Differences of nucleotide stacking patterns in a crystal and in binary complexes— the case of adenine

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Abstract
Calculations of the intermolecular interaction energy between stacked planar molecules show that, for this type of configuration, there is no well‐defined minimum. (The energy surface exhibits a rather large flat basin and not a deep, sharply defined, minimum.) As a consequence, the relative position of the molecules is very likely to change under environmental modifications, e.g., when the molecules become part of a crystal. Detailed calculations are carried out for the case of adenine and show that the experimental structure actually displays the lowest energy among all structures tried, although no binary configuration in the crystal is identical with that giving a minimum for a binary complex. On the contrary, for a column of stacked molecules, the minimum of the total interaction energy is still practically obtained when the successive stacked pairs of the column are in the binary minimum configuration. It is concluded that, for such configurations with a loosely defined minimum like stacking, crystal structure data may be used only with great caution for assigning a precise configuration to the binary complex.