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Hirshfeld Surface Analysis and Interactions Energy Calculations of Metal (II) 4-Cyanobenzoate with Nicotinamide / N,N'-Diethylnicotinamide Complexes

Yıl 2021, Cilt: 8 Sayı: 1, 125 - 136, 28.02.2021
https://doi.org/10.18596/jotcsa.824551

Öz

Hirshfeld surface analysis, a suitable tool for investigating intermolecular interactions, has been widely used in crystallography in recent years. A breakdown of related fingerprint graphics is presented as a color chart, allowing a quantitative analysis of intermolecular interaction types. In this study, the intermolecular interactions of di¬aqua¬bis¬(4-cyano-benzoato-κO)bis¬(nicotinamide-κN1)cobalt(II) (I), di¬aqua¬bis¬(4-cyano¬benzoato-κO)bis-(nicotinamide-κN1)copper(II) (II), di¬aqua¬bis¬(4-cyano¬benzoato-κO)bis¬(nicotinamide-κN1)nickel(II) (III), triaqua(4-cyanobenzoato-κ2O,O')(nicotinamide-κN)zinc(II) 4-cyanobenzoate (IV), diaquabis(4-cyanobenzoato-κO)bis(N,N’-diethylnicotinamide-κN)cadmium(II) (V), di¬aqua¬bis¬(4-cyano¬benzoato-κO)bis¬(N,N’-di¬ethyl¬nicotinamide-κN)zinc(II) (VI) and catena-poly[[aquabis(4-cyanobenzoato-κO)copper(II)]-μ-N,N’-diethylnicotinamide-κ2N1:O] (VII) complexes, which are the crystal structures were previously determined, were and investigated by using Hirshfeld surface analysis via CrystalExplorer Program Version 17.5. In addition, the intermolecular interaction energies of the complexes were calculated using CE-HF/3-21G and CE-B3LYP/6-31G (d,p) energy models that involved in CrystalExplorer (CE) program. Related to the obtained Hirshfeld surface analysis results, H…H, H…C/C…H, H…O/O…H, H…N/N…H, C…C, C…N/N…C and C…O/O…C constitute the intermolecular interactions of the complexes. Additionally, N…O/O…N and N…N interactions only in I, II, III, IV and VII complexes, H...Cu/Cu...H, O...Cu/Cu...O only in complexes II and VII and O...O interactions only in complexes II, V and VI were also found. The most significant interactions of all of the complexes were found as the H…H interactions. These results support the existence of π-π interactions between benzene and pyridine rings and medium strength hydrogen bonds which contribute to the stability of the crystal packing of the complexes that are determined by single crystal X-ray diffraction method. Depending on the intermolecular interactions and the energy-framework analysis the O-H...O and N-H...O hydrogen bonds, and π···π stacking and C−H···π interaction energies are the most significant forces in the crystal packaging. The estimation of the intermolecular interactions and electrostatic energy values of the complexes are very important for the classification of them for their electrical, magnetic and optical properties.

Teşekkür

The authors would like to thank Ömer Aydoğdu and Gamze Yılmaz Nayir for their valuable contributions.

Kaynakça

  • 1. Philp D, Stoddart JF. Self-Assembly in Natural and Unnatural Systems. Angew Chem Int Ed Engl. 1996;35(11):1154-96.
  • 2. Głowacki ED, Irimia-Vladu M, Bauer S, Sariciftci NS. Hydrogen-bonds in molecular solids – from biological systems to organic electronics. J Mater Chem B. 2013;1(31):3742.
  • 3. Seth SK, Manna P, Singh NJ, Mitra M, Jana AD, Das A, vd. Molecular architecture using novel types of non-covalent π-interactions involving aromatic neutrals, aromatic cations and π-anions. CrystEngComm. 2013;15(7):1285.
  • 4. Martin AD, Britton J, Easun TL, Blake AJ, Lewis W, Schröder M. Hirshfeld Surface Investigation of Structure-Directing Interactions within Dipicolinic Acid Derivatives. Crystal Growth & Design. 2015;15(4):1697-706.
  • 5. Maity T, Mandal H, Bauzá A, Samanta BC, Frontera A, Seth SK. Quantifying conventional C–H⋯π(aryl) and unconventional C–H⋯π(chelate) interactions in dinuclear Cu( II ) complexes: experimental observations, Hirshfeld surface and theoretical DFT study. New J Chem. 2018;42(12):10202-13.
  • 6. Kirste B. Applications of Density Functional Theory to Theoretical Organic Chemistry. Chem Sci J [İnternet]. 2016 [a.yer 07 Mayıs 2020];7(2). Link: https://www.omicsonline.com/open-access/applications-of-density-functional-theory-to-theoretical-organicchemistry-2150-3494-1000127.php?aid=73993
  • 7. Turner MJ, McKinnon JJ, Wolff SK, Grimwood DJ, Spackman PR, Jayatilaka D, Spackman MA. CrystalExplorer17 (2017). University of Western Australia.
  • 8. Tan SL, Jotani MM, Tiekink ERT. Utilizing Hirshfeld surface calculations, non-covalent interaction (NCI) plots and the calculation of interaction energies in the analysis of molecular packing. Acta Crystallogr E Cryst Commun. 2019;75(3):308-18.
  • 9. Hirshfeld FL. Bonded-atom fragments for describing molecular charge densities. Theoret Chim Acta. 1977;44(2):129-38.
  • 10. McKinnon JJ, Jayatilaka D, Spackman MA. Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chem Commun. 2007;(37):3814.
  • 11. Spackman MA, Jayatilaka D. Hirshfeld surface analysis. CrystEngComm. 2009;11(1):19-32.
  • 12. Aşkın GŞ, Necefoğlu H, Yılmaz Nayir G, Çatak Çelik R, Hökelek T. Crystal structure of trans -diaquabis(4-cyanobenzoato-κ O )bis(nicotinamide-κ N 1 )cobalt(II). Acta Crystallogr E Cryst Commun. 2015;71(5):561-3.
  • 13. Özbek FE, Sertçelik M, Yüksek M, Necefoğlu H, Çelik RÇ, Nayir GY, vd. Cu(II) and Ni(II) 4-cyanobenzoate complexes with nicotinamide: Synthesis, spectral, structural and optical characterization and thermal behavior. Journal of Molecular Structure. 2017;1150:112-7.
  • 14. Aşkın GŞ, Necefoğlu H, Yılmaz Nayir G, Çatak Çelik R, Hökelek T. Crystal structure of triaqua(4-cyanobenzoato-κ 2 O , O ′)(nicotinamide-κ N 1 )zinc 4-cyanobenzoate. Acta Crystallogr E Cryst Commun. 2015;71(6):684-6.
  • 15. Akduran N, Sertçelik M, Aydoğdu Ö, Necefoğlu H, Hökelek T. Crystal structure of trans -diaquabis(4-cyanobenzoato-κ O )bis( N , N -diethylnicotinamide-κ N )cadmium. Acta Crystallogr E Cryst Commun. 2016;72(12):1827-9.
  • 16. Akduran N, Necefoğlu H, Aydoğdu Ö, Hökelek T. Crystal structure of trans -diaquabis(4-cyanobenzoato-κ O )bis( N , N -diethylnicotinamide-κ N )zinc(II). Acta Crystallogr E Cryst Commun. 2016;72(10):1374-6.
  • 17. Akduran N, Necefoğlu H, Aydoğdu Ö, Hökelek T. Crystal structure of catena -poly[[aquabis(4-cyanobenzoato-κ O )copper(II)]-μ- N , N -diethylnicotinamide-κ 2 N 1 : O ]. Acta Crystallographica Section E Crystallographic Communications. 2016;72(8):1183-6.
  • 18. Özbek FE, Sertçelik M, Yüksek M, Uğurlu G, Tonbul AM, Necefoğlu H, vd. Synthesis and Crystallographic, Absorption and Emission Studies of 4-Pyridine Carboxamide of Zn(II) 4-Chlorophenylacetate. J Fluoresc. 2019;29(5):1265-75.
  • 19. Jayatilaka D, Grimwood DJ. Tonto: A Fortran Based Object-Oriented System for Quantum Chemistry and Crystallography. in: Sloot PMA, Abramson D, Bogdanov AV, Gorbachev YE, Dongarra JJ, Zomaya AY, Eds. Computational Science — ICCS 2003 [İnternet]. Berlin, Heidelberg: Springer Berlin Heidelberg; 2003 [a.yer 01 Ekim 2020]. s. 142-51. (Goos G, Hartmanis J, van Leeuwen J. Lecture Notes in Computer Science; c. 2660). Link: http://link.springer.com/10.1007/3-540-44864-0_15
  • 20. Mackenzie CF, Spackman PR, Jayatilaka D, Spackman MA. CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCrJ. 2017;4(5):575-87.
  • 21. Spackman MA, McKinnon JJ, Jayatilaka D. Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm. 2008;10.1039.b715227b.
  • 22. Caracelli I, Zukerman-Schpector J, Schwab RS, Silva EM da, Jotani MM, Tiekink ERT. 2-Methyl-4-(4-nitrophenyl)but-3-yn-2-ol: crystal structure, Hirshfeld surface analysis and computational chemistry study. Acta Crystallogr E Cryst Commun. 2019;75(8):1232-8.
  • 23. Etse KS, Lamela LC, Zaragoza G, Pirotte B. Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. Eur J Chem. 2020;11(2):91-9.
  • 24. Madan Kumar S. 3D energy frameworks of dimethylbenzophenone tetramorphs. Heliyon. 2019;5(2):e01209.
Yıl 2021, Cilt: 8 Sayı: 1, 125 - 136, 28.02.2021
https://doi.org/10.18596/jotcsa.824551

Öz

Kaynakça

  • 1. Philp D, Stoddart JF. Self-Assembly in Natural and Unnatural Systems. Angew Chem Int Ed Engl. 1996;35(11):1154-96.
  • 2. Głowacki ED, Irimia-Vladu M, Bauer S, Sariciftci NS. Hydrogen-bonds in molecular solids – from biological systems to organic electronics. J Mater Chem B. 2013;1(31):3742.
  • 3. Seth SK, Manna P, Singh NJ, Mitra M, Jana AD, Das A, vd. Molecular architecture using novel types of non-covalent π-interactions involving aromatic neutrals, aromatic cations and π-anions. CrystEngComm. 2013;15(7):1285.
  • 4. Martin AD, Britton J, Easun TL, Blake AJ, Lewis W, Schröder M. Hirshfeld Surface Investigation of Structure-Directing Interactions within Dipicolinic Acid Derivatives. Crystal Growth & Design. 2015;15(4):1697-706.
  • 5. Maity T, Mandal H, Bauzá A, Samanta BC, Frontera A, Seth SK. Quantifying conventional C–H⋯π(aryl) and unconventional C–H⋯π(chelate) interactions in dinuclear Cu( II ) complexes: experimental observations, Hirshfeld surface and theoretical DFT study. New J Chem. 2018;42(12):10202-13.
  • 6. Kirste B. Applications of Density Functional Theory to Theoretical Organic Chemistry. Chem Sci J [İnternet]. 2016 [a.yer 07 Mayıs 2020];7(2). Link: https://www.omicsonline.com/open-access/applications-of-density-functional-theory-to-theoretical-organicchemistry-2150-3494-1000127.php?aid=73993
  • 7. Turner MJ, McKinnon JJ, Wolff SK, Grimwood DJ, Spackman PR, Jayatilaka D, Spackman MA. CrystalExplorer17 (2017). University of Western Australia.
  • 8. Tan SL, Jotani MM, Tiekink ERT. Utilizing Hirshfeld surface calculations, non-covalent interaction (NCI) plots and the calculation of interaction energies in the analysis of molecular packing. Acta Crystallogr E Cryst Commun. 2019;75(3):308-18.
  • 9. Hirshfeld FL. Bonded-atom fragments for describing molecular charge densities. Theoret Chim Acta. 1977;44(2):129-38.
  • 10. McKinnon JJ, Jayatilaka D, Spackman MA. Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chem Commun. 2007;(37):3814.
  • 11. Spackman MA, Jayatilaka D. Hirshfeld surface analysis. CrystEngComm. 2009;11(1):19-32.
  • 12. Aşkın GŞ, Necefoğlu H, Yılmaz Nayir G, Çatak Çelik R, Hökelek T. Crystal structure of trans -diaquabis(4-cyanobenzoato-κ O )bis(nicotinamide-κ N 1 )cobalt(II). Acta Crystallogr E Cryst Commun. 2015;71(5):561-3.
  • 13. Özbek FE, Sertçelik M, Yüksek M, Necefoğlu H, Çelik RÇ, Nayir GY, vd. Cu(II) and Ni(II) 4-cyanobenzoate complexes with nicotinamide: Synthesis, spectral, structural and optical characterization and thermal behavior. Journal of Molecular Structure. 2017;1150:112-7.
  • 14. Aşkın GŞ, Necefoğlu H, Yılmaz Nayir G, Çatak Çelik R, Hökelek T. Crystal structure of triaqua(4-cyanobenzoato-κ 2 O , O ′)(nicotinamide-κ N 1 )zinc 4-cyanobenzoate. Acta Crystallogr E Cryst Commun. 2015;71(6):684-6.
  • 15. Akduran N, Sertçelik M, Aydoğdu Ö, Necefoğlu H, Hökelek T. Crystal structure of trans -diaquabis(4-cyanobenzoato-κ O )bis( N , N -diethylnicotinamide-κ N )cadmium. Acta Crystallogr E Cryst Commun. 2016;72(12):1827-9.
  • 16. Akduran N, Necefoğlu H, Aydoğdu Ö, Hökelek T. Crystal structure of trans -diaquabis(4-cyanobenzoato-κ O )bis( N , N -diethylnicotinamide-κ N )zinc(II). Acta Crystallogr E Cryst Commun. 2016;72(10):1374-6.
  • 17. Akduran N, Necefoğlu H, Aydoğdu Ö, Hökelek T. Crystal structure of catena -poly[[aquabis(4-cyanobenzoato-κ O )copper(II)]-μ- N , N -diethylnicotinamide-κ 2 N 1 : O ]. Acta Crystallographica Section E Crystallographic Communications. 2016;72(8):1183-6.
  • 18. Özbek FE, Sertçelik M, Yüksek M, Uğurlu G, Tonbul AM, Necefoğlu H, vd. Synthesis and Crystallographic, Absorption and Emission Studies of 4-Pyridine Carboxamide of Zn(II) 4-Chlorophenylacetate. J Fluoresc. 2019;29(5):1265-75.
  • 19. Jayatilaka D, Grimwood DJ. Tonto: A Fortran Based Object-Oriented System for Quantum Chemistry and Crystallography. in: Sloot PMA, Abramson D, Bogdanov AV, Gorbachev YE, Dongarra JJ, Zomaya AY, Eds. Computational Science — ICCS 2003 [İnternet]. Berlin, Heidelberg: Springer Berlin Heidelberg; 2003 [a.yer 01 Ekim 2020]. s. 142-51. (Goos G, Hartmanis J, van Leeuwen J. Lecture Notes in Computer Science; c. 2660). Link: http://link.springer.com/10.1007/3-540-44864-0_15
  • 20. Mackenzie CF, Spackman PR, Jayatilaka D, Spackman MA. CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCrJ. 2017;4(5):575-87.
  • 21. Spackman MA, McKinnon JJ, Jayatilaka D. Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm. 2008;10.1039.b715227b.
  • 22. Caracelli I, Zukerman-Schpector J, Schwab RS, Silva EM da, Jotani MM, Tiekink ERT. 2-Methyl-4-(4-nitrophenyl)but-3-yn-2-ol: crystal structure, Hirshfeld surface analysis and computational chemistry study. Acta Crystallogr E Cryst Commun. 2019;75(8):1232-8.
  • 23. Etse KS, Lamela LC, Zaragoza G, Pirotte B. Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. Eur J Chem. 2020;11(2):91-9.
  • 24. Madan Kumar S. 3D energy frameworks of dimethylbenzophenone tetramorphs. Heliyon. 2019;5(2):e01209.
Toplam 24 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular İnorganik Kimya
Bölüm Makaleler
Yazarlar

Füreya Elif Öztürkkan 0000-0001-6376-4161

Mustafa Sertçelik 0000-0001-7919-7907

Mustafa Yüksek 0000-0003-2169-1827

Hacali Necefoğlu 0000-0003-2901-3748

Tuncer Hökelek 0000-0002-8602-4382

Yayımlanma Tarihi 28 Şubat 2021
Gönderilme Tarihi 11 Kasım 2020
Kabul Tarihi 2 Aralık 2020
Yayımlandığı Sayı Yıl 2021 Cilt: 8 Sayı: 1

Kaynak Göster

Vancouver Öztürkkan FE, Sertçelik M, Yüksek M, Necefoğlu H, Hökelek T. Hirshfeld Surface Analysis and Interactions Energy Calculations of Metal (II) 4-Cyanobenzoate with Nicotinamide / N,N’-Diethylnicotinamide Complexes. JOTCSA. 2021;8(1):125-36.