ArticleJournal of chemical information and modeling2022
QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Quantum Pharmacophore-Based Virtual Screening Enables Prospective Discovery of Chemotype-Diverse Dengue NS5 Inhibitors.Journal of chemical information and modeling · 2026Article
- Article
- Exploring the Reaction Mechanism of Polyethylene Terephthalate Biodegradation through QM/MM Approach.The journal of physical chemistry. B · 2024Article
- Explainable chemical artificial intelligence from accurate machine learning of real-space chemical descriptors.Nature communications · 2024Article
- Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis.Journal of chemical information and modeling · 2023Article
- The IQA Energy Partition in a Drug Design Setting: A Hepatitis C Virus RNA-Dependent RNA Polymerase (NS5B) Case Study.Pharmaceuticals (Basel, Switzerland) · 2022Article
- A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems.Molecules (Basel, Switzerland) · 2022Article
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Authors and funding
5 authors.
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Abstract
The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal-water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)- and Mg(II)-water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM-PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology.
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