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Kumaran M, Sivaranjani T, Suresh S, Periandy S, Soundhariya S, Alibrahim KA, Alodhayb AN. Investigation of the molecular structure of CHBP, biological activities and SARS-CoV-2 protein binding interaction by molecular and biomolecular spectroscopy approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124853. [PMID: 39053114 DOI: 10.1016/j.saa.2024.124853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The objective of this investigation is to learn more about the structural, electrical, spectroscopic, and physiochemical characteristics of biologically active cyano-4'-hydroxybiphenyl (CHBP). The title molecule's optimized conformational analysis was computed using the DFT/B3LYP/6-311++G (d, p) level of theory. The observed wavenumbers were compared with theoretical FT-IR and FT-Raman spectra. 1H and 13C NMR experimental spectra in CDCl3 solution (solvent phase) were recorded and the chemical shift was calculated. NBO analysis was used to examine the transfer of charge as well as the intermolecular and intramolecular bonding of orbitals. The TD-DFT (time-dependent DFT) approach was used to estimate theoretical values for both the gas and solvent (ethanol) in the corresponding transitional research, which was conducted using UV-Vis's spectra. Energy gap (Eg = 0.26764 eV) implies that the strong potential for charge transfer, and the stability of the CHBP compound. CHBP compound's has bioactive nature, its drug-likeness and biological properties were evaluated. The predicted topological polar surface area of 44.02 \AA2 for the molecule falls within the permissible range of < 140 \AA2. Based on the docking results, the most stable docking score value is -6.84 kcal/mol. In that interaction, MET 165 affects both phenyl rings in a pi-sulphur fashion and a single bond hydrogen with protein moieties GLN 192. This suggests that the pi-alkyl in PRO 168 is a hydroxyl substitutional ring. Our findings demonstrate the CHBP compound is a good inhibitor against the SAR COVID-19 viral protein.
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Affiliation(s)
- M Kumaran
- Department of Physics, Sri ManakulaVinayagar Engineering College, Pondicherry 605107, India
| | - T Sivaranjani
- Department of Physics, Sri ManakulaVinayagar Engineering College, Pondicherry 605107, India.
| | - S Suresh
- Department of Physics, Saveetha Engineering College (Autonomous), Thandalam, Chennai 602105, Tamil Nadu, India.
| | - S Periandy
- Department of Physics, Kanchi Mamunivar Centre for Post Graduate Studies and Research, Pondicherry, India
| | - S Soundhariya
- Department of Physics, Kanchi Mamunivar Centre for Post Graduate Studies and Research, Pondicherry, India
| | - Khuloud A Alibrahim
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Abdullah N Alodhayb
- Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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2
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Manogaran K, Sivaranjani T, Sengeny P, Venkatachalapathy VSK, Mahadevan M, Elangovan K, Armaković S, Armaković SJ, Abramović BF. Investigation on molecular and biomolecular spectroscopy of the novel 2BCA molecule to analyse its biological activities and binding interaction with nipah viral protein. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 321:124737. [PMID: 38963946 DOI: 10.1016/j.saa.2024.124737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/08/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024]
Abstract
The molecule of 2-Biphenyl Carboxylic Acid (2BCA), which contains peculiar features, was explored making use of density functional theory (DFT) and experimental approaches in the area of quantum computational research. The optimised structure, atomic charges, vibrational frequencies, electrical properties, electrostatic potential surface (ESP), natural bond orbital analysis and potential energy surface (PES) were obtained applying the B3LYP approach with the 6-311++ G (d,p) basis set.. The 2BCA molecule was examined for possible conformers using a PES scan. The methods applied for spectral analyses included FT-IR, FT-RAMAN, NMR, and UV-Vis results. Vibrational frequencies for all typical modes of vibration were found using the Potential Energy Distribution (PED) data. The UV-Vis spectrum was simulated using the TD-DFT technique, which is also seen empirically. The Gauge-Invariant Atomic Orbital (GIAO) approach was employed to model and study the 13C and 1H NMR spectra of the 2BCA molecule in a CDCL3 solution. The spectra were then exploited experimentally to establish their chemical shifts. To predict the donor and acceptor interaction, the NBO analysis was used. The electrostatic potential surface was employed to anticipate the locations of nucleophilic and electrophilic sites. Hirshfeld surfaces and their related fingerprint plots are exploited for the investigation of intermolecular interactions. Reduced Density Gradient (RDG) helps to measure and illustrate electron correlation effects, offering precise insights into chemical bonding, reactivity, and the electronic structure of 2BCA. According to Lipinski and Veber's drug similarity criteria, 2BCA exhibits the typical physicochemical and pharmacokinetic properties that make it a potential oral pharmaceutical candidate. According to the findings of a molecular docking study, the 2BCA molecule has promise as a treatment agent for the Nipah virus (PDB ID: 6 EB9), which causes severe respiratory and neurological symptoms in humans.
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Affiliation(s)
- Kumaran Manogaran
- Department of Physics, Sri Manakula Vinayagar Engineering College, Madagadipet, Puducherry 605107, India
| | - T Sivaranjani
- Department of Physics, Sri Manakula Vinayagar Engineering College, Madagadipet, Puducherry 605107, India.
| | - Periandy Sengeny
- Department of Physics, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Puducherry 605008, India
| | - V S K Venkatachalapathy
- Department of Physics, Sri Manakula Vinayagar Engineering College, Madagadipet, Puducherry 605107, India
| | - M Mahadevan
- Saveetha School of Engineering, Saveetha Institute of Medical and Technical Science (SIMATS), Chennai, Tamil Nadu 602105, India
| | - K Elangovan
- Department of Physics, Malla Reddy Engineering College for Women (Autonomous), Maisammaguda, Dhulapally (Kompally), Secunderabad, Telangana 500 100, India
| | - Stevan Armaković
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg D. Obradovića 4, 21000 Novi Sad, Serbia
| | - 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
| | - Biljana F Abramović
- University of Novi Sad, Faculty of Sciences, Department of Chemistry, Biochemistry and Environmental Protection, Trg D. Obradovića 3, 21000 Novi Sad, Serbia
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Dexlin XDD, Tarika JDD, Kumar AA, Beaula TJ. Hypothetical confirmation for the anti-bacterial compound potassium succinate-succinic acid in comparison with certain succinate derivatives. J Biomol Struct Dyn 2024; 42:1237-1248. [PMID: 37021491 DOI: 10.1080/07391102.2023.2199078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
The development of antibacterial medications has recently been promoted due to the non- effective usage of antibiotics and the rise in severe bacterial infections. The effectiveness of antimicrobial therapy alternatives is constrained due to the prevalence of germs that are resistant to medications. Our current study's goal is to favor metallic compounds for antibiotic delivery in order to increase the effectiveness of the antibacterial regimen. Due to its bioactivity, potassium succinate-succinic acid is preferred because in general, the succinic acid compound has the greatest potential against microbial infections and a natural antibiotic because of its relative acidic nature. In the current study, the molecular geometry, band gap energies, molecular electrostatic interactions and potential energy distribution of the molecule were compared with those of certain succinate derivatives. The potential compound potassium succinate succinic acid was probed using FT-IR and FT-Raman analyses. Vibrational assignments pertaining to different modes of vibration with potential energy distribution have been improved by normal coordinate analysis. The chemical bond stability which is largely important for biological activity is studied using NBO analysis. The molecular docking study suggests that the molecule possesses antibacterial action and displays a minimal binding energy of -5.3 kcal/mol which can be endorsed for the prevention of any bacterial illness. From the results of our studies, the material would be stable and bioactive according to the FMO study, which indicates a band gap value of 4.35 eV and the pharmacokinetic features of the molecule, was predicted using the ADMET factors and the drug-likeness test.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- X D Divya Dexlin
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - J D Deephlin Tarika
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
| | - A Arun Kumar
- Department of Physics (H & Sc), Methodist College of Engineering & Technology (Autonomous), Hyderabad, India
| | - T Joselin Beaula
- Department of Physics and Research Centre, Malankara Catholic College, Mariagiri, Tamilnadu, India
- Manonmaniam Sundaranar University, Tirunelveli, Tamilnadu, India
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Zahid MN, Kosar N, Sajid H, Ibrahim KE, Gatasheh MK, Mahmood T. Unveiling the Potential of B 3O 3 Nanoflake as Effective Transporter for the Antiviral Drug Favipiravir: Density Functional Theory Analysis. Molecules 2023; 28:8092. [PMID: 38138581 PMCID: PMC10746011 DOI: 10.3390/molecules28248092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, for the first time, boron oxide nanoflake is analyzed as drug carrier for favipiravir using computational studies. The thermodynamic stability of the boron oxide and favipiravir justifies the strong interaction between both species. Four orientations are investigated for the interaction between the favipiravir and the B3O3 nanoflake. The Eint of the most stable orientation is -26.98 kcal/mol, whereas the counterpoise-corrected energy is -22.59 kcal/mol. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses are performed to obtain insights about the behavior and the types of interactions that occur between B3O3 nanoflake and favipiravir. The results indicate the presence of hydrogen bonding between the hydrogen in the favipiravir and the oxygen in the B3O3 nanoflake in the most stable complex (FAV@B3O3-C1). The electronic properties are investigated through frontier molecular orbital analysis, dipole moments and chemical reactivity descriptors. These parameters showed the significant activity of B3O3 for favipiravir. NBO charge analysis transfer illustrated the charge transfer between the two species, and UV-VIS analysis confirmed the electronic excitation. Our work suggested a suitable drug carrier system for the antiviral drug favipiravir, which can be considered by the experimentalist for better drug delivery systems.
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Affiliation(s)
- Muhammad Nauman Zahid
- Department of Biology, College of Science, University of Bahrain, Sakhir P.O. Box 32038, Bahrain;
| | - Naveen Kosar
- Department of Chemistry, University of Management and Technology (UMT), C-11, Johar Town Lahore, Lahore 54770, Pakistan;
| | - Hasnain Sajid
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK;
| | - Khalid Elfaki Ibrahim
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Mansour K. Gatasheh
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - Tariq Mahmood
- Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Sakhir P.O. Box 32038, Bahrain
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Azougagh O, Jilal I, Jabir L, El-Hammi H, Essayeh S, Mohammed N, Achalhi N, El Yousfi R, El Idrissi A, El Ouardi Y, Laatikainen K, Abou-Salama M, El Barkany S. Dissolution mechanism of cellulose in a benzyltriethylammonium/urea deep eutectic solvent (DES): DFT-quantum modeling, molecular dynamics and experimental investigation. Phys Chem Chem Phys 2023; 25:22870-22888. [PMID: 37587837 DOI: 10.1039/d3cp02335d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
In this paper, a benzyltriethylammonium/urea DES was investigated as a new green and eco-friendly medium for the progress of organic chemical reactions, particularly the dissolution and the functionalization of cellulose. In this regard, the viscosity-average molecular weight of cellulose (M̄w) during the dissolution/regeneration process was investigated, showing no significant degradation of the polymer chains. Moreover, X-ray diffraction patterns indicated that the cellulose dissolution process in the BTEAB/urea DES decreased the crystallinity index from 87% to 75%, and there was no effect on type I cellulose polymorphism. However, a drastic impact of the cosolvents (water and DMSO) on the melting point of the DES was observed. Besides, to understand the evolution of cellulose-DES interactions, the formation mechanism of the system was studied in terms of H-bond density and radial distribution function (RDF) using molecular dynamics modeling. Furthermore, density functional theory (DFT) was used to evaluate the topological characteristics of the polymeric system such as potential energy density (PED), laplacian electron density (LED), energy density, and kinetic energy density (KED) at bond critical points (BCPs) between the cellulose and the DES. The quantum theory of atoms in molecules (AIM), Bader's quantum theory (BQT), and reduced density gradient (RDG) scatter plots have been exploited to estimate and locate non-covalent interactions (NCIs). The results revealed that the dissolution process is attributed to the physical interactions, mainly the strong H-bond interactions.
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Affiliation(s)
- Omar Azougagh
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Issam Jilal
- LIMOME Laboratory, Dhar El Mehraz Faculty of Sciences, Sidi Mohamed Ben Abdellah University, B.P. 1796 Atlas, Fes 30000, Morocco
| | - Loubna Jabir
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Hayat El-Hammi
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Soumya Essayeh
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Nor Mohammed
- Applied Chemistry Unit, Sciences and Technologies Faculty, Abdelmalek Essaadi University, 32 003 Al Hoceima, Morocco
| | - Nafea Achalhi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohammed 1st University, 60000 Oujda, Morocco
| | - Ridouan El Yousfi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohammed 1st University, 60000 Oujda, Morocco
| | - Abderrahmane El Idrissi
- Laboratory Applied Chemistry and Environmental (LCAE-URAC18), Faculty of Sciences of Oujda, Mohammed 1st University, 60000 Oujda, Morocco
| | - Youssef El Ouardi
- LIMOME Laboratory, Dhar El Mehraz Faculty of Sciences, Sidi Mohamed Ben Abdellah University, B.P. 1796 Atlas, Fes 30000, Morocco
- Laboratory of Separation Technology, Lappeenranta University of Technology, P.O. Box 20, FI-53851 Lappeenranta, Finland
| | - Katri Laatikainen
- Laboratory of Separation Technology, Lappeenranta University of Technology, P.O. Box 20, FI-53851 Lappeenranta, Finland
| | - Mohamed Abou-Salama
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
| | - Soufian El Barkany
- Laboratory of Molecular Chemistry, Materials and Environment (LMCME), Department of Chemistry, Faculty Multidisciplinary Nador, Mohammed 1st University, P. B. 300, Nador 62700, Morocco.
- Applied Chemistry Unit, Sciences and Technologies Faculty, Abdelmalek Essaadi University, 32 003 Al Hoceima, Morocco
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Chérif I, Raissi H, Abiedh K, Gassoumi B, Caccamo MT, Magazu S, Said AH, Hassen F, Boubaker T, Ayachi S. Exploration of intramolecular charge transfer in para-substituted nitrobenzofurazan: Experimental and theoretical analyses. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 301:122939. [PMID: 37285745 DOI: 10.1016/j.saa.2023.122939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/09/2023]
Abstract
The present work aims at exploring the high electrophilic character of 4-chloro-7-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) toward the morpholine group by an SNAr reaction in acetonitrile or water (thereafter referred to as NBD-Morph). The electron-donating ability of the morpholine causes intra-molecular charge transfer (ICT). In this report, we present a comprehensive study on the optical characteristics using UV-Vis, photoluminescence (cw-PL) and its time-resolved (TR-PL) to determine the properties of the emissive intramolecular charge transfer (ICT) in the NBD-Morph donor-acceptor system. An exhaustive theoretical investigation utilizing the density functional theory (DFT) and its extension TD-DFT methods is an essential complement of experiments to rationalize and understand the molecular structure and related properties. The findings from QTAIM, ELF, and RDG analyses establish that the bonding between morpholine and NBD moieties is of the electrostatic or hydrogen bond type. In addition, the Hirshfeld surfaces have been established to explore the types of interactions. Further, the non-linear optical (NLO) responses of the compound have been examined. The structure-property relationships obtained through the combined experimental and theoretical offer valuable insights for designing efficient NLO material.
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Affiliation(s)
- Imen Chérif
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the environment, 5019 Monastir, Tunisia
| | - Hanen Raissi
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Khouloud Abiedh
- Laboratoire de Micro-Optoélectronique et Nanostructures (LR99/ES29), Faculté des Sciences, Université de Monastir, Monastir, Tunisia
| | - Bouzid Gassoumi
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Maria Teresa Caccamo
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra Università di Messina Viale Ferdinando Stagno D', Alcontres n°31, S. Agata, 98166 Messina Italy
| | - Salvatore Magazu
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra Università di Messina Viale Ferdinando Stagno D', Alcontres n°31, S. Agata, 98166 Messina Italy
| | - Ayoub Haj Said
- Laboratoire Interfaces et Matériaux Avancés (LIMA), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia; Centre de Recherche en Microélectronique et Nanotechnologie, Technopôle de Sousse, BP 334, Sahloul, 4054 Sousse, Tunisia
| | - Fredj Hassen
- Laboratoire de Micro-Optoélectronique et Nanostructures (LR99/ES29), Faculté des Sciences, Université de Monastir, Monastir, Tunisia
| | - Taoufik Boubaker
- Laboratoire de Chimie Hétérocyclique, Produits Naturels et Réactivité (LR11ES39), Faculté des Sciences, Université de Monastir, Avenue de l'Environnement, 5019 Monastir, Tunisia
| | - Sahbi Ayachi
- Laboratory of Physico-Chemistry of Materials (LR01ES19), Faculty of Sciences, University of Monastir, Avenue of the environment, 5019 Monastir, Tunisia.
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Akman F, Demirpolat A, Kazachenko AS, Kazachenko AS, Issaoui N, Al-Dossary O. Molecular Structure, Electronic Properties, Reactivity (ELF, LOL, and Fukui), and NCI-RDG Studies of the Binary Mixture of Water and Essential Oil of Phlomis bruguieri. Molecules 2023; 28:molecules28062684. [PMID: 36985656 PMCID: PMC10056484 DOI: 10.3390/molecules28062684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Essential oils are volatile oil-like liquids with a characteristic strong smell and taste. They are formed in plants and are then extracted. Essential oils have extremely strong physiological and pharmacological properties, which are used in the medicine, cosmetics, and food industries. In this study, the molecules caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene, which are the molecules with the highest contents in the essential oil of the plant mentioned in the title, were selected and theoretical calculations describing their interactions with water were performed. Because oil–water mixtures are very important in biology and industry and are ubiquitous in nature, quantum chemical calculations for binary mixtures of water with caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene were performed using the density functional theory (DFT)/B3LYP method with a basis of 6–31 G (d, p). Molecular structures, HOMO–LUMO energies, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG and molecular electrostatic potential (MEP) on surfaces of the main components of Phlomis bruguieri Desf. essential oil were calculated and described.
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Affiliation(s)
- Feride Akman
- Vocational School of Food, Agriculture and Livestock, University of Bingöl, Bingöl 12000, Turkey
- Correspondence: (F.A.); or (A.S.K.)
| | - Azize Demirpolat
- Vocational School of Food, Agriculture and Livestock, University of Bingöl, Bingöl 12000, Turkey
| | - Aleksandr S. Kazachenko
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Pr. Svobodny 79, 660041 Krasnoyarsk, Russia
- Siberian Branch, FRC “Krasnoyarsk Scientific Center”, Institute of Chemistry and Chemical Technology, Russian Academy of Sciences, Akademgorodok 50, Bld. 24, 660036 Krasnoyarsk, Russia
- Department of Biological Chemistry with Courses in Medical, Pharmaceutical and Toxicological Chemistry, Krasnoyarsk State Medical University, St. Partizan Zheleznyak, Bld. 1, 660022 Krasnoyarsk, Russia
- Correspondence: (F.A.); or (A.S.K.)
| | - Anna S. Kazachenko
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Pr. Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Noureddine Issaoui
- Laboratory of Quantum and Statistical Physics, LR18ES18, Faculty of Sciences, University of Monastir, Monastir 5079, Tunisia
| | - Omar Al-Dossary
- Departement of Physics and Astronomy, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Nauman Zahid M, Asif M, Sajid H, Kosar N, Akbar Shahid M, Allangawi A, Ayub K, Azeem M, Mahmood T. Therapeutic efficiency of B3O3 quantum dot as a targeted drug delivery system toward Foscarnet anti-HIV drug. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2023.114107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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9
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Experimental spectroscopy, eco-friendly solvents effect on transitions, reactive sites and biological research on methyl gallate – MTT assay (cytotoxicity). J Mol Liq 2023. [DOI: 10.1016/j.molliq.2022.121092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Abisha W, Dhas DA, Balachandran S, Joe IH. Synthesis, Structural, and Quantum Chemical Spectroscopic, Hydrogen Bonding, and Molecular Docking Investigation of Antifungal Compound Pyrazole-Pyrazolium Picrate. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2149571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- W. Abisha
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, India
- Manonmaniam Sundaranar University Abishekapatti, Tirunelveli, India
| | - D. Arul Dhas
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, India
- Manonmaniam Sundaranar University Abishekapatti, Tirunelveli, India
| | - S. Balachandran
- Department of Chemistry, NSS College Ottapalam, Palakkad, India
| | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvanathapuram, India
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Demirpolat A, Akman F, Kazachenko AS. An Experimental and Theoretical Study on Essential Oil of Aethionema sancakense: Characterization, Molecular Properties and RDG Analysis. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186129. [PMID: 36144861 PMCID: PMC9504168 DOI: 10.3390/molecules27186129] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 01/18/2023]
Abstract
This study aims to experimentally and theoretically examine the plant Aethionema sancakense, which was determined as a new species and whose essential oil and fatty acid compositions were characterized by GC/GC-MS technique. Linoleic acid (23.1%), α-humulene (19.8%), camphene (13.9%), and heptanal (9.7%) were found to be the major essential oil components of A. sancakense aerial part structures. The quantum chemical calculations of these four molecules that are very important to this plant were performed using the density functional method (DFT)/B3LYP with the 6-31 G (d, p) basis set in the ground state for the gas phase. The molecular structures, HOMO-LUMO energies, electronic properties, Fukui functions, and molecular electrostatic potential (MEP) surfaces of the major constituents of Aethionema sancakense essential oil were calculated and interpreted. Finally, the RDG-NCI analysis of these molecules was performed to determine the non-covalent interactions present within the molecules.
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Affiliation(s)
- Azize Demirpolat
- Vocational School of Food, Agriculture and Livestock, University of Bingöl, Bingöl 12000, Turkey
- Correspondence: (A.D.); (F.A.); (A.S.K.)
| | - Feride Akman
- Vocational School of Food, Agriculture and Livestock, University of Bingöl, Bingöl 12000, Turkey
- Correspondence: (A.D.); (F.A.); (A.S.K.)
| | - Aleksandr S. Kazachenko
- Krasnoyarsk Scientific Center, Department of Chemistry of Natural Organic Raw Materials, Institute of Chemistry and Chemical Technology, Siberian Branch, Russian Academy of Sciences, Akademgorodok, 50, bld. 24, Krasnoyarsk 660036, Russia
- Department of Non-Ferrous Metals and Materials Science, Siberian Federal University, pr. Svobodny 79, Krasnoyarsk 660041, Russia
- Department of Biological Chemistry with Elements of Pharmaceutical, Medical and Toxicological Chemistry, Krasnoyarsk State Medical University of the Ministry of Healthcare of the Russian Federation, st. Partizan Zheleznyak, bld. 1, Krasnoyarsk 660022, Russia
- Correspondence: (A.D.); (F.A.); (A.S.K.)
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Competitor hydrogen-bond acceptors in the SP(NH)3-based structures: Comparison of structural features - computational/database and experimental. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.116157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Divya Dexlin X, Deephlin Tarika J, Sethuram M, Joselin Beaula T. Synthesis, vibrational Depictions, IRI interpretations and docking research on coordination metal complex Diaqua aspartato zinc (II) monohydrate using DFT approach. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Dexlin XD, Tarika JD, Kumar SM, Mariappan A, Beaula TJ. Synthesis and DFT computations on structural, electronic and vibrational spectra, RDG analysis and molecular docking of novel Anti COVID-19 molecule 3, 5 Dimethyl Pyrazolium 3, 5 Dichloro Salicylate. J Mol Struct 2021; 1246:131165. [DOI: 10.1016/j.molstruc.2021.131165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/15/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
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Sagaama A, Issaoui N, Al-Dossary O, Kazachenko AS, Wojcik M. Non covalent interactions and molecular docking studies on morphine compound. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2021. [DOI: 10.1016/j.jksus.2021.101606] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Miah MH, Hossain MR, Islam MS, Ferdous T, Ahmed F. A theoretical study of allopurinol drug sensing by carbon and boron nitride nanostructures: DFT, QTAIM, RDG, NBO and PCM insights. RSC Adv 2021; 11:38457-38472. [PMID: 35493251 PMCID: PMC9044057 DOI: 10.1039/d1ra06948a] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022] Open
Abstract
The application of low-dimensional nanomaterials in clinical practice as efficient sensors has been increasing day by day due to progress in the field of nanoscience. In this research work, we have conducted a theoretical investigation to nominate a potential electrochemical sensor for the allopurinol (APN) drug molecule via studying the fundamental interactions of the drug molecule with two nanocages (carbon nanocage/CNC - C24 and boron nitride nanocage/BNNC - B12N12) and two nanosheets (graphene - C54H18 and boron nitride - B27N27H18) by means of the DFT B3LYP/6-31G(d,p) level of theory in both gas and water phases. The adsorption energies of APN-BNNC conjugated structures are in the range of -20.90 kcal mol-1 to -22.33 kcal mol-1, which indicates that weak chemisorption has occurred. This type of interaction happened due to charge transfer from the APN molecule to BNNC, which was validated and characterized based on the quantum theory of atoms in molecules, natural bond analysis, and reduced density gradient analysis. The highest decreases in energy gap (36.22% in gas and 26.79% in water) and maximum dipole moment (10.48 Debye in gas and 13.88 Debye in water) were perceived for the APN-BNNC conjugated structure, which was also verified via frontier molecular orbital (FMO) and MEP analysis. Also, the highest sensitivity (BNNC > BNNS > CNC > GNS) and favorable short recovery time (in the millisecond range) of BNNC can make it an efficient detector for the APN drug molecule.
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Affiliation(s)
- Md Helal Miah
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj-8100 Bangladesh
| | - Md Rakib Hossain
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj-8100 Bangladesh
| | - Md Saiful Islam
- Department of Physics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University Gopalganj-8100 Bangladesh
| | - Tahmina Ferdous
- Department of Physics, Jahangirnagar University Savar Dhaka-1342 Bangladesh
| | - Farid Ahmed
- Department of Physics, Jahangirnagar University Savar Dhaka-1342 Bangladesh
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Sagdinc SG, Akcay BK, Yildiz SZ, Isik IB. Single-crystal X-ray structural characterization, Hirshfeld surface analysis, electronic properties, NBO, and NLO calculations and vibrational analysis of the monomeric and dimeric forms of 5-nitro-2-oxindole. NEW J CHEM 2021. [DOI: 10.1039/d1nj00264c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The information of interactions is given by RDG versus sign(λ2)ρ product of the sign of the second largest eigenvalue of electron density Hessian matrix and electron density) investigated by RDG surface analysis.
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Affiliation(s)
| | - Banu Kevser Akcay
- Department of Physics, Science and Art Faculty
- Kocaeli University
- 41380 Umuttepe
- Turkey
| | - Salih Zeki Yildiz
- Department of Chemistry
- Faculty of Arts and Sciences
- Sakarya University
- 54187 Serdivan
- Turkey
| | - Ilknur Baldan Isik
- Department of Physics, Science and Art Faculty
- Kocaeli University
- 41380 Umuttepe
- Turkey
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Khan S, Sajid H, Ayub K, Mahmood T. Adsorption behaviour of chronic blistering agents on graphdiyne; excellent correlation among SAPT, reduced density gradient (RDG) and QTAIM analyses. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113860] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Sajid H, Ullah F, Yar M, Ayub K, Mahmood T. Superhalogen doping: a new and effective approach to design materials with excellent static and dynamic NLO responses. NEW J CHEM 2020. [DOI: 10.1039/d0nj02291h] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The first-ever example where superhalogen doping alone is introduced as a new and effective approach to impart large NLO responses.
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Affiliation(s)
- Hasnain Sajid
- Department of Chemistry
- COMSATS University Islamabad
- Abbottabad-22060
- Pakistan
| | - Faizan Ullah
- Department of Chemistry
- COMSATS University Islamabad
- Abbottabad-22060
- Pakistan
| | - Muhammad Yar
- Department of Chemistry
- COMSATS University Islamabad
- Abbottabad-22060
- Pakistan
| | - Khurshid Ayub
- Department of Chemistry
- COMSATS University Islamabad
- Abbottabad-22060
- Pakistan
| | - Tariq Mahmood
- Department of Chemistry
- COMSATS University Islamabad
- Abbottabad-22060
- Pakistan
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