| Autor: |
Yuan Y; School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China., Ma Y; School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China., Huo D; School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China., Mills MJL; 3M Corporate Research Analytical Laboratory, Saint Paul, Minnesota 55114, United States., Wei J; School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China., Su W; School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China., Zhang R; School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou 730000, China. |
| Abstrakt: |
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. |
