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Chemek M, Rhouma FIH, Chemek M, Safi Z, Kadi A, Naili S, Wazzan N, Kamel A. Impact of the chemical insertion of the dimethylamino group on the electronic and optical properties of the 4-(methoxyphenyl acetonitrile) monomer (MPA): a DFT theoretical investigation. J Mol Model 2024; 30:271. [PMID: 39017741 DOI: 10.1007/s00894-024-06062-4] [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: 04/28/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
CONTEXT Density functional theory (DFT) calculations on the ground and the first excited state are performed on the modified and unmodified 4-(methoxyphenyl acetonitrile) monomer (referred to as MPA). The modified monomer named MFA is obtained by Knoevenagel condensation of MPA with dimethylformamide dimethyl acetal (DMF-DMA). DFT computations show that the chemical grafting of the dimethylamino group onto the MPA unit induces a great change in the geometric, electronic, and optical properties. Going from MPA to MFA monomer, a great change in the frontier orbitals of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) in the ground and the first excited state is observed. Consequently, a reduction in the energy gap HOMO-LUMO and an enhancement in the absorption and emission properties are observed under the chemical modification. The observed modifications in the electronics and optical properties are the result of the charge transfer appearing between the cyano (C≡N) acceptor group and the dimethylamino (DMF-DMA)-grafted group donor ring. METHODS Quantum chemical calculations were performed in the ground and the first excited state using the density functional theory (DFT), and it extends the time-dependent density functional theory (TD-DFT), implemented in the Gaussian 09 software package. The ground state is obtained by optimization of the studied molecular geometries by employing the DFT/M062X/6-31G(d,p) level of theory. The first excited state is obtained by re-optimization of the ground state geometries using the TD-DFT/M062X/6-31G(d,p) level of theory. The contour plots of the frontier orbitals and the molecular electrostatic potential (MEP) maps are obtained from the ground and the first excited state, optimized geometries, and drawn using Gaussview software.
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Affiliation(s)
- Mourad Chemek
- Laboratoire de Recherche: Synthèse asymétrique et ingénierie moléculaire de matériaux organiques pour l'électronique organique (LR18ES19), Faculté des Sciences de Monastir, 5000, Monastir, Tunisia.
- Institut Supérieur des Sciences Appliquées et de Technologie de Sousse (ISSAT-Sousse), Université de Sousse-Tunisie, Sousse, Tunisia.
| | - F I H Rhouma
- Laboratory of Nanomaterials and Renewable Energy Systems, Research and Technology Center of Energy, Borj-Cedria Science and Technology Park, BP 95, 2050, Hammam-Lif, Tunisia
| | - Marouane Chemek
- Department of Food and Biotechnology, South Ural State University, Chelyabinsk, 454080, Russia
| | - Zaki Safi
- Chemistry Department, Faculty of Science, Al Azhar University-Gaza, P.O Box 1277, Gaza, Palestine
| | - Ammar Kadi
- Department of Food and Biotechnology, South Ural State University, Chelyabinsk, 454080, Russia
| | - Salem Naili
- Department of Physics, College of Science, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Nuha Wazzan
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O Box 42805, Jeddah, 21589, Saudi Arabia
| | - Alimi Kamel
- Laboratoire de Recherche: Synthèse asymétrique et ingénierie moléculaire de matériaux organiques pour l'électronique organique (LR18ES19), Faculté des Sciences de Monastir, 5000, Monastir, Tunisia
- Institut National de Recherche et d'Analyse Physico-chimique, Biotechpôle Sidi Thabet, Ariana, 2020, Tunisia
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Gupta S, Saha M, Singh R, Ahmed SB, Asati V. Multistage in silico approach to identify novel quinoline derivatives as potential c-kit kinase inhibitors. J Biomol Struct Dyn 2024:1-18. [PMID: 38287494 DOI: 10.1080/07391102.2024.2308759] [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: 08/11/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024]
Abstract
The type II-C-KIT signaling network has been extensively studied for its potential as a target for cancer treatment, leading to the investigation of quinoline derivatives as compounds with inhibitory effects on c-Kit kinase. In this study, a multistage approach was employed, including the creation of pharmacophore models, 3D QSAR analysis, virtual screening, docking investigations, and molecular dynamics stimulation. The pharmacophore evaluation included a data set of 29 ligands, which resulted in the generation of the ADDHR_1pharmacophore model as the most promising, with a survival score of 5.6812. The main objective was to utilize the atom-based 3D-QSAR approach for generating robust 3D-QSAR models aimed at identifying new TypeII-C-kit kinase inhibitors. The evaluations of these models have convincingly demonstrated their high predictive power (Q2 = 0.6547, R2 = 0.9947). Using atom-based 3D-QSAR data, a total of 7564 novel compounds were generated from R-group enumeration. Molecular docking and MM-GBSA study revealed that compound A1 exhibited the highest binding score of -9.30 kcal/mol and a Δ GBind value of -90.56 kcal/mol. The ZINC compounds were then screened using the pharmacophore model, followed by virtual screening, which identified ZINC65798256, ZINC09317958, ZINC73187176, and ZINC76176670 as potential candidates with promising docking scores. Among these, ZINC65798256 demonstrated the best binding interactions with amino acid residues, ASP810, LYS623, CYS673, and THR670 (PDB ID: 1T46). To further analyze the structural features and molecular interactions, molecular dynamics simulation was conducted for a time scale of 100 ns.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shankar Gupta
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Moumita Saha
- Department of Pharmaceutical Analysis, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Samia Ben Ahmed
- Department of Chemistry, College of Sciences, King Khalid University, Abha, Saudi Arabia
| | - Vivek Asati
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
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Kandhasamy K, Surajambika RR, Velayudham PK. Pyrazolo - Pyrimidines as Targeted Anticancer Scaffolds - A Comprehensive Review. Med Chem 2024; 20:293-310. [PMID: 37885114 DOI: 10.2174/0115734064251256231018104623] [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: 03/06/2023] [Revised: 09/08/2023] [Accepted: 09/15/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND Globally, cancer is the leading cause of death, which causes 10 million deaths yearly. Clinically, several drugs are used in treatment but due to drug resistance and multidrug resistance, there occurs a failure in the cancer treatment. OBJECTIVES The present review article is a comprehensive review of pyrazole and pyrimidine hybrids as potential anticancer agents. METHODS The review comprises more than 60 research works done in this field. The efficiency of the reported pyrazolopyrimidine fused heterocyclic with their biological data and the influence of the structural aspects of the molecule have been discussed. RESULTS This review highlighted pyrazolo-pyrimidines as targeted anticancer agents with effect on multiple targets. CONCLUSION The review will be helpful for the researchers involved in targeted drugs for cancer therapy for designing new scaffolds with pyrazolo-pyrimidine moieties.
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Affiliation(s)
- Kesavamoorthy Kandhasamy
- Department of Pharmaceutical Chemistry, C.L. Baid Metha College of Pharmacy, Chennai- 600 097, India
| | | | - Pradeep Kumar Velayudham
- Department of Pharmaceutical Chemistry, C.L. Baid Metha College of Pharmacy, Chennai- 600 097, India
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Desai NC, Khasiya AG, Jadeja DJ, Monapara JD, Jethawa AM, Dave BP, Sivan SK, Manga V, Mhaske PC, Chaudhary DR. Synthesis, Antifungal Ergosterol Inhibition, Antibiofilm Activities, and Molecular Docking on β-Tubulin and Sterol 14-Alpha Demethylase along with DFT-Based Quantum Mechanical Calculation of Pyrazole Containing Fused Pyridine-Pyrimidine Derivatives. ACS OMEGA 2023; 8:37781-37797. [PMID: 37867649 PMCID: PMC10586022 DOI: 10.1021/acsomega.3c01722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 10/24/2023]
Abstract
Multidrug-resistant fungal infections have become much more common in recent years, especially in immune-compromised patients. Therefore, researchers and pharmaceutical professionals have focused on the development of novel antifungal agents that can tackle the problem of resistance. In continuation to this, a novel series of pyrazole-bearing pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione derivatives (4a-4o) have been developed. These compounds have been screened against Candida albicans, Aspergillus niger, and Aspergillus clavatus. The synthesized compounds were characterized by well-known spectroscopic techniques, i.e., IR, 1H NMR, 13C NMR, and mass spectrometry. In vitro antifungal results revealed that compound 4n showed activity against C. albicans having MIC value of 200 μg/mL. To know the plausible mode of action, the active derivatives were screened for anti-biofilm and ergosterol biosynthesis inhibition activities. The compounds 4h, 4j, 4k, and 4n showed greater ergosterol biosynthesis inhibition than the control DMSO. To comprehend how molecules interact with the receptor, studies of molecular docking of 4k and 4n have been performed on the homology-modeled protein of β-tubulin. The molecular docking revealed that the active compounds 4h, 4j, 4k, 4l, and 4n interacting with the active site amino acid of sterol 14-alpha demethylase (PDB ID: 5v5z) indicate one of the possible modes of action of ergosterol inhibition activity. The synthesized compounds 4c, 4e, 4h, 4i, 4j, 4k, 4l, and 4n inhibited biofilm formation and possessed the potential for anti-biofilm activity. DFT-based quantum mechanical calculations were carried out to optimize, predict, and compare the vibration modes of the molecule 4a.
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Affiliation(s)
- Nisheeth C. Desai
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Ashvinkumar G. Khasiya
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Dharmpalsinh J. Jadeja
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Jahnvi D. Monapara
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Aratiba M. Jethawa
- Division
of Medicinal Chemistry, Department of Chemistry, Mahatma Gandhi Campus, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat 364002, India
| | - Bharti P. Dave
- School
of Science, Indrashil University, Rajpur, Gujarat 382 740, India
| | - Sree Kanth Sivan
- Department
of Chemistry, University College for Women,
Osmania University, Koti, 500095 Hyderabad, India
| | - Vijjulatha Manga
- Department
of Chemistry, University College for Women,
Osmania University, Koti, 500095 Hyderabad, India
| | - Pravin C. Mhaske
- Post-Graduate
Department of Chemistry, S. P. Mandali’s
Sir Parashurambhau College, Tilak Road, Pune 411030, Maharashtra, India
| | - Doongar R. Chaudhary
- CSIR-Central
Salt and Marine Chemicals Research Institute, Bhavnagar 364002, Gujarat, India
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R S, Mahalakshmi S, Kumaran S, Kadaikunnan S, Abbas G, Muthu S. Structural, electronic, intermolecular interaction, reactivity, vibrational spectroscopy, charge transfer, Hirshfeld surface analysis, pharmacological and hydropathy plot on 5-Bromo nicotinic acid - Antiviral study (Hepatitis A, B, and C). Heliyon 2023; 9:e19965. [PMID: 37809934 PMCID: PMC10559560 DOI: 10.1016/j.heliyon.2023.e19965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
The therapeutic properties of 5-Bromonicotinatic acid (5BNA) were studied for antiviral illnesses like Hepatitis A, Hepatitis B and Hepatitis C and the influence of electron-donating and electron-withdrawing properties of functional groups on the nicotinic acid was evaluated and represented in this study using the DFT approach. The molecular parameters were determined for both gases as well as for various solvent phases. The reactive areas in the compound are examined utilising Fukui analysis. The molecular interactions are accomplished by recognising the different types of bonding found in the compound using the AIM, ELF, LOL, RDG and IRI. Solvation investigations were demonstrated to have an influence on molecular orbital energy, ESP, UV-Vis and NLO analyses. Electron-hole, NBO and Hirshfeld investigations are used to investigate the transfer of charges and interactions inside the molecule. The method of vibrational spectroscopy (IR and Raman) is used to differentiate and identify the various types of vibrations displayed by the compound. The hydropathy plots for the proteins 2A4O, 6CWD and 2OC8 associated with Hepatitis A, Hepatitis B and Hepatitis C illustrate the disquiet and attraction of the amino acids towards the water.
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Affiliation(s)
- Sravanthi R
- Department of Physics, Ethiraj College for Women, Chennai, 600008, Tamil Nadu, India
- University of Madras, Chennai, 600005, Tamil Nadu, India
| | - S. Mahalakshmi
- Department of Physics, Ethiraj College for Women, Chennai, 600008, Tamil Nadu, India
| | - S. Kumaran
- Department of ECE, Saveetha Engineering College, Thandalam, Chennai, 602105, Tamil Nadu, India
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ghulam Abbas
- Institute of Inorganic Chemistry, Karlsruhe Institute of Technology, Engesserstr 15, 76131, Karlsruhe, Germany
| | - S. Muthu
- Department of Physics, Arignar Anna Govt. Arts College, Cheyyar, 604407, Tamil Nadu, India
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6
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Selvakumari S, Irfan A, Muthu S. Solvent –solute interactions, electronic properties, topological and biological explorations of 6-Bromo-7-methylimidazo[1,2-a]pyridine. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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7
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Bhaskaran RP, Sreelekha MK, Babu BP. Metal‐free Synthesis of Trisubstituted Pyrazoles by the Reaction Between Hydrazones and Activated Olefins. ChemistrySelect 2022. [DOI: 10.1002/slct.202202773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Rasmi P. Bhaskaran
- Department of Chemistry National Institute of Technology Karnataka Surathkal Mangalore INDIA – 575025
| | - Mariswamy K. Sreelekha
- Department of Chemistry National Institute of Technology Karnataka Surathkal Mangalore INDIA – 575025
| | - Beneesh P. Babu
- Department of Chemistry National Institute of Technology Karnataka Surathkal Mangalore INDIA – 575025
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8
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Cherian Parakkal S, Datta R, Saral A, Muthu S, Irfan A, Jeelani A. Solvent polarity, Structural and Electronic Properties with Different Solvents and Biological Studies of 3,3,5-triphenylfuran-2(3H)-one- Cancers of the blood cells. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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9
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Dutta D, Sharma P, Gomila RM, Frontera A, Barcelo-Oliver M, Verma AK, Baishya T, Bhattacharyya MK. Supramolecular assemblies involving unconventional non-covalent contacts in pyrazole-based coordination compounds of Co(II) and Cu(II) pyridinedicarboxylates: Antiproliferative evaluation and theoretical studies. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116025] [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]
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10
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Parakkal SC, Datta R, Muthu S, Irfan A, Jeelani A. Computational investigation into structural, topological, electronic properties, and biological evaluation of spiro[1H-indole-3,2′-3H-1,3-benzothiazole]-2-one. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119234] [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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Aarthi K, Rajagopal H, Muthu S, Narayana B, Basha Asif F, Irfan A, Javed S. Experimental spectra, electronic energies (liquid and gaseous phases) quantum computational strategies and potential biological activity studies of (1E, 4E)-1, 5-bis (4-methoxyphenyl) penta-1,4-dien-3-one: An antiviral agent. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119012] [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]
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12
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Sangeetha P, Sangeetha R, Mullainathan S, Irfan A, Sevvanthi S, Muthu S. Molecular docking evaluation and spectroscopic study of 2-amino-1,4-benzenedisulfonic acid using the IEFPCM model, electronic properties of different solvents. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100543] [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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13
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Structural and Vibrational Investigation of Benzil-(1,2-Diphenylethane-1,2-Dione): Experimental and Theoretical Studies. J CHEM-NY 2022. [DOI: 10.1155/2022/5968496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Single crystals of benzil commonly known as 1,2-diphenylethane-1,2-dione are grown by the slow evaporation method at room temperature. Gaussian 09 program is applied for theoretical calculations with B3LYP/6-311++G(d,p) basis set. The structure is optimized, and the energy, structural parameters, vibrational frequencies, IR, and Raman intensities are determined. Complete natural bonding orbital (NBO) analysis is carried out to analyze the intramolecular electronic interactions and their stabilization energies. From the second-order perturbation theory analysis of the benzil molecule, it is observed that there exists a hyperconjugative intramolecular stabilization energy between 17.45 and 22.76 KJmol-1. HOMO-LUMO analysis has been performed to identify the charges transferred within the molecule. The energy gap is calculated to be 2.919 eV and thus establishes the soft nature of the molecule. The molecular electrostatic potential (MEP) of the grown crystal was analyzed using the B3LYP method with 6-311++G(d,p) basis set. First-order hyperpolarizability calculations reveal the nonlinear optical microscopic behavior of the benzil molecule with nonzero values. The total value of the first-order hyperpolarizability (
) is of the order of
, which is found to be 11.135 times that of urea. Hence, benzil can be referred to as a good material for nonlinear optical applications.
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Pooventhiran T, Gangadharappa BS, Abu Ali OA, Thomas R, Saleh DI. Study of the structural features and solvent effects using ab initio molecular dynamics and energy decomposition analysis of atogepant in water and ammonia. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118672] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Al-Otaibi JS, Sheena Mary Y, Shyma Mary Y, Thomas R. Electronic Structure, Solvation Effects and Wave Function Based Properties of a New Triazole Based Symmetric Chromene Derivative of Apigenin. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2055583] [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)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Renjith Thomas
- Deparment of Chemistry, St Berchmans College, (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
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Pham EC, Thi TVL, Phan LT, Nguyen HGT, Le KN, Truong TN. Design, synthesis, antimicrobial evaluations and in silico studies of novel pyrazol-5(4H)-one and 1H-pyrazol-5-ol derivatives. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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17
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Electronic properties (in different solvents), spectroscopic progression and evaluation on 4-morpholinepropane sulfonic acid along with molecular docking analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Wahan SK, Chawla PA. Recent advances of heterocycle based anticancer hybrids. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cancer is one of the major causes of death across the world. Cancer is a broad word that encompasses a wide range of illnesses that can affect any part of the body. Cancer research has increased understanding of molecular biology and cellular biology, resulting in new cancer therapies. Despite of adverse effects, surgery, radiation, and anticancer medicines are the modern cancer treatments. Keeping in mind the excellent anticancer activity exhibited by various heterocyclics, various medicines with heterocyclic moiety have been developed to identify particular target regions. The chapter aims to discuss new discoveries in the field of anticancer pharmaceuticals comprising the thiazole, pyrazole, oxazole, and triazole rings over the last five years. The proposed anticancer drugs have a lot of future significance due to their high potency.
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Affiliation(s)
- Simranpreet K. Wahan
- Department of Pharmaceutical Chemistry , ISF College of Pharmacy , Moga , Punjab - 142001 , India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry , ISF College of Pharmacy , Moga , Punjab - 142001 , India
- Department of Pharmaceutical Analysis , ISF College of Pharmacy , Moga - 142001 , India
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Radhika B, Prashanth J, Basavoju S, Jyothi S, Venkatram Reddy B. Synthesis, single-crystal X-ray diffraction, NLO and DFT studies of centrosymmetric 4-amino-3,5-dimethyl-1H-pyrazolium citrate monohydrate salt. Mol Phys 2022. [DOI: 10.1080/00268976.2021.2022797] [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)
- B. Radhika
- Department of Chemistry, Kakatiya University, Warangal, India
| | - J. Prashanth
- Department of Physics, Kakatiya University, Warangal, India
| | - Srinivas Basavoju
- Department of Chemistry, National Institute of Technology, Warangal, India
| | - S. Jyothi
- Department of Chemistry, Kakatiya University, Warangal, India
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Surendar P, Pooventhiran T, Rajam S, Irfan A, Thomas R. Schiff Bases from α-ionone with Adenine, Cytosine, and l-leucine Biomolecules: Synthesis, Structural Features, Electronic Structure, and Medicinal Activities. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416522500016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tea is a very important source of the terepenoid [Formula: see text]-ionone, which is much appreciated as a medicinal beverage. Schiff bases are a very important class of organic compounds usually formed by the condensation of carbonyl compounds with amines. [Formula: see text]-ionone is a carbonyl terpenoid obtained from Schiff bases on condensation with nucleobases like adenine and cytosine and the amino acid [Formula: see text]-leucine. We synthesized these three Schiff bases and characterized them using UV, FTIR, and H1 and C13-NMR spectra. The molecules were optimized using B3LYP/6-311+G(2d,p) level followed by the simulation of FT-IR spectra, of which the simulated and experimental spectra showed complete agreement. The UV spectra were simulated using TD-DFT, and the electronic excitations were carefully analyzed. Natural bond orbitals provided an analysis of the stability of the compound, which is supplemented by the data from frontier molecular orbital analysis. Detailed wavefunction analysis is reported which predicts the active centers, reactivity profile, and the extent of non-covalent interactions. PASS indicated that compounds show antieczemic properties and antiarthritic properties, which is confirmed with the help of molecular docking results.
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Affiliation(s)
- P. Surendar
- Department of Chemistry, Bishop Heber’s College (Autonomous), Tiruchirappalli 600017, Tamil Nadu, India
- UPASI Tea Research Institute Nirardam (BPO), Valparai 642127, Tamil Nadu, India
| | - T. Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Mahatma Gandhi University, Changanaserry 686101, Kerala, India
| | - Shameela Rajam
- Department of Chemistry, Bishop Heber’s College (Autonomous), Tiruchirappalli 600017, Tamil Nadu, India
| | - Ahmad Irfan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P. O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P. O. Box 9004, Abha 61413, Saudi Arabia
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Mahatma Gandhi University, Changanaserry 686101, Kerala, India
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Electronic properties of solvents (Water, Benzene, Ethanol) using IEFPCM model, spectroscopic exploration with drug likeness and assessment of molecular docking on 1-Octanesulfonic Acid Sodium Salt. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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22
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Elangovan N, Sowrirajan S, Manoj K, Kumar AM. Synthesis, structural investigation, computational study, antimicrobial activity and molecular docking studies of novel synthesized (E)-4-((pyridine-4-ylmethylene)amino)-N-(pyrimidin-2-yl)benzenesulfonamide from pyridine-4-carboxaldehyde and sulfadiazine. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130544] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Pooventhiran T, Marondedze EF, Govender PP, Bhattacharyya U, Rao DJ, Aazam ES, Kuthanapillil JM, E TJ, Thomas R. Energy and reactivity profile and proton affinity analysis of rimegepant with special reference to its potential activity against SARS-CoV-2 virus proteins using molecular dynamics. J Mol Model 2021; 27:276. [PMID: 34480634 PMCID: PMC8416574 DOI: 10.1007/s00894-021-04885-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/18/2021] [Indexed: 12/23/2022]
Abstract
Rimegepant is a new medicine developed for the management of chronic headache due to migraine. This manuscript is an attempt to study the various structural, physical, and chemical properties of the molecules. The molecule was optimized using B3LYP functional with 6-311G + (2d,p) basis set. Excited state properties of the compound were studied using CAM-B3LYP functional with same basis sets using IEFPCM model in methanol for the implicit solvent atmosphere. The various electronic descriptors helped to identify the reactivity behavior and stability. The compound is found to possess good nonlinear optical properties in the gas phase. The various intramolecular electronic delocalizations and non-covalent interactions were analyzed and explained. As the compound contain several heterocyclic nitrogen atoms, they have potential proton abstraction features, which was analyzed energetically. The most important result from this study is from the molecular docking analysis which indicates that rimegepant binds irreversibly with three established SARS-CoV-2 proteins with ID 6LU7, 6M03, and 6W63 with docking scores − 9.2988, − 8.3629, and − 9.5421 kcal/mol respectively. Further assessment of docked complexes with molecular dynamics simulations revealed that hydrophobic interactions, water bridges, and π–π interactions play a significant role in stabilizing the ligand within the binding region of respective proteins. MMGBSA-free energies further demonstrated that rimegepant is more stable when complexed with 6LU7 among the selected PDB models. As the pharmacology and pharmacokinetics of this molecule are already established, rimegepant can be considered as an ideal candidate with potential for use in the treatment of COVID patients after clinical studies.
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Affiliation(s)
- T Pooventhiran
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - Ephraim Felix Marondedze
- Department of Chemical Sciences, Doornfontein Campus, University of Johannesburg, P. O. Box 17011, Johannesburg, 2028, South Africa
| | - Penny Poomani Govender
- Department of Chemical Sciences, Doornfontein Campus, University of Johannesburg, P. O. Box 17011, Johannesburg, 2028, South Africa
| | - Utsab Bhattacharyya
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - D Jagadeeswara Rao
- Department of Physics, Dr. Lankapalli Bullayya College, Visakhapatnam, Andhra Pradesh, India
| | - Elham S Aazam
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 23622, Saudi Arabia
| | - Jinesh M Kuthanapillil
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - Tomlal Jose E
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Mahatma Gandhi University, Changanassery, Kerala, India.
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Raajaraman BR, Sheela NR, Muthu S. Spectroscopic, quantum computational, molecular docking and biological parameters of 4-phenylbutyrophenone: a neuroleptic agent. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01617-8] [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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25
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Al-Otaibi JS, Albrycht P, Mary YS, Mary YS, Księżopolska-Gocalska M. Concentration-dependent SERS profile of olanzapine on silver and silver-gold metallic substrates. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01783-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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26
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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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27
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Surendar P, Pooventhiran T, Rajam S, Bhattacharyya U, Bakht MA, Thomas R. Quasi liquid Schiff bases from trans-2-hexenal and cytosine and l-leucine with potential antieczematic and antiarthritic activities: Synthesis, structure and quantum mechanical studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116448] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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28
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Pooventhiran T, Cheriet M, Bhattacharyya U, Irfan A, Puchta R, Sowrirajan S, Thomas R. Detailed Structural Examination, Quantum Mechanical Studies of the Aromatic Compound Solarimfetol and Formation of Inclusion Compound with Cucurbituril. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1937238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- T. Pooventhiran
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Mouna Cheriet
- Unité de Recherche sur les Plantes Médicinales (URPM.3000, Laghouat) Rattachée au Centre de Recherche en Biotechnologie CRBt 2500, Constantine, Algeria
| | - Utsab Bhattacharyya
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Ahmad Irfan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Ralph Puchta
- Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
- Computer Chemistry Center, Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, Erlangen, Germany
- Central Institute for Scientific Computing (ZISC), University of Erlangen-Nuremberg, Erlangen, Germany
- Fakultät Angewandte Mathematik, Physik und Allgemeinwissenschaften, Technische Hochschule Nürnberg Georg Simon Ohm, Nürnberg, Germany
| | - S. Sowrirajan
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Kingdom of Saudi Arabia
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
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Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, molecular docking and SERS (concentration and solvent dependant) investigations of a methylisoxazole derivative with potential antimicrobial activity. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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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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31
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Concentration and solvent dependent SERS, DFT, MD simulations and molecular docking studies of a thioxothiazolidine derivative with antimicrobial properties. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115582] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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32
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Fazilath Basha A, Liakath Ali Khan F, Muthu S, Raja M. Computational evaluation on molecular structure (Monomer, Dimer), RDG, ELF, electronic (HOMO-LUMO, MEP) properties, and spectroscopic profiling of 8-Quinolinesulfonamide with molecular docking studies. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113169] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Sehout I, Boulebd H, Boulcina R, Nemouchi S, Bendjeddou L, Bramki A, Merazig H, Debache A. Synthesis, crystal structure, Hirshfeld surface analysis, biological evaluation, DFT calculations, and in silico ADME analysis of 4-arylidene pyrazolone derivatives as promising antibacterial agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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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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35
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Sheena Mary Y, Shyma Mary Y, Krátký M, Vinsova J, Baraldi C, Gamberini MC. DFT, SERS-concentration and solvent dependent and docking studies of a bioactive benzenesulfonamide derivative. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129680] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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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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37
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Alharthi FA, Al-Zaqri N, Alsalme A, Al-Taleb A, Pooventhiran T, Thomas R, Rao DJ. Excited-state electronic properties, structural studies, noncovalent interactions, and inhibition of the novel severe acute respiratory syndrome coronavirus 2 proteins in Ripretinib by first-principle simulations. J Mol Liq 2021; 324:115134. [PMID: 33390634 PMCID: PMC7765765 DOI: 10.1016/j.molliq.2020.115134] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/02/2022]
Abstract
Ripretinib is a recently developed drug for the treatment of adults with advanced gastrointestinal stromal tumors. This paper reports an attempt to study this molecule by electronic modeling and molecular mechanics to determine its composition and other specific chemical features via the density-functional theory (DFT), thereby affording sufficient information on the electronic properties and descriptors that can enable the estimation of its molecular bioactivity. We explored most of the physico-chemical properties of the molecule, as well as its stabilization, via the studies of the natural bond orbitals and noncovalent interactions. The electronic excitation, which is a time-dependent process, was examined by the time-dependent DFT with a CAM-B3LYP functional. The molecular docking study indicated that Ripretinib strongly docks with three known novel severe acute respiratory syndrome coronavirus 2 (SARS-n-CoV-2) proteins with a reasonably good docking score.
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Affiliation(s)
- Fahad A Alharthi
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Afnan Al-Taleb
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - D Jagadeeswara Rao
- Department of Physics, Dr. Lankapalli Bullayya College, Visakhapatnam, Andhra Pradesh, India
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38
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Mary YS, Mary YS. DFT Analysis and Molecular Docking Studies of the Cocrystals of Sulfathiazole-Theophylline and Sulfathiazole-Sulfanilamide. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1873809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Structural, physico-chemical landscapes, ground state and excited state properties in different solvent atmosphere of Avapritinib and its ultrasensitive detection using SERS/GERS on self-assembly formation with graphene quantum dots. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114555] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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40
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Ahmed MF, Santali EY, El-Haggar R. Novel piperazine-chalcone hybrids and related pyrazoline analogues targeting VEGFR-2 kinase; design, synthesis, molecular docking studies, and anticancer evaluation. J Enzyme Inhib Med Chem 2020; 36:307-318. [PMID: 33349069 PMCID: PMC7758046 DOI: 10.1080/14756366.2020.1861606] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
New piperazine–chalcone hybrids and related pyrazoline derivatives have been designed and synthesised as potential vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors. The National Cancer Institute (NCI) has selected six compounds to evaluate their antiproliferative activity in vitro against 60 human cancer cells lines. Preliminary screening of the examined compounds indicated promising anticancer activity against number of cell lines. The enzyme inhibitory activity against VEGFR-2 was evaluated and IC50 of the tested compounds ranged from 0.57 µM to 1.48 µM. The most potent derivatives Vd and Ve were subjected to further investigations. A cell cycle analysis showed that both compounds mainly arrest HCT-116 cell cycle in the G2/M phase. Annexin V-FITC apoptosis assay showed that Vd and Ve induced an approximately 18.7-fold and 21.2-fold total increase in apoptosis compared to the control. Additionally, molecular docking study was performed against VEGFR (PDB ID: 4ASD) using MOE 2015.10 software and Sorafenib as a reference ligand.
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Affiliation(s)
- Marwa F Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Taif University, Taif, Kingdom of Saudi Arabia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Eman Y Santali
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Taif University, Taif, Kingdom of Saudi Arabia
| | - Radwan El-Haggar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Helwan University, Cairo, Egypt
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Al-Zaqri N, Pooventhiran T, Alharthi FA, Bhattacharyya U, Thomas R. Structural investigations, quantum mechanical studies on proton and metal affinity and biological activity predictions of selpercatinib. J Mol Liq 2020; 325:114765. [PMID: 33746318 PMCID: PMC7957184 DOI: 10.1016/j.molliq.2020.114765] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Cancer of the lungs and thyroid is particularly difficult to manage and treat. Notably, selpercatinib has recently been suggested as an effective drug to combat these diseases. The entire world is currently tackling the pandemic caused by the SARS-CoV-19 virus. Numerous pharmaceuticals have been evaluated for the management of the disease caused by SARS-CoV-19 (i.e., COVID-19). In this study, selpercatinib was proposed as a potential inhibitor of different SARS-CoV-19 proteins. Several intriguing effects of the molecule were found during the conducted computational investigations. Selpercatinib could effectively act as a proton sponge and exhibited high proton affinity in solution. Moreover, it was able to form complexes with metal ions in aqueous solutions. Specifically, the compound displayed high affinity towards zinc ions, which are important for the prevention of virus multiplication inside human cells. However, due to their charge, zinc ions are not able to pass the lipid bilayer and enter the cell. Thus, it was determined that selpercatinib could act as an ionophore, effectively transporting active zinc ions into cells. Furthermore, various quantum mechanical analyses, including energy studies, evaluation of the reactivity parameters, examination of the electron localisation and delocalisation properties, as well as assessment of the nonlinear optical (NLO) properties and information entropy, were conducted herein. The performed docking studies (docking scores -9.3169, -9.1002, -8.1853 and -8.1222 kcal mol-1) demonstrated that selpercatinib strongly bound with four isolated SARS-CoV-2 proteins.
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Chemistry, College of Science, Ibb University, P. O. Box 70270, Ibb, Yemen
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Fahad A Alharthi
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Utsab Bhattacharyya
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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Akhtar W, Marella A, Alam MM, Khan MF, Akhtar M, Anwer T, Khan F, Naematullah M, Azam F, Rizvi MA, Shaquiquzzaman M. Design and synthesis of pyrazole-pyrazoline hybrids as cancer-associated selective COX-2 inhibitors. Arch Pharm (Weinheim) 2020; 354:e2000116. [PMID: 33015829 DOI: 10.1002/ardp.202000116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/22/2020] [Accepted: 09/11/2020] [Indexed: 12/25/2022]
Abstract
In continuation of our previous work on cancer and inflammation, 15 novel pyrazole-pyrazoline hybrids (WSPP1-15) were synthesized and fully characterized. The formation of the pyrazoline ring was confirmed by the appearance of three doublets of doublets in 1 H nuclear magnetic resonance spectra exhibiting an AMX pattern for three protons (HA , HM , and HX ) of the pyrazoline ring. All the synthesized compounds were screened for their in vitro anticancer activity against five cell lines, that is, MCF-7, A549, SiHa, COLO205, and HepG2 cells, using the MTT growth inhibition assay. 5-Fluorouracil was taken as the positive control in the study. It was observed that, among them, WSPP11 was found to be active against A549, SiHa, COLO205, and HepG2 cells, with IC50 values of 4.94, 4.54, 4.86, and 2.09 µM. All the derivatives were also evaluated for their cytotoxicity against HaCaT cells. WSPP11 was also found to be nontoxic against normal cells (cell line HaCaT), with an IC50 value of more than 50 µM. The derivatives were also evaluated for their in vitro anti-inflammatory activity by the protein (egg albumin) denaturation assay and the red blood cell membrane stabilizing assay, using diclofenac sodium and celecoxib as standard. Compounds that showed significant anticancer and anti-inflammatory activities were further studied for COX-2 inhibition. The manifestation of a higher COX-2 selectivity index of WSPP11 as compared with other derivatives and an in vitro anticancer activity against four cell lines further established that compounds that were more selective toward COX-2 also exhibited a better spectrum of activity against various cancer cell lines.
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Affiliation(s)
- Wasim Akhtar
- Drug Design and Medicinal Chemistry Laboratory, Jamia Hamdard, New Delhi, India
| | - Akranth Marella
- Fryer Global Regulatory Solutions and Services, Hyderabad, Telangana, India
| | | | - Mohemmed F Khan
- Drug Design and Medicinal Chemistry Laboratory, Jamia Hamdard, New Delhi, India
| | - Mymoona Akhtar
- Drug Design and Medicinal Chemistry Laboratory, Jamia Hamdard, New Delhi, India
| | - Tariq Anwer
- Department of Pharmacology, College of Pharmacy, Jazan University, Gizan, Saudi Arabia
| | - Farah Khan
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Md Naematullah
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Faizul Azam
- Department of Pharmaceutical Chemistry & Pharmacognosy, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
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43
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DFT and molecular docking studies of self-assembly of sulfone analogues and graphene. J Mol Model 2020; 26:273. [DOI: 10.1007/s00894-020-04546-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/14/2020] [Indexed: 01/30/2023]
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44
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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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Al-Zaqri N, Pooventhiran T, Alsalme A, Warad I, John AM, Thomas R. Structural and physico-chemical evaluation of melatonin and its solution-state excited properties, with emphasis on its binding with novel coronavirus proteins. J Mol Liq 2020; 318:114082. [PMID: 32863490 PMCID: PMC7443329 DOI: 10.1016/j.molliq.2020.114082] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Melatonin is a natural hormone from the pineal gland that regulates the sleep-wake cycle. We examined the structure and physico-chemical properties of melatonin using electronic structure methods and molecular-mechanics tools. Density functional theory (DFT) was used to optimise the ground-state geometry of the molecule from frontier molecular orbitals, which were analysed using the B3LYP functional. As its electrons interacted with electromagnetic radiation, electronic excitations between different energy levels were analysed in detail using time-dependent DFT with CAM-B3LYP orbitals. The results provide a wealth of information about melatonin's electronic properties, which will enable the prediction of its bioactivity. Molecular docking studies predict the biological activity of the molecules against the coronavirus2 protein. Excellent docking scores of −7.28, −7.20, and −7.06 kcal/mol indicate that melatonin can help to defend against the viral load in vulnerable populations. Hence it can be investigated as a candidate drug for the management of COVID. Detailed quantum mechanical studies of the sleep regulating hormone melatonin Analysed the intramolecular stabilisation and nonlinear properties Excited state properties using TD-DFT formalism Compound active binds to three known novel coronavirus 2019 proteins.
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Chemistry, College of Science, Ibb University, P.O. Box 70270, Ibb, Yemen
| | - T Pooventhiran
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ismail Warad
- Department of Chemistry, Science College, An-Najah National University, P.O. Box 7, Nablus, Palestine
| | - Athira M John
- Department of Chemistry, CHRIST (Deemed to be University), Bangalore, Karnataka, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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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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Pooventhiran T, Bhattacharyya U, Rao DJ, Chandramohan V, Karunakar P, Irfan A, Mary YS, Thomas R. Detailed spectra, electronic properties, qualitative non-covalent interaction analysis, solvatochromism, docking and molecular dynamics simulations in different solvent atmosphere of cenobamate. Struct Chem 2020. [DOI: 10.1007/s11224-020-01607-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Al-Otaibi JS, Mary YS, Thomas R, Narayana B. Theoretical Studies into the Spectral Characteristics, Biological Activity, and Photovoltaic Cell Efficiency of Four New Polycyclic Aromatic Chalcones. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1747097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Jamelah S. Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
| | - B. Narayana
- Department of Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
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Haruna K, Kumar VS, Armaković SJ, Armaković S, Mary YS, Thomas R, Popoola SA, Almohammedi AR, Roxy MS, Al-Saadi AA. Spectral characterization, thermochemical studies, periodic SAPT calculations and detailed quantum mechanical profiling various physico-chemical properties of 3,4-dichlorodiuron. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117580. [PMID: 31748158 DOI: 10.1016/j.saa.2019.117580] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/16/2019] [Accepted: 09/28/2019] [Indexed: 06/10/2023]
Abstract
A set of experimental and computational techniques have been applied for the understanding of fundamental spectroscopic and reactive properties of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (diuron) compound. Experimental techniques employed in this study encompassed spectroscopic characterization via IR and Raman approaches, while optical properties were studied by measurements of UV/Vis spectra. The thermogravimetric analysis was also studied in order to analyze the stability of diuron. Aside from the determination of reactive properties, DFT calculations on isolated molecules were also used to thoroughly visualize and analyze spectroscopic properties such as IR and UV/Vis. MD simulations were used in order to understand interactions with water, while periodic DFT calculations were used in order to analyze band structure and density of states of the diuron crystal structure. Since the crystal structure of diuron is known, it was used in order to extract the relevant molecular pairs and investigate interactions between them by DFT and symmetry adapted perturbation theory approaches (SAPT).
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Affiliation(s)
- K Haruna
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Veena S Kumar
- Department of Physics, SN College, Kollam, Kerala, India; Research Centre, University of Kerala, Kerala, India
| | - Sanja J Armaković
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000, Novi Sad, Serbia
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000, Novi Sad, Serbia
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, 686101, Kerala, India.
| | - Saheed A Popoola
- Department of Chemistry, Islamic University of Madinah, Saudi Arabia
| | - A R Almohammedi
- Department of Physics, Islamic University of Madinah, Saudi Arabia
| | - M S Roxy
- Department of Physics, SN College, Kollam, Kerala, India
| | - A A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
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Priya YS, Rao KR, Chalapathi P, Veeraiah A, Srikanth KE, Mary YS, Thomas R. Intricate spectroscopic profiling, light harvesting studies and other quantum mechanical properties of 3-phenyl-5-isooxazolone using experimental and computational strategies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127461] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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