Several recent developments in the area of QM/MM simulations of biological systems will be discussed. First, with SCC-DFTB as the QM level, we discuss a new QM/MM Hamiltonian that avoids the over-polarization of the QM region and better describes short-range interactions between QM and MM atoms. The impact of this development on the description of reactions involving highly charged systems will be illustrated with the study of phosphate mono-ester hydrolysis in solution and the alkaline phosphatase superfamily. Second, we discuss the treatment of boundary potential in QM/MM simulations of biomolecules. In particular, we critically evaluate the performance of the generalized boundary solvent potential (GSBP) and its variant, the solvated macromolecular boundary potential (SMBP) approaches by comparing the results to those from periodic boundary condition simulations for processes that change the net charge of the system. Potential caveats and solutions will be discussed using several solution and protein examples. Finally, if time permits, we will also describe progress in integrating SCC-DFTB/MM and higher-level QM/MM simulations for efficiently computing free energies for condensed phase reactions.

Recent developments and applications of QM/MM methods with SCC-DFTB and ab initio QM methods

244th National Meeting (2012)

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