the amino group seems to be the absolute energy minimum in the gas phase and the most stable neutral form in solution. The absolute energy minimum in solution is a zwitterionic form. The energy barrier for proton transfer is predicted to be very small, in particular when zero-point-energy contributions are added. Our calculations allow the dynamic aspects of the ionization mechanism to be discussed by incorporating nonequilibrium effects.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002149900109
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular dynamics simulation in aqueous solution of N-methylazetidinone as a model of β-lactam antibiotics (1999)
    Springer
    Theoretical chemistry accounts 101 (1999), S. 336-342 
    Details
    ISSN: 1432-2234
    Keywords: Key words:N-Methylazetidinone ; Molecular dynamics ; β-Lactam hydrolysis ; Solvent effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having similar energy barriers at the rate-limiting step of the reaction path. In the first type, the β-lactam-water interaction takes place through the oxygen carbonyl atom and there is agreement between the maxima of the RDFs obtained here and the ab initio structure of the complexes previously reported. In the second type, the interaction takes place through the nitrogen atom and we do not predict a coordination layer around the β-lactam nitrogen atom. The results suggest that in aqueous solution hydrolysis of the carbonyl group is the most probable starting point for the overall hydrolysis reaction. Some discussion on the use of cluster models to represent the solvent effect is included.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050450
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  • 10
    Electronic Resource
    Electronic Resource
    Conformational analysis of 2-cyano-1,1-dihydroxyethane in solution (1996)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 9 (1996), S. 119-127 
    Details
    ISSN: 0894-3230
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: The conformational space of the 2-cyano-1,1-dihydroxyethane molecule was studied at the semi-empirical PM3 level and ab initio MP2/6-31G**//6-31G level in the gas phase and in a low-polarity medium. This system has been chosen as a model compound for 2-cyanocyclohexanone propylene and ethylene acetals. This has allowed the study of the role of polar groups on the relative conformation of two adjacent OH groups, which is of interest also in relation to the anomeric effect in carbohydrate chemistry. Solvent effects are taken into account using a continuum model with general cavity shapes.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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