A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.

摘要: Abstract A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229–234). metal⋯metal distances are significantly shorter (~ 0.5 A) in QM/MM model than structure. As result, argentophilic interactions feasible between silver(I) ions neighboring metal-mediated Using computationally determined distances, re-refined solution obtained. In this new structure, all constraints remain fulfilled. shows less deviation from regular B-type conformation one. This investigation that application generate additional be used during structural refinements represents an elegant approach obtaining high-resolution structures.