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Salah M, Belghiti ME, Aitouna AO, Zeroual A, Jorio S, El Alaoui Abdellaoui H, El Hadki H, Marakchi K, Komiha N. MEDT study of the 1,3-DC reaction of diazomethane with Psilostachyin and investigation about the interactions of some pyrazoline derivatives with protease (M pro) of nCoV-2. J Mol Graph Model 2020; 102:107763. [PMID: 33069124 PMCID: PMC7515590 DOI: 10.1016/j.jmgm.2020.107763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/08/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023]
Abstract
The molecular electronic density theory (MEDT) was invested to elucidate the chemo-, regio- and stereo-selectivity of the 1,3-dipolar cycloaddition between Diazomethane (DZM) and Psilostachyin (PSH). The DFT method at B3LYP/6-31 + G (d,p) level of theory was used. Reactivity indices, transition structures theory, IGM and ELF analysis were employed to reveal the mechanism of the reaction. The addition of DZM to PSH takes place through a one-step mechanism and an asynchronous transition states. Eight possible addition channels of reaction were investigated (addition of C (sp2) to Diazomethane at C4, C5, C6 or C7). The addition of C (sp2) at C5 leading to P1 product is the preferred channel. The addition of ether does not affect the chemo-, regio- and stereo-selectivity of the reaction. Analysis of transfer of charges along the IRC path associated with the P1 product shows a polar character for the studied reaction. We have also used the noncovalent interaction (NCI) which is very helpful to reveal the most favored addition channel of the reaction, by analyzing the weak interactions in different TSs. Finally, we investigate about the potential of inhibition of some pyrazoline compounds against COVID-19-Mpro by performing a molecular docking calculations. The 1,3-DC reaction between Diazomethane and Psilostachyin has been investigated by MEDT. The asynchronicity of TSs has been revealed by IGM and Wiberg indices. The electronic description of mechanism of reaction has been performed by ELF analysis. The NCI analysis allow a deep description of weak interactions. The pyrazolines products possess a potential effect against COVID-19.
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Affiliation(s)
- M Salah
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco; LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco.
| | - M E Belghiti
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - A O Aitouna
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - A Zeroual
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - S Jorio
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - H El Alaoui Abdellaoui
- Molecular Modeling and Spectroscopy Research Team, Department of Chemistry, Faculty of Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - H El Hadki
- LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco
| | - K Marakchi
- LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco
| | - N Komiha
- LS3MN2E, Department of Chemistry, Mohammed V University, Faculty of Sciences Rabat, Morocco
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Dalbouha S, Senent ML, Komiha N, Domínguez-Gómez R. Structural and spectroscopic characterization of methyl isocyanate, methyl cyanate, methyl fulminate, and acetonitrile N-oxide using highly correlated ab initio methods. J Chem Phys 2017; 145:124309. [PMID: 27782665 DOI: 10.1063/1.4963186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Various astrophysical relevant molecules obeying the empirical formula C2H3NO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CH3NCO), methyl cyanate (CH3OCN), methyl fulminate (CH3ONC), and acetonitrile N-oxide (CH3CNO). A CH3CON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CH3CON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C3v symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton.
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Affiliation(s)
- S Dalbouha
- Departamento de Química y Física Teóricas, Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, Madrid 28006, Spain
| | - M L Senent
- Departamento de Química y Física Teóricas, Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, Madrid 28006, Spain
| | - N Komiha
- LS3ME-Equipe de chimie théorique et Modélisation, Faculté des Sciences Rabat-Université Mohammed V, 4 Avenue Ibn Battouta B.P. 1014 RP, Rabat, Morocco
| | - R Domínguez-Gómez
- E.T.S. de Ingeniería Civil, Universidad Politécnica de Madrid, Alfonso XII, 3-5, Madrid 28014, Spain
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Dalbouha S, Boussessi R, Komiha N, Jaïdane N, Senent M. Stability of van der Waals complexes of the greenhouse effect gases NH3, SO2 and CO with imidazole in gas mixtures containing CO2. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Boussessi R, Dalbouha S, Timón V, Komiha N, Jaïdane N, Senent M. Stability of Van der Waals complexes of the greenhouse effect gases CH4 and SF6 with imidazole in gas mixtures containing CO2. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Salah M, Marakchi K, Dalbouha S, Senent M, Kabbaj O, Komiha N. Influence of the functionalization of imidazole on its CO 2 uptake efficiency. A theoretical contribution. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Boussouf K, Khairat T, Prakash M, Komiha N, Chambaud G, Hochlaf M. Structure, Spectroscopy, and Bonding within the Zn(q+)-Imidazole(n) (q = 0, 1, 2; n = 1-4) Clusters and Implications for Zeolitic Imidazolate Frameworks and Zn-Enzymes. J Phys Chem A 2015; 119:11928-40. [PMID: 26565743 DOI: 10.1021/acs.jpca.5b09500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using density functional theory (DFT) with dispersion correction and ab initio post Hartree-Fock methods, we treat the bonding, the structure, the stability, and the spectroscopy of the complexes between Zn(q+) and imidazole (Im), Zn(q+)Imn (where q = 0, 1 and 2; n = 1-4). These entities are subunits of zeolitic imidazolate frameworks (ZIFs) and Zn-enzymes, which possess relevant roles in industrial and biological domains, respectively. We also investigate the Imn (n = 2-4) clusters for comparison. For each species, we determine several new structures that were not found previously. Our calculations show a competition between atomic metal solvation, by either σ-type interactions or π-stacking type interaction, and proton transfer through hydrogen bonding (H-bonding) in charged species. This results in several geometrical environments around the metal. These are connected with structural properties and the functional role of Zn cation within ZIFs and Zn-enzymes. Moreover, we show that the Zn(2+)Imn subunits do not absorb in the visible domain, which may be related to the photostability of ZIFs. Our findings are important for the development of new applications of ZIFs and metalloenzymes.
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Affiliation(s)
- K Boussouf
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco.,Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - T Khairat
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - M Prakash
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - N Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation, Faculté des Sciences Rabat, Université Mohamed V , Rabat, Morocco
| | - G Chambaud
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - M Hochlaf
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est , 5 bd Descartes, 77454 Marne-la-Vallée, France
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Dalbouha S, Prakash M, Timón V, Komiha N, Hochlaf M, Senent ML. Explicitly correlated interaction potential energy profile of imidazole + CO2 complex. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1657-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dalbouha S, Senent ML, Komiha N. Theoretical spectroscopic characterization at low temperatures of methyl hydroperoxide and three S-analogs. J Chem Phys 2015; 142:074304. [DOI: 10.1063/1.4907941] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- S. Dalbouha
- Departamento de Química y Física Teóricas, Instituto de Estructura de la Materia, IEM-C.S.I.C., Serrano 121, Madrid 28006, Spain
| | - M. L. Senent
- Departamento de Química y Física Teóricas, Instituto de Estructura de la Materia, IEM-C.S.I.C., Serrano 121, Madrid 28006, Spain
| | - N. Komiha
- LS3ME-Équipe de Chimie Théorique et Modélisation, Faculté des Sciences, Université Mohamed V—Agdal, Rabat, Morocco
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Boussouf K, Boulmene R, Prakash M, Komiha N, Taleb M, Mogren Al-Mogren M, Hochlaf M. Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods. Phys Chem Chem Phys 2015; 17:14417-26. [DOI: 10.1039/c4cp06108j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Benchmarking DFts for the characterization of the Znq+–imidazole (q= 0, 1, 2) complexes.
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Affiliation(s)
- K. Boussouf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - R. Boulmene
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - M. Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - N. Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation
- Université Mohamed
- Faculté des Sciences
- Rabat
- Maroc
| | - M. Taleb
- Laboratoire LIMME
- Université Sidi Med Ben Abdellah
- Fac des Sciences Dhar El Mehrez
- Fès
- Maroc
| | - M. Mogren Al-Mogren
- Chemistry Department
- Faculty of Science
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - M. Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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Abbiche K, Marakchi K, Komiha N, Francisco J, Linguerri R, Hochlaf M. Accurate theoretical spectroscopy of the lowest electronic states of CP radical. Mol Phys 2014. [DOI: 10.1080/00268976.2014.901567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Guennoun L, Zaydoun S, El Jastimi J, Marakchi K, Komiha N, Kabbaj OK, El Hajji A, Guédira F. Molecular structure and vibrational study of diprotonated guanazolium using DFT calculations and FT-IR and FT-Raman spectroscopies. Spectrochim Acta A Mol Biomol Spectrosc 2012; 97:975-985. [PMID: 22925973 DOI: 10.1016/j.saa.2012.07.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 06/01/2023]
Abstract
The purpose of this manuscript is to discuss our investigations of diprotonated guanazolium chloride using vibrational spectroscopy and quantum chemical methods. The solid phase FT-IR and FT-Raman spectra were recorded in the regions 4000-400cm(-1) and 3600-50cm(-1) respectively, and the band assignments were supported by deuteration effects. Different sites of diprotonation have been theoretically examined at the B3LYP/6-31G level. The results of energy calculations show that the diprotonation process occurs with the two pyridine-like nitrogen N2 and N4 of the triazole ring. The molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated for this form by DFT/B3LYP methods, using a 6-31G basis set. Both the optimized geometries and the theoretical and experimental spectra for diprotonated guanazolium under a stable form are compared with theoretical and experimental data of the neutral molecule reported in our previous work. This comparison reveals that the diprotonation occurs on the triazolic nucleus, and provide information about the hydrogen bonding in the crystal. The scaled vibrational wave number values of the diprotonated form are in close agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PED) using the VEDA 4 program.
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Affiliation(s)
- L Guennoun
- Laboratoire de Spectroscopie Infrarouge, Département de Chimie, Faculté des Sciences, Université Mohammed V-Agdal, Avenue Ibn Batouta, Rabat, Morocco.
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Marakchi K, Kabbaj O, Komiha N, Jalal R, Esseffar M. Ab initio and DFT studies on the mechanism of the 1,3-dipolar cycloaddition reaction between nitrone and sulfonylethene chloride. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(02)00611-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Komiha N, Kabbaj O, Chraibi M. A density functional study of alizarin two of its isomers and its transition metals and rare-earth complexes. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00140-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Lahmidi A, Hliwa M, Komiha N, Kabbaj O. Etude théorique par la méthode DFT des structures non-classiques des systèmes X2H2F2 (X=Si, Ge, Sn). J Fluor Chem 2002. [DOI: 10.1016/s0022-1139(01)00552-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Komiha N, Kabbaj O, Lhamyani-Chraibi M. Theoretical study of the electron attachment dissociation of methyl halides and freon molecules: CF 3 Cl, CF 2 Cl 2 , CFCl 3. J Fluor Chem 2001. [DOI: 10.1016/s0022-1139(01)00351-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Naji N, Marakchi K, Kabbaj O, Komiha N, Joffre J, Chraı̈bi M, Soufiaoui M. Approche théorique de la cycloaddition dipolaire-1,3 sur des dipolarophiles fluorés. J Fluor Chem 1999. [DOI: 10.1016/s0022-1139(98)00317-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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