Energy barriers of proton transfer reactions between amino acid side chain analogs and water fromab initio calculations

2006 ◽  
Vol 27 (13) ◽  
pp. 1534-1547 ◽  
Author(s):  
Elena Herzog ◽  
Tomaso Frigato ◽  
Volkhard Helms ◽  
C. Roy D. Lancaster
Keyword(s):  
Amino Acid ◽  
Proton Transfer ◽  
Transfer Reactions ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Energy Barriers ◽  
Proton Transfer Reactions

The effect of water-mediated catalysis on the intramolecular proton-transfer reactions of the isomers of 5-chlorouracil: a theoretical study

2019 ◽  
Vol 75 (5) ◽  
pp. 554-561
Author(s):  
Jian Zhang ◽  
Xiu Li
Keyword(s):  
Proton Transfer ◽  
Density Functional ◽  
Dft Method ◽  
Intramolecular Proton Transfer ◽  
Transfer Reactions ◽  
Energy Barriers ◽  
Transfer Energy ◽  
Geometrical Structures ◽  
Proton Transfer Reactions ◽  
Mediated Catalysis

The geometrical structures and thermal energies (E), enthalpies (H) and Gibbs free energies (G) of 13 isomers of 5-chlorouracil (5ClU) in the gas and water phases were investigated using the density functional theory (DFT) method at the M06-2X/6-311++g(3df,3pd) level. The isomers of 5ClU can be microhydrated at different molecular target sites. The mono- and dihydrated forms are the most stable in both the gas and water phases, and, because of the intermolecular interactions, the hydrations lead to a degree of change in the stability trend. Two types of isomerizations were considered: the internal H—O bond rotations in which the H atom rotates 180° around the C—O bond and the intramolecular proton-transfer reactions in which an H atom is transferred between an O atom and a neighbouring N atom. The forward and backward energy barriers for isomerizations of nonhydrated 5ClU were calculated. In addition, 16 optimized transition-state structures for water-mediated catalysis on isomerizations of 5ClU were investigated. The forward and backward proton-transfer energy barriers of water-mediated catalysis on isomerizations of 5ClU were obtained. The results indicate that the catalytic effect of two H2O molecules is much greater than that of one H2O molecule in isomerizations of 5ClU.

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