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

Abstract

synopsisCalculations 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.

On the conformational varieties of adrenaline: the free molecule and the molecule in the crystal

“…Conceptionally the situation is thus analogous to that encountered in our previous study of the effect of the crystal environment on the stacking pattern of adenines (Caillet & Claverie, 1974): namely, the optimal geometry of the isolated subunit [binary complex in Caillet & Claverie (1974) or the free molecule in the present case] need not necessarily be identical to the optimal geometry in a crystal, corresponding to the interaction of such subunits. These examples stress the necessity of explicitly taking into account environmental factors in cases in which the experimental results are at variance with predictions referring to free molecules and show also the possibility of arriving at an agreement between the two aspects with the presently available methodologies and computational techniques.…”

“…The evaluation of lattice energies from simple intermolecular potential functions (involving essentially atom-atom terms) has been accomplished successfully in several recent works (Caillet & Claverie, 1974, 1975Momany, Carruthers, McGuire & Scheraga, 1974;Hagler, Huler & Lifson, 1974;Huler & Warshel, 1974;and references therein). A detailed description of our own method may be found in Caillet & Claverie (1975); thus we only recall here the main practical features in §2(a)-(d), and describe in §2(e) the modification applied for very short interatomic distances which was not described in Caillet & Claverie (1974, 1975.…”

“…A detailed description of our own method may be found in Caillet & Claverie (1975); thus we only recall here the main practical features in §2(a)-(d), and describe in §2(e) the modification applied for very short interatomic distances which was not described in Caillet & Claverie (1974, 1975.…”

“…The total lattice energy is calculated from these intermolecular potentials as indicated in Caillet & Claverie (1974, 1975.…”

“…We have employed the procedure for the evaluation of crystal lattice energies from intermolecular potential functions described by Caillet & Claverie (1974, 1975 and applied in these publications for a comparative study of relative configurations of neighbouring molecules in the crystal with the optimal configurations of isolated binary complexes.…”