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Transition metal-catalyzed hydrogenation
Published in Ilya D. Gridnev, Pavel A. Dub, Enantioselection in Asymmetric Catalysis, 2016
The behavior of chemical reactions occurring in solution, however, is largely dictated by solvent effects.220 Solute-solvent interactions have dramatic effects on molecular structures, energies and properties221–223 as well as on the outcome of the reaction, including the sense of enantioselection.224,225 Within the gas-phase, reactions without charge separation or charge distribution are common (e.g., radical and pericyclic reactions), but in solution, most reactions do involve charge separation and charge distribution.220 Solvent effects can be grouped into two distinct components.220,226Nonspecific solvation or macrosolvation describes interactions between solute molecules and the solvent polarization electric field (reaction field) around the solute in solution. Specific solvation or microsolvation is defined as the formation of kinetically stable complexes between the solute and solvent, originating from hydrogen-bonding, charge transfer or electron-pair donor-acceptor complexes and other weak chemical interactions. A computational description of nonspecific solvation can be achieved by treating the solvent as a continuous medium characterized by its macroscopic dielectric constant.227–233 This gives rise to the continuum or implicit solvation model.222,234 When the solvent and solute interact only slightly, the continuum model is an efficient tool for a proper description of chemical systems, accounting for the effects of solvation on a molecular structure, its energetics, and dynamics.228,230 A computational description of specific solvation can be achieved via explicit inclusion of one or more solvent molecules into gas-phase calculations. This gives rise to the discrete or explicit solvation model.51,55 The best approach to take into account both nonspecific and specific interactions is to compute the solute properties by including a few explicit solvent molecules in the continuum solvent, thus giving rise to a continuum/discrete solvation model.230,235–239 Usually the inclusion of only a small number of solvent molecules is sufficient to fill most of the discrepancy between energy diagrams calculated in the gas-phase and in solution.240–242
The deamination mechanism of the 5,6-dihydro-6-hydro-6-hydroxylcytosine and 5,6-dihydro-5-methyl-6-hydroxylcytosine under typical bisulfite conditions
Published in Molecular Physics, 2019
Lingxia Jin, Gongwei Qin, Caibin Zhao, Xiaohu Yu, Jiufu Lu, Hao Meng
As seen from Figures 1 and S1, except for A-RC that H2O is farther from HOHCytN3+ than that in the gas phase, the distances of O1-H4, O1-N4, O2-H1, and O3-H4 in A-RC are elongated to 4.640, 4.581, 1.792, and 1.829 Å, respectively. It indicates that the interaction between ···H2O group and HOHCytN3+ has substantially been weakened. The rest of stationary structures of path A in the aqueous phase are similar with those in the gas phase. Similar with path A, the optimised geometry in B-TS2 for path B changes a lot in the aqueous phase, and the H2SO3 migrates from the right side to the left side of the HOHCytN3+. In addition, the same case happens in D-TS3, and the position of the H2SO3 group in D-TS3 is very different with that in the gas phase. The H2SO3 migrates from the right side to the above of the 5-HOHMeCytN3+. The solvent effects obviously change the geometries of reaction complexes, and also change the free energy barrier. On the contrary, the stationary structures of path C in the aqueous phase are similar with those in the gas phase, implying that the small geometrical changes are induced by the presence of the bulk water.