Bai Junhao, Zhang Yan, Yin Shuhui, Che Li, Yang Songqiu
School of Science, Dalian Maritime University, Linghai Road 1, Dalian 116026, China.
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Zhongshan Road 457, Dalian 116023, China.
Molecules. 2025 May 19;30(10):2213. doi: 10.3390/molecules30102213.
QM/MM simulations were performed to investigate the ionizations of four DNA nucleotides in the explicit solution. The vertical ionization energies (VIEs) and adiabatic ionization energies (AIEs) were averaged over 40 snapshots to calculate mean values. The QM/MM VIEs (6.92-7.63 eV) were ~0.70 eV lower than those of the corresponding nucleosides. This suggests that the water environment cannot fully screen the effect of the phosphate group on ionizations. The result is inconsistent with computations using implicit solvent models. The distributions of holes in both adiabatic and vertical ionizations suggest that bulk-water polarization drives the hole transfer from first-shell water to nucleobases, resulting in increases in VIEs and AIEs. Moreover, we computed the released energies in the structural relaxations after ionizations. The results indicate that the minimal energies are released by the structural relaxations of both the bulk-water and the QM region. The redistributions of the electron density on first-shell water molecules and nucleobases produce the primary contributions to released energies.
进行了量子力学/分子力学（QM/MM）模拟，以研究四种DNA核苷酸在明确溶液中的电离情况。垂直电离能（VIEs）和绝热电离能（AIEs）在40个快照上进行平均以计算平均值。QM/MM的VIEs（6.92 - 7.63电子伏特）比相应核苷的VIEs低约0.70电子伏特。这表明水环境不能完全屏蔽磷酸基团对电离的影响。该结果与使用隐式溶剂模型的计算结果不一致。绝热电离和垂直电离中孔洞的分布表明，本体水极化驱动孔洞从第一壳层水转移到核碱基，导致VIEs和AIEs增加。此外，我们计算了电离后结构弛豫中释放的能量。结果表明，本体水和QM区域的结构弛豫释放的能量最小。第一壳层水分子和核碱基上电子密度的重新分布对释放的能量起主要作用。
