ArticleThe journal of physical chemistry. B2016
Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 152 citations in OpenAlex.
- Are QM/MM models systematically improvable? A case study on carbonic anhydrase binding affinities.Journal of computer-aided molecular design · 2026Article
- Systematically Improvable and Locality Accelerated Enzymatic Reactivity Modeling: Toward Chemical Accuracy at Affordable Cost.Journal of chemical theory and computation · 2026Article
- Uncertainty Quantification forChemical reviews · 2026Review
- Quantum medicine: A quantum-mechanical framework for redox biology, disease and precision medicine.Clinical and translational medicine · 2026Review
- Computational approaches to enzymatic reaction assignment: a review of methods, validations, and future directions.Briefings in bioinformatics · 2025Review
- Mechanistic Insights into SAM-Dependent Methyltransferases: A Review of Computational Approaches.International journal of molecular sciences · 2025Review
- Challenges and Advances in the Simulation of Targeted Covalent Inhibitors Using Quantum Computing.The journal of physical chemistry letters · 2025Review
- Adaptive Restraints to Accelerate Geometry Optimizations of Large Biomolecular Systems.Journal of computational chemistry · 2025Article
- The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems.Journal of computational chemistry · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Exploring the Reaction Mechanism of Polyethylene Terephthalate Biodegradation through QM/MM Approach.The journal of physical chemistry. B · 2024Article
- Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.Chemical reviews · 2024Review
- CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods.Journal of chemical theory and computation · 2024Article
- Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations.The Journal of chemical physics · 2024Article
- Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase.ACS catalysis · 2023Article
- Unraveling the Pivotal Roles of Various Metal Ion Centers in the Catalysis of Quercetin 2,4-Dioxygenases.Molecules (Basel, Switzerland) · 2023Article
- High-throughput computational investigation of protein electrostatics and cavity for SAM-dependent methyltransferases.Protein science : a publication of the Protein Society · 2023Article
- Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.Annual review of biophysics · 2023Review
- Insights into the Degradation of Polymer-Drug Conjugates by an Overexpressed Enzyme in Cancer Cells.Journal of medicinal chemistry · 2023Article
- Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis.Journal of chemical information and modeling · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Although QM/MM calculations are the primary current tool for modeling enzymatic reactions, the reliability of such calculations can be limited by the size of the QM region. Thus, we examine in this work the dependence of QM/MM calculations on the size of the QM region, using the reaction of catechol-O-methyl transferase (COMT) as a test case. Our study focuses on the effect of adding residues to the QM region on the activation free energy, obtained with extensive QM/MM sampling. It is found that the sensitivity of the activation barrier to the size of the QM is rather limited, while the dependence of the reaction free energy is somewhat larger. Of course, the results depend on the inclusion of the first solvation shell in the QM regions. For example, the inclusion of the Mg(2+) ion can change the activation barrier due to charge transfer effects. However, such effects can easily be included in semiempirical approaches by proper parametrization. Overall, we establish that QM/MM calculations of activation barriers of enzymatic reactions are not highly sensitive to the size of the QM region, beyond the immediate region that describes the reacting atoms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.