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Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies.

Year 2022, Volume: 9 Issue: 2, 153 - 167, 31.12.2022
https://doi.org/10.48138/cjo.1205712

Abstract

CrystalExplorer program is a program that has been used frequently in the field of theoretical chemistry in recent years and its popularity has increased. First of all, Hirshfeld surface analysis of molecules can be done in this program. Thanks to Hirshfeld surface analysis, intermolecular interactions and their contributions to the crystal surface can be determined. In this study, Hirshfeld surface analyzes and energy frameworks of nicotinamide complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-formylbenzoate were investigated. Dnorm index, shape index, curvature index and 2D fingerprint graphs were examined for all complexes. In addition, the intermolecular interaction energies of the complexes were calculated using the CE-B3LYP/6-31G (d,p) and CEHF/3-21G energy models. As a result of all these, it was seen that the most important interaction in the four isostructured complexes was H...H interactions.
According to Hirshfeld surface analysis and energy frameworks, O-H...O and N-H...O hydrogen bonds and π•••π stacking and C−H••π interaction energies are seen as the most important interaction types in the crystal structure.

References

  • Etse, K. S., Lamela, L. C., Zaragoza, G., & Pirotte, B. (2020). Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. European Journal of Chemistry, 11(2), Article 2. https://doi.org/10.5155/eurjchem.11.2.91-99.1973
  • Huseynova, M., Farzaliyev, V., Medjidov, A., Aliyeva, M., Taslimi, P., Sahin, O., & Yalçın, B. (2020). Novel zinc compound with thiosemicarbazone of glyoxylic acid: Synthesis, crystal structure, and bioactivity properties. Journal of Molecular Structure, 1200, 127082. https://doi.org/10.1016/j.molstruc.2019.127082
  • Huseynova, M., Medjidov, A., Taslimi, P., & Aliyeva, M. (2019). Synthesis, characterization, crystal structure of the coordination polymer Zn (II) with thiosemicarbazone of glyoxalic acid and their inhibitory properties against some metabolic enzymes. Bioorganic Chemistry, 83, 55–62. https://doi.org/10.1016/j.bioorg.2018.10.012
  • Huseynova, M. T. (2021). DFT calculations, hirshfeld analysis, antimicrobial, antifungal properties of the Cu(II) polymeric complex with thiosemicarbazone of glyoxylic acid. Azerbaijan Chemical Journal, 4, 77–81. Scopus. Irak, Z. T., & Beytur, M. (2019). 4-Benzilidenamino-4,5-dihidro-1H-1,2,4-triazol-5-on Türevlerinin Antioksidan Aktivitelerinin Teorik Olarak İncelenmesi. Journal of the Institute of Science and Technology, 9(1), Article 1. https://doi.org/10.21597/jist.481990
  • Jayatilaka, D., Grimwood, D. J., Lee, A., Lemay, A., Russel, A. J., Taylor, C., Wolff, S. K., Cassam-Chenai, P., & Whitton, A. (2005). TONTO - A System for Computational Chemistry. Available at: Http://hirshfeldsurface.net/. Kirste, B. (2016). Applications of Density Functional Theory to Theoretical Organic Chemistry. https://doi.org/10.4172/2150-3494.1000127
  • Koç, E., Yüksek, H., Beytur, M., Akyıldırım, O., Akçay, M., Beytur, C. (2020). In vivo determination of antioxidant property of heterocyclic 4,5 dihydro-1H-1, 2, 4- triazol 5-one derivate in male rats (wistar albino). Bitlis Eren University Journal of Science, 9, 542-548.
  • Kotan, G., Gökce, H., Akyıldırım, O., Yüksek, H., Beytur, M., Manap, S., & Medetalibeyoğlu, H. (2020). Synthesis, Spectroscopic and Computational Analysis of 2-[(2-Sulfanyl-1H-benzo[d]imidazol-5-yl)iminomethyl]phenyl Naphthalene-2-sulfonate. Russian Journal of Organic Chemistry, 56(11), 1982–1994. https://doi.org/10.1134/S1070428020110135
  • Mackenzie, C. F., Spackman, P. R., Jayatilaka, D., & Spackman, M. A. (2017). CrystalExplorer model energies and energy frameworks: Extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCrJ, 4(Pt 5), 575–587. https://doi.org/10.1107/S205225251700848X
  • Madan Kumar, S. (2019). 3D energy frameworks of dimethylbenzophenone tetramorphs. Heliyon, 5(2), e01209. https://doi.org/10.1016/j.heliyon.2019.e01209
  • McKinnon, J. J., Jayatilaka, D., & Spackman, M. A. (2007). Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chemical Communications (Cambridge, England), 37, 3814–3816.
  • Omoregie, H. O., Oloba-Whenu, O. A., Olowu, O. J., Fasina, T. M., Friedrich, A., Haehnel, M., & Marder, T. B. (2022). Mixed-ligand complexes of copper(II) with thienoyltrifluoroacetonate and nitrogen containing ligands: Synthesis, structures, antimicrobial activity, cytotoxicity, Hirshfeld surface analysis and DFT studies. RSC Advances, 12(36), 23513–23526. https://doi.org/10.1039/D2RA02428D
  • Sertçelik, M. (2021). Synthesis, spectroscopic properties, crystal structures, DFT studies, and the antibacterial and enzyme inhibitory properties of a complex of Co(II) 3,5-difluorobenzoate with 3-pyridinol. Journal of Chemical Research, 45(1–2), 42–48. https://doi.org/10.1177/1747519820924636
  • Sertçelik, M., Çaylak Delibaş, N., Çevik, S., Necefoğlu, H., & Hökelek, T. (2012). Poly[(μ5-2,2′-bipyridine-5,5′-dicarboxyl­ato)lead(II)]. Acta Crystallographica Section E: Structure Reports Online, 68(9), Article 9. https://doi.org/10.1107/S1600536812035647
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012a). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)copper(II). Acta Crystallographica Section E: Structure Reports Online, 68(7), Article 7. https://doi.org/10.1107/S1600536812028814
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012b). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)nickel(II). Acta Crystallographica Section E: Structure Reports Online, 68(7), Article 7. https://doi.org/10.1107/S1600536812026943
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012c). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)cobalt(II). Acta Crystallographica Section E: Structure Reports Online, 68(8), Article 8. https://doi.org/10.1107/S1600536812032205
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012d). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)zinc. Acta Crystallographica Section E: Structure Reports Online, 68(8), Article 8. https://doi.org/10.1107/S160053681203320X
  • Sertcelik, M., & Durman, M. (2020). Synthesis, Characterization, and Antibacterial Activity of Cd(II) Complexes with 3-/4-Fluorobenzoates and 3-Hydroxypiridine as Co-Ligands. Russian Journal of Inorganic Chemistry, 65(9), 1351–1359. https://doi.org/10.1134/S0036023620090168
  • Sertçeli̇k, M., Sugeçti̇, S., Büyükgüzel, E., Necefoğlu, H., & Büyükgüzel, K. (2018). Diaquabis N,N-dietilnikotinamid-lN1 bis 4-formilbenzoato-lO kobalt II Kompleksinin Model Organizma Galleria mellonella L. Lepidoptera: Pyralidae Üzerindeki Toksikolojik ve Fizyolojik Etkileri. Karaelmas Fen ve Mühendislik Dergisi, 8(1), Article 1. Spackman, M. A., & Jayatilaka, D. (2009). Hirshfeld surface analysis. CrystEngComm, 11(1), 19–32. https://doi.org/10.1039/B818330A
  • Spackman, M. A., McKinnon, J. J., & Jayatilaka, D. (2008). Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm, 10(4), 377–388. https://doi.org/10.1039/B715227B
  • Sugeçti, S., & Büyükgüzel, K. (2022). Effects of Ni (II) p-hydroxybenzoate with caffeine on metabolic, antioxidant, andbiochemical parameters of model insect Galleria mellonella L. (Lepidoptera: Pyralidae). Turkish Journal of Zoology, 46(1), 167–174. https://doi.org/10.3906/zoo-2110-6
  • Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D., & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia.
  • Venkatesan, P., Thamotharan, S., Ilangovan, A., Liang, H., & Sundius, T. (2016). Crystal structure, Hirshfeld surfaces and DFT computation of NLO active (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid. Spectrochimica Acta Part A-Molecular and Biomolecular Spectroscopy, 153, 625–636. https://doi.org/10.1016/j.saa.2015.09.002
Year 2022, Volume: 9 Issue: 2, 153 - 167, 31.12.2022
https://doi.org/10.48138/cjo.1205712

Abstract

References

  • Etse, K. S., Lamela, L. C., Zaragoza, G., & Pirotte, B. (2020). Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione. European Journal of Chemistry, 11(2), Article 2. https://doi.org/10.5155/eurjchem.11.2.91-99.1973
  • Huseynova, M., Farzaliyev, V., Medjidov, A., Aliyeva, M., Taslimi, P., Sahin, O., & Yalçın, B. (2020). Novel zinc compound with thiosemicarbazone of glyoxylic acid: Synthesis, crystal structure, and bioactivity properties. Journal of Molecular Structure, 1200, 127082. https://doi.org/10.1016/j.molstruc.2019.127082
  • Huseynova, M., Medjidov, A., Taslimi, P., & Aliyeva, M. (2019). Synthesis, characterization, crystal structure of the coordination polymer Zn (II) with thiosemicarbazone of glyoxalic acid and their inhibitory properties against some metabolic enzymes. Bioorganic Chemistry, 83, 55–62. https://doi.org/10.1016/j.bioorg.2018.10.012
  • Huseynova, M. T. (2021). DFT calculations, hirshfeld analysis, antimicrobial, antifungal properties of the Cu(II) polymeric complex with thiosemicarbazone of glyoxylic acid. Azerbaijan Chemical Journal, 4, 77–81. Scopus. Irak, Z. T., & Beytur, M. (2019). 4-Benzilidenamino-4,5-dihidro-1H-1,2,4-triazol-5-on Türevlerinin Antioksidan Aktivitelerinin Teorik Olarak İncelenmesi. Journal of the Institute of Science and Technology, 9(1), Article 1. https://doi.org/10.21597/jist.481990
  • Jayatilaka, D., Grimwood, D. J., Lee, A., Lemay, A., Russel, A. J., Taylor, C., Wolff, S. K., Cassam-Chenai, P., & Whitton, A. (2005). TONTO - A System for Computational Chemistry. Available at: Http://hirshfeldsurface.net/. Kirste, B. (2016). Applications of Density Functional Theory to Theoretical Organic Chemistry. https://doi.org/10.4172/2150-3494.1000127
  • Koç, E., Yüksek, H., Beytur, M., Akyıldırım, O., Akçay, M., Beytur, C. (2020). In vivo determination of antioxidant property of heterocyclic 4,5 dihydro-1H-1, 2, 4- triazol 5-one derivate in male rats (wistar albino). Bitlis Eren University Journal of Science, 9, 542-548.
  • Kotan, G., Gökce, H., Akyıldırım, O., Yüksek, H., Beytur, M., Manap, S., & Medetalibeyoğlu, H. (2020). Synthesis, Spectroscopic and Computational Analysis of 2-[(2-Sulfanyl-1H-benzo[d]imidazol-5-yl)iminomethyl]phenyl Naphthalene-2-sulfonate. Russian Journal of Organic Chemistry, 56(11), 1982–1994. https://doi.org/10.1134/S1070428020110135
  • Mackenzie, C. F., Spackman, P. R., Jayatilaka, D., & Spackman, M. A. (2017). CrystalExplorer model energies and energy frameworks: Extension to metal coordination compounds, organic salts, solvates and open-shell systems. IUCrJ, 4(Pt 5), 575–587. https://doi.org/10.1107/S205225251700848X
  • Madan Kumar, S. (2019). 3D energy frameworks of dimethylbenzophenone tetramorphs. Heliyon, 5(2), e01209. https://doi.org/10.1016/j.heliyon.2019.e01209
  • McKinnon, J. J., Jayatilaka, D., & Spackman, M. A. (2007). Towards quantitative analysis of intermolecular interactions with Hirshfeld surfaces. Chemical Communications (Cambridge, England), 37, 3814–3816.
  • Omoregie, H. O., Oloba-Whenu, O. A., Olowu, O. J., Fasina, T. M., Friedrich, A., Haehnel, M., & Marder, T. B. (2022). Mixed-ligand complexes of copper(II) with thienoyltrifluoroacetonate and nitrogen containing ligands: Synthesis, structures, antimicrobial activity, cytotoxicity, Hirshfeld surface analysis and DFT studies. RSC Advances, 12(36), 23513–23526. https://doi.org/10.1039/D2RA02428D
  • Sertçelik, M. (2021). Synthesis, spectroscopic properties, crystal structures, DFT studies, and the antibacterial and enzyme inhibitory properties of a complex of Co(II) 3,5-difluorobenzoate with 3-pyridinol. Journal of Chemical Research, 45(1–2), 42–48. https://doi.org/10.1177/1747519820924636
  • Sertçelik, M., Çaylak Delibaş, N., Çevik, S., Necefoğlu, H., & Hökelek, T. (2012). Poly[(μ5-2,2′-bipyridine-5,5′-dicarboxyl­ato)lead(II)]. Acta Crystallographica Section E: Structure Reports Online, 68(9), Article 9. https://doi.org/10.1107/S1600536812035647
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012a). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)copper(II). Acta Crystallographica Section E: Structure Reports Online, 68(7), Article 7. https://doi.org/10.1107/S1600536812028814
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012b). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)nickel(II). Acta Crystallographica Section E: Structure Reports Online, 68(7), Article 7. https://doi.org/10.1107/S1600536812026943
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012c). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)cobalt(II). Acta Crystallographica Section E: Structure Reports Online, 68(8), Article 8. https://doi.org/10.1107/S1600536812032205
  • Sertçelik, M., Çaylak Delibaş, N., Necefoğlu, H., & Hökelek, T. (2012d). Diaqua­bis­(4-formyl­benzoato-κO1)bis­(nicotinamide-κN1)zinc. Acta Crystallographica Section E: Structure Reports Online, 68(8), Article 8. https://doi.org/10.1107/S160053681203320X
  • Sertcelik, M., & Durman, M. (2020). Synthesis, Characterization, and Antibacterial Activity of Cd(II) Complexes with 3-/4-Fluorobenzoates and 3-Hydroxypiridine as Co-Ligands. Russian Journal of Inorganic Chemistry, 65(9), 1351–1359. https://doi.org/10.1134/S0036023620090168
  • Sertçeli̇k, M., Sugeçti̇, S., Büyükgüzel, E., Necefoğlu, H., & Büyükgüzel, K. (2018). Diaquabis N,N-dietilnikotinamid-lN1 bis 4-formilbenzoato-lO kobalt II Kompleksinin Model Organizma Galleria mellonella L. Lepidoptera: Pyralidae Üzerindeki Toksikolojik ve Fizyolojik Etkileri. Karaelmas Fen ve Mühendislik Dergisi, 8(1), Article 1. Spackman, M. A., & Jayatilaka, D. (2009). Hirshfeld surface analysis. CrystEngComm, 11(1), 19–32. https://doi.org/10.1039/B818330A
  • Spackman, M. A., McKinnon, J. J., & Jayatilaka, D. (2008). Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm, 10(4), 377–388. https://doi.org/10.1039/B715227B
  • Sugeçti, S., & Büyükgüzel, K. (2022). Effects of Ni (II) p-hydroxybenzoate with caffeine on metabolic, antioxidant, andbiochemical parameters of model insect Galleria mellonella L. (Lepidoptera: Pyralidae). Turkish Journal of Zoology, 46(1), 167–174. https://doi.org/10.3906/zoo-2110-6
  • Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D., & Spackman, M. A. (2017). CrystalExplorer17. University of Western Australia.
  • Venkatesan, P., Thamotharan, S., Ilangovan, A., Liang, H., & Sundius, T. (2016). Crystal structure, Hirshfeld surfaces and DFT computation of NLO active (2E)-2-(ethoxycarbonyl)-3-[(1-methoxy-1-oxo-3-phenylpropan-2-yl)amino] prop-2-enoic acid. Spectrochimica Acta Part A-Molecular and Biomolecular Spectroscopy, 153, 625–636. https://doi.org/10.1016/j.saa.2015.09.002
There are 23 citations in total.

Details

Primary Language English
Subjects Environmental Sciences
Journal Section Articles
Authors

Mustafa Sertçelik 0000-0001-7919-7907

Publication Date December 31, 2022
Submission Date November 16, 2022
Acceptance Date December 22, 2022
Published in Issue Year 2022 Volume: 9 Issue: 2

Cite

APA Sertçelik, M. (2022). Determination of Intermolecular Interactions of Nicotinamide Liganded Complexes of Co(II), Cu(II), Ni(II) and Zn(II) 4-Formilbenzoates by Hirshfeld Surface Analysis and Investigation of Interaction Energies. Caucasian Journal of Science, 9(2), 153-167. https://doi.org/10.48138/cjo.1205712

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