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Khaled NA, Ibrahim MA, Mohamed NA, Ahmed SA, Ahmed NS. DFT studies on N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 323:124864. [PMID: 39067358 DOI: 10.1016/j.saa.2024.124864] [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: 04/30/2024] [Revised: 07/01/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
In this work, molecular descriptors of N-(1-(2-bromobenzoyl)-4-cyano-1H-pyrazol-5-yl) halogenated benzamides (1a-h) have been computed using a quantum chemical technique through DFT. Prior work involved the synthesis of compounds (1a-h) and the assessment of their anticancer activity on breast, colon, and liver tumors: MCF-7, HCT-116, and HepG-2 cell lines respectively. Since 1a, 1b, and 1d showed the most potential anticancer impact, their ability to inhibit EGFRWT was investigated. Based on the biological data, 1b inhibited EGFRWT the most. According to the docking evaluation, an H-bond with the threonine residue was one of the main non-covalent contacts between 1b and the EGFRWT active site residues. PES, MESP, HOMOs, LUMOs, energy band gap, global reactivity indices [electron affinity (A), ionization energies (I), electrophilicity index (ω), nucleophilicity index (ε), chemical potential (μ), electronegativity (χ), hardness (η), and softness (S)], condensed Fukui functions, NBO, and NCIs are the molecular descriptors of 1a-h that were computed using DFT technique. According to the theoretical investigation results, compounds (1a-h) might have anticancer effects; these findings are consistent with the biological findings from our previous research. Compound 1b had the lowest binding energy, according to an assessment of the binding energies between the threonine and the three most active compounds (1a, 1b, and 1d). This is consistent with the outcomes of the docking study and the biological examination of the influence of 1a, 1b, and 1d on EGFRWT.
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Affiliation(s)
- Nada A Khaled
- Therapeutical Chemistry Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Medhat A Ibrahim
- Spectroscopy Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt; Molecular Modeling and Spectroscopy Laboratory, Centre of Excellence for Advanced Science, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt.
| | - Neama A Mohamed
- Therapeutical Chemistry Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Sayed A Ahmed
- Department of Chemistry, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt; Basic Science Department, Faculty of Engineering, Nahda University Beni-Suef (NUB), Beni Suef, Egypt
| | - Nesreen S Ahmed
- Therapeutical Chemistry Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
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Wang Y, Lin Q, Liu Y, Li C, Liu Z, Yu X, Wang KN. Lighting Up Nucleolus To Report Mitochondria Damage Using a Mitochondria-to-Nucleolus Migration Probe. Anal Chem 2024; 96:9808-9816. [PMID: 38833718 DOI: 10.1021/acs.analchem.3c05629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Visualization of the mitochondrial state is crucial for tracking cell life processes and diagnosing disease, while fluorescent probes that can accurately assess mitochondrial status are currently scarce. Herein, a fluorescent probe named "SYN" was designed and prepared, which can target mitochondria via the mitochondrial membrane potential. Upon pathology or external stimulation, SYN can be released from the mitochondria and accumulate in the nucleolus to monitor the status of mitochondria. During this process, the brightness of the nucleolus can then serve as an indicator of mitochondrial damage. SYN has demonstrated excellent photostability in live cells as well as an extremely inert fluorescence response to bioactive molecules and the physiological pH environment of live cells. Spectroscopic titration and molecular docking studies have revealed that SYN can be lit up in nucleoli due to the high viscosity of the nucleus and the strong electrostatic interaction with the phosphate backbone of RNA. This probe is expected to be an exceptional tool based on its excellent imaging properties for tracking mitochondrial state in live cells.
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Affiliation(s)
- Yumeng Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Qiaowen Lin
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Yang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Chi Li
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Zhiqiang Liu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
| | - Xiaoqiang Yu
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Kang-Nan Wang
- State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
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Singh M, Jain P, Mohammad F, Singh P, Bahadur I, Abedigamba OP. Significant Increase in the Dipole Moment of Graphene on Functionalization: DFT Calculations and Molecular Dynamics Simulations. ACS OMEGA 2024; 9:16458-16468. [PMID: 38617684 PMCID: PMC11007824 DOI: 10.1021/acsomega.4c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/16/2024]
Abstract
The limited solubility of graphene in water can be attributed to the existence of π-π bonds connecting its layers. Functionalized graphene or graphene oxide (GO) is frequently produced in order to overcome the shortcomings of graphene. Using density functional theory (DFT) calculation, functionalized graphene with various combinations of hydroxyl, epoxy, and carboxylic functional groups were investigated computationally. The study focused on the effects of functional group combinations on the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, giving information about the chemical reactivity and stability of the molecules under investigation. Global chemical reactivity descriptors, including chemical hardness, softness, electronegativity, chemical potential, and electrophilicity index, were calculated to further elucidate the overall stability and reactivity of the molecules. The results demonstrated that the introduction of oxygen-containing functional groups on graphene significantly influenced its electronic properties, leading to variations in the chemical reactivity and stability. Molecular electrostatic potential (MEP) maps highlighted the susceptibility of specific regions to electrophilic and nucleophilic attacks. The flexibility and stability of functionalized graphene through root mean square fluctuation (RMSF) and root mean square deviation (RMSD) analyses indicate the stability of functionalized graphene in water. This comprehensive computational investigation provides valuable insights into the design and understanding of functionalized graphene for potential applications in drug delivery.
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Affiliation(s)
- Madhur
Babu Singh
- Department
of Chemistry, Atma Ram Sanatan Dharma College,
University of Delhi, Delhi 110021, India
- Department
of Chemistry, SRM Institute of Science &
Technology, NCR Campus, Ghaziabad 201204, India
| | - Pallavi Jain
- Department
of Chemistry, SRM Institute of Science &
Technology, NCR Campus, Ghaziabad 201204, India
| | - Faruq Mohammad
- Department
of Chemistry, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Kingdom
of Saudi Arabia
| | - Prashant Singh
- Department
of Chemistry, Atma Ram Sanatan Dharma College,
University of Delhi, Delhi 110021, India
| | - Indra Bahadur
- Department
of Chemistry, Material Science, Innovation and Modelling (MaSIM) Research
Focus Area, North-West University (Mafikeng
Campus), Private Bag X2046, Mmabatho 2735, South Africa
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Muhammad S, Zahir N, Bibi S, Alshahrani MY, Shafiq-urRehman, Chaudhry AR, Sarwar F, Tousif MI. Computational prediction for designing novel ketonic derivatives as potential inhibitors for breast cancer: A trade-off between drug likeness and inhibition potency. Comput Biol Chem 2024; 109:108020. [PMID: 38286082 DOI: 10.1016/j.compbiolchem.2024.108020] [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: 08/24/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
Unlike simple molecular screening, a combined hybrid computational methodology has been applied which includes quantum chemical methods, molecular docking, and molecular dynamics simulations to design some novel ketonic derivatives. The current study contains the derivatives of an experimental ligand which are designed as a trade-off between drug likeness and inhibition strength. We investigate the interaction of various newly designed ketonic compounds with the breast cancer receptor known as the Estrogen Receptor Alpha (ERα). The molecular structures of all newly designed ligands were studied quantum chemically in terms of their fully optimized structures, 3-D molecular orbital distributions, global chemical descriptors, molecular electrostatic potentials and energies of frontier molecular orbitals (FMOs). All ligands under study show good binding affinities with the ERα protein. The ligands CMR2 and CMR4 exhibit improved molecular docking interactions. The intermolecular interactions indicate that CMR4 demonstrates better hydrophobic and hydrogen bonding interactions with protein (ERα). Furthermore, molecular dynamics simulations were conducted on ligands and reference drugs interacting with the ERα protein over a time span of 120 nanoseconds. The molecular dynamics results are interpreted in terms of ligand-protein stability and flexible behaviour based on their respective values of RMSD, RMSF, H-bonds, the radius of gyration, and SASA graphs. To analyse ligand-protein interactions throughout the entire 120 ns trajectory, a more advanced MM/PBSA method is utilized, where six selected ligands (CMR1, CMR2, CMR3, CMR4, CMR5 and CMR9) illustrate promising results for inhibition of the ERα receptor as assessed through MM/BBSA analysis. The CMR9 has the highest MM/BBSA binding free energy (-14.46 kcal/mol). The ADMET analysis reveals that CMR4 has maximum intestinal absorption (6.68) and clearance rate (0.1). All the compounds are non-toxic and safe to use. These findings indicate the potential of involving different computational techniques to design the ligand structures and to study the ligand-protein interactions for better understanding and achieving more potent synthetic inhibitors for breast cancer.
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Affiliation(s)
- Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.
| | - Nimra Zahir
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shamsa Bibi
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia
| | - Shafiq-urRehman
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Aijaz Rasool Chaudhry
- Department of Physics, College of Science, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Fatima Sarwar
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Imran Tousif
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
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Agarwal N, Fatima A, Bhattacharya P, Muthu S, Arora H, Siddiqui N, Javed S. Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine. J Biomol Struct Dyn 2023; 41:10430-10449. [PMID: 36562198 DOI: 10.1080/07391102.2022.2159530] [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: 04/03/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Agarwal
- Department of chemistry, Institute of H. Science, Dr. Bhimrao-Ambedkar University, Agra, Uttar Pradesh, India
| | - Aysha Fatima
- S.O.S in chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | | | - S Muthu
- Department of Physics, Aringnar Anna Government Arts College, Cheyyar, India
| | - Himanshu Arora
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
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Fatima A, Khanum G, Srivastava SK, Bhattacharya P, Ali A, Arora H, Siddiqui N, Javed S. Exploring quantum computational, molecular docking, and molecular dynamics simulation with MMGBSA studies of ethyl-2-amino-4-methyl thiophene-3-carboxylate. J Biomol Struct Dyn 2023; 41:10411-10429. [PMID: 37942665 DOI: 10.1080/07391102.2023.2180667] [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: 08/22/2022] [Accepted: 12/10/2022] [Indexed: 02/24/2023]
Abstract
2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (1H-NMR and 13C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV-Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H--H/H--H/C--H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, India
- Department of Chemistry, CMP College, University of Allahabad, Prayagraj, India
| | | | | | | | - Akram Ali
- Department of Chemistry, CMP College, University of Allahabad, Prayagraj, India
| | - Himanshu Arora
- Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, India
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Ahmed MT, Roy D, Roman AA, Islam S, Ahmed F. A first-principles investigation of Cr adsorption on C 8 and B 4N 4 nanocages in aqueous mediums. Phys Chem Chem Phys 2023; 25:32261-32272. [PMID: 37988166 DOI: 10.1039/d3cp04225a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Heavy metal removal from polluted environments is one of the vital research areas for better and healthier living. In this research, C8 and B4N4 nanocage-like quantum dots are investigated for heavy metal (Cr) removal applications via density functional theory calculations. The adsorption of up to two Cr atoms has been studied in both air and a water medium. The adsorption of Cr atoms results in significant structural deformation of the adsorbents with a high adsorption energy of -8.74 and -5.77 eV for C8 and B4N4 nanostructures, respectively, which is further increased with an increasing number of Cr atoms. All adsorbents and complex structures showed real vibrational frequencies. Mulliken charge and electrostatic potential analysis reveal a significant charge transfer between adsorbate-adsorbent. The adsorption process causes a decrease in the energy gap of the adsorbents. All the reactions in this study were spontaneous and thermodynamically ordered. QTAIM analysis verifies that the interactions of the adsorbents with Cr atoms are strong partial covalent. The study's findings make C8 and B4N4 nanostructures potential candidates for Cr-detection and removal applications.
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Affiliation(s)
- Mohammad Tanvir Ahmed
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Debashis Roy
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Abdullah Al Roman
- Department of Physics, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Shariful Islam
- Department of Physics, Jahangirnagar University, Dhaka, Bangladesh
| | - Farid Ahmed
- Department of Physics, Jahangirnagar University, Dhaka, Bangladesh
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Perveen M, Noreen L, Waqas M, Mehmood RF, Iqbal J, Manzoor S, Nazir S, Shawky AM, Khera RA. A DFT approach for finding therapeutic potential of graphyne as a nanocarrier in the doxorubicin drug delivery to treat cancer. J Mol Graph Model 2023; 124:108537. [PMID: 37321062 DOI: 10.1016/j.jmgm.2023.108537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/19/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
In the present work, the drug-loading efficacy of graphyne (GYN) for doxorubicin (DOX) drug is investigated for the first time by using density functional theory (DFT). Doxorubicin drug is effective in the cure of numerous types of cancer including bone cancer, gastric, thyroid, bladder, ovarian, breast, and soft tissue cancer. Doxorubicin drug prevents the cell division process by intercalating in the double-helix of DNA and stopping its replication. The optimized, geometrical, energetic, and excited-state characteristics of graphyne (GYN), doxorubicin drug (DOX), and doxorubicin-graphyne complex (DOX@GYN complex) are calculated to see how effective it is as a carrier. The DOX drug interacted with GYN with an adsorption-energy of -1.57 eV (gas-phase). The interaction of GYN with DOX drug is investigated using NCI (non-covalent interaction) analysis. The findings of this analysis showed that the DOX@GYN complex has weak forces of interaction. Charge transfer from doxorubicin drug to GYN during DOX@GYN complex formation is described by charge-decomposition analysis and HOMO-LUMO analysis. The increased dipole-moment (8.41 D) of the DOX@GYN in contrast with therapeutic agent DOX and GYN indicated that the drug will move easily in the biochemical system. Furthermore, the photo-induced electron-transfer process is explored for excited states, and it reveals that upon interaction, fluorescence-quenching will occur in the complex DOX@GYN. In addition, the influence of the positive and negative charge states on the GYN and DOX@GYN is also considered. Overall, the findings indicated that the GYN could be exploited as an effective drug-transporter for the delivery of doxorubicin drug. Investigators will be inspired to look at another 2D nanomaterials for drug transport applications as a result of this theoretical work.
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Affiliation(s)
- Mehvish Perveen
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Lubna Noreen
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Muhammad Waqas
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Rana Farhat Mehmood
- Department of Chemistry, University of Education, Township, Lahore, 54770, Pakistan
| | - Javed Iqbal
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan.
| | - Sidra Manzoor
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan
| | - Sidra Nazir
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Rasheed Ahmad Khera
- Department of Chemistry, University of Agriculture, 38000 Faisalabad, Pakistan.
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Guan T, Bian C, Ma Z. In vitro and in silico perspectives on the activation of antioxidant responsive element by citrus-derived flavonoids. Front Nutr 2023; 10:1257172. [PMID: 37674886 PMCID: PMC10478098 DOI: 10.3389/fnut.2023.1257172] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023] Open
Abstract
Introduction Oxidative stress plays an essential role in the pathogenesis of chronic diseases. Disrupting the Keap1-Nrf2 pathway by binding Keap1 is identified as a potential strategy to prevent oxidative stress-related chronic diseases. Therefore, of special interest is the utilization of dietary antioxidations from citrus, including narirutin, naringenin, hesperetin, hesperidin, naringin, neohesperidin dihydrochalcone, neohesperidin, and nobiletin, has been exploited as a prospective way to treat or prevent several human pathologies as Keap1-Nrf2 inhibitors for modulation of antioxidant properties. Methods To probe into the structural foundation of the molecular identification of citrus-derived antioxidations, we calculated the antioxidant responsive element activation ability of citrus-derived flavonoids after binding with Keap1. Also, the quantum chemistry properties and binding mode were performed theoretically with frontier molecular orbitals, molecular electrostatic potential analysis, molecular docking, and absorption, distribution, metabolism, excretion (ADME) calculation. Results and discussion Experimental findings combining computational assays revealed that the tested citrus-derived flavonoids can be grouped into strong agonists and weak agonists. The citrus-derived antioxidations were well housed in the bound zone of Keap1 via stable hydrogen bonding and hydrophobic interaction. Eventually, three of eight antioxidations were identified after ADME and physicochemical evaluations. The citrus-derived flavonoids were identified as potential dietary antioxidants of the Keap1-Nrf2 interaction, and can be used to improve oxidative stress-related chronic diseases.
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Affiliation(s)
- Tianzhu Guan
- School of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Canfeng Bian
- School of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Zheng Ma
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
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M JP, Dhas DA, Joe IH, Balachandran S. Structural, Spectroscopic, Quantum Chemical, RDG, AIM, ELF, Fukui, O–H…N Hydrogen Bonding and NLO Activity of 2-Hydroxy-2-Phenyl Acetophenone Oxime: Experimental and Theoretical Approach. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2022.2164016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jini Pramila M
- Department of Physics, Manonmanium Sundaranar University, Abishekapatti, India
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - D. Arul Dhas
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvananthapuram, India
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Kiven DE, Nkungli NK, Tasheh SN, Ghogomu JN. In silico screening of ethyl 4-[(E)-(2-hydroxy-4-methoxyphenyl)methyleneamino]benzoate and some of its derivatives for their NLO activities using DFT. ROYAL SOCIETY OPEN SCIENCE 2023; 10:220430. [PMID: 36686549 PMCID: PMC9832297 DOI: 10.1098/rsos.220430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The nonlinear optical (NLO) properties of ethyl 4-[(E)-(2-hydroxy-4-methoxyphenyl)methyleneamino]benzoate (EMAB) and some of its derivatives are investigated herein using the density functional theory (DFT) and time-dependent (TD)-DFT methods. The density functionals B3LYP, CAM-B3LYP, M06-2X and ωB97XD, and basis sets 6-31 + G**, 6-311 + + G** and Def2-TZVPP have been used. From the results, EMAB and its substituted derivatives studied are promising candidates for NLO materials. In all cases, the static first and second hyperpolarizabilities (31.7-86.5 × 10-30 and 84.4-273 × 10-36 electrostatic units (esu), respectively) and the frequency-dependent NLO properties are found to be significantly larger (about 43-103 and 28-76 times greater) than those of the NLO prototypical molecule, para-nitroaniline. Furthermore, the maximum absorption wavelengths of the molecules fall within the UV region of the electromagnetic spectrum. Relative to EMAB, the derivatives have shown improved transparency-nonlinearity trade-offs. Natural bond orbital (NBO) and density of states (DOS) analyses herein revealed effective charge transfer within the molecules studied, especially those with stronger electron donors than that in EMAB (methoxy group). Among the molecules studied, the derivative obtained by substituting EMAB's methoxy group with the pyrrolyl group was found to exhibit the best NLO properties. Conclusively, the NLO activities of EMAB can be significantly improved through the substitution of its methoxy group with stronger electron donors.
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Affiliation(s)
- Dinyuy Emmanuel Kiven
- Department of Chemistry, Faculty of Science, The University of Bamenda, P.O. Box 39, Bambili-Bamenda, Cameroon
| | - Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, P.O. Box 39, Bambili-Bamenda, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, P.O. Box 39, Bambili-Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, Research Unit of Noxious Chemistry and Environmental Engineering, P.O. Box 67, Dschang, Cameroon
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, P.O. Box 39, Bambili-Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, Research Unit of Noxious Chemistry and Environmental Engineering, P.O. Box 67, Dschang, Cameroon
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12
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Structural insights, spectral, flourescence, Z-scan, C-H…O/N-H…O hydrogen bonding and AIM, RDG, ELF, LOL, FUKUI analysis, NLO activity of N-2(Methoxy phenyl) acetamide. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Mishra SK, Parikh A, Rangan K, Sah AK. Crystal Structure of
N
‐(2‐Hydroxynapthylidene)‐L‐isoleucinyl‐4,6‐
O
‐ethylidene‐β‐D‐glucopyranosylamine and an Insight from Experimental and Theoretical Calculations. CRYSTAL RESEARCH AND TECHNOLOGY 2022. [DOI: 10.1002/crat.202200209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Santosh K. Mishra
- Department of Chemistry Birla Institute of Technology and Science, Pilani Pilani Campus Pilani Rajasthan 333031 India
| | - Anuvasita Parikh
- Department of Chemistry Birla Institute of Technology and Science, Pilani Pilani Campus Pilani Rajasthan 333031 India
| | - Krishnan Rangan
- Department of Chemistry Birla Institute of Technology and Science, Pilani Hyderabad Campus Hyderabad Telangana 500078 India
| | - Ajay K. Sah
- Department of Chemistry Birla Institute of Technology and Science, Pilani Pilani Campus Pilani Rajasthan 333031 India
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14
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M JP, Samson Y, Dhas DA, Joe IH. Exploration of Non Covalent Interactions, Structural, Vibrational, Chemical Reactivity and NLO Properties of 1, 2-Diphenyl-2-Methoxyethanone Oxime: A Theoretical Approach. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2135547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jini Pramila M
- Manonmanium Sundaranar University, Tirunelveli, India
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - Y. Samson
- Department of Physics, Annai Velankanni College, Tholayavattam, India
| | - D. Arul Dhas
- Department of Physics and Research Centre, Nesamony Memorial Christian College, Marthandam, India
| | - I. Hubert Joe
- Department of Physics, Centre for Molecular and Biophysics Research, Mar Ivanios College, Thiruvananthapuram, India
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15
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Exploration of Electronic and Non-Linear Optical Properties of Novel 4-Aryl-2-methylpyridine Based Compounds Synthesized via High-Yielding Pd(0) Catalysed Reaction. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Saba A, Sarwar F, Muhammad S, Ilyas M, Iqbal J, Al-Sehemi AG, Ayub K, Amjad Gilani M, Adnan M. Insighting the inhibitory potential of novel modafinil drug derivatives against estrogen alpha (ERα) of breast cancer through a triple hybrid computational methodology. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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17
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Romeu MC, Freire PT, Ayala AP, Barreto AC, Oliveira LS, de Oliveira MR, Bandeira PN, dos Santos HS, Teixeira AM, Vasconcelos DL. Synthesis, crystal structure and ATR-FTIR, FT-Raman and UV–Vis spectroscopic analysis of dihydrochalcone (3R)-3-(4-chlorophenyl)-3-hydroxy-1-(2-hydroxyphenyl)propan-1-one. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133516] [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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18
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Effect of surfactants addition on physical, structure and antimicrobial activity of (Na-CMC/Na–Alg) biofilms. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-022-04189-z] [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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19
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Fatima A, Khanum G, Verma I, Butcher RJ, Siddiqui N, Srivastava SK, Javed S. Synthesis, Characterization, Crystal Structure, Hirshfeld Surface, Electronic Excitation, Molecular Docking, and DFT Studies on 2-Amino Thiophene Derivative. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2032769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, UP, India
| | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | | | | | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
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20
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Synthesis, computational, spectroscopic, hirshfeld surface, electronic state and molecular docking studies on diethyl-5-amino-3-methylthiophene-2,4-dicarboxylate. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Structural and spectroscopic analysis of the Cis-Trans isomers of the captopril in the gaseous and aqueous phases. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130872] [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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22
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Hajam TA, Saleem H, Syed Ali Padhusha M, Mohammed Ameen KK. Quantum Mechanical Study, Spectroscopic (FT-IR, FT-Raman and UV-Vis) Study, NBO, NLO Analysis and Molecular Docking Studies of 2-Ethoxy-4-(Pyridine-2yliminomethyl)-Phenol. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1896561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - H. Saleem
- Department of Physics, Annamalai University, Annamalainagar, India
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23
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Uzzaman M, Hasan MK, Mahmud S, Yousuf A, Islam S, Uddin MN, Barua A. Physicochemical, spectral, molecular docking and ADMET studies of Bisphenol analogues; A computational approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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24
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Hajam TA, Saleem H, Padhusha MSA, Mohammed Ameen KK. Synthesis, quantum chemical calculations and molecular docking studies of 2-ethoxy-4[(2-trifluromethyl-phenylimino)methyl]phenol. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1781945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - H. Saleem
- Department of Physics, Annamalai University, Annamalainagar, India
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25
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Quantum chemical calculations, spectroscopic investigation and molecular docking analysis of 4-chloro-N-methylpyridine-2-carboxamide. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Potla KM, Poojith N, Osório FA, Valverde C, Chinnam S, Suchetan P, Vankayalapati S. An analysis of spectroscopic, computational and biological activity studies of L-shaped sulfamoylbenzoic acid derivatives: A third order nonlinear optical material. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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27
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Fonkem C, Ejuh GW, Tchangnwa Nya F, Yossa Kamsi RA, Ndjaka JMB. Theoretical study of optoelectronic properties of the molecule 2-cyano-3-[4-(diphenylamino)phenyl] acrylic acid. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-019-01790-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Saji RS, Prasana JC, Muthu S, George J, Kuruvilla TK, Raajaraman BR. Spectroscopic and quantum computational study on naproxen sodium. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 226:117614. [PMID: 31606674 DOI: 10.1016/j.saa.2019.117614] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/05/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
The spectroscopic (FT-IR, FT-Raman, NMR), electronic (UV--Vis.), structural and thermodynamical properties of an anti-inflammatory analgesic called Naproxen Sodium, (s)-6-methoxy-α-methyl-2-naphthaleneacetic acid sodium salt are submitted by using both experimental techniques and theoretical methods as quantum chemical calculations in this work. The equilibrium geometry and vibrational spectra are calculated by using DFT (B3LYP) with 6-311++G (d,p) basis set using GAUSSIAN 09. The vibrational wavenumbers are also corrected with scale factor to take better results for the calculated data. The HOMO-LUMO calculations are carried out on the title compound. The theoretical and experimental NMR peaks were found to be in good agreement. In addition, the detailed study on the Non-Bonding Orbitals, the excitation energies, AIM charges, condensed fukui calculations, thermodynamical properties, Localized Orbital Locator (LOL) and Electron Localization Function (ELF) are also performed. Furthermore, the study is extended to calculate the first order hyperpolarizability and to predict its NLO properties. The docking studies details helped on predicting the binding with different proteins.
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Affiliation(s)
- Rinnu Sara Saji
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India; University of Madras, Chennai, 600005, Tamilnadu, India
| | | | - S Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, 604407, Tamil Nadu, India.
| | - Jacob George
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India
| | - Tintu K Kuruvilla
- Department of Physics, Madras Christian College, East Tambaram, 600059, Tamil Nadu, India
| | - B R Raajaraman
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur, 602 117, Tamil Nadu, India
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29
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Synthesis, characterization, theoretical calculations and biochemical evaluation of a novel oxime ligand with complexes. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.03.169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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Gul M, Eryılmaz S. Synthesis, Antioxidant Activity and Theoretical Investigation of Isoxazolines Derivatives of Monoterpenoids. LETT ORG CHEM 2019. [DOI: 10.2174/1570178616666181226154540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 3+2 cycloaddition reactions are important to generate five-membered heterocyclic compounds
as well as altering biological activity effects based on structure. In the study, we synthesized
new isoxazoline derivatives of different monoterpenoids and examined the structure analysis using
spectroscopical analysis methods, reveal changes in the theoretical analysis related to the biological activity.
These new compounds exhibit antioxidant activities; DPPH radical scavenging, ferric reducing,
metal chelating activities which are significantly higher than the related commercial monoterpenoids.
Theoretical approaches on the compounds containing isoxazole moiety have been performed by the
DFT/B3LYP/method, 6-31G(d,p) basis set in the ground state. The global and local chemical reactivity
properties of the compounds were investigated by considering the values of electronegativity, global
hardness-softness, electronic chemical potential, electrophilicity index and condensed Fukui functions,
local softness and local electrophilicity index. Furthermore, total energy, FMOs energy values and the
dipole moment (µ), mean polarizability (α), and first order hyperpolarizability (β) values were analysed
at the theoretical level to examine the polarizability characteristics of the compounds. The antioxidant
activity values of the newly synthesized compounds were compared with a finding of the computational
study. The results obtained exhibited good correlation on some parameters.
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Affiliation(s)
- Melek Gul
- Department of Chemistry, Science-Art Faculty, Amasya University, Amasya, Turkey
| | - Serpil Eryılmaz
- Department of Physics, Science-Art Faculty, Amasya University, Amasya, Turkey
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31
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Devi P, Fatma S, Shukla S, Kumar R, Singh V, Bishnoi A. Synthesis, spectroscopic investigation, molecular docking and DFT studies of novel (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA). Heliyon 2018; 4:e01009. [PMID: 30582037 PMCID: PMC6299111 DOI: 10.1016/j.heliyon.2018.e01009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/16/2018] [Accepted: 11/30/2018] [Indexed: 11/29/2022] Open
Abstract
The synthesized compound (2Z,4Z)-2,4-bis(4-chlorobenzylidene)-5-oxo-1-phenylpyrrolidine-3-carboxylic acid (BCOPCA) was characterised by Ultraviolet, FT-Infra Red, 1H, 13C Nuclear Magnetic Resonance and mass spectroscopy. The compound was further subjected to quantum chemical calculations at the level of density functional theory (DFT) using 6-31G (d,p) basis sets method with B3LYP and CAM-B3LYP hybrid functionals. The intramolecular interactions, polarizability, hyperpolarizability and nonlinear optical properties of the title compound were also incorporated in the study. The total first static hyperpolarizability (β0 = 19.477 × 10−30 and 16.924 × 10−30 esu) value was also computed and indicated the title molecule as an interesting forthcoming NLO material. The other thermodynamic properties (entropy, heat capacity and zero vibrational energy) were also discussed. The study also includes NBO computations, complete vibrational assignments, Mulliken charges, UV–Visible spectral analysis and HOMO–LUMO energies. The regions of low and high electron density were obtained from MESP and ESP maps. The calculated parameters for BCOPCA using aforementioned functions are harmonious with the experimental findings. The in-vitro antimicrobial activity and molecular docking studies of BCOPCA were also done and showed a good correlation.
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Affiliation(s)
- Poornima Devi
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Shaheen Fatma
- Department of Chemistry, Shri Ramswaroop Memorial University, Lucknow Dewa Road, Barabanki 225003, India
| | - Shraddha Shukla
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Roop Kumar
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
| | - Vineeta Singh
- Department of Biotechnology, Institute of Engineering and Technology, Lucknow 226021, India
| | - Abha Bishnoi
- Department of Chemistry, University of Lucknow, Lucknow 226007, India
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32
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Vibrational and electronic absorption spectroscopic profiling, natural hybrid orbital, charge transfer, electron localization function and molecular docking analysis on 3-amino-3-(2-nitrophenyl) propionic acid. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.06.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Chapman S, O'Malley AJ, Parker SF, Raja R. Comprehensive Vibrational Spectroscopic Characterization of Nylon-6 Precursors for Precise Tracking of the Beckmann Rearrangement. Chemphyschem 2018; 19:3196-3203. [PMID: 30253015 DOI: 10.1002/cphc.201800721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Indexed: 11/05/2022]
Abstract
As a key step in nylon-6 synthesis, the Beckmann rearrangement is an ongoing target of catalytic studies that seek to improve the sustainability of polymer manufacture. Whilst solid-acid catalysts (predominantly zeotypes) have proven effective for this transformation, the development of more active and selective systems demands an understanding of fundamental catalytic mechanisms. In this undertaking, in situ and operando characterization techniques can be informative, provided rigorous spectroscopic groundwork is in place. Thus, to facilitate mechanistic studies we present a detailed investigation of the vibrational spectra of cyclohexanone, cyclohexanone oxime, ϵ-caprolactam and their D10-isotopomers, in the solid state. Variable-temperature infrared (150-300 K) and Raman (10-300 K) spectra are reported alongside inelastic neutron scattering data. Moreover, where key vibrational modes have been assigned with the aid of periodic density functional theory calculations, it has been possible to include hydrogen-bonding interactions explicitly.
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Affiliation(s)
- Stephanie Chapman
- School of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Alexander J O'Malley
- Centre for Sustainable Chemical Technologies (CSCT), Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, CF10 3AT, UK
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Oxon, OX11 0QX, UK
| | - Stewart F Parker
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Oxon, OX11 0QX, UK
- ISIS Pulsed Neutron and Muon Facility, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Oxon, OX11 0QX, UK
| | - Robert Raja
- School of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
- UK Catalysis Hub, Research Complex at Harwell, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Oxon, OX11 0QX, UK
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34
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The vibrational spectroscopic studies and molecular property analysis of Estradiol, Tamoxifen and their interaction by density functional theory. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Zülfikaroğlu A, Batı H, Dege N. A theoretical and experimental study on isonitrosoacetophenone nicotinoyl hydrazone: Crystal structure, spectroscopic properties, NBO, NPA and NLMO analyses and the investigation of interaction with some transition metals. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.079] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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36
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Growth, density functional theory (DFT) and spectral studies on L-2-aminobutyric acid –biologically active material. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Conjugates of natural chlorins with cyclen as chelators of transition metals. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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38
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Kaya EÇ, Kaya AA, Demircioğlu Z, Büyükgüngör O. Synthesis, spectroscopic characterization, X-ray structure and DFT calculations of Ni(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate. HETEROCYCL COMMUN 2017. [DOI: 10.1515/hc-2016-0099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractA single crystal of Ni(II)bis(3,4 dimethoxybenzoate)bis(nicotinamide) dihydrate, formulated as C30H34N4NiO12 (I), was characterized in the solid state by infra-red (IR), ultra-violet (UV) and single crystal X-ray diffraction analysis at 296 K as mononuclear with a distorted octahedral stereochemistry. The complex consists of a six-coordinate Nickel atom in a distorted octahedral environment constructed from two N atoms and four O atoms and crystallizes in the monoclinic space group C 2/c with a=27.7680(16) Å, b=8.5748(3) Å, c=17.8018(9) Å, α=90°, β=108.154(4)°, γ=90°, Z=4. The molecular structure and geometry was also optimized using the B3LYP density functional theory method employing the 6-31G(d) basis set. The molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, nonlinear optical properties (NLO) and natural bond analysis (NBO), Mulliken population analyis, natural population analysis (NPA) and Fukui function analysis were also described.
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Affiliation(s)
- Elif Çelenk Kaya
- 1School of Health, Gümüşhane University, TR-29100, Gümüşhane, Turkey
| | - Afşin Ahmet Kaya
- 1School of Health, Gümüşhane University, TR-29100, Gümüşhane, Turkey
| | - Zeynep Demircioğlu
- 2Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Kurupelit-Samsun, Turkey
| | - Orhan Büyükgüngör
- 2Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Kurupelit-Samsun, Turkey
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39
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Kose E, Karabacak M, Bardak F, Atac A. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.088] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Molecular structure, experimental and theoretical spectroscopic characterization and non-linear optical properties studies of a new non-centrosymmetric hybrid material. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Eryılmaz S, Gül M, İnkaya E, İdil Ö, Özdemir N. Synthesis, crystal structure analysis, spectral characterization, quantum chemical calculations, antioxidant and antimicrobial activity of 3-(4-chlorophenyl)-3a,4,7,7a-tetrahydro-4,7-methanobenzo[d]isoxazole. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Durgun M, Ceylan Ü, Yalçın ŞP, Türkmen H, Özdemir N, Koyuncu İ. Synthesis, molecular structure, spectroscopic characterization, NBO, NLO and NPA analysis and in vitro cytotoxicity study of 3-chloro-N-(4-sulfamoylphenethyl)propanamide with experimental and computational study. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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43
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Isoxazole derivatives of alpha-pinene isomers: Synthesis, crystal structure, spectroscopic characterization (FT-IR/NMR/GC–MS) and DFT studies. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.11.079] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Baykara H, Ilhan S, Oztomsuk A, Seyitoglu MS, Levent A, Okumus V, Dündar A. Synthesis and Characterization of a New Difunctional Ligand and Its Metal Complexes: An Experimental, Theoretical, Cyclic Voltammetric, and Antimicrobial Study. SYNTHESIS AND REACTIVITY IN INORGANIC, METAL-ORGANIC, AND NANO-METAL CHEMISTRY 2015; 45:1795-1807. [DOI: https:/doi.org/10.1080/15533174.2013.872134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 11/24/2013] [Indexed: 07/01/2024]
Affiliation(s)
- Haci Baykara
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Salih Ilhan
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Abdussamet Oztomsuk
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - M. Salih Seyitoglu
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Abdulkadir Levent
- Batman University, Health Services Vocational College, Batman, Turkey
| | - Veysi Okumus
- Faculty of Art and Science, Biology Department, Siirt University, Siirt, Turkey
| | - Abdurrahman Dündar
- Mardin Artuklu University, Vocational Higher School of Health Services, Medical Promotion and Marketing Program, Mardin, Turkey
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45
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Baykara H, Ilhan S, Oztomsuk A, Seyitoglu MS, Levent A, Okumus V, Dündar A. Synthesis and Characterization of a New Difunctional Ligand and Its Metal Complexes: An Experimental, Theoretical, Cyclic Voltammetric, and Antimicrobial Study. ACTA ACUST UNITED AC 2015. [DOI: 10.1080/15533174.2013.872134] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Haci Baykara
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Salih Ilhan
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Abdussamet Oztomsuk
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - M. Salih Seyitoglu
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Abdulkadir Levent
- Batman University, Health Services Vocational College, Batman, Turkey
| | - Veysi Okumus
- Faculty of Art and Science, Biology Department, Siirt University, Siirt, Turkey
| | - Abdurrahman Dündar
- Mardin Artuklu University, Vocational Higher School of Health Services, Medical Promotion and Marketing Program, Mardin, Turkey
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46
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Ceylan Ü, Durgun M, Türkmen H, Yalçın ŞP, Kilic A, Özdemir N. Theoretical and experimental investigation of 4-[(2-hydroxy-3-methylbenzylidene)amino]benzenesulfonamide: Structural and spectroscopic properties, NBO, NLO and NPA analysis. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.02.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Arshad MN, Asiri AM, Alamry KA, Mahmood T, Gilani MA, Ayub K, Birinji AS. Synthesis, crystal structure, spectroscopic and density functional theory (DFT) study of N-[3-anthracen-9-yl-1-(4-bromo-phenyl)-allylidene]-N-benzenesulfonohydrazine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 142:364-74. [PMID: 25721652 DOI: 10.1016/j.saa.2015.01.101] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 12/23/2014] [Accepted: 01/30/2015] [Indexed: 05/28/2023]
Abstract
N-[3-anthracen-9-yl-1-(4-bromo-phenyl)-allylidene]-N-benzenesulfonohydrazine has been synthesized and characterized by various spectroscopic techniques including FT-IR, UV-vis, (1)H-NMR, (13)C-NMR spectroscopy, and the structure was unequivocally confirmed by single crystal X-ray diffraction studies. The compound crystallized in monoclinic system with P21/n space group, and adopted cis-geometry around the azomethine CN double bond. The X-ray crystal structure revealed that the intermolecular packing was stabilized by C-H⋯O type hydrogen bonding interaction, whereas NH was not involved in hydrogen bonding due to steric hindrance. Absorption wavelength was studied by scanning UV-vis. absorption spectrum in different solvents to explore excited state stability of the molecule in polar solvent. Density functional theory calculations were performed at B3LYP/6-31G (d, p) level in order to compare the experimental results with the theoretical results. The simulated molecular electrostatic potential (MEP), Mulliken charges and NPA (natural population analysis) also confirmed the presence of specific intermolecular hydrogen bonding (C-H⋯O). In addition natural bond orbital (NBO) analysis (intra and inter molecular bonding and interaction among bonds), frontier molecular orbital analysis (electronic properties) and first hyperpolarizability analysis (nonlinear optical response) were simulated at B3LYP/6-31G (d, p) level of theory.
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Affiliation(s)
- Muhammad Nadeem Arshad
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Khalid A Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Tariq Mahmood
- Department of Chemistry, COMSATS Institute of Information Technology, University Road, Tobe Camp, 22060 Abbottabad, Pakistan.
| | - Mazhar Amjad Gilani
- Department of Chemical Engineering, COMSATS Institute of Information Technology, Defence Road, Off Raiwind Road, Lahore, Pakistan.
| | - Khurshid Ayub
- Department of Chemistry, COMSATS Institute of Information Technology, University Road, Tobe Camp, 22060 Abbottabad, Pakistan; Department of Chemistry, College of Science, King Faisal University, Al-Hafouf 31982, Saudi Arabia
| | - Abdulhadi Salih Birinji
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; Centre of Excellence for Advanced Materials Research (CEAMR), King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
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48
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Demircioğlu Z, Kaştaş ÇA, Büyükgüngör O. The spectroscopic (FT-IR, UV-vis), Fukui function, NLO, NBO, NPA and tautomerism effect analysis of (E)-2-[(2-hydroxy-6-methoxybenzylidene)amino]benzonitrile. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 139:539-548. [PMID: 25579656 DOI: 10.1016/j.saa.2014.11.078] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 10/17/2014] [Accepted: 11/23/2014] [Indexed: 06/04/2023]
Abstract
A new o-hydroxy Schiff base, (E)-2-[(2-hydroxy-6-methoxybenzylidene)amino]benzonitrile was isolated and investigated by experimental and theoretical methodologies. The solid state molecular structure was determined by X-ray diffraction method. The vibrational spectral analysis was carried out by using FT-IR spectroscopy in the range of 4000-400cm(-)(1). Theoretical calculations were performed by density functional theory (DFT) method using 6-31G(d,p) basis set. The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The UV-vis spectrum of the compound was recorded in the region 200-800 nm in several solvents and electronic properties such as excitation energies, and wavelengths were calculated by TD-DFT/B3LYP method. The most prominent transitions were corresponds to π→π∗. Hybrid density functional theory (DFT) was used to investigate the enol-imine and keto-amine tautomers of titled compound. The titled compound showed the preference of enol form, as supported by X-ray and spectroscopic analysis results. The geometric and molecular properties were compaired for both enol-imine and keto-amine forms. Additionally, geometry optimizations in solvent media were performed with the same level of theory by the integral equation formalism polarizable continuum (IEF-PCM). Stability of the molecule arises from hyperconjugative interactions, charge delocalization and intramolecular hydrogen bond has been analyzed using natural bond orbital (NBO) analysis. Mulliken population method and natural population analysis (NPA) have been studied. Also, condensed Fukui function and relative nucleophilicity indices calculated from charges obtained with orbital charge calculation methods (NPA). Molecular electrostatic potential (MEP) and non linear optical (NLO) properties are also examined.
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Affiliation(s)
- Zeynep Demircioğlu
- Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, TR-55139 Kurupelit-Samsun, Turkey.
| | - Çiğdem Albayrak Kaştaş
- Department of Chemistry, Faculty of Arts and Science, Sinop University, TR-57000 Sinop, Turkey
| | - Orhan Büyükgüngör
- Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, TR-55139 Kurupelit-Samsun, Turkey
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49
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Govindasamy P, Gunasekaran S. Spectroscopic (FT-IR, FT-Raman and UV) investigation, NLO, NBO, molecular orbital and MESP analysis of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt C:1543-1556. [PMID: 25459716 DOI: 10.1016/j.saa.2014.10.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/27/2014] [Accepted: 10/15/2014] [Indexed: 06/04/2023]
Abstract
In this work, FT-IR and FT-Raman spectra of 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetic acid (abbreviated as 2DCPAPAA) have been reported in the regions 4000-450cm(-1) and 4000-50cm(-1), respectively. The molecular structure, geometry optimization, intensities, vibrational frequencies were obtained by the ab initio and DFT levels of theory B3LYP with 6-311++G(d,p) standard basis set and a different scaling of the calculated wave numbers. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using vibrational energy distribution analysis (VEDA 4) program. The harmonic frequencies were calculated and the scaled values were compared with experimental FT-IR and FT-Raman data. The observed and the calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The thermodynamic properties of the title compound at different temperature reveal the correlations between standard heat capacities (C) standard entropies (S) standard enthalpy changes (ΔH). The important non-linear optical properties such as electric dipole momentum, polarizability and first hyperpolarizability of 2DCPAPAA have been computed using B3LYP/6-311++G(d,p) quantum chemical calculations. The Natural charges, HOMO, LUMO, chemical hardness (η), chemical potential (μ), Electro negativity (χ) and electrophilicity values (ω) are calculated and reported. The oscillator's strength, wave length, and energy calculated by TD-DFT and 2DCPAPAA is approach complement with the experimental findings. The molecular electrostatic potential (MESP) surfaces of the molecule were constructed.
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Affiliation(s)
- P Govindasamy
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India.
| | - S Gunasekaran
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India; Research and Development St. Peter's Institute of Higher Education and Research, St. Peter's University, Avadi, Chennai 600054, TN, India
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50
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Quantum mechanical calculations and spectroscopic (FT-IR, FT-Raman and UV) investigations, molecular orbital, NLO, NBO, NLMO and MESP analysis of 4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl] benzene-1-sulfonamide. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.10.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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