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1 Supporting Information Energies and 2 -hydroxyl group orientations of RNA backbone conformations. Benchmark CCSD(T)/CBS database, electronic analysis and assessment of DFT methods and MD simulations Arnošt Mládek,* 1 Pavel Banáš, 2 Petr Jurečka, 2 Michal Otyepka, 2 Marie Zgarbová, 2 and Jiří Šponer* 1,3 1 Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic. 2 Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17. listopadu 12, , Olomouc, Czech Republic. 3 CEITEC Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno, Czech Republic. * Corresponding authors: arnost.mladek@gmail.com, sponer@ncbr.muni.cz
2 Table S1 List of solvent relative energies (kcal.mol -1 ) referenced against the 1a conformation. Applied methods are tagged as follows: M1: B-LYP, M2: PBE, M3: revpbe, M4: TPSS, M5: otpss, M6: B3-LYP, M7: PW6B95, M8: MPW1B95, M9: PWPB95, M10: DSD-B- LYP, M11: MP2(D,T), and M12: MP2(T,Q). For further details see Methods. MAD and MAX (both in kcal.mol -1 ) represent the mean absolute deviation and the maximum absolute deviation from the reference CBS(T) energies. MM labels force field calculations. Listed DFT energies include D3 correction; MAD and MAX values are quoted for DFs with and without D3 term. Label GGA meta-gga Hybrid Double-Hyb. MP2/CBS M1 M2 M3 M4 M5 M6 M7 M8 M9 M10 M11 M12 CBS(T) MM 1a m L &a a a a g d d d e c f j b [ b z z p t q o r a a a #a g g d d d h n i n j [ b b p p s o MAD- D MAX- D N/A N/A N/A MAD MAX
3 Table S2 List of O2 H group acceptors and respective H-bond strengths estimated by AIM analysis for RNA backbone conformations. The (i+1) designates that respective H-bond acceptor belongs to the i+1-th (i.e. 5-3 downstream) nucleotide. Electronic densities (ρ) and magnitudes of electronic density Laplacians ( ρ) at the H-bond critical point are given in a.u. δ, δ + 1, γ + 1 Group Label ρ ρ O2 H Acceptor 1a O3 1m O3 1L O3 &a O5 (i+1) O4 (i+1) 3, 3, p 7a O3 3a O3 Group I 9a O3 1g O3 7d O3 3d O3 5d O3 1e O4 (i+1) 3, 3, t 1c O5 (i+1) 1f O5 (i+1) 5j O3 1b O3 1[ O3 3, 2, p 3b O3 1z O3 Group II 5z O2P (i+1) 7p O3 3, 2, t 1t O5 (i+1) 5q O3 3, 2, m 1o O3 7r O3 2a O3 4a O3 0a O1P (i+1) O3 2, 3, p #a O1P (i+1) 4g O3 Group III 6g O3 8d O3 4d O3 6d O3 2h O3 2, 3, t 4n O1P (i+1) 0i O3 6n O3
4 6j O3 2[ O3 4b O3 2, 2, p 0b O3 Group IV 4p O3 6p O3 2, 2, t 4s O3 2, 2, m 2o O3 Comment on MD simulation protocol The simulation protocol was as follows both systems (SRL and glms, for more details see main text) were minimized, by first optimizing the waters and ions, while the positions of the RNA molecule remained constrained. Subsequently, all RNA atoms were frozen and the solvent molecules with counter-ions were allowed to move during a 1000-step minimization, followed by 10 ps long MD runs under [NpT] conditions (p = 1 atm., T = K) in order to relax the total density. After this, the solute and nucleobases were relaxed by several minimization runs, with decreasing force constants applied to the sugar-phosphate backbone atoms. After the relaxation, each system was heated from K to K for 100 ps. The particle-mesh Ewald (PME) method for treating electrostatic interactions was used, and all simulations were performed under periodic boundary conditions in the [NpT] ensemble at K using weak-coupling Berendsen thermostat with coupling time of 1 ps. The SHAKE algorithm, with a tolerance of 10 5 Å, was used to fix the positions of all hydrogen atoms, and a 10.0 Å cutoff was applied to non-bonding interactions to allow a 2 fs integration step. The simulation lengths of production phases of the simulations were 1 µs.
5 Figure S1 Hydroxyl group rotation energy profiles (kcal.mol -1 ). The zero energy refers to C3 -C2 -O2 -O2 H torsion of 180. The sequence of conformations corresponds to that in Table 1 in the main text. For methodology details, see Methods in the main text.
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17 Cartesian coordinates (xyz format) of the conformations optimized in gas phase with respective relative CBS(T) energies (kcal.mol -1 ). System: 1a, CBS(T): 0.00 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1m, CBS(T): C C O C C O C O P O O
18 O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1L, CBS(T): 2.60 C C O C C O C O P O O O C C O C C C O H H H H H H H H H
19 H H H H H H H H H System: &a, CBS(T): C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 7a, CBS(T): 1.20 C C O C C
20 O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 3a, CBS(T): 0.64 C C O C C O C O P O O O C C O C C C O H H H
21 H H H H H H H H H H H H H H H System: 9a, CBS(T): 0.56 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H
22 System: 1g, CBS(T): 0.89 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 7d, CBS(T): C C O C C O C O P O O O C C O C
23 C C O H H H H H H H H H H H H H H H H H H System: 3d, CBS(T): 1.04 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H
24 H H H H System: 5d, CBS(T): 0.60 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1e, CBS(T): 1.92 C C O C C O C O P O
25 O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1c, CBS(T): 1.22 C C O C C O C O P O O O C C O C C C O H H H H H H H H
26 H H H H H H H H H H System: 1f, CBS(T): 2.15 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 5j, CBS(T): 4.75 C C O C
27 C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1b, CBS(T): C C O C C O C O P O O O C C O C C C O H H
28 H H H H H H H H H H H H H H H H System: 1[, CBS(T): C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H
29 System: 3b, CBS(T): C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1z, CBS(T): C C O C C O C O P O O O C C O
30 C C C O H H H H H H H H H H H H H H H H H H System: 5z, CBS(T): C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H
31 H H H H H System: 7p, CBS(T): C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 1t, CBS(T): 2.45 C C O C C O C O P
32 O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 5q, CBS(T): 3.19 C C O C C O C O P O O O C C O C C C O H H H H H H H
33 H H H H H H H H H H H System: 1o, CBS(T): 0.11 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 7r, CBS(T): 0.77 C C O
34 C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 2a, CBS(T): C C O C C O C O P O O O C C O C C C O H
35 H H H H H H H H H H H H H H H H H System: 4a, CBS(T): 1.06 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H
36 System: 0a, CBS(T): 0.52 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: #a, CBS(T): 0.05 C C O C C O C O P O O O C C
37 O C C C O H H H H H H H H H H H H H H H H H H System: 4g, CBS(T): 3.62 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H
38 H H H H H H System: 6g, CBS(T): C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 8d, CBS(T): 1.69 C C O C C O C O
39 P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 4d, CBS(T): 1.63 C C O C C O C O P O O O C C O C C C O H H H H H H
40 H H H H H H H H H H H H System: 6d, CBS(T): 1.99 C C O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 2h, CBS(T): 3.10 C C
41 O C C O C O P O O O C C O C C C O H H H H H H H H H H H H H H H H H H System: 4n, CBS(T): 6.51 C C O C C O C O P O O O C C O C C C O
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