Table 1.

Relative energies (kcal/mol) of 2-quartet G-DNA stems. Solvent screening is included by the method used in the optimization.^a

Method/ Stem	AA	SA-aabb	SA-abab	SA-abab-2	SA- aaab	3AA+1SS	AS	SA-aaaa
QMoptb	0	+0.4 (+7.4)	+9.8	−4.4 (+2.6)	+3.9	+6.8	+16.7	−21.5 (+6.5)
QM→MMoptc	0	−27.0 (−20.3)	−14.8	−31.3 (−25.6)	−22.9	+2.1	−2.7	−53.9(−20.9)
Differenced	0	−27.4 (−27.7)	−24.6	−26.9 (−28.2)	−26.8	−4.7	−19.4	−32.4 (−27.4)
QM→MMoptOL4e	0	−34.0	−17.7	−39.6	−31.4	+3.7	−4.9	−58.4
Cang et al. 34f	0	−14.6(−20.2)	−14.4(−20.0)	−14.4(−20.0)	−13.4(−19.0)	+4.6(+6.0)	+ ~14	N/A

^aIntramolecular O5′H…N3(G) H-bonds in 5′-terminal syn guanosines are present in the following structures: SA-aabb, one interaction; SA-abab-2, one interaction; SA-aaaa, four interactions. All these interactions exist in the original X-ray structures. There is one O5′H…N2(G) H-bond in the SA-abab system. The H-bonds are consistently present/absent in both QM_opt and QM→MM_opt structures and thus should not systematically affect the comparison of QM and MM relative energies.

^bOptimization using the DFT-D3 COSMO approach starting from the initial structure. The estimates in parentheses were obtained by deducting 7 kcal/mol per each syn nucleotide terminal O5′H…N3(G) H-bond (see the text).

^cOptimization using the parmbsc0 force field and PB method starting from the QM_opt structure. Values in parentheses show the energies with elimination of the terminal O5′H…N3(G) H-bonds (see the text).

^dDifference between MM and QM relative energies. The estimates in parentheses were obtained when considering the deductions of the energies of the terminal O5′H…N3(G) H-bonds.

^eOptimization using the parmbsc0+χ_OL4 force field and PB method starting from the QM_opt structure.

^fMD MM-PBSA free energy computations compiled from the Table 1 by Cang et al³⁴ with −4.4 (−3.0 in parenthesis) kcal/mol correction per each 5′-terminal syn base to deduct contributions of all O5′H…N3(G) intramolecular H-bonds (for more details see the original study and the Method section).