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Aghahosseini A, Edjlali L, Jamehbozorgi S, Rezvani M, Ghasemi E. Theoretical investigations of functionalization of graphene and ZnO monolayers with Mercaptopurine at aqueous media: a dispersion-corrected DFT calculations and Molecular dynamic simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yang K, Bi F, Zhang J, Xue Q, Zhang J, Wang K, Wang B. Comparative Research on Promising Energetic 1,3-Diazinane and 1,3-Oxazinane Structures. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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3
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Bakhshandeh A, Ardestani F, Ghorbani HR, Darvish Ganji M. Structural and molecular properties of complexes of biomolecules and metal-organic frameworks: dispersion-corrected DFT treatment. J Mol Model 2022; 28:32. [PMID: 35018501 DOI: 10.1007/s00894-021-04947-2] [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: 06/11/2021] [Accepted: 10/13/2021] [Indexed: 11/27/2022]
Abstract
Investigation of complexes of nanostructured materials and biomolecules has attracted much attention by various researchers as it can contribute to coherent growth and extended application of nanostructures in different technologies. In this research, following a comprehensive approach, we examined the interaction between different amino acids and metal-organic frameworks (MOFs) at atomic scale using computational chemistry. For this purpose, we employed the density functional theory (DFT-D2) calculations to afford a molecular description of the interaction properties of the amino acids and MOF-5 by examining the interaction energy and the electronic structure of the amino acid/MOF complexes. We found strong interactions between the amino acids and MOF through their polar groups as well as aromatic rings in the gas phase. However, our findings were significantly different in solvent media, where water molecules prevent the amino acids from approaching the active sites of MOF, causing weak attractions between them. The evaluation of nature of interaction between the amino acids and MOF by the atoms-in-molecules (AIM) theory shows that the electrostatic attractions are the main force contributing to bond formation between the interacting entities. Furthermore, our DFT-PBE model of theory was validated against the comprehensive MP2 quantum level of theory.
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Affiliation(s)
- Anahita Bakhshandeh
- Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran
| | - Fatemeh Ardestani
- Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.
| | - Hamid Reza Ghorbani
- Department of Chemical Engineering, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran
| | - Masoud Darvish Ganji
- Department of Nanochemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran.
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Chen B, Li L, Liu L, Cao J. Molecular simulation of adsorption properties of thiol-functionalized titanium dioxide (TiO2) nanostructure for heavy metal ions removal from aqueous solution. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Synthesis, enzymes inhibitory properties and characterization of 2- (bis (4-aminophenyl) methyl) butan-1-ol compound: Quantum simulations, and in-silico molecular docking studies. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Fatima M, Liaqat F, Shabbir M, Ahmad I, Akhter Z, Fatima R, Yousaf S. Synthesis, characterization, antioxidant, DNA binding and density functional studies of novel bisamides. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Trenzado JL, Rodríguez Y, Gutiérrez A, Cincotti A, Aparicio S. Experimental and molecular modeling study on the binary mixtures of [EMIM][BF4] and [EMIM][TFSI] ionic liquids. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Rozas S, Alomari N, Atilhan M, Aparicio S. Theoretical insights into the cineole-based deep eutectic solvents. J Chem Phys 2021; 154:184504. [PMID: 34241002 DOI: 10.1063/5.0048369] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Deep eutectic solvents based on cineole as hydrogen bond acceptors and organic acids (succinic, malic, and lactic) as hydrogen bond donors are studied using a theoretical approach. The nature, strength, and extension of hydrogen bonding are analyzed, thus quantifying this prevailing interaction and its role in the fluid properties. Density functional theory was used to study small molecular clusters, and the topological characterization of the intermolecular forces was carried out using atoms in a molecule theory. Classical molecular dynamics simulations were considered to study nanoscopic bulk liquid properties and their relationship with relevant macroscopic properties such as density or thermal expansion. The reported results provide the characterization of environmentally friendly deep eutectic solvents and show the suitability of cineole for developing these sustainable materials.
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Affiliation(s)
- Sara Rozas
- Department of Chemistry, University of Burgos, 09001 Burgos, Spain
| | - Noor Alomari
- Department of Chemical and Paper Engineering, Western Michigan University, Kalamazoo, Michigan 49008, USA
| | - Mert Atilhan
- Department of Chemical and Paper Engineering, Western Michigan University, Kalamazoo, Michigan 49008, USA
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Atilhan M, Cincotti A, Aparicio S. Nanoscopic characterization of type II porous liquid and its use for CO2 absorption from molecular simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Effect of Hydrogen Bond Donors and Acceptors on CO2 Absorption by Deep Eutectic Solvents. Processes (Basel) 2020. [DOI: 10.3390/pr8121533] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The effects of a hydrogen bond acceptor and hydrogen bond donor on carbon dioxide absorption via natural deep eutectic solvents were studied in this work. Naturally occurring non-toxic deep eutectic solvent constituents were considered; choline chloride, b-alanine, and betaine were selected as hydrogen bond acceptors; lactic acid, malic acid, and fructose were selected as hydrogen bond donors. Experimental gas absorption data were collected via experimental methods that uses gravimetric principles. Carbon dioxide capture data for an isolated hydrogen bond donor and hydrogen bond acceptor, as well as natural deep eutectic solvents, were collected. In addition to experimental data, a theoretical study using Density Functional Theory was carried out to analyze the properties of these fluids from the nanoscopic viewpoint and their relationship with the macroscopic behavior of the system, and its ability for carbon dioxide absorption. The combined experimental and theoretical reported approach work leads to valuable discussions on what is the effect of each hydrogen bond donor or acceptor, as well as how they influence the strength and stability of the carbon dioxide absorption in deep eutectic solvents. Theoretical calculations explained the experimental findings, and combined results showed the superiority of the hydrogen bond acceptor role in the gas absorption process, with deep eutectic solvents. Specifically, the cases in which choline chloride was used as hydrogen bond acceptor showed the highest absorption performance. Furthermore, it was observed that when malic acid was used as a hydrogen bond donor, it led to low carbon dioxide solubility performance in comparison to other studied deep eutectic solvents. The cases in which lactic acid was used as a hydrogen bond donor showed great absorption performance. In light of this work, more targeted, specific, deep eutectic solvents can be designed for effective and alternative carbon dioxide capture and management.
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Synthesis, characterization, antioxidant evaluation, molecular docking and density functional theory studies of phenyl and naphthyl based esters. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127812] [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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12
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Gutiérrez A, Atilhan M, Aparicio S. Theoretical Study on Deep Eutectic Solvents as Vehicles for the Delivery of Anesthetics. J Phys Chem B 2020; 124:1794-1805. [DOI: 10.1021/acs.jpcb.9b11756] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Mert Atilhan
- Department of Chemical Engineering, Texas A&M University at Qatar, Doha, Qatar
- Gas and Fuels Research Center, Texas A&M University, College Station, Texas 77843, United States
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Atilhan M, Altamash T, Aparicio S. Quantum Chemistry Insight into the Interactions Between Deep Eutectic Solvents and SO 2. Molecules 2019; 24:molecules24162963. [PMID: 31443291 PMCID: PMC6720665 DOI: 10.3390/molecules24162963] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/22/2019] [Accepted: 07/27/2019] [Indexed: 01/08/2023] Open
Abstract
A systematic research work on the rational design of task specific Deep Eutectic Solvents (DES) has been carried out via density functional theory (DFT) in order to increase knowledge on the key interaction parameters related to efficient SO2 capture by DES at a molecular level. A total of 11 different DES structures, for which high SO2 affinity and solubility is expected, have been selected in this work. SO2 interactions in selected DES were investigated in detail through DFT simulations and this work has generated a valuable set of information about required factors at the molecular level to provide high SO2 solubility in DES, which is crucial for enhancing the current efficiency of the SO2 capture process and replacing the current state of the art with environmentally friendly solvents and eventually implementing these materials in the chemical industry. Results that were obtained from DFT calculations were used to deduce the details of the type and the intensity of the interaction between DES and SO2 molecules at various interaction sites as well as to quantify short-range interactions by using various methods such as quantum theory of atoms in a molecule (QTAIM), electrostatic potentials (ESP) and reduced density gradients (RDG). Systematic research on the molecular interaction characterization between DES structures and SO2 molecule increases our knowledge on the rational design of task-specific DES.
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Affiliation(s)
- Mert Atilhan
- Department of Chemical Engineering, Texas A&M University at Qatar, Doha 23874, Qatar.
- Gas and Fuels Research Center, Texas A&M University, College Station, TX 77843, USA.
| | - Tausif Altamash
- Qatar Environment and Energy Research Institute, Hamad Bin Khalifa University, Doha 23874, Qatar
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Gutiérrez A, Aparicio S, Atilhan M. Design of arginine-based therapeutic deep eutectic solvents as drug solubilization vehicles for active pharmaceutical ingredients. Phys Chem Chem Phys 2019; 21:10621-10634. [PMID: 31080981 DOI: 10.1039/c9cp01408j] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The solvation of lidocaine in three newly designed deep eutectic solvents is studied using combined experimental and theoretical methods that include density functional theory and molecular dynamics methods. The intermolecular forces between lidocaine and the hydrogen bond acceptors and hydrogen bond donors of the deep eutectic solvents were analysed regarding the type and the strength of inter- and intra-molecular bonding. The structure, composition and properties of the lidocaine solvation shells are analysed together with the possible lidocaine-clustering around the studied deep eutectic solvents and their constituent molecules. Furthermore, the changes in the solvent structures upon lidocaine solubilization are also studied. Natural product-based eutectic solvents showed considerably high solvation of lidocaine in all three deep eutectics based on the strong solute-solvent intermolecular interactions accompanied by a slight volume expansion and minor solvent structural changes. These non-toxic and almost null-volatile therapeutic deep eutectic solvents can be considered as suitable solubilization media for developing pharmaceutical applications and they can be considered as effective drug delivery vehicles for active pharmaceutical ingredients.
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Affiliation(s)
| | | | - Mert Atilhan
- Department of Chemical Engineering, Texas A&M University at Qatar, Doha, Qatar. and Gas and Fuels Research Center, Texas A&M University, College Station, TX, USA
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