Karışık 2,2'-dimetilmalonat/2,2'-bipiridin ligandlı Cu(II) kompleksinin sentezi, spektroskopik, kristal yapı ve DFT incelemesi

Abstract

Bu çalışmada; karışık ligantlı Cu(II) kompleksi, [Cu(Me2mal)(bpy)(H2O)]∙H2O (Me2mal-2= Dimetilmalonat dianyonu, bpy=2,2'-bipiridin) sentezlenmiştir. Sentezlenen kompleks IR, UV ve tek kristal X-ışını kırınımı yöntemleri ile deneysel ve kuantum mekaniksel hesaplama yöntemleri kullanılarak teorik olarak karakterize edilmiştir. Kompleks, Pnnm uzay grubunda ortorombik kristal sisteminde kristallenmiştir. Komplekste Cu merkezi; bir Me2mal-2 dianyonu ve bir bpy molekülü tarafından koordine edilmiştir ve N2O2 kare-düzlemsel geometri sergilemektedir. Eksensel pozisyonda ise su molekülü bulunmaktadır. Kompleksin kristal paketlenmesi O-H...O hidrojen bağları ve etkileşimleri ile kararlı bir yapı oluşturmuştur. Çalışmada hidrojen bağlarının ve  istifleme etkileşimlerinin kristal paketlenmeye katkısı da araştırılmıştır. Bu çalışmada DFT yöntemi kullanılarak teorik hesaplamalar da yapılmıştır. Sentezlenen kompleksin geometrik, titreşimsel ve elektronik özelliklerini elde etmek için DFT (B3LYP/6-31G) ve TD-DFT (B3LYP/LanL2DZ) hesaplama yöntemleri kullanılmıştır. Elde edilen teorik hesaplama sonuçları ve deneysel sonuçlar karşılaştırmalı olarak verilmiştir.

Keywords

• Dimetilmalonat
• Cu(II) Koordinasyon Kompleksi
• Kuantum Kimyasal Hesaplama
• Kristal Yapı
• IR
• UV-Vis

Supporting Institution

State of Planning Organization, Aksaray University Science and Technology Application and Research Center in Aksaray, Turkey, (Grant No:2010K120480 ) and The Research Fund of Giresun University (BAP) under the project FEN-BAP-C-220413-22

Project Number

Grant No:2010K120480 and FEN-BAP-C-220413-22

Thanks

The author expresses sincere gratitude to Dr. Nefise Dilek for her invaluable contribution in collecting X-ray data. Additionally, we extend our acknowledgments to the Aksaray University Science and Technology Application and Research Center in Aksaray, Turkey, for generously providing access to the Bruker SMART BREEZE CCD diffractometer

Synthesis, spectroscopic, crystal structure and DFT investigation of the Cu(II) complex with mixed 2,2’-dimethylmalonate/2,2'-bipyridine ligands

Abstract

In this study; a mixed ligand Cu(II) complex, [Cu(Me2mal)(bpy)(H2O)]∙H2O (Me2mal-2= Dimethylmalonate dianion, bpy=2,2'-bipyridine) was synthesized and characterized experimentally and theoretically by IR, UV and single crystal X-ray diffraction. The complex crystallizes in the orthorhombic system with space group Pnnm. In the complex, the Cu center is coordinated by a Me2mal-2 dianion and a bpy molecule, and the N2O2 exhibits square-planar geometry. The axial position was occupied by the water molecule. The crystal packing of the complex is stabilized by O-H…O hydrogen bonds and  interactions. The contribution of hydrogen bonding and  stacking interactions to crystal packing was also investigated. Theoretical calculations using the DFT method were also carried out in this study. DFT (B3LYP/6-31G) and TD-DFT (B3LYP/LanL2DZ) calculation methods were used to obtain the geometric, vibrational and electronic properties of the synthesized complex and the obtained theoretical calculation results and experimental results are presented comparatively in this study.

Keywords

• Dimethylmalonate
• Cu(II) Coordination Complex
• Quantum Chemical Computation
• Crystal Structure
• IR
• UV-Vis

Project Number

Grant No:2010K120480 and FEN-BAP-C-220413-22

References

1. Pasán, J., Delgado, F.S., Rodrı́guez-Martı́n, Y., Hernández-Molina, M., Ruiz-Pérez, C., Sanchiz, J., Lloret, F., Julve, M., Malonate-based copper(II) coordination compounds: ferromagnetic coupling controlled by dicarboxylates, Polyhedron 22, 2143-2153 (and references therein), (2003).
2. Alderighi, L., Cecconi, F., Ghilardi, C. A., Mederos, A., Midollini, S., Orlandini, A. and Vacca, A., Complexes of beryllium(II) with substituted malonates. Crystal structure of K2[Be(C4H6(COO)2)2]·2H2O. Polyhedron, 18, 3305-3312, (1999).
3. Deniz, M., Hernandez-Rodriguez, I., Pasan, J., Fabelo, O., Canadillas-Delgado, L., Yuste, C., Julve, M., Lloret, F. and Ruiz-Perez, C., Pillaring Role of 4,4′-Azobis(pyridine) in Substituted Malonate-Containing Manganese(II) Complexes: Syntheses, Crystal Structures, and Magnetic Properties. Crystal Growth & Design 12, 4505-4518, (2012).
4. Farnum, G. A., Nettleman, J. H. and LaDuca, R. L., Structure and physical properties of substituted malonate divalent metal coordination polymers with dipyridylamine co-ligands: acentric chain, herringbone layer, and novel binodal network topologies. Crystengcomm, 12, 888-897, (2010).
5. Guo, M.-L. and Wang, F.-Q., Poly[diaquabis([]3-2,2dimethylpropanedioato) calcium(II)copper(II)] Acta Crystallographica Section C-Crystal Structure Communications, 66, M184-M187, (2010a).
6. Guo, M.-L. and Wang, F.-Q., Poly [[aqua-μ3-2, 2-dimethylmalonato-copper (II)] monohydrate] and poly [aqua-μ3-2,2-dimethylmalonato-copper(II)]. Acta Crystallographica Section C-Crystal Structure Communications, 66, M379-M383, (2010b).
7. Guo, M.-L. and Zhao, Y.-N., Poly [aqua-μ3-2,2-dimethylmalonato-zinc(II)]. Acta Crystallographica Section C-Crystal Structure Communications, 62, M563-M565, (2006).
8. Mukhopadhyay, U., Thurston, J. H., Whitmire, K. H. and Khokhar, A. R., Synthesis and characterization of cis-bis-heptamethyleneimine platinum(II) dicarboxylate complexes: crystal structure of cis-[Pt(heptamethyleneimine)2(malonate)]·H2O. Polyhedron, 21, 2369-2374, (2002).

9. Zhang, Y. J., Livens, F. R., Collison, D., Helliwell, M., Heatley, F., Powell, A. K., Wocadlo, S. and Eccles, H., Synthesis and characterisation of uranyl substituted malonato complexes: Part I. Structural diversity with dimethylmalonate and different counter-cations. Polyhedron, 21, 69-79, (2002).
10. Guo, M.-L. and Guo, C.-H., Poly[[aqua­([m]-2,2-dimethyl­malonato)­barium(II)] 2,2-dimethyl­malonic acid solvate]. Acta Crystallographica Section C-Crystal Structure Communications, 64, M398-M400, (2008).
11. Guo, M.-L. and Guo, C.-H., Poly[[diaqua­([m]3-2,2-dimethyl­malonato)­cadmium(II)] tetra­hydrate]. Acta Crystallographica Section C-Crystal Structure Communications, 65, M266-M268, (2009).
12. Yoshinobu Yokomori, Y., Flaherty, K. A., Hodgson, D. J., Barium binding to .gamma.-carboxyglutamate and .beta.-carboxyaspartate residues: structures of barium complexes of benzylmalonate, dimethylmalonate, and ethylmalonate ions. Inorg. Chem. 27, 13, 2300–2306, (1998).
13. Deniz, M., Hernandez-Rodriguez, I., Pasan, J., Fabelo, O., Canadillas-Delgado, L., Vallejo, J., Julve, M., Lloret, F. and Ruiz-Perez, C., Syntheses, crystal structures and magnetic properties of five new Manganese(II) complexes: influence of the conformation of different alkyl/aryl substituted malonate ligands on the crystal packing. Crystengcomm, 16, 2766-2778, (2014).
14. Drommi, D., Saporita, M., Bruno, G., Faraone, F., Scafato, P. and Rosini, C., Origin of enantioselectivity in palladium-catalyzed asymmetric allylic alkylation reactions using chiral N, N-ligands with different rigidity and flexibility. Dalton Transactions, 15, 1509-1519, (2007).
15. Schmeier, T. J., Nova, A., Hazari, N. and Maseras, F., Synthesis of PCP‐Supported Nickel Complexes and their Reactivity with Carbon Dioxide. Chemistry-a European Journal, 18, 6915-6927, (2012).
16. Saenger, W., Defining Terms for the Nucleic Acids. In: Principles of Nucleic Acid Structure. Springer Advanced Texts in Chemistry. Springer, New York, pp 9-28, (1984).
17. Sigel, R. K., and Pyle, A. M., Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry. Chemical reviews, 107(1), 97-113, (2007).
18. Erat, M. C., Zerbe, O., Fox, T., and Sigel, R. K., Solution structure of domain 6 from a self‐splicing group II intron ribozyme: A Mg2+ binding site is located close to the stacked branch adenosine. ChemBioChem, 8(3), 306-314, (2007).
19. Yamauchi, O., Odani, A., Masuda, H., & Sigel, H., Stacking interactions involving nucleotides and metal ion complexes. Metal Ions in Biological Systems, 32, 207-270, (1996).
20. Bruker, SADABS, Bruker AXS Inc., Madison, WI, (2005).
21. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A., & Puschmann, H., OLEX2: a complete structure solution, refinement and analysis program. Journal of applied crystallography, 42(2), 339-341, (2009).
22. Sheldrick, G. M., SHELX-97–Programs for crystal structure determination (SHELXS) and refinement (SHELXL). Acta Crystallogr. A, 64, 112, (2008).
23. Brandenburg, K., DIAMOND Demonstrated Version, Crystal Impact GbR. Bonn, Germany, (2005).
24. Becke, A. D., Density‐functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics, 98 (7), 5648–5652, (1993).
25. Lee, C., Yang, W. and Parr, R.G., Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron Density. Physical Review B, 37, 785-789, (1988).
26. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; PetStefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A., Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford CT, (2004).
27. Frisch, A., Dennington, I. I. R., Keith, T., Millam, J., Nielsen, A. B., Holder, A. J., and Hiscocks, J., Version 4.0, Gaussian Inc, (2007).
28. Jamroz, M. H., Vibrational energy distribution analysis. VEDA 4, Warsaw, (2004).
29. Gross, E. K. U., and Kohn, W., Local density-functional theory of frequency-dependent linear response. Physical review letters, 55(26), 2850-2852, (1985).
30. Caricato, M., Mennucci, B., Tomasi, J., Ingrosso, F., Cammi, R., Corni, S., and Scalmani, G., Formation and relaxation of excited states in solution: A new time dependent polarizable continuum model based on time dependent density functional theory. The Journal of chemical physics, 124(12), 124520, (2006).
31. Kwik, W. L., Ang, K. P., Chan, H. S. O., Chebolu, V., and Koch, S. A., Thermal, spectroscopic, and structural properties of aqua (malonato-O,O′)(1,10-phenanthroline) Copper (II) hydrate (1/1.5). Journal of the Chemical Society, Dalton Transactions, (12), 2519-2523, (1986).
32. Zhang, Q.-Z., Lu, C.-Z., and Yang, W.-B., Synthesis and crystal structure of a Cu(II) complex with mixed malonate/1,10-phenanthroline ligands. Journal of Coordination Chemistry, 58:18, 1759-1764, (2005).
33. Shen, H. Y., Bu, W. M., Liao, D. Z., Jiang, Z. H., Yan, S. P., and Wang, G. L., A new mixed-ligand one dimensional complex via hydrogen bonds: Cu (Mal)(bpy)· 2H2O (Mal= Malonate ion, bpy= 2, 2′-bipyridine). Inorganic Chemistry Communications, 3(9), 497-500, (2000).
34. I.B. Bersuker (Ed.), The Jahn–Teller Effect, Cambridge University Press, Cambridge, p. 609, (2006).
35. Jahn, H. A. and Teller, E., Stability of polyatomic molecules in degenerate electronic states-I—Orbital degeneracy. Proceedings of the Royal Society of London. Series A-Mathematical and Physical Sciences, 161(905), 220-235, (1937).
36. Jahn, H. A., Stability of polyatomic molecules in degenerate electronic states II-Spin degeneracy. Proceedings of the Royal Society of London. Series A-Mathematical and Physical Sciences, 164(916), 117-131, (1938).
37. Moore, E. A. and Janes, R., Metal-Ligand Bonding. Royal Society of Chemistry, p. 108, (2007).
38. B. J. Hathaway, Structure and Bonding, 57, Springer Verlag, New York-Berlin-Heidelberg, p. 56, (1984).
39. Veidis, M. V., Schreiber, G. H., Gough, T. E., and Palenik, G. J., Jahn-Teller distortions in octahedral copper (II) complexes. Journal of the American Chemical Society, 91(7), 1859-1860, (1969).
40. Belicchi, M. F., Gasparri, G. F., Pelizzi, C., and Tarasconi, P., Synthesis and X-ray structures of dinitrato-bis [2-(2′-thienyl)-1-(2′-thienylmethyl) benzimidazole] copper (II) and dichloro-bis-[2-(2′-thienyl)-benzimidazole] copper (II)-ethanol. Transition Metal Chemistry, 10(8), 295-299, (1985).
41. Pearson, R. G., Concerning jahn-teller effects. Proceedings of the National Academy of Sciences, 72(6), 2104-2106, (1975).
42. Reinen, D., and Atanasov, M., Fluxionality and stereochemistry of 5-coordinate Cu2+ complexes. The potential energy surface and spectroscopic implications. Chemical physics, 136(1), 27-46, (1989).
43. Addison, A. W., Rao, T. N., Reedijk, J., van Rijn, J., and Verschoor, G. C., Synthesis, structure, and spectroscopic properties of copper (II) compounds containing nitrogen–sulphur donor ligands; the crystal and molecular structure of aqua [1, 7-bis (N-methylbenzimidazol-2′-yl)-2, 6-dithiaheptane] copper (II) perchlorate. Journal of the Chemical Society, Dalton Transactions, (7), 1349-1356, (1984).
44. Kočanová, I., Kuchár, J., Orendáč, M. and Černák, J., Cu–Ni heterobimetallic compounds. Part 2: Study of the system Cu(II)–bpy–[Ni(CN)4] 2−(bpy= 2, 2′-bipyridine). Polyhedron, 29(18), 3372-3379, (2010).
45. Ferlay, S., Francese, G., Schmalle, H. W. and Decurtins, S., A new bidimensional compound containing (μ-thiocyanate)(bpy) copper(II) molecules: synthesis, crystal structure and magnetic properties of [Cu(bpy)(NCS)2]n (bpy=2,2′-bipyridyl). Inorganica chimica acta, 286(1), 108-113, (1999).
46. Phuengphai, P., Youngme, S., Chaichit, N., Pakawatchai, C., van Albada, G. A., Quesada, M. and Reedijk, J., Crystal structures and magnetic properties of two new phosphate-metal complexes: [Cu2 (bpy) 2 (μ, η2-HPO4)(μ, η1-H2PO4)(μ, η2-H2PO4)] n and [Cu4 (phen)4 (μ3, η2-HPO4)2 (μ, η2-H2PO4) 2(H2PO4)2](H2O)4. Polyhedron, 25(11), 2198-2206, (2006).
47. Youngme, S., Chaichit, N., Pakawatchai, C. and Booncoon, S., The coordination chemistry of mono and bis(di-2-pyridylamine) copper(II) complexes: preparation, characterization and crystal structures of [Cu(L)(NO2)2],[Cu (L)(H2O)2(SO4)],[Cu(L)2(NCS)](SCN)·0.5DMSO and [Cu(L)2(SCN)2]. Polyhedron, 21(12-13), 1279-1288, (2002).
48. Kumar, U., Thomas, J., Nagarajan, R. and Thirupathi, N., 3, 5-Lutidine coordinated zinc (II) aryl carboxylate complexes: Precursors for zinc (II) oxide. Inorganica Chimica Acta, 372(1), 191-199, (2011).
49. Mehrotra R. C. and Bohra, R., Metal Carboxylates, Academic Press, New York, p. 396, (1983).
50. Deacon, G. B. and Phillips, R. J., 1980. Relationships between the carbon-oxygen stretching frequencies of carboxylato complexes and the type of carboxylate coordination. Coordination chemistry reviews, 33(3), 227-250, (1983).
51. Nakamoto, K., Infrared and Raman Spectra of Inorganic and Coordination Compounds: Theory and Applications in Inorganic Chemistry, 5th ed.; John Wiley & Sons: New York, p. 350, (1997).
52. Zeleňák, V., Vargová, Z. and Györyová, K., Correlation of infrared spectra of zinc (II) carboxylates with their structures. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 66(2), 262-272, (2007).
53. Fleming, I., Frontier Orbitals and Organic Chemical Reactions, John Wiley & Sons, New York, p. 249, (1976).
54. Obot, I. B., Obi-Egbedi, N. O., Eseola, A.O., Anticorrosion Potential of 2-Mesityl-1H-imidazo[4,5-f][1,10]phenanthroline on Mild Steel in Sulfuric Acid Solution: Experimental and Theoretical Study, Industrial & Engineering Chemistry Research, 50, 2098, (2011).
55. Obot, I. B., Obi-Egbedi, N. O., Theoretical study of benzimidazole and its derivatives and their potential activity as corrosion inhibitors, Corrosion Science, Volume 52, Issue 2, Pages 657-660, (2010).
56. Obreedot, I. B. and Obi-Egbedi, N. O., Anti-corrosive properties of xanthone on mild steel corrosion in sulphuric acid: Experimental and theoretical investigations, Current Applied Physics, Volume 11, Issue 3, Pages 382-392, (2011)
57. Foster, A. J. and Weinhold, F., Natural hybrid orbitals. Journal of the American Chemical Society, 102(24), 7211-7218, (1980).
58. Reed, A. E. and Weinhold, F., Natural bond orbital analysis of near‐Hartree–Fock water dimer. The Journal of Chemical Physics, 78(6), 4066-4073, (1983).
59. Reed, A. E., Weinstock, R. B., and Weinhold, F., Natural population analysis. The Journal of Chemical Physics, 83(2), 735-746, (1985).
60. Reed, A. E. and Weinhold, F., Natural localized molecular orbitals. The Journal of Chemical Physics, 83(4), 1736-1740, (1985).
61. Carpenter, J. E. and Weinhold, F., Analysis of the geometry of the hydroxymethyl radical by the “different hybrids for different spins” natural bond orbital procedure. Journal of Molecular Structure: THEOCHEM, 169, 41-62, (1988).
62. Reed, A. E., Curtiss, L. A. and Weinhold, F., Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chemical Reviews, 88(6), 899-926, (1988).