Skip to main content
SpringerLink
Log in

The role of water molecular structuring in the formation of the inclusion compounds based on cucurbit[8]uril and trans-[Co(en)2Cl2]+, trans-[Ru(en)2Cl2]+ complexes: a DFT examination

  • Original Article
  • Published:
Journal of Inclusion Phenomena and Macrocyclic Chemistry Aims and scope Submit manuscript

Abstract

This paper presents the results of studying the structural features of inclusion compounds based on the cucurbit[8]uril macrocycle and the cobalt(III) and ruthenium(III) complexes (trans-[Co(en)2Cl2]+ and trans-[Ru(en)2Cl2]+) within the framework of the density functional theory taking into account the course of the reaction in the aqueous solution. Formation thermodynamics of the complexes in the cavitands was evaluated by taking into account the most probable number of water molecules inside cucurbit[8]uril. In this methodology, the complexation was considered as a substitution reaction in which the guest complex displaces partially or completely the water molecules that are located inside the cavity. The water molecules present in the cavitand were shown to play an important role in the fixation of the guest complex inside the cavity due to the hydrogen bonds with the oxygen portals. The role of water molecules in the fixation of the complex in the cavity of the macrocycle with the formation of a particular structure is shown. The symmetrical arrangement of the fixing water molecules in the portals leads to a more symmetric arrangement of the metal complex in the cucurbit[8]uril cavity, while their asymmetric localization leads to a significant turn of the complex. Comparison of the main geometric characteristics according to the calculation and X-ray structural analysis showed good agreement. The thermodynamic parameters of the formation of the inclusion compound are estimated. It is shown that the energy contribution of macrocycle deformation to the energetics of formation of the inclusion compound is insignificant.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Abbreviations

CB[n]:

Cucurbit[n]uril

CB[8]:

Cucurbit[8]uril

References

  1. Lagona, J., Mukhopadhyay, P., Chakrabarti, S., Isaacs, L.: The cucurbit[n]uril family. Angew. Chem. Int. Ed. (2005). https://doi.org/10.1002/anie.200460675

    Article  Google Scholar 

  2. Kim, K., Selvapalam, N., Ko, Y.H., Park, K.M., Kim, D., Kim, J.: Functionalized cucurbiturils and their applications. Chem. Soc. Rev. (2007). https://doi.org/10.1039/B603088M

    Article  PubMed  Google Scholar 

  3. Maslii, A.N., Grishaeva, T.N., Kuznetsov, A.M., Bakovets, V.V.: Quantum chemical investigation of structural and thermodynamic peculiarities of the formation of cucurbit[n]urils. J. Struct. Chem. (2007). https://doi.org/10.1007/s10947-007-0083-z

    Article  Google Scholar 

  4. Grishaeva, T.N., Maslii, A.N., Bakovets, V.V., Kuznetsov, A.M.: Quantum-chemical study of the formation mechanism of cucurbit[n]uril nanocavitands. Russ. J. Inorg. Chem. (2010). https://doi.org/10.1134/S0036023610100165

    Article  Google Scholar 

  5. Ko, Y.H., Hwang, I., Lee, D.-W., Kim, K.: Ultrastable host–guest complexes and their applications. Isr. J. Chem. (2011). https://doi.org/10.1002/ijch.201100041

    Article  Google Scholar 

  6. Biedermann, F., Uzunova, V.D., Scherman, O.A., Nau, W.M., De Simone, A.: Release of high-energy water as an essential driving force for the high-affinity binding of cucurbit[n]urils. J. Am. Chem. Soc. (2012). https://doi.org/10.1021/ja303309e

    Article  PubMed  Google Scholar 

  7. Biedermann, F., Vendruscolo, M., Scherman, O.A., De Simone, A., Nau, W.M.: Cucurbit[8]uril and blue-box: high-energy water release overwhelms electrostatic interactions. J. Am. Chem. Soc. (2013). https://doi.org/10.1021/ja407951x

    Article  PubMed  Google Scholar 

  8. Saleh, N., Ghosh, I., Nau, W.M.: Cucurbiturils in drug delivery and for biomedical applications. In: Schneider, H.-J. (ed.) Supramolecular Systems in Biomedical Fields, pp. 164–212. Royal Society of Chemistry, Cambridge (2013). https://doi.org/10.1039/9781849737821

    Chapter  Google Scholar 

  9. Walker, S., Oun, R., McInnes, F.J., Wheate, N.J.: The potential of cucurbit[n]urils in drug delivery. Isr. J. Chem. (2011). https://doi.org/10.1002/ijch.201100033

    Article  Google Scholar 

  10. Urbach, A.R., Ramalingam, V.: Molecular recognition of amino acids, peptides, and proteins by cucurbit[n]uril receptors. Isr. J. Chem. (2011). https://doi.org/10.1002/ijch.201100035

    Article  Google Scholar 

  11. Masson, E., Ling, X., Joseph, R., Kyeremeh-Mensah, L., Lu, X.: Cucurbituril chemistry: a tale of supramolecular success. RSC Adv. (2012). https://doi.org/10.1039/C1RA00768H

    Article  Google Scholar 

  12. Assaf, K.I., Nau, W.M.: Cucurbiturils: from synthesis to high-affinity binding and catalysis. Chem. Soc. Rev. (2015). https://doi.org/10.1039/C4CS00273C

    Article  PubMed  Google Scholar 

  13. Kovalenko, E.A., Maynichev, D.A., Masliy, A.N., Kuznetsov, A.M.: Supramolecular chemistry of macrocyclic cavitandcucurbit[7]uril with isoleucine. Russ. Chem. Bull. (2015). https://doi.org/10.1007/s11172-015-1092-2

    Article  Google Scholar 

  14. Grishaeva, T.N., Masliy, A.N., Bakovets, V.V., Kuznetsov, A.M.: Inclusion compound based on bis(ethylenediamine)copper(II) complex and cucurbit[8]uril: quantum chemical prediction for structure and formation thermodynamic parameters. Russ. J. Inorg. Chem. (2015). https://doi.org/10.1134/S0036023615100071

    Article  Google Scholar 

  15. Grishaeva, T.N., Maslii, A.N., Bakovets, V.V., Kuznetsov, A.M.: Inclusion compounds based on nickel(II) dimethylglyoxymate and cucurbit[8]uril: a quantum chemical prediction of the structure and thermodynamic parameters of formation. J. Struct. Chem. (2015). https://doi.org/10.1134/S0022476615080016

    Article  Google Scholar 

  16. Gerasko, O.A., Kovalenko, E.A., Fedin, V.P.: Macrocyclic cavitands cucurbit[n]urils: prospects for application in biochemistry, medicine and nanotechnology. Russ. Chem. Rev. (2016). https://doi.org/10.1070/RCR4595

    Article  Google Scholar 

  17. Kovalenko, E., Vilaseca, M., Díaz-Lobo, M., Masliy, A.N., Vicent, C., Fedin, V.P.: Supramolecular adducts of cucurbit[7]uril and amino acids in the gas phase. J. Am. Soc. Mass Spectrom. (2016). https://doi.org/10.1007/s13361-015-1274-z

    Article  PubMed  Google Scholar 

  18. Kovalenko, E.A., Pashkina, E.A., Kozlov, V.A., Kanazhevskaya, L.Y., Masliy, A.N.: Chemical and biological properties of a supramolecular complex of tuftsin and cucurbit[7]uril. Int. Immunopharmacol. (2017). https://doi.org/10.1016/j.intimp.2017.03.032

    Article  PubMed  Google Scholar 

  19. Uzunova, V.D., Cullinane, C., Brix, K., Nau, W.M., Day, A.I.: Toxicity of cucurbit[7]uril and cucurbit[8]uril: an exploratory in vitro and in vivo study. Org. Biomol. Chem. (2010). https://doi.org/10.1039/B925555A

    Article  PubMed  Google Scholar 

  20. Chen, H., Chan, J.Y.W., Yang, X., Wyman, I.W., Bardelang, D., Macartney, D.H., Lee, S.M.Y., Wang, R.: In vivo reversal of general anesthesia by cucurbit[7]uril with zebrafish models. RSC Adv. (2015). https://doi.org/10.1039/C5RA09406B

    Article  PubMed  Google Scholar 

  21. Wheate, N.J., Day, A.I., Blanch, R.J., Collins, J.G.: UNISEARCH Limited, Australia. PCT Int. Appl. 63 (2005)

  22. Kim, K., Jeon, Y.J..Kim, S.-Y., Ko, Y.H.: Postech Foundation, S. Korea. PCT Int. Appl. 42 (2002)

  23. Kim, K., Kim, J., Jung, I.-S., Kim, S.Y., Lee, E., Kang, J.-K.: US Pat. 7160466, 2007; Chem. Abstr. 134, 326547 (2001)

  24. Kim, K., Jeon, Y.J., Kim, S.Y., Ko, Y.H., PCT Int. Appl. WO 2003/024978, 2003; Chem. Abstr. 138, 264767 (2003)

  25. Masliy, A.N., Grishaeva, T.N., Kuznetsov, A.M.: Formation of aqua and tetraammine Cu(II) complexes inside the cavities of cucurbit[6,8]urils: a DFT forecast. Int. J. Quantum Chem. (2019). https://doi.org/10.1002/qua.25877

    Article  Google Scholar 

  26. Grishaeva, T.N., Masliy, A.N., Kuznetsov, A.M.: Structural features of the inclusion compound based on the trans-[Co(en)2Cl2]+ complex and cucurbit[8]uril: a DFT study. J. Struct. Chem. (2019). https://doi.org/10.1134/S0022476619120035

    Article  Google Scholar 

  27. Kovalenko, E.A., Mitkina, T.V., Gerasko, O.A., Naumov, Yu.D., Samsonenko, D.G., Fedin, V.P.: Inclusion compounds of cucurbit[8]uril with noble metal polyamine complexes. Russ. Chem. Bull. (2010). https://doi.org/10.1007/s11172-010-0357-z

    Article  Google Scholar 

  28. Laikov, D.N.: Fast evaluation of density functional exchange-correlation terms using the expansion of the electron density in auxiliary basis sets. Chem. Phys. Lett. (1997). https://doi.org/10.1016/S0009-2614(97)01206-2

    Article  Google Scholar 

  29. Mitkina, T.V., Sokolov, M.N., Naumov, D.Y., Kuratieva, N.V., Gerasko, O.A., Fedin, V.P.: Jørgensen complex within a molecular container: Selective encapsulation of trans-[Co(en)2 Cl2]+ into Cucurbit[8]uril and Influence of Inclusion on Guest’s Properties. Inorg. Chem. (2006). https://doi.org/10.1021/ic060502z

  30. Laikov, D.N.: A new class of atomic basis functions for accurate electronic structure calculations of molecules. Chem. Phys. Lett. (2005). https://doi.org/10.1016/j.cplett.2005.09.046

    Article  Google Scholar 

  31. Klamt, A., Schürmann, G.: COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J. Chem. Soc. Perkin. Trans. (1993). https://doi.org/10.1039/P29930000799

    Article  Google Scholar 

  32. Neese, F.: ORCA—an ab initio, Density Functional and Semiempirical Program Package, Version 2.4, Max-Planck Institut für Bioanorganische Chemie, Mülheim an der Ruhr, Germany (2004)

  33. Grimme, S., Antony, J., Ehrlich, S., Krieg, H.: A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. (2010). https://doi.org/10.1063/1.3382344

    Article  PubMed  Google Scholar 

  34. Becke, A.D., Johnson, E.R.: A density-functional model of the dispersion interaction. J. Chem. Phys. (2005). https://doi.org/10.1063/1.2065267

    Article  PubMed  Google Scholar 

  35. Becke, A.D., Johnson, E.R.: Exchange-hole dipole moment and the dispersion interaction. J. Chem. Phys. (2005). https://doi.org/10.1063/1.1884601

    Article  PubMed  Google Scholar 

  36. Grimme, S., Ehrlich, S., Goerigk, L.: Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. (2011). https://doi.org/10.1002/jcc.21759

    Article  PubMed  Google Scholar 

  37. Schafer, A., Horn, H., Ahlrichs, R.: Fully optimized contracted Gaussian basis sets for atoms Li to Kr. J. Chem. Phys. (1992). https://doi.org/10.1063/1.463096

    Article  Google Scholar 

  38. ChemCraft, Tool for Treatment of Chemical Data. http://www.chemcraftprog.com. Accessed July 2011.

  39. Maslii, A.N., Grishaeva, T.N., Kuznetsov, A.M., Bakovets, V.V.: Quantum-chemical study of structurization of water in the cavity of cucurbit[6]uril. J. Struct. Chem. (2009). https://doi.org/10.1007/s10947-009-0059-2

    Article  Google Scholar 

  40. Grishaeva, T.N., Masliy, A.N., Kuznetsov, A.M.: Water structuring inside the cavities of cucurbit[n]urils (n = 5–8): a quantum-chemical forecast. J. Incl. Phenom. Macrocycl. Chem. (2017). https://doi.org/10.1007/s10847-017-0751-3

    Article  Google Scholar 

  41. Samsonenko, D.G., Virovets, A.V., Lipkowski, J., Geras’ko, O.A., Fedin, V.P.: Distortion of the cucurbituril molecule by an included 4-methylpyridinum cation. J. Struct. Chem. (2002). https://doi.org/10.1023/A:1022008822653

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Inorganic Chemistry Named After Professor N.S. Akhmetov, Kazan National Research Technological University, K. Marx Street 68, Kazan, Russian Federation, 420015

    Tatiana N. Grishaeva, Alexey N. Masliy & Andrey M. Kuznetsov

Authors
  1. Tatiana N. Grishaeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alexey N. Masliy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Andrey M. Kuznetsov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tatiana N. Grishaeva.

Ethics declarations

Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 54 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Grishaeva, T.N., Masliy, A.N. & Kuznetsov, A.M. The role of water molecular structuring in the formation of the inclusion compounds based on cucurbit[8]uril and trans-[Co(en)2Cl2]+, trans-[Ru(en)2Cl2]+ complexes: a DFT examination. J Incl Phenom Macrocycl Chem 102, 653–662 (2022). https://doi.org/10.1007/s10847-022-01146-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10847-022-01146-1

Keywords

Search

Navigation