Synthesis, crystal structure, Hirshfeld surface and interaction energies analysis of 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione

Koffi Senam Etse; Laura Comeron Lamela; Guillermo Zaragoza; Bernard Pirotte

doi:10.5155/eurjchem.11.2.91-99.1973

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Published: Jun 30, 2020

DOI: https://doi.org/10.5155/eurjchem.11.2.91-99.1973

Keywords:

Thymine, Crystal structure, Hirshfeld surfaces, Hydrogen bonding, Interaction energies, 3-Nitrobenzylbromide

Section

Research Article

Issue

Vol. 11 No. 2 (2020): June 2020

Dates

Received 2020-02-19
Accepted 2020-03-24
Published 2020-06-30

Koffi Senam Etse

Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium

http://orcid.org/0000-0001-8495-4327

Laura Comeron Lamela

Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium

http://orcid.org/0000-0002-5940-3002

Guillermo Zaragoza

Unidade de Difracción de Raios X, RIAIDT, Universidade de Santiago de Compostela, Campus VIDA, 15782 Santiago de Compostela, Spain

http://orcid.org/0000-0002-2550-6628

Bernard Pirotte

Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium

http://orcid.org/0000-0001-8251-8257

Abstract

The title compound 5-methyl-1,3-bis(3-nitrobenzyl)pyrimidine-2,4(1H,3H)-dione was obtained by reaction of thymine with 3-nitrobenzylbromide in the presence of cesium carbonate. Characterization of the product was achieved by NMR spectroscopy and its stability was probed in basic condition using UV-Visible analysis. Furthermore, the molecular structure was confirmed by X-ray diffraction analysis. The compound crystallizes in orthorhombic Pna21 space group with unit cell parameters a = 14.9594 (15) Å, b = 25.711 (3) Å, c = 4.5004 (4) Å, V = 1731.0 (3) Å³ and Z = 4. The crystal packing of the title compound is stabilized by intermolecular hydrogen bond, π···π and C−H···π stacking interactions. The intermolecular interactions were furthermore analyzed through the mapping of different Hirshfeld surfaces. The two-dimensional fingerprint revealed that the most important contributions to these surfaces come from O···H (37.1%), H···H (24%) and H···C/C···H (22.6%) interactions. The interaction energies stabilizing the crystal packing were calculated and were presented graphically as framework energy diagrams. Finally, the energy-framework analysis reveals that π···π and C−H···π interactions energies are mainly dispersive and are the most important forces in the crystal.

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Etse, K. S.; Lamela, L. C.; 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, 91-99.

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References

[1]. Lagoja I. M. Chem. Biodivers. 2005, 2, 1-50.
https://doi.org/10.1002/cbdv.200490173

[2]. Honda, T.; Inagawa, H.; Fukushima, M.; Moriyama, A.; Soma, G. Clin. Chim. Acta. 2002, 322, 59-66.
https://doi.org/10.1016/S0009-8981(02)00132-8

[3]. Hadj-Bouazza, A.; Teste, K.; Colombeau, L.; Chaleix, V.; Zerrouki, R.; Kraemer, M.; Sainte Catherine, O. Nucleosides Nucleotides Nucleic Acids 2008, 27, 439-448.
https://doi.org/10.1080/15257770802086872

[4]. Balzarini, J.; Baba, M.; De Clercq. E. Antimicrob. Agents Chemother. 1995, 39, 998-1002.
https://doi.org/10.1128/AAC.39.4.998

[5]. Adamska, A.; Rumijowska-Galewicz, A.; Ruszczynska, A.; Studzinska, M.; Jablonska, A.; Paradowska, E.; Bulska, E.; Munier-Lehmann, H.; Dziadek, J.; Lesnikowski, Z. J.; Olejniczak, A. B. Eur. J. Med. Chem. 2016, 121, 71-81.
https://doi.org/10.1016/j.ejmech.2016.05.030

[6]. Bialek-Pietras, M.; Olejniczak, A. B.; Paradowsk, E.; Studzinska, M.; Jablonska, A.; Lesnikowski, Z. J. J. Organomet. Chem. 2018, 865, 166-172.
https://doi.org/10.1016/j.jorganchem.2018.03.026

[7]. Li, G.; Zhu, Y.; Yang, F.; Yang, H. Hecheng Huaxue. 2011, 19, 111-114.

[8]. Lin, T. S.; Wang, L.; Antonini, I.; Cosby, L. A.; Shiba, D. A.; Kirkpatrick, D. L.; Sartorelli, A. C. J. Med. Chem. 1986, 29, 84-89.
https://doi.org/10.1021/jm00151a014

[9]. Weaver, D. F.; Guillain, B. M.; Carran, J. R.; Jones, K. US Patent. 2002, No. 7, 501, 429 B2.

[10]. Kim, B. R.; Park, J. Y.; Jeong, H. J.; Kwon, H. J.; Park, S. J.; Lee, I. C.; Ryu, Y. B.; Lee, W. S. J. Enzyme Inhib. Med. Chem. 2018, 33, 1256-1265.
https://doi.org/10.1080/14756366.2018.1488695

[11]. Li, M.; Cai, X.; Zhu, Y.; Liu, K.; Hu, M. Acta Chim. Sinica (Chinese Edition) 2011, 69, 425-430.

[12]. Etse, K. S.; Dassonneville, B.; Zaragoza, G.; Demonceau, A. Tetrahedron Lett. 2017, 58, 789-793.
https://doi.org/10.1016/j.tetlet.2017.01.041

[13]. Manos‐Turvey, A.; Becker, G.; Francotte, P.; Serrano, M. E.; Luxen, A.; Pirotte, B.; Plenevaux, A.; Lemaire, C. Chem. Med. Chem. 2019, 14, 788-795.
https://doi.org/10.1002/cmdc.201800816

[14]. Goffin, E.; Drapier, T.; Larsen, A. P.; Geubelle, P.; Ptak, C. P.; Laulumaa, S.; Rovinskaja, K.; Gilissen, J.; Tullio, P.; Olsen, L.; Frydenvang, K.; Pirotte, B.; Hanson, J.; Oswald, R. E.; Kastrup, J. S.; Francotte, P. J. Med. Chem. 2018, 61, 1251-1264.

[15]. Etse, K. S.; Zaragoza, G.; Pirotte, B. Eur. J. Chem. 2019, 10, 189-194.
https://doi.org/10.5155/eurjchem.10.3.189-194.1903

[16]. Dolman, N. P.; More, J. C.; Alt, A.; Knauss, J. L.; Troop, H. M.; Bleakman, D.; Collingridge, G. L.; Jane, D. E. J. Med. Chem. 2006, 49, 2579-2592.
https://doi.org/10.1021/jm051086f

[17]. Drapier, T.; Geubelle, P.; Bouckaert, C.; Nielsen, L.; Laulumaa, S.; Goﬃn, E.; Dilly, S.; Francotte, P.; Hanson, J.; Pochet, L.; Kastrup, J. S.; Pirotte, B. J. Med. Chem. 2018, 61, 5279-529.
https://doi.org/10.1021/acs.jmedchem.8b00250

[18]. Bruker APEX II Bruker AXS Inc., Madison, WI, USA, 2004.

[19]. Sheldrick, G. M. Acta Cryst. A 2015, 71, 3-8.
https://doi.org/10.1107/S2053229614024218

[20]. Sheldrick, G. M. Acta Cryst. C 2015, 71, 3-8.
https://doi.org/10.1107/S2053229614024218

[21]. Farrugia, L. J. J. Appl. Cryst. 2012, 45, 849-854.
https://doi.org/10.1107/S0021889812029111

[22]. 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. J. Appl. Cryst. 2008, 41, 466-470.
https://doi.org/10.1107/S0021889807067908

[23]. Kaspar, K.; Giessmann, R. T.; Krausch, N.; Neubauer, P.; Wagner, A.; Gimpel, M. Methods Protoc. 2019, 2, 60-72.
https://doi.org/10.3390/mps2030060

[24]. Turner, M. J.; McKinnon, J. J.; Wolff, S. K.; Grimwood, D. J.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. CrystalExplorer17, The University of Western Australia. http://hirshfeldsurface. net, 2017.

[25]. Spackman, M. A.; Jayatilaka, D. CrystEngComm. 2009, 11, 19-32.
https://doi.org/10.1039/B818330A

[26]. Demircioglu, Z.; Yesil, A. E.; Altun, M.; Bal-Demirci, T.; Ozdemir, N. J. Mol. Struct. 2018, 1162, 96-108.
https://doi.org/10.1016/j.molstruc.2018.02.093

[27]. 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, J. A. Jr.; 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. Gaussian16. Gaussian Inc. Wallingford, Connecticut, USA, 2016.

[28]. Turner, M. J.; Thomas, S. P.; Shi, M. W.; Jayatilaka, D.; Spackman, M. A. Chem. Commun. 2015, 51, 3735-3738.
https://doi.org/10.1039/C4CC09074H

[29]. Mackenzie, C. F.; Spackman, P. R.; Jayatilaka, D.; Spackman, M. A. IUCrJ. 2017, 4, 575-587.
https://doi.org/10.1107/S205225251700848X

[30]. Tan, S. L.; Jotani, M. M.; Tiekink, E. R. T. Acta Cryst. E 2019, 75, 308-318.
https://doi.org/10.1107/S2056989019001129

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University of Liège, Liège, Belgium

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