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Dague Y, Koyambo-Konzapa SJ, Nose H, Minguirbara A, Nsangou M, Amolo G. DFT investigation on the structural and vibrational behaviours of the non-protein amino acids in hybrid explicit/continuum solvent: a case of the zwitterions γ-aminobutyric and α - aminoisobutyric acids. J Mol Model 2023; 30:17. [PMID: 38157064 DOI: 10.1007/s00894-023-05817-9] [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: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND The influence of hybrid solvation models on the molecular structures and vibrational characteristics of g-aminobutyric acid (GABA) and a-aminoisobutyric acid (AIB) zwitterions was assessed by employing a variety of Density Functional Theory (DFT). The quantum chemical methods included the B3LYP and B3PW91 hybrid functionals and the 6‑311++G(d,p) basis set. METHODS The most stable conformation derived from the potential energy surface (PES) scans using the B3LYP/6-311++G(d,p) model chemistry for each studied molecule was predicted within a continuum environment represented by the COSMO and SMD solvation models. The stable structures were subsequently immersed in explicit/COSMO and explicit/SMD hybrid solvation models, where 10 and 8 water molecules were explicitly positioned around the functional groups of the GABA and AIB zwitterions, respectively. The number of water molecules chosen was sufficient to prevent proton transfer among the carboxylate group (COO-) and the ammonium group (NH3+) within each molecule under investigation. After optimizing the geometry of each hydrated complex, the normal vibrational modes were determined. The scaled theoretical frequencies obtained from the various model chemistries were then compared to available experimental data from infrared (IR) and Raman spectroscopy. RESULTS In the case of GABA and AIB molecules, the comparisons revealed that the B3LYP/6-311++G(d,p) model chemistry yielded wavenumber values that closely matched the experimental IR and Raman data, particularly when the explicit/SMD solvent was employed. The computed results indicate deviations of less than 4% when compared to the experimental data for the two molecules under investigation.
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Affiliation(s)
- Yves Dague
- Higher Teacher's Training College, The University of Maroua, P.O. Box 46, Maroua, Cameroon
| | - Stève-Jonathan Koyambo-Konzapa
- Laboratoire Matière, Energie et Rayonnement (LAMER), Université de Bangui, P.O. Box 1450, Bangui, Central African Republic.
| | - Holliness Nose
- School of Chemistry and Material Science, The Technical University of Kenya, Nairobi, 52428-00200, Kenya
| | - Alain Minguirbara
- Higher Teacher's Training College, The University of Maroua, P.O. Box 46, Maroua, Cameroon
| | - Mama Nsangou
- Higher Teacher's Training College, The University of Maroua, P.O. Box 46, Maroua, Cameroon.
- Department of Physics, Faculty of Sciences, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon.
| | - George Amolo
- Materials Modeling Group, School of Physics and Earth Science, The Technical University of Kenya, Nairobi, 52428-00200, Kenya
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Zeng R, Zou X, Huang C, Si H, Song J, Zhang J, Luo H, Wang Z, Wang P, Fan G, Rao X, Liao S, Chen S. Novel Design of Citral-Thiourea Derivatives for Enhancing Antifungal Potential against Colletotrichum gloeosporioides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:3173-3183. [PMID: 36760014 DOI: 10.1021/acs.jafc.2c07851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Although much progress has been made in developing botanical fungicides to combat fungal diseases in crops, there remains a great need to improve the efficiency and long-term safety of these fungicides. This study proposes a novel strategy for designing citral-thiourea derivatives that feature such desirable properties. The motivation of the work herein was to enhance the antifungal activity of citral against C. gloeosprioides by exploiting the synergistic effect that arises from combining citral and thiourea compounds, thereby producing citral-thiourea derivatives that exhibit good long-term safety. The results revealed that the generated compounds e1, e3, e6, e18, and g showed remarkable antifungal activities against C. gloeosprioides, with corresponding EC50 values reaching 0.16, 1.66, 1.37, 4.76, and 4.60 mg/L, respectively, showing that the compounds significantly outperformed both the positive control kresoxim-methyl and the commercially available fungicide carbendazim. Furthermore, compound g showed stronger protective efficacy against C. gloeosprioides than carbendazim on mango fruit at 25 mg/L. Investigating the preliminary structure-activity relationship (SAR) of the compounds also revealed that the citral-thiourea derivatives exhibited higher antifungal activities against C. gloeosprioides compared to citral and thiourea compounds. This reinforcement of antifungal activity observed in the derivatives was found to be attributable to the two characteristics of low molecular size and the presence of a fluorine atom in the meta-position of the benzene ring. Beyond this, it was determined from QSAR that two molecular descriptors (the Kier-Hall index (order 3) and Tot dipole of the molecules) were negatively related to the antifungal activity of the citral-thiourea derivatives, while one other (the maximum resonance energy of a C-H bond) was positively related to their antifungal activity. More importantly, the citral-thiourea derivatives with high antifungal activities (i.e., compounds e1, e3, e6, e14, e15, e18, and g) exhibited negligible cytotoxicity to LO2 and HEK293T cell lines. The antifungal mechanism of the generated citral-thiourea derivatives was investigated by scanning electron microscopy (SEM) and relative conductivity. The derivatives were found to affect mycelial morphology and increase fungal cell membrane permeability, thereby resulting in the destruction of fungal cell membranes. These promising results provide novel insights into the study and potential application value of citral-thiourea derivatives as high-efficiency antifungal agents against C. gloeosprioides.
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Affiliation(s)
- Rong Zeng
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Xiuxiu Zou
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Cong Huang
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Hongyan Si
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Jie Song
- Department of Natural Sciences, University of Michigan-Flint, 303E Kearsley, Flint, Michigan 48502, United States
| | - Ji Zhang
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Hai Luo
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Zongde Wang
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Peng Wang
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Guorong Fan
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Xiaoping Rao
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, People's Republic of China
| | - Shengliang Liao
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
| | - Shangxing Chen
- College of Forestry, Jiangxi Agricultural University; East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration; Camphor Engineering Research Center of National Forestry and Grassland Administration/Jiangxi Province, Nanchang 330045, People's Republic of China
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Energetic, conformational and vibrational features of the tripeptide (Gly)3. Data from MP2 and DFT calculations. COMPUT THEOR CHEM 2023. [DOI: 10.1016/j.comptc.2022.113989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Koyambo-Konzapa SJ, Mbesse Kongbonga GY, R P, Ramlina Vamhindi BSD, Nsangou M, Franklin Benial AM. Spectroscopic, quantum chemical, molecular docking and molecular dynamics investigations of hydroxylic indole-3-pyruvic acid: a potent candidate for nonlinear optical applications and Alzheimer's drug. J Biomol Struct Dyn 2022; 40:10651-10664. [PMID: 34263703 DOI: 10.1080/07391102.2021.1947380] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this paper, a complete theoretical investigation of hydroxylic indole-3-pyruvic acid (HIPyA) molecule was performed using the DFT quantum chemical, molecular docking and molecular dynamics calculations. The conformational analysis of HIPyA molecule was carried out using density functional theory quantum chemical calculations. The most stable structure of the studied molecule was predicted by means of DFT/B3LYP method with cc-pVTZ basis set. The simulated vibrational frequencies were assigned and proved to be in agreement with the available experimental FT-IR data. The effects of gas phase and solvents on UV-visible spectra of HIPyA molecule were simulated using TD-DFT/B3LYP method with cc-pVTZ basis set. The analysis of the density of states spectrum validates the frontier molecular orbitals results, which reveals the charge transfer interaction in HIPyA molecule. The molecular electrostatic potential surface confirms the electrophilic and nucleophilic reactive sites of the studied molecule. The natural bond orbital analysis evidences the bioactivity of the studied molecule. The obtained first order hyperpolarizability value is 33.596 times greater than urea, which confirms the nonlinear optical activity of HIPyA molecule. The molecular docking analysis reveals that the studied molecule under interest can act as a potent inhibitor against the amyloid β-protein (Aβ) enzyme, which causes the Alzheimer's disease. The molecular dynamics analysis confirms the reliability of the docking results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Premkumar R
- PG and Research Department of Physics, N. M. S. S. V. N College, Madurai, Tamil Nadu, India
| | | | - Mama Nsangou
- Departement of Physics, Faculty of Science, The University of Ngaoundere, Ngaoundere, Cameroon.,Higher Teacher's Training College, The University of Maroua, Maroua, Cameroon
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Electronic, spectroscopic, molecular docking and molecular dynamics studies of neutral and zwitterionic forms of 3, 4-dihydroxy-l-phenylalanine: A novel lung cancer drug. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Premkumar R, Hussain S, Jayram ND, Koyambo-Konzapa SJ, Revathy M, Mathavan T, Milton Franklin Benial A. Adsorption and orientation characteristics of 1-methylpyrrole-2-carbonyl chloride using SERS and DFT investigations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Tao P, Wu C, Hao J, Gao Y, He X, Li J, Shang S, Song Z, Song J. Antifungal Application of Rosin Derivatives from Renewable Pine Resin in Crop Protection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4144-4154. [PMID: 32191457 DOI: 10.1021/acs.jafc.0c00562] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the current work, we synthesized two series of dehydroabietyl amide derivatives from natural product rosin and evaluated their antifungal effects on Valsa mali, Phytophthora capsici, Botrytis cinerea, Sclerotinia sclerotiorum, and Fusarium oxysporum. In vitro and in vivo antifungal activities results indicated that rosin-based amide compounds containing thiophene heterocycles had better inhibitory effects on B. cinerea. In particular, compound 5b (5-fluoro-2-thiophene dehydroabietyl amide) exhibited the excellent antifungal properties against B. cinerea with an EC50 of 0.490 mg/L, which was lower compared to the positive control penthiopyrad (0.562 mg/L). Physiological and biochemical studies showed that the primary action mechanism of compound 5b on B. cinerea changes mycelial morphology, increases cell membrane permeability, and inhibits the TCA pathway in respiratory metabolism. Furthermore, QSAR and SAR studies revealed that charge distribution of rosin-based amides derivatives have a key role in the antifungal activity through the hydrogen bonding, conjugation, and electrostatic interaction between the compounds and the receptors of the target. To sum up, this study contributes to the development of rosin-based antifungal agents with a novel structure and preferable biological activity.
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Affiliation(s)
- Pan Tao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Chengyu Wu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jin Hao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Yanqing Gao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiaohua He
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jian Li
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Shibin Shang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing, Jiangsu 210042, People's Republic of China
| | - Zhanqian Song
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing, Jiangsu 210042, People's Republic of China
| | - Jie Song
- Department of Chemistry and Biochemistry, University of Michigan-Flint, Flint, Michigan 48502, United States
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