ArticleJournal of computational chemistry2015
Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.
Article in Journal of computational chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- ABEEM/MM Magnesium Force Field for Proteins and Aqueous Solutions.Interdisciplinary sciences, computational life sciences · 2026Article
- Single-engineered-residue solvation perturbations regulate global protein architecture and function.Nature communications · 2026Article
- A Transferable Force Field for Simulating Adsorption in Metal-Organic Frameworks with Open Metal Sites Based on the 12-6-4 Lennard-Jones Potential.Journal of chemical information and modeling · 2026Article
- Force fields matter in DNA polProtein science : a publication of the Protein Society · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems.Journal of chemical theory and computation · 2025Article
- Surface-Accelerated String Method for Locating Minimum Free Energy Paths.Journal of chemical theory and computation · 2024Article
- Molecular View on theJournal of chemical information and modeling · 2023Article
- Molecular basis of MgNature communications · 2023Article
- The effect of MgThe FEBS journal · 2022Article
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- Article
- Systematic Evaluation of Ion Diffusion and Water Exchange.Journal of chemical theory and computation · 2022Article
- Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence.Molecules (Basel, Switzerland) · 2022Article
- Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.Journal of chemical theory and computation · 2022Article
- Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis.ACS catalysis · 2021Article
- Extension of the Variational Free Energy Profile and Multistate Bennett Acceptance Ratio Methods for High-Dimensional Potential of Mean Force Profile Analysis.The journal of physical chemistry. A · 2021Article
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3 authors.
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Abstract
The prevalence of Mg(2+) ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg(2+) ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion-centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg(2+) model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion-water and ion-solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single-site Mg(2+) ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12-6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg(2+) ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next-generation models that target specific binding sites in biomolecules.
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