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Agarwal N, Fatima A, Bhattacharya P, Muthu S, Arora H, Siddiqui N, Javed S. Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine. J Biomol Struct Dyn 2023; 41:10430-10449. [PMID: 36562198 DOI: 10.1080/07391102.2022.2159530] [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: 04/03/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Agarwal
- Department of chemistry, Institute of H. Science, Dr. Bhimrao-Ambedkar University, Agra, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | | | - S Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, India
| | - Himanshu Arora
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
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Ait Elmachkouri Y, Irrou E, Thiruvalluvar AA, Anouar EH, Varadharajan V, Ouachtak H, Mague JT, Sebbar NK, Essassi EM, Labd Taha M. Synthesis, crystal structure, spectroscopic characterization, DFT calculations, Hirshfeld surface analysis, molecular docking, and molecular dynamics simulation investigations of novel pyrazolopyranopyrimidine derivatives. J Biomol Struct Dyn 2023:1-19. [PMID: 37817543 DOI: 10.1080/07391102.2023.2268187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
A series of new pyrazolopyranopyrimidine derivatives (3-9) were synthesized from 5-amino-2,4-dihydro-3-methyl-4-phenylpyrano-[2,3-c]pyrazole-5-carbonitrile (2) by multicomponent reactions (MCR) involving malononitrile, benzaldehyde, and pyrazolone under refluxing ethanol in the presence of piperidine. Compound (2) was then converted to 2-acetylpyrazolopyranopyrimidine (3) through a reaction with acetic anhydride. The deprotection of 3 using ammonium hydroxide in ethanol, leads to 4. Subsequent chlorination of 4 by phosphorus oxychloride affords 5 which was alkylated using methyl iodide and ethyl bromoacetate in DMF, leading to regioisomers 6-9. The products were characterized by spectroscopic techniques (1H and 13C NMR) and confirmed by single crystal X-ray diffraction (XRD) studies for 2, 5, 6, and 9. Moreover, the geometrical parameters, molecular orbital calculations, and spectral data of 2, 5, 6, and 9 were compared by DFT at the B3LYP/6-311G(d,p) level of theory. There is good agreement between the calculated results and the experimental data. The intermolecular contacts for 2, 5, 6, and 9 were studied by Hirshfeld surface analysis. In addition, the molecular docky study was conducted to investigate the binding patterns of 2, 5, 6, and 9 within the binding site of cyclin-dependent kinase 2 (CDK2) and penicillin-binding protein 1 A. After the docking process, molecular dynamics (MD) simulations for 100 ns were performed on CDK2 and PBP 1 A proteins in the complex with 5.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Younesse Ait Elmachkouri
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco
| | - Ezaddine Irrou
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco
| | | | - El Hassane Anouar
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | | | - Hassan Ouachtak
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Nada Kheira Sebbar
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco
- Laboratory of Heterocyclic Organic Chemistry, Pharmacochemistry Competence, Center, Drug Science Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - El Mokhtar Essassi
- Laboratory of Heterocyclic Organic Chemistry, Pharmacochemistry Competence, Center, Drug Science Research Center, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Mohamed Labd Taha
- Laboratory of Organic and Physical Chemistry, Applied Bioorganic Chemistry Team, Faculty of Sciences, Ibnou Zohr University, Agadir, Morocco
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Nikoofar K, Sadathosainy M. Phthalic anhydride (PA): a valuable substrate in organic transformations. RSC Adv 2023; 13:23870-23946. [PMID: 37588043 PMCID: PMC10426397 DOI: 10.1039/d3ra03378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023] Open
Abstract
This review has been centralized on applications of phthalic anhydride (PA) as a valuable and significant heterocyclic substrate in two- and multicomponent organic reactions. The article has been subdivided into the following parts: (i) PA introduction by focusing on its characterization, synthesizing procedure, and multiple-aspect applications. In addition, the previous review articles based on PA have also been indicated; (ii) the applications of PA as a substrate have been subdivided into parts with a glance on the reaction components numbers; (iii) the applications of PA in esterification reactions; and (iv) some examples of PA in multistep synthesis. The review covers the corresponding literature up to the end of 2022. According to the abovementioned classifications, PA is a potent substrate to design a wide range of heterocyclic compounds that possess various kinds of properties and applications in chemistry, industry, and pharmaceuticals.
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Affiliation(s)
- Kobra Nikoofar
- Department of Organic Chemistry, Faculty of Chemistry, Alzahra University P.O. Box 1993891176 Tehran Iran +98 2188041344 +98 2188041344
| | - Mansoorehsadat Sadathosainy
- Department of Organic Chemistry, Faculty of Chemistry, Alzahra University P.O. Box 1993891176 Tehran Iran +98 2188041344 +98 2188041344
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Fatima A, Ali A, Rajan R, Verma I, Muthu S, Siddiqui N, Garg P, Javed S. Experimental Spectroscopic, DFT, Molecular Docking, and Molecular Dynamics Simulation Investigations on m-Phenylenediamine (Monomer and Trimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2150655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, India
| | - Akram Ali
- Department of Chemistry, CMP College, Allahabad, India
| | - Ramya Rajan
- Department of Chemistry, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Govt. Arts College, Cheyyar, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, India
| | - Pankaj Garg
- Department of Chemistry, GLA University, Mathura, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, India
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M JP, Samson Y, Dhas DA, Joe IH. Exploration of Non Covalent Interactions, Structural, Vibrational, Chemical Reactivity and NLO Properties of 1, 2-Diphenyl-2-Methoxyethanone Oxime: A Theoretical Approach. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2135547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jini Pramila M
- Manonmanium Sundaranar University, Tirunelveli, India
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - Y. Samson
- Department of Physics, Annai Velankanni College, Tholayavattam, India
| | - D. Arul Dhas
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvananthapuram, India
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Femi-Frederic N, Arul-Dhas D, Hubert-Joe I, Gunasekaran B, Sindhusha S, Vinitha G. Synthesis, structure, spectroscopic, topological analysis of novel intermolecular N-H…N and N-H…O hydrogen bonded NLO active melaminium cyanoacetate single crystal: Experimental and Theoretical approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134515] [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]
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Manhas FM, Fatima A, Verma I, Siddiqui N, Muthu S, AlSalem HS, Savita S, Singh M, Javed S. Quantum computational, spectroscopic (FT-IR, NMR and UV–Vis) profiling, Hirshfeld surface, molecular docking and dynamics simulation studies on pyridine-2,6-dicarbonyl dichloride. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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DFT, Molecular Docking, Molecular Dynamics Simulation (MMGBSA) and Hirshfeld Surface Analysis of 5-Sulfosalicylic Acid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Sharma S, Fatima A, Manhas FM, Agarwal N, Singh M, Muthu S, Siddiqui N, Javed S. Experimental Spectroscopic, Quantum Chemical, Molecular Docking, and Molecular Dynamic Simulation Studies on Hydantoin (Monomer and Dimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Shikha Sharma
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Farah Manzer Manhas
- Department of Chemistry, Shoolini University, Solan, Himachal Pradesh, India
| | - Neha Agarwal
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Meenakshi Singh
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, Tamil Nadu, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Central University of Allahabad, Prayagraj, Uttar Pradesh, India
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Fatima A, Khanum G, Sharma A, Siddiqui N, Muthu S, Butcher R, Srivastava SK, Javed S. Synthesis, Single crystal X-ray, DFT, Hirshfeld Surface and molecular docking studies of 9-(2,4-dichlorophenyl)-4a-hydroxy-tetramethyl-octahydro-1H-xanthene-1,8(2H)-dione. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Abuelizz HA, Bakheit AH, Marzouk M, Abdellatif MM, Al-Salahi R. Reactivity of 4,5-Dichlorophthalic Anhydride towards Thiosemicarbazide and Amines: Synthesis, Spectroscopic Analysis, and DFT Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113550. [PMID: 35684489 PMCID: PMC9182083 DOI: 10.3390/molecules27113550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 12/05/2022]
Abstract
The cyclic anhydrides are broadly employed in several fields, such as the chemical, plastic, agrochemical, and pharmaceutical industries. This study describes the chemical reactivity of 4,5-dichlorophthalic anhydride towards several nucleophiles, including thiosemicarbazide and different amines, to produce the carboxylic acid derivatives resulting from anhydride’s opening, namely, phthalimide and dicarboxylic acid (1–12) products. Their chemical structures are confirmed by NMR, IR and MS spectra analyses. Density–functional theory (DFT) studies are performed using (DFT/B3LYP) with the 6-311G(d, p) basis sets to recognize different chemical and physical features of the target compounds.
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Affiliation(s)
- Hatem A. Abuelizz
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Correspondence: (H.A.A.); (R.A.-S.); Tel.: +96-61-1467-7194 (H.A.A. & R.A.-S.)
| | - Ahmed H. Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed Marzouk
- Chemistry of Tanning Materials and Leather Technology Department, Chemical Industries Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo 12622, Egypt;
| | - Mohamed M. Abdellatif
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami Osawa, Tokyo 192-0397, Japan;
| | - Rashad Al-Salahi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Correspondence: (H.A.A.); (R.A.-S.); Tel.: +96-61-1467-7194 (H.A.A. & R.A.-S.)
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Çakmak Ş, Kansiz S, Azam M, Veyisoglu A, Yakan H, Min K. Synthesis, Spectroscopic Characterization, Single-Crystal Structure, Hirshfeld Surface Analysis, and Antimicrobial Studies of 3-Acetoxy-2-methylbenzoic Anhydride. ACS OMEGA 2022; 7:17192-17201. [PMID: 35647448 PMCID: PMC9134421 DOI: 10.1021/acsomega.2c00879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
We report a novel anhydride derivative, 3-acetoxy-2-methylbenzoic anhydride (AMA), obtained from the interaction of 3-acetoxy-2-methylbenzoyl chloride with 3-acetoxy-2-methylbenzoic acid. The synthesized compound was characterized by elemental analysis, IR, 1H NMR, and 13C NMR spectroscopic studies and single-crystal X-ray crystallography which revealed the crystallization of AMA as monoclinic with space group P21/c. A Hirshfeld surface analysis was performed to record various intermolecular interactions, indicating the stabilization of the AMA structure by the intermolecular weak C-H···O hydrogen bonds and π···π interactions. The title compound was screened for antibacterial and antifungal activities using a serial dilution technique under aseptic conditions. The results indicate that the title compound has significant antibacterial properties but showed no antifungal behavior.
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Affiliation(s)
- Şükriye Çakmak
- Department
of Medical Services and Techniques, Vocational School of Health Services, Sinop University, 57000 Sinop, Turkey
| | - Sevgi Kansiz
- Department
of Fundamental Sciences, Faculty of Engineering, Samsun University, Samsun 55420, Turkey
| | - Mohammad Azam
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Aysel Veyisoglu
- Department
of Medical Services and Techniques, Vocational School of Health Services, Sinop University, 57000 Sinop, Turkey
| | - Hasan Yakan
- Department
of Science and Mathematics Education, Ondokuz
Mayıs University, Samsun 55139, Turkey
| | - Kim Min
- Department
of Safety Engineering, Dongguk University, 123 Dongdae-ro, Gyeongju 780714, Gyeongbuk, South Korea
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Vibrational Spectroscopy, Quantum Computational and Molecular Docking Studies on 2-[(1H-Benzimidazol-1-yl)-methyl]benzoic Acid. CRYSTALS 2022. [DOI: 10.3390/cryst12030337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Experimental and theoretical investigations on the optimized geometrical structure, electronic and vibrational features of 2-[(1H-benzimidazol-1-yl)-methyl]benzoic acid are provided using the B3LYP/6-311++G(d,p) basis set. The Vibrational Energy Distribution Analysis (VEDA) program was used to perform the vibrational assignments and calculate the Potential Energy Distribution (PED). The acquired FT-IR and FT Raman data were used to complete the vibrational assignment and characterization of the compound fundamental modes. Theoretical and actual NMR chemical shifts were found to be quite similar. The UV-vis spectrum of 21HBMBA, as well as effects of solvents, have been investigated. The calculated HOMO and LUMO energies reveal that charge transfer happens within the molecule and MEP surface to be a chemically reactive area appropriate for drug action. Furthermore, a thorough examination of Non-Bonding Orbitals, excitation energies, AIM charges, Fukui functions and the Electron Localization Function (ELF) is carried out. The research is also expanded to compute first-order hyperpolarizability and forecast NLO characteristics. The details of the docking studies aided in the prediction of protein binding.
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Isik IB, Tekin N, Sagdinc SG. The analyses of solvent effects on infrared spectra and thermodynamic parameters, Hirshfeld surface, reduced density gradient and molecular docking of ketoprofen as a member of nonsteroidal anti-inflammatory drugs. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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