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Chng CP, Dowd A, Mechler A, Hsia KJ. Molecular dynamics simulations reliably identify vibrational modes in far-IR spectra of phospholipids. Phys Chem Chem Phys 2024; 26:18715-18726. [PMID: 38932689 DOI: 10.1039/d4cp00521j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The properties of self-assembled phospholipid membranes are of essential importance in biochemistry and physical chemistry, providing a platform for many cellular life functions. Far-infrared (far-IR) vibrational spectroscopy, on the other hand, is a highly information-rich method to characterize intermolecular interactions and collective behaviour of lipids that can help explain, e.g., chain packing, thermodynamic phase behaviour, and sequestration. However, reliable interpretation of the far-IR spectra is still lacking. Here we present a molecular dynamics (MD) based approach to simulate vibrational modes of individual lipids and in an ensemble. The results are a good match to synchrotron far-IR measurements and enable identification of the molecular motions corresponding to each vibrational mode, thus allowing the correct interpretation of membrane spectra with high accuracy and resolving the longstanding ambiguities in the literature in this regard. Our results demonstrate the feasibility of using MD simulations for interpreting far-IR spectra broadly, opening new avenues for practical use of this powerful method.
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Affiliation(s)
- Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore.
| | - Annette Dowd
- School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Adam Mechler
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - K Jimmy Hsia
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore.
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore 637459, Republic of Singapore
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Hamouda RA, Alharbi AA, Al-Tuwaijri MM, Makharita RR. The Antibacterial Activities and Characterizations of Biosynthesized Zinc Oxide Nanoparticles, and Their Coated with Alginate Derived from Fucus vesiculosus. Polymers (Basel) 2023; 15:polym15102335. [PMID: 37242910 DOI: 10.3390/polym15102335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/07/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Zinc oxide nanoparticles have many advantages for nano-biotechnologists due to their intense biomedical applications. ZnO-NPs are used as antibacterial agents, which influence bacterial cells through the rupture of the cell membrane and the generation of reactive free radicals. Alginate is a polysaccharide of natural origin due to its excellent properties that are used in various biomedical applications. Brown algae are good sources of alginate and are used as a reducing agent in the synthesis of nanoparticles. This study aims to synthesize ZnO-NPs by using brown alga Fucus vesiculosus (Fu/ZnO-NPs) and also to extract alginate from the same alga, which is used in coating the ZnO-NPs (Fu/ZnO-Alg-NCMs). The characterizations of Fu/ZnO-NPs and Fu/ZnO-Alg-NCMs were determined by FTIR, TEM, XRD, and zeta potential. The antibacterial activities were applied against multidrug resistance bacteria of both gram-positive and negative. The results obtained in FT-TR showed there are some shifts in the peak positions of Fu/ZnO-NPs and Fu/ZnO-Alg-NCMs. The peak at 1655 cm-1, which assigned amide I-III, is present in both Fu/ZnO-NPs and Fu-Alg-ZnO-NCMs; this band is responsible for bio-reductions and stabilization of both nanoparticles. The TEM images proved the Fu/ZnO-NPs have rod shapes with sizes ranging from 12.68 to 17.66 and are aggregated, but Fu/ZnO/Alg-NCMs are spherical in shape with sizes ranging from 12.13 to 19.77. XRD-cleared Fu/ZnO-NPs have nine sharp peaks that are considered good crystalline, but Fu/ZnO-Alg-NCMs have four broad and sharp peaks that are considered semi-crystalline. Both Fu/ZnO-NPs and Fu/ZnO-Alg-NCMs have negative charges (-1.74 and -3.56, respectively). Fu/ZnO-NPs have more antibacterial activities than Fu/ZnO/Alg-NCMs in all tested multidrug-resistant bacterial strains. Fu/ZnO/Alg-NCMs had no effect on Acinetobacter KY856930, Staphylococcus epidermidis, and Enterobacter aerogenes, whereas there was an apparent effect of ZnO-NPs against the same strains.
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Affiliation(s)
- Ragaa A Hamouda
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21959, Saudi Arabia
- Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City, Sadat City 32897, Egypt
| | - Asrar A Alharbi
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21959, Saudi Arabia
| | - Majdah M Al-Tuwaijri
- Department of Biology, Faculty of Applied Science, Umm-Al-Qura University, Makkah Al-Mukarramah 21955, Saudi Arabia
| | - Rabab R Makharita
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21959, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
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Abdul Hussein SA, Razzak Mahmood AA, Tahtamouni LH, Balakit AA, Yaseen YS, Al-Hasani RA. New Combretastatin Analogs as Anticancer Agents: Design, Synthesis, Microtubules Polymerization Inhibition, and Molecular Docking Studies. Chem Biodivers 2023; 20:e202201206. [PMID: 36890635 DOI: 10.1002/cbdv.202201206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/16/2023] [Indexed: 03/10/2023]
Abstract
A new series of 4-(4-methoxyphenyl)-5-(3,4,5-trimethoxyphenyl)-4H-1,2,4-triazole-3-thiol derivatives were synthesized as analogs for the anticancer drug combretastatin A-4 (CA-4) and characterized using FT-IR, 1 H-NMR, 13 CNMR, and HR-MS techniques. The new CA-4 analogs were designed to meet the structural requirements of the highest expected anticancer activity of CA-4 analogs by maintaining ring A 3,4,5-trimethoxyphenyl moiety, and at the same time varying the substituents effect of the triazole moiety (ring B). In silico analysis indicated that compound 3 has higher total energy and dipole moment than colchicine and the other analogs, and it has excellent distribution of electron density and is more stable, resulting in an increased binding affinity during tubulin inhibition. Additionally, compound 3 was found to interact with three apoptotic markers, namely p53, Bcl-2, and caspase 3. Compound 3 showed strong similarity to colchicine, and it has excellent pharmacokinetics properties and a good dynamic profile. The in vitro anti-proliferation studies showed that compound 3 is the most cytotoxic CA-4 analog against cancer cells (IC50 of 6.35 μM against Hep G2 hepatocarcinoma cells), and based on its selectivity index (4.7), compound 3 is a cancer cytotoxic-selective agent. As expected and similar to colchicine, compound 3-treated Hep G2 hepatocarcinoma cells were arrested at the G2/M phase resulting in induction of apoptosis. Compound 3 tubulin polymerization IC50 (9.50 μM) and effect on Vmax of tubulin polymerization was comparable to that of colchicine (5.49 μM). Taken together, the findings of the current study suggest that compound 3, through its binding to the colchicine-binding site at β-tubulin, is a promising microtubule-disrupting agent with excellent potential to be used as cancer therapeutic agent.
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Affiliation(s)
- Shaker A Abdul Hussein
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Babylon, 51001, Babylon, Iraq
| | - Ammar A Razzak Mahmood
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Baghdad, 10001, Baghdad, Iraq
| | - Lubna H Tahtamouni
- Department of Biology and Biotechnology, Faculty of Science, The Hashemite University, 13133, Zarqa, Jordan
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, 80523 Colorado, USA
| | - Asim A Balakit
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Babylon, 51001, Babylon, Iraq
| | - Yahya S Yaseen
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Tikrit, 34001, Tikrit, Iraq
| | - Rehab A Al-Hasani
- Department of Chemistry, College of Science, Al-Mustansiriyah University, 10052, Baghdad, Iraq
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Elkaeed EB, Metwaly AM, Alesawy MS, Saleh AM, Alsfouk AA, Eissa IH. Discovery of Potential SARS-CoV-2 Papain-like Protease Natural Inhibitors Employing a Multi-Phase In Silico Approach. Life (Basel) 2022; 12:1407. [PMID: 36143445 PMCID: PMC9505301 DOI: 10.3390/life12091407] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
As an extension of our research against COVID-19, a multiphase in silico approach was applied in the selection of the three most common inhibitors (Glycyrrhizoflavone (76), Arctigenin (94), and Thiangazole (298)) against papain-like protease, PLpro (PDB ID: 4OW0), among 310 metabolites of natural origin. All compounds of the exam set were reported as antivirals. The structural similarity between the examined compound set and S88, the co-crystallized ligand of PLpro, was examined through structural similarity and fingerprint studies. The two experiments pointed to Brevicollin (28), Cryptopleurine (41), Columbamine (46), Palmatine (47), Glycyrrhizoflavone (76), Licochalcone A (87), Arctigenin (94), Termilignan (98), Anolignan B (99), 4,5-dihydroxy-6″-deoxybromotopsentin (192), Dercitin (193), Tryptanthrin (200), 6-Cyano-5-methoxy-12-methylindolo [2, 3A] carbazole (211), Thiangazole (298), and Phenoxan (300). The binding ability against PLpro was screened through molecular docking, disclosing the favorable binding modes of six metabolites. ADMET studies expected molecules 28, 76, 94, 200, and 298 as the most favorable metabolites. Then, molecules 76, 94, and 298 were chosen through in silico toxicity studies. Finally, DFT studies were carried out on glycyrrhizoflavone (76) and indicated a high level of similarity in the molecular orbital analysis. The obtained data can be used in further in vitro and in vivo studies to examine and confirm the inhibitory effect of the filtered metabolites against PLpro and SARS-CoV-2.
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Affiliation(s)
- Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria 21934, Egypt
| | - Mohamed S. Alesawy
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Abdulrahman M. Saleh
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
| | - Aisha A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
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Structural and computational analysis, spectroscopic and electrochemical elucidation of a Schiff base. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02571-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Isolation and In Silico Inhibitory Potential against SARS-CoV-2 RNA Polymerase of the Rare Kaempferol 3-O-(6″-O-acetyl)-Glucoside from Calligonum tetrapterum. PLANTS 2022; 11:plants11152072. [PMID: 35956550 PMCID: PMC9370365 DOI: 10.3390/plants11152072] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022]
Abstract
The phytochemical constituents of Calligonum tetrapterum Jaub. & Spach (Family Polygonaceae) were studied for the first time. The study resulted in the isolation of the rare flavonol glycoside, kaempferol 3-O-(6″-O-acetyl)-glucoside,(K3G-A). The potential inhibitive activity of K3G-A toward SARS-CoV-2 was investigated utilizing several in silico approaches. First, molecular fingerprints and structural similarity experiments were carried out for K3G-A against nine co-crystallized ligands of nine proteins of SARS-CoV-2 to reveal if there is a structural similarity with any of them. The conducted studies showed the high similarity of K3G-A and remdesivir, the co-crystallized ligand of SARS-CoV-2 RNA-dependent RNA polymerase (PDB ID: 7BV2), RdRp. To validate these findings, a DFT study was conducted and confirmed the proposed similarity on the electronic and orbital levels. The binding of K3G-A against RdRp was confirmed through molecular docking studies exhibiting a binding energy of −27.43 kcal/mol, which was higher than that of remdesivir. Moreover, the RdRp-K3G-A complex was subjected to several MD studies at 100 ns that authenticated the accurate mode of binding and the correct dynamic behavior. Finally, in silico ADMET and toxicity evaluation of K3G-A was conducted and denoted the safety and the drug-likeness of K3G-A. In addition to K3G-A, two other metabolites were isolated and identified to be kaempferol (K) and β-sitosterol (β-S).
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A Multistage In Silico Study of Natural Potential Inhibitors Targeting SARS-CoV-2 Main Protease. Int J Mol Sci 2022; 23:ijms23158407. [PMID: 35955547 PMCID: PMC9369012 DOI: 10.3390/ijms23158407] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
Among a group of 310 natural antiviral natural metabolites, our team identified three compounds as the most potent natural inhibitors against the SARS-CoV-2 main protease (PDB ID: 5R84), Mpro. The identified compounds are sattazolin and caprolactin A and B. A validated multistage in silico study was conducted using several techniques. First, the molecular structures of the selected metabolites were compared with that of GWS, the co-crystallized ligand of Mpro, in a structural similarity study. The aim of this study was to determine the thirty most similar metabolites (10%) that may bind to the Mpro similar to GWS. Then, molecular docking against Mpro and pharmacophore studies led to the choice of five metabolites that exhibited good binding modes against the Mpro and good fit values against the generated pharmacophore model. Among them, three metabolites were chosen according to ADMET studies. The most promising Mpro inhibitor was determined by toxicity and DFT studies to be caprolactin A (292). Finally, molecular dynamics (MD) simulation studies were performed for caprolactin A to confirm the obtained results and understand the thermodynamic characteristics of the binding. It is hoped that the accomplished results could represent a positive step in the battle against COVID-19 through further in vitro and in vivo studies on the selected compounds.
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Suleimen YM, Jose RA, Suleimen RN, Ishmuratova MY, Toppet S, Dehaen W, Alsfouk AA, Elkaeed EB, Eissa IH, Metwaly AM. Isolation and In Silico SARS-CoV-2 Main Protease Inhibition Potential of Jusan Coumarin, a New Dicoumarin from Artemisia glauca. Molecules 2022; 27:2281. [PMID: 35408682 PMCID: PMC9000794 DOI: 10.3390/molecules27072281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
A new dicoumarin, jusan coumarin, (1), has been isolated from Artemisia glauca aerial parts. The chemical structure of jusan coumarin was estimated, by 1D, 2D NMR as well as HR-Ms spectroscopic methods, to be 7-hydroxy-6-methoxy-3-[(2-oxo-2H-chromen-6-yl)oxy]-2H-chromen-2-one. As the first time to be introduced in nature, its potential against SARS-CoV-2 has been estimated using various in silico methods. Molecular similarity and fingerprints experiments have been utilized for 1 against nine co-crystallized ligands of COVID-19 vital proteins. The results declared a great similarity between Jusan Coumarin and X77, the ligand of COVID-19 main protease (PDB ID: 6W63), Mpro. To authenticate the obtained outputs, a DFT experiment was achieved to confirm the similarity of X77 and 1. Consequently, 1 was docked against Mpro. The results clarified that 1 bonded in a correct way inside Mpro active site, with a binding energy of -18.45 kcal/mol. Furthermore, the ADMET and toxicity profiles of 1 were evaluated and showed the safety of 1 and its likeness to be a drug. Finally, to confirm the binding and understand the thermodynamic characters between 1 and Mpro, several molecular dynamics (MD) simulations studies have been administered. Additionally, the known coumarin derivative, 7-isopentenyloxycoumarin (2), has been isolated as well as β-sitosterol (3).
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Affiliation(s)
- Yerlan M. Suleimen
- The International Centre for Interdisciplinary Solutions on Antibiotics and Secondary Metabolites, Republican Collection of Microorganisms, Nur-Sultan 010000, Kazakhstan;
- The Laboratory of Engineering Profile of NMR Spectroscopy, Sh. Ualikhanov Kokshetau University, Kokshetau 020000, Kazakhstan
| | - Rani A. Jose
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
- Department of Chemistry, St. Dominic’s College, Mahatma Gandhi University, Kanjirappally 686512, India
| | - Raigul N. Suleimen
- Department of Technical Physics, Faculty of Physics and Technology, L.N. Gumilyov Eurasian National University, Nur-Sultan 010010, Kazakhstan
| | | | - Suzanne Toppet
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
| | - Wim Dehaen
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
| | - Aisha A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia;
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Product Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria 21934, Egypt
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Suleimen YM, Jose RA, Suleimen RN, Arenz C, Ishmuratova MY, Toppet S, Dehaen W, Alsfouk BA, Elkaeed EB, Eissa IH, Metwaly AM. Jusanin, a New Flavonoid from Artemisia commutata with an In Silico Inhibitory Potential against the SARS-CoV-2 Main Protease. Molecules 2022; 27:1636. [PMID: 35268738 PMCID: PMC8911936 DOI: 10.3390/molecules27051636] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 01/07/2023] Open
Abstract
A new flavonoid, Jusanin, (1) has been isolated from the aerial parts of Artemisia commutata. The chemical structure of Jusanin has been elucidated using 1D, 2D NMR, and HR-Ms spectroscopic methods to be 5,2',4'-trihydroxy-6,7,5'-trimethoxyflavone. Being new in nature, the inhibition potential of 1 has been estimated against SARS-CoV-2 using different in silico techniques. Firstly, molecular similarity and fingerprint studies have been conducted for Jusanin against co-crystallized ligands of eight different SARS-CoV-2 essential proteins. The studies indicated the similarity between 1 and X77, the co-crystallized ligand SARS-CoV-2 main protease (PDB ID: 6W63). To confirm the obtained results, a DFT study was carried out and indicated the similarity of (total energy, HOMO, LUMO, gap energy, and dipole moment) between 1 and X77. Accordingly, molecular docking studies of 1 against the target enzyme have been achieved and showed that 1 bonded correctly in the protein's active site with a binding energy of -19.54 Kcal/mol. Additionally, in silico ADMET in addition to the toxicity evaluation of Jusanin against seven models have been preceded and indicated the general safety and the likeness of Jusanin to be a drug. Finally, molecular dynamics simulation studies were applied to investigate the dynamic behavior of the Mpro-Jusanin complex and confirmed the correct binding at 100 ns. In addition to 1, three other metabolites have been isolated and identified to be сapillartemisin A (2), methyl-3-[S-hydroxyprenyl]-cumarate (3), and β-sitosterol (4).
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Affiliation(s)
- Yerlan M. Suleimen
- The International Centre for Interdisciplinary Solutions on Antibiotics and Secondary Metabolites, Republican Collection of Microorganisms, Nur-Sultan 010000, Kazakhstan;
- The Laboratory of Engineering Profile of NMR Spectroscopy, Sh. Ualikhanov Kokshetau University, Kokshetau 020000, Kazakhstan
| | - Rani A. Jose
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
- Department of Chemistry, St. Dominic’s College, Mahatma Gandhi University, Kanjirappally 686512, India
| | - Raigul N. Suleimen
- Department of Technical Physics, Faculty of Physics and Technology, L.N. Gumilyov Eurasian National University, Nur-Sultan 010010, Kazakhstan
| | - Christoph Arenz
- Institut für Chemie der Humboldt-Universität zu, D-12489 Berlin, Germany;
| | | | - Suzanne Toppet
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
| | - Wim Dehaen
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
| | - Bshra A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia;
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria 21934, Egypt
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Alesawy MS, Elkaeed EB, Alsfouk AA, Metwaly AM, Eissa IH. In Silico Screening of Semi-Synthesized Compounds as Potential Inhibitors for SARS-CoV-2 Papain-like Protease: Pharmacophoric Features, Molecular Docking, ADMET, Toxicity and DFT Studies. Molecules 2021; 26:6593. [PMID: 34771004 PMCID: PMC8588135 DOI: 10.3390/molecules26216593] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 01/21/2023] Open
Abstract
Papain-like protease is an essential enzyme in the proteolytic processing required for the replication of SARS-CoV-2. Accordingly, such an enzyme is an important target for the development of anti-SARS-CoV-2 agents which may reduce the mortality associated with outbreaks of SARS-CoV-2. A set of 69 semi-synthesized molecules that exhibited the structural features of SARS-CoV-2 papain-like protease inhibitors (PLPI) were docked against the coronavirus papain-like protease (PLpro) enzyme (PDB ID: (4OW0). Docking studies showed that derivatives 34 and 58 were better than the co-crystallized ligand while derivatives 17, 28, 31, 40, 41, 43, 47, 54, and 65 exhibited good binding modes and binding free energies. The pharmacokinetic profiling study was conducted according to the four principles of the Lipinski rules and excluded derivative 31. Furthermore, ADMET and toxicity studies showed that derivatives 28, 34, and 47 have the potential to be drugs and have been demonstrated as safe when assessed via seven toxicity models. Finally, comparing the molecular orbital energies and the molecular electrostatic potential maps of 28, 34, and 47 against the co-crystallized ligand in a DFT study indicated that 28 is the most promising candidate to interact with the target receptor (PLpro).
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Affiliation(s)
- Mohamed S. Alesawy
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, Almaarefa University, Ad Diriyah, Riyadh 13713, Saudi Arabia;
| | - Aisha A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria 21934, Egypt
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
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Eissa IH, Khalifa MM, Elkaeed EB, Hafez EE, Alsfouk AA, Metwaly AM. In Silico Exploration of Potential Natural Inhibitors against SARS-Cov-2 nsp10. Molecules 2021; 26:6151. [PMID: 34684735 PMCID: PMC8539059 DOI: 10.3390/molecules26206151] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 12/24/2022] Open
Abstract
In continuation of our previous effort, different in silico selection methods were applied to 310 naturally isolated metabolites that exhibited antiviral potentialities before. The applied selection methods aimed to pick the most relevant inhibitor of SARS-CoV-2 nsp10. At first, a structural similarity study against the co-crystallized ligand, S-Adenosyl Methionine (SAM), of SARS-CoV-2 nonstructural protein (nsp10) (PDB ID: 6W4H) was carried out. The similarity analysis culled 30 candidates. Secondly, a fingerprint study against SAM preferred compounds 44, 48, 85, 102, 105, 182, 220, 221, 282, 284, 285, 301, and 302. The docking studies picked 48, 182, 220, 221, and 284. While the ADMET analysis expected the likeness of the five candidates to be drugs, the toxicity study preferred compounds 48 and 182. Finally, a density-functional theory (DFT) study suggested vidarabine (182) to be the most relevant SARS-Cov-2 nsp10 inhibitor.
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Affiliation(s)
- Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Mohamed M. Khalifa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, Almaarefa University, Riyadh 13713, Saudi Arabia;
| | - Elsayed E. Hafez
- Department of Plant Protection and Biomolecular Diagnosis, ALCRI, City of Scientific Research and Technological Applications, New Borg El-Arab City 21934, Egypt;
| | - Aisha A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
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12
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Feride Akman. A DFT Study on Molecular Structure, MEP, HOMO–LUMO and Spectroscopic Analysis of Thermoresponsive Monomers Used in Micro/Nanogel Preparations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [DOI: 10.1134/s1990793121030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Jayasudha J, Balachandran V, Narayana B. Molecular Docking, Spectroscopic, and Computational Studies of 2-{3-(4-Chlorophenyl)-5-[4-(Propan-2-yl) Phenyl]-4, 5-Dihydro-1H-Pyrazol-1-yl}-1, 3-Thiazol-4(5H)-One. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1830810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- J. Jayasudha
- Centre for Research – Department of Physics, Arignar Anna Government Arts College, Musiri (Affiliated by Bharathidasan University), Tiruchirappalli, Tamil Nadu, India
| | - V. Balachandran
- Centre for Research – Department of Physics, Arignar Anna Government Arts College, Musiri (Affiliated by Bharathidasan University), Tiruchirappalli, Tamil Nadu, India
| | - B. Narayana
- Deparment of Chemistry, Mangalore University, Mangalagangoti, India
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14
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Al-Wahaibi LH, Sert Y, Ucun F, Al-Shaalan NH, Alsfouk A, El-Emam AA, Karakaya M. Theoretical and experimental spectroscopic studies, XPS analysis, dimer interaction energies and molecular docking study of 5-(adamantan-1-yl)-N-methyl-1,3,4-thiadiazol-2-amine. JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS 2019. [DOI: 10.1016/j.jpcs.2019.109091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Alam M, Park S. Spectroscopic Identifications, Molecular Docking, Neuronal Growth and Enzyme Inhibitory Activities of Steroidal Nitro Olefin: Quantum Chemical Study. ChemistrySelect 2019. [DOI: 10.1002/slct.201902093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mahboob Alam
- Division of Chemistry and BiotechnologyDongguk University Gyeongju 780-714 South Korea
| | - Soonheum Park
- Department of Advanced Materials ChemistryDongguk University Gyeongju 780-714 South Korea
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16
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Adaikalaraj C, Manivarman S, Subashchandrabose S, Dhandapani A. Synthesis, rotational, vibrational and transitional spectra investigation on novel ethyl-4-(3-(benzo[d]1,3di-oxole-5-carboxamido)phenyl)-1,2,3,4-tetrahydro-6-methyl-2-oxopyrimidine-5-carboxylate. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Molecular structure, spectral studies, NBO, HOMO–LUMO profile, MEP and Mulliken analysis of 3β,6β-dichloro-5α-hydroxy-5α–cholestane. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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19
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Lan W, Wang X, He L, Meng Y, Li J, Qiu B, Nie C. Computational insight into asymmetric uranyl‐salophen coordinated with α, β‐unsaturated aldehydes and ketones. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.4137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Wen‐Bo Lan
- School of Public HealthXiangnan University Chenzhou Hunan 423000 China
- School of Chemistry and Chemical EngineeringUniversity of South China Hengyang China
| | - Xiao‐Feng Wang
- School of Public HealthXiangnan University Chenzhou Hunan 423000 China
| | - Li‐Ping He
- School of Public HealthXiangnan University Chenzhou Hunan 423000 China
| | - Yan‐Bin Meng
- School of Public HealthXiangnan University Chenzhou Hunan 423000 China
| | - Jun Li
- School of Public HealthXiangnan University Chenzhou Hunan 423000 China
| | - Bin Qiu
- Chenzhou City Center for Disease Control and Prevention Chenzhou Hunan 423000 China
| | - Chang‐Ming Nie
- School of Chemistry and Chemical EngineeringUniversity of South China Hengyang China
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20
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Karakaya M, Sert Y, Kürekçi M, Eskiyurt B, Çırak Ç. Theoretical and experimental investigations on vibrational and structural properties of tolazamide. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Sert Y, Karakaya M, Çırak Ç, Eskiyurt B, Kürekçi M. Structural optimization and vibrational analysis of an antidiabetic drug: tolbutamide. J Sulphur Chem 2015. [DOI: 10.1080/17415993.2015.1050397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Prasanth S, Varughese M, Joseph N, Mathew P, Manojkumar T, Sudarsanakumar C. Crystal structure, FT-IR, FT-Raman, 1H NMR and computational study of ethyl 2-{[(Z)3-(4-chlorophenyl)-3-hydroxy-2-propene-1-thione] amino} acetate. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.10.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Al-Omary FA, Karakaya M, Sert Y, Haress NG, El-Emam AA, Çırak Ç. Structural and spectroscopic analysis of 3-[(4-phenylpiperazin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4-oxadiazole-2-thione with experimental (FT-IR, Laser-Raman) techniques and ab initio calculations. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.08.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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Çırak Ç, Sert Y, Ucun F. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 127:41-46. [PMID: 24632154 DOI: 10.1016/j.saa.2014.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/26/2014] [Accepted: 02/09/2014] [Indexed: 06/03/2023]
Abstract
In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.
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Affiliation(s)
- Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey.
| | - Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey
| | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta, Turkey
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25
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Yamini D, Mangalaraj D, Ramakrishnan V. Raman spectroscopic and ab initio studies on the molecular interactions in the binary liquid mixtures of 4'-fluoroacetophenone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 116:381-388. [PMID: 23973583 DOI: 10.1016/j.saa.2013.07.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/05/2013] [Accepted: 07/21/2013] [Indexed: 06/02/2023]
Abstract
Raman spectral measurements were carried out for binary liquid mixtures 4'fluoroacetophenone (4F) in different volume concentration ranges at a regular intervals of 0.1 in different solvents. The asymmetric Raman peak observed at 1685 cm(-1) (carbonyl stretching mode) in pure 4F confirms the presence of self association in 4F. The optimization was performed for monomer and dimer structures of 4F as well as 4F dimer with solvents using Gaussian 03 W package. Vibrational wavenumber calculation was performed for monomer and dimer structures of 4F to explain the experimentally observed Raman spectra. The carbonyl stretching mode is the more polar group and its interaction with the solvent molecule plays a vital role in determining the physical and chemical properties of the solute. Hence the observed variation in the peak position and linewidth of carbonyl stretching mode was analysed as a result of intermolecular interactions between the solute and the solvent molecules. Also, interaction energies were calculated to support the results obtained from Raman spectra.
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Affiliation(s)
- D Yamini
- Department of Laser Studies, School of Physics, Madurai Kamaraj University, Madurai 625 021, India
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26
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Çırak Ç, Sert Y, Ucun F. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 113:130-136. [PMID: 23714189 DOI: 10.1016/j.saa.2013.04.102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 04/15/2013] [Accepted: 04/24/2013] [Indexed: 06/02/2023]
Abstract
In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the N-H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H···S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.
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Affiliation(s)
- Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey.
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27
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Yamini D, Ramakrishnan V. An investigation of solute-solvent interactions in binary liquid mixtures of 3'-methoxyacetophenone: using Raman spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 111:14-23. [PMID: 23602954 DOI: 10.1016/j.saa.2013.03.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/07/2013] [Accepted: 03/12/2013] [Indexed: 06/02/2023]
Abstract
Raman spectral measurements have been carried out for neat 3'-methoxy acetophenone (3'-MAP) and binary liquid mixtures of 3'-MAP in three solvents of different polarity. Also Density Functional Theory (DFT) geometry optimization and vibrational wavenumber calculation have been performed on monomer and dimer structures of 3'-MAP to analyze the experimentally observed Raman spectrum. Mulliken charge analysis has also been made on optimized geometries of 3'-MAP with solvents. The changes associated with the observed peak position, intensity and linewidth in the carbonyl stretching mode of 3'-MAP are explained as a consequence of intermolecular interactions between solute-solute and solute-solvent molecules. This analysis reports that the solute-solvent interaction is dominant in the case of binary liquid mixtures of 3'-MAP with ethanol compared to DMF and benzene.
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Affiliation(s)
- D Yamini
- Department of Laser Studies, School of Physics, Madurai Kamaraj University, Madurai 625 021, India
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28
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El-Mansy MAM, El-Nahass MM, Khusayfan NM, El-Menyawy EM. DFT approach for FT-IR spectra and HOMO-LUMO energy gap for N-(p-dimethylaminobenzylidene)-p-nitroaniline (DBN). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 111:217-222. [PMID: 23644446 DOI: 10.1016/j.saa.2013.04.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 03/18/2013] [Accepted: 04/02/2013] [Indexed: 06/02/2023]
Abstract
In the present work, a combined experimental and computational study for the optimized molecular structural parameters, FT-IR spectra, thermo-chemical parameters, total dipole moment and HOMO-LUMO energy gap for N-(p-diethylaminobenzylidene)p-nitroaniline (DBN) have been investigated using B3LYP/6-311G basis set. Our calculated results have showed that the investigated compound possesses a dipole moment of 12 Debye and HOMO-LUMO energy gap of 2.94 eV which indicate high recommendations for photovoltaic devices fabrication.
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Affiliation(s)
- M A M El-Mansy
- Physics Department, Faculty of Education, Ain Shams University, Roxy, Cairo, Egypt.
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29
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El-Nahass MM, Kamel MA, El-Barbary AA, El-Mansy MAM, Ibrahim M. FT-IR spectroscopic analyses of 3-Methyl-5-Pyrazolone (MP). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 111:37-41. [PMID: 23602957 DOI: 10.1016/j.saa.2013.03.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 03/13/2013] [Accepted: 03/16/2013] [Indexed: 06/02/2023]
Abstract
In the present work both experimental and computational FT-IR spectroscopic studies on 3-Methyl-5-Pyrazolone (MP) were reported. Experimental FT-IR spectrum for MP compound is recorded in powder form. Important physical parameters were reported such as structural parameters, vibrational frequencies, entropy, total energy, total dipole moment and HOMO-LUMO energy gap using DFT/B3LYP/6-311G(d,p) basis set. MP molecule has a total dipole moment of 2.83 Debye and HOMO-LUMO energy gap of 5.80 eV. Results indicate also that exposure to UV changes the spin from singlet to doublet state; one can conclude that MP compound may undergo anomalous Zeeman like effect.
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Affiliation(s)
- M M El-Nahass
- Physics Department, Faculty of Education, Ain Shams University, Roxy, Cairo, Egypt
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30
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Sert Y, Çırak Ç, Ucun F. Vibrational analysis of 4-chloro-3-nitrobenzonitrile by quantum chemical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:248-255. [PMID: 23434551 DOI: 10.1016/j.saa.2013.01.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/11/2013] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
In the present study, the experimental and theoretical harmonic and anharmonic vibrational frequencies of 4-chloro-3-nitrobenzonitrile were investigated. The experimental FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) were calculated using ab initio Hartree Fock (HF), density functional B3LYP and M06-2X methods with 6-311++G(d,p) basis set by Gaussian 09 W program, for the first time. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey.
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31
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Soliman HS, Eid KM, Ali HAM, El-Mansy MAM, Atef SM. FT-IR spectroscopic analyses of 2-(2-furanylmethylene) propanedinitrile. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 105:545-549. [PMID: 23353693 DOI: 10.1016/j.saa.2012.12.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/17/2012] [Accepted: 12/13/2012] [Indexed: 06/01/2023]
Abstract
In the present work, a computational study for the optimized molecular structural parameters, thermo-chemical parameters, total dipole moment, HOMO-LUMO energy gap and a combined experimental and computational study for FT-IR spectra for 2-(2-furanylmethylene) propanedinitrile have been investigated using B3LYP utilizing 6-31G and 6-311G basis set. Our calculated results showed that the investigated compound possesses a dipole moment of 7.5D and HOMO-LUMO energy gap of 3.92eV using B3LYP/6-311G which indicates that our investigated compound is highly applicable for photovoltaic solar cell applications.
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Affiliation(s)
- H S Soliman
- Physics Department, Faculty of Education, Ain Shams University, Roxy, Cairo, Egypt
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32
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Arivazhagan M, Jeyavijayan S, Geethapriya J. Conformational stability, vibrational spectra, molecular structure, NBO and HOMO-LUMO analysis of 5-nitro-2-furaldehyde oxime based on DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 104:14-25. [PMID: 23274252 DOI: 10.1016/j.saa.2012.11.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/27/2012] [Accepted: 11/08/2012] [Indexed: 06/01/2023]
Abstract
The FTIR and FT-Raman spectra of 5-nitro-2-furaldehyde oxime (NFAO) have been recorded in the regions 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The total energies of different conformations have been obtained from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The computational results identify the most stable conformer of NFAO as the C1 form. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of NFAO is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. Besides, molecular electrostatic potential (MEP), HOMO and LUMO analysis, and several thermodynamic properties were performed by the DFT method. Mulliken's net charges have been calculated and compared with the natural atomic charges. Ultraviolet-visible spectrum of the title molecule has also been calculated using TD-DFT method.
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Affiliation(s)
- M Arivazhagan
- Department of Physics, A.A. Govt. Arts College, Musiri 621 211, India.
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33
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Soliman HS, Eid KM, Ali HAM, Atef SM, El-Mansy MAM. Vibrational spectroscopic analysis of 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 97:1079-1084. [PMID: 22925985 DOI: 10.1016/j.saa.2012.07.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/14/2012] [Accepted: 07/26/2012] [Indexed: 06/01/2023]
Abstract
In the present work, a combined experimental and computational study for the optimized molecular structural parameters, FT-IR spectra, thermo-chemical parameters, total dipole moment and HOMO-LUMO energy gap for 2-chloro-5-(2,5-dimethoxy-benzylidene)-1,3-diethyl-dihydro-pyrimidine-4,6(1H,5H)-dione have been investigated using B3LYP/6-311G basis set. Our calculated results have showed that the investigated compound possesses a dipole moment of 4.9 Debye and HOMO-LUMO energy gap of 3 eV which indicate high recommendations for photovoltaic devices fabrication.
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Affiliation(s)
- H S Soliman
- Physics Department, Faculty of Education, Ain Shams University, Roxy, Cairo, Egypt
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El-Nahass MM, Kamel MA, El-Deeb AF, Atta AA, Huthaily SY. Density functional theory (DFT) investigation of molecular structure and frontier molecular orbitals (FMOs) of P-N,N-dimethylaminobenzylidenemalononitrile (DBM). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1499-1504. [PMID: 21640638 DOI: 10.1016/j.saa.2011.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 04/28/2011] [Accepted: 05/05/2011] [Indexed: 05/30/2023]
Abstract
P-N,N-dimethylaminobenzylidenemalononitrile (DBM) dye belongs to a class of organic compounds known as molecular rotors. Its optimized geometry and frontier molecular orbitals (FMOs), before and after ultraviolet (UV) irradiation, were obtained by DFT/B3LYP level with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. It is found that the length of C-C bonds of the DBM molecule increases after the UV irradiation, which leads to an increase in its dipole moment making it as a promising material for solar cell applications. Also, its HOMO-LUMO gap decreased from 3.46 to 3.34 eV. From the cyclic voltammetry measurements the value of HOMO-LUMO gap is equal to 3.21 eV. This means that B3LYP/6-311++G(d,p) level of theory is the best one for calculations.
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Affiliation(s)
- M M El-Nahass
- Physics Department, Faculty of Education, Ain Shams University, Roxy, 11757 Cairo, Egypt
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