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首页> 外文期刊>Chemistry: A European journal >Binding of cationic and neutral phenanthridine Intercalators to a DNA oligomer is controlled by dispersion energy: Quantum chemical calculations and molecular mechanics simulations
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Binding of cationic and neutral phenanthridine Intercalators to a DNA oligomer is controlled by dispersion energy: Quantum chemical calculations and molecular mechanics simulations

机译：阳离子和中性菲啶嵌入剂与DNA寡聚物的结合由分散能控制：量子化学计算和分子力学模拟

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摘要

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge-transfer terms are also important. The Delta G of ethidium intercalation to DNA was estimated at -4.5 kcal mol(-1) and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non-covalent stacking (including charge -transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.
机译：使用相关的从头算以及半经验量子化学计算和分子动力学模拟来研究阳离子乙锭，阳离子5-乙基-6-苯基菲啶鎓和不带电荷的3,8-二氨基-6-苯基菲啶对DNA的嵌入。阳离子嵌入剂的稳定能比不带电荷的稳定剂大得多。所有嵌入剂的主要能量贡献由分散能表示。在阳离子嵌入剂的情况下，静电和电荷转移项也很重要。乙et插入DNA的Delta G估计为-4.5 kcal mol（-1），该值与实验结果吻合良好。在最终自由能的六种贡献中，相互作用能的价值至关重要。插层过程受非共价堆叠（包括电荷转移）相互作用的控制，而乙氨基氨基和DNA骨架之间的氢键作用则不那么重要。这通过相互作用能的评估以及自由能变化的计算得到证实。插层在灵活性方面会影响DNA的宏观特性。这解释了另一种嵌入剂分子更容易进入现有的嵌入位点附近。

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