Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

摘要: We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios hairpin ribozyme by evaluating potential and free energy surfaces reactions various hybrid QM/MM methods. The is a unique RNA that achieves rate acceleration similar other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) adenine 38 (A38) been identified as catalytically essential nucleobases. However, their exact roles are still being investigated. In line with available experimental data, we considered two reaction involving protonated A38H+ general acid which further assisted either canonical G8 or deprotonated G8– forms. used spin-component scaled Moller–Plesset (SCS-MP2) method at complete basis set limit reference method. semiempirical AM1/d-PhoT SCC-DFTBPR methods...