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Sankar Ganesan T, Elangovan N, Thirumavalavan M, Seenan S, Sowrirajan S, Chandrasekar S, Arumugam N, Almansour AI, Mahalingam SM, V M DD, Kanchi S, Sivaramakrishnan V. Synthesis, topology, molecular docking and dynamics studies of o-phenylenediamine derivative. J Biomol Struct Dyn 2024:1-20. [PMID: 38577881 DOI: 10.1080/07391102.2024.2317981] [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: 09/06/2023] [Accepted: 02/07/2024] [Indexed: 04/06/2024]
Abstract
The N, N'-(1,2-phenylene) bis (1- (4- chlorophenyl) methanimine) (CS4) was synthesized and characterized by infrared (IR), absorption (UV-vis) and NMR (1H and 13C) spectral analyses. The structural parameters, vibrational frequencies, potential energy and the distribution analysis (PED) were calculated by using DFT with the basis set of B3LYP/cc-pVDZ and these spectral values were compared to the experimental values. HOMO and LUMO studied were performed in order to understand the stability and biological activity of the compound. The most reactive sites on the compound were investigated by utilizing MEP energy surface and Fukui function descriptor with the natural population analysis (NPA) of the charges. The study of the natural bond orbitals (NBO) reveals the delocalization of the intramolecular interaction of the charges in the compound. Additionally, topological investigations (ELF, LOL), determination of thermodynamic parameters and noncovalent interaction (NCI) study by using topology (RDG) analysis were also carried out. Finally, the molecular docking and molecular dynamics simulations was carried out by examining against glycosylphosphatidylinositol phospholipase D inhibitor receptor for distinct protein targets (3MZG).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T Sankar Ganesan
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | | | - Shanthi Seenan
- Department of Chemistry, Saveetha Engineering College, Chennai, Tamil Nadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | - S Chandrasekar
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
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Geetha Priya C, Venkatraman BR, Arockiaraj I, Sowrirajan S, Elangovan N, Islam MS, Mahalingam SM. Antimicrobial activity prediction, inter- and intramolecular charge transfer investigation, reactivity analysis and molecular docking studies of adenine derivatives. J Biomol Struct Dyn 2023:1-14. [PMID: 37978905 DOI: 10.1080/07391102.2023.2281636] [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: 08/21/2023] [Accepted: 11/04/2023] [Indexed: 11/19/2023]
Abstract
The utilization of the density functional theory (DFT) methodology has developed as a highly efficient method for investigating molecular structure and vibrational spectra, and it is increasingly being employed in various applications relating to biological systems. This study focuses on conducting investigations, both experimental and computed, to analyze the molecular structure, electronic properties and features of (E)-4-(((9H-purin-6-yl)imino)methyl)-2-methoxyphenol (ANVA). The expression ANVA should be rewritten as follows: the compound is a derivative of adenine (primary amine), specifically a vanillin (aldehyde). The present study reports the synthesis, characterization, DFT, docking and antimicrobial activity of ANVA. The optimization of the molecular structure was conducted, and the determination of its structural features was performed using DFT with the B3LYP/cc-pVDZ method. The vibrational assignments were determined in detail by analyzing the potential energy distribution. A strong correlation was observed between the spectra that were observed and the spectra that were calculated. The calculation of intramolecular charge transfer was performed using natural bond orbital analysis. In addition, several computational methods were employed, including highest occupied molecular orbital-least unoccupied molecular orbital analysis, molecular electrostatic potential calculations, non-linear optical, reduced density gradient, localization orbital locator and electron localization function analysis. This paper examines the present use of adenine derivatives in combatting bacterial and fungal infections, as well as the inclusion of spectral and quantum chemical calculations in the discussion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- C Geetha Priya
- Department of Chemistry, Thanthai Periyar Government Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - B R Venkatraman
- Department of Chemistry, Thanthai Periyar Government Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - I Arockiaraj
- Department of Chemistry, St. Joseph's College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamil Nadu, India
| | - N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamil Nadu, 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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Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer). Molecules 2023; 28:molecules28052116. [PMID: 36903362 PMCID: PMC10004125 DOI: 10.3390/molecules28052116] [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: 12/02/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule's 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV-Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule's charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO-LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.
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Keskin E, Arslan H. Synthesis, crystal structure, DFT calculations, and Hirshfeld surface analysis of an NNN pincer type compound. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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Syntheses, crystal structure, luminescent properties and Hirshfeld surface of a set of triazole-based salts. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Wang D, Zhan E, Wang S, Liu X, Yan G, Chen L, Wang X. Surface Coordination of Pd/ZnIn 2S 4 toward Enhanced Photocatalytic Activity for Pyridine Denitrification. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010282. [PMID: 36615476 PMCID: PMC9822349 DOI: 10.3390/molecules28010282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
New surface coordination photocatalytic systems that are inspired by natural photosynthesis have significant potential to boost fuel denitrification. Despite this, the direct synthesis of efficient surface coordination photocatalysts remains a major challenge. Herein, it is verified that a coordination photocatalyst can be constructed by coupling Pd and CTAB-modified ZnIn2S4 semiconductors. The optimized Pd/ZnIn2S4 showed a superior degradation rate of 81% for fuel denitrification within 240 min, which was 2.25 times higher than that of ZnIn2S4. From the in situ FTIR and XPS spectra of 1% Pd/ZnIn2S4 before and after pyridine adsorption, we find that pyridine can be selectively adsorbed and form Zn⋅⋅⋅C-N or In⋅⋅⋅C-N on the surface of Pd/ZnIn2S4. Meanwhile, the superior electrical conductivity of Pd can be combined with ZnIn2S4 to promote photocatalytic denitrification. This work also explains the surface/interface coordination effect of metal/nanosheets at the molecular level, playing an important role in photocatalytic fuel denitrification.
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Affiliation(s)
- Deling Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, China
| | - Erda Zhan
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, China
| | - Shihui Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, China
| | - Xiyao Liu
- Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde 352100, China
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, China
| | - Guiyang Yan
- Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde 352100, China
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, China
- Correspondence: (G.Y.); (L.C.); (X.W.); Tel.: +86-13809566652 (G.Y.); +86-156959097359 (L.C.); +86-13600887951 (X.W.)
| | - Lu Chen
- Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde 352100, China
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, China
- Correspondence: (G.Y.); (L.C.); (X.W.); Tel.: +86-13809566652 (G.Y.); +86-156959097359 (L.C.); +86-13600887951 (X.W.)
| | - Xuxu Wang
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350002, China
- Correspondence: (G.Y.); (L.C.); (X.W.); Tel.: +86-13809566652 (G.Y.); +86-156959097359 (L.C.); +86-13600887951 (X.W.)
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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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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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