ArticleFrontiers in chemistry2018
On the Difference Between Additive and Subtractive QM/MM Calculations.
Article in Frontiers in chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- Reproducibility of QM/MM Calculations for the SARS-CoV-2 Main Protease.Journal of chemical theory and computation · 2025Article
- Predicting Reduction Potentials of Blue Copper Proteins Using Quantum Mechanical Calculations.Inorganic chemistry · 2025Article
- On electrostatic interactions of adenosine triphosphate-insulin-degrading enzyme revealed by quantum mechanics/molecular mechanics and molecular dynamics.Quantitative biology (Beijing, China) · 2024Article
- Article
- Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM.Inorganic chemistry · 2024Article
- Review
- Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of SScientific reports · 2024Article
- Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.Chemical reviews · 2024Review
- Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces.The journal of physical chemistry. C, Nanomaterials and interfaces · 2023Article
- Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6).ACS chemical biology · 2023Article
- Histidine oxidation in lytic polysaccharide monooxygenase.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic 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
- Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase.Molecules (Basel, Switzerland) · 2022Article
- Perspective on the Current State-of-the-Art of Quantum Computing for Drug Discovery Applications.Journal of chemical theory and computation · 2022Review
- QM/MM Study of Partial Dissociation of S2B for the EInorganic chemistry · 2022Article
- Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents.Journal of chemical theory and computation · 2022Article
- Benchmark Study of Redox Potential Calculations for Iron-Sulfur Clusters in Proteins.Inorganic chemistry · 2022Article
- Can Water Act as a Nucleophile in CO Oxidation Catalysed by Mo/Cu CO-Dehydrogenase? Answers from Theory.Chemphyschem : a European journal of chemical physics and physical chemistry · 2022Article
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2 authors.
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Abstract
The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding. In this article, we clarify the similarities and differences of the two approaches. We show that inherently, the two approaches should be identical and in practice require the same sets of parameters. However, the subtractive scheme provides an opportunity to correct errors introduced by the truncation of the QM system, i.e., the link atoms, but such corrections require additional MM parameters for the QM system. We describe and test three types of link-atom correction, viz. for van der Waals, electrostatic, and bonded interactions. The calculations show that electrostatic and bonded link-atom corrections often give rise to problems in the geometries and energies. The van der Waals link-atom corrections are quite small and give results similar to a pure additive QM/MM scheme. Therefore, both approaches can be recommended.
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