Browsing by Author "Amani Direm"
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Item (4S)-4-Benzyl-N-{[(4S)-4-benzyl-2-oxo-1,3-oxazolidin-3- yl]sulfonyl}-2-oxo-1,3-oxazolidine-3-carboxamide(2010) Amani DiremActa Crystallographica Section E: Structure Reports Online is the IUCr’s highly popular open-access structural journal. It provides a simple and easily accessible publication mechanism for the growing number of inorganic, metal-organic and organic crystal structure determinations. The electronic submission, validation, refereeing and publication facilities of the journal ensure very rapid and high-quality publication, whilst key indicators and validation reports provide measures of structural reliability. In 2007, the journal published over 5000 structures. The average publication time is less than one month.Item A Comparative Theoretical and Spectroscopic Study of Aminomethylbenzoic Acid Derivatives as Potential NLO Candidates †(2020-12-25) Amani DiremThree aminomethylbenzoic acid derivatives were theoretically studied at M062X/6-311++G(d,p) level in a vacuum, namely 2-ammonio-5-methylcarboxybenzene perchlorate (1), 4-(ammoniomethyl) carboxybenzene nitrate (2) and 4-(ammoniomethyl)carboxybenze perchlorate (3). The compounds’ structures were fully optimized and compared with the single-crystal X-ray diffraction results, showing a very close agreement with the experimental structural parameters. Their IR, 1H- and 13C-NMR spectra were calculated and examined in detail. Furthermore, the molecular electrostatic potential (MEP) maps of the studied compounds were investigated and the strength of the non-covalent interactions evaluated. In addition to these results, the NLO properties of the three compounds were pItem A Comparative Theoretical and Spectroscopic Study of Aminomethylbenzoic Acid Derivatives as Potential NLO Candidates †(2020-11-13) Amani DiremThree aminomethylbenzoic acid derivatives were theoretically studied at M062X/6-311++G(d,p) level in a vacuum, namely 2-ammonio-5-methylcarboxybenzene perchlorate (1), 4-(ammoniomethyl) carboxybenzene nitrate (2) and 4-(ammoniomethyl)carboxybenze perchlorate (3). The compounds’ structures were fully optimized and compared with the single-crystal X-ray diffraction results, showing a very close agreement with the experimental structural parameters. Their IR, 1H- and 13C-NMR spectra were calculated and examined in detail. Furthermore, the molecular electrostatic potential (MEP) maps of the studied compounds were investigated and the strength of the non-covalent interactions evaluated. In addition to these results, the NLO properties of the three compounds were predicted.Item A rhodanine derivative as a potential antibacterial and anticancer agent: Crystal structure, spectral characterization, DFT calculations, Hirshfeld surface analysis, in silico molecular docking and ADMET studies(2023-01-23) Amani DiremA novel rhodanine derivative, namely 5-(4-dimethylaminobenzylidene) rhodanine “C12H12N2OS2”, was successfully crystallized from condensation route and characterized by NMR, FT-IR, UV–Vis spectral methods as well as single-crystal X-ray diffraction. This rhodanine derivate crystallizes in the monoclinic P21/c space group, with the cell parameters: a = 3.93590(10), b = 11.2480(3), c = 26.6703(7) A˚ and β = 93.8530(10)°. The molecular structure displays intra- (C − S···H) and intermolecular (N − H···O) hydrogen-bonding interactions. Micro-spectroscopy performed on single-crystals of the studied compound revealed the first absorption transition at 2.25 eV, and a well-structured luminescence peaked at 2.01 eV (0.15 eV broad). Density functional theory (DFT) calculations allowed the structure optimization, the electronic properties, the IR-vibrational modes and frequencies as well as the 1H and 13C NMR chemical shifts’ calculation. Furthermore, time-dependent DFT (TD-DFT) calculations were performed for the vertical transition energies. Hirshfeld surface analysis (HSA) showed the presence of non-conventional C–H···H–C, C–H···π and π···lp interactions and π−π stacking. The anti-cancer and anti-bacterial activities of the studied compound towards the Polo-like kinase PLK1 and the Escherichia coli MurB enzymes were in silico evaluated by performing molecular docking simulations. The results suggest that the molecule can significantly inhibit the enzymes’ active sites. Additionally, the physicochemical and pharmacokinetic characteristics of the molecule were evaluated through absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis, and the results ensure its good drug-likeness propertiesItem Ammonium tris(tetraethylammonium) hexacosaoxidooctamolybdate(2008) Amani DiremActa Crystallographica Section E: Structure Reports Online is the IUCr’s highly popular open-access structural journal. It provides a simple and easily accessible publication mechanism for the growing number of inorganic, metal-organic and organic crystal structure determinations. The electronic submission, validation, refereeing and publication facilities of the journal ensure very rapid and high-quality publication, whilst key indicators and validation reports provide measures of structural reliability. In 2007, the journal published over 5000 structures. The average publication time is less than one month.Item Atmospheric reaction of chlorine radical and cyclic amide: A theoretical approach(2024-02-29) Amani DiremThe atmosphere is considered a chemical reactor where many chemical reactions occur. Theoretical investigations are useful for understanding the mechanisms involved in the reaction with atmospheric radicals. Density functional theory (DFT) with B3LYP, CBS-QB3 and G3B3 methods were used to investigate the reactivity, mechanism and structure–reactivity relationship as well as the kinetics of N-methyl-2-pyrrolidinone (NMP) reaction with chlorine. Furthermore, the Rice–Ramsperger–Kassel–Marcus (RRKM) theory was employed to compute the rate constants. This study provides rate coefficients and a detailed H-abstraction mechanism for the reaction of chlorine with NMP. Kinetic and mechanistic results showed that the mechanism of this reaction goes with small barriers through H-atom transfer from the –N–CH3 group and –CH2– adjacent to the –N–CH3 site within a branching ratio slightly in favour of the –N–CH3 site.Item Carboxyanilinium hydrogensulfate(2007-03-18) Amani DiremThe cohesion in the title structure (p-CPABS), C7H8NO2+- HSO4 , is assured by an intricate three-dimensional hydrogen-bonded network of types N—H O and O— H O involving anions, carboxyl and amino groups in addition to the ionic interactions.Item Creatinium perchlorate(2009) Amani DiremActa Crystallographica Section E: Structure Reports Online is the IUCr’s highly popular open-access structural journal. It provides a simple and easily accessible publication mechanism for the growing number of inorganic, metal-organic and organic crystal structure determinations. The electronic submission, validation, refereeing and publication facilities of the journal ensure very rapid and high-quality publication, whilst key indicators and validation reports provide measures of structural reliability. In 2007, the journal published over 5000 structures. The average publication time is less than one month.Item Crystal structure, Hirshfeld surface analysis and theoretical calculations of an oxalato‑bridged copper(II) complex: μ‑oxalato‑bis[(2,2’‑bipyridine) hydrate copper(II) nitrate](2019-11-05) Amani DiremThe copper complex [Cu2(Bipy)2(H2O)2(C2O4)(NO3)2] (Bipy = 2,2′-bipyridine; C2O42− = oxalate) has been synthesized and characterized by single-crystal X-ray diffraction and FTIR spectroscopy. The structure determination revealed that the title compound contains centrosymmetric doubly charged dinuclear oxalato-bridged copper(II) complex cations, nitrate counter ions and water molecules. In this complex, the oxalate ligand is coordinated in a bis-bidentate bridging mode to the copper atoms. Each Cu(II) atom has a distorted tetragonal–bipyramidal environment, being coordinated by two N atoms of a chelating 2,2′-bipyridine ligand and two O atoms of the doubly deprotonated oxalate anion. Pairs of monodentate nitrate anions and aqua ligands are linked to the metallic cations in an axial position. The H-bonds occurring in the crystal structure result in the formation of 2D supramolecular chains and 3D networks. The Hirshfeld surface analysis of the complex has shown the presence of strong O–H…O and C–H…O hydrogen bonds together with non-classical weak C–H…π, π…π, π…lp/lp…π and lp …lp interactions. Furthermore, the theoretical calculations results are in agreement with the experimental geometric parameters. The NMR spectra and the MEP maps were also calculated.Item Crystal structure, physical study and Hirshfeld surface analysis of (C9H26N4) [SnCl6]Cl2·2H2O(2020-05-26) Amani Direm(C9H26N4)[SnCl6]Cl2·2H2O has been synthesized in solution and its structure confirmed by single-crystal X-ray diffraction. It crystallizes in the monoclinic system, with space group P21/n (14), Z = 4, with refined cell parameters (Å,°) a = 10.7550(3), b = 15.3981(7), c = 13.8750(5), β = 103.095(3), V = 2238.04(15) Å3. The 3D framework of the title compound is made of free molecules 1,4,7,10-tetraazacyclotridecane, [SnCl6], Cl atoms and water molecules, interacting through an intricate network of hydrogen-bonds and H…Cl interactions. The 1,4,7,10-tetraazacyclotridecane moiety is also confirmed by Raman spectroscopy. The Hirshfeld surface analysis of (C9H26N4)[SnCl6]Cl2·2H2O is elucidated. Preliminary investigations of the electrochemical performance of the title compound as an active material in a Li-ion battery have also been carried out.Item Cu2(ox)(dien)2](NO3)3, a precursor for preparation of CuO nanoparticles: Synthesis, structural, Hirshfeld surface analyses, and physico-chemical investigations(2023-02-28) Amani Direm[Cu2(ox)(dien)2](NO3)3 with (ox=oxalate, dien=diethylenetriamine) has been synthesized and characterized by single-crystal X-ray diffraction as well as FTIR and UV–Vis spectroscopic techniques. The complex crystallizes in the monoclinic space group (P2/c) with the following cell parameters (A, ˚ °): a = 23.7888(10), b = 6.7055(3), c = 12.7842(6) and β = 95.534(2). The 3D network consists of (C2O4) groups bridging binuclear Cu(II) cations, in which the copper atoms are in a distorted square-pyramidal coordination environment. Experimental and computed FT-IR results confirmed the presence of characteristic bands of diethylenetriamine tridentate, nitrate and oxalate bidentate groups. UV–Vis spectrum of the complex was recorded and the characteristic transitions were determined. TG-DSC measurements revealed thermal stability of the studied complex until 473 K. Calcination of the complex under air led to the production of CuO nanoparticles. Moreover, the morphology and the size of the complex and its CuO nanoparticles were monitored by scanning electron microscopy (SEM). Magnetization and a.c. susceptibility were measured and discussed. The complex molecular structure was optimized and the simulated geometric parameters compared with the crystal structure values. Hirshfeld surface and topological analyses were performed to describe the intermolecular interactions and to simplify the 3D networks of [Cu2(ox)(dien)2](NO3)3. Moreover, its antioxidant activity was assessed using DPPH, ferric reducing power tests and phosphomolybdenum assay.Item Cytosinium–hydrogen maleate–cytosine(2009-11-04) Amani DiremThe title organic salt, C4H6N3O+ C4H3O4ÿ C4H5N3O, was synthesized from cytosine base and maleic acid. An intramolecular O—H O hydrogen bond occurs in the hydrogen maleate anion. The crystal packing is stabilized by intermolecular N—H O, N—H N and C—H O hydrogen bonds, giving rise to a nearly planar two-dimensional network parallel to (101)Item Diaquabis(ethylenediamine-j2N,N00)- copper(II) bis(sulfamerazinate)(2014-05-09) Amani DiremThe asymmetric unit of the title compound, [Cu(C2H8N2)2- (H2O)2](C11H11N4O2S)2, contains one sulfamerazinate anion in a general position and one half-cation that is located on a center of inversion. The CuII cation shows a strong Jahn–Teller distortion. It is coordinated by four N atoms of two ethylenediamine ligands in the basal plane and two O atoms at much longer distances in the axial positions in a bipyramidal coordination. In the crystal, the building blocks are connected by N—H N, O—H N, N—H O and O—H O hydrogen bonding into a two-dimensional network parallel to (001)Item Diaquabis(ethylenediamine-j2N,N00)- copper(II) bis(sulfamerazinate)(2014-05-09) Amani DiremThe asymmetric unit of the title compound, [Cu(C2H8N2)2- (H2O)2](C11H11N4O2S)2, contains one sulfamerazinate anion in a general position and one half-cation that is located on a center of inversion. The CuII cation shows a strong Jahn–Teller distortion. It is coordinated by four N atoms of two ethylenediamine ligands in the basal plane and two O atoms at much longer distances in the axial positions in a bipyramidal coordination. In the crystal, the building blocks are connected by N—H N, O—H N, N—H O and O—H O hydrogen bonding into a two-dimensional network parallel to (001).Item Dual inhibition of S. aureus TyrRS and S. aureus gyrase by two 4-amino-4′-acetyldiphenyl sulfide-based Schiff bases: Structural features, DFT study, Hirshfeld surface analysis and molecular docking(Inorganic Chemistry Communications 143 (2022) 109779, 2022) Soumia Kadri; Amani Direm; Athmani Hamza; Brahim El Bali; Cemal Parlak; Rabihe HebbachiTwo 4-amino-4′ -acetyldiphenyl sulfide-based Schiff bases, namely 1-[4-({4-[(E)-(2hydroxynaphthalen-1-yl) methylideneamino]phenyl}sulfanyl)-phenyl]ethanone (I) and (E)-1-[4-({4-[(4methoxybenzylidene)amino] phenyl}-sulfanyl)phenyl]ethan-1-one (II) were structurally studied. They crystallize respectively in the monoclinic Cc and the triclinic P1 space groups, with the respective cell parameters: [10.695(3) Å, 44.458(14) Å, 4.4437(11) Å, 99.004(9)°] and [5.7708(2) Å, 8.0867(3) Å, 19.6929(8) Å, 81.844(2)◦, 86.664(3)◦, 85.662(3)◦]. The asymmetric units of (I) and (II) are composed of one molecule and two crystallographically independent molecules, respectively. Their molecular structures were optimized by the density functional theory and correlated correspondingly to the crystal structures. Moreover, the IR vibration modes were assigned to the calculate wavenumbers, the Mulliken atomic charges obtained and the frontier molecular orbitals evaluated. The hydrogen bonding and the non-classical intermolecular interactions within the two frameworks were investigated using Hirshfeld surface analysis which indicated the presence of C–H…H–C, C–H⋅⋅⋅π, C–H⋅⋅⋅O, C–H⋅⋅⋅N, C–H⋅⋅⋅S and π⋅⋅⋅lp interactions as well as π⋅⋅⋅π stacking. Additionally, in order to understand the interacting binding sites of the two molecules with the bacterial S. aureus protein receptors, the studied compounds were in silico eval- uated by molecular docking against tyrosyl-tRNA synthetase 1JIJ and topoisomerase II DNA gyrase 2XCT en- zymes. The results revealed consequently potent antimicrobial efficacy through the formed hydrogen bonds, hydrophobic contacts, π-cation interactions and π…π stacking.Item Dual inhibition of S. aureus TyrRS and S. aureus gyrase by two 4-amino-4′-acetyldiphenyl sulfide-based Schiff bases: Structural features, DFT study, Hirshfeld surface analysis and molecular docking(2023-07-19) Amani DiremTwo 4-amino-4′-acetyldiphenyl sulfide-based Schiff bases, namely 1-[4-({4-[(E)-(2-hydroxynaphthalen-1-yl) methylideneamino]phenyl}sulfanyl)-phenyl]ethanone (I) and (E)-1-[4-({4-[(4-methoxybenzylidene)amino] phenyl}-sulfanyl)phenyl]ethan-1-one (II) were structurally studied. They crystallize respectively in the monoclinic Cc and the triclinic P1 space groups, with the respective cell parameters: [10.695(3) Å, 44.458(14) Å, 4.4437(11) Å, 99.004(9)◦] and [5.7708(2) Å, 8.0867(3) Å, 19.6929(8) Å, 81.844(2)◦, 86.664(3)◦, 85.662(3)◦]. The asymmetric units of (I) and (II) are composed of one molecule and two crystallographically independent molecules, respectively. Their molecular structures were optimized by the density functional theory and correlated correspondingly to the crystal structures. Moreover, the IR vibration modes were assigned to the calculated wavenumbers, the Mulliken atomic charges obtained and the frontier molecular orbitals evaluated. The hydrogen bonding and the non-classical intermolecular interactions within the two frameworks were investigated using Hirshfeld surface analysis which indicated the presence of C–H…H–C, C–H⋅⋅⋅π, C–H⋅⋅⋅O, C–H⋅⋅⋅N, C–H⋅⋅⋅S and π⋅⋅⋅lp interactions as well as π⋅⋅⋅π stacking. Additionally, in order to understand the interacting binding sites of the two molecules with the bacterial S. aureus protein receptors, the studied compounds were in silico evaluated by molecular docking against tyrosyl-tRNA synthetase 1JIJ and topoisomerase II DNA gyrase 2XCT enzymes. The results revealed consequently potent antimicrobial efficacy through the formed hydrogen bonds, hydrophobic contacts, π-cation interactions and π…π stackingItem Experimental and computational studies of di-μ-chlorido-bis[chlorido(1,10-phenanthroline-K2N,N′)nickel(II)] NiCl2(H2O)(C12N2H8): Crystal structure, quantitative analysis of the intermolecular interactions and electronic properties(2020-11-03) Amani DiremNiCl2(H2O)(C12N2H8) was synthesized in solution and its structure was studied by single-crystal X-ray diffraction. It crystallizes in the monoclinic system (S. G.: P21/n), Z = 4, with the cell parameters (A, ˚ °): a = 12.6640(5), b = 6.8322(3), c = 14.2054(5) and β = 93.569(3). The final residual factors of the refined structure model R/Rω were 0.031/0.082 for 2156 independent reflexions and 172 parameters. The crystal structure is described in terms of Ni2Cl4(H2O)2(Phen)2 dimmers interacting through weak intermolecular O–H…Cl Hydrogen bonds. The 2D fingerprint plots, built using the Hirshfeld surface analysis, helped analyzing and quantifying all the intermolecular contacts and revealed the main intermolecular interactions around the title complex. The computational investigation was undertaken at M06–2X/6– 31G(d)(LANL2DZ) level by using Gaussian.Item Experimental and in silico studies of dichloro-tetrakis(1H-pyrazole)-cobalt(II): Structural description, photoluminescent behavior and molecular docking(2021-03-10) Amani DiremA novel pyrazole-based Co(II) complex, namely dichloro-tetrakis(1H-pyrazole)-cobalt(II), was synthesized and characterized. Its X-ray crystal structure showed that it crystallizes in the monoclinic C2/c space group with discrete [CoPz4Cl2] units held together via intra- and intermolecular hydrogen bonds. The non-covalent interactions were explicitly analyzed by means of the topological and Hirshfeld surface analyses, revealing the presence of 0-periodic binodal 1,6-connected 1,6M7–1 and 14-connected uninodal bcu–x topologies built up through N—H…Cl and C—H…Cl hydrogen-bonding networks in addition to weak non-classical H…H, N–H…C, C–H…N, N—H…π, π…lp/lp…π and lp…lp interactions. Additionally, interactions energy and energy frameworks analyses were performed in order to compute the total energies of the possible intermolecular interactions. The empty space in the crystal lattice was analyzed using void mapping which lead to the presence of small cavities. The structure was furthermore optimized showing a very good agreement with the experimental results, the molecular electrostatic potential (MEP) maps were obtained with their active regions and the non-linear optical properties estimated. Additionally, the optical properties of the title complex were investigated at room temperature using optical UV-visible absorption and photoluminescence spectroscopy, exhibiting π →π ∗, n → π ∗, d → d and ligand-field transitions which result in a large variety of emission bands predominant by a bright red photoluminescence. An in silico study was carried out and the binding ability of the title complex with Staphylococcus aureus tyrosyl-tRNA synthetase and Pyrococcus kodakaraensis aspartyl-tRNA synthetase was evaluated displaying a good inhibition activity towards the last one.Item Experimental and in silico studies of dichloro-tetrakis(1H-pyrazole)-cobalt(II): Structural description, photoluminescent behavior and molecular docking(2021-03-10) Amani DiremA novel pyrazole-based Co(II) complex, namely dichloro-tetrakis(1H-pyrazole)-cobalt(II), was synthesized and characterized. Its X-ray crystal structure showed that it crystallizes in the monoclinic C2/c space group with discrete [CoPz4Cl2] units held together via intra- and intermolecular hydrogen bonds. The non-covalent interactions were explicitly analyzed by means of the topological and Hirshfeld surface analyses, revealing the presence of 0-periodic binodal 1,6-connected 1,6M7–1 and 14-connected uninodal bcu–x topologies built up through N—H…Cl and C—H…Cl hydrogen-bonding networks in addition to weak non-classical H…H, N–H…C, C–H…N, N—H…π, π…lp/lp…π and lp…lp interactions. Additionally, interactions energy and energy frameworks analyses were performed in order to compute the total energies of the possible intermolecular interactions. The empty space in the crystal lattice was analyzed using void mapping which lead to the presence of small cavities. The structure was furthermore optimized showing a very good agreement with the experimental results, the molecular electrostatic potential (MEP) maps were obtained with their active regions and the non-linear optical properties estimated. Additionally, the optical properties of the title complex were investigated at room temperature using optical UV-visible absorption and photoluminescence spectroscopy, exhibiting π →π ∗, n → π ∗, d → d and ligand-field transitions which result in a large variety of emission bands predominant by a bright red photoluminescence. An in silico study was carried out and the binding ability of the title complex with Staphylococcus aureus tyrosyl-tRNA synthetase and Pyrococcus kodakaraensis aspartyl-tRNA synthetase was evaluated displaying a good inhibition activity towards the last one.Item Hydrogen bonding in 2-carboxyanilinium dihydrogen phosphite at 100 K(2009) Amani DiremActa Crystallographica Section E: Structure Reports Online is the IUCr’s highly popular open-access structural journal. It provides a simple and easily accessible publication mechanism for the growing number of inorganic, metal-organic and organic crystal structure determinations. The electronic submission, validation, refereeing and publication facilities of the journal ensure very rapid and high-quality publication, whilst key indicators and validation reports provide measures of structural reliability. In 2007, the journal published over 5000 structures. The average p