European Journal of Chemistry 2020, 11(2), 91-99 | doi: https://doi.org/10.5155/eurjchem.11.2.91-99.1973 | Get rights and content

Issue cover




Crossmark

  Open Access OPEN ACCESS | Open Access PEER-REVIEWED | RESEARCH ARTICLE | DOWNLOAD PDF | VIEW FULL-TEXT PDF | TOTAL VIEWS

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 (1,*) orcid , Laura Comeron Lamela (2) orcid , Guillermo Zaragoza (3) orcid , Bernard Pirotte (4) orcid

(1) Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
(2) Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
(3) Unidade de Difracción de Raios X, RIAIDT, Universidade de Santiago de Compostela, Campus VIDA, 15782 Santiago de Compostela, Spain
(4) Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Quartier Hôpital B36 Av. Hippocrate 15 B-4000 Liège, Belgium
(*) Corresponding Author

Received: 19 Feb 2020 | Revised: 22 Mar 2020 | Accepted: 24 Mar 2020 | Published: 30 Jun 2020 | Issue Date: June 2020

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.


Announcements


Our editors have decided to support scientists to publish their manuscripts in European Journal of Chemistry without any financial constraints.

1- The article processing fee will not be charged from the articles containing the single-crystal structure characterization between July 1, 2022 and August 15, 2022 (Voucher code: SINGLE2022).

2. Young writers will not be charged for the article processing fee between July 1, 2022 and August 15, 2022 (Voucher code: YOUNG2022).

3. The article processing fee will not be charged from the articles containing a part of the PhD thesis between July 1, 2022 and August 15, 2022 (Voucher code: PhD2022).

Editor-in-Chief

European Journal of Chemistry

Keywords


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

Full Text:

PDF
PDF    Open Access

DOI: 10.5155/eurjchem.11.2.91-99.1973

Links for Article


| | | | | | |

| | | | | | |

| | | |

Related Articles




Article Metrics

icon graph This Abstract was viewed 934 times | icon graph PDF Article downloaded 311 times

Funding information


University of Liège, Liège, Belgium

Citations

/


[1]. Koffi Sénam Etsè, Albert Demonceau, Guillermo Zaragoza, Didier Serteyn, Ange Mouithys-Mickalad
Design, synthesis and biochemical evaluation of novel 2-amino-3-(7-methoxybenzo[d][1,3]dioxol-5-yl)propanoic acid using Horseradish peroxidase (HRP) activity, cellular ROS inhibition and molecular docking study
Journal of Molecular Structure  1250, 131668, 2022
DOI: 10.1016/j.molstruc.2021.131668
/


[2]. Koffi Sénam Etsè, Guillermo Zaragoza, Kodjo Djidjolé Etsè
Easy preparation of novel 3,3-dimethyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide: Molecular structure, Hirshfeld surface, NCI analyses and molecular docking on AMPA receptors
Journal of Molecular Structure  1238, 130435, 2021
DOI: 10.1016/j.molstruc.2021.130435
/


[3]. Tufan Topal, Ghodrat Mahmoudi, Canan Onac, Ennio Zangrando
Thermal and kinetic analysis of a new hydrazone-oxime ligand and its cadmium(II) complex: Synthesis, spectral characterization, crystallographic determination and Hirshfeld surface analysis
Journal of Molecular Structure  , 133887, 2022
DOI: 10.1016/j.molstruc.2022.133887
/


[4]. Füreya Elif ÖZBEK, Mustafa SERTÇELİK, Mustafa YÜKSEK
Hirshfeld Surface Analysis and Interaction Energy Calculations of Bis(4-chlorophenylacetate)bis(pyridine-4-carboxamide)Zinc(II)
Caucasian Journal of Science  , , 2020
DOI: 10.48138/cjo.803919
/


[5]. Koffi Sénam Etsè, Guillermo Zaragoza
Insight into structural description of novel 1,4-Diacetyl-3,6-bis(phenylmethyl)-2,5-piperazinedione: synthesis, NMR, IR, Raman, X-ray, Hirshfeld surface, DFT and docking on breast cancer resistance protein
Journal of Molecular Structure  1248, 131435, 2022
DOI: 10.1016/j.molstruc.2021.131435
/


[6]. Kodjo Djidjole Etse, Koffi Senam Etse, Marie-Luce Akossiwoa Quashie
Describing auxin solid state intermolecular interactions using contact descriptors, shape property and molecular fingerprint: comparison of pure auxin crystal and auxin-TIR1 co-crystal
European Journal of Chemistry  13(2), 172, 2022
DOI: 10.5155/eurjchem.13.2.172-179.2271
/


[7]. Füreya Elif ÖZTÜRKKAN, Mustafa SERTÇELİK, Mustafa YÜKSEK, Hacali NECEFOĞLU, Tuncer HÖKELEK
Hirshfeld Surface Analysis and Interactions Energy Calculations of Metal (II) 4-Cyanobenzoate with Nicotinamide / N,N'-Diethylnicotinamide Complexes
Journal of the Turkish Chemical Society Section A: Chemistry  , 125, 2021
DOI: 10.18596/jotcsa.824551
/


[8]. Koffi Sénam Etsè, Kodjo Djidjolé Etsè, Guillermo Zaragoza, Ange Mouithys-Mickalad
Structural description, IR, TGA, antiradical, HRP activity inhibition and molecular docking exploration of N-cyclohexyl-N-tosylformamide
Journal of Molecular Structure  1269, 133731, 2022
DOI: 10.1016/j.molstruc.2022.133731
/


[9]. K. Sooryakala, S. Ramalingam, S. Periandy, R. Aarthi
NLO evaluation on opto-electronic application and chemical potential oscillation analysis of 2-Chloro-4-nitro-N-methylaniline crystal using crystallographic, spectroscopic and theoretical tools
Journal of Molecular Structure  1231, 129961, 2021
DOI: 10.1016/j.molstruc.2021.129961
/


[10]. Tufan Topal
Synthesis, X-ray, characterization and HSA and energy framework analysis of novel pyridine-hydrazone based ligand and its Co(II) complex biological activity prediction and experimental antibacterial properties
Molecular Crystals and Liquid Crystals  , 1, 2022
DOI: 10.1080/15421406.2022.2060617
/


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


Supporting information


The Supplementary Material for this article can be found online at: Supplementary files

How to cite


Etse, K.; Lamela, L.; Zaragoza, G.; Pirotte, B. Eur. J. Chem. 2020, 11(2), 91-99. doi:10.5155/eurjchem.11.2.91-99.1973
Etse, K.; Lamela, L.; 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), 91-99. doi:10.5155/eurjchem.11.2.91-99.1973
Etse, K., Lamela, L., 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), 91-99. doi:10.5155/eurjchem.11.2.91-99.1973
Etse, Koffi, Laura Comeron Lamela, Guillermo Zaragoza, & Bernard Pirotte. "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 [Online], 11.2 (2020): 91-99. Web. 16 Aug. 2022
Etse, Koffi, Lamela, Laura, Zaragoza, Guillermo, AND Pirotte, Bernard. "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 [Online], Volume 11 Number 2 (30 June 2020)

The other citation formats (EndNote | Reference Manager | ProCite | BibTeX | RefWorks) for this article can be found online at: How to cite item



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

CrossRef | Scilit | GrowKudos | Researchgate | Publons | ScienceGate | scibey | Scite | Lens | OUCI

WorldCat Paperbuzz | LibKey Citeas | Dimensions | Semanticscholar | Plumx | Kopernio | Zotero | Mendeley

ZoteroSave to Zotero MendeleySave to Mendeley



European Journal of Chemistry 2020, 11(2), 91-99 | doi: https://doi.org/10.5155/eurjchem.11.2.91-99.1973 | Get rights and content

Refbacks

  • There are currently no refbacks.




Copyright (c) 2020 Authors

Creative Commons License
This work is published and licensed by Atlanta Publishing House LLC, Atlanta, GA, USA. The full terms of this license are available at http://www.eurjchem.com/index.php/eurjchem/pages/view/terms and incorporate the Creative Commons Attribution-Non Commercial (CC BY NC) (International, v4.0) License (http://creativecommons.org/licenses/by-nc/4.0). 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 (http://www.eurjchem.com/index.php/eurjchem/pages/view/terms) are administered by Atlanta Publishing House LLC (European Journal of Chemistry).



© Copyright 2010 - 2022  Atlanta Publishing House LLC All Right Reserved.

The opinions expressed in all articles published in European Journal of Chemistry are those of the specific author(s), and do not necessarily reflect the views of Atlanta Publishing House LLC, or European Journal of Chemistry, or any of its employees.

Copyright 2010-2022 Atlanta Publishing House LLC. All rights reserved. This site is owned and operated by Atlanta Publishing House LLC whose registered office is 2850 Smith Ridge Trce Peachtree Cor GA 30071-2636, USA. Registered in USA.