Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory

• DOI: 10.1039/c3cp44383c
• Publication Date: 2013-03-18T15:05:55Z
• Authors: Arnošt Mládek; Miroslav Krepl; Daniel Svozil; Petr Čech; Michal Otyepka; Pavel Banáš; Marie Zgarbová; Petr Jurečka; Jiří Šponer
• Keywords: Benchmark (surveying); Basis (linear algebra)

The DNA sugar–phosphate backbone has a substantial influence on the structural dynamics. Structural biology and bioinformatics studies revealed that in experimental structures samples wide range of distinct conformational substates, known as rotameric families. Their correct description is essential for methods used to model nucleic acids be Achilles heel force field computations. In this study we report benchmark database MP2 calculations extrapolated complete basis set atomic orbitals with aug-cc-pVTZ aug-cc-pVQZ sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. are performed gas phase well using COSMO solvent model. This includes 18 established biochemically most important families conformations several other salient identified structures. We utilize an electronically sufficiently sugar–phosphate–sugar (SPS) system truncated prevent undesired intramolecular interactions. then compared QM methods. BLYP TPSS functionals supplemented Grimme's D3(BJ) dispersion term provide best tradeoff between computational demands accuracy can recommended preliminary searches large systems. Among tested methods, agreement been obtained double-hybrid DSD-BLYP functional combination quadruple-ζ set, which is, however, computationally very demanding. new hybrid density PW6B95-D3 MPW1B95-D3 yield outstanding results even slightly outperform more demanding PWPB95 functional. B3LYP-D3 somewhat less accurate hybrids. Extrapolated MP2(D,T) not DFT-D3 Preliminary tests charge sets reveal almost order magnitude larger deviations from reference data modern DFT-D3, underlining challenges facing simulations acids. As expected, inclusion environment approximated continuum approach impact relative stabilities different substates when comparing data.