Accurate ab initio study on the hydrogenbond pairs in protein secondary structures

Abstract: Ab initio calculations up to the MP2/aug-cc-pVQZ//MP2/6-311+G* * level have been carried out to characterize the four patterns of hydrogen-bond (H-bond) pairs in protein secondary structures. The unblocked and methyl-blocked glycine dipeptide dimers were arranged to model the H-bond pairs in R-helix (RHH) and antiparallel (Aââ-C5 and Aââ-C7) and parallel â-sheet (Pââ) secondary structures. The study uncovers that, in addition to the primary COâââNH H-bonds and the crossing secondary interactions, the CHâââOC H-bonds and the tertiary effect (as we call it) also contribute substantially. The tertiary effect is due to the interpolarization between the donor and acceptor of a H-bond. This effect, which enhances the dipole-dipole interactions between two nearby H-bonds, stabilizes the â-sheet-like but destabilizes the helix-like H-bond pairs. The MP2 binding energies of the complexes were further refined by extrapolating to the complete basis set limit (CBS) according to Truhlar and co-workers and by a three-basis-set-based method. The best extrapolated CBS(aD-aT-aQ) binding energies of the unblocked dimers are-13.1 (RHH),-11.3 (Aââ-C5),-19.2 (Aââ-C7), and-14.8 kcal/mol (Pââ). For the methyl-blocked counterparts, the best extrapolated CBS(D-T-Q) binding energies are-14.8,-13.4,-20.8, and-16.7 kcal/mol, respectively. The interactions in the parallel â conformations are very close to the averages of the C5 and C7 antiparallel â conformations, and both are stronge