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

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

Polish Journal of Chemistry

2007

tom Vol. 81, nr 3

369-380

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.

Tautomers of styrylquinoline derivatives containing a methoxy substituent: Computation of their population in aqueous solution and their interaction with RSV integrase catalytic core.

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Ouali M. , Laboulais C. , Leh H. , Gill D. , Xhuvani E. , Zouhiri F. , Desmaële D. , d'Angelo J. , Auclair C. , Mouscadet J.-F. , Bret M. L.

Acta Biochimica Polonica

2000

tom 47

nr 1

11-22

8-Hydroxy-2-[2-(3-hydroxy-4-methoxyphenyl)ethenyl]-7-quinoline carboxylic acid and 8-hydroxy-2-[2-(3-methoxy-4-hydroxyphenyl)ethenyl]-7-quinoline carboxylic acid inhibit the processing and strand transfer reactions catalyzed by HIV-1 integrase with an IC50 of 2 μM. Some of their spectral properties are briefly reported. Their fluorescence is so weak that it is of no use in an experimental determination of the binding to the protein and we resorted to computer simulation. Both styrylquinoline derivatives, in their monoanionic form, have several dozens of tautomers and each of these forms has four planar rotamers. In this work computer simulations have been performed to determine which tautomer is the most abundant in aqueous solution and which binds to the Rous sarcoma virus (RSV) integrase catalytic core. As the substituents on the quinoline moiety are the same as on salicylic acid, the energies of hydroxy benzoic acid tautomers were also computed both in vacuo and embedded in a continuous medium which had the dielectric constant of bulk water, using the recent CPCM technique. The CPCM method was then applied to the two integrase inhibitors to estimate the tautomer population in water. The binding site of the compounds on the RSV integrase catalytic core was determined through a docking protocol, consisting of coupling a grid search method with full energy minimization. The designed method is a way leading to identification of potent integrase inhibitors using in silico experiments.