Abstract
Combined quantum mechanical and molecular mechanical (QM/MM) methods are the most powerful available methods for high-level treatments of subsystems of very large systems. The treatment of the QM−MM boundary strongly affects the accuracy of QM/MM calculations. For QM/MM calculations having covalent bonds cut by the QM−MM boundary, it has been proposed previously to use a scheme with system-specific tuned fluorine link atoms. Here, we propose a broadly parametrized scheme where the parameters of the tuned F link atoms depend only on the type of bond being cut. In the proposed new scheme, the F link atom is tuned for systems with a certain type of cut bond at the QM−MM boundary instead of for a specific target system, and the resulting link atoms are call bond-tuned link atoms. In principle, the bond-tuned link atoms can be as convenient as the popular H link atoms, and they are especially well adapted for high-throughput and accurate QM/MM calculations. Here, we present the parameters for several kinds of cut bonds along with a set of validation calculations that confirm that the proposed bond-tuned link-atom scheme can be as accurate as the system-specific tuned F link-atom scheme.
Highlights
The combined quantum mechanical and molecular mechanical (QM/MM) method is well established for molecular simulations of large and complex chemical systems that are too big to be treated accurately by full QM methods [1,2,3,4,5,6]
The treatment of the QM−MM boundary is a challenging issue within the framework of QM/MM, especially when the boundary between the QM fragment and the MM surroundings passes through a covalent bond, which is unavoidable in treating enzymes and metal-organic frameworks (MOFs)
A QM/MM calculation proceeds by dividing the entire system (ES) into two parts: a subsystem that will be treated by QM and a subsystem that will be treated by MM
Summary
The combined quantum mechanical and molecular mechanical (QM/MM) method is well established for molecular simulations of large and complex chemical systems that are too big to be treated accurately by full QM methods [1,2,3,4,5,6]. Examples include catalytic systems where one needs to include effects beyond the active site and QM/MM methods have been widely applied to both enzyme kinetics [5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22] and metal-organic frameworks (MOFs) [23,24,25,26,27,28,29,30,31]. A number of approaches have been proposed to cap the dangling bonds of the QM subsystem, such as a link atom or pseudoatom [32,33,34,35,36,37,38,39,40,41,42,43,44,45], or localized or generalized hybrid orbitals [46,47,48,49].
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