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1. EE-ONIOM-CT Method to Efficiently Account for the Missing Interactions in ONIOM: Energies and Analytic Gradients

   https://doi.org/10.1021/acs.jctc.3c00497  

   Tripathy, Vikrant; Raghavachari, Krishnan (September 2023, Journal of Chemical Theory and Computation)
2. Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study

   https://doi.org/10.1002/jcc.25528  

   Jayasinghe‐Arachchige, Vindi M.; Hu, Qiaoyu; Sharma, Gaurav; Paul, Thomas J.; Lundberg, Marcus; Quinonero, David; Parac‐Vogt, Tatjana N.; Prabhakar, Rajeev (September 2018, Journal of Computational Chemistry)

   In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH)(PW₁₁O₃₉)]⁴⁻(ZrK) have been investigated using the hybrid two‐layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392‐Glu393 site of HSA is predicted to occur in the rate‐limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392‐Glu393, Ala257‐Asp258, Lys313‐Asp314, and Arg114‐Leu115) for the hydrolysis of all four sites of HSA. © 2018 Wiley Periodicals, Inc. 

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3. Weighted-Graph-Theoretic Methods for Many-Body Corrections within ONIOM: Smooth AIMD and the Role of High-Order Many-Body Terms

   https://doi.org/10.1021/acs.jctc.0c01287  

   Zhang, Juncheng Harry; Ricard, Timothy C.; Haycraft, Cody; Iyengar, Srinivasan S. (May 2021, Journal of Chemical Theory and Computation)
4. Reformulation of All ONIOM-Type Molecular Fragmentation Approaches and Many-Body Theories Using Graph-Theory-Based Projection Operators: Applications to Dynamics, Molecular Potential Surfaces, Machine Learning, and Quantum Computing

   https://doi.org/10.1021/acs.jpca.3c05630  

   Iyengar, Srinivasan S.; Ricard, Timothy C.; Zhu, Xiao (January 2024, The Journal of Physical Chemistry A)

   We present a graph-theory-based reformulation of all ONIOM-based molecular fragmentation methods. We discuss applications to (a) accurate post-Hartree–Fock AIMD that can be conducted at DFT cost for medium-sized systems, (b) hybrid DFT condensed-phase studies at the cost of pure density functionals, (c) reduced cost on-the-fly large basis gas-phase AIMD and condensed-phase studies, (d) post-Hartree–Fock-level potential surfaces at DFT cost to obtain quantum nuclear effects, and (e) novel transfer machine learning protocols derived from these measures. Additionally, in previous work, the unifying strategy discussed here has been used to construct new quantum computing algorithms. Thus, we conclude that this reformulation is robust and accurate. 

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