Development of novel schemes for treating subsystem boundaries and electrostatic potentials in simulations of complex systems

Abstract

Fragmentation schemes provide a powerful strategy for calculating the potential energy surfaces of complex systems. The combined quantum mechanical and molecular mechanical (QM/MM) method, the electrostatically embedded many-body (EE-MB) method, and the molecular tailoring approach (MTA) are three examples. Two critical issues to be addressed in these methods are the treatment of the boundary between the subsystems when it passes between bonded atoms and the inclusion of the electrostatic potential of one subsystem in the Hamiltonian of another. This thesis involves the development and application of new schemes to treat both issues. The first part focuses on the development of a tuned pseudoatom scheme with a balanced redistributed charge algorithm to accurately model the QM-MM boundary that passes through a covalent bond, especially a polar covalent bond. Various redistribution schemes and ways of tuning the boundary treatments are tested and compared for the QM/MM method and the EE-MTA method. The second part of this thesis involves the development of screened charge models to include charge penetration and screening effects in generating electrostatic potentials for use in various methods, including QM/MM and EE-MB methods. The screened charge models are also used to derive partial atomic charges by fitting electrostatic potentials.