. Author manuscript; available in PMC: 2020 Sep 15.

Published in final edited form as: J Chem Theory Comput. 2019 Apr 2;15(5):3288–3305. doi: 10.1021/acs.jctc.8b00955

Table 6.

Population (%) of native RNA A-form (including both A-major and A-minor states) and artificial intercalated structures as obtained in standard χ_OL3CP and with the suggested $gHBfix (\begin{matrix} 2 - OH \dots nbO / bO \\ - 0.5 \end{matrix}) (\begin{matrix} NH \dots N \\ + 1.0 \end{matrix})$ modification.

sequence	A-form		Intercalated
	χ_OL3CP	gHBfix	χ_OL3CP	gHBfix
r(CAAU)	<~2% ^a	~21% ^d	~50% ^a,b	~51% ^d
r(CCCC)	~20% ^b,c	~54% ^d	~56% ^b,c	~39% ^d
r(AAAA)	~21% ^a,b	~25% ^d	~23% ^a,b	~11% ^d
r(UUUU)	~4% ^a,b	~5% ^d	~18% ^b	~3% ^d

Ref.²⁷

Ref.³³

Ref.¹⁴

this study. Note that we used the implementation of modified vdW parameters of phosphates by Case et al.⁶³ including correction for the affected dihedrals (see Methods).