Yuan Yongna, Ma Yan, Huo Dongxu, Mills Matthew J L, Wei Jiaxuan, Su Wei, Zhang Ruisheng
School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China.
3M Corporate Research Analytical Laboratory, Saint Paul, Minnesota 55114, United States.
J Phys Chem B. 2020 Nov 12;124(45):10089-10103. doi: 10.1021/acs.jpcb.0c06757. Epub 2020 Nov 3.
Molecular force field simulation is an effective method to explore the properties of DNA molecules in depth. Almost all current popular force fields calculate atom-atom electrostatic interaction energies for DNAs based on the atomic charge and dipole or quadrupole moments, without considering high-rank atomic multipole moments for more accurate electrostatics. Actually, the distribution of electrons around atomic nuclei is not spherically symmetric but is geometry dependent. In this work, a multipole expansion method that allows us to combine polarizability and anisotropy was applied. One single-stranded DNA and one double-stranded DNA were selected as pilot systems. Deoxynucleotides were cut out from pilot systems and capped by mimicking the original DNA environment. Atomic multipole moments were integrated instead of fixed-point charges to calculate atom-atom electrostatic energies to improve the accuracy of force fields for DNA simulations. Also, the applicability of modeling the behavior of both single-stranded and double-stranded DNAs was investigated. The calculation results indicated that the models can be transferred from pilot systems to test systems, which is of great significance for the development of future DNA force fields.
分子力场模拟是深入探索DNA分子性质的有效方法。目前几乎所有流行的力场都是基于原子电荷和偶极矩或四极矩来计算DNA的原子间静电相互作用能，而没有考虑高阶原子多极矩以获得更精确的静电作用。实际上，原子核周围电子的分布不是球对称的，而是与几何形状有关。在这项工作中，应用了一种允许我们结合极化率和各向异性的多极展开方法。选择了一条单链DNA和一条双链DNA作为试点系统。从试点系统中切出脱氧核苷酸，并通过模拟原始DNA环境进行封端。通过积分原子多极矩而非定点电荷来计算原子间静电能，以提高DNA模拟力场的准确性。此外，还研究了对单链和双链DNA行为进行建模的适用性。计算结果表明，这些模型可以从试点系统转移到测试系统，这对未来DNA力场的发展具有重要意义。
