. 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 12.

Dihedral angles and pucker (in °) of Z-DNA, Na⁺ -net neutral simulations in TIP3P, reference values (the first item on each line) and median simulation values (the 220–250 ns period). Both ZI and ZII substates are listed where relevant. Numbers in parentheses indicate occupation time of given substate. Terminal residues are not considered. See Figure S7 (supporting information) for the values obtained for the individual nucleotides. Note that the simulations are mixing ZI-like and ZII-like values for different dihedrals (see the text).

Dihedral	Cytosine nucleotides
	reference	ff99	bsc0	bsc0χ_OL3	bsc0χ_OL4
α^a	210 / 169	254	218	190	199
β	233 / 162	225(8%) / 164(92%)	225(25%) / 169(75%)	191^a	194^a
γ^a	54 / 44^a	44	55	59	59
δ	144	134	133	121	128
ε	264	272	274	282	279
ζ	76	69	70	76	74
χ	205	198	199	195	193
P	155	141	139	126	134

Dihedral	Guanine nucleotides
	reference	ff99	bsc0	bsc0χ_OL3	bsc0χ_OL4
α	66	71	87	186	161
β	186	186	185	176	175
γ	179	182	166	80	106
δ	95	104	100	132	103
ε^a	242 / 187	277	257	205	224
ζ	292 / 63	305(88%) / 50(12%)	304(86%) / 50(14%)	300^a	305(94%) / 41(6%)
χ	60.7	57	60	104	70
P	30~90	38	42	141	77

Distinct ZI / ZII values were not stabilized in simulations. The dihedral fluctuates wildly.

ZII value of γ dihedral was observed for ff99 and ZI value for bsc0, bsc0χ_OL3 and bsc0χ_OL4.