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Hu F, Chang F, Tao L, Sun X, Liu L, Zhao Y, Han Z, Li C. Prediction of Protein Allosteric Sites with Transfer Entropy and Spatial Neighbor-Based Evolutionary Information Learned by an Ensemble Model. J Chem Inf Model 2024; 64:6197-6204. [PMID: 39075972 DOI: 10.1021/acs.jcim.4c00544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Allostery is one of the most direct and efficient ways to regulate protein functions. The diverse allosteric sites make it possible to design allosteric modulators of differential selectivity and improved safety compared with those of orthosteric drugs targeting conserved orthosteric sites. Here, we develop an ensemble machine learning method AllosES to predict protein allosteric sites in which the new and effective features are utilized, including the entropy transfer-based dynamic property, secondary structure features, and our previously proposed spatial neighbor-based evolutionary information besides the traditional physicochemical properties. To overcome the class imbalance problem, the multiple grouping strategy is proposed, which is applied to feature selection and model construction. The ensemble model is constructed where multiple submodels are trained on multiple training subsets, respectively, and their results are then integrated to be the final output. AllosES achieves a prediction performance of 0.556 MCC on the independent test set D24, and additionally, AllosES can rank the real allosteric sites in the top three for 83.3/89.3% of allosteric proteins from the test set D24/D28, outperforming the state-of-the-art peer methods. The comprehensive results demonstrate that AllosES is a promising method for protein allosteric site prediction. The source code is available at https://github.com/ChunhuaLab/AllosES.
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Affiliation(s)
- Fangrui Hu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Fubin Chang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lianci Tao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lamei Liu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Yingchun Zhao
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
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2
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Alhagri IA, Alsowayan R, Ghannay S, Al-Hazmy SM, Ahmad I, Patel H, Kadri A, Aouadi K. Synthesis, optical properties, DNA, β-cyclodextrin interactions, and antioxidant evaluation of novel isoxazolidine derivative (ISoXD2): A multispectral and computational analysis. Heliyon 2024; 10:e34561. [PMID: 39113987 PMCID: PMC11305329 DOI: 10.1016/j.heliyon.2024.e34561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/06/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024] Open
Abstract
ISoXD2 are well explored among versatile and outstanding class of pharmacophores for the preparation and discovery of drugs. Herein, the electronic absorption and emission spectra of ISoXD2 were investigated in three different solvents. The observed transition was attributed to π-π* with charge transfer character. Changes in the excited state and shift of the absorption and emission peaks to longer wavelengths are observed as a result of increasing solvent polarity, due to the interactions between the ISoXD2 molecule and the solvent molecules surrounding it. Changing the solvent confirms its solvatochromic effect. UV-vis and fluorescence analysis revealed that ISoXD2 binds to deoxyribonucleic acid (DNA) by intercalation mode, with a stoichiometric ratio of 1:1.5. Moreover, the fluorescence intensity of DNA bound to ethidium bromide (EB) in the presence of ISoXD2 was investigated. From this analysis, the Stern-Volmer quenching constant (Ksv), quenching rate constant (kq), binding constant (Kb) and binding sites number (n) were found to be 5.654 × 103 M-1, 2.827 × 1011 M-1 s-1, 3.81 × 104 M-1 and 1.225, respectively. The interaction between ISoXD2 and β-CD was investigated through absorption spectra analysis. Kb for this interaction was determined to be 4.9 × 104 M-1. The free radical-scavenging ability of the prepared ISoXD2, examined by DPPH and ABTS assays have shown a good antioxidant activity. Furthermore, modeling study was conducted to explore their plausible binding mechanism with ISoXD2 and to support the experimental results.
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Affiliation(s)
- Ibrahim A. Alhagri
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
- Department of Chemistry, Faculty of Sciences, Ibb University, Ibb, Yemen
| | - Raghad Alsowayan
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Siwar Ghannay
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Sadeq M. Al-Hazmy
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
- Department of Chemistry, College of Science, Sana'a University, Sana'a, P.O. Box 1247, Yemen
| | - Iqrar Ahmad
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Adel Kadri
- Faculty of Science and Arts in Baljurashi, Al-Baha University, P.O. Box (1988), Al-Baha, 65527, Saudi Arabia
- Faculty of Science of Sfax, Department of Chemistry, University of Sfax, B.P. 1171, 3000, Sfax, Tunisia
| | - Kaiss Aouadi
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
- Department of Chemistry, Laboratory of Heterocyclic Chemistry Natural Product and Reactivity/CHPNR, Faculty of Science of Monastir, University of Monastir, Avenue of the Environment, Monastir, 5019, Tunisia
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Furia E, Lettera V, Napoli A, Aiello D. Insights on Stability Constants and Structures of Complexes between Coumarin Derivatives and Pb(II) in Aqueous Media. Molecules 2024; 29:1911. [PMID: 38731402 PMCID: PMC11085526 DOI: 10.3390/molecules29091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
In the frame of a systematic study on the sequestering ability of natural antioxidants towards metal cations, here the complexation of coumarin-3-carboxilic acid (HCCA) with Pb(II) and the overall stability constants of the resulting complexes, at 37 °C and in 0.16 M NaClO4, are discussed. Reaction of Pb(ClO4)2 with HCCA in an aqueous medium at a pH range from 2 to 6 and various ratios (1:1-1:10) yielded the Pb-CCA complexes, which were characterized spectrometrically by laser desorption ionization mass spectrometry (LD-MS). LD-MS has provided the composition and structure of Pb-CCA species according to the speciation model proposed on the basis of the potentiometric data. The graphic representation of the complex's concentration curves is given by the distribution diagram, which provides a whole depiction of the species present in the solution at the selected pH ranges.
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Affiliation(s)
| | | | | | - Donatella Aiello
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Rende, Italy; (E.F.); (V.L.); (A.N.)
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Khan MA, Hoque A, Islam MS, Ghosh S, Alam MA. Coumarin Derivative and Gold Nanoparticle Conjugate as a Selective Fluorescent Sensor for Mercury Ion in Real Sample. J Fluoresc 2024:10.1007/s10895-024-03709-6. [PMID: 38647961 DOI: 10.1007/s10895-024-03709-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/05/2024] [Indexed: 04/25/2024]
Abstract
A biphenyl based coumarin fluorescent molecule, N,N'-bis(7-diethylamino-2-oxo-2 H-chromen-3-yl)methylene)biphenyl-2-2'-dicarbohydrazide (molecule 1) has been synthesized and characterised. Photophysical studies of 1 exhibit solvent polarity dependent absorption and emission maxima. Citrate capped gold nanoparticles (AuNPs) have been mixed with molecule 1 for the preparation of AuNPs/1 conjugate. The association constant of the AuNPs/1 conjugate has been calculated to 4.54 × 104 M- 1. The AuNPs/1 conjugate has been found to detect Hg2+ ion selectively by fluorescence enhancement. While addition of molecule 1 into the solution of AuNPs, fluorescence intensity of 1 quenched. On addition of several monovalent, divalent and trivalent metal ion into the solution of AuNPs/1 conjugate separately, there was no change in fluorescence intensity of 1 has been observed. However, upon addition of Hg2+ ion into the solution of AuNPs/1 conjugate, the fluorescence intensity enhancement occurred, indicating released of 1 from the surface of AuNPs and probably aggregation of AuNPs took place in presence of Hg2+ ion. The AuNPs/1 conjugate has been found to have a detection limit of 2.3 × 10- 9 M for Hg2+ ion in aqueous solvent. Meanwhile, the AuNPs/1 conjugate have also been successfully applied for the determination of Hg2+ in real water samples.
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Affiliation(s)
- Mehebub Ali Khan
- Department of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, 700160, India
| | - Anamika Hoque
- Department of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, 700160, India
| | - Md Sanaul Islam
- Department of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, 700160, India
| | - Soumen Ghosh
- Department of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, 700160, India.
| | - Md Akhtarul Alam
- Department of Chemistry, Aliah University, Action Area IIA/27, New Town, Kolkata, 700160, India.
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Hegazy ME, Taher ES, Ghiaty AH, Bayoumi AH. Tailored quinoline hybrids as promising COX-2/15-LOX dual inhibitors endowed with diverse safety profile: Design, synthesis, SAR, and histopathological study. Bioorg Chem 2024; 145:107244. [PMID: 38428284 DOI: 10.1016/j.bioorg.2024.107244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/14/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
Complications of the worldwide use of non-steroidal anti-inflammatory drugs (NSAIDs) sparked scientists to design novel harmless alternatives as an urgent need. So, a unique hybridization tactic of quinoline/pyrazole/thioamide (4a-c) has been rationalized and synthesized as potential COX-2/15-LOX dual inhibitors, utilizing relevant reported studies on these pharmacophores. Moreover, we extended these preceding hybrids into more varied functionality, bearing crucial thiazole scaffolds(5a-l). All the synthesized hybrids were evaluatedin vitroas COX-2/15-LOX dual inhibitors. Initially, series4a-cexhibited significant potency towards 15-LOX inhibition (IC50 = 5.454-4.509 μM) compared to meclofenamate sodium (IC50 = 3.837 μM). Moreover, they revealed reasonable inhibitory activities against the COX-2 enzyme in comparison to celecoxib.Otherwise, conjugates 5a-ldisclosed marked inhibitory activity against 15-LOX and strong inhibitory to COX-2. In particular, hybrids5d(IC50 = 0.239 μM, SI = 8.95), 5h(IC50 = 0.234 μM, SI = 20.35) and 5l (IC50 = 0.201 μM, SI = 14.42) revealed more potency and selectivity outperforming celecoxib (IC50 = 0.512 μM, SI = 4.28). In addition, the most potentcompounds, 4a, 5d, 5h, and 5l have been elected for further in vivoevaluation and displayed potent inhibition of edema in the carrageenan-induced rat paw edema test that surpassed indomethacin. Further, compounds5d, 5h, and 5l decreased serum inflammatory markers including oxidative biomarkersiNO, and pro-inflammatory mediators cytokines like TNF-α, IL-6, and PGE. Ulcerogenic liability for tested compounds demonstrated obvious gastric mucosal safety. Furthermore, a histopathological study for compound 5l suggested a confirmatory comprehensive safety profile for stomach, kidney, and heart tissues. Docking and drug-likeness studies offered a good convention with the obtained biological investigation.
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Affiliation(s)
- Mohamed E Hegazy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt
| | - Ehab S Taher
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut 71524, Egypt; Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa 13110, Jordan.
| | - Adel H Ghiaty
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Ashraf H Bayoumi
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11884, Cairo, Egypt
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AlHazmy SM, Zouaghi MO, Al-Hakimi AN, Alorini T, Alhagri IA, Arfaoui Y, Al-Ashwal R, Mansour L, Hamdi N. Synthesis, characterization, optical properties, biological activity and theoretical studies of a 4 nitrobenzylidene) amino) phenyl)imino)methyl)naphthalen-2-ol -based fluorescent Schiff base. Heliyon 2024; 10:e26349. [PMID: 38495175 PMCID: PMC10943314 DOI: 10.1016/j.heliyon.2024.e26349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
A new Schiff base, 1-(E)-(4-((E) 4nitrobenzylidene) amino) phenyl)imino) methyl)naphthalen-2-ol (4NMN), was prepared from the reaction of p-phenylenediamine with 2-hydroxy-1-naphthaldehyde and 4-nitrobenzaldehyde and characterized with spectroscopic analysis. UV-VIS and NMR. Frontier molecular orbitals, molecular electrostatic potential, and chemical reactivity descriptors of the synthesized compound were studied using molecular modeling methods. The antibacterial and antifungal activities of the Schiff base were studied for its minimum inhibitory concentration. The compound showed a higher effect on yeast than against bacteria. Density functional theory (DFT) calculations were performed to study the mechanism of reaction for the synthesis of 4NMN, and the results were consistent with the experimental findings. 4NMN exhibited moderate antibacterial and antifungal activities and demonstrated higher inhibition potential against different resistant strains compared to the reference drug gentamycin. The absorption and fluorescence spectra of 4NMN were measured in different solvents, and the effect of relative polarity and acidity on the medium was observed. An inner filter effect was observed at high concentrations, and the compound showed considerable fluorescence enhancement with increasing medium viscosity and fluorescence quenching by the addition of traces of Cr1+ and Cu2+. Additionally, molecular docking studies were conducted to investigate the efficiency of antibacterial and antifungal targets.
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Affiliation(s)
- Sadeq M. AlHazmy
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Mohamed Oussama Zouaghi
- Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Ahmed N. Al-Hakimi
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Thamer Alorini
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Ibrahim A. Alhagri
- Department of Chemistry, College of Science, Qassim University, Buraidah, 51452, Saudi Arabia
| | - Youssef Arfaoui
- Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092, Tunis, Tunisia
| | - Rania Al-Ashwal
- School of Biomedical Engineering and Health Sciences, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, 81310, Malaysia
- Advanced Diagnostic and Progressive Human Care Research Group, School of Biomedical Engineering and Health Science Teknologi Malaysia, Johor Bahru, 81310, Malaysia
| | - Lamjed Mansour
- Zoology Department, College of Science, King Saud University, Saudi Arabia, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Naceur Hamdi
- Research Laboratory of Environmental Sciences and Technologies (LR16ES09), Higher Institute of Environmental Sciences and Technology, University of Carthage, Hammam-Lif, Tunisia
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Alotayeq A, Ghannay S, Alhagri IA, Ahmed I, Hammami B, E. A. E. Albadri A, Patel H, Messaoudi S, Kadri A, M. Al-Hazmy S, Aouadi K. Synthesis, optical properties, DNA, β-cyclodextrin interaction, hydrogen isotope sensor and computational study of new enantiopure isoxazolidine derivative (ISoXD). Heliyon 2024; 10:e26341. [PMID: 38404822 PMCID: PMC10884473 DOI: 10.1016/j.heliyon.2024.e26341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
A novel isoxazolidine derivative (ISoXD) dye was successfully synthesized and comprehensively characterized. In this study, we conducted a thorough examination of its various properties, including optical characteristics, interactions with DNA and β-cyclodextrin (β-CD), molecular docking, molecular dynamic simulation, and density functional theory (DFT) calculations. Our investigation encompassed a systematic analysis of the absorption and emission spectra of ISoXD in diverse solvents. The observed variations in the spectroscopic data were attributed to the specific solvent's capacity to engage in hydrogen bonding interactions. Remarkably, the most pronounced intensities were observed in glycol, which can establish many hydrogen bonds with ISoXD. Furthermore, our study revealed a significant distinction in the fluorescence behavior of ISoXD when subjected to different solvents, particularly between CHCl3 and CDCl3. Moreover, we explored the fluorescence intensity of the ISoXD complex in the presence of various metals, both in ethanol and water. The ISoXD complex exhibited a substantial increase of fluorescence upon interaction with different metal ions. The utilization of DFT calculations allowed us to propose an intramolecular charge transfer (ICT) mechanism as a plausible explanation for this quenching phenomenon. The interaction of ISoXD with DNA and β-CD was studied using absorption spectra. The binding constant (K) and the standard Gibbs free energy change (ΔGo) for the interaction between DNA and β-CD with ISoXD were determined. In docking study, ISoXD exhibited significant docking scores (-6.511) and MM-GBSA binding free energies (-66.27 kcal/mol) within the PARP-1 binding cavity. Its binding pattern closely resembles to the co-crystal ligand veliparib, and during a 100ns MD simulation, ISoXD displayed strong stability and formed robust hydrogen bonds with key amino acids. These findings suggest ISoXD's potential as a PARP-1 inhibitor for further investigation in therapeutic development.
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Affiliation(s)
- Afnan Alotayeq
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
| | - Siwar Ghannay
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
| | - Ibrahim A. Alhagri
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
- Department of Chemistry, Faculty of Sciences, Ibb University, Ibb, Yemen
| | - Iqrar Ahmed
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, 424002, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Bechir Hammami
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
| | - Abuzar E. A. E. Albadri
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
| | - Harun Patel
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, 425405, Maharashtra, India
| | - Sabri Messaoudi
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
- Faculty of Sciences of Bizerte, Carthage University, Jarzouna, Bizerte 7021, Tunisia
| | - Adel Kadri
- Faculty of Science of Sfax, Department of Chemistry, University of Sfax, B.P. 1171, 3000 Sfax, Tunisia
- Department of Chemistry, Faculty of Science and Arts of Baljurashi, Al- Baha University, Saudi Arabia
| | - Sadeq M. Al-Hazmy
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
| | - Kaiss Aouadi
- Department of Chemistry, College of Science, Qassim University, Buraidah 51452, Saudi Arabia
- Department of Chemistry, Laboratory of Heterocyclic Chemistry Natural Product and Reactivity/CHPNR, Faculty of Science of Monastir, University of Monastir, Avenue of the Environment, Monastir, 5019, Tunisia
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Zouaghi MO, Amri N, Hassen S, Arfaoui Y, Özdemir N, Özdemir I, Hamdi N. Biological determination, Molecular Docking and Hirshfeld surface analysis of rhoduim(I)-N-heterocyclic carbene complex: Synthesis, crystal structure, DFT calculations, Optical and Non Linear Optical properties. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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