ArticleThe journal of physical chemistry. B2024
Thermodynamics of Metal-Acetate Interactions.
Article in The journal of physical chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- Parameterization of the PA Endonuclease Bimetallic Center Reveals the Dynamics of Clinically Relevant Mutations.Journal of chemical theory and computation · 2026Article
- Scalable mechanochemical synthesis of a cyclic dehydroalanine peptide.Organic & biomolecular chemistry · 2026Article
- An N-terminal amphipathic helix governs activity and conformational dynamics of Nramp metal transporters.bioRxiv : the preprint server for biology · 2026Article
- The locking mechanism of human TRPV6 inhibition by intracellular magnesium.Nature communications · 2025Article
- Simulating Metal Complex Formation and Ligand Exchange: Unraveling the Interplay between Entropy, Kinetics, and Mechanisms on the Chelate Effect.Journal of chemical theory and computation · 2025Article
- Recent Developments in Amber Biomolecular Simulations.Journal of chemical information and modeling · 2025Article
- Ion-Induced Dipole Interactions Matter in Metadynamics Simulation of Transition Metal Ion Transporters.Journal of chemical theory and computation · 2025Article
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- Molecular insights into substrate translocation in an elevator-type metal transporter.Nature communications · 2024Article
- Molecular insights into substrate translocation in an elevator-type metal transporter.bioRxiv : the preprint server for biology · 2024Article
- Simulating Metal-Imidazole Complexes.Journal of chemical theory and computation · 2024Article
- Binding of Phosphate Species to CaJournal of chemical theory and computation · 2024Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Metal ions play crucial roles in protein- and ligand-mediated interactions. They not only act as catalysts to facilitate biological processes but are also important as protein structural elements. Accurately predicting metal ion interactions in computational studies has always been a challenge, and various methods have been suggested to improve these interactions. One such method is the 12-6-4 Lennard-Jones (LJ)-type nonbonded model. Using this model, it has been possible to successfully reproduce the experimental properties of metal ions in aqueous solution. The model includes induced dipole interactions typically ignored in the standard 12-6 LJ nonbonded model. In this we expand the applicability of this model to metal ion-carboxylate interactions. Using 12-6-4 parameters that reproduce the solvation free energies of the metal ions leads to an overestimation of metal ion-acetate interactions, thus, prompting us to fine-tune the model to specifically handle the latter. We also show that the standard 12-6 LJ model significantly falls short in reproducing the experimental binding free energy between acetate and 11 metal ions (Ni(II), Mg(II), Cu(II), Zn(II), Co(II), Cu(I), Fe(II), Mn(II), Cd(II), Ca(II), and Ag(I)). In this study, we describe optimized C
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Registered trials
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.