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  • 1
    Electronic Resource
    Electronic Resource
    Pectic substances in raw and cooked, fresh or processed Spanish vegetables (1983)
    s.l. : American Chemical Society
    Journal of agricultural and food chemistry 31 (1983), S. 949-953 
    Details
    ISSN: 1520-5118
    Source: ACS Legacy Archives
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Process Engineering, Biotechnology, Nutrition Technology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/jf00119a007
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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
    Two differentially regulated nitrate reductases required for nitrate-dependent, microaerobic growth of Bradyrhizobium japonicum (1994)
    Springer
    Archives of microbiology 162 (1994), S. 310-315 
    Details
    ISSN: 1432-072X
    Keywords: Bradyrhizobium japonicum ; Nitrate ; Membrane-bound nitrate reductase ; Nitrate reductase mutants ; Microaerobiosis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Native PAGE of Triton x-100-solubilized membranes from Bradyrhizobium japonicum strain PJ17 grown microaerobically (2% O2, v/v) in defined nitrate-containing medium resolved two catalytically active nitrate reductase (NR) species with apparent molecular masses of 160 kDa (NRI) and 200 kDa (NRII). NRI and NRII were also found in membranes from cells of strain PJ17 that were first grown in defined medium with glutamate and further incubated microaerobically in the presence of 5 mmol/l KNO3. However, only NRI was detected in cell membranes of strain PJ17 when nitrate was omitted from the microaerobic incubation medium. Four mutants unable to grow at low O2 tension in the presence of nitrate were isolated after transposon Tn5 mutagenesis. Membranes from mutants GRF110 and GRF116 showed mainly NRI, while the other two mutants, GRF3 and GRF4, expressed mostly NRII. These results indicate that the ability of B. japonicum PJ17 to grow under microaerobic conditions depends upon the presence of two membrane-bound NR enzymes whose synthesis seem to be independently induced by microaerobiosis (NRI) or by both microaerobiosis and nitrate (NRII).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00263777
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  • 4
    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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  • 5
    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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  • 6
    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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  • 7
    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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  • 8
    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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  • 9
    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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  • 10
    Electronic Resource
    Electronic Resource
    Changes in the glycosylation pattern at the reducing end of azorhizobial Nod factors affect nodulation efficiency (1998)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 158 (1998), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The Nod factors of Azorhizobium caulinodans ORS571 are lipo-chitooligosaccharides that at the reducing end can be unsubstituted, substituted with a l-fucosyl group, with a d-arabinose, or with both groups at the same time. These lipo-chitooligosaccharides are the compounds produced by the bacteria during the signal exchange with their host plant at the onset of the nodulation process. By the use of wild-type and mutant strains, the role of the different Nod factor glycosylations on the nodulation behavior was checked. The mere presence of the d-arabinosyl group at the reducing end of the lipo-chitooligosaccharides resulted in a higher number of nodules on roots of Sesbania rostrata, whereas the presence or absence of l-fucose had no effect. The situation is the opposite in other tropical legumes that respond to A. caulinodans ORS571: the l-fucose is the major determinant of nodulation, whereas the presence of d-arabinose is less significant. By the use of a β-glucuronidase reporter fusion, A. caulinodans ORS571 was shown to colonize nodules or nodule-like tissues induced on cowpea and bean, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.1998.tb12826.x
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