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. Author manuscript; available in PMC: 2010 May 11.
Published in final edited form as: J Phys Chem B. 2008 Jan 16;112(5):1515–1524. doi: 10.1021/jp709827m

Figure 2.

Figure 2

Schematic representation of the protocol used for the calculation of intrastrand (a), interstrand (b), and overall (c) stacking interactions of a given base (e.g. S1-B2 in the present example). (a) Interaction energy of S1-B2 with S1-B1 and S1-B3 is the intrastrand interaction energy; (b) interaction energy of S1-B2 with S2-B1 and S2-B3 is the interstrand interaction energy and (c) the overall interaction energy of S1B2 is computed as the interaction between S1-B2, and S1-B1, S1-B3, S2-B1 & S2-B3.