European Journal of Chemistry

Synthesis, X-ray crystal structure, DFT, Hirshfeld surfaces, energy frameworks, and molecular docking analysis of a bicyclic ortho-aminocarbonitrile derivative

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Published: Jun 30, 2022
DOI: https://doi.org/10.5155/eurjchem.13.2.135-144.2225
Keywords:
Hirshfeld surface, Molecular docking, X-ray crystallography, 3D energy framework, Density functional theory, Molecular electrostatic potential
Section
Research Article
Issue
Vol. 13 No. 2 (2022): June 2022
Dates
Received 2022-01-21
Accepted 2022-02-20
Published 2022-06-30
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Ruchika Sharma
Chemical Crystallography Laboratory, Department of Physics, University of Jammu, Jammu Tawi-180006, India
https://orcid.org/0000-0002-5698-4067
Sandeep Ashok Sankpal
Department of Chemistry, Shivaji University, Kolhapur, Maharashtra-416004, India
https://orcid.org/0000-0001-8209-5899
Pradeep Jangonda Patil
Department of Chemistry, Shivaji University, Kolhapur, Maharashtra-416004, India
https://orcid.org/0000-0002-2880-8226
Saminathan Murugavel
Department of Physics, Thanthai Periyar Government Institute of Technology, Vellore-632002, Tamil Nadu, India
https://orcid.org/0000-0002-4626-8104
Sonachalam Sundramoorthy
Department of Physics, Agni College of Technology OMR, Thalambur, Chennai-600130, Tamil Nadu, India
https://orcid.org/0000-0002-5310-0692
Rajni Kant
Chemical Crystallography Laboratory, Department of Physics, University of Jammu, Jammu Tawi-180006, India
https://orcid.org/0000-0001-8043-2329

Abstract

2-Amino-4-(2, 5-dimethoxyphenyl)-4a,5,6,7-tetrahydronaphthalene-1,3,3(4H)-tricarbonitrile has been synthesized and characterized by conventional spectroscopic techniques (FT-IR and 1H NMR) and the three-dimensional structure elucidated by single crystal X-ray diffraction studies (SC-XRD). It exists in monoclinic crystal system with space group P21/c and lattice parameters: a = 14.641(13) Å, b = 8.653(4) Å, c = 16.609(10) Å, β = 116.34(3)°, and Z = 4. In the crystal packing, molecules are connected through N-H···O and N-H···N intermolecular and intramolecular C-H···O interactions. The N1-H11···N2 interaction results in the formation of a dimer corresponding to R22(12) graph-set motif. The molecular structure has been theoretically optimized by using density functional theory (DFT) with the basis set B3LYP/6-311G (d,p). The optimized bond geometry shows consistency with the SC-XRD data. Besides this, the molecular electrostatic potential (MEP), Mulliken charges, and frontier molecular orbital analysis have been described. The dnorm, shape index, curvedness, crystal voids, 2D fingerprint (FP) plots, and 3D energy frameworks using Hirshfeld surface (HS) studies have also been computed and investigated. The molecular docking studies for 2-amino-4-(2, 5-dimethoxyphenyl)-4a,5,6,7-tetrahydronaphthalene-1,3,3(4H)-tricarbonitrile with DNA gyrase/lanosterol 14α-demethylase suggest that the compound may act as an active antimicrobial drug.


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Sharma, R.; Sankpal, S. A.; Patil, P. J.; Murugavel, S.; Sundramoorthy, S.; Kant, R. Synthesis, X-Ray Crystal Structure, DFT, Hirshfeld Surfaces, Energy Frameworks, and Molecular Docking Analysis of a Bicyclic Ortho-Aminocarbonitrile Derivative. Eur. J. Chem. 2022, 13, 135-144.

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References

[1]. Enders, D.; Hüttl, M. R. M.; Grondal, C.; Raabe, G. Control of four stereocentres in a triple cascade organocatalytic reaction. Nature 2006, 441, 861-863.
https://doi.org/10.1038/nature04820

[2]. Padwa, A. Domino reactions of rhodium(II) carbenoids for alkaloid synthesis. Chem. Soc. Rev. 2009, 38, 3072-3081.
https://doi.org/10.1039/b816701j

[3]. Mojtahedi, M. M.; Pourabdi, L.; Abaee, M. S.; Jami, H.; Dini, M.; Halvagar, M. R. Facile one-pot synthesis of novel ortho-aminocarbonitriles and dicyanoanilines fused to heterocycles via pseudo four-component reactions. Tetrahedron 2016, 72, 1699-1705.
https://doi.org/10.1016/j.tet.2016.02.023

[4]. Rong, L.; Tao, S.; Xia, S.; Liu, L.; Yin, S.; Shi, Y. An efficient synthesis of 2-amino-4-aryl-6,7,8,9-tetrahydro-5H-benzo[7]annulene-1,3-dicarbonitriles in THF with DBU as catalyst. Res. chem. intermed. 2012, 38, 1647-1654.
https://doi.org/10.1007/s11164-012-0491-3

[5]. Shabalala, N. G.; Maddila, S.; Jonnalagadda, S. B. Facile one-pot green synthesis of tetrahydrobiphenylene-1,3-dicarbonitriles in aqueous media under ultrasound irradiation. Res. chem. intermed. 2016, 42, 8097-8108.
https://doi.org/10.1007/s11164-016-2581-0

[6]. Abaee, M. S.; Ehteshami, F.; Forghani, S.; Mojtahedi, M. M.; Hadizadeh, A. Facile one-pot synthesis of novel dicyanoanilines fused to dithiane ring via a pseudo-four-component reaction. J. Iran. Chem. Soc. 2017, 14, 1151-1157.
https://doi.org/10.1007/s13738-017-1065-5

[7]. Cui, S.-L.; Lin, X.-F.; Wang, Y.-G. Parallel synthesis of strongly fluorescent polysubstituted 2,6-dicyanoanilines via microwave-promoted multicomponent reaction. J. Org. Chem. 2005, 70, 2866-2869.
https://doi.org/10.1021/jo047823h

[8]. Sepioł, J.; Milart, P. Elimination of the nitrile group from o-aminonitriles-IV. Tetrahedron 1985, 41, 5261-5265.
https://doi.org/10.1016/S0040-4020(01)96775-4

[9]. Kurreck, H.; Huber, M. Modellreaktionen für die Photosynthese - photoinduzierter Ladungs- und Energietransfer zwischen verknüpften Porphyrin- und Chinon-Einheiten. Angew. Chem. Weinheim Bergstr. Ger. 1995, 107, 929-947.
https://doi.org/10.1002/ange.19951070804

[10]. Moshtaghi Zonouz, A.; Eskandari, I.; Notash, B. An efficient and green procedure for the synthesis of highly substituted polyhydronaphthalene derivatives via a one-pot, multi-component reaction in aqueous media. Curr. Chem. Lett. 2015, 85-92.
https://doi.org/10.5267/j.ccl.2015.4.004

[11]. Singh, F. V.; Vatsyayan, R.; Roy, U.; Goel, A. Arylanthranilodinitriles: a new biaryl class of antileishmanial agents. Bioorg. Med. Chem. Lett. 2006, 16, 2734-2737.
https://doi.org/10.1016/j.bmcl.2006.02.012

[12]. Elinson, M. N.; Ilovaisky, A. I.; Merkulova, V. M.; Barba, F.; Batanero, B. General approach to spiroacenaphthylene pentacyclic systems: direct multicomponent assembling of acenaphthenequinone and cyclic carbonyl compounds with two molecules of malononitrile. Tetrahedron 2013, 69, 7125-7130.
https://doi.org/10.1016/j.tet.2013.06.015

[13]. Ghosh, K.; Kar, D.; Panja, S.; Bhattacharya, S. Ion conducting cholesterol appended pyridinium bisamide-based gel for the selective detection of Ag+and Cl−ions. RSC Adv. 2014, 4, 3732-3737.
https://doi.org/10.1039/C3RA44718A

[14]. Chinchkar, S. M.; Patil, J. D.; Korade, S. N.; Gokavi, G. S.; Shejawal, R. V.; Pore, D. M. DABCO: An efficient catalyst for pseudo multi-component reaction of cyclic ketone, aldehyde and malononitrile. Lett. Org. Chem. 2017, 14(6), 403-408.
https://doi.org/10.2174/1570178614666170426163442

[15]. Yan, S.; Dong, D.; Xie, C.; Wang, W.; Wang, Z. Synthesis of bicyclic ortho-aminocarbonitrile derivatives catalyzed by 1,4-diazabicyclo [2.2.2]octane. Youji huaxue 2019, 39, 2560-2566.
https://doi.org/10.6023/cjoc201901023

[16]. Hari Babu, T.; Abragam Joseph, A.; Muralidharan, D.; Perumal, P. T. A novel method for the synthesis of functionalized spirocyclic oxindoles by one-pot tandem reaction of vinyl malononitriles with isatylidene malononitriles. Tetrahedron Lett. 2010, 51, 994-996.
https://doi.org/10.1016/j.tetlet.2009.12.082

[17]. Elinson, M. N.; Vereshchagin, A. N.; Nasybullin, R. F.; Bobrovsky, S. I.; Ilovaisky, A. I.; Merkulova, V. M.; Bushmarinov, I. S.; Egorov, M. P. General approach to a spiro indole-3,1′-naphthalene tetracyclic system: stereoselective pseudo four-component reaction of isatins and cyclic ketones with two molecules of malononitrile. RSC Adv. 2015, 5, 50421-50424.
https://doi.org/10.1039/C5RA03452C

[18]. Wang, J.; Li, Q.; Qi, C.; Liu, Y.; Ge, Z.; Li, R. Primary 1,2-diamine catalysis III: an unexpected domino reaction for the synthesis of multi substituted cyclohexa-1,3-dienamines. Org. Biomol. Chem. 2010, 8, 4240-4242.
https://doi.org/10.1039/c0ob00089b

[19]. Gaikwad, D. S.; Undale, K. A.; Patil, D. B.; Patravale, A. A.; Kamble, A. A. A task-specific biodegradable ionic liquid: a novel catalyst for synthesis of bicyclic ortho-aminocarbonitriles. J. Iran. Chem. Soc. 2018, 15, 1175-1180.
https://doi.org/10.1007/s13738-018-1315-1

[20]. Lohar, T.; Kumbhar, A.; Barge, M.; Salunkhe, R. DABCO functionalized dicationic ionic liquid (DDIL): A novel green benchmark in multicomponent synthesis of heterocyclic scaffolds under sustainable reaction conditions. J. Mol. Liq. 2016, 224, 1102-1108.
https://doi.org/10.1016/j.molliq.2016.10.039

[21]. Wan, Y.; Zhang, X.-X.; Zhao, L.-L.; Wang, C.; Chen, L.-F.; Liu, G.-X.; Huang, S.-Y.; Yue, S.-N.; Zhang, W.-L.; Wu, H. Tandem synthesis of bicyclicortho-aminocarbonitrile derivatives in ionic liquids: Tandem synthesis of bicyclicortho-aminocarbonitrile derivatives in ionic liquids. J. Heterocycl. Chem. 2015, 52, 623-627.
https://doi.org/10.1002/jhet.2088

[22]. Wang, X.-S.; Wu, J.-R.; Zhou, J.; Zhang, M.-M. A green method for the synthesis of thiochromene derivatives in ionic liquids. J. Heterocycl. Chem. 2011, 48, 1056-1060.
https://doi.org/10.1002/jhet.688

[23]. Zhang, M.-M.; Wu, J.-R.; Zhou, J.; Wang, X.-S. Green method for the synthesis of polysubstituted chromene derivatives in ionic liquids. Synth. Commun. 2012, 42, 599-607.
https://doi.org/10.1080/00397911.2010.528128

[24]. Wehenkel, A.; Fernandez, P.; Bellinzoni, M.; Catherinot, V.; Barilone, N.; Labesse, G.; Jackson, M.; Alzari, P. M. The structure of PknB in complex with mitoxantrone, an ATP-competitive inhibitor, suggests a mode of protein kinase regulation in mycobacteria. FEBS Lett. 2006, 580, 3018-3022.
https://doi.org/10.1016/j.febslet.2006.04.046

[25]. Chtita, S.; Aoumeur, N.; Belaidi, S.; Tchouar, N.; Ouassaf, M.; Lanez, T. Molecular docking studies for the identifications of novel antimicrobial compounds targeting of staphylococcus aureus. Moroccan J. Chem. 2021, 9 (2), 274-289.

[26]. El-Feky, S. M.; Abou-Zeid, L. A.; Massoud, M. A.; Shokralla, S. G.; Eisa, H. M. Computational design, molecular modeling and synthesis of new 1,2,4 -triazole analogs with potential antifungal activities. SMU Med. J. 2014, 1 (2), 224-242.

[27]. Jordá, T.; Puig, S. Regulation of ergosterol biosynthesis in Saccha-romyces cerevisiae. Genes (Basel) 2020, 11, 795-795.
https://doi.org/10.3390/genes11070795

[28]. Azizi, N.; Ahooie, T. S.; Hashemi, M. M. Multicomponent domino reactions in deep eutectic solvent: An efficient strategy to synthesize multisubstituted cyclohexa-1,3-dienamines. J. Mol. Liq. 2017, 246, 221-224.
https://doi.org/10.1016/j.molliq.2017.09.049

[29]. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. A 2008, 64, 112-122.
https://doi.org/10.1107/S0108767307043930

[30]. Spek, A. L. Structure validation in chemical crystallography. Acta Crystallogr. D Biol. Crystallogr. 2009, 65, 148-155.
https://doi.org/10.1107/S090744490804362X

[31]. Sheldrick, G. M. Crystal structure refinement with SHELXL. Acta Crystallogr. C Struct. Chem. 2015, 71, 3-8.
https://doi.org/10.1107/S2053229614024218

[32]. Wilson, A. J. C. International tables for crystallography. Volume C. corrigenda and addenda to the first edition. Acta Crystallogr. A 1995, 51, 441-444.
https://doi.org/10.1107/S0108767395099958

[33]. Macrae, C. F.; Bruno, I. J.; Chisholm, J. A.; Edgington, P. R.; McCabe, P.; Pidcock, E.; Rodriguez-Monge, L.; Taylor, R.; van de Streek, J.; Wood, P. A. Mercury CSD 2.0- new features for the visualization and investigation of crystal structures. J. Appl. Crystallogr. 2008, 41, 466-470.
https://doi.org/10.1107/S0021889807067908

[34]. Nardelli, M. PARST95 - an update to PARST: a system of Fortran routines for calculating molecular structure parameters from the results of crystal structure analyses. J. Appl. Crystallogr. 1995, 28, 659-659.
https://doi.org/10.1107/S0021889895007138

[35]. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H.P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O. ; Nakai, H.; Vreven, T.; Montgomery Jr., J. A.; Peralta, J. E.; Ogliaro, F. ; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N., Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, rev. A.01, Gaussian. Inc., Wallingford, CT, 2013.

[36]. Spackman, P. R.; Turner, M. J.; McKinnon, J. J.; Wolff, S. K.; Grimwood, D. J.; Jayatilaka, D.; Spackman, M. A. CrystalExplorer: a program for Hirshfeld surface analysis, visualization and quantitative analysis of molecular crystals. J. Appl. Crystallogr. 2021, 54, 1006-1011.
https://doi.org/10.1107/S1600576721002910

[37]. Trott, O.; Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455-461.
https://doi.org/10.1002/jcc.21334

[38]. Wang, X.-S.; Wu, J.-R.; Zhou, J.; Tu, S.-J. Green method for the synthesis of highly substituted cyclohexa-1,3-diene, polyhydroindene, polyhydronaphthalene, isochromene, isothiochromene, and isoquinoline derivatives in ionic liquids. J. Comb. Chem. 2009, 11, 1011-1022.
https://doi.org/10.1021/cc9000482

[39]. Zhang, L.-Z.; Wan, Y.; Zhang, X.-X.; Cui, H.; Zou, H.; Zhou, Q.-J.; Wu, H. Noncovalent catalysis of glucose-containing imidazolium salt in solvent-free one-pot synthesis of Ortho-aminocarbonitriles. Tetrahedron Lett. 2015, 56, 4934-4937.
https://doi.org/10.1016/j.tetlet.2015.06.094

[40]. Uzun, S.; Esen, Z.; Koç, E.; Usta, N. C.; Ceylan, M. Experimental and density functional theory (MEP, FMO, NLO, Fukui functions) and antibacterial activity studies on 2-amino-4- (4-nitrophenyl) -5,6-dihydrobenzo [h] quinoline-3-carbonitrile. J. Mol. Struct. 2019, 1178, 450-457.
https://doi.org/10.1016/j.molstruc.2018.10.001

[41]. Edwards, A. J.; Mackenzie, C. F.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. Intermolecular interactions in molecular crystals: what's in a name? Faraday Discuss. 2017, 203, 93-112.
https://doi.org/10.1039/C7FD00072C

[42]. Murugavel, S.; Sundramoorthy, S.; Lakshmanan, D.; Subashini, R.; Pavan Kumar, P. Synthesis, crystal structure analysis, spectral (NMR, FT-IR, FT-Raman and UV-Vis) investigations, molecular docking studies, antimicrobial studies and quantum chemical calculations of a novel 4-chloro-8-methoxyquinoline-2(1H)-one: An effective anti microbial agent and an inhibition of DNA gyrase and lanosterol-14α-demethylase enzymes. J. Mol. Struct. 2017, 1131, 51-72.
https://doi.org/10.1016/j.molstruc.2016.11.035

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The University of Jammu for funding under the RUSA-2.0 project of the Government of India
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