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Feng L, Zhong K, Majdi HS, Aallaei M, Andreevna Rushchitc A. Advanced computational study of different boron nitride-based nanospheres for removal of organic contaminants from wastewater system. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Molecular Modeling and Simulation of glycine functionalized B12N12 and B16N16 nanoclusters as potential inhibitors of proinflammatory cytokines. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117494] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Aghaei M, Ramezanitaghartapeh M, Javan M, Hoseininezhad-Namin MS, Mirzaei H, Rad AS, Soltani A, Sedighi S, Lup ANK, Khori V, Mahon PJ, Heidari F. Investigations of adsorption behavior and anti-inflammatory activity of glycine functionalized Al 12N 12 and Al 12ON 11 fullerene-like cages. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119023. [PMID: 33049473 DOI: 10.1016/j.saa.2020.119023] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/12/2020] [Accepted: 09/27/2020] [Indexed: 05/24/2023]
Abstract
The adsorption behavior of the amino acid, glycine (Gly), via the carboxyl, hydroxyl, and amino groups onto the surfaces of Al12N12 and Al16N16 fullerene-like cages were computationally evaluated by the combination of density functional theory (DFT) and molecular docking studies. It was found that Gly can chemically bond with the Al12N12 and Al16N16 fullerene-like cages as its amino group being more favorable to interact with the aluminum atoms of the adsorbents compared to carboxyl and hydroxyl groups. Oxygen and carbon doping were reported to reduce steric hindrance for Glycine interaction at Al site of Al12ON11/Gly and Al12CN11/Gly complexes. Interaction was further enhanced by oxygen doping due to its greater electron withdrawing effect. Herein, the Al12ON11/Gly complex where two carbonyl groups of Gly are bonded to the aluminum atoms of the Al12N12 fullerene-like cage is the most stable interaction configuration showing ∆adsH and ∆adsG values of -81.74 kcal/mol and -66.21 kcal/mol, respectively. Computational studies also revealed the frequency shifts that occurred due to the interaction process. Molecular docking analysis revealed that the Al12N12/Gly (-11.7 kcal/mol) and the Al12ON11/Gly (-9.2 kcal/mol) complexes have a good binding affinity with protein tumor necrosis factor alpha (TNF-α). TNF-α was implicated as a key cytokine in various diseases, and it has been a validated therapeutic target for the treatment of rheumatoid arthritis. These results suggest that the Al12N12/Gly complex in comparison with the Al16N16/Gly, Al12ON11/Gly, and the Al12CN11/Gly complexes could be efficient inhibitors of TNF-α.
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Affiliation(s)
- Mehrdad Aghaei
- Golestan Rheumatology Research Center, Golestan University of Medical Science, Gorgan, Iran
| | | | - Masoud Javan
- Department of Physics, Faculty of Sciences, Golestan University, Gorgan, Iran
| | - Mir Saleh Hoseininezhad-Namin
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Mirzaei
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ali Shokuhi Rad
- Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran
| | - Alireza Soltani
- Golestan Rheumatology Research Center, Golestan University of Medical Science, Gorgan, Iran.
| | - Sima Sedighi
- Golestan Rheumatology Research Center, Golestan University of Medical Science, Gorgan, Iran.
| | - Andrew Ng Kay Lup
- School of Energy and Chemical Engineering, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900 Sepang, Selangor Darul Ehsan, Malaysia
| | - Vahid Khori
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Peter J Mahon
- Department of Chemistry and Biotechnology, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Fatemeh Heidari
- Golestan Rheumatology Research Center, Golestan University of Medical Science, Gorgan, Iran
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Molpeceres G, Timón V, Jiménez-Redondo M, Escribano R, Maté B, Tanarro I, Herrero VJ. Structure and infrared spectra of hydrocarbon interstellar dust analogs. Phys Chem Chem Phys 2017; 19:1352-1360. [PMID: 27975091 DOI: 10.1039/c6cp06043a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A theoretical study of the structure and mid infrared (IR) spectra of interstellar hydrocarbon dust analogs is presented, based on DFT calculations of amorphous solids. The basic molecular structures for these solids are taken from two competing literature models. The first model considers small aromatic units linked by aliphatic chains. The second one assumes a polyaromatic core with hydrogen and methyl substituents at the edges. The calculated spectra are in reasonably good agreement with those of aliphatic-rich and graphitic-rich samples of hydrogenated amorphous carbon (HAC) generated in our laboratory. The theoretical analysis allows the assignment of the main vibrations in the HAC spectra and shows that there is a large degree of mode mixing. The calculated spectra show a marked dependence on the density of the model solids, which evinces the strong influence of the environment on the strengths of the vibrational modes. The present results indicate that the current procedure of estimating the hydrogen and graphitic content of HAC samples through the decomposition of IR features into vibrational modes of individual functional groups is problematic owing to the mentioned mode mixing and to the difficulty of assigning reliable and unique band strengths to the various molecular vibrations. Current band strengths from the literature might overestimate polyaromatic structures. Comparison with astronomical observations suggests that the average structure of carbonaceous dust in the diffuse interstellar medium lies probably in between those of the two models considered, though closer to the more aliphatic structure.
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Affiliation(s)
- Germán Molpeceres
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Vicente Timón
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | | | - Rafael Escribano
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Belén Maté
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Isabel Tanarro
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
| | - Víctor J Herrero
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 123, 28006 Madrid, Spain.
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