羟基自由基破坏DNA与RNA的碱基、黄酮类化合物清理羟基自由基反应机理的量子化学研究及电子密度拓扑学分析
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摘要
本论文主要内容分为三部分,第一部分对羟基自由基破坏DNA碱基的反应机理进行了量子化学研究,并对反应物和过渡态结构进行了电子密度拓扑学分析。第二部分和第三部分分别讨论了黄酮类化合物B环与A环酚羟基清理羟基自由基的反应机理,以及反应物和过渡态结构的电子密度拓扑学分析。
论文第一部分采用密度泛函(DFT)理论中的B3LYP方法对羟基自由基破坏DNA碱基分子结构的反应机理进行了量子化学研究。结果表明,腺嘌呤、鸟嘌呤、胞嘧啶以及胸腺嘧啶均能为羟基自由基所破坏,从IRC结果以及对过渡态结构的电子密度拓扑学分析的结果可以确定,其反应历程为羟基自由基破坏碱基环结构的加成机理。嘌呤与羟基自由基反应的活化能在32～35kJ/mol之间,明显高于嘧啶与羟基自由基反应的活化能11～15kJ/mol。另外,对于胸腺嘧啶以及组成RNA的尿嘧啶还存在羟基夺取碱基特定位置氢原子的抽氢机理,论文利用密度泛函(DFT)理论中的B3LYP方法搜索了抽氢机理的过渡态结构,并对其进行了电子密度拓扑学分析。计算结果显示,抽氢机理中羟基自由基抽取反应底物中特定位置的氢原子形成水分子脱去,其过渡态反应位形成了六元环结构。
论文第二部分采用密度泛函(DFT)理论中的B3LYP方法对黄酮类化合物中的几种典型化合物B环酚羟基清理羟基自由基的反应机理进行了量子化学研究。结果表明,黄酮类化合物B环上未形成分子内氢键的酚羟基可以与羟基自由基发生反应。从IRC结果以及对过渡态结构的电子密度拓扑学分析结果可以确定,在反应过程之中羟基自由基抽取了黄酮类化合物B环上未参与分子内氢键结构的酚羟基上的氢原子形成水分子及稳定性更高的半醌式大环自由基,在整个过程之中羟基自由基从反应物一侧接近反应底物,并随着反应的进行逐渐扭转,直至形成一个近平面结构的过渡态结构。另外,随着反应的进行,黄酮化合物分子中B环与A、C环结构之间的夹角呈现出减小的趋势,整个基元反应的活化能在16～20kJ/mol之间。
论文第三部分继续采用密度泛函(DFT)理论中的B3LYP方法对黄酮类化合物中的几种典型化合物A环酚羟基清理羟基自由基的反应机理进行了量子化学研究。结果表明,黄酮类化合物A环上未形成分子内氢键的酚羟基也可以与羟基自由基发生反应。从IRC结果以及对过渡态结构的电子密度拓扑学分析结果可以确定,羟基自由基在反应过程之中抽取了黄酮类化合物A环上未参与分子内氢键结构的酚羟基上的氢原子形成水分子及稳定性更高的半醌式大环自由基,在整个过程之中羟基自由基从反应物一侧进攻并逐渐发生扭转,直至形成一个进平面结构的过渡态结构,这与上一章关于黄酮类化合物B环的研究结果基本一致。但是A环反应中随着反应的进行,黄酮化合物分子中A,C环与B环结构之间夹角的变化呈现一定的不规律性,大部分呈现出了增加的趋势,但个别分子也呈现减小的趋势。A环酚羟基清理羟基自由基的基元反应活化能为14～19kJ/mol之间。另外对反应过渡态的电子密度拓扑学分析表明:B环酚羟基清理羟基自由基的反应过渡态结构之中即将脱去的水分子中的氧原子与黄酮分子中参加反应的酚羟基相邻位置的氢原子之间只有抽甙配基存在弱相互作用,可以形成一个六元环结构,其余分子均不存在该结构。而A环的反应中却只有漆树黄酮不存在该结构,其余分子则全部存在该弱相互作用。
This dissertation contains three parts.The first part is the theoretical study of the Purine and Pyrimidine react with hydroxyl radical.The second and the third parts are the quantum study of the free radical scavenging capacity of bioflavoinoids(B ring and A ring).
The additional mechanism of Purine and Pyrimidine react with hydroxyl radical has been theoretically studied by DFT B3LYP/6-31G in the first part of the dissertation.The results show that Guanine,Adenosine,Cytosine and Thymine all can react with hydroxyl radical.The topological study of transition states and IRC results show that the hydroxyl radical added to the ring structure of Purine and Pyrimidine as the reaction carry out.The activation energy of Purine react with hydroxyl radical is between 32～35kJ/mol,higher than that of Pyrimidine(11～15kJ/mol).In addition,the abstraction hydrogen Mechanism of Thymine and Uracil(the base Included in the RNA) has been studied,and the topological study of the transiton state has also been carded out of them.The hydroxyl radical snatch the hydrogen atom of Thymine and Uracil,formimg a 6-membered-ring structure.
The mechanism of hydroxyl free radical scavenging of flavoinoids compounds (B ring) has been theoretical studied under the DFT B3LYP/6-31g.The IRC also has been carried under the same theory.The results show that the phenolic hydroxyl of flavoinoids(B ring) reacts with hydroxyl radical to produce H_2O and Quinone-type radical which is more stable.The hydroxyl free radical close to the flavoinoids(B ring) from one side of the molecular.The dihedral angel of B ring and A,C ring becomes smaller during the reaction process.The activation energy of B ring elementary reaction is between 16～20kJ/mol.
The mechanism of hydroxyl free radical,scavenging of flavoinoids compounds (A ring) has been theoretical studied under the DFT B3LYP/6-31 g.The IRC also has been carded under the same theory.The results show that the phenolic hydroxyl of flavoinoids(A ring) reacts with hydroxyl radical to produce H_2O and Quinone-type radical which is more stable.The hydroxyl free radical close to the bioflavoinoids(A ring) from one side of the molecular.The dihedral angel of A,C ring and B ring becomes larger during the reaction process for most of the reaction. The activation energy of B ring elementary reaction is between 14～19kJ/mol.The AIM analysis show that there is no weak interaction between oxygen of hydroxyl free radical and the hydrogen of flavoinoids which is adjacent to the phenolic hydroxyl which is losing hydrogen in the reaction,except naringonin in B ring reaction.But for A ring reaction,except fisotin,there is weak interaction and a six membered ring in the reaction area,which is mentioned above.
论文第一部分采用密度泛函(DFT)理论中的B3LYP方法对羟基自由基破坏DNA碱基分子结构的反应机理进行了量子化学研究。结果表明,腺嘌呤、鸟嘌呤、胞嘧啶以及胸腺嘧啶均能为羟基自由基所破坏,从IRC结果以及对过渡态结构的电子密度拓扑学分析的结果可以确定,其反应历程为羟基自由基破坏碱基环结构的加成机理。嘌呤与羟基自由基反应的活化能在32～35kJ/mol之间,明显高于嘧啶与羟基自由基反应的活化能11～15kJ/mol。另外,对于胸腺嘧啶以及组成RNA的尿嘧啶还存在羟基夺取碱基特定位置氢原子的抽氢机理,论文利用密度泛函(DFT)理论中的B3LYP方法搜索了抽氢机理的过渡态结构,并对其进行了电子密度拓扑学分析。计算结果显示,抽氢机理中羟基自由基抽取反应底物中特定位置的氢原子形成水分子脱去,其过渡态反应位形成了六元环结构。
论文第二部分采用密度泛函(DFT)理论中的B3LYP方法对黄酮类化合物中的几种典型化合物B环酚羟基清理羟基自由基的反应机理进行了量子化学研究。结果表明,黄酮类化合物B环上未形成分子内氢键的酚羟基可以与羟基自由基发生反应。从IRC结果以及对过渡态结构的电子密度拓扑学分析结果可以确定,在反应过程之中羟基自由基抽取了黄酮类化合物B环上未参与分子内氢键结构的酚羟基上的氢原子形成水分子及稳定性更高的半醌式大环自由基,在整个过程之中羟基自由基从反应物一侧接近反应底物,并随着反应的进行逐渐扭转,直至形成一个近平面结构的过渡态结构。另外,随着反应的进行,黄酮化合物分子中B环与A、C环结构之间的夹角呈现出减小的趋势,整个基元反应的活化能在16～20kJ/mol之间。
论文第三部分继续采用密度泛函(DFT)理论中的B3LYP方法对黄酮类化合物中的几种典型化合物A环酚羟基清理羟基自由基的反应机理进行了量子化学研究。结果表明,黄酮类化合物A环上未形成分子内氢键的酚羟基也可以与羟基自由基发生反应。从IRC结果以及对过渡态结构的电子密度拓扑学分析结果可以确定,羟基自由基在反应过程之中抽取了黄酮类化合物A环上未参与分子内氢键结构的酚羟基上的氢原子形成水分子及稳定性更高的半醌式大环自由基,在整个过程之中羟基自由基从反应物一侧进攻并逐渐发生扭转,直至形成一个进平面结构的过渡态结构,这与上一章关于黄酮类化合物B环的研究结果基本一致。但是A环反应中随着反应的进行,黄酮化合物分子中A,C环与B环结构之间夹角的变化呈现一定的不规律性,大部分呈现出了增加的趋势,但个别分子也呈现减小的趋势。A环酚羟基清理羟基自由基的基元反应活化能为14～19kJ/mol之间。另外对反应过渡态的电子密度拓扑学分析表明:B环酚羟基清理羟基自由基的反应过渡态结构之中即将脱去的水分子中的氧原子与黄酮分子中参加反应的酚羟基相邻位置的氢原子之间只有抽甙配基存在弱相互作用,可以形成一个六元环结构,其余分子均不存在该结构。而A环的反应中却只有漆树黄酮不存在该结构,其余分子则全部存在该弱相互作用。
This dissertation contains three parts.The first part is the theoretical study of the Purine and Pyrimidine react with hydroxyl radical.The second and the third parts are the quantum study of the free radical scavenging capacity of bioflavoinoids(B ring and A ring).
The additional mechanism of Purine and Pyrimidine react with hydroxyl radical has been theoretically studied by DFT B3LYP/6-31G in the first part of the dissertation.The results show that Guanine,Adenosine,Cytosine and Thymine all can react with hydroxyl radical.The topological study of transition states and IRC results show that the hydroxyl radical added to the ring structure of Purine and Pyrimidine as the reaction carry out.The activation energy of Purine react with hydroxyl radical is between 32～35kJ/mol,higher than that of Pyrimidine(11～15kJ/mol).In addition,the abstraction hydrogen Mechanism of Thymine and Uracil(the base Included in the RNA) has been studied,and the topological study of the transiton state has also been carded out of them.The hydroxyl radical snatch the hydrogen atom of Thymine and Uracil,formimg a 6-membered-ring structure.
The mechanism of hydroxyl free radical scavenging of flavoinoids compounds (B ring) has been theoretical studied under the DFT B3LYP/6-31g.The IRC also has been carried under the same theory.The results show that the phenolic hydroxyl of flavoinoids(B ring) reacts with hydroxyl radical to produce H_2O and Quinone-type radical which is more stable.The hydroxyl free radical close to the flavoinoids(B ring) from one side of the molecular.The dihedral angel of B ring and A,C ring becomes smaller during the reaction process.The activation energy of B ring elementary reaction is between 16～20kJ/mol.
The mechanism of hydroxyl free radical,scavenging of flavoinoids compounds (A ring) has been theoretical studied under the DFT B3LYP/6-31 g.The IRC also has been carded under the same theory.The results show that the phenolic hydroxyl of flavoinoids(A ring) reacts with hydroxyl radical to produce H_2O and Quinone-type radical which is more stable.The hydroxyl free radical close to the bioflavoinoids(A ring) from one side of the molecular.The dihedral angel of A,C ring and B ring becomes larger during the reaction process for most of the reaction. The activation energy of B ring elementary reaction is between 14～19kJ/mol.The AIM analysis show that there is no weak interaction between oxygen of hydroxyl free radical and the hydrogen of flavoinoids which is adjacent to the phenolic hydroxyl which is losing hydrogen in the reaction,except naringonin in B ring reaction.But for A ring reaction,except fisotin,there is weak interaction and a six membered ring in the reaction area,which is mentioned above.
引文
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