Article
Chemistry, Physical
Mehdi Shakourian-Fard, Hamid Reza Ghenaatian, Vali Alizadeh, Ganesh Kamath, Behzad Khalili
Summary: The study on amino acid extraction using deep eutectic solvents revealed strong hydrogen bonding interactions, mainly influenced by the charges present. AAs with positive and negative charges showed a greater tendency to interact with the deep eutectic solvent, indicating increased strength in electrostatic interactions.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemical Research Methods
Hamid Reza Ghenaatian, Mehdi Shakourian-Fard, Vali Alizadeh, Ganesh Kamath
Summary: In this study, density functional theory calculations were used to investigate the stability, reactivity, and interactions of Palladium Pd-n nanoparticles with ChCl:U and ChCl:EG based deep eutectic solvents. The DES Pd-n complexes were found to be stabilized by two types of binding, with charge transfer playing an important role in their stability.Overall, these DESs are potentially promising green solvents for nanoparticle synthesis and activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Chemistry, Physical
Mehdi Shakourian-Fard, S. Maryamdokht Taimoory, Hamid Reza Ghenaatian, Ganesh Kamath, John F. Trant
Summary: The study utilized DFT to evaluate the interaction of four DESs with various forms of graphene nanoflakes, finding that the presence of defects increases adsorption energy and interactions are noncovalent with dispersive forces being dominant. The aromatic moieties in DESs were observed to enhance van der Waals interactions with surfaces.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Engineering, Environmental
Chun-Chi Chen, Chiun-Yao Wang, Yen-Hui Huang
Summary: The study demonstrates a new strategy for capturing nitrogen dioxide (NO2) using deep eutectic solvents (DESs) and their aqueous mixtures. The results show that ChCl-based DESs have excellent NO2 absorption capability, which increases with increasing HBD content. Additionally, the DES aqueous mixtures retain high NO2 solubility while exhibiting a lower viscosity after the introduction of water.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Physical
Usman Saeed, Asim Laeeq Khan, Mazhar Amjad Gilani, Muhammad Roil Bilad, Asad Ullah Khan
Summary: This study focused on utilizing deep eutectic solvents (DESs) impregnated into PVDF membranes for the separation of CO2 from CH4. The DES-SLMs showed high CO2 permeability and selectivity, indicating potential for new pathways in CO2 capture using DESs.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Engineering, Environmental
Jisha Kuttiani Ali, Chahd Maher Chabib, Maguy Abi Jaoude, Emad Alhseinat, Satish Teotia, Shashikant Patole, Dalaver Hussain Anjum, Issam Qattan
Summary: The novel composite UF membranes with silica-based nanofillers show enhanced vacuum-filtration removal of small polar organics from water. The DES@SiO2@PI UF membranes exhibit exceptional water permeate flux and removal efficiency for phenol compared with native polymer membranes, with an optimum nanofiller loading of 2 wt%.
CHEMICAL ENGINEERING JOURNAL
(2021)
Article
Chemistry, Analytical
Eman O. Osman, Amr M. Mahmoud, Sally S. El-Mosallamy, Hala B. El-Nassan
Summary: This study reported the first synthesis of 4H-pyran derivatives using electrochemical synthesis conditions and deep eutectic solvents in a one pot reaction. By optimizing the reaction conditions, high yields of pure pyran derivatives could be obtained in a short amount of time. The use of deep eutectic solvents also eliminated the need for a supporting electrolyte, improving the sustainability of the catalyst.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Kimia Jafari, Mohammad Hossein Fatemi, Luis Lugo
Summary: This study presents the preparation and characterization of new nanofluids based on deep eutectic solvents (DESs) consisting of ethylene glycol (EG), choline chloride (ChCl), and water. The nanofluids with dispersed spherical MgO nanoparticles in DESs of different compositions were designed and their stability was tested. The thermophysical properties, such as thermal conductivity and density, were measured and the effects of nanoparticles' mass fraction, temperature, and water content were examined. The study found that the nanofluids based on DES 1ChCl:5EG showed the best stability and the addition of water increased the thermal conductivity of the nanofluids.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Engineering, Chemical
Karzan A. Omar, Rahmat Sadeghi
Summary: A novel lacmoid-based deep eutectic solvent was prepared and used as a writing ink with interesting characteristics of no feathering, fading, and penetrating the reverse side of paper. It showed high stability and the ability to replace traditional compounds used in writing ink.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2022)
Article
Chemistry, Physical
Mila Manolova, Reinhard Boeck, Ingolf Scharf, Thomas Mehner, Thomas Lampke
Summary: This study investigates the electrodeposition of palladium alloys using different metal components in a choline chloride/urea based deep eutectic solvent. The addition of Ag(I) is found to enhance the overall metal deposition rate, while the layer thickness and composition of the produced alloys can be varied by changing the deposition mode.
JOURNAL OF ALLOYS AND COMPOUNDS
(2021)
Article
Chemistry, Physical
Poonam Patyar, Akhtar Ali, Naved Malek
Summary: This study investigates the effect of water on the thermodynamic properties of deep eutectic solvents composed of choline chloride as a hydrogen bond acceptor and different hydrogen bond donors. The findings provide insights into the non-ideal behavior of the mixtures through measurements of density and discussion of excess molar volume, which can be utilized in industrial processes and thermodynamic modeling of DES systems.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Engineering, Environmental
Filipa Lima, Luis C. Branco, Nuno Lapa, Isabel M. Marrucho
Summary: Deep eutectic solvents (DES) have shown potential in the pre-treatment of lignocellulosic biomass, but their toxicity to microbial consortia during Anaerobic Digestion (AD) needs to be further evaluated. This study found that the presence of ChCl: OA DES had both beneficial and detrimental effects on the anaerobic consortium, with the inhibitory concentrations of OA potentially limiting its application.
Article
Chemistry, Physical
Rixuan Wang, Ying Ma, Picheng Chen, Luyang Sun, Yuetao Liu, Chuanhui Gao
Summary: This study successfully prepared a double-network composite hydrogel with excellent mechanical properties and low temperature resistance by filling the porous structure of polyacrylamide hydrogel with deep eutectic solvent. The composite hydrogel exhibited good conductivity and mechanical properties, opening up new possibilities for future applications in flexible electronics.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2023)
Article
Chemistry, Multidisciplinary
Wrya O. Karim
Summary: This study utilizes deep eutectic solvent for facile and efficient electropolishing of metallic titanium, resulting in a smooth, mirror-like surface with reduced surface roughness. Surface passivation after electropolishing is the main mechanism for removing the microscopic roughness and achieving the desired mirror-like surface.
ARABIAN JOURNAL OF CHEMISTRY
(2021)
Article
Polymer Science
Yuan Zhu, Benkun Qi, Xinquan Liang, Jianquan Luo, Yinhua Wan
Summary: In this study, it was found that acidified solutions of ChCl and glycerol were more efficient at removing lignin and xylan from corn stover compared to DES. Acidified ChCl solution showed better pretreatment performance than acidified glycerol solution. Additionally, the presence of 20% water in DES reduced its capability for delignification and xylan removal. Enzymatic saccharification of pretreated CS was highly correlated to delignification and cellulose crystallinity, but less correlated to xylan removal.
Article
Chemistry, Physical
Mehdi Shakourian-Fard, Hamid Reza Ghenaatian, Ganesh Kamath, S. Maryamdokht Taimoory
JOURNAL OF MOLECULAR LIQUIDS
(2020)
Article
Chemistry, Physical
Aboozar Khajeh, Mehdi Shakourian-Fard, Khalil Parvaneh
Summary: New QSPR models were developed to predict the melting and freezing points of deep eutectic solvents (DESs) using MPSO and MLR to select subsets of descriptors, resulting in two linear models. Experimental data sets were divided into training and test sets, with the models showing good predictive capability.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Mehdi Shakourian-Fard, S. Maryamdokht Taimoory, Hamid Reza Ghenaatian, Ganesh Kamath, John F. Trant
Summary: The study utilized DFT to evaluate the interaction of four DESs with various forms of graphene nanoflakes, finding that the presence of defects increases adsorption energy and interactions are noncovalent with dispersive forces being dominant. The aromatic moieties in DESs were observed to enhance van der Waals interactions with surfaces.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Aboozar Khajeh, Khalil Parvaneh, Mehdi Shakourian-Fard
Summary: New QSPR and GC models were developed for predicting the refractive index of chloride and bromide-based deep eutectic solvents (DESs) with high accuracy and reliability, indicating that these models are proper approaches for modeling other properties of DESs as well.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Mehdi Shakourian-Fard, Hamid Reza Ghenaatian, Vali Alizadeh, Ganesh Kamath, Behzad Khalili
Summary: The study on amino acid extraction using deep eutectic solvents revealed strong hydrogen bonding interactions, mainly influenced by the charges present. AAs with positive and negative charges showed a greater tendency to interact with the deep eutectic solvent, indicating increased strength in electrostatic interactions.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemical Research Methods
Hamid Reza Ghenaatian, Mehdi Shakourian-Fard, Vali Alizadeh, Ganesh Kamath
Summary: In this study, density functional theory calculations were used to investigate the stability, reactivity, and interactions of Palladium Pd-n nanoparticles with ChCl:U and ChCl:EG based deep eutectic solvents. The DES Pd-n complexes were found to be stabilized by two types of binding, with charge transfer playing an important role in their stability.Overall, these DESs are potentially promising green solvents for nanoparticle synthesis and activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2022)
Article
Chemistry, Physical
Aboozar Khajeh, Mehdi Shakourian-Fard
Summary: Linear and nonlinear QSPR models were proposed to predict the density of deep eutectic solvents. By using experimental data and optimization methods, the models were developed and validated for accuracy and reliability.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Mehdi Shakourian-Fard, S. Maryamdokht Taimoory, Hamid Reza Ghenaatian, Ganesh Kamath, John F. Trant
Summary: In this study, the interaction between deep eutectic solvents (DESs) and defective boron nitride was investigated using computational experiments. The results demonstrate that DESs have higher affinity to defective boron nitride and the interaction is primarily non-covalent. The solvents have minimal effect on the properties of pristine boron nitride but significantly alter the adsorption spectrum of defective boron nitride nanoflakes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Hamid Reza Ghenaatian, Mehdi Shakourian-Fard, Ganesh Kamath, John F. Trant, Farouq S. Mjalli
Summary: In this study, the interaction between four deep eutectic solvents and carbon nanotubes and their defects was investigated using density functional theory calculations. The results show that the presence of defects and the volume of the solvents affect the adsorption energy, while the solvents have a small impact on the optical response of the carbon nanotubes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemical Research Methods
Farouq S. Mjalli, Mehdi Shakourian-Fard, Ganesh Kamath, Ghulam Murshid, Jamil Naser, Suhaib Al Ma'awali
Summary: In this study, a novel eutectic solvent composed of Imidazole and Monoethanolamine (MEA) was synthesized and investigated. The physicochemical properties were measured and modeled, and the molecular interaction between the two solvent molecules was explored through molecular dynamics simulations and density functional theory calculations. The results revealed the electrostatic H-bonding nature of the interaction, with the binding energy proportional to the amount of MEA in the eutectic solvent.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Thermodynamics
Fatma R. Al-Fazari, Farouq S. Mjalli, Mehdi Shakourian-Fard, Ganesh Kamath, Jamil Naser, Ghulam Murshid, Suhaib Al Ma'awali
Summary: Imidazole (IMI) and monoethanolamine (MEA) are mixed in different ratios to form a nonionic deep eutectic solvent (DES) for carbon dioxide (CO2) capture. The addition of water to the DES significantly increases the CO2 absorption capacity due to weakened interactions between MEA and IMI. Molecular dynamics simulations confirm the increased CO2 physisorption in the presence of water. This fundamental study provides insights for further investigations on IMI/MEA-based DES for selective absorption of flue gases.
JOURNAL OF CHEMICAL AND ENGINEERING DATA
(2023)
Article
Chemistry, Physical
Farshad Boorboor Ajdari, Abolfazl Fathollahi Zonouz, Ali Heydari, Hassan Shokoui Mehrabani, Mehdi Shakourian-Fard, Ganesh Kamath, Fatemeh Ghasemi, Meisam Kahrizi
Summary: Concerns have arisen regarding the recyclability, performance, and safety of commercial Li-ion batteries. The addition of DMMP and DOP improves cycle life and reversible capacity by reducing flammability and increasing Li-ion conductivity. Molecular dynamics simulations show that these additives increase the solvation-free energy of Li+ ions in the electrolyte.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Biochemical Research Methods
Nousheen Parvaiz, Asma Abro, Syed Sikander Azam
Summary: Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of insulin signaling pathways and has potential as a medicinal target. This study explores the binding and conformational orientation of zinc(II) complexes in PTP1B using advanced computational methods. The findings suggest that zinc(II) complexes can bind to important residues in the enzyme and inhibit its activity.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Hira Zubair, Muhamed Salim Akhter, Muhammad Waqas, Mariam Ishtiaq, Ijaz Ahmed Bhatti, Javed Iqbal, Ahmed M. Skawky, Rasheed Ahmad Khera
Summary: Improving open-circuit voltage is crucial for enhancing the overall efficiency of organic solar cells. This study successfully improved the open-circuit voltage by modulating the molecular structure and proposed a promising design concept for acceptor molecules that may contribute to the development of advanced organic solar cells.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Jerica Wilson, Bahrad A. Sokhansanj, Wei Chuen Chong, Rohan Chandraghatgi, Gail L. Rosen, Hai-Feng Ji
Summary: Fragment-based drug design is a computer-aided drug discovery method, however, it has limitations in processing time and success rate. In this study, a new method called Fragment Databases from Screened Ligands Drug Design (FDSL-DD) was proposed, which intelligently incorporates fragment characteristics into the drug design process to improve the binding affinity between drugs and protein targets.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
M. Chamani, G. H. Farrahi
Summary: This paper employs the Generalized Particle (GP) method to simulate nanoindentation and nanoscratching, showing that this method maintains consistent atomic properties across different scales and achieves results consistent with full atomic simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Paola Vottero, Elena Carlotta Olivetti, Lucia Chiara D'Agostino, Luca Di Grazia, Enrico Vezzetti, Maral Aminpour, Jacek Adam Tuszynski, Federica Marcolin
Summary: This study aims to characterize the spike protein of the SARS-CoV-2 virus and investigate its interaction with the ACE2 receptor using a geometric analysis. The 3D depth maps of the proteins are filtered using a specific convolutional filter to obtain geometric features. Geometric descriptors and a Support Vector Machine classifier are used for feature extraction and classification, revealing the geometrical reasons for the higher contagiousness of the Omicron variant compared to other variants.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Diana Margarita Mojica-Munoz, Karla Lizbeth Macias-Sanchez, Estefania Odemaris Juarez-Hernandez, Aurora Rodriguez-Alvarez, Jean-Michel Grevy, Armando Diaz-Valle, Mauricio Carrillo-Tripp, Jose Marcos Falcon-Gonzalez
Summary: By employing molecular dynamics simulations, we investigated the molecular mechanisms underlying the plasticization of starch. Our study revealed that chain size affects the solubility of starch, temperature influences its diffusivity and elastic properties, and oleic acid shows potential as an alternative plasticizer. Blending glycerol or oleic acid with water enhances the elasticity of starch.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Farid Faraji Chanzab, Saber Mohammadi, Fatemeh Alemi Mahmoudi
Summary: A comprehensive study using molecular dynamics technique was conducted to investigate the behavior of PAP molecules in a n-heptane/toluene solution and the role of SWCNTs, both bare and functionalized with carboxyl groups, in the aggregation of PAP molecules. The study found that the CNTs hindered the association of PAP molecules through steric hindrance and adsorption mechanisms. The presence of carboxyl groups on the CNTs improved the stability and adsorption of PAP molecules. The results have implications for future research on controlling asphaltene precipitation in the oil industry.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Ramin Bairami Habashi, Mohammad Najafi, Reza Zarghami
Summary: A vigorous Monte Carlo strategy was developed to simulate the copolymerization of ethylene and 1-butene using a dual-site metallocene catalyst. The results showed that the second catalyst site had higher activity than the first site, with ethylene and 1-butene consumption rates five times higher and hydrogen transfer rates three times faster. The molar percentage of 1-butene in the copolymers synthesized from the second site was around 12%, while in the copolymers from the first site it was around 2%. Increasing the 1-butene concentration led to an increase in overall molecular weight, while increasing the hydrogen concentration resulted in a decrease in molecular weight. The ratio of ethylene to 1-butene affected the melt index and the weight fraction of crystals, with higher ratios leading to smaller melt indexes and higher weight fractions of crystals. Increasing the temperature caused changes in molecular weight, bimodal molecular weight distribution, crystal thickness and weight fraction, and density of HDPE.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Yufan Lu, Xingmin Guo, Shuya Liu
Summary: This paper investigates how to control the nontrivial topological structures of DNA nanocages by adjusting the number of ssDNA strands. A new algorithm and program are developed to calculate the component number of polyhedral links, filling the gap in computer programs on this aspect. The study provides a complete list of topological structures with different component numbers for DNA octahedrons assembled from one or more ssDNA strands.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Peng Cui, Shideng Yuan, Heng Zhang, Shiling Yuan
Summary: Understanding the mechanisms of viscosity enhancement in crude oil phases is crucial for optimizing extraction and transportation processes. This study employed molecular dynamics simulations to investigate the behavior and viscosification mechanism of asphaltene molecules in complex oil phases. The research suggests that electrostatic interactions and interactions between asphaltene and crude oil molecules contribute to the enhanced viscosity. The findings provide insight into the viscosity enhancement mechanisms in crude oil phases.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Kun Lv, Jin Zhang, Xiaohua Liu, Yuqiao Zhou, Kai Liu
Summary: In this paper, the authors propose a robust method for evaluating the interactions between chiral catalysts and substrates using computer simulations. The method involves constructing 3D models from point cloud data, filtering out non-interacting points, determining interacting points, and accurately calculating interacted volumes. Experimental results demonstrate the effectiveness of the method in removing non-interacting points and calculating interacted volumes with low errors.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Crisciele Fontana, Joao Luiz de Meirelles, Hugo Verli
Summary: By using the GROMOS force field and molecular simulations, this study assessed the dynamics of STA-analogs in aqueous solution and their interaction with water, expanding the knowledge of the conformational space of these ligands and providing potential implications for understanding conformational selection during complexation.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Wei Zhao, Wenjie Zou, Fengyang Liu, Fang Zhou, N. Emre Altun
Summary: The effect of grafting rate on the water solubility of chitosan-grafted polyacrylamide (Chi-gPAM) was investigated using molecular dynamics simulations. The results showed that the intramolecular hydrogen bonding of Chi-gPAM played a dominant role in its water solubility. Additionally, the interaction between Chi-gPAM and water increased with grafting rate.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
Article
Biochemical Research Methods
Nassima Bachir, Samir Kenouche, Jorge I. Martinez-Araya
Summary: This study investigates the local chemical reactivity of FOX-7 and explores the interaction between the compound and different metals. The findings suggest that the stability and charge transfers of the compound are influenced by the metal involved, and the interaction between Metallocene Methyl Cations and the compound shows potential for neutralization.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)
