<br>开发用于 G-四分体和 GGX(8-oxo-G) 四分体中中性和阳离子自由基去质子化的 QM/MM(ABEEM) 方法,Physical Chemistry Chemical Physics

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开发用于 G-四分体和 GGX(8-oxo-G) 四分体中中性和阳离子自由基去质子化的 QM/MM(ABEEM) 方法
Physical Chemistry Chemical Physics ( IF 2.9 ) Pub Date : 2023-11-28 , DOI: 10.1039/d3cp04357f
Yue Wang ₁ , Linlin Liu ₁ , Yue Gao ₁ , Jiayue Zhao ₁ , Cui Liu ₁ , Lidong Gong ₁ , Zhongzhi Yang ₁

Affiliation

DNA链中G˙ ⁺的快速去质子化阻碍了正电荷（空穴）转移，而G-四分体中G˙ ⁺的缓慢去质子化速率使其成为更适合空穴传导的载体。 QM/MM(ABEEM) 组合方法涉及 QM 和 ABEEM 极化力场 (ABEEM PFF) 的集成，用于研究 G-四分体和 GGX(8-oxo) 中中性自由基和阳离子自由基的去质子化-G)四联体（黄嘌呤和8-氧代鸟嘌呤双取代的G-四联体）。通过结合价态电负性分段函数χ *( r ) 并实现电荷局域守恒条件，QM/MM(ABEEM) 具有精确模拟去质子化过程中的电荷转移和极化效应的优势。 X˙的QM方法计算出的活化能是GGX(8-oxo-G)四分体中其他碱基中最低的，这得到了ABEEM PFF计算的平均电负性计算的支持。利用QM/MM(ABEEM)和双向自由能微扰法，确定GGX(8-oxo-G)四分体中X˙的去质子化活化能为33.0 ± 2.1 kJ mol ⁻¹ ，而G-四分体中的G˙ ⁺为20.7 ± 0.6 kJ mol ⁻¹ ，与实验测量的20 ± 1.0 kJ mol ⁻¹一致。这些结果表明，GGX(8-oxo-G) 四分体中的 X˙ 表现出比 G-四分体中的 G˙ ⁺更慢的去质子化速率，表明 GGX(8-oxo-G) 四分体可能作为更有利的去质子化速率。空穴传输载体。此外，GGX(8-oxo-G)四分体中碱基的不相等的平均电负性阻碍了去质子化速率。这项研究为研究DNA电子器件的微观机制提供了潜在的基础。

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Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad

The rapid deprotonation of G˙⁺ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙⁺ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions χ*(r) and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation. The activation energy calculated by the QM method of X˙ is the lowest among other bases in the GGX(8-oxo-G) tetrad, which is supported by the computation of the average electronegativity calculated by ABEEM PFF. By utilizing QM/MM(ABEEM) with a two-way free energy perturbation method, the deprotonation activation energy of X˙ in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol⁻¹, while that of G˙⁺ in the G-tetrad is 20.7 ± 0.6 kJ mol⁻¹, consistent with the experimental measurement of 20 ± 1.0 kJ mol⁻¹. These results manifest that X˙ in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G˙⁺ in the G-tetrad, suggesting that the GGX(8-oxo-G) tetrad may serve as a more favorable hole transport carrier. Furthermore, the unequal average electronegativities of bases in the GGX(8-oxo-G) tetrad impede the deprotonation rate. This study provides a potential foundation for investigating the microscopic mechanism of DNA electronic devices.

更新日期：2023-11-28

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