title: A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations.
abstract: A new method to account for long range electrostatic contributions is proposed and implemented for quantum mechanics/molecular mechanics long range electrostatic correction (QM/MM-LREC) calculations. This method involves the use of the minimum image convention under periodic boundary conditions and a new smoothing function for energies and forces at the cutoff boundary for the Coulomb interactions. Compared to conventional QM/MM calculations without long-range electrostatic corrections, the new method effectively includes effects on the MM environment in the primary image from its replicas in the neighborhood. QM/MM-LREC offers three useful features including the avoidance of calculations in reciprocal space (k-space), with the concomitant avoidance of having to reproduce (analytically or approximately) the QM charge density in k-space, and the straightforward availability of analytical Hessians. The new method is tested and compared with results from smooth particle mesh Ewald (PME) for three systems including a box of neat water, a double proton transfer reaction, and the geometry optimization of the critical point structures for the rate limiting step of the DNA dealkylase AlkB. As with other smoothing or shifting functions, relatively large cutoffs are necessary to achieve comparable accuracy with PME. For the double-proton transfer reaction, the use of a 22 Å cutoff shows a close reaction energy profile and geometries of stationary structures with QM/MM-LREC compared to conventional QM/MM with no truncation. Geometry optimization of stationary structures for the hydrogen abstraction step by AlkB shows some differences between QM/MM-LREC and the conventional QM/MM. These differences underscore the necessity of the inclusion of the long-range electrostatic contribution.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Fang
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Duke
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
authors.forename: G Andrés
authors.initials: GA
authors.lastname: Cisneros
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004735:Energy Transfer; D029968:Escherichia coli Proteins; D006859:Hydrogen / Q000737:chemistry*; D006899:Mixed Function Oxygenases; D011789:Quantum Theory; D055672:Static Electricity; D014867:Water / Q000737:chemistry*
chemical_list: D029968:Escherichia coli Proteins; D014867:Water; D006859:Hydrogen; D004247:DNA; D006899:Mixed Function Oxygenases; C466427:AlkB protein, E coli