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Irrou E, Elmachkouri YA, Oubella A, Ouchtak H, Dalbouha S, Mague JT, Hökelek T, El Ghayati L, Sebbar NK, Taha ML. Crystal structure determination, Hirshfeld surface, crystal void, inter-molecular inter-action energy analyses, as well as DFT and energy framework calculations of 2-(4-oxo-4,5-di-hydro-1 H-pyra-zolo[3,4- d]pyrimidin-1-yl)acetic acid. Acta Crystallogr E Crystallogr Commun 2022; 78:953-960. [PMID: 36072525 PMCID: PMC9443805 DOI: 10.1107/s2056989022008489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022]
Abstract
In the title mol-ecule, C7H6N4O3, the bicyclic ring system is planar with the carb-oxy-methyl group inclined by 81.05 (5)° to this plane. In the crystal, corrugated layers parallel to (010) are generated by N-H⋯O, O-H⋯N and C-H⋯O hydrogen-bonding inter-actions. The layers are associated through C-H⋯π(ring) inter-actions. A Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯O/O⋯H (34.8%), H⋯N/N⋯H (19.3%) and H⋯H (18.1%) inter-actions. The volume of the crystal voids and the percentage of free space were calculated to be 176.30 Å3 and 10.94%, showing that there is no large cavity in the crystal packing. Computational methods revealed O-H⋯N, N-H⋯O and C-H⋯O hydrogen-bonding energies of 76.3, 55.2, 32.8 and 19.1 kJ mol-1, respectively. Evaluations of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated via dispersion energy contributions. Moreover, the optimized mol-ecular structure, using density functional theory (DFT) at the B3LYP/6-311G(d,p) level, was compared with the experimentally determined one. The HOMO-LUMO energy gap was determined and the mol-ecular electrostatic potential (MEP) surface was calculated at the B3LYP/6-31G level to predict sites for electrophilic and nucleophilic attacks.
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Affiliation(s)
- Ezaddine Irrou
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Younesse Ait Elmachkouri
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Ali Oubella
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
- Laboratory of Organic Synthesis and Molecular Physico-Chemistry, Department of Chemistry, Faculty of Sciences, Semlalia, BP 2390, Marrakech 40001, Morocco
| | - Hassan Ouchtak
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
| | - Samira Dalbouha
- Laboratory of Organic Chemistry and Physical Chemistry, Research Team: Molecular Modeling, Materials and Environment, Department of Chemistry, Faculty of Sciences of Agadir, University Ibn Zohr, BP 8106 Agadir, Morocco
- Laboratory of Spectroscopy, Molecular Modeling, Materials, Nanomaterials, Water and Environment, CERNE2D, Faculty of Sciences, Mohammed V University in Rabat, Av. Ibn Battouta, BP 1014, Rabat, Morocco
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Tuncer Hökelek
- Department of Physics, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Lhoussaine El Ghayati
- Laboratory of Heterocyclic Organic Chemistry, Medicines Science Research Center, Pharmacochemistry Competence Center, Mohammed V University in Rabat, Faculty of Sciences, Av. Ibn Battouta, BP 1014, Rabat, Morocco
| | - Nada Kheira Sebbar
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
- Laboratory of Heterocyclic Organic Chemistry, Medicines Science Research Center, Pharmacochemistry Competence Center, Mohammed V University in Rabat, Faculty of Sciences, Av. Ibn Battouta, BP 1014, Rabat, Morocco
| | - Mohamed Labd Taha
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibn Zohr University, Agadir, Morocco
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Al Ati G, Chkirate K, Mague JT, Abad N, Achour R, Essassi EM. Crystal structure, Hirshfeld surface analysis and DFT study of N-(2-amino-5-methyl-phen-yl)-2-(5-methyl-1 H-pyrazol-3-yl)acetamide. Acta Crystallogr E Crystallogr Commun 2021; 77:638-642. [PMID: 34164143 PMCID: PMC8183437 DOI: 10.1107/s205698902100503x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/11/2021] [Indexed: 12/04/2022]
Abstract
The title mol-ecule, C13H16N4O, adopts an angular conformation. In the crystal a layer structure is generated by N-H⋯O and N-H⋯N hydrogen bonds together with C-H⋯π(ring) inter-actions. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (53.8%), H⋯C/C⋯H (21.7%), H⋯N/N⋯H (13.6%), and H⋯O/O⋯H (10.8%) inter-actions. The optimized structure calculated using density functional theory (DFT) at the B3LYP/ 6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated HOMO-LUMO energy gap is 5.0452 eV.
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Affiliation(s)
- Gamal Al Ati
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Karim Chkirate
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - Nadeem Abad
- Department of Biochemistry, Faculty of Education & Science, Al-Baydha University, Yemen
| | - Redouane Achour
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - El Mokhtar Essassi
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Taia A, Ibrahimi BE, Benhiba F, Ashfaq M, Tahir MN, Essaber M, Aatif A, Hökelek T, Mague JT, Sebbar NK, Essassi EM. Syntheses, single crystal X-ray structure, Hirshfeld surface analyses, DFT computations and Monte Carlo simulations of New Eugenol derivatives bearing 1,2,3-triazole moiety. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130189] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Idrissi A, Chkirate K, Abad N, Djerrari B, Achour R, Essassi EM, Van Meervelt L. Crystal structure, Hirshfeld surface analysis and density functional theory study of 6-methyl-2-[(5-methyl-isoxazol-3-yl)meth-yl]-1 H-benzimidazole. Acta Crystallogr E Crystallogr Commun 2021; 77:396-401. [PMID: 33936764 PMCID: PMC8025869 DOI: 10.1107/s2056989021002723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/12/2021] [Indexed: 11/10/2022]
Abstract
In the title mol-ecule, C13H13N3O, the isoxazole ring is inclined to the benzimidazole ring at a dihedral angle of 69.28 (14)°. In the crystal, N-H⋯N hydrogen bonds between neighboring benzimidazole rings form chains along the a-axis direction. Hirshfeld surface analysis indicates that the most important contributions to the crystal packing are from H⋯H (48.8%), H⋯C/C⋯H (20.9%) and H⋯N/N⋯H (19.3%) inter-actions. The optimized structure calculated using density functional theory at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined structure in the solid state. The calculated highest occupied mol-ecular orbital (HOMO) and lowest unoccupied mol-ecular orbital (LUMO) energy gap is 4.9266 eV.
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Affiliation(s)
- Ahlam Idrissi
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Karim Chkirate
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Nadeem Abad
- Department of Biochemistry, Faculty of Education & Science, Al-Baydha University, Yemen
| | - Bahia Djerrari
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Redouane Achour
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - El Mokhtar Essassi
- Laboratory of Heterocyclic Organic Chemistry URAC 21, Pharmacochemistry Competence Center, Av. Ibn Battouta, BP 1014, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Luc Van Meervelt
- KU Leuven, Chemistry Department, Celestijnenlaan 200F box 2404, Leuven, (Heverlee), B-3001, Belgium
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