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. Author manuscript; available in PMC: 2013 Jan 10.
Published in final edited form as: J Chem Theory Comput. 2011 Dec 8;8(1):335–347. doi: 10.1021/ct200712b

Figure 6.

Figure 6

A symbolic flowchart describing the complete sequence of computations. The numbered steps, denoted by arrows, are as follows: (1) extraction of model systems (numerals in parentheses in the second row of boxes denote the number of systems); (2) M06/6-31+G(d,p) and subsequent TPSS-D/LP constrained geometrical optimizations; (3) calculation of RI-MP2/CBS single-point energies; (4) removal of the sugar-phosphate backbone segment followed by attachment of terminal methyl groups to N1/N9 of pyrimidines/purines; (5) relaxation of methyl groups at the M06/6-31+G(d,p) level of theory; (6) location of H-bonds via AIM analysis; (7) evaluation of DF-MP2/aug-cc-pVDZ base…base interaction energies; (8) manual attachment of nucleobases to optimized idealized rSPSOMs and inspection of mutual compatibility to form a dinucleotide platform submotif; and (9) assignment of backbone conformational class. The experimental structures out of which idealized rSPSOMs were derived are listed in the footnote of Table 1.