. Author manuscript; available in PMC: 2010 Jun 24.

Published in final edited form as: J Am Chem Soc. 2009 Jun 24;131(24):8416–8424. doi: 10.1021/ja809543j

Table 1.

Occupancy of the Hydroxyl Group by the Hydrogen Bond Acceptors During Molecular Dynamics Simulations, and the Distances and Angles of the Corresponding Atoms in the Average Structure of the (R)-γ-Hydroxytrimethylene Cross-link.

potential hydrogen bond	occupancy of OH (%) ^a		distance (Å)	angle (°)
potential hydrogen bond	from A-DNA	from B-DNA	distance (Å)	angle (°)
Carbinol OH→C²⁰ O²	62	74	2.1	177
Carbinol OH→C²⁰ O4′	22	14	3.0	97
Carbinol OH→Y¹⁹ N3	2.7	1.7	3.2	103
Carbinol OH→C⁶ O²	1.0	0.70	3.6	93
Carbinol OH→solvent	0.20	0

The criteria for a hydrogen bond formation: distance ≤ 3.5 Å and angle ≥ 120°.