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A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA

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Abstract

Force fields are actively used to study RNA. Development of accurate force fields relies on a knowledge of how the variation of properties of molecules depends on their structure. Detailed scrutiny of RNA’s conformational preferences is needed to guide such development. Towards this end, minimum energy structures for each of a set of 16 small RNA-derived molecules were obtained by geometry optimization at the HF/6-31G(d,p), B3LYP/apc-1, and MP2/cc-pVDZ levels of theory. The number of minima computed for a given fragment was found to be related to both its size and flexibility. Atomic electrostatic multipole moments of atoms occurring in the [HO-P(O3)-CH2-] fragment of 30 sugar-phosphate-sugar geometries were calculated at the HF/6-31G(d,p) and B3LYP/apc-1 levels of theory, and the transferability of these properties between different conformations was investigated. The atomic multipole moments were found to be highly transferable between different conformations with small standard deviations. These results indicate necessary elements of the development of accurate RNA force fields.

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This work was supported by the National Natural Science Foundation of China (No. 21503101), the Fundamental Research Funds for the Central Universities (Grant No. lzujbky-2019-cd05), the National Natural Science Foundation of China (No.81973786), and the Science Foundation of Guangxi (AA17204096, AD16380076).

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  1. Zhuangzhuang Zhang

    Present address: **’an Microelectronic Technology Institute, No.198 Taibai South Road, **’an, 710000, China

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  1. School of Information Science & Engineering, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China

    Yongna Yuan, Zhuangzhuang Zhang, Yan Ma & Wei Su

  2. 3M Corporate Research Analytical Laboratory, Saint Paul, MN, 55114, USA

    Matthew J. L. Mills

  3. School of Pharmacy, Lanzhou University, No. 222 South Tianshui Road, Lanzhou, 730000, China

    Chunyan Zhao

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Supporting Information Available: Supporting Information contains Cartesian coordinates of all the 22 B3LYP/apc-1 minima of SPS.

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Yuan, Y., Mills, M.J.L., Zhang, Z. et al. A general RNA force field: comprehensive analysis of energy minima of molecular fragments of RNA. J Mol Model 27, 137 (2021). https://doi.org/10.1007/s00894-021-04746-9

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