Implementation and Application of QM/MM Hybrid Methods

• Main Author: Sauer, Susanne
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: 2021
• Subjects: Quantenmechanik; Molekularmechanik; ddc:540; Orca
• Online Access: https://opus.bibliothek.uni-wuerzburg.de/frontdoor/index/index/docId/24321; https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-243213; https://doi.org/10.25972/OPUS-24321; https://opus.bibliothek.uni-wuerzburg.de/files/24321/Sauer_Susanne_QMMM.pdf

Within this work, an additive and a subtractive QM/MM interface were implemented into CAST. The interactions between QM and MM system are described via electrostatic embedding. Link atoms are used to saturate dangling bonds originating from the separation of QM and MM system. Available energy evaluation methods to be combined include force fields (OPLSAA and AMBER), semi-empirical programs (Mopac and DFTB+), and quantum-chemical methods (from Gaussian, Orca, and Psi4). Both the additive and the subtractive interface can deal with periodic boundary conditions. The subtractive scheme was extended to enable QM/QM, three-layer, and multi-center calculations. Another feature only available within the subtractive interface is the microiteration procedure for local optimizations. The novel QM/MM methods were applied to the investigation of the reaction path for the complex formation between rhodesain and K11777. Benchmark calculations show a very good agreement with results from Gaussian-ONIOM. When comparing the relative energies obtained with different options to a computation where the whole system was treated with the “QM method” DFTB3, the electrostatic embedding scheme with option “delM3” gives the best results. “delM3” means that atoms with up to three bonds distance to the QM region are ignored when creating the external charges. This is done in order to avoid a double counting of Coulomb interactions between QM and MM system. The embedding scheme for the inner system in a three-layer calculation, however, does not have a significant influence on the energies. The same is true for the choice of the coupling scheme: Whether the additive or the subtractive QM/MM interface is applied does not alter the results significantly. The choice of the QM region, though, proved to be an important factor. As can be seen from the comparison of two QM systems of different size, bigger is not always better here. Instead, one has to make sure not to separate important (polar) interactions by the QM/MM border. After this ...