Departamento de Física, Universidade Federal de Juiz de Fora, Juiz de Fora, CP 36036-330, Minas Gerais, Brasil.
J Mol Model. 2024 May 27;30(6):187. doi: 10.1007/s00894-024-05983-4.
A systematic study of hydrogen bonds in base pairs and the interaction of cisplatin with DNA fragments was carried out. Structure, binding energies, and electron density were analyzed. xTB has proven to be an accurate method for obtaining structures and binding energies in DNA structures. Our xTB values for DNA base binding energy were in the same order and in some cases better than CAM-B3LYP values compared to experimental values. Double-stranded DNA-cisplatin structures have been calculated and the hydrogen bonds of water molecules are a decisive factor contributing to the preference for the cisplatin-Guanine interaction. Higher values of the water hydrogen bonding energies were obtained in cisplatin-Guanine structures. Furthermore, the electrostatic potential was used to investigate and improve the analysis of DNA-cisplatin structures.
We applied the xTB method and the CAM-B3LYP functional combined with def2-SVP basis set to perform and analyze of the bonding energies of the cisplatin interaction and the effects of the hydrogen bonds. Results were calculated employing the xTB and the ORCA software.
本研究对碱基对中的氢键以及顺铂与 DNA 片段的相互作用进行了系统研究。分析了结构、结合能和电子密度。xTB 已被证明是一种获得 DNA 结构中结构和结合能的准确方法。与实验值相比，我们对 DNA 碱基结合能的 xTB 值在相同的顺序，在某些情况下优于 CAM-B3LYP 值。计算了双链 DNA-顺铂结构，并且水分子的氢键是导致顺铂-鸟嘌呤相互作用偏好的决定性因素。在顺铂-鸟嘌呤结构中获得了更高的水氢键能值。此外，还利用静电势来研究和改进 DNA-顺铂结构的分析。
我们应用了 xTB 方法和结合了 def2-SVP 基组的 CAM-B3LYP 函数来进行顺铂相互作用的结合能和氢键影响的分析。结果是使用 xTB 和 ORCA 软件计算的。
