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Single Water Molecule (single + water_molecule)
Selected AbstractsCatalytic Action of a Single Water Molecule in a Proton-Migration Reaction,ANGEWANDTE CHEMIE, Issue 29 2010Yoshiyuki Matsuda Dr. Ein kleiner Schritt: Der Mechanismus der Protonenverschiebung in ionisiertem Aceton durch Wasser wurde IR-spektroskopisch untersucht. Im Anschluss an die Ionisation spaltet das Wassermolekül ein Proton von einer Methylgruppe des Acetonmoleküls ab und überträgt es auf die Carbonylgruppe (siehe Bild). [source] Keto-enol tautomerism in linear and cyclic ,-diketones: A DFT study in vacuo and in solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 10 2008Giuliano Alagona Abstract DFT geometry optimizations have been performed at the B3LYP/6-31G* level in the gas phase and at the IEF-PCM/B3LYP/6-31G* level in tetrahydrofuran (THF) and aqueous solutions using scaled radii for the diketo and ketoenol forms of acetylacetone and cyclohexanedione. To evaluate basis set effects, starting from the aforementioned minima, the 6-311++G** optimized structures have been obtained. A number of complexes of both systems including one explicit water molecule have been considered up to the B3LYP/6-311++G** level, for cyclohexanedione taking into account the B3LYP/6-31G* basis set superposition errors as well. The diketo,ketoenol interconversion mechanisms have been investigated at the B3LYP/6-31G* level in vacuo. Interestingly, the geometric constraint due to the presence of the ring facilitates the description of the reaction mechanism in cyclohexanedione. Despite the very different flexibility of the two systems that in the case of acetylacetone prevents a straightforward interconversion of the diketo to the most stable of its ketoenol forms, both reactions occur with a very high barrier (about 62,63 kcal/mol), unaffected by continuum solvents, that decreases by 2.5,3.5 kcal/mol after the inclusion of thermal corrections. The barriers are almost halved, becoming ,31,35 kcal/mol, for the addition of a single water molecule according to various model reaction paths. Thermal corrections are limited (0.8,1.6 kcal/mol) for those adducts. The formation of a 1,1-diol, explored in the case of acetylacetone, might facilitate the obtainment of the most stable diketo conformation, featuring the carbonyl groups in distinct orientations. Inclusion of dispersion and basis set effects via the G2MP2 protocol does not alter the relative stability of both system tautomers. In contrast, the G2MP2 interconversion barriers for the isolated systems in vacuo are close to the B3LYP ones, whereas they turn out to be somewhat higher than the free energy-based B3LYP barriers in the presence of a catalytic water molecule. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Intra and intermolecular hydrogen bonding in formohydroxamic acid,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2008Damanjit Kaur Abstract The presence of hydrogen bonding interactions in several tautomeric forms of formohydroxamic acid (FHA) and 1:1 association among the tautomeric forms and water-coordinated tautomeric forms of FHA is explored theoretically. Out of the seven equilibrium structures, four tautomeric forms have been selected for aggregation with single water molecule and dimer formation. Fifteen aggregates of FHA with H2O have been optimized at MP2/AUG-cc-PVDZ level and analyzed for intramolecular and intermolecular H-bond interactions. Twenty-seven dimers of the four tautomeric forms have been obtained at MP2/6-31+G* level. The stabilization energies associated with dimerization and adduct formation with water are the result of H-bond interactions and range from very weak to medium. The atomic charges and NBO analysis indicate that the electrostatic and the charge transfer are the important components favoring H-bond formation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse-turn ScaffoldsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 2 2007Ye Che Reverse turns are common structural motifs and recognition sites in protein/protein interactions. The design of peptidomimetics is often based on replacing the amide backbone of peptides by a non-peptidic scaffold while retaining the biologic mode of action. This study evaluates the potential of metal complexes of chiral pentaazacrowns conceptually derived by reduction of cyclic pentapeptides as reverse-turn mimetics. The possible conformations of metal complexes of chiral pentaazacrown scaffolds have been probed by analysis of 28 crystal structures complexed with six different metals (Mn, Fe, Co, Ni, Cu, and Zn). The solvated structures as well as the impact of complexation with different metals/oxidation states have been examined with density functional theory (DFT) calculation as explicitly represented by interactions with a single water molecule. The results suggest that most reverse-turn motifs seen in proteins could be mimicked effectively with a subset of metal complexes of chiral pentaazacrown scaffolds with an RMSD of approximately 0.3 Å. Due to the relatively fixed orientation of the pendant chiral side groups in these metal complexes, one can potentially elicit information about the receptor-bound conformation of the parent peptide from their binding affinities. The presence of 20 H-atoms on the pentaazacrown ring that could be functionalized as well as the conformational perturbations available from complexation with different metals offer a desirable diversity to probe receptors for reverse-turn recognition. [source] Molecular Mechanism of the Hydration of Candida antarctica Lipase B in the Gas Phase: Water Adsorption Isotherms and Molecular Dynamics SimulationsCHEMBIOCHEM, Issue 18 2009Ricardo J. F. Branco Dr. Abstract Hydration is a major determinant of activity and selectivity of enzymes in organic solvents or in gas phase. The molecular mechanism of the hydration of Candida antarctica lipase B (CALB) and its dependence on the thermodynamic activity of water (aw) was studied by molecular dynamics simulations and compared to experimentally determined water sorption isotherms. Hydration occurred in two phases. At low water activity, single water molecules bound to specific water binding sites at the protein surface. As the water activity increased, water networks gradually developed. The number of protein-bound water molecules increased linearly with aw, until at aw=0.5 a spanning water network was formed consisting of 311 water molecules, which covered the hydrophilic surface of CALB, with the exception of the hydrophobic substrate-binding site. At higher water activity, the thickness of the hydration shell increased up to 10 Å close to aw=1. Above a limit of 1600 protein-bound water molecules the hydration shell becomes unstable and the formation of pure water droplets occurs in these oversaturated simulation conditions. While the structure and the overall flexibility of CALB was independent of the hydration state, the flexibility of individual loops was sensitive to hydration: some loops, such as those part of the substrate-binding site, became more flexible, while other parts of the protein became more rigid upon hydration. However, the molecular mechanism of how flexibility is related to activity and selectivity is still elusive. [source] Structure and Dynamics of Water Confined in Dimethyl SulfoxideCHEMPHYSCHEM, Issue 1 2006A. Wulf Abstract We study the structure and dynamics of hydrogen-bonded complexes of H2O/D2O and dimethyl sulfoxide (DMSO) by infrared spectroscopy, NMR spectroscopy and ab initio calculations. We find that single water molecules occur in two configurations. For one half of the water monomers both OH/OD groups form strong hydrogen bonds to DMSO molecules, whereas for the other half only one of the two OH/OD groups is hydrogen-bonded to a solvent molecule. The H-bond strength between water and DMSO is in the order of that in bulk water. NMR deuteron relaxation rates and calculated deuteron quadrupole coupling constants yield rotational correlation times of water. The molecular reorientation of water monomers in DMSO is two-and-a-half times slower than in bulk water. This result can be explained by local structure behavior. [source] | ||||||||||