The complementary “lock and key” patterns of weakly
interacting molecules are explored by mapping the
topography of respective molecular electrostatic potentials (MESP).
A new model, viz., electrostatic potential
for intermolecular complexation (EPIC), which incorporates such MESP
features, has been employed for
studying interactions between DNA base pairs. A wide variety of
pairs of bases involving adenine (A),
guanine (G), and cytosine (C) are chosen as test cases. The
interaction energy within the EPIC model is
expressed as
(1/2){∑V
A,
i
q
B,
i
+
∑V
B,
i
q
A,
i
},
where V
A,
i
is the MESP
value due to A at the ith atom of molecule
B and q
B,
i
is the
MESP-derived charge at this site. The interaction energies and
geometrical parameters
obtained by this model agree remarkably well with the corresponding
literature values obtained by full geometry
optimization at the ab initio level. Being intuitively appealing
and simple in application, the EPIC model
seems to have the potential of being a good predictive tool for
investigating weak intermolecular interactions.
Triplexes involving major groove binding of a third oligomer to
the DNA duplex structure have gathered
much interest in recent years. The study of base trimer
interactions in the gas phase is expected to provide
useful information regarding orientational preferences and inherent
stabilities. A recently developed electrostatic
potential for intermolecular complexation (EPIC) model has been found
to be quite useful for exploring the
structures and energetics in base pairs [Gadre, S. R.; Pundlik, S. S.
J. Phys. Chem.
1996, 101, 3298].
This
model makes use of complementary electrostatic features of the
interacting species that are determined by ab
initio theory. We report here the investigations on various
trimers including TAT, TAG, ATG, CGG, and
TCG using this model. The overall good agreement of the trimer
interaction energies with the corresponding
single-point SCF values made at the model-predicted geometries reveals
the suitability of the EPIC model
for studying DNA base complexes.
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