Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, Campinas 13083-859, SP, Brazil.
Instituto de Geociências e Ciências Exatas de Rio Claro, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro 13506-900, SP, Brazil.
J Chem Theory Comput. 2022 Nov 8;18(11):6463-6471. doi: 10.1021/acs.jctc.2c00756. Epub 2022 Oct 28.
The early DNA damage induced by ionizing radiation depends on how ionizing particles transfer energy to this molecule and the surrounding medium, mostly water. In preliminary studies, we found that the energy transferred by a 4 keV proton to a cytosine-guanine base pair in a classical simulation collision using the ReaxFF potential is much smaller than that obtained by a quantum calculation using time-dependent density functional theory (TDDFT). We observed that there are two main reasons for that: no accurate force-field for this situation and problems while dealing with the proton charge during the collision. Here, we only focus on the interaction potential. We calibrated the van der Waals energy term of the ReaxFF potential using TDDFT calculations and a genetic algorithm, specifically for the interaction of a proton with the DNA constituent atoms (carbon, hydrogen, phosphorus, nitrogen, and oxygen). We obtained a significant improvement in the interaction potential and, consequently, in the scattering angle of the proton colliding with the target atoms in question. However, we conclude that despite the improvement for the force-field and scattering angle, the classical charge equilibration method should also be improved to properly describe the proton-DNA collision process.
电离辐射引起的早期 DNA 损伤取决于电离粒子将能量传递给该分子和周围介质（主要是水）的方式。在初步研究中，我们发现使用 ReaxFF 势能进行经典模拟碰撞时，4keV 质子传递给胞嘧啶-鸟嘌呤碱基对的能量远小于使用含时密度泛函理论（TDDFT）的量子计算获得的能量。我们观察到有两个主要原因：这种情况下没有准确的力场，以及在碰撞过程中处理质子电荷时存在问题。在这里，我们只关注相互作用势能。我们使用 TDDFT 计算和遗传算法对 ReaxFF 势能的范德华能量项进行了校准，特别是针对质子与 DNA 组成原子（碳、氢、磷、氮和氧）的相互作用。我们得到了相互作用势能的显著改善，进而提高了质子与目标原子碰撞的散射角度。然而，我们得出结论，尽管力场和散射角度得到了改善，但经典的电荷平衡方法也应该得到改进，以正确描述质子-DNA 碰撞过程。
