. Author manuscript; available in PMC: 2013 Jul 10.

Published in final edited form as: J Chem Theory Comput. 2012 Jun 5;8(7):2506–2520. doi: 10.1021/ct300275s

Table 5.

Populations (in %) of different α/γ syn nucleotides combinations of antiparallel G-DNA stem in Na⁺ -net neutral simulations in TIP3P (the 50–100 ns period). The canonical α(−)/γ(+) combination is not in agreement with the experiment. G9 and 21 should be α(+)/γ(t) and the remaining nucleotides are compatible with both α(+)/γ(−) and α(−)/γ(−).

α/γ combinations of syn nucleotides	nucleotides	α(−)/γ(+)	α(+)/γ(−)	α(+)/γ(t)	α(−)/γ(−)

x-ray		---	G3, 15, 23	G9, 21	G11
ff99	G3	92	3	0	0
	G9	0	0	100	0
	G11	97	0	0	1
	G15	93	1	0	5
	G21	0	0	100	0
	G23	84	4	0	7

bsc0	G3	100	0	0	0
	G9	41	0	59	0
	G11	100	0	0	0
	G15	100	0	0	0
	G21	1	0	99	0
	G23	100	0	0	0

bsc0χ_OL3	G3	100	0	0	0
	G9	18	0	82	0
	G11	52	17	0	30
	G15	69	25	0	6
	G21	14	0	86	0
	G23	36	35	0	29

bsc0χ_OL4	G3	34	41	0	25
	G9	0	0	100	0
	G11	36	36	0	27
	G15	55	27	0	19
	G21	49	0	51	0
	G23	21	55	0	24