Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Density functional theoretical study on attachment sites of Mg2+ and Ca2+ and metal ion affinity to Crenulatin molecule

Abstract

Crenulatin (C25H20O10) is a flavonol derivative and has been isolated from the roots of Rhodiola crenulata (Hook. F. et Thoms.), a widely used medicinal herb. Magnesium and calcium cations play an important physiological role in biological systems. In this work, interactions of magnesium and calcium divalent cations with Crenulatin molecule were studied. Density functional theory (DFT) was used to determine coordination geometries and absolute metal ion affinities (MIA) for all possible stable complexes. The results show that calcium and magnesium cations are able to interact with the Crenulatin molecule through mono-, bi-, and tricoordination. B3LYP/6-31G(d) bond energies for all complexes reveal that magnesium cation has a greater affinity to Crenulatin molecule than calcium cation. The calculated value of Mg2+ cation affinity, including the zero-point vibrational energy (ZPE) and basis set superposition error (BSSE), is 231.8 kcal mol−1 for the most stable complex. Entropy (ΔS) and free energy (ΔG) variations for the metalation processes considered here have also been reported.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4

References

  1. 1.

    Darbinyan V, Kteyan A, Panossian A (2000) Phytomedicine 7:365

  2. 2.

    Seo WG, Pae HO, Oh GS (2001) J Ethnopharmacol 76:119

  3. 3.

    Pae HO, Seo WG, Oh GS (2001) Immunopharmacol Immunotoxicol 23:25

  4. 4.

    Xu KJ, Zhang SF, Lu GZ (1999) Med J NDFNC 20:172

  5. 5.

    Hao LM, Jiang WH, Meng XT (2000) Chin J Gerontol 20:230

  6. 6.

    Li Y, Cui L, Pan L (2001) Chin J Gerontol 21:55

  7. 7.

    Guan GM, Wang YP, Dong Z (1999) Chin J Otorhinolaryngol 34:227

  8. 8.

    Ma Y, Zhang XZ, Chen XS (2001) Chin Ment Health J 15:117

  9. 9.

    Chi AQ, Zhang XS, Lu XM (2000) Chin Tradit Herb Drugs 31:442

  10. 10.

    Du M, Xie JM (1994) Acta Chimi Sini 52:927

  11. 11.

    Su XF, Zhang H, Shao JX, Wu HY (2007) J Mol Struct (THEOCHEM) 847:59

  12. 12.

    Belrhali H, Yaremchuk A, Tukalo M, Berthetcolominas C, Rasmussen B, Bosecke P, Diat O, Cusack S (1995) Structure 3:341

  13. 13.

    Arnez JG, Moras D (1997) Trends Biochem Sci 22:211

  14. 14.

    Desogus G, Todone F, Brick P, Onesti S (2000) Biochemistry 39:8418

  15. 15.

    Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D (2003) J Mol Biol 331:201

  16. 16.

    Airas RK (1996) Eur J Biochem 240:223

  17. 17.

    Zurek J, Bowman AL, Sokalski WA, Mulholland AJ (2004) Struct Chem 15:405

  18. 18.

    Frick DN, Banik S, Rypma RS (2007) J Mol Biol 365:1017

  19. 19.

    Falcke M (2003) New J Phys 5:961

  20. 20.

    Berridge MJ, Bootman MD, Lipp P (1998) Nature 395:45

  21. 21.

    Trofimova MS, Andreev IM, Kuznetsov VV (1999) Physiol Plant 105:67

  22. 22.

    Liang H, Yuan QP, Xiao Q (2006) J Mol Catal B-Enzym 43:9

  23. 23.

    Russo N, Toscano M, Grand A (2003) J Phys Chem A 107:1533

  24. 24.

    Russo N, Toscano M, Grand A (2001) J Am Chem Soc 123:10272

  25. 25.

    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW,Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (1998) Gaussian 98, Revision A.9, Gaussian, Inc. Pittsburgh, PA

  26. 26.

    Becke ADJ (1993) Chem Phys 98:648

  27. 27.

    Lee C, Yang W, Parr RG (1988) Phys Rev B 37:85

  28. 28.

    Remko M, Rode BM (2004) Struct Chem 15:23

  29. 29.

    Russo N, Toscano M, Grand A (2003) J Mass Spectrom 38:65

  30. 30.

    Frisch MJ, Del Bene JE, Binkley JS, Schaefer HF (1986) J Chem Phys 84:279

  31. 31.

    Eller K, Schwarz H (1991) Chem Rev 91:121

  32. 32.

    Fontijn A (ed) (1992) Gas-phase metal reactions. North-Holland, Amsterdam

  33. 33.

    Freiser BS (ed) (1995) Organometallic ion chemistry. Kluwer Academic Publishers, Dordrecht

  34. 34.

    Cerda BA, Wesdemiotis C (1996) J Am Chem Soc 118:1884

  35. 35.

    Armentrout PB (2000) J Am Soc Mass Spectrom 11:71

  36. 36.

    Wilson MA, Brunger AT (2000) J Mol Biol 301:1237

Download references

Acknowledgments

This project was supported by the National Natural Science Foundation of China and China Academia Engineering Physics under Grant No. 10676025.

Author information

Correspondence to Xinlu Cheng.

Electronic supplementary material

Below is the link to the electronic supplementary material. The optimized geometry parameters, including bond lengths, bond angles and dihedrals, of Crenulatin-a, Crenulatin-b, and their complexes at B3LYP/6-31G(d) level (Table S1–S20).

ESM 1 (DOC 2354 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Cheng, X., Su, X., Zhao, X. et al. Density functional theoretical study on attachment sites of Mg2+ and Ca2+ and metal ion affinity to Crenulatin molecule. Struct Chem 19, 541–548 (2008). https://doi.org/10.1007/s11224-008-9315-x

Download citation

Keywords

  • Crenulatin
  • Density functional theory
  • Stability
  • Metal ion affinity