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Assisted and Protected Effects of Methanol Molecules on Intramolecular Proton Transfer in Formamide Studied with the Density Functional Theory

Du M., Qin M., Fu A., Zhou Z.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 3

369-380

EN

Methanol assisted and protected proton transfers from the amide nitrogen to carbonyl oxygen atom inmodel peptide compound formamide have been investigated employing the B3LYP/6-311++G(d,p) level of theory. In the vicinity of formamide (F) and formamidic acid (FA), three different regions are considered to form hydrogen bond with methanol. Methanol molecule only in one of them can assist the proton transfer reaction while in other two sites can protect formamide from tautomerization. Totally, 27 geometries, including nine important transition states, were optimized, and their geometric parameters have also been discussed in detail. The thermodynamic and kinetic parameters, such as tautomeric energies, equilibrium constants, barrier heights, and rate constants have been predicted, respectively. In addition, the factors influencing the thermodynamic and kinetic parameters, such as temperature dependences, and solvent effects have also been explored qualitatively. Computational results show that the lowest proton transfer barrier heights are 83.30 (61.61) kJ/mol without (with) ZPVE correction for the assistance of two methanol molecules, which are also lower than that of the water-assisted process. Nonspecific solvent effects have also been taken into account by using the IPCM model of methanol. The tautomerization energies and the barrier heights are increased for these proton transfer systems because of the bulk solvent, which imply that the tautomerization of F becomes less favorable in the polar medium.

2

A Study on the Electrochemical and Structural Properties of a Schiff Base SAM on Au(111) Surface

Kong D. S., Gu K. Q., Feng Y. Y., Qin M.

Polish Journal of Chemistry

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2007

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Vol. 81, nr 9

1611-1620

EN

The electrochemical and structural properties of Schiff base V-hp self-assembled monolayer (SAM) on Au(111) surface have been studied using electrochemical technique and electrochemical scanning tunneling microscopy (ECSTM) in 0.1 M HClO4 solution. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) measurements revealed that the adlayer of V-hp on Au(111) surface inhibits the oxidization of Au and reduces the surface double-layer capacitance. The electronic charges for V-hp-SAM covered Au(111) electrode, resulting from capacitive charging and discharging process in volved in the double-layer potential region, become one or more orders of magnitude lower than that for bare Au(111). STM investigation demonstrated that V-hp molecules can adsorb with a flat-lying orientation on Au(111) and formed a long-range two-dimensional ordered SAM with a (2 square root 3 x square root 21) adlattice symmetry structure. A model structure with one molecule per unit cell was proposed, which yields a surface concentration of 1.28x10-10 mol/cm2.

3

Ionization of Organic Acids in Dimethyl Sulfoxide Solution: Different Methods of the Ab Initio Calculation of the pKa Using the Polarizable Continuum Model

Qin M., Zhao G., Duan C., Zhou Z., Lu J.

Polish Journal of Chemistry

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2006

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Vol. 80, nr 11

1865-1876

EN

The pKa values of ten organic acids in dimethyl sulfoxide (DMSO) solution were calculated using the density functional theory (DFT), second-order Moller-Plesset Perturbation (MP2) and Hartree-Fock (HF) methods at the 6-31+G(d) basis set level. The solvation was included through the polarizable continuum model (PCM). The major work was to compare the different PCM methods to calculate the pKa, as well as coupled with the experimental data. The average error over this set of molecules using the HF method is smaller than those using B3LYP orMP2 methods, not only in theoretical calculation but also in the mix approach (coupled with the experimental data). The present result suggests that the HF method in PCM model could be used for predicting the pKa values.