ArticleThe journal of physical chemistry. B2015
Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed.
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- Engineered MgO Nanoparticles with Tunable Electronic Signatures for Energy Applications.ACS omega · 2026Article
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- Parametrization of Zirconium for DFTB3/3OB: A Pathway to Study Complex Zr-Compounds for Biomedical and Material Science Applications.Journal of computational chemistry · 2025Article
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- Comparative Study of UMCM-9 Polymorphs: Structural, Dynamic, and Hydrogen Storage Properties via Atomistic Simulations.The journal of physical chemistry. C, Nanomaterials and interfaces · 2025Article
- Tight Binding Simulation of the MgO and Mg(OH)Journal of chemical theory and computation · 2025Article
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- Hybrid Materials Based on Carbon Nanotubes and Tetra- and Octa-Halogen-Substituted Zinc Phthalocyanines: Sensor Response Toward Ammonia from the Quantum-Chemical Point of View.Sensors (Basel, Switzerland) · 2024Article
- Polarity profiling of porous architectures: solvatochromic dye encapsulation in metal-organic frameworks.Journal of materials chemistry. C · 2024Article
- Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure HJournal of chemical theory and computation · 2024Article
- Flexibility of Binding Site is Essential to the CaJournal of the American Chemical Society · 2024Article
- Conformational Changes and ATP Hydrolysis in Zika Helicase: The Molecular Basis of a Biomolecular Motor Unveiled by Multiscale Simulations.Journal of the American Chemical Society · 2023Article
- Storage and Diffusion of Carbon Dioxide in the Metal Organic Framework MOF-5─A Semi-empirical Molecular Dynamics Study.The journal of physical chemistry. B · 2023Article
- Accurate and Efficient Multilevel Free Energy Simulations with Neural Network-Assisted Enhanced Sampling.Journal of chemical theory and computation · 2023Article
11 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
We report the parametrization of the approximate density functional theory, DFTB3, for magnesium and zinc for chemical and biological applications. The parametrization strategy follows that established in previous work that parametrized several key main group elements (O, N, C, H, P, and S). This 3OB set of parameters can thus be used to study many chemical and biochemical systems. The parameters are benchmarked using both gas-phase and condensed-phase systems. The gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization (MIO). The results indicate that DFTB3/3OB is particularly successful at predicting structures, including rather complex dinuclear metalloenzyme active sites, while being semiquantitative (with a typical mean absolute deviation (MAD) of ∼3-5 kcal/mol) for energetics. Single-point calculations with high-level quantum mechanics (QM) methods generally lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic properties. DFTB3/MM simulations for solution and two enzyme systems also lead to encouraging structural and energetic properties in comparison to available experimental data. The remaining limitations of DFTB3, such as the treatment of interaction between metal ions and highly charged/polarizable ligands, are also discussed.
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