Browsing by Author "Amani Direm"
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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 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 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 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 pItem Hydrogen bonding in 4-carboxyanilinium dihydrogenphosphate(2007-03-27) Amani DiremThe crystal structure analysis of the title compound, C7H8NO2+H2PO4 , has revealed a three-dimensional hydrogen-bonded network structure, involving the dihydrogenphosphate anions, the carboxyl groups and the ammonium groups. The anions are held together via strong O—H O hydrogen bonds. In addition to the N—H O and O—H O interactions, involving all the H atoms covalently bonded to the anion, the nitrogen and the carboxyl group, the crystal structure is also stabilized by C—H O and C—H short contacts.Item Interaction between escitalopram and ibuprofen or paracetamol: DFT and molecular docking on the drug–drug interactions(2023-04-12) Amani DiremMusa Daboe, Cemal Parlak, Amani Direm, Özgür Alver & Ponnadurai Ramasami (2023): Interaction between escitalopram and ibuprofen or paracetamol: DFT and molecular docking on the drug–drug interactions, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2023.2195004Item Intermolecular interactions of proton transfer compounds: synthesis, crystal structure and Hirshfeld surface analysis(2010-06-10) Amani DiremThree new proton transfer compounds, [2-ammonio-5-methylcarboxybenzene perchlorate (1), (C8H10NO2+ClO4 ), 4-(ammoniomethyl)carboxybenzene nitrate (2), (C8H10NO2+NO3 ), and 4-(ammoniomethyl)carboxybenzene perchlorate (3), (C8H10NO2+ClO4 )], have been synthesized, their IR modes of vibrations have been assigned and their crystal structures studied by means of singlecrystal X-ray diffraction. Their asymmetric units consist of one cation and one anion for both compounds (1) and (2). However, the crystal structure of compound (3) is based on a pair of cations and a pair of anions in its asymmetric unit. The three-dimensional Hirshfeld surface analysis and the two-dimensional fingerprint maps revealed that the three structures are dominated by H O/ O H and H H contacts. The strongest hydrogen-bonding interactions are associated with O—H O and N—H O constituting the highest fraction of approximately 50%, followed by those of the H H type contributing 20%. Other close contacts are also present, including weak C H/H C contacts (with about 10%)Item Sev and pcu topological nets in one-pot newly synthesized mixed-ligand imidazole-containing Cu(II) coordination frameworks: Crystal structure, intermolecular interactions, theoretical calculations, magnetic behavior and biological activity(2018-03-30) Amani DiremNovel mixed-ligand coordination frameworks, occurring concomitantly namely [Cu(Im)3(H2Cit)] (1) and [Cu(Im)2(HCit)] HIm (2) (with Im = imidazole and H4Cit = citric acid) were obtained as a result of the onepot reaction between imidazole, citric acid and copper chloride. The complexes were structurally characterized by elemental analysis, FTIR spectroscopy and X-ray diffraction. The two structures were found to be connected through 3D hydrogen-bonding networks examined by means of the Hirshfeld surface analysis which highlighted the presence of O–H O, N–H O and C–H O H-bonds together with the p lp interactions. A topological analysis of the underlying nets corresponding to the two hydrogen-bonded frameworks was carried out. Moreover, quantum chemical calculations were performed using the HF method with 6-31G(d) and LANL2DZ levels in the gas phase, and therefore the optimized structures, the IR, 1H NMR, 13C NMR spectra and the electronic structure descriptors were examined in detail. Furthermore, the magnetic properties of (1) and (2) were also investigated. The complexes showed remarkable antimicrobial and antifungal inhibition activities.Item Spectroscopic characterization, DFT calculations, in vitro pharmacological potentials, and molecular docking studies of N, N, O-Schiff base and its trivalent metal complexes(2024-02-29) Amani DiremIn this study, trivalent metal complexes of the category: [M(L)(H2O)nCly] obtained from the interaction of metal3+ ion salts with organic N, N, O-Schiff base (HL) (where: HL = 4-{(Z)-((2-{(E)-((2-hydroxyphenyl)methylidene)amino}ethyl)imino)methyl}-2-methoxyphenol; n, y = 1 or 2 and M = Ti(III), Fe(III), Ru(III), Cr(III) and Al(III)) were synthesized and characterized viz molar conductance, FT-IR, and UV–Vis spectroscopies, elemental analyses, thermal analyses (TGA and DTA), and UV–Vis spectroscopy, theoretical calculations. A distorted octahedral structure around the metal ions was proposed based on the obtained experimental and calculated data. Thermal examination of the complexes signposts the step-by-step disintegration to give the final decomposition product as metal oxides. Moreover, DFT calculations were executed utilizing the B3LYP/LANL2DZ theory level, which revealed that the synthesized metal (III) complexes were more stable than the free ligand (HL). The value of ΔE for HL is 4.60 eV while the related values for the complexes of Cr(III) (C1), Ru(III) (C2), Fe (III) (C3), Al(III) (C4), and Ti(III) (C5) are respectively 2.59, 3.68, 3.15, 1.64, and 2.75 eV. Scavenging abilities of DPPH and ABTS radicals by the test compounds revealed promising antioxidant behavior. It was observed that the compounds are proficient DPPH radical scavengers in a dose-dependent configuration. Ru(III); IC50 = 1.69 ± 2.68 µM for DPPH and Ti(III); IC50 = 8.70 ± 2.78 µM for ABTS performed best. Similarly, the complexes demonstrated higher antimicrobial activities compared to HL against the designated strains, while ciprofloxacin acted as a standard antibiotic. Furthermore, the ligand and its most effective complexes C2 and C5 were docked against the targets S. aureus DNA gyrase (2XCT), S. pneumoniae DNA gyrase (5BOD), and E. coli DNA gyrase (5L3J). The binding sites were evaluated and the docking results showed that the studied molecules bind to the targets through classical O—H…O and/or N—H…O hydrogen bonds, as well as via hydrophobic contacts.