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S Al-Otaibi J, Mary YS, Mary YS, Cristina Gamberini M. SERS analysis, DFT, and solution effects regarding the structural and optical characteristics of folic acid biomolecule adsorbed on a Cu 3 metal cluster. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124161. [PMID: 38493513 DOI: 10.1016/j.saa.2024.124161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
The optical characteristics of folic acid (ABP) and metal clusters of copper (Cu3) at various locations were investigated by means of density functional theory (DFT) computations. Mulliken charge analysis and molecular electrostatic potential (MEP) surface show how charge moves from Cu3 to ABP through the various groups. The peak in the UV-Vis spectra of ABP-Cu3 is caused by bonding and anti-bonding orbitals. In both vacuum and aqueous conditions, the polarizability values of ABP-Cu3 cluster are significantly higher than those of pure ABP, indicating a possible enhancement of the nonlinear optical (NLO) effect. Our research investigates the possibility of using ABP adsorbed metal clusters for NLO materials. Surface enhanced Raman scattering (SERS) in the ABP adsorbed metal clusters enhances the vibrational modes of ABP. Adsorption energies are found to be in the range -17.08 to -58.52 kcal/mol in vacuum and -53.34 to -93.44 kcal/mol in aqueous medium for the different configurations for ABP-Cu3. It indicates that metal clusters adsorbed by ABP are stable in the aqueous media. Experimental IR and UV-Vis of ABP is in agreement with theoretically predicted ones.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Y Sheena Mary
- Department of Physics, FMN College (Autonomous), Kollam, Kerala, University of Kerala, India
| | | | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
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Hassan SA, Aziz DM, Abdullah MN, Bhat AR, Dongre RS, Hadda TB, Almalki FA, Kawsar SMA, Rahiman AK, Ahmed S, Abdellattif MH, Berredjem M, Sheikh SA, Jamalis J. In vitro and in vivo evaluation of the antimicrobial, antioxidant, cytotoxic, hemolytic activities and in silico POM/DFT/DNA-binding and pharmacokinetic analyses of new sulfonamide bearing thiazolidin-4-ones. J Biomol Struct Dyn 2024; 42:3747-3763. [PMID: 37402503 DOI: 10.1080/07391102.2023.2226713] [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: 11/24/2022] [Accepted: 05/11/2023] [Indexed: 07/06/2023]
Abstract
In this work, Schiff bases and Thiazolidin-4-ones, were synthesized using Sonication and Microwave techniques, respectively. The Schiff base derivatives (3a-b) were synthesized via the reaction of Sulfathiazole (1) with benzaldehyde derivatives (2a-b), followed by the synthesis of 4-thiazoledinone (4a-b) derivatives by cyclizing the synthesized Schiff bases through thioglycholic acid. All the synthesized compounds were characterized by spectroscopic techniques such as FT IR, NMR and HRMS. The synthesized compounds were tested for their in vitro antimicrobial and antioxidant and in vivo cytotoxicity and hemolysis ability. The synthesized compounds displayed better antimicrobial and antioxidant activity and low toxicity in comparison to reference drugs and negative controls, respectively. The hemolysis test revealed the compounds exhibit lower hemolytic effects and hemolytic values are comparatively low and the safety of compounds is in comparison with standard drugs. Theoretical calculations were carried out by using the molecular operating environment (MOE) and Gaussian computing software and observations were in good agreement with the in vitro and in vivo biological activities. Petra/Osiris/Molinspiration (POM) results indicate the presence of three combined antibacterial, antiviral and antitumor pharmacophore sites. The molecular docking revealed the significant binding affinities and non-bonding interactions between the compounds and Erwinia Chrysanthemi (PDB ID: 1SHK). The molecular dynamics simulation under in silico physiological conditions revealed a stable conformation and binding pattern in a stimulating environment. HighlightsNew series of Thaiazolidin-4-one derivatives have been synthesized.Sonication and microwave techniques are used.Antimicrobial, Antioxidant, cytotoxicity, and hemolysis activities were observed for all synthesized compounds.Molecular Docking and DFT/POM analyses have been predicted.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sangar Ali Hassan
- Department of Chemistry, College of Science, University of Raparin, Sulaymaniyah, Iraq
| | - Dara Muhammed Aziz
- Department of Chemistry, College of Science, University of Raparin, Sulaymaniyah, Iraq
| | | | - Ajmal R Bhat
- Department of Chemistry, R.T.M. Nagpur University, Nagpur, India
| | | | - Taibi Ben Hadda
- Laboratory of Applied Chemistry & Environment, Faculty of Sciences, Mohammed Premier University, Oujda, Morocco
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Faisal A Almalki
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sarkar M A Kawsar
- Laboratory of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong, Bangladesh
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai, India
| | - Magda H Abdellattif
- Department of Chemistry, College of Science, Taif University, Al-Haweiah, Taif, Saudi Arabia
| | - Malika Berredjem
- Laboratory of Applied Organic Chemistry LCOA, Synthesis of Biomolecules and Molecular Modelling Group, Badji-Mokhtar - Annaba University, Annaba, Algeria
| | - S A Sheikh
- Department of physics, National Institute of Technology, Srinagar, Kashmir, India
| | - Joazaizulfazli Jamalis
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor, Malaysia
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Tian B, Mao J, Zu M, Wu R, Xiao C. Study of the Mechanism of Hydrolysis of Hemicellulose from Lignocellulose during Alkali Thermal Pretreatment by Density Functional Theory and Experiment. J Org Chem 2024. [PMID: 38191296 DOI: 10.1021/acs.joc.3c01668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The covalent bond fracture of hemicellulose leads to hemicellulose hydrolysis during lignocellulosic alkali thermal pretreatment, which has not previously been reported. Density functional theory was used to study the mechanism of hydrolysis of the hemicellulose model compounds under alkali conditions. There are four reaction paths for xylose formation, among which the reaction path with the lowest energy barrier is that in which the nucleophile captures H30 to generate water. The deprotonated hydroxyl group attacks the carbon on the glycoside bond, resulting in the cleavage of the glycoside bond and the formation of a new carbon-oxygen covalent bond, with an energy barrier of 154.2 kJ/mol. The nucleophile further attacks the glycosidic bond to form a new xylose residue with an energy barrier of 111.9 kJ/mol. When the glycosidic bond breaks, the orbital interaction with the largest proportion causes the transfer of ∼0.511 electron from the glycosidic bond oxygen to the deprotonated hydroxy oxygen. In situ Fourier transform infrared spectroscopy is used for the identification of functional groups during the alkali thermal pretreatment. As the temperature increases, the feasibility of the reaction increases. This study lays a theoretical foundation for the development of the alkali thermal pretreatment of lignocellulose.
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Affiliation(s)
- Bobing Tian
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Jiahua Mao
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Mingfu Zu
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Ruilin Wu
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Chao Xiao
- Department of Energy and Power Engineering, College of Electrical Engineering, Guizhou University, Huaxi District, Guiyang 550025, China
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Al-Otaibi JS, Mary YS, Mary YS, Krátký M, Vinsova J, Mahmood T, Gamberini MC, Rajendran Nair DS. TD-DFT, DFT, docking, MD simulations, and concentration-dependent SERS investigations of a bioactive trifluoromethyl derivative having human acetylcholinesterase and butyrylcholinesterase in silver colloids. J Mol Model 2023; 29:271. [PMID: 37535185 DOI: 10.1007/s00894-023-05679-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
CONTEXT Various concentrations of (E)-4-methoxy-N'-(2-(trifluoromethyl)benzylidene) benzohydrazide (EMT) adsorbed on colloidal silver nanoparticles were studied using SERS and results were compared to the normal Raman spectrum. DFT calculations were used to validate experimental findings. Theoretically, the structures of the EMT and EMT-Ag6 systems were optimized. The UV-Vis spectral analysis's red shift and lower intensity behavior show that EMT has chemisorbed onto Ag nanoparticles. Charge transfer (CT) from Ag to EMT is highlighted by FMO analysis. The CT interaction in EMT and EMT-Ag6 was further verified by MEP and Mulliken charge analyses. The EMT was adsorbed on Ag nanoparticles with tilted orientation and orientation changes with colloidal concentration, according to SERS spectrum analysis. Docking EMT with 4PQE and 5DYW binding affinities are found to be -9.7 and -8.1 kcal/mol. MD simulations give the competence of 5DYW-EMT and 4PQE-EMT in their intended binding interactions and their ability to establish enduring associations with the protein of interest. METHODS DFT was used to optimize the molecular structures of EMT and EMT-Ag6 using B3LYP/6-311++G* (LANL2DZ basis set for Ag). A molecular dynamics simulation study was conducted on the 4PQE-EMT and 5DYW-EMT systems using the Desmond software for 100 ns.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Y Sheena Mary
- Department of Physics, FMNC, University of Kerala, Kollam, Kerala, India.
- Thushara, Neethinagar, Kollam, Kerala, India.
| | | | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05, Hradec Králové, Czech Republic
| | - Tariq Mahmood
- Department of Chemistry, College of Science, University of Bahrain, Manama, Bahrain
| | - Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125, Modena, Italy
| | - Deepthi S Rajendran Nair
- Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
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Al-Otaibi JS, Mary YS, Mary YS, Thomas R. Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions. J Mol Model 2023; 29:246. [PMID: 37442832 DOI: 10.1007/s00894-023-05623-3] [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: 04/22/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
CONTEXT Theoretical investigation of indole (IND) and its binary combination with dichloromethane (DC) in various solvents were computed to track the impact of molecular interactions on spectral characteristics. When transitioning from plain drug to complexes, different modes of IND display a substantial shift in peak location. The 3561.26 cm-1 band shows (~15.58 cm-1) red shift upon dilution. The geometry in various solvents was calculated using quantum chemical calculation utilizing density functional theory (DFT). The highest ALIE values are located at the indole skeleton and on complexation with DC, and the ring atoms become more electron rich. The atom-centered density matrix propagation (ADMP) molecular dynamic (MD) calculation shows that the geometries optimized through the DFT calculation match the global minima effectively. MD simulations indicate that indole is more stable in water and methanol. METHODS DFT studies have been employed to study the interaction between indole and dichloromethane. CAM-B3LYP/6-311++G(d)(6D,7F) level of theory was employed using Gaussian 16 W suite. Quantum topological descriptors were discussed using quantum theory of atoms in molecules (QTAIM) with the help of Multiwfn software. Reduced density gradient (RDG) plot describes the nature of the interaction, while average local ionization energy (ALIE) explained the variation in local ionization energy of the molecular surface before and after complexation.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | | | | | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
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Synthesis, crystal structure, molecular dynamics, docking and in-vitro studies of cyclododecanonethiosemicarbazone, a promising anti tuberculosis agent. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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Al-Otaibi JS, Mary YS, Mary YS, Krátký M, Vinsova J, Gamberini MC. DFT, TD-DFT and SERS analysis of a bioactive benzohydrazide’s adsorption in silver hydrosols at various concentrations. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Vennila P, Al-Otaibi JS, Venkatesh G, Sheena Mary Y, Raj V, Acharjee N, Tamilselvi P. Structural, Spectral, Molecular Docking, and Molecular Dynamics Simulations of Phenylthiophene-2-Carboxylate Compounds as Potential Anticancer Agents. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2172052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- P. Vennila
- Department of Chemistry, Thiruvalluvar Government Arts College, Rasipuram, India
| | - Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - G. Venkatesh
- Department of Chemistry, Muthayammal Memorial College of Arts & Science, Rasipuram, India
| | | | - V. Raj
- Department of Chemistry, Periyar University, Salem, India
| | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, Paschim Bardhaman, India
| | - P. Tamilselvi
- Department of Chemistry, Muthayammal Memorial College of Arts & Science, Rasipuram, India
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Spectroscopic, reactivity analysis and docking studies of 3-(adamantan-1-yl)-4-(4-fluorophenyl)-1-[(4-phenylpiperazin-1-yl)methyl]-4,5-dihdyro-1H-1,2,4-triazole—5-thione: DFT and MD simulations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Quantum control of optoelectronic and thermodynamic properties of dopamine molecule in external electric field : A DFT and TD-DFT study. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Novel fluorophenyl tethered thiazole and chalcone analogues as potential anti-tubercular agents: Design, synthesis, biological and in silico evaluations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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S.Al-Otaibi J, Mary Y, Mary Y, Armaković SJ, Armaković S, Van Alsenoy C, Yathirajan H. Insights into the reactivity properties, docking, DFT and MD simulations of orphenadrinium dihydrogen citrate in different solvents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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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Fatima A, Khanum G, Sharma A, Siddiqui N, Butcher RJ, Srivastava SK, Javed S. Synthesis, X-Ray Diffraction, DFT and Hirshfeld Surface Studies of 9-(4-Hydroxyphenyl-Tetramethyl-Hexahydro-1H-Xanthene-1,8(2H)-Dione. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2127804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Aysha Fatima
- S.O. S in Chemistry, Jiwaji University, Gwalior, M.P., India
| | - Ghazala Khanum
- S.O. S in Chemistry, Jiwaji University, Gwalior, M.P., India
| | - Arun Sharma
- S.O. S in Chemistry, Jiwaji University, Gwalior, M.P., India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, U.P., India
| | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | | | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, U.P., India
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Understanding the mechanism of thioguanine's binding to Ag6 and bimetallic (Ag3–Au3 and Ag3–Cu3) clusters. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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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Zochedh A, Priya M, Chakaravarthy C, Sultan AB, Kathiresan T. Experimental and Computational Evaluation of Syringic Acid – Structural, Spectroscopic, Biological Activity and Docking Simulation. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2118332] [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)
- Azar Zochedh
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Mohana Priya
- Department of Bioinformatics, School of Distance Education, Bharathiar University, Coimbatore, India
| | - Cibe Chakaravarthy
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Asath Bahadur Sultan
- Condensed Matter Physics Laboratory, Department of Physics, International Research Centre, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Thandavarayan Kathiresan
- Department of Biotechnology, Kalasalingam Academy of Research and Education, Krishnankoil, India
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Krishna Priya M, Reuben Jonathan D, Muthu S, Sivasankaran B, Usha G. Synthesis and Chemical Exploration of an Organic Exocyclic Chalcone Derivative for Its Therapeutic Proficiency against Breast Cancer. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2118331] [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)
- M. Krishna Priya
- PG and Research Department of Physics, Queen Mary’s College(A), University of Madras, Chennai, India
| | - D. Reuben Jonathan
- Department of Chemistry, Madras Christian College(A), University of Madras, Chennai, India
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, India
| | | | - G. Usha
- PG and Research Department of Physics, Queen Mary’s College(A), University of Madras, Chennai, India
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Koparir P, Omar RA, Sarac K, Ahmed LO, Karatepe A, Taskin-Tok T, Safin DA. Synthesis, Characterization and Computational Analysis of Thiophene-2,5-Diylbis((3-Mesityl-3-Methylcyclobutyl)Methanone). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2112712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Pelin Koparir
- Institute of Forensic, Department of Chemistry, Firat University, Elazig, Turkey
| | - Rebaz Anwar Omar
- Department of Chemistry, Faculty of Science and Health, Koya University–University Park, Daniel Mitterrand Boulevard, Koya, Kurdistan Region, F. R. Iraq
| | - Kamuran Sarac
- Department of Chemistry, Faculty of Art and Sciences, Bitlis Eren University, Bitlis, Turkey
| | - Lana Omer Ahmed
- Department of physics, Faculty of Science and Health, Koya University – University Park, Daniel Mitterrand Boulevard, Koya, Kurdistan Region, F. R. Iraq
| | - Arzu Karatepe
- Department of Chemistry, Faculty of Sciences, Firat University, Elazığ, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, University of Gaziantep, Gaziantep, Turkey
- Department of Bioinformatics and Computational Biology, Institute of Health Sciences, University of Gaziantep, Gaziantep, Turkey
| | - Damir A. Safin
- «Advanced Materials for Industry and Biomedicine» Laboratory, Kurgan State University, Kurgan, Russia Federation
- Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University Named after the First President of Russia B.N. Yeltsin, Ekaterinburg, Russia Federation
- University of Tyumen, Tyumen, Russia Federation
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Synthesis, characterization, In-silico and In-vitro investigation of sulfonamide based esters. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Al-Otaibi JS, Mary YS, Mary YS. Spectroscopic analyses on an azatricycloderivative by DFT with different solvents, reactivity analysis and MD simulations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Al-Otaibi JS, Shabeer M, Mary YS, Mary YS, Thomas R. Adsorption of a thione derivative on carbon, AlN, and BN nanotubes: a detailed DFT and MD investigation. J Mol Model 2022; 28:181. [PMID: 35668144 DOI: 10.1007/s00894-022-05179-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/30/2022] [Indexed: 12/30/2022]
Abstract
The performance of nanotubes (NT) of carbon (CC), aluminium-nitrogen (AlN), and boron-nitrogen (BN) as a sensor and nanocarrier for mercaptopurine (MCP) was investigated by means of a theoretical approach. The calculated negative values of adsorption energy showed the interaction and adsorption of MCP. Highest-occupied molecular orbital (HOMO) and lowest-unoccupied molecular orbital (LUMO) distributions were only found on the NT counter portion of the drug-nanotube not on MCP for AlN-NT and BN-NT while HOMO is over MCP and LUMO is over NT for CC-NT. The polarizability of MCP-NTs is greater than that of MCP. Raman wavenumbers of MCP are enhanced in NTs, and hence, NTs can act as a sensor for the detection of MCP. Solvent dependency on adsorption behaviour is also presented in the manuscript, where we found that the AlN nanotube showed exceptionally high free energy of adsorption over other nanotubes in all solvent mediums. Solvation-free energies were also reported. Noncovalent interaction scattered plot also showed significant intermolecular interaction between AlN nanotubes and the mercaptopurine when compared to other nanotubes under study. To find the antiviral activity of MCP and MCP-NTs against antiviral activities, docking and molecular dynamics simulations were performed with 1HMP PDB. Recovery times show that MCP desorption occurs quickly. The MD simulations and docking results show that BN and CC-NTs with MCP show good activity as drug carriers.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | - Muhammad Shabeer
- School of Science, Westlake University, Hangzhou, People's Republic of China
| | | | | | - Renjith Thomas
- Deparment of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
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Co-crystals of ethenzamide with 2-nitrobenzoic acid - Conformational analysis, MD simulations and DFT investigations. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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In Silico study for acyclovir, ganciclovir and its derivatives to fight the COVID-19: Molecular docking, DFT calculations, ADME and td-Molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC8931996 DOI: 10.1016/j.jics.2022.100433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the present work, we have designed three molecules, acyclovir (A), ganciclovir (G) and derivative of hydroxymethyl derivative of ganciclovir (CH2OH of G, that is D) and investigated their biological potential against the Mpro of nCoV via in silico studies. Further, density functional theory (DFT) calculations of A, G and D were performed using Gaussian 16 on applying B3LYP under default condition to collect the information for the delocalization of electron density in their optimized geometry. Authors have also calculated various energies including free energy of A, G and D in Hartree per particle. It can be seen that D has the least free energy. As mentioned, the molecular docking of the A, G and D against the Mpro of nCoV was performed using iGemdock, an acceptable computational tool and the interaction has been studied in the form of physical data, that is, binding energy for A, G and D were calculated in kcal/mol. It can be seen the D showed effective binding, that is, maximum inhibition that A and G. For a better understanding for the inhibition of the Mpro of nCoV by A, G and D, temperature dependent molecular dynamics simulations were performed. Different trajectories like RMSD, RMSF, Rg and hydrogen bond were extracted and analyzed. The results of molecular docking of A, G and D corroborate with the td-MD simulations and hypothesized that D could be a promising candidate to inhibit the activity of Mpro of nCoV.
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Manimozhi PK, Kavitha R, Thilagavathi R, Gokilavani GM. Theoretical, Experimental Studies on Molecular Structure and Vibrational Spectra of 2,6-Dibromo-4-Nitrophenol. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- P. K. Manimozhi
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - R. Kavitha
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - R. Thilagavathi
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - G. M. Gokilavani
- PG and Research Department of Physics, Seethalakshmi Ramaswami College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Investigation of the electronic properties of solvents (water, benzene, methanol) using IEFPCM model, spectroscopic investigation with docking and MD simulations of a thiadiazole derivative with anti-tumor activities. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Das N, Bhattacharjee M, Boruah S, Chowdhury S, Dutta Purkayastha R. Some contribution to W(VI)-peroxo-chemistry: Synthesis, spectroscopic characterization, reactivity and DFT studies. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2021.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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28
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Evidence of cluster formation of pyrrole with mixed silver metal clusters, Agx-My (x = 4,5, y = 2/1 and M = Au/Ni/Cu) using DFT/SERS analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113569] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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S.Al-Otaibi J, Mary Y, Mary Y. Adsorption of a thione bioactive derivative over different silver/gold clusters – DFT investigations. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113497] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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30
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Shyni V, Leenaraj DR, Ittyachan R, Shyju GJ, Joseph L, Sajan D. Spectroscopic studies, quantum chemical investigations, and in silico and in vitro scrutiny of the diuretic drug trichlormethiazide adsorbed on AuNPs. J Mol Recognit 2021; 35:e2939. [PMID: 34850458 DOI: 10.1002/jmr.2939] [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: 06/22/2021] [Revised: 08/26/2021] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
Experimental and theoretical study was employed to study the adsorption of the diuretic drug, trichlormethiazide (TCM) molecule on AuNPs (TCMA). The stereoelectronic properties of the molecular structure of most stable conformers of TCM and TCMA were studied using DFT/B3LYP-6-311++G (d, p) together with LANL2DZ methodology. The Fourier transform Raman and Infrared spectra of TCM were recorded and analyzed. Quantum chemical calculations of TCM and TCMA molecules were used to evaluate the stability of the molecule, hyper-conjugative interactions, electron delocalization, and binding interactions. The calculated and experimentally observed vibrational frequencies of the molecule were assigned and compared. The shifting and intensity enhancement of the CCl2 band manifests the back-donation and conjugation effect, which are the result of the presence of nitrogen atom adjoining the dichloromethyl groups and the oxygen in the sulfur dioxide group attached among the amino group and the chlorophenyl ring, respectively, which enhances bioactivity. Anticancer activity was examined based on molecular docking analysis, and it was identified that TCM and TCMA molecules act as good inhibitors against lung cancer. SERS analysis and MTT assay confirmed the molecular docking analysis results.
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Affiliation(s)
- V Shyni
- Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, India
| | - D R Leenaraj
- Department of Physics, Mar Ivanios College, Thiruvananthapuram, India
| | - Reena Ittyachan
- Department of Physics, Sacred Heart College, Chalakudy, India
| | - G J Shyju
- Department of Physics, Christian College, Thiruvananthapuram, India
| | - Lynnette Joseph
- Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, India
| | - D Sajan
- Centre for Advanced Functional Materials, Department of Physics, Bishop Moore College, Mavelikara, India
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Yadav T, Brahmachari G, Karmakar I, Saha S, Chowdhury J, Pathak A, Kumar R, Sharma R, Bento RRF, Yadav NP. Spectroscopic Investigation of Electron-Releasing Functional Groups Substituted N- Iso-Butyl, S-2-Nitro-1-Phenylethyl Dithiocarbamate – A DFT Approach. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1993940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Tarun Yadav
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Goutam Brahmachari
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (A Central University), Santiniketan, West Bengal, India
| | - Indrajit Karmakar
- Laboratory of Natural Products & Organic Synthesis, Department of Chemistry, Visva-Bharati (A Central University), Santiniketan, West Bengal, India
| | - Saumen Saha
- Department of Physics, Jadavpur University, Kolkata, India
| | | | - Amit Pathak
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Rajneesh Kumar
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - R. Sharma
- Department of Physics, Rabindranath Tagore University, Hojai, Assam, India
| | | | - Nagendra P. Yadav
- School of Electrical and Electronics Information Engineering, Hubei Polytechnic University, Huangshi, Hubei, China
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32
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Ramuthai M, Jeyavijayan S, Jayram ND. Molecular Structure, Spectroscopic Investigation, Docking and in Vitro Cytotoxicity Studies of 7-Methoxycoumarin as anti-Leukemia Agent. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1994430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M. Ramuthai
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - S. Jeyavijayan
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, India
| | - Naidu Dhanpal Jayram
- Department of Physics, Kalasalingam Academy of Research and Education, Krishnankoil, India
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Dodeja KK, Bhola YO, Socha BN, Alalawy MD, Dubey RP, Pandya SB, Padariya TJ, Naliapara YT. Lipophilicity, gas-phase optimized geometry, quantum chemical calculations, Hirshfeld surface analysis, energy frameworks, and molecular docking studies of novel (Z)-2-((3-(4-chlorophenyl)-1-phenyl-1H-pyrazol-4-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one. INORG NANO-MET CHEM 2021. [DOI: 10.1080/24701556.2021.1983839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Khushbu K. Dodeja
- Department of Chemistry, Saurashtra University, Rajkot, Gujarat, India
| | - Yogesh O. Bhola
- College of Computer, Science, and Information Technology, Junagadh, Gujarat, India
| | - Bhavesh N. Socha
- Department of Physics, Sardar Patel University, Anand, Gujarat, India
| | - Mohammed Dawood Alalawy
- Department of Physics, Faculty of Education & Science, University of Al-Baydha, Al-Baydha, Yemen
| | - Rahul P. Dubey
- Department of Physics, Sardar Patel University, Anand, Gujarat, India
| | - Sachin B. Pandya
- Department of Chemistry, Saurashtra University, Rajkot, Gujarat, India
| | | | - Y. T. Naliapara
- Department of Chemistry, Saurashtra University, Rajkot, Gujarat, India
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34
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Sheena Mary Y, Shyma Mary Y. Adsorption of Phenothiazine Derivatives on Graphene – DFT, Docking and MD Simulation. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1946570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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