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首页> 外文期刊>The journal of physical chemistry, A. Molecules, spectroscopy, kinetics, environment, & general theory >Hydrolytic Deamination of 5-Methylcytosine in Protic MediumsA Theoretical Study
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Hydrolytic Deamination of 5-Methylcytosine in Protic MediumsA Theoretical Study

机译：质子介质中5-甲基胞嘧啶的水解脱氨基理论研究

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摘要

The mechanism for the deamination reaction of 5-methylcytosine with H2O in protic medium was investigated using DFT calculations at the B3LYP/6-311G(d,p) level of theory. Two pathways were found. Pathway 5mA is a two-step mechanism where the N3-protonated 5-MeCyt undergoes a nucleophilic attack to carbon C4 by a water dimer before the elimination of an ammonium cation. Pathway 5mB is a three-step mechanism where neutral 5-MeCyt is directly attacked by a water dimer. The resulting intermediate is then protonated to allow the elimination of an ammonium cation. Both pathways lead to the formation of thymine in interaction with an ammonium cation and a water molecule. Pathway 5mA can explain the spontaneous deamination of 5-MeCyt in protic medium at acidic pH, whereas pathway 5mB is more representative of the deamination in protic medium at neutral pH. The nucleophilic addition of the water dimer is rate-determining in both pathways and is associated with an activation free energy in aqueous solution of 137.4 kJ/mol for pathway 5mA and 134.1kJ/mol for pathway 5mB. This latter value is in agreement with the experimental observation that 5-MeCyt deaminates four- to fivefold faster than Cyt at neutral pH. Both electrostatic and electron-transfer contributions appear to have significant importance. In vacuum, the former one dominates when the substrate is positively charged and the latter one when it is neutral.
机译：在理论水平的B3LYP / 6-311G（d，p）水平上使用DFT计算研究了质子介质中5-甲基胞嘧啶与H2O脱氨反应的机理。发现了两个途径。途径5mA是一个两步机制，其中N3质子化的5-MeCyt在消除铵阳离子之前通过水二聚体对碳C4进行亲核攻击。途径5mB是三步机制，其中中性5-MeCyt被水二聚体直接攻击。然后使所得的中间体质子化以消除铵阳离子。两种途径都导致与铵阳离子和水分子相互作用的胸腺嘧啶的形成。途径5mA可以解释在酸性pH下质子培养基中5-MeCyt的自发脱氨，而途径5mB更能代表中性pH下质子培养基中的脱氨。水二聚体的亲核加成在两个途径中都是速率决定的，并且对于水溶液5mA而言，其水溶液中的活化自由能为137.4kJ / mol，对于途径5mB而言，其与水溶液中的活化自由能为134.1kJ / mol。后一个值与在中性pH下5-MeCyt脱氨速度比Cyt快四到五倍的实验观察结果一致。静电和电子转移的贡献似乎都非常重要。在真空中，当基材带正电时，前者占主导，而中性时，后者占主导。

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