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Rasool A, Zahid S, Alfryyan N, Ayub AR, Ayub K, Akhter MS, Iqbal J, Al-Buriahi M, Yousef ES. Remarkable non-linear optical properties of gold cluster doped graphyne (GY): A DFT study. J Mol Graph Model 2022; 114:108204. [DOI: 10.1016/j.jmgm.2022.108204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/14/2022] [Accepted: 04/22/2022] [Indexed: 01/18/2023]
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Haribabu J, Garisetti V, Malekshah RE, Srividya S, Gayathri D, Bhuvanesh N, Mangalaraja RV, Echeverria C, Karvembu R. Design and synthesis of heterocyclic azole based bioactive compounds: Molecular structures, quantum simulation, and mechanistic studies through docking as multi-target inhibitors of SARS-CoV-2 and cytotoxicity. J Mol Struct 2022; 1250:131782. [PMID: 34697505 PMCID: PMC8528790 DOI: 10.1016/j.molstruc.2021.131782] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/16/2021] [Accepted: 10/19/2021] [Indexed: 01/04/2023]
Abstract
Two heterocyclic azole compounds, 3-(2,3-dihydrobenzo[d]thiazol-2-yl)-4H-chromen-4-one (SVS1) and 5-(1H-indol-3-yl)-4-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (SVS2) were obtained unexpectedly from 2-aminothiophenol and 4-oxo-4H-chromene-3-carbaldehyde (for SVS1), and (E)-2-((1H-indol-3-yl)methylene)-N-methylhydrazine-1-carbothioamide in the presence of anhydrous FeCl3 (for SVS2), respectively. The compounds were well characterized by analytical and spectroscopic tools. The molecular structures of both the compounds were determined by single crystal X-ray diffraction (XRD) study. The results obtained from density functional theory (DFT) study revealed the molecular geometry and electron distribution of the compounds, which were correlated well with the three-dimensional structures obtained from the single crystal XRD. DMol3 was used to calculate quantum chemical parameters [chemical potential (µ), global hardness (η), global softness (σ), absolute electronegativity (χ) and electrophilicity index (ω)] of SVS1 and SVS2. Molecular docking study was performed to elucidate the binding ability of SVS1 and SVS2 with SARS-CoV-2 main protease and human angiotensin-converting enzyme-2 (ACE-2) molecular targets. Interestingly, the binding efficiency of the compounds with the molecular targets was comparable with that of remdesivir (SARS-CoV-2), chloroquine and hydroxychloroquine. SVS1 showed better docking energy than SVS2. The molecular docking study was complemented by molecular dynamics simulation study of SARS-CoV-2 main protease-SVS1 complex, which further exemplified the binding ability of SVS1 with the target. In addition, SVS1, SVS2 and cisplatin were assessed for their cytotoxicity against a panel of three human cancer cells such as HepG-2 (hepatic carcinoma), T24 (bladder) and EA.hy926 (endothelial), as well as Vero (kidney epithelial cells extracted from an African green monkey) normal cells using MTT assay. The results showed that SVS2 has significant cytotoxicity against HepG-2 and EA.hy926 cells with the IC50 values of 33.8 μM (IC50 = 49.9 μM-cisplatin and 8.6 μM-doxorubicin) and 29.2 (IC50 = 26.6 μM-cisplatin and 3.8 μM-doxorubicin), respectively.
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Affiliation(s)
- Jebiti Haribabu
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India,Facultad de Medicina, Universidad de Atacama, Los Carreras 1579, 1532502 Copiapo, Chile
| | - Vasavi Garisetti
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India
| | - Rahime Eshaghi Malekshah
- Medical Biomaterial Research Centre (MBRC), Tehran University of Medical Sciences, Tehran, Iran,Department of Chemistry, Iran University of Science and Technology, Tehran 16846‒13114, Iran
| | - Swaminathan Srividya
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India
| | - Dasararaju Gayathri
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India
| | - Nattamai Bhuvanesh
- Department of Chemistry, Texas A & M University, College Station, TX 77842, USA
| | - Ramalinga Viswanathan Mangalaraja
- Advanced Ceramics and Nanotechnology Laboratory, Department of Materials Engineering, Faculty of Engineering, University of Concepcion, Concepcion, Chile
| | - Cesar Echeverria
- Facultad de Medicina, Universidad de Atacama, Los Carreras 1579, 1532502 Copiapo, Chile,Corresponding authors
| | - Ramasamy Karvembu
- Department of Chemistry, National Institute of Technology, Tiruchirappalli 620015, India,Corresponding authors
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Baillargeon P, Seidler T, Champagne B, Soldera A. Polar and Helical Isomorphous Crystals of Proline Derivatives: Influence of a Fluorine Atom on the Electric Susceptibility. CHEMISTRY AFRICA 2021. [DOI: 10.1007/s42250-021-00236-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractTwo novel nonlinear optical isomorphous crystals of proline derivatives with alkyne functionality have been obtained (Boc-L-ProNH(CH2)2CCH and Boc-cis-4-fluoro-L-ProNH(CH2)2CCH). Both derivatives, which differ only by the substitution of a H atom to a F atom, adopt the same polar and columnar right-handed helix arrangement in the crystalline state. In addition, adjacent polar helical columns all point in the same direction, thus generating a macrodipole and a crystalline system conducive for second harmonic generation (SHG) properties. This isomorphous crystal system constitutes an interesting tool to study the effect of the fluorine atom on the dipole moment and on the first hyperpolarizability. Starting from the PBC optimized geometries of the crystals, the macroscopic second-order nonlinearity, χ(2), of the newly synthesized crystals has been estimated by quantum chemical calculations. These χ(2) responses are of the same order of magnitude as those of inorganic proline derivatives while smaller than those observed in crystals of push–pull π-conjugated molecules.
Graphic Abstract
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Gholivand K, Sabaghian M, Eshaghi Malekshah R. Synthesis, characterization, cytotoxicity studies, theoretical approach of adsorptive removal and molecular calculations of four new phosphoramide derivatives and related graphene oxide. Bioorg Chem 2021; 115:105193. [PMID: 34339976 DOI: 10.1016/j.bioorg.2021.105193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/26/2021] [Accepted: 07/17/2021] [Indexed: 01/05/2023]
Abstract
In this study, four novel phosphoramide ligands (L1-L4) are synthesized and characterized by 31PNMR, 1HNMR, MASS, and FT-IR spectroscopies. In vitro cell growth inhibition is studied by the MTT assay to evaluate the cytotoxicity of ligands against MCF-7 cell line; the result of the assay demonstrates that all ligands significantly suppress the proliferation of breast cancer cells in a concentration-dependent manner. The calculated IC50 values are in the range of 3.6-10.77 µg ml-1, of which the lowest value is attributed to L1. Then a facile approach was developed to functionalize graphene oxide (GO) surface by L1. The data which are obtained by XRD, FT-IR, and EDX analysis confirmed the deposition of phosphoramide on the surface of GO. The cell viability of GO-L1 compound at different concentrations is investigated in 24 h experiment. Excellent synergistic antitumor effects of GO and L1 lead to a decrease in IC50 value up to 2.13 μg ml-1. The Quantum calculations of compounds are used to study energies and HOMO and LUMO values, dipole moments (µ), global hardness (η), global softness (σ), and electrophilicity index (ω) using DMol3 module in Material studio2017. The docking calculations are performed to describe the mode of the binding to DNA and DNA polymerase IIα. Adsorption calculations of ligands (L1-L4) on GO sheet in the presence of water showed that L1 and L2 were located on GO via π electrons of anisole ring. While, L3 and L4 were located on GO by π - π interactions of aniline ring.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
| | - Marzie Sabaghian
- Department of Chemistry, Faculty of Science, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
| | - Rahime Eshaghi Malekshah
- Medical Biomaterial Research Centre (MBRC), Tehran University of Medical Sciences, Tehran, Iran.
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Synthesis, molecular dynamics simulation and adsorption study of different pollutants on functionalized mesosilica. Sci Rep 2021; 11:1967. [PMID: 33479295 PMCID: PMC7820229 DOI: 10.1038/s41598-020-80566-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/23/2020] [Indexed: 11/08/2022] Open
Abstract
Experimental and computational works were carried out on a new type of mesoporous silica. In the experimental section, functionalized hollow mesosilica spheres were prepared via a facile technique and then evaluated using some analytical techniques (FESEM, TEM, L-XRD, FTIR, BET-BJH, and TGA). The obtained results revealed that the synthesized material had hollow structure with a diamino-grafted porous shell. The molecular separation of crystal Violet (CV) and neutral Red (NR) dyes from water were investigated by adsorption process using the synthesized powder. Influence of adsorbent loading was evaluated as adsorption ability and dyes removal efficiency. Also, the obtained modeling results revealed appropriate fitting of data with non-linear Langmuir model. The theoretical studies were employed to study the adsorption and removal mechanism of cationic (CV and NR) and anionic (orange II (OII)) dyes using molecular dynamics calculations. Moreover, the simulation outcomes provided valuable information about quantum chemical properties including the HOMO-LUMO maps, chemical reactivity, global softness (σ) and hardness (η) for silica-linker-water-dyes components.
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Pelalak R, Soltani R, Heidari Z, Malekshah RE, Aallaei M, Marjani A, Rezakazemi M, Kurniawan TA, Shirazian S. Molecular dynamics simulation of novel diamino-functionalized hollow mesosilica spheres for adsorption of dyes from synthetic wastewater. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114812] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Venkateshan M, Muthu M, Suresh J, Ranjith Kumar R. Azafluorene derivatives as inhibitors of SARS CoV-2 RdRp: Synthesis, physicochemical, quantum chemical, modeling and molecular docking analysis. J Mol Struct 2020; 1220:128741. [PMID: 32834110 PMCID: PMC7309803 DOI: 10.1016/j.molstruc.2020.128741] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 01/18/2023]
Abstract
The crystal structures of 2-(1H-indol-3-yl)-4-phenyl-5H-indeno [( Cheng et al., 2007; Lee et al., 2003) 1,21,2-b]pyridine-3-carbonitrile (Ia) and 2-(1H-indol-3-yl)-4-(4-methoxyphenyl)-5H-indeno [( Cheng et al., 2007; Lee et al., 2003) 1,21,2-b]pyridine-3-carbonitrile (Ib) were determined using single crystal X-ray diffraction. Both the compounds belong to the triclinic system with the P-1 space group. The azafluorene ring system in both the compounds is effectively planar. The intermolecular interactions present in the compounds are discussed using Hirshfeld surface analysis, QTAIM and NCI. Compound Ib formed a strong interaction (-24.174 kJ/mol) with the solvent molecule. Both the compounds were geometry optimized using DFT/B3LYP level of theory. The compound's drug-like behaviors were studied using HOMO-LUMO analysis. The homology modeling of SARS CoV-2 RdRp was done utilizing the PDB 6NUR_A as a template. The model showed above 99% similarity with its preceder SARS CoV. The molecular docking analysis of the synthesized compounds was carried out along with some suggested drugs for COVID-19 and some phytochemicals. The docking results were then analyzed. The binding free energy of the complexes were calculated using MM-PB(GB)SA and ADMET properties of Ia and Ib were also predicted. Some suggestions are given from this analysis.
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Affiliation(s)
- M Venkateshan
- Department of Physics, The Madura College, Madurai, 625011, Tamilnadu, India
| | - M Muthu
- Department of Organic Chemistry, Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
| | - J Suresh
- Department of Physics, The Madura College, Madurai, 625011, Tamilnadu, India
| | - R Ranjith Kumar
- Department of Organic Chemistry, Madurai Kamaraj University, Madurai, 625021, Tamilnadu, India
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Azaphenantherene derivatives as inhibitor of SARS CoV-2 Mpro: Synthesis, physicochemical, quantum chemical and molecular docking analysis. CHEMICAL DATA COLLECTIONS 2020. [PMCID: PMC7332229 DOI: 10.1016/j.cdc.2020.100470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The crystal structure of 2-(1H-indol-3-yl)-4-phenyl-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (Ia) and 2-(5-bromo-1H-indol-3-yl)-4-(4-methoxyphenyl)-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (Ib) were elucidated using single crystal X-ray diffraction. The cyclohexadiene ring adopts screw boat conformation in compound (Ia) and distorted screw boat in compound (Ib). The pyridine ring is effectively planar. The qualitative and quantitative analyses of hydrogen bonding interactions in the compounds were done using Hirshfeld surface analysis, QTAIM and NCI. DFT/B3LYP level of theory was used to optimize both the compounds. These compounds drug-like behaviors were studied using HOMO-LUMO analysis. The molecular docking analysis against Mpro was carried out for the synthesized compounds and some suggested drugs for COVID-19. The docking results were then analyzed.
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