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Salih RHH, Hasan AH, Hussen NH, Hawaiz FE, Hadda TB, Jamalis J, Almalki FA, Adeyinka AS, Coetzee LCC, Oyebamiji AK. Thiazole-Pyrazoline Hybrids as Potential Antimicrobial Agent: Synthesis, Biological Evaluation, Molecular Docking, DFT Studies and POM analysis. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
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2
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Experimental and theoretical studies of novel Schiff base based on diammino benzophenone with formyl chromone – BPAMC. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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3
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Latha A, Elangovan N, Manoj K, Keerthi M, Balasubramani K, Sowrirajan S, Chandrasekar S, Thomas R. Synthesis, XRD, spectral, structural, quantum mechanical and anticancer studies of di(p-chlorobenzyl) (dibromo) (1, 10-phenanthroline) tin (IV) complex. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100540] [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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4
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Roy P, Pandey N, Kumari N, Baidya R, Mary YS, Mary YS, Ghosh A. Development of Sulfamethoxazole-Succinimide cocrystal by mechanochemical cocrystallization- an insight into spectroscopic, electronic, chemical conformation and physicochemical properties. Chem Eng Res Des 2022. [DOI: 10.1016/j.cherd.2022.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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5
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Computational Study of Furosemide-Piperazine (FS – PZ) and 2,3,5,6-tetramethylpyrazine (FS-TP) Co-Crystals. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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6
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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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Al-Wahaibi LH, Abdalla M, Mary YS, Mary YS, Costa RA, Rana M, El-Emam AA, Hassan HM, Al-Shaalan NH. Spectroscopic, Solvation Effects and MD Simulation of an Adamantane-Carbohydrazide Derivative, a Potential Antiviral Agent. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2039233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Lamya H. Al-Wahaibi
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, P.R. China
| | | | | | - Renyer Alves Costa
- Department of Chemistry, Federal University of Amazonas (DQ-UFAM), Manaus, Brazil
| | - Meenakshi Rana
- Department of Physics, School of Sciences, Uttarakhand Open University, Haldwani, India
| | - Ali A. El-Emam
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Hanan M. Hassan
- Department of Pharmacology and Biochemistry, Faculty of Pharmacy, Delta University for Science and Technology, International Costal Road, Gamasa City, Mansoura, Egypt
| | - Nora H. Al-Shaalan
- Department of Chemistry, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
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8
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Investigation of the electronic properties of solvents (water, benzene, methanol) using IEFPCM model, spectroscopic investigation with docking and MD simulations of a thiadiazole derivative with anti-tumor activities. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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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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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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11
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Al-Otaibi JS, Mary YS, Mary YS, Yadav R. Structural and reactivity studies of pravadoline –An ionic liquid, with reference to its wavefunction-relative properties using DFT and MD simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Al-Otaibi JS, Sheena Mary Y, Mary YS, Resmi KS. Computational Evaluation of Molecular Structures and Spectroscopic Properties of Tryptamine Derivatives on Its Binding With Novel Corona Virus Proteins. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.2006248] [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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13
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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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Molecular docking, DFT analysis, and dynamics simulation of natural bioactive compounds targeting ACE2 and TMPRSS2 dual binding sites of spike protein of SARS CoV-2. J Mol Liq 2021; 342:116942. [PMID: 34305216 PMCID: PMC8267125 DOI: 10.1016/j.molliq.2021.116942] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/20/2021] [Accepted: 07/05/2021] [Indexed: 12/26/2022]
Abstract
The scientific community is continuously working to discover drug candidates against potential targets of SARS-CoV-2, but effective treatment has not been discovered yet. The virus enters the host cell through molecular interaction with its enzymatic receptors i.e., ACE2 and TMPRSS2, which, if, synergistically blocked can lead to the development of novel drug candidates. In this study, 1503 natural bioactive compounds were screened by HTVS, followed by SP and XP docking using Schrodinger Maestro software. Bio-0357 (protozide) and Bio-597 (chrysin) were selected for dynamics simulation based on synergistic binding affinity on S1 (docking score −9.642 and −8.78 kcal/mol) and S2 domains (-5.83 and −5.3 kcal/mol), and the RMSD, RMSF and Rg analyses showed stable interaction. The DFT analysis showed that the adsorption of protozide/chrysin, the band gap of protozide/chrysin-F/G reduced significantly. From SERS, results, it can be concluded that QDs nanocluster will act as a sensor for the detection of drugs. The docking study showed Bio-0357 and Bio-0597 bind to both S1 and S2 domains through stable molecular interactions, which can lead to the discovery of new drug candidates to prevent the entry of SARS-CoV-2. This in-silico study may be helpful to researchers for further in vitro experimental validation and development of new therapy for COVID-19.
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15
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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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16
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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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Mary YS, Mary YS, Resmi KS, Sarala S, Yadav R, Celik I. Modeling the structural and reactivity properties of hydrazono methyl-4H-chromen-4-one derivatives-wavefunction-dependent properties, molecular docking, and dynamics simulation studies. J Mol Model 2021; 27:186. [PMID: 34036470 DOI: 10.1007/s00894-021-04800-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/17/2021] [Indexed: 11/29/2022]
Abstract
This study explains the vibration and interaction of three pharmaceutically active hydrazine derivatives, (E)-3-((2-(2,5-difluorophenyl)hydrazono)methyl)-4H-chromen-4-one (DFH), (E)-3-((2-(4-(trifluoromethyl)phenyl)hydrazono)methyl)-4H-chromen-4-one (TMH), and (E)-3-((2-(3,5-bis(trifluoromethyl)phenyl)hydrazono)methyl)-4H-chromen-4-one (BPH) using theoretical approach. The trend in chemical reactivity and stability of the studied compounds was observed to show increasing stability and decreasing reactivity and this was obtained from orbital energies. The effect of bromine and chlorine atoms, instead of fluorine atoms, is also noted. Surface analysis on the covalent bond was attained by ELF and LOL analysis. Biological activities were predicted using molecular docking studies. Docking results were analyzed with standard drugs, 5-fluorouracil/piperine. Antitumor activity of hydrazine derivatives was found to be higher than reference ones. Molecular dynamics (MD) simulation was performed for 100 ns to validate the stability behavior of hydrazine derivatives with the dual specificity threonine tyrosine kinase (TTK) protein. RMSD, RMSF, Rg, SASA, and intermolecular analysis of DFH, TMH, and BPH with threonine tyrosine kinase forms stable ligand-protein interactions. The molecular and predictive biological properties of three pharmaceutically active hydrazine derivatives which can be helpful to researchers in future experimental validation through in vitro and in vivo studies.
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Affiliation(s)
- Y Sheena Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India.
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar-64, Kollam, Kerala, India
| | - K S Resmi
- Researcher, Thiruvalluvarpuram Main Street Number 5, Chennai, India
| | - S Sarala
- Department of Physics, Kanchi Shri Krishna College of Arts and Science, Kanchipuram, Tamilnadu, 631551, India
| | - Rohitash Yadav
- Department of Pharmacology, All India Institute of Medical Sciences, Rishikesh, 249203, India
| | - Ismail Celik
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Erciyes University, Kayseri, Turkey
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Al-Otaibi JS, Mary YS, Mary YS, Serdaroglu G. Adsorption of adipic acid in Al/B-N/P nanocages: DFT investigations. J Mol Model 2021; 27:113. [PMID: 33765215 DOI: 10.1007/s00894-021-04742-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Drug delivery clusters based on nanocages recently have been the most capable to study. Adipic acid (ADPA) interaction mechanism over nanocages of X(Al/B)12Y(N/P)12 was investigated. We analyzed various electronic, chemical, and spectroscopic properties with nanocages of the adsorbed ADPA molecule. Adsorption energies were calculated to study the adsorption of ADPA with nanocages. Raman enhanced surface scattering is used to track the drug as an effective approach to vibrational spectroscopy. Detection of the drug has been investigated using the SERS properties of nanocages. Title drug acts as a donor of electrons and adsorbs at the electrophilic site of nanocages. Variations in chemical descriptors to recognize the sensing property of ADPA-nanocages are also noted. Analysis of various properties explains enhancement which makes it possible to detect the drug in other products. • Interaction of adipic acid with fullerene-like metal nanocages • Enhancement of spectral properties • Changes in charge transfer values in nanocage-drug system • Docking studies identify the drug delivery property.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Goncagül Serdaroglu
- Faculty of Education, Math. and Sci. Edu., Sivas Cumhuriyet University, 58140, Sivas, Turkey
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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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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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21
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Biological perspective of a triazine derivative with isatin/chalcone/acridone: DFT and docking investigations. Struct Chem 2021. [DOI: 10.1007/s11224-020-01609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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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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23
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Al-Otaibi JS, Almuqrin AH, Sheena Mary Y, Shyma Mary Y. Utilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations. J Biomol Struct Dyn 2021; 40:5320-5327. [PMID: 33410367 DOI: 10.1080/07391102.2020.1870155] [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
Nanocluster based drug delivery systems are very useful in modern medical treatment and interaction mechanism of desflurane (DES), isoflurane ISO), sevoflurane (SEV) over carboxyl substituted graphene-doped with O and S atoms were investigated in the present study. Different electronic and chemical properties of adsorbed desflurane, isoflurane and sevoflurane with nanoclusters are analyzed. To track the drugs, SERS is used as an efficient method and drug's detection was analyzed using SERS. DES's energy over GQD-S is greater than that over GQD-O nanocluster and for ISO and SEV, adsorption energies over the O/S nanoclusters are same. The title drugs work on the reactives sites and got adsorbed. For ISO, there is an increase in fluorine atom charges and for DES and SEV, the fluorine atom charge decreases due to adsorption in both O/S nanoclusters. Changes in chemical descriptors are identified for the sensing property of drug-nanoclusters.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia
| | - Y Sheena Mary
- Researcher, Thushara, Neethinagar, Kollam, Kerala, India
| | - Y Shyma Mary
- Researcher, Thushara, Neethinagar, Kollam, Kerala, India
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Mary YS, Mary YS. Utilization of doped/undoped graphene quantum dots for ultrasensitive detection of duphaston, a SERS platform. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 244:118865. [PMID: 32889339 DOI: 10.1016/j.saa.2020.118865] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Recently nanocluster based drug delivery systems have become the most skillful to study. Interaction mechanism of duphaston (DPH) over graphene (G), carboxyl substituted graphene (COG) and doped COG-X (X = O/S/N/B) were investigated. We studied different spectroscopic properties of adsorbed DPH with nanoclusters. To study effect adsorption of DPH with nanoclusters, the adsorption energies were measured. To track DPH, surface enhanced Raman scattering is used since it is an efficient approach to vibrational spectroscopy. The DPH detection was investigated using GQDs SERS property. For the adsorption of DPH with COG-B nanocluster maximum energy interaction is determined. DPH works on the electrophilic site of nanoclusters as donor of electrons and adsorbs. Charge transfer is higher for to COG-B nanocluster than for other nanoclusters. Variations in chemical descriptors are also noted to understand sensing property of DPH molecule-nanoclusters. The analysis of different properties demonstrates enhancement effect which makes it significant in detecting DPH in other products.
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Affiliation(s)
- Y Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India.
| | - Y Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
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Mary YS, Kumar VS, Mary YS, K. S. R, Thomas R. Detailed Quantum Mechanical Studies on Three Bioactive Benzimidazole Derivatives and Their Raman Enhancement on Adsorption over Graphene Sheets. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1852267] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Veena S. Kumar
- Department of Physics, SN College, Kollam, Kerala, India
- Research Centre, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Resmi K. S.
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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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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Spectral analysis and DFT investigation of some benzopyran analogues and their self-assemblies with graphene. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113924] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jayasudha J, Balachandran V, Narayana B. Molecular Docking, Spectroscopic, and Computational Studies of 2-{3-(4-Chlorophenyl)-5-[4-(Propan-2-yl) Phenyl]-4, 5-Dihydro-1H-Pyrazol-1-yl}-1, 3-Thiazol-4(5H)-One. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1830810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- J. Jayasudha
- Centre for Research – Department of Physics, Arignar Anna Government Arts College, Musiri (Affiliated by Bharathidasan University), Tiruchirappalli, Tamil Nadu, India
| | - V. Balachandran
- Centre for Research – Department of Physics, Arignar Anna Government Arts College, Musiri (Affiliated by Bharathidasan University), Tiruchirappalli, Tamil Nadu, India
| | - B. Narayana
- Deparment of Chemistry, Mangalore University, Mangalagangoti, India
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Kumar VS, Mary YS, Pradhan K, Brahman D, Mary YS, Serdaroğlu G, Rad AS, Roxy M. Conformational analysis and quantum descriptors of two new imidazole derivatives by experimental, DFT, AIM, molecular docking studies and adsorption activity on graphene. Heliyon 2020; 6:e05182. [PMID: 33072922 PMCID: PMC7548447 DOI: 10.1016/j.heliyon.2020.e05182] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/29/2020] [Accepted: 10/02/2020] [Indexed: 11/15/2022] Open
Abstract
1-[2-(2-hydroxy-3-methoxy-5-(4-methoxyphenylazo)benzaldeneamino)ethyl]-3-methyl-3H-imidazole (HMY) and 1-[2-(2-hydroxy-3-methoxy-5-(4-methylphenylazo)benzaldene amino)ethyl]-3-methyl-3H-imidazole (HMM) were synthesized and characterized using spectral analysis. Conformational analysis has been achieved using potential energy scan for different rotable bonds for obtaining the lowest energy conformer. Conformer with minimum energy is obtained along the dihedral angle N30-C31-C34-N37. QTAIM analysis gives nature and strength of hydrogen bonding interactions. UV-Vis, electrostatic potential and chemical descriptors are analyzed. Interaction of HMY and HMM with graphene is analyzed in terms of SERS activity. Chemical reactivity descriptors were investigated for graphene-drug systems. NLO activity of parent drugs and its graphene complexes show good activity. The wavenumber downshift of different modes is noted. Title molecules exhibit inhibitory activity against cytochrome C peroxidase. Interactions with graphene sheets are theoretically predicted for the title compounds.
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Affiliation(s)
- Veena S. Kumar
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Kerala, India
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - Kiran Pradhan
- Department of Chemistry, St. Joseph's College, P.O. North Point, Dist. Darjeeling 734104, India
| | - Dhiraj Brahman
- Department of Chemistry, St. Joseph's College, P.O. North Point, Dist. Darjeeling 734104, India
| | - Y. Shyma Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - Goncagül Serdaroğlu
- Sivas Cumhuriyet University, Faculty of Education, Math. and Sci. Edu., 58140 Sivas TURKEY
| | - Ali Shokuhi Rad
- Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran
| | - M.S. Roxy
- Department of Physics, SN College, Kollam, Research Centre, University of Kerala, Kerala, India
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Almuqrin AH, Al-Otaibi JS, Mary YS, Thomas R, Kaya S, Işın DÖ. Spectral analysis and detailed quantum mechanical investigation of some acetanilide analogues and their self-assemblies with graphene and fullerene. J Mol Model 2020; 26:254. [PMID: 32876867 DOI: 10.1007/s00894-020-04485-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/21/2020] [Indexed: 01/21/2023]
Abstract
Spectroscopic analysis and different quantum mechanical studies of four pharmaceutically active compounds phenacetin, p-acetanisidide, 4'-butoxyacetanilide, and 4'-(3-chloropropoxy)acetanilide are reported in this manuscript. Simulated IR spectrum of these compounds was compared with experimentally available data, and essential functional group assignments were made. We also report the frontier orbital properties and other derived local energy descriptors which talks about the relative stability and reactivity. Photovoltaic efficiency of the compounds was studied from the simulated electronic spectra. The compound was found to interact with graphene and fullerene, to form molecular self-assembly. These self-assemblies showed tremendous enhancement in various physicochemical properties when compared with its constituents. The nature of the interactions between studied chemical species was discussed with the help of chemical reactivity principles. Biological activity of the compounds was predicted using molecular docking studies. It is interesting to see that on adsorption with a graphene/fullerene surface, all adsorbed complex shows enhancement in the Raman activity giving surface enhanced Raman spectra (SERS). This can be used for the detection of these drugs in a pharmacological or biological sample. Interestingly the graphene/fullerene drug molecular assembly shows enhanced biological activity when compared with individual drug molecules. Graphical abstract.
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Affiliation(s)
- Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - 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), Changanacherry, Kerala, India
| | - Savaş Kaya
- Department of Pharmacy, Sivas Cumhuriyet University, Health Services Vocational School, 58140, Sivas, Turkey
| | - Dilara Özbakır Işın
- Department of Chemistry, Sivas Cumhuriyet University Faculty of Science, Sivas, Turkey
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31
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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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32
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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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33
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Almuqrin AH, Al-Otaibi JS, Mary YS, Mary YS, Thomas R. Structural study of letrozole and metronidazole and formation of self-assembly with graphene and fullerene with the enhancement of physical, chemical and biological activities. J Biomol Struct Dyn 2020; 39:5509-5515. [PMID: 32657232 DOI: 10.1080/07391102.2020.1790420] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Letrozole and metronidazole are two commonly used drugs for the management of breast cancer and parasitic infections, respectively. This manuscript attempts to study their structure, geometry, search for stable conformers using relaxed potential energy scan, spectral properties, quantum mechanical properties like energy and reactivity descriptors, intra molecular electron transfer properties, non-linear properties etc using various computational tools. It is found that these compounds will form a self-assembly with graphene sheets and fullerenes and exhibit a surface-enhanced Raman spectra and enhancement in non-linear optical properties when compared to the single molecule. The electronic absorption behavior of the compounds was studied using TD-DFT method. Global chemical reactivity descriptors and activity sites toward electrophilic and nucleophilic attack have been discussed. Studies of intra molecular electron transfer gave information about the relative stability of the compounds. Molecular docking studies indicate that the pure compounds and their self-assemblies with graphene have excellent biological activities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aljawhara H Almuqrin
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.,Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Jamelah S Al-Otaibi
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.,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
| | - Y Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanacherry, Kerala, India
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34
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Al-Otaibi JS. Detailed quantum mechanical studies on bioactive benzodiazepine derivatives and their adsorption over graphene sheets. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 235:118333. [PMID: 32272424 DOI: 10.1016/j.saa.2020.118333] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
Estazolam (Z1) and related derivatives, adinazolam (Z2), alprazolam (Z3), 4-hydroxyalprazolam (Z4) and triazolam (Z5) have been studied by using various computational tools to analyze their geometry and spectral characteristics. The compounds were found to interact with graphene monolayer results shows that there is enhancement in various physico-chemical descriptors and surface enhanced Raman spectra (SERS). The various reactive descriptors obtained from the FMO analysis predict the reactive nature of the compound. The various lone pair/sigma to pi conjugation was analyzed using NBO formalism, which provides valuable information about intra molecular electron transfer which is vital in predicting the inherent stability of the molecule. Simulated electronic spectra using TD-DFT and CAM-B3LYP functional are discussed in detail with respect to electronic transitions and light harvesting efficiency. Suitability of candidates as a photo sensitizer in dye sensitized solar cells was studied and 4-Hydroxyalprazolam is identified as a suitable candidate. Nucleophilic and electrophilic regions of the molecules are identified using MESP, which adds to the reactivity information. It can be seen that the highest interaction energy has been obtained in the case of the Z5-graphene system, while the lowest interaction energy has been obtained in the case of the Z1-graphene system. Docking indicates that the ligands adsorbed over graphene also form stable complexes with the receptors as indicated by the high binding affinity energy values.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Saudi Arabia.
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35
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Detailed molecular structure (XRD), conformational search, spectroscopic characterization (IR, Raman, UV, fluorescence), quantum mechanical properties and bioactivity prediction of a pyrrole analogue. Heliyon 2020; 6:e04106. [PMID: 32529077 PMCID: PMC7276443 DOI: 10.1016/j.heliyon.2020.e04106] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/08/2020] [Accepted: 05/27/2020] [Indexed: 01/21/2023] Open
Abstract
Pyrroles are an exciting class of organic compounds with immense medicinal activities. This manuscript presents the structural and quantum mechanical studies of 1-(2-aminophenyl) pyrrole using X-Ray diffraction and various spectroscopic methods like Infra-Red, Raman, Ultra-violet and Fluorescence spectroscopy and its comparison with theoretical simulations. The single-crystal X-ray diffraction values and optimized geometry parameters also were within the agreeable range. A fully relaxed potential energy scan revealed the stability of the possible conformers of this molecule. We present the density functional theory results and assignment of the vibrational modes in the infrared spectrum. The experimental and scaled simulated vibrations matched when density functional theory simulations (B3LYP functional with 6–311++G∗∗). The electronic spectrum was simulated using time-dependent density functional theory with CAM-B3LYP functional in dimethylsulphoxide solvent. The fluorescence spectrum of the compound was studied at different excitation wavelengths in the dimethylsulphoxide solvent. The stability of the molecule by intramolecular electron transfer by hyperconjugation was studied with the natural bond orbital analysis. Frontier molecular orbitals and molecular electrostatic potentials of the compound gave an idea about the reactive behaviour of the compounds. Prediction of activity spectral studies followed by docking analysis indicated that the molecule is active against arylacetonitrilase inhibitor.
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36
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Experimental and computational analysis of 1-(4-chloro-3-nitrophenyl)-3-(3,4-dichlorophenyl)thiourea. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127587] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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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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38
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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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39
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Al-Otaibi JS, Mary YS, Armaković S, Thomas R. Hybrid and bioactive cocrystals of pyrazinamide with hydroxybenzoic acids: Detailed study of structure, spectroscopic characteristics, other potential applications and noncovalent interactions using SAPT. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127316] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Kumar VS, Mary YS, Pradhan K, Brahman D, Mary YS, Thomas R, Roxy M, Alsenoy CV. Synthesis, spectral properties, chemical descriptors and light harvesting studies of a new bioactive azo imidazole compound. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127035] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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41
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Rao DJ, Mary YS, Mary YS, Resmi KS, Thomas R. Structure, Spectral Features, Bioactivity and Light Harvesting Properties of Methyl and Dimethyl Anthracene: Experimental and First Principle Studies. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1709083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- D. Jagadeeswara Rao
- Department of Physics, Dr. Lankapalli Bullayya College, Visakhapatnam, Andhra Pradesh, India
| | - Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Y. Shyma 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
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, Kerala, India
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42
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Sheena Mary Y, Shyma Mary Y, Thomas R, Resmi KS, Narayana B, Samshuddin S, Sarojini BK. Spectroscopic and Theoretical Studies of Potential Anti-Inflammatory Polycyclic Aromatic Fluorophenyl Substituted Acyclic and Heterocyclic Analogues Synthesized from 4,4′-Difluorophenylchalcone. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1699836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - Y. Shyma Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanassery, India
| | - K. S. Resmi
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, India
| | - B. Narayana
- Department of Chemistry, Mangalore University, Mangalagangothri, India
| | - S. Samshuddin
- Department of Chemistry, Mangalore University, Mangalagangothri, India
| | - B. K. Sarojini
- Department of Industrial Chemistry, Mangalore University, Mangalagangothri, India
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Smitha M, Mary YS, Pradhan K, Brahman D, Mary YS, Thomas R, Pavithran R, Alsenoy CV. RETRACTED: Synthesis, spectral characterisation, quantum mechanical analysis and light harvesting properties of two azoimidazole analogues. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.05.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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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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Haruna K, Kumar VS, Sheena Mary Y, Popoola SA, Thomas R, Roxy MS, Al-Saadi AA. Conformational profile, vibrational assignments, NLO properties and molecular docking of biologically active herbicide1,1-dimethyl-3-phenylurea. Heliyon 2019; 5:e01987. [PMID: 31304416 PMCID: PMC6600072 DOI: 10.1016/j.heliyon.2019.e01987] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 11/22/2022] Open
Abstract
1,1-Dimethyl-3-phenylurea (known as fenuron) which is a phenyl urea-based widely used herbicide exhibits interesting structural and conformational properties and a notable biological activity. A detailed analysis on the vibrational, molecular and electronic characteristics of fenuron has been carried out. Potential energy scans (PESs) performed at the B3LYP/6-311++G(d,p) level of theory predicted two possible minima corresponding to the optimized anti and synforms resulting from the internal rotation about the N-C bond. The presence of an auxochrome together with the interaction with DMSO solvent exhibited a blue shift corresponding to the C=O orbitals. Delocalization of HOMO and LUMO orbital facilitated the charge transfer effect in the molecule. The calculated HOMO-LUMO energies, chemical potential, energy gap and global hardness suggested a low softness value for the compound while its biological activity was described by the value of electrophilicity. Chlorine substitution in the phenyl ring influenced the orbital delocalization for ortho and para substitutions but that of meta remained unaffected. NLO properties were noticed to increase due to chlorine substitution in the parent molecule. The docking results suggested that the compound exhibits an inhibitory activity against mitochondrial ubiquinol-cytochrome-c reductase and can be developed as a potential anticancer agent.
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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
| | - Y Sheena Mary
- Department of Physics, Fatima Mata National College(Autonomous), Kollam, Kerala, India
| | - S A Popoola
- Department of Chemistry, Islamic University of Madinah, MadinahMunawara, Saudi Arabia
| | - Renjith Thomas
- Department of Chemistry, St. Berchmans College (Autonomous), Changanacherry, Kerala, India
| | - 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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Mary YS, Mary YS, Thomas R, Narayana B, Samshuddin S, Sarojini BK, Armaković S, Armaković SJ, Pillai GG. Theoretical Studies on the Structure and Various Physico-Chemical and Biological Properties of a Terphenyl Derivative with Immense Anti-Protozoan Activity. Polycycl Aromat Compd 2019. [DOI: 10.1080/10406638.2019.1624974] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Y. Sheena Mary
- Department of Physics, Fatima Mata National College (Autonomous), Kollam, Kerala, India
| | - Y. Shyma 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
| | - S. Samshuddin
- Department of Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
- Department of Chemistry, SDM Institute of Technology, Ujire, Karnataka, India
| | - B. K. Sarojini
- Department of Industrial Chemistry, Mangalore University, Mangalagangothri, Karnataka, India
| | - Stevan Armaković
- Department of Physics, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - Sanja J. Armaković
- Department of Chemistry, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
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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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Marzouk AA, Mohamed SK, Aljohani ET, Abdelhamid AA. New Method for Synthesis of Multi-substituted Imidazoles. J Heterocycl Chem 2018. [DOI: 10.1002/jhet.3215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Adel A. Marzouk
- Pharmaceutical Chemistry Department, Faculty of Pharmacy; Al Azhar University; Cairo Egypt
| | - Shaaban K. Mohamed
- Chemistry and Environmental Division; Manchester Metropolitan University; Manchester M1 5GD UK
- Chemistry Department, Faculty of Science; Minia University; El-Minia 61519 Egypt
| | - Enas T. Aljohani
- Chemistry Department, College of Science; Majmaah University; Majmaah 11952 Saudi Arabia
| | - Antar A. Abdelhamid
- Chemistry Department, Faculty of Science; Sohag University; Sohag 82524 Egypt
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