ReviewJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2009
Recent developments of the quantum chemical cluster approach for modeling enzyme reactions.
Review in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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52 citing papers in PubMed.
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- Capturing Dichotomic Solvent Behavior in Solute-Solvent Reactions with Neural Network Potentials.Journal of chemical theory and computation · 2024Article
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- Nucleolar Essential Protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by molecular dynamics simulation and quantum mechanics study.Computational and structural biotechnology journal · 2023Article
- Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Role of water coordination at zinc binding site and its catalytic pathway of dizinc creatininase: insights from quantum cluster approach.Journal of computer-aided molecular design · 2022Article
- Theoretical Modeling of Redox Potentials of Biomolecules.Molecules (Basel, Switzerland) · 2022Review
- Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences.Topics in catalysis · 2022Article
- Ocean Acidification Amplifies the Olfactory Response to 2-Phenylethylamine: Altered Cue Reception as a Mechanistic Pathway?Journal of chemical ecology · 2021Article
- Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography.Acta crystallographica. Section D, Structural biology · 2021Review
- The Se-S Bond Formation in the Covalent Inhibition Mechanism of SARS-CoV-2 Main Protease by Ebselen-like Inhibitors: A Computational Study.International journal of molecular sciences · 2021Article
- Thermochemical and Quantum Descriptor Calculations for Gaining Insight into Ricin Toxin A (RTA) Inhibitors.ACS omega · 2021Article
- Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family.eLife · 2021Article
- First-Principles Calculations on Ni,Fe-Containing Carbon Monoxide Dehydrogenases Reveal Key Stereoelectronic Features for Binding and Release of COInorganic chemistry · 2021Article
- What Does the Brønsted Slope Measure in the Phosphoryl Transfer Transition State?ACS catalysis · 2020Article
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Abstract
The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.
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