Supramolecular Interactions and Hirshfeld Surface Analysis of Three 3-Carboxamidecoumarin Derivatives
Abstract
1. Introduction
2. Materials and Methods
2.1. General Methods
2.2. Computational Details
2.2.1. Hirshfeld Surfaces and 2D Fingerprint Plots
2.2.2. Pair-Wise Interaction-Energy Calculations
2.2.3. Energy-Framework Analysis
2.3. Crystal Structure Determination and Refinement
3. Results and Discussion
3.1. X-Ray Crystal Structure Determination of 3b, 3c and 4
3.2. Crystal Packing of Compounds 3b, 3c and 4
3.3. Hirshfeld Surface and 2D Fingerprint Plots
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Dharavath, R.; Nagaraju, N.; Reddy, M.R.; Ashok, D.; Sarasija, M.; Vijjulatha, M.; Vani, T.; Jyothi, K.; Prashanthi, G. Microwave-Assisted Synthesis, Biological Evaluation and Molecular Docking Studies of New Coumarin-Based 1,2,3-Triazoles. RSC Adv. 2020, 10, 11615–11623. [Google Scholar] [CrossRef]
- Irfan, A.; Rubab, L.; Rehman, M.U.; Anjum, R.; Ullah, S.; Marjana, M.; Qadeer, S.; Sana, S. Coumarin Sulfonamide Derivatives: An Emerging Class of Therapeutic Agents. Heterocycl. Commun. 2020, 26, 46–59. [Google Scholar] [CrossRef]
- García-Báez, E.V.; Martínez-Martínez, F.J.; Höpfl, H.; Padilla-Martínez, I.I. π-Stacking Interactions and CH···X (X = O, Aryl) Hydrogen Bonding as Directing Features of the Supramolecular Self-Association in 3-Carboxy and 3-Amido Coumarin Derivatives. Cryst. Growth Des. 2003, 3, 35–45. [Google Scholar] [CrossRef]
- Magaña-Vergara, N.E.; Martínez-Martínez, F.J.; Padilla-Martínez, I.I.; Höpfl, H.; García-Báez, E.V. N-Cyclohexyl-2-Oxo-2H-1-Benzopyran-3-Carboxamide. Acta Crystallogr. E Struct. Rep. Online 2004, 60, o2306–o2308. [Google Scholar] [CrossRef]
- Chimenti, F.; Bizzarri, B.; Bolasco, A.; Secci, D.; Chimenti, P.; Granese, A.; Carradori, S.; Rivanera, D.; Zicari, A.; Scaltrito, M.M.; et al. Synthesis, Selective Anti-Helicobacter Pylori Activity, and Cytotoxicity of Novel N-Substituted-2-Oxo-2H-1-Benzopyran-3-Carboxamides. Bioorg. Med. Chem. Lett. 2010, 20, 4922–4926. [Google Scholar] [CrossRef]
- Thacker, P.S.; Alvala, M.; Arifuddin, M.; Angeli, A.; Supuran, C.T. Design, Synthesis and Biological Evaluation of Coumarin-3-Carboxamides as Selective Carbonic Anhydrase IX and XII Inhibitors. Bioorg. Chem. 2019, 86, 386–392. [Google Scholar] [CrossRef]
- Robert, S.; Bertolla, C.; Masereel, B.; Dogné, J.-M.; Pochet, L. Novel 3-Carboxamide-Coumarins as Potent and Selective FXIIa Inhibitors. J. Med. Chem. 2008, 51, 3077–3080. [Google Scholar] [CrossRef]
- Phutdhawong, W.; Chuenchid, A.; Taechowisan, T.; Sirirak, J.; Phutdhawong, W.S. Synthesis and Biological Activity Evaluation of Coumarin-3-Carboxamide Derivatives. Molecules 2021, 26, 1653. [Google Scholar] [CrossRef]
- Yu, X.; Teng, P.; Zhang, Y.-L.; Xu, Z.-J.; Zhang, M.-Z.; Zhang, W.-H. Design, Synthesis and Antifungal Activity Evaluation of Coumarin-3-Carboxamide Derivatives. Fitoterapia 2018, 127, 387–395. [Google Scholar] [CrossRef]
- Abdizadeh, R.; Hadizadeh, F.; Abdizadeh, T. In Silico Analysis and Identification of Antiviral Coumarin Derivatives against 3-Chymotrypsin-like Main Protease of the Novel Coronavirus SARS-CoV-2. Mol. Divers. 2022, 26, 1053–1076. [Google Scholar] [CrossRef]
- El-Haggar, R.; Al-Wabli, R. Anti-Inflammatory Screening and Molecular Modeling of Some Novel Coumarin Derivatives. Molecules 2015, 20, 5374–5391. [Google Scholar] [CrossRef]
- Tian, G.; Zhang, Z.; Li, H.; Li, D.; Wang, X.; Qin, C. Design, Synthesis and Application in Analytical Chemistry of Photo-Sensitive Probes Based on Coumarin. Crit. Rev. Anal. Chem. 2020, 51, 565–581. [Google Scholar] [CrossRef]
- Cao, D.; Liu, Z.; Verwilst, P.; Koo, S.; Jangjili, P.; Kim, J.S.; Lin, W. Coumarin-Based Small-Molecule Fluorescent Chemosensors. Chem. Rev. 2019, 119, 10403–10519. [Google Scholar] [CrossRef]
- Gayathry, T.C.; Gaur, M.; Mishra, L.; Mishra, M.; Barooah, N.; Bhasikuttan, A.C.; Mohanty, J. Supramolecular Assembly of Coumarin 7 with Sulfobutylether-β-Cyclodextrin for Biomolecular Applications. Front. Chem. 2023, 11, 1245518. [Google Scholar] [CrossRef]
- Yabuuchi, K.; Matsuo, N.; Maeda, H.; Moriyama, M. Photoinduced Reinforcement of Supramolecular Gels Based on a Coumarin-Containing Gelator. Polym. J. 2018, 50, 1093–1097. [Google Scholar] [CrossRef]
- Ji, W.; Yuan, C.; Wang, F.; Liu, J.; Qin, M.; Yan, X.; Feng, C. Deciphering the Structure-Property Relationship in Coumarin-Based Supramolecular Organogel Materials. Colloids Surf. A Physicochem. Eng. Asp. 2020, 597, 124744. [Google Scholar] [CrossRef]
- Flores-Larios, I.Y.; López-Garrido, L.; Martínez-Martínez, F.J.; González, J.; García-Báez, E.V.; Cruz, A.; Padilla-Martínez, I.I. Thermal [4 + 2] Cycloadditions of 3-Acetyl-, 3-Carbamoyl-, and 3-Ethoxycarbonyl-Coumarins with 2,3-Dimethyl-1,3-Butadiene under Solventless Conditions: A Structural Study. Molecules 2010, 15, 1513–1530. [Google Scholar] [CrossRef]
- 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. [Google Scholar] [CrossRef]
- Spackman, M.A.; Jayatilaka, D. Hirshfeld Surface Analysis. CrystEngComm 2009, 11, 19–32. [Google Scholar] [CrossRef]
- Spackman, M.A.; McKinnon, J.J. Fingerprinting Intermolecular Interactions in Molecular Crystals. CrystEngComm 2002, 4, 378–392. [Google Scholar] [CrossRef]
- McKinnon, J.J.; Jayatilaka, D.; Spackman, M.A. Towards Quantitative Analysis of Intermolecular Interactions with Hirshfeld Surfaces. Chem. Commun. 2007, 7, 3814–3816. [Google Scholar] [CrossRef]
- Mackenzie, C.F.; Spackman, P.R.; Jayatilaka, D.; Spackman, M.A. CrystalExplorer Model Energies and Energy Frameworks: Extension to Metal Coordination Compounds, Organic Salts, Solvates and Open-Shell Systems. IUCrJ 2017, 4, 575–587. [Google Scholar] [CrossRef]
- Turner, M.J.; Thomas, S.P.; Shi, M.W.; Jayatilaka, D.; Spackman, M.A. Energy Frameworks: Insights into Interaction Anisotropy and the Mechanical Properties of Molecular Crystals. Chem. Commun. 2015, 51, 3735–3738. [Google Scholar] [CrossRef]
- Bruker APEX2, version 2012.10-0; Bruker AXS, Inc.: Madison, WI, USA, 2012.
- SAINT, version 8.27B; Bruker AXS, Inc.: Madison, WI, USA, 2012.
- SADABS, version 8.27B; Bruker AXS, Inc.: Madison, WI, USA, 2012.
- Blessing, R.H. An Empirical Correction for Absorption Anisotropy. Acta Crystallogr. A 1995, 51, 33–38. [Google Scholar] [CrossRef]
- Farrugia, L.J. WinGX and ORTEP for Windows: An Update. J. Appl. Cryst. 2012, 45, 849–854. [Google Scholar] [CrossRef]
- Sheldrick, G. SHELXT: Integrated space-group and crystal-structure determination. Acta Crystallogr. A 2015, 71, 3–8. [Google Scholar] [CrossRef]
- Sheldrick, G.M. A Short History of SHELX. Acta Crystallogr. A 2008, 64, 112–122. [Google Scholar] [CrossRef]
- Spek, A.L. Structure Validation in Chemical Crystallography. Acta Crystallogr. D Biol. Crystallogr. 2009, 65, 148–155. [Google Scholar] [CrossRef]
- 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. Cryst. 2008, 41, 466–470. [Google Scholar] [CrossRef]
- Santos-Contreras, R.J.; Martínez-Martínez, F.J.; Mancilla-Margalli, N.A.; Peraza-Campos, A.L.; Morín-Sanchez, L.M.; García-Baez, E.V.; Padilla-Martínez, I.I. Formation of Intramolecular Three-Centred Hydrogen Bond in 3-Acyl Coumarins. CrystEngComm 2009, 11, 1451–1461. [Google Scholar] [CrossRef]
- Bernstein, J.; Davis, R.E.; Shimoni, L.; Chang, N.-L. Patterns in hydrogen bonding: Functionality and graph set analysis. Angew. Chem. Int. Ed. 1995, 34, 1555–1573. [Google Scholar] [CrossRef]








| 3b | 3c | 4 | |
|---|---|---|---|
| Chemical formula | C16H16ClNO3 | C16H16N2O5 | C16H12N2O3 |
| Mr | 305.75 | 316.31 | 279.27 |
| Crystal system, space group | Triclinic, P-1 | Triclinic, P-1 | Monoclinic P21 |
| a, b, c (Å) | 6.068(2), 8.595(3), 14.642(6) | 5.984(4), 8.760(7), 14.763(2) | 6.135(13), 6.453(12), 16.382(3) |
| α, β, γ (°) | 97.464(7), 100.590(6), 101.315(7) | 97.930(18), 100.847(19), 100.13(2) | 90, 95.800(7), 90 |
| V (Å3) | 725.1 (5) | 736.4 (9) | 645.3 (2) |
| Z | 2 | 2 | 2 |
| Dx, g cm−3 | 1.401 | 1.426 | 1.44 |
| µ (mm−1) | 0.27 | 0.11 | 0.10 |
| Crystal size (mm) | 0.3 × 0.2 × 0.1 | 0.26 × 0.18 × 0.09 | 0.3 × 0.2 × 0.1 |
| Data collection | |||
| Diffractometer | Bruker APEXII Diffractometer (Madison, WI, USA) | Bruker APEXII Diffractometer | Bruker APEXII diffractometer |
| Radiation type | Mo Kα (λ = 0.71073) | Mo Kα (λ = 0.71073) | Mo Kα (λ = 0.71073) |
| No. of measured, independent and observed [I > 2σ(I)] reflections | 7126, 2554, 1920 | 26718, 3516, 2768 | 23748, 2462, 2170 |
| Rint | 0.031 | 0.062 | 0.128 |
| Index ranges | −7 ≤ h ≤ 7, −10 ≤ k ≤ 10, −17 ≤ l ≤ 17 | −7 ≤ h ≤ 7, −11 ≤ k ≤ 11, −19 ≤ l ≤ 19 | −7 ≤ h ≤ 7, −7 ≤ k ≤ 7, −20 ≤ l ≤ 20 |
| Refinement | |||
| R[F2 > 2σ(F2)], wR(F2), S | 0.057, 0.143, 1.04 | 0.061, 0.174, 1.05 | 0.095, 0.255, 1.17 |
| No. of reflections | 2554 | 3516 | 2462 |
| No. of parameters | 194 | 213 | 190 |
| No. of restraints | 0 | 0 | 1 |
| Δρmax, Δρmin (e Å−3) | 0.42, −0.17 | 0.38, −0.29 | 0.86, −0.74 |
| Bond lengths (Å) | |||
| 3b | 3c | 4 | |
| O1–C2 | 1.362(3) | 1.371(2) | 1.360(3) |
| C2–O2 | 1.204(3) | 1.211(2) | 1.202(3) |
| C3–C4 | 1.340(2) | 1.346(2) | 1.329(3) |
| C11–O11 | 1.217(3) | 1.2257(19) | 1.231(3) |
| C11–N12 | 1.331(3) | 1.333(2) | 1.338(3) |
| N12–C13 | 1.449(3) | 1.460(2) | 1.407(3) |
| Torsion angles (°) | |||
| O1–C9–C10–C4 | −0.6(3) | −0.3(2) | 0.04(1) |
| C2–C3–C11–N12 | 12.8(3) | 13.1(2) | −3.23(1) |
| C2–C3–C11–O11 | −169.1(2) | −167.68(15) | 177.19(1) |
| C4–C3–C11–O11 | 12.5(4) | 15.0(2) | −2.01(1) |
| C4–C3–C11–N12 | −165.5(2) | −164.23(15) | 177.58(1) |
| O11–C11–N12–H12 | −171.0(2) | −175.5(18) | −173 |
| Comp. | Interaction | Lengths/Å | Angle/deg | ||
|---|---|---|---|---|---|
| D–H⋯A | D–H | H⋯A | D⋯A | D–H⋯A | |
| Hydrogen-bonding interactions | |||||
| 3b | C4–H4∙∙∙O11 i | 0.93 | 2.55 | 3.358(3) | 146 |
| C5–H5∙∙∙O11 ii | 0.93 | 2.51 | 3.329(3) | 146 | |
| C8–H8∙∙∙O2 iii | 0.93 | 2.44 | 3.333(3) | 161 | |
| C13–H13⋯Cg(2) iv | 0.93 | 3.173 | 3.857 | 128 | |
| 3c | C4–H4∙∙∙O11 v | 0.93 | 2.49 | 3.315(3) | 148 |
| C5–H5∙∙∙O11 vi | 0.93 | 2.53 | 3.344(3) | 146 | |
| C8–H8∙∙∙O2 vii | 0.93 | 2.46 | 3.351(3) | 161 | |
| C13–H13⋯Cg(2) viii | 0.93 | 3.303 | 3.955 | 125 | |
| C15–H15B∙∙∙O6A ix | 0.93 | 2.710 | 3.586 | 150 | |
| 4 | C6–H6∙∙∙O2 x | 0.93 | 2.47 | 3.229(7) | 139 |
| O11⋯H19B xi | 0.93 | 2.87 | - - | 120 | |
| N14⋯H5 xii | 0.93 | 2.80 | - - | 123 | |
| O11⋯H15 xiii | 0.93 | 2.92 | - - | 135 | |
| Lone pair → π interactions | |||||
| 3b | C2–O2∙∙∙Cg (2) xiv | 3.837(3) | 65.34(15) | ||
| C(11)–O(11)∙∙∙Cg(1) xv | 3.215(2) | 85.15(15) | |||
| 3c | C11–O11∙∙∙Cg(1) xvi | 3.119(3) | 89.46(11) | ||
| 4 | C7–H7∙∙∙Cg(3) xvii | 3.597(8) | 137 | ||
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content. |
© 2026 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
Share and Cite
Madrigal-Angulo, J.L.; Flores-Pérez, M.d.J.; Rodríguez-Romero, J.; González-González, J.S.; Pineda-Urbina, K.; García-Baez, E.V.; Padilla-Martínez, I.I.; Martínez-Martínez, F.J. Supramolecular Interactions and Hirshfeld Surface Analysis of Three 3-Carboxamidecoumarin Derivatives. Crystals 2026, 16, 355. https://doi.org/10.3390/cryst16060355
Madrigal-Angulo JL, Flores-Pérez MdJ, Rodríguez-Romero J, González-González JS, Pineda-Urbina K, García-Baez EV, Padilla-Martínez II, Martínez-Martínez FJ. Supramolecular Interactions and Hirshfeld Surface Analysis of Three 3-Carboxamidecoumarin Derivatives. Crystals. 2026; 16(6):355. https://doi.org/10.3390/cryst16060355
Chicago/Turabian StyleMadrigal-Angulo, José L., María de J. Flores-Pérez, Jesús Rodríguez-Romero, Juan Saulo González-González, Kayim Pineda-Urbina, Efrén V. García-Baez, Itzia I. Padilla-Martínez, and Francisco J. Martínez-Martínez. 2026. "Supramolecular Interactions and Hirshfeld Surface Analysis of Three 3-Carboxamidecoumarin Derivatives" Crystals 16, no. 6: 355. https://doi.org/10.3390/cryst16060355
APA StyleMadrigal-Angulo, J. L., Flores-Pérez, M. d. J., Rodríguez-Romero, J., González-González, J. S., Pineda-Urbina, K., García-Baez, E. V., Padilla-Martínez, I. I., & Martínez-Martínez, F. J. (2026). Supramolecular Interactions and Hirshfeld Surface Analysis of Three 3-Carboxamidecoumarin Derivatives. Crystals, 16(6), 355. https://doi.org/10.3390/cryst16060355

