Toward more efficient density‐based adaptive QM/MM methods

Abstract

Funding informationDeutsche Forschungsgemeinschaft (DFG).Adaptive QM/MM (quantum mechanical/molecular mechanical) methods repartition molecules on-the-fly into the QM and MM regions based on a partitioning criterion. A density-based partitioning scheme offers a unique way of carrying out QM and MM assignments on the presence/ absence of (non) covalent interactions between non-QM core molecules and the QM core. Here, we present two improvements to promote our density-based adaptive partitioning strategy for adaptive QM/MM calculations. First, bond formation/breaking processes between non-QM core molecules and the QM core are monitored using a density-based descriptor, to define an adaptive QM core region on the fly. Second, the density-based adaptive QM/MM partitioning scheme is made efficient enough for large systems by utilizating an adaptive search region and a Voronoi style-partitioning scheme. The adaptive search region is used to preselect the subset of molecules that may interact strongly enough with the QM core region, and then a density-based interaction calculation is only carried out on this subset. A Voronoi style-partitioning scheme achieves an efficient assignment of the density-based interactions. K E Y W O R D S adaptive multiscale modeling, density-based adaptive, noncovalent interactions, Voronoi partitioning 1 | I N T R O D U C T I O N Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow accurate calculations on large complex systems by describing the chemically most relevant (active) region with a high-level electronic structure method, while the remaining environment is modeled bylower-level methods. [1][2][3][4][5][6][7] The chemically relevant part is usually small, such as a solute, an enzyme's active site, [8,9] or a local defect in a material. [10] In traditional QM/MM methods, the contents of these regions are fixed and cannot change during a geometry optimization or molecular dynamics simulation. [11] This fixed composition of the two regions is not ideal for systems such as complex gas-phase reactive systems, solution processes, diffusion through liquid or solid, defect propagation, or reactions on catalytic surfaces such as nanoparticles.A number of so-called adaptive QM/MM schemes have been developed to effectively expand the research areas for traditional QM/ MM methodology. Adaptive methods allow atoms, or groups of atoms, to enter or leave the "active zone" which is typically centered on the QM core. [12][13][14][15][16][17][18][19][20][21][22][23][24][25] In adaptive schemes, the partitioning of the entire system into QM and MM regions is not rigid, and the molecules are continually being repartitioned into QM and MM subsystems. [26][27][28][29][30] The repartitioning of the QM and MM regions was initially accomplished by adopting a geometric criterion in the form of a distance cutoff, R QM . [14,[17][18][19][20][21] For each of the molecules in a given molecular system, assignment of QM versus MM character is determined by its distance from a predefined QM core r...

Yoink: An interaction‐based partitioning API

“…Second, a number‐based approach, which enables a pre‐determined integer number of molecules to surround the QM core. Third, our density‐based adaptive QM/MM (DBA‐QM/MM) partitioning, where the system is analyzed and partitioned based on interactions.…”

“…In the new DBA partitioning method, RDG is replaced by DORI and SEDD, which enabled the detection (presence or absence) of (non)‐covalent interactions in a system. In addition, the computationally expensive pairwise interaction analysis between each molecule and the QM core was discarded, and replaced with a Voronoi based scheme . Molecules having interactions with the QM core are located nearby the QM core, so there is no need to perform interaction analysis for the entire system.…”

“…F) QM and MM regions of the whole system. For more details, please see our recent publication . [Color figure can be viewed at http://wileyonlinelibrary.com]…”

“…Grid spacing and cube size can be adjusted. To address the computational efficiency of the intermolecular interaction calculation, Voronoi‐based partitioning was implemented to allocate the intermolecular region of any two molecules and assign the corresponding interaction result to them …”

“…Moreover, only the presence/absence of NCI was considered in the interaction‐based partitioning. In subsequent work, the interaction‐based partitioning approach was further developed to investigate large complex systems, and was adapted by replacing RDG with DORI and SEDD to be able to consider bond forming and bond breakage …”