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Khadka M, Sah M, Chaudhary R, Sahani SK, Sahani K, Pandey BK, Pandey D. Spectroscopic, quantum chemical, and topological calculations of the phenylephrine molecule using density functional theory. Sci Rep 2025; 15:208. [PMID: 39747169 PMCID: PMC11697212 DOI: 10.1038/s41598-024-81633-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 11/27/2024] [Indexed: 01/04/2025] Open
Abstract
In this work, Density Functional Theory (DFT) on Gaussian 09 W software was utilized to investigate the phenylephrine (PE) molecule (C9H13NO2). Firstly, the optimized structure of the PE molecule was obtained using B3LYP/6-311 + G (d, p) and CAM-B3LYP/6-311 + G (d, p) basis sets. The electron charge density is shown in Mulliken atomic charge as a bar chart and also as a color-filled map in Molecular Electrostatic Potential (MEP). Using these properties, the possibility of different charge transfers occurring within the molecule was evaluated. The calculated values of the energy gap from HOMO-LUMO mapping, illustrated in Frontier Molecular Orbitals (FMO) and Density of State (DOS), were found to be similar for both the neutral and anion states in the gaseous and water solvent phases. Both the global and local reactivity were studied to understand the reactivity of the PE molecule. Using the thermodynamic parameters, the thermochemical property of the title molecule was understood. Non-covalent interaction was studied to understand the Van der Waals interactions, hydrogen bonds, and steric repulsion in the title molecule. Natural Bond Orbital (NBO) Analysis was performed to understand the strongest stabilization interaction. In the vibrational analysis, Total Electron Density (TED) assignments were done in the intense region where the frequency of the title molecule was shifted distinctly. For vibrational spectroscopy, FT-IR and Raman spectra in the neutral and anion states were plotted and compared. Using the TD-DFT technique, the UV-Vis spectra along with Tauc's plot were studied. Finally, topological analysis, electron localized function (ELF), and localized orbital locator (LOL) were performed in the PE molecule.
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Affiliation(s)
- Mukesh Khadka
- Department of Physics, St.Xavier College, Maitighar, Kathmandu, Nepal
| | - Manoj Sah
- Department of Physics, St.Xavier College, Maitighar, Kathmandu, Nepal
| | - Raju Chaudhary
- Department of Physics, St.Xavier College, Maitighar, Kathmandu, Nepal
| | - Suresh Kumar Sahani
- Department of Science and Technology, Rajarshi Janak University, Janakpurdham, Nepal.
| | - Kameshwar Sahani
- Department of Civil Engineering, Kathmandu University, Kathmandu, Nepal
| | - Binay Kumar Pandey
- Department of Information Technology, College of Technology Govind Ballabh Pant, University of Agriculture and Technology, Pantnagar, Uttrakhand, India
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Hrubaru MM, Draghici C, Ngounoue Kamga FA, Diacu E, Egemonye TC, Ekennia AC, Ungureanu EM. Experiments and Calculation on New N,N- bis-Tetrahydroacridines. Molecules 2024; 29:4082. [PMID: 39274930 PMCID: PMC11396808 DOI: 10.3390/molecules29174082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 09/16/2024] Open
Abstract
Tetrahydroacridines arouse particular interest due to the potential possibilities of application in the medical field and protection against corrosion. Bis-tetrahydroacridines were newly synthesized by Pfitzinger condensation of 5,5'-(ethane-1,2-diyl) diindoline-2,3-dione with several cyclanones. NMR, MS, and FT-IR were used to prove their molecular structure. In addition, a computer-aided study was performed for the lowest energy conformers of each structure, in vacuum conditions, at ground state using DFT models to assess their electronic properties. UV-Vis and voltammetric methods (cyclic voltammetry, differential pulse voltammetry, and rotating disk electrode voltammetry) were used to investigate their optical and electrochemical properties. The results obtained for these π-conjugated heteroaromatic compounds lead to the conclusion that they have real potential in applications in different fields such as pharmaceuticals and especially as corrosion inhibitors.
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Affiliation(s)
- Madalina-Marina Hrubaru
- "C. D. Nenitzescu" Institute of Organic and Supramolecular Chemistry, Romanian Academy, Bucharest, Sector 6, Splaiul Independentei 202B, P.O. Box 35-108, 060023 Bucharest, Romania
- Faculty of Chemical Engineering and Biotechnologies, National University of Science and Technology Politehnica Bucharest, 1-7 Polizu Street, Sector 1, 011061 Bucharest, Romania
| | - Constantin Draghici
- "C. D. Nenitzescu" Institute of Organic and Supramolecular Chemistry, Romanian Academy, Bucharest, Sector 6, Splaiul Independentei 202B, P.O. Box 35-108, 060023 Bucharest, Romania
| | - Francis Aurelien Ngounoue Kamga
- Coordination Chemistry Laboratory, Department of Inorganic Chemistry, Faculty of Science, University of Yaounde, Yaounde P.O. Box 812, Cameroon
| | - Elena Diacu
- Doctoral School Chemical Engineering and Biotechnologies, National University of Science and Technology Politehnica Bucharest, 1-7 Polizu Street, Sector 1, 011061 Bucharest, Romania
| | - ThankGod C Egemonye
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar 540281, Cross River State, Nigeria
| | - Anthony C Ekennia
- Department of Chemistry, Alex Ekwueme Federal University, Ndufu-Alike, P.M.B. 1010, Abakiliki 482131, Ebonyi State, Nigeria
| | - Eleonora-Mihaela Ungureanu
- Doctoral School Chemical Engineering and Biotechnologies, National University of Science and Technology Politehnica Bucharest, 1-7 Polizu Street, Sector 1, 011061 Bucharest, Romania
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Shanmuganathan R, Devanesan S, Oza G, Sharma A. Assessment of antimicrobial, antidiabetic, and anti-inflammatory properties of acetone extract of Aerva lanata (L.) by in-vitro approach and bioactive compounds characterization. ENVIRONMENTAL RESEARCH 2024; 248:118348. [PMID: 38295976 DOI: 10.1016/j.envres.2024.118348] [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: 12/07/2023] [Revised: 01/22/2024] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
The antimicrobial, antidiabetic, and anti-inflammatory activities efficiency of Aerva lanata plant extracts (aqueous (Aqu-E), acetone (Ace-E), and ethanol (Eth-E)) were investigated in this study. Furthermore, the active molecules exist in the crude extract were characterized by UV-Visible spectrophotometer, Fourier transform infrared (FTIR), High-performance liquid chromatography (HPLC), and Gas Chromatography-Mass Spectrometry (GC-MS) analyses. The preliminary phytochemical study revealed that the Ace-E restrain more phytochemicals like alkaloids, saponins, anthraquinone, tannins, phenolics, flavonoids, glycosides, terpenoids, amino acid, steroids, protein, coumarin, as well as quinine than Aqu-E and Eth-E. Accordingly to this Ace-E showed considerable antimicrobial activity as the follows: for bacteria S. aureus > E. coli > K. pneumoniae > P. aeruginosa > B. subtilis and for fungi T. viride > A.flavus > C. albicans > A.niger at 30 mg ml concentration. Similarly, Ace-E showed considerable antidiabetic (α-amylase: 71.7 % and α-glucosidase: 70.1 %) and moderate anti-inflammatory (59 % and 49.8 %) activities. The spectral and chromatogram studies confirmed that the Ace-E have pharmaceutically valuable bioactive molecules such as (Nbutyl)-octadecane, propynoic acid, neophytadiene, and 5,14-di (N-butyl)-octadecane. These findings suggest that Ace-E from A. lanata can be used to purify additional bioactive substances and conduct individual compound-based biomedical application research.
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Affiliation(s)
- Rajasree Shanmuganathan
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam; School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam.
| | - Sandhanasamy Devanesan
- Department of Physics and Astronomy, College of Science, King Saud University, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Goldie Oza
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica (CIDETEQ), Parque Tecnológico Querétaro s/n, Sanfandila. Pedro Escobedo, Querétaro 76703, Mexico
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, NatProLab, Plant Innovation Lab, School of Engineering and Sciences, Queretaro 76130, Mexico.
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Manda T, Barasa GO, Louis H, Irfan A, Agumba JO, Lugasi SO, Pembere AMS. A data-guided approach for the evaluation of zeolites for hydrogen storage with the aid of molecular simulations. J Mol Model 2024; 30:43. [PMID: 38236500 DOI: 10.1007/s00894-024-05837-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024]
Abstract
CONTEXT This study employs a data-guided approach to evaluate zeolites for hydrogen storage, utilizing molecular simulations. The development of efficient and practical hydrogen storage materials is crucial for advancing clean energy technologies. Zeolites have shown promise as potential candidates due to their unique porous structure and tunable properties. However, the selection and design of suitable zeolites for hydrogen storage remain challenging. Therefore, this work aims to address this materials science question by utilizing molecular simulations and data-guided approaches to evaluate zeolites' performance for hydrogen storage. The results obtained from this study provide valuable insights into the evaluation of zeolites for hydrogen storage. Through molecular simulations, we analyze the adsorption behavior of hydrogen molecules in various zeolite structures. The performance of different zeolite frameworks in terms of hydrogen storage capacity, adsorption energy, and diffusion properties is assessed. Linde type A zeolite (LTA) had the highest capacity with a hydrogen capacity of 4.8wt% out of the 233 investigated zeolites. Furthermore, we investigate the influence of different factors such as mass (M), density (D), helium void fraction (HVF), accessible pore volume (APV), gravimetric surface area (GSA), and largest overall cavity diameter (Di) on the hydrogen storage performance of zeolites. The results show that Di, D, and M have a negative effect on the percentage weight capacity, while GSA and VSA have the highest positive contribution to the percentage weight. This study, therefore, provides new insights into the factors that affect their hydrogen storage capacity by exhibiting the importance of considering multiple factors when evaluating the performance of zeolites and demonstrates the potential of combining different computational methods to provide a more comprehensive understanding of materials. The current study contributes to the understanding of zeolite-based materials for hydrogen storage applications, aiding in the development of more efficient and practical hydrogen storage systems. METHODS Computational techniques were employed to investigate the hydrogen storage properties of zeolites. Molecular simulations were performed using classical force fields and molecular dynamics methods. The calculations were carried out at a force field level of theory with the GGA functional. To accurately capture the thermodynamics and kinetics of hydrogen adsorption, enhanced sampling techniques such as Monte Carlo simulations and molecular dynamics with metadynamics were utilized. We employed Grand Canonical Monte Carlo (GCMC) simulations to model hydrogen adsorption in zeolite structures for hydrogen storage. Our approach involved performing a substantial number of Monte Carlo steps (10,000) to ensure system equilibration and precise results. We defined a cutoff distance for particle interactions as 12.5 Ǻ and considered 0.000e framework charge per cell and 0.000e sorbate charge in energy calculations. The choice of an appropriate simulation cell size (50 × 50 × 50) Ǻ was crucial, mirroring real-world conditions. We specified lower and upper fugacity values (1 to 10 atm) to capture the range of gas pressures in the simulations. These methodical steps collectively enabled us to accurately model hydrogen adsorption within zeolites, forming the core of our hydrogen storage evaluation. In this research, we utilized DFT calculations to thoroughly investigate the interactions between zeolites and hydrogen. We employed pseudopotentials to describe electron behavior in zeolite systems, choosing them in line with DFT norms and basis set compatibility. Our simulation cell design replicated zeolite periodicity and eliminated boundary effects. Pre-geometry optimization was performed with HyperChem29, ensuring stable conformations with strict convergence criteria. We utilized 6-31 + G(d) and LanL2DZ basis sets for light and heavy atoms, aligning with field standards for computational efficiency and precision. A machine learning algorithm was used to rank the importance of various structural features such as mass (M), density (D), helium void fraction (HVF), accessible pore volume (APV), gravimetric surface area (GSA), and largest overall cavity diameter (Di) and how they affect the capacity of the zeolites. Machine learning analysis was performed with the Scikit-learn library, an open-source Python tool. We employed a range of machine learning models, including SVMs, random forests, and neural networks, primarily for data analysis and feature extraction. Pearson correlation analysis, a classical statistical technique, was used to evaluate linear relationships between variables and assess the strength and direction of these relationships. It served as a complementary tool to understand the interplay of variables in our dataset, distinguishing it from machine learning algorithms. Further quantum chemical calculations were also performed to calculate the adsorption energy, global reactivity electronic descriptors, and natural bond orbital analysis in order to provide insights into the interaction of the zeolites with hydrogen. The simulations and data analysis were performed using BIOVIA material studio software, Gaussian, and Origin Pro software.
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Affiliation(s)
- Timothy Manda
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya
| | - Godfrey Okumu Barasa
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya.
| | - Hitler Louis
- Computational Quantum Chemistry Research Group, Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, 1115, Nigeria
| | - Ahmad Irfan
- Department of Chemistry, College of Science, King Khalid University, 61413, Abha, Saudi Arabia
| | - John Onyango Agumba
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya
| | - Solomon Omwoma Lugasi
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya
| | - Anthony M S Pembere
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology, P.O Box 210, Bondo, 40601, Kenya
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Mo Y, Yang Y, Zeng J, Ma W, Guan Y, Guo J, Wu X, Liu D, Feng L, Jia X, Yang B. Enhancing the Biopharmacological Characteristics of Asperosaponin VI: Unveiling Dynamic Self-Assembly Phase Transitions in the Gastrointestinal Environment. Int J Nanomedicine 2023; 18:7335-7358. [PMID: 38084126 PMCID: PMC10710790 DOI: 10.2147/ijn.s436372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE Asperosaponin VI (ASP VI) as an active ingredient of Dipsacus asperoides, which has a wide range of biological and pharmacological activity. However, its development and application are restricted due to the poor gastrointestinal permeability and oral bioavailability. This investigation aims to reveal the influence of the self-assembled structure by the interaction between ASP VI and endogenous components NaTC and/or DOPC in the gastrointestinal environment on its biopharmaceutical properties, and novelty elucidated the molecular mechanism for the formation of self-assembled nanomicelles. METHODS This change in phase state in gastrointestinal fluids is characterized by dynamic light scattering (DLS) and transmission electron microscope (TEM). UPLC-Q-TOF-MS was used to analyze the composition of phase components and the exposure of nanomicelles in vivo. Molecular dynamics simulation (MDS) was applied to preliminarily elucidate the self-assembly mechanism of ASP VI in the gastrointestinal environment. Furthermore, theS8 promoting absorption mechanism of nanomicelles were investigated through in vivo pharmacokinetic experiments, parallel artificial membrane permeability assay (PAMPA), quadruple single-pass intestinal perfusion in rats, and Caco-2 cell monolayer model. RESULTS We demonstrated that the ASP VI could spontaneously form dynamic self-assembled structures with sodium taurocholate (NaTC) and dipalmitoyl phosphatidylcholine (DOPC) during gastrointestinal solubilization, which promoted the gastrointestinal absorption and permeability of ASP VI and increased its exposure in vivo, thus improving the biopharmacological characteristics of ASP VI. Moreover, ASP VI-NaTC-DOPC-self-assembled nanostructures (ASP VI-NaTC-DOPC-SAN) manifested higher cellular uptake in Caco-2 cells as evidenced by flow cytometry and confocal microscopy, and this study also preliminarily revealed the mechanism of self-assembly formation of ASP VI with endogenous components NaTC and DOPC driven by electrostatic and hydrogen bonding interactions. CONCLUSION This study provides evidence that the dynamic self-assembled phase transition may play a key role in improving the biopharmacological characteristics of insoluble or low permeability active ingredients during the gastrointestinal dissolution of Chinese medicines.
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Affiliation(s)
- Yulin Mo
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Yanjun Yang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Jingqi Zeng
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Weikun Ma
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Yuxin Guan
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Jingxi Guo
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Xiaochun Wu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Dingkun Liu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Liang Feng
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Xiaobin Jia
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
| | - Bing Yang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, People’s Republic of China
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Eno EA, Cheng CR, Louis H, Gber TE, Emori W, Ita IAT, Unimke TO, Ling L, Adalikwu SA, Agwamba EC, Adeyinka AS. Investigation on the molecular, electronic and spectroscopic properties of rosmarinic acid: an intuition from an experimental and computational perspective. J Biomol Struct Dyn 2023; 41:10287-10301. [PMID: 36546691 DOI: 10.1080/07391102.2022.2154841] [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: 05/16/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
Various drugs such as corticosteroids, salbutamol, and β2 agonist are available for the treatment of asthma an inflammatory disease and its symptoms, although the ingredient and the mode of action of these drugs are not clearly elucidated. Hence this research aimed at carrying out improved scientific research with respect to the use of natural product rosmarinic acid which poses minima, side effects. Herein, we first carried out extraction, isolation, and spectroscopic (FT-IR, 1H-NMR and 13C-NMR) investigation, followed by molecular modeling analysis on the naturally occurring rosmarinic acid extracted from Rosmarinus officinalis. A detailed comparison of the experimental and theoretical vibrational analysis has been carried out using five DFT functionals: BHANDH, HSEH1PBE, M06-2X, MPW3PBE and THCTHHYB with the basis set 6-311++G (d, p) to investigate into the structural, reactivity, and stability of the isolated compound. Frontier molecular orbital analysis and appropriate quantum descriptors were calculated. Results showed that the compound was more stable at M06-2X and more reactive at HSEH1PBE with an energy gap of 6.43441 eV and 3.8047 eV, respectively, which was later affirmed by the global quantum reactivity parameters. From natural bond orbital analysis, π* → π* is the major contributor to electron transition with the summation perturbation energy of 889.57 kcal/mol, while π → π* had the perturbation energy totaling of 145.3 kcal/mol. Geometry analysis shows BHANDH to have lower bond length values and lesser deviation from 120° in carbon-carbon angle. The potency of the title molecule as an asthma drug was tested via a molecular docking approach and the binding score of -8.2 kcal/mol was observed against -7.0 of salbutamol standard drug, suggesting romarinic acid as a potential natural organic treatment for asthma.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ededet A Eno
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Chun-Ru Cheng
- Key Laboratory of Material Corrosion and Protection of Sichuan Province, Zigong, Sichuan, PR China
- College of Chemical Engineering, Institute of Pharmaceutical Engineering Technology and Application, Key Laboratory of Green Chemistry of Sichuan Institutes of Higher Education, Sichuan University of Science & Engineering, Zigong, Sichuan, PR China
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Terkumbur E Gber
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Wilfred Emori
- Key Laboratory of Material Corrosion and Protection of Sichuan Province, Zigong, Sichuan, PR China
- School of Materials Science and Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan, PR China
| | - Ima-Abasi T Ita
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Tomsmith O Unimke
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Liu Ling
- College of Chemical Engineering, Institute of Pharmaceutical Engineering Technology and Application, Key Laboratory of Green Chemistry of Sichuan Institutes of Higher Education, Sichuan University of Science & Engineering, Zigong, Sichuan, PR China
| | - Stephen A Adalikwu
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Ernest C Agwamba
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
- Department of Chemistry, Covenant University Ota, Ota, Nigeria
| | - Adedapo S Adeyinka
- Research Centre for Synthesis and Catalysis, Department of Chemical sciences, University of Johannesburg, Johannesburg, South Africa
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Sanakarganesan data T, Elangovan data N, Chandrasekar S, Ganesan E, Balachandran data V, Sowrirajan data S, Balasubramani K, Thomas R. Synthesis, Hirshfeld surface analysis, Computational, Wave function properties, Anticancer and Cytotoxicity activity of di[(p-chlorobenzyl) (dibromo)] (4,7-dimethyl-1,10-phenanthroline)tin (IV) complex. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Louis H, Mathias GE, Unimuke TO, Emori W, Ling L, Owen AE, Adeyinka AS, Ntui TN, Cheng CR. Isolation, characterization, molecular electronic structure investigation, and in-silico modeling of the anti-inflammatory potency of trihydroxystilbene. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Emori W, Ogunwale GJ, Louis H, Agwamba EC, Wei K, Unimuke TO, Cheng CR, Ejiofor EU, Asogwa FC, Adeyinka AS. Spectroscopic (UV–vis, FT-IR, FT-Raman, and NMR) analysis, structural benchmarking, molecular properties, and the in-silico cerebral anti-ischemic activity of 2-amino-6-ethoxybenzothiazole. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133318] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Latha A, Elangovan N, Manoj K, Maheswari V, Balachandran V, Balasubramani K, Sowrirajan S, Chandrasekar S, Thomas R. Synthesis, single crystal (XRD), spectral characterization, computational (DFT), quantum chemical modelling and anticancer activity of di(p-bromobenzyl) (dibromo) (1, 10-phenanthroline) tin (IV) complex. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Osigbemhe IG, Oyoita EE, Louis H, Khan EM, Etim EE, Edet HO, Ikenyirimba OJ, Oviawe AP, Obuye F. Antibacterial potential of N-(2-furylmethylidene)-1, 3, 4-thiadiazole-2-amine: Experimental and theoretical investigations. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Ethanol Conversion to Butanol over Small Coinage Metal Clusters: An Experimental and Computational Study. J CLUST SCI 2022. [DOI: 10.1007/s10876-022-02344-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Evidence of significant non-covalent interactions in the solution of Levetiracetam in water and methanol. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Synthesis, characterization, DFT studies, and molecular modeling of 2-(-(2-hydroxy-5-methoxyphenyl)-methylidene)-amino) nicotinic acid against some selected bacterial receptors. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02550-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Antibacterial Potential of 2-(-(2-Hydroxyphenyl)-methylidene)-amino)nicotinic Acid: Experimental, DFT Studies, and Molecular Docking Approach. Appl Biochem Biotechnol 2022; 194:5680-5701. [PMID: 35802239 DOI: 10.1007/s12010-022-04054-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 11/02/2022]
Abstract
The problems associated with antibacterial drug discovery have kept the model of antibacterial drug to an extraordinary low level. Humans carry millions of bacteria; some species of bacteria can cause infectious disease, while some are pathogenic. Infectious bacteria which can reproduce quickly in the body can cause diseases such as tuberculosis, cholera, pneumonia, and typhoid, thus arises an urgent need to develop new drugs. Herein, 2-{[(2-hydroxyphenyl)methylidene]amino}nicotinic acid was synthesized from the condensation of o-phenylenediamine and 5-nitrosalicaldehyde followed by detailed characterization by ultraviolet-visible spectroscopy, vibrational studies FT-IR, nuclear magnetic resonance (1H-NMR, 13C-NMR), and gas chromatography coupled with mass spectroscopy (GC-MS). The complex synthesized was screened against selected microbes in order to establish their potential antimicrobial activity using selected known drugs as reference. From the results obtained, the Schiff base exhibited antimicrobial activity against all the tested microorganisms except Candida albicans isolate, which exhibited zero diameter zone of inhibition. The theoretical investigations of the synthesized compounds were computed using density functional theory (DFT) at the B3LYP/6-311 + + G(d, p) level of theory and in silico molecular docking simulation. By comparing binding affinity of the studied compound and the standard drug (ampicillin), the studied compound docked against bacterial protein showed a high binding affinity for E. coli 6.6 kcal/mol and makes it effective as an antibacterial agent for E. coli.
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Wei K, Louis H, Emori W, Idante PS, Agwamba EC, Cheng CR, Eno EA, Unimuke TO. Antispasmodic activity of carnosic acid extracted from rosmarinus officinalis: Isolation, spectroscopic characterization, DFT studies, and in silico molecular docking investigations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132795] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Synthesis, vibrational analysis, molecular property investigation, and molecular docking of new benzenesulphonamide-based carboxamide derivatives against Plasmodium falciparum. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133796] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Eno EA, Louis H, Unimuke TO, Egemonye TC, Adalikwu SA, Agwupuye JA, Odey DO, Abu AS, Eko IJ, Ifeatu CE, Ntui TN. Synthesis, characterization, and theoretical investigation of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)asmino-4-(2,4-dichlorophenyl)thiazol-5-yl-diazenyl)phenyl as potential SARS-CoV-2 agent. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Abstract
The synthesis of 4-chloro-6(phenylamino)-1,3,5-triazin-2-yl)amino-4-(2,4 dichlorophenyl)thiazol-5-yl-diazenyl)phenyl is reported in this work with a detailed structural and molecular docking study on two SARS-COV-2 proteins: 3TNT and 6LU7. The studied compound has been synthesized by the condensation of cyanuric chloride with aniline and characterized with various spectroscopic techniques. The experimentally obtained spectroscopic data has been compared with theoretical calculated results achieved using high-level density functional theory (DFT) method. Stability, nature of bonding, and reactivity of the studied compound was evaluated at DFT/B3LYP/6-31 + (d) level of theory. Hyper-conjugative interaction persisting within the molecules which accounts for the bio-activity of the compound was evaluated from natural bond orbital (NBO) analysis. Adsorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) properties of the experimentally synthesized compound was studied to evaluate the pharmacological as well as in silico molecular docking against SARS-CoV-2 receptors. The molecular docking result revealed that the investigated compound exhibited binding affinity of −9.3 and −8.8 for protein 3TNT and 6LU7 respectively. In conclusion, protein 3TNT with the best binding affinity for the ligand is the most suitable for treatment of SARS-CoV-2.
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Affiliation(s)
- Ededet A. Eno
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Tomsmith O. Unimuke
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - ThankGod C. Egemonye
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Stephen A. Adalikwu
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
| | - John A. Agwupuye
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences , University of Calabar , Calabar , Nigeria
| | - Diana O. Odey
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Biochemistry, Faculty of Physical Sciences , Cross River University of Technology , Calabar , Nigeria
| | - Abu Solomon Abu
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Marine Biology, Faculty of Biology Sciences , University of Calabar , Calabar , Nigeria
| | - Ishegbe J. Eko
- Department of Polymer and Textile Engineering , Ahmadu Bello University Zaria , Kaduna , Nigeria
| | - Chukwudubem E. Ifeatu
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
| | - Tabe N. Ntui
- Computational and Bio-Simulation Research Group , University of Calabar, Calabar , Nigeria
- Department of Chemistry, Faculty of Physical Sciences , Cross River University of Technology , Calabar , Nigeria
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Eno EA, Louis H, Ekoja P, Benjamin I, Adalikwu SS, Orosun MM, Unimuke TO, Asogwa FC, Agwamba EC. Experimental and computational modeling of the biological activity of benzaldehyde sulphur trioxide as a potential drug for the treatment of Alzheimer disease. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100532] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Eno EA, Mbonu JI, Louis H, Patrick-Inezi FS, Gber TE, Unimke TO, Okon EE, Benjamin I, Offiong OE. Antimicrobial activities of 1-phenyl-3-methyl-4-trichloroacetyl-pyrazolone: Experimental, DFT studies, and molecular docking investigation. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100524] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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21
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Undiandeye UJ, Louis H, Gber TE, Egemonye TC, Agwamba EC, Undiandeye IA, Adeyinka AS, Ita BI. Spectroscopic, conformational analysis, structural benchmarking, excited state dynamics, and the photovoltaic properties of Enalapril and Lisinopril. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100500] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Vibrational Characterization and Molecular Electronic Investigations of 2-acetyl-5-methylfuran using FT-IR, FT-Raman, UV-VIS, NMR, and DFT Methods. J Fluoresc 2022; 32:1005-1017. [PMID: 35247130 DOI: 10.1007/s10895-022-02903-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/13/2022] [Indexed: 12/11/2022]
Abstract
Spectroscopic (FT-IR, FT-Raman, UV-vis, and NMR) techniques have been extensively used for structural elucidation of compounds along with the study of geometrical and vibrational properties. Herein, 2-acetyl-5-methylfuran, a derivative of furan, was experimentally characterized and analyzed in details using FT-IR, FT-Raman, UV-vis, and 1H NMR spectroscopic techniques conducted in different solvents. The experimentally analyzed spectral results were carefully compared with theoretical values obtained using density functional theory (DFT) calculations at the B3LYP/6-311 + + G (d, p) method to support, validate, and provide more insights on the structural characterizations of the titled compound. The correlated experimental and theoretical structural vibrational assignments along with their potential energy distributions (PEDs) and all the spectroscopic spectral investigations of the titled structure were observed to be in good agreements with calculated results.
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Shobana D, Sudha S, Ramarajan D, Dimić D. Synthesis, crystal structure, spectral characterization and Hirshfeld surface analysis of (E)-N′-(3-ethoxy-4-hydroxybenzylidene)-4-fluorobenzohydrazide single-crystal – a novel NLO active material. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131856] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Louis H, Ifediora LP, Enudi OC, Unimuke TO, Asogwa FC, Moshood YL. Evaluation of the excited state dynamics, photophysical properties, and the influence of donor substitution in a donor-
π
-acceptor system. J Mol Model 2021; 27:284. [PMID: 34515856 DOI: 10.1007/s00894-021-04875-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
There have been numerous attempts for the theoretical design of a better donor-π -acceptor structural framework with improved absorption and emission properties. However, for effective dye designing, it is necessary to understand the electronic and photophysical properties of the dye systems. In this work, we report a detailed density functional theory (DFT) and time-dependent density functional theory (TD-DFT) investigations of the excited state characteristics and the influence of various groups (-HCO, =CH2, (-CH3)2, (HCO)2, and (-OCH3)2) attached to the donor group (-NH2) in a p-nitroaniline D-π -A system which are symbolized respectively as p-nitroaniline (A), N,N-dimethylnitroaniline (A2), N,N-dicarbonylnitroaniline (A3), N-methylenenitroaniline (A4), and N,N-dimethoxynitroaniline (A5). The first principles DFT and TD-DFT calculations from the ground state (S0) to the first five excited states: (S0→S1), (S0→S2), (S0→S3), (S0→S4), and (S0→S5) were utilized to explore the reactivity of D-π -A system using the conceptual DFT approach, characterization of electron excitation using the hole-electron analysis, visual study of the various real space functions in the hole-electron framework, density of states (DOS), measurement of charge transfer (CT) length of electron excitation (Δ r ), measurement of the overlapping degrees of hole and electron of electron excitation (Λ ), interfragment charge transfer (IFCT) during electron excitation, and the second-order perturbation energy analysis from the natural bond orbitals (NBO) computation. Results of the excitation studies show that all the studied compounds exhibited an n→π * localized type for first excitations (S0→S1) on -NO2 group in A, A2, A4, and A5 and -NCl2 in A3.π →π * charge transfer excitations were confirmed for S0→S2/S4/S5 in A and A2, S0→S3/S4/S5 in A3 and A5, and S0→S4/S5 in A4. The NBO second-order perturbation energy analysis suggest that the most significant hyperconjugative interactions wereπ ( C 1 − C 2 ) → L P ∗ ( 1 ) C 6 (54.43kcal/mol),π C 1 − C 2 → L P ( 1 ) C 3 (40.82kcal/mol),π N 14 − O 16 → L P ( 3 ) O 15 (11.67kcal/mol),π ( C 1 − C 6 ) → π ∗ ( N 12 − O 13 ) (29.52kcal/mol),π ( N 12 − O 13 ) → L P ( 3 ) O 14 (11.55kcal/mol),π ( C 3 − C 4 ) → π ∗ ( C 5 − C 6 ) (23.40kcal/mol), andπ ( C 5 − C 6 ) → π ∗ ( N 12 − O 14 ) (24.88kcal/mol)π ( C 3 − C 4 ) → π ∗ ( C 5 − C 6 ) (24.64kcal/mol), which respectively corresponds to the A, A2, A3, A4, and A5 D-π -A systems under investigation, and these strong interactions stabilize the systems.
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Affiliation(s)
- Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria.
| | - Linda P Ifediora
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Obieze C Enudi
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Tomsmith O Unimuke
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Fredrick C Asogwa
- Computational and Bio-Simulation Research Group, University of Calabar, Calabar, Nigeria
| | - Yusuff L Moshood
- UFR Chimie at Biologie, Universite Grenoble Alpes, Grenoble, France
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Louis H, Onyebuenyi IB, Odey JO, Igbalagh AT, Mbonu MT, Eno EA, Pembere AMS, Offiong OE. Synthesis, characterization, and theoretical studies of the photovoltaic properties of novel reactive azonitrobenzaldehyde derivatives. RSC Adv 2021; 11:28433-28446. [PMID: 35480716 PMCID: PMC9038037 DOI: 10.1039/d1ra05075c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
All dyes conduct but at different degrees of absorption; it is interesting to study the degree of conductivity and absorptivity of novel reactive azo-dyes in respect to dye-sensitized solar cells (DSSCs) to ascertain their viability for such applications. In this study, four novel reactive azo-dyes were experimentally synthesized from p-aminobenzaldehyde, 4-amino-3-nitrobenzaldehyde, and aniline through series of condensation and coupling reactions. The various functional groups, molecular connectivities, and molecular weight of the various fragments of the synthesized dyes were elucidated using the GC-MS, FT-IR, UV-vis, and NMR respectively. The experimentally determined structures were modeled and investigated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) approaches to computationally compute the electronic structure properties, reactivity, absorption and solvatochromism in four different phases: gas, ethanol, acetone, and water, and the photovoltaic properties for possible applications in dye-sensitized solar cells (DSSCs). By comparing the HOMO (E H) and the LUMO (E L) energies from the results obtained demonstrates that dye D has the highest E L energy value of -2.48 eV with a relatively lowest E H energy value of -5.63 eV such that it lies underneath the conduction band edge of TiO2 which is necessary to enable charge regeneration. Pi-electron delocalization was observed from the natural bond orbital (NBO) calculations between the different aromatic rings with dye B and A having the relatively highest and least second-order stabilization energies between σ* → σ* and LP* → LP interacting orbitals respectively. It is also observed in all the solvents that the Gibbs free energy of injection (ΔG inject) is greater than 0.2 eV and hence, all the studied azo structures in the four phases provided efficient electron injection and light harvesting efficiency (LHE), however, the value of ΔG inject for dyes B and D is greatest in all the four phases and thus, provided the highest electron injection of all the dyes. From the fact-findings of quantum theory of atoms-in-molecules (QTAIM), dyes A and C have extra-stability due to their relatively high numbers of intramolecular H-bond interactions along with some additional intra-atomic bonding between atoms within the studied compounds. Hence, all the four dyes are good for DSSCs applications.
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Affiliation(s)
- Hitler Louis
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Izubundu B Onyebuenyi
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Joseph O Odey
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Azuaga T Igbalagh
- Department of Chemical Sciences, Federal University of Wukari Wukari Nigeria
| | - MaryJane T Mbonu
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Ededet A Eno
- Computational and Bio-Simulation Research Group, Department of Pure and Applied Chemistry, University of Calabar Calabar Nigeria
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
| | - Anthony M S Pembere
- Department of Physical Sciences, Jaramogi Oginga Odinga University of Science and Technology Bondo Kenya
| | - Offiong E Offiong
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar Calabar Nigeria
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Agwupuye JA, Neji PA, Louis H, Odey JO, Unimuke TO, Bisiong EA, Eno EA, Utsu PM, Ntui TN. Investigation on electronic structure, vibrational spectra, NBO analysis, and molecular docking studies of aflatoxins and selected emerging mycotoxins against wild-type androgen receptor. Heliyon 2021; 7:e07544. [PMID: 34345733 PMCID: PMC8319581 DOI: 10.1016/j.heliyon.2021.e07544] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/17/2021] [Accepted: 07/07/2021] [Indexed: 01/21/2023] Open
Abstract
The geometry, frontier molecular orbitals (FMOs), vibrational, NBO analysis, and molecular docking simulations of aflatoxins (B1, B2, M1, M2, G1, G2), zearalenone (ZEA) emodin (EMO), alternariol (AOH), alternariol monoethyl ether (AMME), and tenuazonic acid (TeA) mycotoxins have been extensively theoretically studied and discussed based on quantum density functional theory calculations using Gaussian 16 software package. The theoretical computation for the geometry optimization, NBOs, and the molecular docking interaction was conducted using Density Functional Theory with B3LYP/6-31+G(d,p), NBO program, and AutoDock Vina tools respectively. Charge delocalization patterns and second-order perturbation energies of the most interacting natural bond orbitals (NBOs) of these mycotoxins have also been computed and predicted. Interestingly, among the mycotoxins investigated, aflatoxin G1 is seen to give the strongest stabilization energy while Zearalenone shows the highest tendency to accept electron(s) and emodin, an emerging mycotoxin gave the best binding pose within the androgen receptor pocket with a mean binding affinity of -7.40 kcal/mol.
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Affiliation(s)
- John A. Agwupuye
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
- Computational Quantum Chemistry Research Group, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Peter A. Neji
- Department of Chemistry, Faculty of Sciences, Cross River University of Technology, Calabar, Nigeria
| | - Hitler Louis
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
- Computational Quantum Chemistry Research Group, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Joseph O. Odey
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Tomsmith O. Unimuke
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Emmanuel A. Bisiong
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Ededet A. Eno
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Patrick M. Utsu
- Department of Pure and Applied Chemistry, Faculty of Physical Sciences, University of Calabar, Calabar, Nigeria
| | - Tabe N. Ntui
- Department of Chemistry, Faculty of Sciences, Cross River University of Technology, Calabar, Nigeria
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Synthesis, characterization, DFT, and TD-DFT studies of (E)-5-((4,6-dichloro-1,3,5-triazin-2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2,7-diylbis(hydrogen sulfite). SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04688-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
AbstractIn this study, (E)-5-((4,6-dichloro-1,3,5-triazin-2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2,7-diylbis(hydrogen sulfite), a cyanurated H-acid (CHA) azo dye, was synthesized and characterized using FT-IR spectrophotometer and GC-MS spectroscopy. A density functional theory (DFT) based B3LYP and CAM-B3LYP method with 6–311 + G (d,p) basis set analysis was computed for HOMO-LUMO, natural bonding orbitals (NBO), UV-Vis absorptions and excitation interactions, in order to understand its molecular orbital excitation properties. A low Energy gap (Eg) of 2.947 eV was obtained from the molecular orbital analysis, which showed that HOMO to LUMO transition is highly feasible; hence CHA is adequate for diverse electronic and optic applications. Studies of the first five excitations (S0 → S1/S2/S3/S4/S5) of CHA revealed that S0 → S1 and S0 → S3 are π → π* type local excitations distributed around the –N=N– group; S0 → S2, a Rydberg type local excitation; S0 → S4, a highly localized π → π* excitation; while S0 → S5 is an n → π* charge transfer from a benzene ring to –N=N– group. From NBO analysis, we obtained the various donor–acceptor orbital interactions contributing to the stabilization of the studied compound. Most significantly, some strong hyper-conjugations (n → n*) within fragments, and non-bondingand anti-bonding intermolecular (n → n*/π* and π → n*/π*) interactions were observed to contribute appreciable energies. This study is valuable for understanding the molecular properties of the azo dyes compounds and for synthesizing new ones in the future.
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Bisong EA, Louis H, Unimuke TO, Bassey VM, Agwupuye JA, Peter LI, Ekpen FO, Adeleye AT. Theoretical investigation of the stability, reactivity, and the interaction of methyl-substituted peridinium-based ionic liquids. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2020-0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This research work focuses on the reactivity, stability, and electronic interaction of pyridinium hydrogen nitrate (PHN)-based ionic liquids and the influence of methyl substituent on this class of ionic liquids: Ortho- (O-MPHN), meta- (M-MPHN), and para- (P-MPHN) substitution. Natural bond orbital (NBO) calculations were performed at the density functional theory (DFT) with Becke’s Lee Yang and Parr functional (B3LYP) methods and DFT/B3LYP/6-311++G(d,p) as basis set using GAUSSIAN 09W and GAUSSVIEW 6.0 software and the most important interaction between donor (Filled Lewis-type NBO’s) and the acceptor (vacant non-Lewis NBOs) were observed. From our natural bond orbital (NBO) result, it could be deduced that the higher the stabilization energy value, the greater the interaction between the donor and acceptor NBOs. The stability of the studied compounds is said to follow the order from O-MPHN > PHN > P-MPHN > M-MPHN based on the hyperconjugative interaction (stabilization energy) of the most significant interaction. The result of the highest occupied molecular orbital (HOMO), shows that PHN has the highest HOMO while the substituted derivatives have similar HOMO values between −7.70 and −7.98 eV thus PHN complex is the best electron donor while the substituted derivatives act as electron acceptors due to the presence of methyl group substituent which is observed to be electron deficient as a result of its withdrawal effect from the aromatic ring. Furthermore, the electron density, real space functions such as energy density and Laplacian of electron density at bond critical point (BCP) of the hydrogen bond interaction of the studied compounds were analyzed using Multifunctional Wavefunction analyzer software version 3.7 and it was observed that the hydrogen at position 6 and oxygen at position 11 (H6–O11) of M-methyl pyridinium nitrate with bond distance of 4.59 (Å) gave binding energy with the strongest electrostatic interaction between the cation and anion of the compounds under investigation. We also observed from our results that, substitution at the ortho position enhances the stability and strengthen the extent of charge transfer. This therefore implies that substitution at ortho position is more favorable for inter- and intramolecular interactions resulting to stabilization of the studied molecules.
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Affiliation(s)
- Emmanuel A. Bisong
- Department of Pure and Applied Chemistry , Computational and Bio-Simulation Research Group, Faculty of Physical Sciences, University of Calabar , Calabar , Cross River State , Nigeria
| | - Hitler Louis
- Department of Pure and Applied Chemistry , Computational and Bio-Simulation Research Group, Faculty of Physical Sciences, University of Calabar , Calabar , Cross River State , Nigeria
| | - Tomsmith O. Unimuke
- Department of Pure and Applied Chemistry , Computational and Bio-Simulation Research Group, Faculty of Physical Sciences, University of Calabar , Calabar , Cross River State , Nigeria
| | - Victoria M. Bassey
- Department of Pure and Applied Chemistry , Computational and Bio-Simulation Research Group, Faculty of Physical Sciences, University of Calabar , Calabar , Cross River State , Nigeria
| | - John A. Agwupuye
- Department of Pure and Applied Chemistry , Computational and Bio-Simulation Research Group, Faculty of Physical Sciences, University of Calabar , Calabar , Cross River State , Nigeria
| | - Linda I. Peter
- Department of Pure and Applied Chemistry , Computational and Bio-Simulation Research Group, Faculty of Physical Sciences, University of Calabar , Calabar , Cross River State , Nigeria
| | - Francis O. Ekpen
- Department of Science Education , Faculty of Education, University of Calabar , Calabar , Cross River State , Nigeria
| | - Aderemi T. Adeleye
- Dalian Institute of Chemical Physics, University of Chinese Academy of Sciences , Dalian , P. R. China
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Edim MM, Louis H, Bisong EA, Chioma AG, Enudi OC, Unimuke TO, Bassey AB, Prince D, Sam QO, Ubana EI, Mujong TH. Electronic structure theory study of the reactivity and structural molecular properties of halo-substituted (F, Cl, Br) and heteroatom (N, O, S) doped cyclobutane. PHYSICAL SCIENCES REVIEWS 2021. [DOI: 10.1515/psr-2020-0138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cyclobutane and its halo-substituted derivatives and its heteroatom doped derivatives have been extensively investigated in this study because of the vast applications and interesting chemistry associated with them, the vibrational assignments, Natural Bond Orbital (NBO) analysis, Conceptual Density Functional Theory, Quantum Mechanical Descriptors and Molecular Electrostatic Potential (MEP) analysis have been explored in this study. The corresponding wavenumbers of the studied compounds have as well been assigned by Potential Energy Distribution analysis. Several inter and intramolecular hyperconjugative interactions within the studied compounds have been revealed by the NBO analysis with a confirmation of geometric hybridization and electronic occupancy. The compounds reactivity was observed to decrease down the halo group in manners such as the stability, both were observed to decrease from azetidine to thietane. The distribution of charge was observed to be affected by the ring substituent as observed from the charge population analysis; in addition, adjacent atoms are very much affected by the inherent properties of the substituted atoms. The NBO result suggests that the molecules are stabilized by lone pair delocalization of electrons from the substituted atoms and molecular electrostatic potential (MEP) studies revealed that substituted halogens and doped heteroatoms are important and most probable sites of electrostatic interactions.
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Affiliation(s)
- Moses M. Edim
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
- Department of Chemistry , Cross River University of Technology , Calabar Nigeria
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Emmanuel A. Bisong
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Apebende G. Chioma
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Obieze C. Enudi
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Tomsmith O. Unimuke
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Asuquo B. Bassey
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - David Prince
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Queen O. Sam
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
| | - Emmanuel I. Ubana
- Computational and Bio-Simulation Research Group, University of Calabar , Calabar , Nigeria
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30
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Aromaticity indices, electronic structural properties, and fuzzy atomic space investigations of naphthalene and its aza-derivatives. Heliyon 2021; 7:e06138. [PMID: 33553781 PMCID: PMC7856479 DOI: 10.1016/j.heliyon.2021.e06138] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/21/2020] [Accepted: 01/26/2021] [Indexed: 11/23/2022] Open
Abstract
The aromaticity and CDFT properties of naphthalene and its aza-derivatives were theoretically investigated using density functional theory (DFT) electronic structure method. The reactivity and chemistry of Azanaphthalene (1-AN), 1, 2-diazanaphthalene (1, 2-DAN), 1, 3-diazanaphthalene (1, 3-DAN), 1, 4-diazanaphthalene (1,4-DAN), 1, 5-diazanaphthalene (1, 5-DAN), 1, 6-diazanaphthalene (1, 6-DAN), 1, 7-diazanaphthalene (1,7-DAN) and 1, 8-diazanaphthalene (1, 8-DAN) were thoroughly explored and predicted focusing more on the fuzzy atomic space analysis, quantum chemical descriptors (CDFT), natural bond orbital (NBO), and structural electronic properties. The CDFT is focused on predicting the condensed Fukui function and dual descriptors along with condensed local electrophilicity and nucleophilicity investigation. From the aromaticity computational study, 1,7-DAN gave PDI, FLU, FLU- π , PLR, HOMA, BIRD and LOLIPOP values of approximately one (1) was found to be the most aromatic in the group, and strongest π -stacking ability. The aromaticity follows the trend: 1, 7-DAN > 1, 8-DAN > 1, 5-DAN > 1, 6-DAN > 1, 4-DAN > 1, 2-DAN > 1-AN > naphthalene. The second order perturbation energy NBO analysis revealed that the 3 highest stabilization energies in the molecules are C6-Na to C3-C4 ( π ∗ - π ∗ 236.90 kcal/mol) of 1, 6-DAN, C3-C4 to C1-C2 ( π ∗ - π ∗ 236.37 kcal/mol) of 1-AN and C7-N10 to C2-C4 ( π ∗ - π ∗ 235 kcal/mol) of 1, 3-DAN.
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