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NMR and computational studies of ammonium ion binding to dibenzo-18-crown-6

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Abstract

Dibenzo-18-crown-6 (DB18C6) is a single-crown ether that can act as a host for a guest ion. In an effort to illuminate the relationships among structure, dynamics, and thermodynamics of ligand binding in a simple model for understanding the affinity and specificity of ligand interactions, nuclear magnetic resonance (NMR) experiments and density functional theory (DFT) were used to study the interaction of DB18C6 with ammonium ion. 1H-NMR was used to follow the titration of DB18C6 with ammonium chloride in deuterated methanol, a solvent chosen for its amphipathic character. Ammonium ion binds strongly to DB18C6 with a dissociation equilibrium constant at least as low as ~ \({10}^{-6}\) M. DFT calculations were used to identify optimized conformations of bound and free DB18C6 and to estimate its binding energy with ammonium ion in implicit solvent. An approach is described that accounts for geometry relaxation in addition to solvation correction and basis set superposition error; to our knowledge, this is the first such report that includes the energy difference from optimizing species geometry. The lowest-energy conformer of free DB18C6 in implicit methanol acquires an open, W-shaped structure that is also the lowest-energy conformer found for the DB18C6-ammonium ion complex. These results form a foundation for further studies of this system by molecular dynamics simulations.

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The data generated and/or analyzed during this study are available from the corresponding authors on request.

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Funding

B. M. and D. R acknowledge access to modeling facilities supported by the Czech research infrastructure for systems biology C4SYS (project no. LM2015055) and computational resources provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the program “Projects of Large Research, Development, and Innovations Infrastructures.” This work was carried out when B. S. was an undergraduate research participant in an NSF REU Training Site in Molecular Biophysics supported by awards DBI13-58737 and DBI16-59726 to J.C.

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Author notes

  1. Brielle Shope and D. Brandon Magers contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry, Taylor University, Upland, IN, 46989, USA

    Brielle Shope & D. Brandon Magers

  2. Department of Chemistry and Physics, Belhaven University, Jackson, MS, 39202, USA

    D. Brandon Magers

  3. Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA

    István Pelczer & Jannette Carey

  4. Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zamek 136, 37333, Nové Hrady, Czech Republic

    David Řeha, Babak Minofar & Jannette Carey

  5. Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA

    Brielle Shope

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Contributions

Study conception and design: J. C. and D. B. M.; materials preparation and NMR data collection: B. S. and I. P.; computational data coysellection: B. S., B. M., D. B. M., D. R. All authors contributed to data analysis. The first draft of the manuscript was written by B. S. and J. C., and all authors contributed to intermediate versions. All authors have read and approved the final manuscript.

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Correspondence to D. Brandon Magers or Jannette Carey.

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Supplementary Information

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11224_2022_2017_MOESM1_ESM.docx

Alist of coordinates for the optimized structures of conformers I through VI and the details of Psi4 and Gaussiancomputations are supplied as Supporting Information. Gas phase, implicitwater, and implicit methanol structures are available for both the complexedand uncomplexed DB18C6. Additionally, counterpoise correction and basis setsuperposition error calculation details for implicit solvent are includedwithin the Supporting Information (DOCX 259 KB)

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Shope, B., Magers, D.B., Pelczer, I. et al. NMR and computational studies of ammonium ion binding to dibenzo-18-crown-6. Struct Chem 34, 713–722 (2023). https://doi.org/10.1007/s11224-022-02017-8

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  • DOI: https://doi.org/10.1007/s11224-022-02017-8

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