European Journal of Chemistry

Molecular self-assembly in indole-based benzamide derivative: Crystal structure, Hirshfeld surfaces and antimicrobial activity


Main Article Content

Ilkay Gumus
Ummuhan Solmaz
Serpil Gonca
Hakan Arslan


Two new compounds, 1H-indole-7-amine (1) and N-(1H-indol-7-yl)-2-methylbenzamide (2) were synthesized and structurally characterized by NMR and FT-IR spectroscopic techniques. The molecular structure of compound 2 was further elucidated by single-crystal X-ray diffraction technique. Moreover, the crystal packing of compound 2 is analyzed in terms of non-covalent N-H···O, C-H···π, and parallel displaced π···π interactions. Hirshfeld surface analysis and decomposed fingerprint plots of the compound 2 were performed to visualize the presence of strong hydrogen bond N-H···O and C-H···π stacking interactions. Hirshfeld surface analysis and decomposed fingerprint plots show that the structure of compound 2 is stabilized by H···H, N-H···O, C-H···π and π···π intermolecular interactions and these interactions contribute mostly to molecular self-assembly in the crystal. In addition, compound 2 was evaluated for both their in-vitro antibacterial and antifungal activity. The obtained results have been reported, explained and compared with fluconazole and ampicillin used as reference drugs.

icon graph This Abstract was viewed 2020 times | icon graph Article PDF downloaded 734 times icon graph Article CIF FILE downloaded 0 times

How to Cite
Gumus, I.; Solmaz, U.; Gonca, S.; Arslan, H. Molecular Self-Assembly in Indole-Based Benzamide Derivative: Crystal Structure, Hirshfeld Surfaces and Antimicrobial Activity. Eur. J. Chem. 2017, 8, 349-357.

Article Details

Crossref - Scopus - Google - European PMC

[1]. Barluenga, J.; Valdes, C. Mod. Heterocycl. Chem. 2011, 1, 377-531.

[2]. Chadha, N.; Silakari, O. Eur. J. Med. Chem. 2017, 134, 159-184.

[3]. Baeyer, A.; Emmerling, A. Ber. Dtsch. Chem. Ges. 1869, 2, 679-682.

[4]. Joule, J. A. 'Indoles' in 'Science of Synthesis'; Thomas, E. J., Ed.; Georg Thieme: Stuttgart, New York, 2011; Vol. 10 Knowledge Update 2010/2, pp. 526.

[5]. Faulkner, D. J. Nat. Prod. Rep. 2001, 18, 1-49.

[6]. Chelucci, G. Coord. Chem. Rev. 2017, 331, 37-53.

[7]. Sharma, V.; Kumar, P.; Pathak, D. J. Heterocycl. Chem. 2010, 47, 491-502.

[8]. Kaushik, N. K.; Kaushik, N.; Attri, P.; Kumar, N.; Kim, C. H.; Verma, A. K.; Choi, E. H. Molecules 2013, 18, 6620-6662.

[9]. Suzen, S.; Buyukbingol, E. Il Farmaco 2000, 55, 246-248.

[10]. Buyukbingol, E.; Suzen, S.; Klopman, G. Il Farmaco 1994, 49, 443-447.

[11]. Pojarova, M.; Kaufmann, D.; Gastpar, R.; Nishino, T.; Reszka, P.; Bednarskib, P. J.; Angerer, E. V. Med. Chem. 2007, 15, 7368-7379.

[12]. Morteza, S.; Mohammad, A. Z.; Hendrik, G. K.; Zahra, T. Chem. Rev. 2010, 110, 2250-2293.

[13]. Chyan, Y. J.; Poeggler, B.; Omar, R. A.; Chain, D. G.; Frangione, B.; Ghiso, J.; Pappolla, M. A. J. Biol. Chem. 1999, 274, 21937-21942.

[14]. Suzen, S.; Buyukbingol, E. Il Farmaco 1998, 53, 525-527.

[15]. Darehkordi, A.; Rahmani, F.; Hashemi V. Tetrahedron Lett. 2013, 54, 4689-4692.

[16]. Srivastava, N.; Banik, B. K. J. Org. Chem. 2003, 68, 2109-2114.

[17]. Shimazakia, Y.; Yajimab, T.; Takanic, M.; Yamauchi, O. Coord. Chem. Rev. 2009, 253, 479-492.

[18]. Kordic, B.; Kovacevic, M.; Sloboda, T.; Vidovic A.; Jovic, B. J. Mol. Struct. 2017, 1144, 159-165.

[19]. Nocek, J. M.; Zhou, J. S.; De Forest, S.; Priyadarshy, S.; Beratan, D. N.; Onuchic, J. N.; Hoffman, B. M. Chem. Rev. 1996, 96, 2459-2489.

[20]. Dougherty, D. A. Science 1996, 271, 163-168.

[21]. Ma, J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303-1324.

[22]. Gallivan, J. P.; Dougherty, D. A. Proc. Natl. Acad. Sci. USA 1999, 96, 9459-9464.

[23]. Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H. J. Appl. Cryst. 2009, 42, 339-341.

[24]. Palatinus, L.; Chapuis, G. J. Appl. Cryst. 2007, 40, 786-790.

[25]. Palatinus, L.; VanderLee, A. J. Appl. Cryst. 2008, 41, 975-984.

[26]. Palatinus, L.; Prathapa, S. J.; VanSmaalen, S. J. Appl. Cryst. 2012, 45, 575-580.

[27]. Sheldrick, G. M. Acta Cryst. C 2015, 71, 3-8.

[28]. Zielinski, T.; Dydio, P.; Jurczak, J. Tetrahedron 2008, 64, 568-574.

[29]. Turner, M. J.; McKinnon, J. J.; Wolff, S. K.; Grimwood, D. J.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. CrystalExplorer17, University of Western Australia, 2017.

[30]. Burlesson, F. G.; Chambers, T. M.; Wedbrauk, D. L. Virology. A Laboratory Manual, Academic Press, New York, 1992.

[31]. National Committee for Clinical Laboratory Standards. Reference method for broth dilution antifungal susceptibility testing of yeasts. Approved standard NCCLS document M27-A. National Committee for Clinical Laboratory Standards, Wayne, Pa., (2002).

[32]. Arslan, H.; Duran, N.; Borekci, G.; Ozer, C. K.; Akbay, C. Molecules 2009, 14, 519‐527.

[33]. Planas J. G.; Masalles, C.; Sillanpa, R.; Kivekas, R.; Teixidor, F.; Vinas, C. Cryst. Eng. Comm. 2006, 8, 75-83.

Supporting Agencies

This work was supported by Mersin University Research Fund [Project No, 2015-AP4-1162].
Most read articles by the same author(s)

Most read articles by the same author(s)

1 2 3 4 5 6 7 8 9 10 > >> 

Dimensions - Altmetric - scite_ - PlumX

Downloads and views


Download data is not yet available.


Metrics Loading ...
License Terms

License Terms


Copyright © 2024 by Authors. This work is published and licensed by Atlanta Publishing House LLC, Atlanta, GA, USA. The full terms of this license are available at and incorporate the Creative Commons Attribution-Non Commercial (CC BY NC) (International, v4.0) License ( By accessing the work, you hereby accept the Terms. This is an open access article distributed under the terms and conditions of the CC BY NC License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited without any further permission from Atlanta Publishing House LLC (European Journal of Chemistry). No use, distribution, or reproduction is permitted which does not comply with these terms. Permissions for commercial use of this work beyond the scope of the License ( are administered by Atlanta Publishing House LLC (European Journal of Chemistry).