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QMMM References

QM/MM References

It is worth citing some papers dealing with the QM/MM method 123, its implementation in NWChem4567 and some more recent discussions of the QM/MM parameters89

References

  1. Warshel, A.; Levitt, M. Theoretical Studies of Enzymic Reactions: Dielectric, Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme. Journal of Molecular Biology 1976, 103 (2), 227–249. https://doi.org/10.1016/0022-2836(76)90311-9. ↩

  2. Zhang, Y.; Lee, T.-S.; Yang, W. A Pseudobond Approach to Combining Quantum Mechanical and Molecular Mechanical Methods. The Journal of Chemical Physics 1999, 110 (1), 46–54. https://doi.org/10.1063/1.478083. ↩

  3. Lin, H.; Truhlar, D. G. Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations. The Journal of Physical Chemistry A 2005, 109 (17), 3991–4004. https://doi.org/10.1021/jp0446332. ↩

  4. Valiev, M.; Kowalski, K. Hybrid Coupled Cluster and Molecular Dynamics Approach: Application to the Excitation Spectrum of Cytosine in the Native DNA Environment. The Journal of Chemical Physics 2006, 125 (21), 211101. https://doi.org/10.1063/1.2403847. ↩

  5. Valiev, M.; Garrett, B. C.; Tsai, M.-K.; Kowalski, K.; Kathmann, S. M.; Schenter, G. K.; Dupuis, M. Hybrid Approach for Free Energy Calculations with High-Level Methods: Application to the SN2 Reaction of CHCl3 and OH− in Water. The Journal of Chemical Physics 2007, 127 (5), 051102. https://doi.org/10.1063/1.2768343. ↩

  6. Fan, P.-D.; Valiev, M.; Kowalski, K. Large-Scale Parallel Calculations with Combined Coupled Cluster and Molecular Mechanics Formalism: Excitation Energies of Zinc–Porphyrin in Aqueous Solution. Chemical Physics Letters 2008, 458 (1), 205–209. https://doi.org/10.1016/j.cplett.2008.04.071. ↩

  7. Valiev, M.; Bylaska, E. J.; Dupuis, M.; Tratnyek, P. G. Combined Quantum Mechanical and Molecular Mechanics Studies of the Electron-Transfer Reactions Involving Carbon Tetrachloride in Solution. The Journal of Physical Chemistry A 2008, 112 (12), 2713–2720. https://doi.org/10.1021/jp7104709. ↩

  8. Giudetti, G.; Polyakov, I.; Grigorenko, B. L.; Faraji, S.; Nemukhin, A. V.; Krylov, A. I. How Reproducible Are QM/MM Simulations? Lessons from Computational Studies of the Covalent Inhibition of the SARS-CoV-2 Main Protease by Carmofur. Journal of Chemical Theory and Computation 2022, 18 (8), 5056–5067. https://doi.org/10.1021/acs.jctc.2c00286. ↩

  9. Zlobin, A.; Belyaeva, J.; Golovin, A. Challenges in Protein QM/MM Simulations with Intra-Backbone Link Atoms. Journal of Chemical Information and Modeling 2023, 63. https://doi.org/10.1021/acs.jcim.2c01071. ↩