10.1021/ja402525c.s002 Jiří Šponer Jiří Šponer Arnošt Mládek Arnošt Mládek Naďa Špačková Naďa Špačková Xiaohui Cang Xiaohui Cang Thomas E. Cheatham Thomas E. Cheatham Stefan Grimme Stefan Grimme Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations American Chemical Society 2013 QM energy data stability force field modeling acid force fields DNA building blocks QM computations COSMO limitation MM Different DNA Guanine Quadruplex Stem Topologies Derived DNA force field calculation 2013-07-03 00:00:00 Dataset https://acs.figshare.com/articles/dataset/Relative_Stability_of_Different_DNA_Guanine_Quadruplex_Stem_Topologies_Derived_Using_Large_Scale_Quantum_Chemical_Computations/2399686 We provide theoretical predictions of the intrinsic stability of different arrangements of guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have applied Molecular Mechanics (MM) approaches using simple pairwise-additive force fields. The principle limitation of such calculations is the highly approximate nature of the force fields. In this study, we for the first time apply accurate QM computations (DFT-D3 with large atomic orbital basis sets) to essentially complete DNA building blocks, seven different folds of the cation-stabilized two-quartet G-DNA stem, each having more than 250 atoms. The solvent effects are approximated by COSMO continuum solvent. We reveal sizable differences between MM and QM descriptions of relative energies of different G-DNA stems, which apparently reflect approximations of the DNA force field. Using the QM energy data, we propose correction to earlier free energy estimates of relative stabilities of different parallel, hybrid, and antiparallel G-stem folds based on classical simulations. The new energy ranking visibly improves the agreement between theory and experiment. We predict the 5′-<i>anti-anti</i>-3′ GpG dinucleotide step to be the most stable one, closely followed by the 5′-<i>syn-anti</i>-3′ step. The results are in good agreement with known experimental structures of 2-, 3-, and 4-quartet G-DNA stems. Besides providing specific results for G-DNA, our study highlights basic limitations of force field modeling of nucleic acids. Although QM computations have their own limitations, mainly the lack of conformational sampling and the approximate description of the solvent, they can substantially improve the quality of calculations currently relying exclusively on force fields.