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Comparative cation sensing properties of a newly designed urea linked ferrocene-benzimidazole dyad: a DFT study

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Herein, our primary motivation was to elucidate the electronic and physicochemical properties of a novel molecular dyad consisting of ferrocene (Fc; electron donor), urea (u; linker), and amphoteric benzimidazole (BI; electron acceptor) entities. The sensor responses were investigated for various divalent transition metal cations (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+) and the selectivity of this cationophore molecule (Fc-u-BI) to copper ion (Cu2+) was demonstrated by using B3LYP/LANL2DZ method. According to the thermochemical calculations, we justified that Fc-u-BI⋯Cu2+ reached to the lowest binding energy (∆E), enthalpy (∆H), and Gibbs free energy (∆G) changes. In the light of the calculated global descriptors, Fc-u-BI⋯Cu2+ was found to be the softer and thus the most reactive complex. The complex stabilities and their corresponding non-covalent interactions were also investigated by NBO and NCI analyses, respectively.

The mechanistic insight into metal cation sensing by the modeled cationophore dyad

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  1. 1.

    Electronic supplementary information (ESI†) is available comprising Cartesian coordinates, representative diagrams of the total dipole moments’ components, HOMO-LUMO counter plots including their orbital contributions.


  1. 1.

    Prodi L, Montalti M, Zaccheroni N, Dolci LS Probes and sensors for cations. Top. fluoresc. spectrosc. Springer US, Boston, pp 1–57

  2. 2.

    Trigo-López M, Muñoz A, Ibeas S et al (2016) Colorimetric detection and determination of Fe (III), Co (II), Cu (II) and Sn (II) in aqueous media by acrylic polymers with pendant terpyridine motifs. Sensors Actuators B Chem 226:118–126. https://doi.org/10.1016/j.snb.2015.11.116

  3. 3.

    Ye J, Wang L, Wang H et al (2018) A cation-selective and anion-controlled benzothiazolyl-attached macrocycle for NLO-based cation detection: variational first hyperpolarizabilities. New J Chem 42:6091–6100. https://doi.org/10.1039/C8NJ00360B

  4. 4.

    Tanaka K, Kumagai T, Aoki H et al (2001) Application of 2-(3,5,6-Trifluoro-2-hydroxy-4-methoxyphenyl) benzoxazole and- benzothiazole to fluorescent probes sensing pH and metal cations. J Organomet Chem 66:7328–7333. https://doi.org/10.1021/jo010462a

  5. 5.

    Narin I (2000) Determination of trace metal ions by AAS in natural water samples after preconcentration of pyrocatechol violet complexes on an activated carbon column. Talanta 52:1041–1046. https://doi.org/10.1016/S0039-9140(00)00468-9

  6. 6.

    Prestel H, Gahr A, Niessner R (2000) Detection of heavy metals in water by fluorescence spectroscopy: on the way to a suitable sensor system. Fresenius J Anal Chem 368:182–191. https://doi.org/10.1007/s002160000379

  7. 7.

    Wang S, Forzani ES, Tao N (2007) Detection of heavy metal ions in water by high-resolution surface plasmon resonance spectroscopy combined with anodic stripping voltammetry. Anal Chem 79:4427–4432. https://doi.org/10.1021/ac0621773

  8. 8.

    Wu D, Sedgwick AC, Gunnlaugsson T et al (2017) Fluorescent chemosensors: the past, present and future. Chem Soc Rev 46:7105–7123. https://doi.org/10.1039/C7CS00240H

  9. 9.

    Bargossi C, Fiorini MC, Montalti M et al (2000) Recent developments in transition metal ion detection by luminescent chemosensors. Coord Chem Rev 208:17–32. https://doi.org/10.1016/S0010-8545(00)00252-6

  10. 10.

    Prodi L (2000) Luminescent chemosensors for transition metal ions. Coord Chem Rev 205:59–83. https://doi.org/10.1016/S0010-8545(00)00242-3

  11. 11.

    Waggoner DJ, Bartnikas TB, Gitlin JD (1999) The role of copper in neurodegenerative disease. Neurobiol Dis 6:221–230. https://doi.org/10.1006/nbdi.1999.0250

  12. 12.

    Chan S, Gerson B, Subramaniam S (1998) The role of copper, molybdenum, selenium, and zinc in nutrition and health. Clin Lab Med 18:673–685. https://doi.org/10.1016/S0272-2712(18)30143-4

  13. 13.

    Yruela I (2005) Copper in plants. Braz J Plant Physiol 17:145–156. https://doi.org/10.1590/S1677-04202005000100012

  14. 14.

    Dringen R, Scheiber IF, Mercer JFB (2013) Copper metabolism of astrocytes. Front Aging Neurosci. https://doi.org/10.3389/fnagi.2013.00009

  15. 15.

    Flemming CA, Trevors JT (1989) Copper toxicity and chemistry in the environment: a review. Water Air Soil Pollut 44:143–158. https://doi.org/10.1007/BF00228784

  16. 16.

    Harris ZL, Gitlin JD (1996) Genetic and molecular basis for copper toxicity. Am J Clin Nutr 63:836S–841S. https://doi.org/10.1093/ajcn/63.5.836

  17. 17.

    Theophanides T, Anastassopoulou J (2002) Copper and carcinogenesis. Crit Rev Oncol Hematol 42:57–64. https://doi.org/10.1016/S1040-8428(02)00007-0

  18. 18.

    Di Toro DM, Allen HE, Bergman HL et al (2001) Biotic ligand model of the acute toxicity of metals. 1. Technical basis. Environ Toxicol Chem 20:2383–2396. https://doi.org/10.1002/etc.5620201034

  19. 19.

    Yang H, Zhou Z, Li F et al (2007) New Hg2+ and Ag+ selective colorimetric sensor based on thiourea subunits. Inorg Chem Commun 10:1136–1139. https://doi.org/10.1016/j.inoche.2007.06.022

  20. 20.

    Fabbrizzi L (2000) The design of luminescent sensors for anions and ionisable analytes. Coord Chem Rev 205:85–108. https://doi.org/10.1016/S0010-8545(00)00239-3

  21. 21.

    Caballero A, Tormos R, Espinosa A et al (2004) Selective fluorescence sensing of Li + in an aqueous environment by a ferrocene−anthracene-linked dyad. Org Lett 6:4599–4602. https://doi.org/10.1021/ol047972m

  22. 22.

    Zapata F, Caballero A, Molina P, Tarraga A (2010) A ferrocene-quinoxaline derivative as a highly selective probe for colorimetric and redox sensing of toxic mercury (II) cations. Sensors 10:11311–11321. https://doi.org/10.3390/s101211311

  23. 23.

    Molina P, Tárraga A, Caballero A (2008) Ferrocene-based small molecules for multichannel molecular recognition of cations and anions. Eur J Inorg Chem 2008:3401–3417. https://doi.org/10.1002/ejic.200800474

  24. 24.

    Basurto S, Riant O, Moreno D et al (2007) Colorimetric detection of Cu [II] cation and acetate, benzoate, and cyanide anions by cooperative receptor binding in new α,α‘-Bis-substituted donor−acceptor ferrocene sensors. J Organomet Chem 72:4673–4688. https://doi.org/10.1021/jo0702589

  25. 25.

    Zapata F, Caballero A, Espinosa A et al (2008) Cation coordination induced modulation of the anion sensing properties of a ferrocene−imidazophenanthroline dyad: multichannel recognition from phosphate-related to chloride anions. J Organomet Chem 73:4034–4044. https://doi.org/10.1021/jo800296c

  26. 26.

    Caballero A, Espinosa A, Tárraga A, Molina P (2008) Ferrocene-based small molecules for dual-channel sensing of heavy- and transition-metal cations. J Organomet Chem 73:5489–5497. https://doi.org/10.1021/jo800709v

  27. 27.

    Valério C, Fillaut J-L, Ruiz J et al (1997) The dendritic effect in molecular recognition: ferrocene dendrimers and their use as supramolecular redox sensors for the recognition of small inorganic anions. J Am Chem Soc 119:2588–2589. https://doi.org/10.1021/ja964127t

  28. 28.

    Casas-Solvas JM, Ortiz-Salmerón E, Fernández I et al (2009) Ferrocene-β-cyclodextrin conjugates: synthesis, supramolecular behavior, and use as electrochemical sensors. Chem Eur J 15:8146–8162. https://doi.org/10.1002/chem.200900593

  29. 29.

    Beall LS, Mani NS, White AJP et al (1998) Porphyrazines and norphthalocyanines bearing nitrogen donor pockets: metal sensor properties. J Organomet Chem 63:5806–5817. https://doi.org/10.1021/jo9802574

  30. 30.

    Li A-F, Wang J-H, Wang F, Jiang Y-B (2010) Anion complexation and sensing using modified urea and thiourea-based receptors. Chem Soc Rev 39:3729. https://doi.org/10.1039/b926160p

  31. 31.

    Zhou X-H, Yan J-C, Pei J (2004) Exploiting an imidazole-functionalized polyfluorene derivative as a chemosensory material. Macromolecules 37:7078–7080. https://doi.org/10.1021/ma049057m

  32. 32.

    Udhayakumari D, Velmathi S, Boobalan M susai, et al (2015) Heterocyclic ring based colorimetric and fluorescent chemosensor for transition metal ions in an aqueous medium. J Lumin 158:484–492. doi: https://doi.org/10.1016/j.jlumin.2014.10.040

  33. 33.

    Persson JC, Josefsson K, Jannasch P (2006) Polysulfones tethered with benzimidazole. Polymer (Guildf) 47:991–998. https://doi.org/10.1016/j.polymer.2005.12.077

  34. 34.

    Purakayastha A, Baruah JB (1999) Thermal effects on urea–copper binding within a supramolecular assembly. New J Chem 23:1141–1142. https://doi.org/10.1039/a907123g

  35. 35.

    Savyasachi AJ, Kotova O, Shanmugaraju S et al (2017) Supramolecular chemistry: a toolkit for soft functional materials and organic particles. Chem 3:764–811. https://doi.org/10.1016/j.chempr.2017.10.006

  36. 36.

    Dennington R, Keith T, Millam J (2009) GaussView, Version 5. Semichem Inc, Shawnee Mission

  37. 37.

    Frisch MJ, Trucks GW, Schlegel HB et al (2009) Gaussian 09, Revision B.01. Gaussian 09, Revis. B.01. Gaussian, Inc, Wallingford

  38. 38.

    Skylaris C-K, Oks E, Abu-Awwad FM et al (2016) NBO version 3.1. Angew Chemie Int Ed. https://doi.org/10.1002/anie.199004491

  39. 39.

    Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem. https://doi.org/10.1002/jcc.22885

  40. 40.

    Gorelsky SI (2019) AOMix: program for molecular orbital analysis

  41. 41.

    Gorelsky SI, Lever ABP (2001) Electronic structure and spectra of ruthenium diimine complexes by density functional theory and INDO/S. Comparison of the two methods. J Organomet Chem 635:187–196. https://doi.org/10.1016/S0022-328X(01)01079-8

  42. 42.

    Irving H, Williams RJP (1953) 637. The stability of transition-metal complexes. J Chem Soc:3192. https://doi.org/10.1039/jr9530003192

  43. 43.

    Chapman D (1954) Electronegativity and the stability of metal complexes. Nature 174:887–888. https://doi.org/10.1038/174887a0

  44. 44.

    Tanaka M, Tabata M (2009) Stability constants of metal (II) complexes with amines and aminocarboxylates with special reference to chelation. Bull Chem Soc Jpn 82:1258–1265. https://doi.org/10.1246/bcsj.82.1258

  45. 45.

    Kaviani S, Shahab S, Sheikhi M, Ahmadianarog M (2019) DFT study on the selective complexation of meso-2,3-dimercaptosuccinic acid with toxic metal ions (Cd2+, Hg2+ and Pb2+) for pharmaceutical and biological applications. J Mol Struct 1176:901–907. https://doi.org/10.1016/j.molstruc.2018.09.027

  46. 46.

    Gapeev A, Dunbar RC (2002) Reactivity and binding energies of transition metal halide ions with benzene. J Am Soc Mass Spectrom 13:477–484. https://doi.org/10.1016/S1044-0305(02)00373-2

  47. 47.

    He H-T, Xing L-C, Zhang J-S, Tang M (2016) Binding characteristics of Cd 2+ , Zn 2+ , Cu 2+ , and Li + with humic substances: implication to trace element enrichment in low-rank coals. Energy Explor Exploit 34:735–745. https://doi.org/10.1177/0144598716656067

  48. 48.

    Cramer CJ, Truhlar DG (2009) Density functional theory for transition metals and transition metal chemistry. Phys Chem Chem Phys 11:10757. https://doi.org/10.1039/b907148b

  49. 49.

    Hieringer W, Baerends EJ (2006) First hyperpolarizability of a sesquifulvalene transition metal complex by time-dependent density-functional theory. J Phys Chem A 110:1014–1021. https://doi.org/10.1021/jp0540297

  50. 50.

    Weinhold F, Landis CR, Glendening ED (2016) What is NBO analysis and how is it useful? Int Rev Phys Chem 35:399–440. https://doi.org/10.1080/0144235X.2016.1192262

  51. 51.

    Boto RA, Contreras-García J, Tierny J, Piquemal J-P (2016) Interpretation of the reduced density gradient. Mol Phys 114:1406–1414. https://doi.org/10.1080/00268976.2015.1123777

  52. 52.

    Bine FK, Nkungli NK, Numbonui TS, Numbonui Ghogomu J (2018) Structural properties and reactive site selectivity of some transition metal complexes of 2,2′(1E,1′E)-(ethane-1,2-diylbis (azan-1-yl-1-ylidene)) (phenylmethan-1-yl-1-ylidene) dibenzoic acid: DFT, conceptual DFT, QTAIM, and MEP studies. Bioinorg Chem Appl 2018:1–11. https://doi.org/10.1155/2018/4510648

  53. 53.

    Stefaniu A, Pintilie L (2018) Molecular descriptors and properties of organic molecules. Symmetry (gr Theory). Math Treat Chem. https://doi.org/10.5772/intechopen.72840

  54. 54.

    Parr RG, Donnelly RA, Levy M, Palke WE (1978) Electronegativity: the density functional viewpoint. J Chem Phys 68:3801–3807. https://doi.org/10.1063/1.436185

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The numerical calculations reported in this paper were performed at TUBITAK ULAKBIM, High Performance, and Grid Computing Center (TRUBA resources).

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Correspondence to Fatma Sevin.

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Sarikavak, K., Kurtay, G. & Sevin, F. Comparative cation sensing properties of a newly designed urea linked ferrocene-benzimidazole dyad: a DFT study. J Mol Model 26, 50 (2020). https://doi.org/10.1007/s00894-020-4304-0

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  • Cation sensing
  • Global descriptors
  • NBO analysis
  • NCI
  • DFT