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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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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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A H, C PP, Mary Y, G ST, Raghunandan R. Spectral, Thermal, Structural, and DFT studies of New Luminescent Heterobimetallic MOF of Lead and Sodium based on Diglycolic acid ligand having unusual coordination environment for Photodegradation and Antibacterial applications. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Al-Otaibi JS, Mary YS, Mary YS, Krátký M, Vinsova J, Gawad J, Gamberini MC. SERS spectra of a bioactive carboximidamide derivative at different concentrations: Experimental and DFT investigations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Sheena Mary Y, Shyma Mary Y, Armaković S, Armaković SJ, Yadav R, Celik I, Razavi R. Investigation of reactive properties, adsorption on fullerene, DFT, molecular dynamics simulation of an anthracene derivative targeting dihydrofolate reductase and human dUTPase. J Biomol Struct Dyn 2022; 40:10952-10961. [PMID: 34278966 DOI: 10.1080/07391102.2021.1953602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Anthracenes are aromatic compounds with flexible structure and reactivity which are of great interest to theoretical and experimental chemists. Theoretical investigations of 1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]anthracene-9,10-dione (Mitoxantrone) (DDEA) based on density functional theory, molecular dynamics and adsorption on fullerene are reported in the present research. The suitable situation for adsorption with fullerene (C60) is the cyclohex-2-ene-1,4-dione ring of DDEA. Selected quantum-molecular descriptors have been calculated to predict the most reactive sites of the DDEA molecule. Interactions of DDEA with water have been studied using MD simulations. MD simulations were also used to study solubility parameter, a significant quantity for the development of pharmaceutical formulations. The affinity of DDEA on human dihydrofolate reductase and deoxyuridine triphosphatase enzymes was investigated by MD simulation of the protein-ligand complex obtained by molecular docking study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Stevan Armaković
- Faculty of Sciences, Department of Physics, University of Novi Sad, Novi Sad, Serbia
| | - Sanja J Armaković
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Novi Sad, Serbia
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, India
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
| | - Razieh Razavi
- Department of Chemistry, Faculty of Science, University of Jiroft, Jiroft, Iran
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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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Bayrakdar A, Mert S, Kasımoğulları R, Bangaru S, Manivannan P. Synthesis, spectroscopic (FT-IR and NMR), DFT and molecular docking studies of ethyl 1-(3-nitrophenyl)-5-phenyl-3-((4-(trifluoromethyl)phenyl)carbamoyl)-1H-pyrazole-4-carboxylate. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04681-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Al-Otaibi JS, Mary YS, Mary YS. Theoretical Insights into the Solvation, Electronic, Chemical Properties and Molecular Docking of Some Thiazole Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2030767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Sudhakar C, Saravanabhavan M, Ramesh K, Badavath V, Chandrasekar S, Babu B, Sekar M. Pharmacological and quantum chemical studies of 2-aminobenzo[d]thiazol-3-ium 4-chlorobenzenesulphonate: Synthesis, spectral, thermal analysis and structural elucidation. RESULTS IN CHEMISTRY 2022. [DOI: 10.1016/j.rechem.2022.100442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Al-Otaibi JS, Mary Y, Mary Y. Exploring the Detailed Spectroscopic Characteristics, Chemical and Biological Activity of Three Pyrone Derivatives Using Experimental and Theoretical Tools. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2020136] [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)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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Mary YS, Mary YS, Bielenica A, Armaković S, Armaković SJ, Chandramohan V, Dammalli M. Investigation of the reactivity properties of a thiourea derivative with anticancer activity by DFT and MD simulations. J Mol Model 2021; 27:217. [PMID: 34218339 DOI: 10.1007/s00894-021-04835-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/23/2021] [Indexed: 11/27/2022]
Abstract
Spectroscopic analysis of 1-(2-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (FPTT) is reported. Experimental and theoretical analyses of FPTT, with molecular dynamics (MD) simulations, are reported for finding different parameters like identification of suitable excipients, interactions with water, and sensitivity towards autoxidation. Molecular dynamics and docking show that FPTT can act as a potential inhibitor for new drug. Additionally, local reactivity, interactivity with water, and compatibility of FPTT molecule with frequently used excipients have been studied by combined application of density functional theory (DFT) and MD simulations. Analysis of local reactivity has been performed based on selected fundamental quantum-molecular descriptors, while interactivity with water was studied by calculations of radial distribution functions (RDFs). Compatibility with excipients has been assessed through calculations of solubility parameters, applying MD simulations. Graphical abstract Reactive sites identified.
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Affiliation(s)
| | | | - Anna Bielenica
- Department of Biochemistry, Medical University of Warsaw, 02-097, Warszawa, Poland
| | - Stevan Armaković
- Faculty of Sciences, Department of Physics, University of Novi Sad, Trg D. Obradovića 4, Novi Sad, 21000, Serbia
| | - Sanja J Armaković
- Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, University of Novi Sad, Trg D. Obradovića 3, Novi Sad, 21000, Serbia
| | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India
| | - Manjunath Dammalli
- Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, 572103, India
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Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Gamberini MC, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a benzoic acid derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119265. [PMID: 33316651 DOI: 10.1016/j.saa.2020.119265] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering of 4-((3-bromo-5-chloro-2-hydroxybenzylidene)amino)benzoic acid (BCHB) have been studied on different silver colloids concentrations in order to know the particular chemical species responsible for the spectra. For Raman and surface enhanced Raman scattering (SERS) wavenumbers, changes are observed. Observed variations in the modes of ring may be due to interaction of the π-electrons and presence of this indicated that RingII is more inclined than RingI and the BCHB assumes inclined orientation for concentration 10-3 M. Changes in orientation are seen in SERS spectra depending on concentration. In order to determine the electron-rich and poor sites of BCHB, the molecular electrostatic potential was also constructed. The molecular docking studies show that the bindings and interactions with the receptors may be supporting evidence for further studies in design further BCHB pharmaceutical applications.
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Affiliation(s)
- Maria Cristina Gamberini
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, 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
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, via G. Campi 103, 41125 Modena, Italy
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Kumar VS, Mary YS, Mary YS, Krátký M, Vinsova J, Baraldi C, Roxy MS, Gamberini MC. Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative. J Biomol Struct Dyn 2021; 40:6952-6964. [PMID: 33645445 DOI: 10.1080/07391102.2021.1891971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Spectroscopic analysis, density functional theory (DFT) studies and surface enhanced Raman scattering (SERS) of (E)-N'-(5-chloro-2-hydroxybenzylidene)-4-trifluoromethyl) benzohydrazide (CHTB) have been studied on different silver colloids in order to know the particular chemical species responsible for the spectra. Very significant shifts are observed for Raman and SERS wavenumbers. Observed changes in the υ-ring modes may be due to surface interaction of the π-electrons and the presence of this suggested that RingII is more tilted in both cases than RingI and the molecule assumes a tilted orientation for the concentration 10-3 M. Orientation changes are seen in concentration dependent SERS spectra. The molecular electrostatic potential has also been constructed to determine the electron rich and poor site of CHTB. The molecular docking studies indicate that the binding affinity and hydrogen bond interactions with the receptors may be supporting evidence for further studies in designing other pharmaceutical applications of CHTB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Veena S Kumar
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | | | | | - Martin Krátký
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Jarmila Vinsova
- Department of Organic and Bioorganic Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Cecilia Baraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - M S Roxy
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
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Kirishnamaline G, Magdaline JD, Chithambarathanu T, Aruldhas D, Anuf AR. Theoretical investigation of structure, anticancer activity and molecular docking of thiourea derivatives. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Spectroscopic and computational study of chromone derivatives with antitumor activity: detailed DFT, QTAIM and docking investigations. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04188-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
AbstractTheoretical investigations of three pharmaceutically active chromone derivatives, (E)-3-((2,3,5,6-tetrafluorophenyl)hydrazono)methyl)-4H-chromen-4-one (TPC), (E)-3-((2-(2,4,6-trifluorophenyl)hydrazono)methyl)-4H-chromen-4-one (FHM) and(E)-3-((2-(perfluorophenyl)hydrazono)methyl)-4H-chromen-4-one (PFH) are reported. Molecular geometries, vibrational spectra, electronic properties and molecular electrostatic potential were investigated using density functional theory. Quantum theory of atoms in molecules (QTAIM) study shows that the maximum of ellipticity parameters in the existing bonds in TPC, FHM and PFH, attributes to the bonds involving in aromatic region points toward the π-bond interactions in the molecules. Based on energy gap (1.870, 1.649 and 1.590 eV) and electrophilicity index (20.233, 22.581 and 23.203 eV) values of TPC, FHM and PFH, we can conclude that all molecules have more biological activity. The molecular electrostatic potential maps were calculated to provide information on the chemical reactivity of the molecule and also to describe the intermolecular interactions. All these studies including docking studies, help a lot in determining the biological activities of chromone derivatives. Activities of chromone derivatives are compared with 5-fluorouracil and azathioprine (antitumor, antiproliferative standards) and were found to be higher than reference ones.
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Conformational analysis and quantum descriptors of two bifonazole derivatives of immense anti-tuber potential by using vibrational spectroscopy and molecular docking studies. Struct Chem 2020. [DOI: 10.1007/s11224-020-01678-7] [Citation(s) in RCA: 6] [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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Cocrystals of hydrochlorothiazide with picolinamide, tetramethylpyrazine and piperazine: quantum mechanical studies, docking and modelling of the photovoltaic efficiency for DSSC. J Mol Model 2020; 26:256. [PMID: 32885337 DOI: 10.1007/s00894-020-04528-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 01/06/2023]
Abstract
Cocrystals are of immense applications in crystal engineering and pharmaceutical chemistry. Hydrochlorothiazide is found to form cocrystals with picolinamide (H1), tetramethylpyrazine (H2) and piperazine (H3). It was characterized using IR spectra, and quantum mechanical calculations for geometry and other properties. Frontier orbital energies are used to predict the energy properties and model the possible charge transfer between the constituents of the cocrystal. The frontier molecular orbital analysis indicates chemical reactivity and bioactivity of the cocrystals. The MEP surface reveals the various reactive surfaces in the cocrystal system, which is very important in deciding various biological activities. The UV-Vis spectra show the possible electronic transitions of the molecules. Simulated electronic spectra using TDDFT method with CAM-B3LYP functional were used to investigate the suitability of the cocrystals to be used in DSSC. Moreover, the molecular docking analysis proves that the cocrystals can act as potential inhibitors and paves the way for developing effective drugs.
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DFT and MD simulations and molecular docking of co-crystals of octafluoro-1,4-diiodobutane with phenazine and acridine. Struct Chem 2020. [DOI: 10.1007/s11224-020-01616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Hu J, Zanca F, Lambe P, Tsuji M, Wijeweera S, Todisco S, Mastrorilli P, Shirley W, Benamara M, Moghadam PZ, Beyzavi H. (Thio)urea-Based Covalent Organic Framework as a Hydrogen-Bond-Donating Catalyst. ACS APPLIED MATERIALS & INTERFACES 2020; 12:29212-29217. [PMID: 32511903 PMCID: PMC7815320 DOI: 10.1021/acsami.0c04957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Two-dimensional urea- and thiourea-containing covalent organic frameworks (COFs) were synthesized at ambient conditions at large scale within 1 h in the absence of an acid catalyst. The site-isolated urea and thiourea in the COF showed enhanced catalytic efficiency as a hydrogen-bond-donating organocatalyst compared to the molecular counterparts in epoxide ring-opening reaction, aldehyde acetalization, and Friedel-Crafts reaction. The COF catalysts also had excellent recyclability.
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Affiliation(s)
- Jiyun Hu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Federica Zanca
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S13JD, United Kingdom
| | - Patricia Lambe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Miu Tsuji
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Samantha Wijeweera
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | | | | | - William Shirley
- Department of Chemistry, Pittsburg State University, Pittsburg, Kansas 66762, United States
| | - Mourad Benamara
- Institute for Nanoscience & Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Peyman Z Moghadam
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield S13JD, United Kingdom
| | - Hudson Beyzavi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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Viji A, Balachandran V, Babiyana S, Narayana B, Saliyan VV. Molecular docking and quantum chemical calculations of 4-methoxy-{2-[3-(4-chlorophenyl)-5-(4-(propane-2-yl) PHENYL)-4, 5-dihydro-1H-pyrazol-1-yl]- 1, 3-thiazol-4-yl}phenol. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127452] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Mary YS, Mary YS, Resmi KS, Kumar VS, Thomas R, Sureshkumar B. Detailed quantum mechanical, molecular docking, QSAR prediction, photovoltaic light harvesting efficiency analysis of benzil and its halogenated analogues. Heliyon 2019; 5:e02825. [PMID: 31763480 PMCID: PMC6861576 DOI: 10.1016/j.heliyon.2019.e02825] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/21/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
The structural, spectroscopic various physico-chemical and biological characteristics of the organic molecule benzil (BZL) and derivatives, 1,2-bis(4-methylphneyl)-1,2-ethanedione (DMB), 4,4′-difluorobenzil (DFB), 4,4′-dichlorobenzil (DCB) and 4,4′-dibromobenzil (DBB) have been studied by various computational methods. The experimental and scaled simulated Raman and IR spectra were compared and found close agreement. Assignments of important peaks are also presented. Detailed information pertaining to the local and global reactivity and other properties like electrophilic and nucleophilic characteristics were analysed. The hyperactive pressure was measured in terms of polarizability and corresponding biological properties were validated to identity reactive sites. Prediction of Activity Spectral Studies (PASS) predicts the biological activity of the compounds and it is found that the candidate molecules can be used as feruloyl esterase inhibitor, bisphosphoglycerate phosphatase inhibitor and Prolylaminopeptidase inhibitor. The crystals structures of those receptors are taken from the protein data bank and docking studies indicates stable complex with the receptors and candidate molecules. Light harvesting efficiency, followed by photovoltaic modelling shows that DMB is the best compound to be used in the DSSC to get the best output.
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Affiliation(s)
- Y Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - K S Resmi
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Veena S Kumar
- Department of Physics, SN College, Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
| | - B Sureshkumar
- Department of Chemistry, SN College, Kollam, Kerala, India
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Thomas R, Mary YS, Resmi K, Narayana B, Sarojini B, Vijayakumar G, Van Alsenoy C. Two neoteric pyrazole compounds as potential anti-cancer agents: Synthesis, electronic structure, physico-chemical properties and docking analysis. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Synthesis and spectroscopic study of two new pyrazole derivatives with detailed computational evaluation of their reactivity and pharmaceutical potential. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.01.014] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Alcívar León CD, Echeverría GA, Piro OE, Ulic SE, Jios JL, Luna Tapia CA, Mera Guzmán MF. New thiourea and urea derivatives containing trifluoromethyl- and bis-triflouromethyl-4H-chromen-3-yl substituents. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1514132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- C. D. Alcívar León
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, Quito, Ecuador
| | - G. A. Echeverría
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata e IFLP (CONICET, CCT-La Plata), La Plata, Argentina
| | - O. E. Piro
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de La Plata e IFLP (CONICET, CCT-La Plata), La Plata, Argentina
| | - S. E. Ulic
- CEQUINOR (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, República Argentina
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Buenos Aires, República Argentina
| | - J. L. Jios
- UNIDAD PLAPIMU-LASEISIC (UNLP-CIC), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - C. A. Luna Tapia
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, Quito, Ecuador
| | - M. F. Mera Guzmán
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, Quito, Ecuador
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Hosna S, Janzen DE, Mary YS, Resmi KS, Thomas R, Mohamed R, Wajda S. Molecular structure, spectroscopic, dielectric and thermal study, nonlinear optical properties, natural bond orbital, HOMO-LUMO and molecular docking analysis of (C 6Cl 2O 4) (C 10H 14N 2F) 2·2H 2O. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 204:328-339. [PMID: 29957411 DOI: 10.1016/j.saa.2018.06.062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/22/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
A new chloranilate compound with 1-(2-fluorophenyl)piperazine has been synthesized and characterized using spectroscopic methods and X-ray diffraction. The atomic arrangement can be described by an H-bonded 3D network, formed by anionic entities, organic cations and H2O molecules linked together via NH…O, OH…Cl, CH…Cl and CH…O hydrogen bonds. The vibrational absorption bands of the various characteristic groups of this compound have been identified by infrared spectroscopy. Moreover, the thermal and dielectric analyses have shown that the title compound has a phase transition at 393 K. The surface mapped over the dnorm property, highlights the A⋯H (AO, C, Cl and F) as the main intermolecular contacts. On the other hand, the geometry, intermolecular bonds and harmonic vibrational frequencies of the title molecule have been investigated using the B3LYP/6-31G (d, p) method. The stability of the structure obtained, as well as the charge transfer within the molecule, have been confirmed by determining the energies of the HOMO and LUMO levels and the theoretical gap energy. Molecular docking studies of the title compound have also been conducted as part of this study.
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Affiliation(s)
- Saadouni Hosna
- Laboratory of Chemical Materials, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, Tunisia
| | - Daron E Janzen
- Department of Chemistry and Biochemistry, St Catherine University, St Paul, MN, USA
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - K S Resmi
- Department of Physics, Fatima Mata National College, Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanacherry, Kerala, India
| | - Rzaigui Mohamed
- Laboratory of Chemical Materials, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, Tunisia
| | - Smirani Wajda
- Laboratory of Chemical Materials, Faculty of Sciences of Bizerte, Carthage University, Zarzouna, Tunisia.
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Mushtaque M, Avecilla F, Khan MS, Hafeez ZB, Rezvi MMA, Srivastava A. Synthesis, characterization, cytotoxicity, cell cycle analysis of 3-(4-methoxyphenyl)-1-(pyridin-2-ylmethyl)thiourea and quantum chemical analyses. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.03.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Daud AI, Khairul WM, Wahid KAA. Cyano substituted acetylide-thiourea as d-π-a semiconductor material for CO2 sensing. AIP CONFERENCE PROCEEDINGS 2017. [DOI: 10.1063/1.5002324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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