Isomers of the uracil dimer: an ab initio benchmark study

Jann A Frey, Andreas Müller, Martin Losada, Samuel Leutwyler
Journal of Physical Chemistry. B 2007 April 5, 111 (13): 3534-42
Benchmark ab initio calculations at the correlated level are reported for ten isomers of the uracil dimer (U.U): six are doubly N-H...O hydrogen bonded, three have a C-H...O and an N-H...O hydrogen bond, and one is doubly C-H...O hydrogen bonded. Their structures were optimized at the correlated level by using second-order Møller-Plesset perturbation theory (MP2), resolution of identity MP2 (RIMP2), and the binding energies D(e) calculated with the coupled-cluster method with singles, doubles, and iterative triples, CCSD(T). The MP2 and RIMP2 binding energies D(e) are extrapolated to the complete basis set (CBS) limit, using the aug-cc-pVXZ (X = D, T, Q) basis sets, giving binding energies accurate to +/-0.07 kcal/mol. With one exception, the correlation energy contributions at the CCSD(T) level increase the binding energies, although the changes are small, +0.03 to -0.27 kcal/mol (or 0.1% to 2.2%). The most stable isomer is the doubly N1-H...O hydrogen-bonded HB4 form, with D(e)[CCSD(T)]= -19.04 kcal/mol. The biologically relevant HB2 dimer has D(e)[CCSD(T)] = -12.64 kcal/mol, and the HB5 dimer that constitutes the main structural motif of the uracil crystal has -13.20 kcal/mol. The "Calcutta" dimer, which occurs in an RNA hexamer, is among the weakest isomers, with D(e)[CCSD(T)] = -9.81 kcal/mol. We compare to the binding energies calculated with the B3LYP, PBE, and PW91 density functionals; the PW91/6-311++G(d,p) binding energies agree with the CBS benchmark values, to within <2%. A useful single-molecule descriptor for the strengths of the individual hydrogen bonds can be derived from the gas-phase acidity DeltaE(0)(A-H) of the N-H or C-H donor groups and the gas-phase proton affinity PA(0)(B) of the C=O groups of the uracil monomer. The calculated hydrogen bond energies D(e)(infinity) correlate well with the difference between gas-phase acidity and basicity, DeltaE(0)(A-H) - PA(0)(B).

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