Quantum Chemical Benchmark Study on 46 RNA Backbone Families Using a Dinucleotide Unit

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Authors	KRUSE Holger MLÁDEK Arnošt GKIONIS Konstantinos HANSEN Andreas GRIMME Sstefan ŠPONER Jiří
Year of publication	2015
Type	Article in Periodical
Magazine / Source	Journal of Chemical Theory and Computation
MU Faculty or unit	Central European Institute of Technology
Citation
Web	http://pubs.acs.org/doi/10.1021/acs.jctc.5b00515
Doi	http://dx.doi.org/10.1021/acs.jctc.5b00515
Field	Physical chemistry and theoretical chemistry
Keywords	MOLECULAR-DYNAMICS SIMULATIONS; DENSITY-FUNCTIONAL THEORY; SUGAR-PHOSPHATE BACKBONE; ELECTRONIC-STRUCTURE CALCULATIONS; MAIN-GROUP THERMOCHEMISTRY; BASIS-SET CALCULATIONS; LONG NONCODING RNAS; NUCLEIC-ACID BASES; AMBER FORCE-FIELD; B-DNA STRUCTURE
Description	We have created a benchmark set of quantum chemical structure energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0 chi(OL3) force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of similar to 0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields.
Related projects:	CEITEC - Central European Institute of Technology SYLICA - Synergies of Life and Material Sciences to Create a New Future Centrum biologie RNA