Skip to main content
SpringerLink
Log in

Selective complexation of alkali metal ions and nanotubular cyclopeptides: a DFT study

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

Abstract

A density functional theory based on interaction of alkali metal cations (Li+, Na+, K+, Rb+ and Cs+) with cyclic peptides constructed from 3 or 4 alanine molecule (CyAla3 and CyAla4), has been investigated using mixed basis set (C, H, O, Li+, Na+ and K+ using 6-31+G(d), and the heavier cations: Rb+ and Cs+ using LANL2DZ). The minimum energy structures, binding energies, and various thermodynamic parameters of free ligands and their metal cations complexes have been determined with B3LYP and CAM-B3LYP functionals. The order of interaction energies were found to be Li+ > K+ > Na+ > Rb+ > Cs+ and Li+ > Na+ > K+ ≫ Rb+ > Cs+, calculated at CAM-B3LYP level for the M/CyAla3 and M/CyAla4 complexes, respectively. Their selectivity trend shows that the highest cation selectivity for Li+ over other alkali metal ions has been achieved on the basis of thermodynamic analysis. The main types of driving force host–guest interactions are investigated, the electron-donating O offers lone pair electrons to the contacting LP* of alkali metal cations.

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
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Chen, G., Su, S., Liu, R.: Theoretical studies of monomer and dimer of cyclo[(−l-Phe1-d-Ala2−)n] and cyclo[(−l-Phe1-d-MeN-Ala2−)n] (n = 3–6). J. Phys. Chem. B 106(7), 1570–1575 (2002)

    Article  CAS  Google Scholar 

  2. Ghadiri, M.R., Granja, J.R., Buehler, L.K.: Artificial transmembrane ion channels from self-assembling peptide nanotubes. Nature 369(6478), 301–304 (1994)

    Article  CAS  Google Scholar 

  3. Ghadiri, M.R., Granja, J.R., Milligan, R.A., McRee, D.E., Khazanovich, N.: Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature 366(6453), 324–327 (1993)

    Article  CAS  Google Scholar 

  4. Ghadiri, M.R., Kobayashi, K., Granja, J.R., Chadha, R.K., McRee, D.E.: The structural and thermodynamic basis for the formation of self-assembled peptide nanotubes. Angew. Chem. Int. Ed. Engl. 34(1), 93–95 (1995)

    Article  CAS  Google Scholar 

  5. Hartgerink, J.D., Granja, J.R., Milligan, R.A., Ghadiri, M.R.: Self-assembling peptide nanotubes. J. Am. Chem. Soc. 118(1), 43–50 (1996)

    Article  CAS  Google Scholar 

  6. Kobayashi, K., Granja, J.R., Ghadiri, M.R.: β-Sheet peptide architecture: measuring the relative stability of parallel vs. antiparallel β-sheets. Angew. Chem. Int. Ed. Engl. 34(1), 95–98 (1995)

    Article  CAS  Google Scholar 

  7. Poteau, R., Trinquier, G.: All-cis cyclic peptides. J. Am. Chem. Soc. 127(40), 13875–13889 (2005)

    Article  CAS  Google Scholar 

  8. Tan, H., Qu, W., Chen, G., Liu, R.: Theoretical investigation of the self-assembly of cyclo[(−β3-HGly)4−]. Chem. Phys. Lett. 369(5–6), 556–562 (2003)

    Article  CAS  Google Scholar 

  9. Teranishi, M., Okamoto, H., Takeda, K., Nomura, K.-i., Nakano, A., Kalia, R.K., Vashishta, P., Shimojo, F.: Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes. J. Phys. Chem. B 113(5), 1473–1484 (2009)

    Article  CAS  Google Scholar 

  10. Bagheri, M., Keller, S., Dathe, M.: Interaction of W-substituted analogs of cyclo-RRRWFW with bacterial lipopolysaccharides: the role of the aromatic cluster in antimicrobial activity. Antimicrob. Agents Chemother. 55(2), 788–797 (2011)

    Article  CAS  Google Scholar 

  11. Vollenbroich, D., Özel, M., Vater, J., Kamp, R.M., Pauli, G.: Mechanism of inactivation of enveloped viruses by the biosurfactant surfactin from Bacillus subtilis. Biologicals 25(3), 289–297 (1997)

    Article  CAS  Google Scholar 

  12. Kracht, M., Rokos, H., Ozel, M., Kowall, M., Pauli, G., Vater, J.: Antiviral and hemolytic activities of surfactin isoforms and their methyl ester derivatives. J. Antibiot. 52(7), 613–619 (1999)

    Article  CAS  Google Scholar 

  13. Tendulkar, S.R., Saikumari, Y.K., Patel, V., Raghotama, S., Munshi, T.K., Balaram, P., Chattoo, B.B.: Isolation, purification and characterization of an antifungal molecule produced by Bacillus licheniformis BC98, and its effect on phytopathogen Magnaporthe grisea. J. Appl. Microbiol. 103(6), 2331–2339 (2007)

    Article  CAS  Google Scholar 

  14. Weber, C., Wider, G., von Freyberg, B., Traber, R., Braun, W., Widmer, H., Wuthrich, K.: The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry 30(26), 6563–6574 (1991)

    Article  CAS  Google Scholar 

  15. Trevisan, G., Maldaner, G., Velloso, N.A., Sant’Anna Gda, S., Ilha, V., Velho Gewehr Cde, C., Rubin, M.A., Morel, A.F., Ferreira, J.: Antinociceptive effects of 14-membered cyclopeptide alkaloids. J. Nat. Prod. 72(4), 608–612 (2009)

    Article  CAS  Google Scholar 

  16. Gang, H.Z., Liu, J.F., Mu, B.Z.: Molecular dynamics simulation of surfactin derivatives at the decane/water interface at low surface coverage. J. Phys. Chem. B 114(8), 2728–2737 (2010)

    Article  CAS  Google Scholar 

  17. Banerjee, A., Yadav, A.: Self-assembling cyclic systems as drug carriers. Appl. Nanosci. 1–14 (2012). doi:10.1007/s13204-012-0154-0

  18. Liu, J., Fan, J., Tang, M., Zhou, W.: Molecular dynamics simulation for the structure of the water chain in a transmembrane peptide nanotube. J. Phys. Chem. A 114(6), 2376–2383 (2010)

    Article  CAS  Google Scholar 

  19. Jishi, R.A., Flores, R.M., Valderrama, M., Lou, L., Bragin, J.: Equilibrium geometry and properties of cyclo[(Gly-d-Ala)4] and {cyclo[(Gly-d-Ala)4]}2 from density functional theory. J. Phys. Chem. A 102(48), 9858–9862 (1998)

    Article  CAS  Google Scholar 

  20. Vijayaraj, R., Sundar Raman, S., Mahesh Kumar, R., Subramanian, V.: Studies on the structure and stability of cyclic peptide based nanotubes using oligomeric approach: a computational chemistry investigation. J. Phys. Chem. B 114(49), 16574–16583 (2010)

    Article  CAS  Google Scholar 

  21. Vijayaraj, R., Van Damme, S., Bultinck, P., Subramanian, V.: Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition. Phys. Chem. Chem. Phys. 14(43), 15135–15144 (2012)

    Article  CAS  Google Scholar 

  22. Żero, P., Pluciński, F., Mazurek, A.P.: Theoretical comparison of molecular properties of linear and cyclic glycine derived peptides and their phosphor analogues. J. Mol. Struct. (Theochem.) 915(1–3), 182–187 (2009)

    Google Scholar 

  23. Ali, S.M., Maity, D.K., De, S., Shenoi, M.R.K.: Ligands for selective metal ion extraction: a molecular modeling approach. Desalination 232(1–3), 181–190 (2008)

    Article  CAS  Google Scholar 

  24. Casanovas, J., Rodríguez-Ropero, F., Zanuy, D., Alemán, C.: Microscopic details of the sensing ability of 15-crown-5-ether functionalized poly(bithiophene). Polymer 51(18), 4267–4272 (2010)

    Article  CAS  Google Scholar 

  25. Hill, S.E., Feller, D.: Theoretical study of cation/ether complexes: 15-crown-5 and its alkali metal complexes. Int. J. Mass Spectrom. 201(1–3), 41–58 (2000)

    Article  CAS  Google Scholar 

  26. Hong, J., Cho, S., Ham, S.: Metal ion shuttling mechanism through thiacalix[4]crown: a computational study. Tetrahedron Lett. 53(15), 2009–2012 (2012)

    Article  CAS  Google Scholar 

  27. Hou, H., Zeng, X., Liu, X.: DFT study of a series of crown-4 ethers and their selectivity trend for alkali metal cations: Li+ and Na+. J. Mol. Model. 15(2), 105–111 (2009)

    Article  CAS  Google Scholar 

  28. Becke, A.D.: Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98(7), 5648–5652 (1993)

    Article  CAS  Google Scholar 

  29. Kamiya, M., Tsuneda, T., Hirao, K.: A density functional study of van der Waals interactions. J. Chem. Phys. 117(13), 6010–6015 (2002)

    Article  CAS  Google Scholar 

  30. Lee, C., Yang, W., Parr, R.G.: Development of the Colle–Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37(2), 785–789 (1988)

    Article  CAS  Google Scholar 

  31. Stephens, P.J., Devlin, F.J., Chabalowski, C.F., Frisch, M.J.: Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98(45), 11623–11627 (1994)

    Article  CAS  Google Scholar 

  32. Yanai, T., Tew, D.P., Handy, N.C.: A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem. Phys. Lett. 393(1–3), 51–57 (2004)

    Article  CAS  Google Scholar 

  33. Frisch, M.J.T., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery Jr., J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, Ö., Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J.: Gaussian 09, Revision A.02. Gaussian Inc, Wallingford (2009)

    Google Scholar 

  34. Foster, J.P., Weinhold, F.: Natural hybrid orbitals. J. Am. Chem. Soc. 102(24), 7211–7218 (1980)

    Article  CAS  Google Scholar 

  35. Reed, A.E., Curtiss, L.A., Weinhold, F.: Intermolecular interactions from a natural bond orbital, donor–acceptor viewpoint. Chem. Rev. 88(6), 899–926 (1988)

    Article  CAS  Google Scholar 

  36. Kubik, S.: Large increase in cation binding affinity of artificial cyclopeptide receptors by an allosteric effect. J. Am. Chem. Soc. 121(25), 5846–5855 (1999)

    Article  CAS  Google Scholar 

  37. De, S., Boda, A., Ali, S.M.: Preferential interaction of charged alkali metal ions (guest) within a narrow cavity of cyclic crown ethers (neutral host): a quantum chemical investigation. J. Mol. Struct. (Theochem.) 941(1–3), 90–101 (2010)

    Article  CAS  Google Scholar 

  38. Kubik, S., Goddard, R.: Intramolecular conformational control in a cyclic peptide composed of alternating -proline and substituted 3-aminobenzoic acid subunits. Chem. Commun. 0(7), 633–634 (2000)

    Article  CAS  Google Scholar 

  39. Praveena, G., Kolandaivel, P.: Interaction of metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide—a theoretical study. J. Mol. Struct. (Theochem.) 900(1–3), 96–102 (2009)

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We would like to acknowledge the Isfahan University of Technology for the financial support of this work.

Author information

Authors and Affiliations

  1. Department of Chemistry, Isfahan University of Technology, 8415483111, Isfahan, Islamic Republic of Iran

    Alireza Najafi Chermahini & Mehdi Rezapour

  2. Chemistry Department, Payame Noor University, 19395-4697, Tehran, Islamic Republic of Iran

    Abbas Teimouri

Authors
  1. Alireza Najafi Chermahini
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mehdi Rezapour
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Abbas Teimouri
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alireza Najafi Chermahini.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Najafi Chermahini, A., Rezapour, M. & Teimouri, A. Selective complexation of alkali metal ions and nanotubular cyclopeptides: a DFT study. J Incl Phenom Macrocycl Chem 79, 205–214 (2014). https://doi.org/10.1007/s10847-013-0346-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10847-013-0346-6

Keywords

Search

Navigation