Editorial Material
Chemistry, Physical
Andrew P. Abbott, Karen J. Edler, Alister J. Page
Summary: When selecting a solvent for a given solute, the commonly used idiom "like dissolves like" suggests using polar solvents for polar solutes. However, in deep eutectic solvents (DES), the components can be of various types, allowing for the solubilization of a wide range of solutes and the control of phase behavior through mixture design.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Engineering, Chemical
Shuzi Liu, Dongkun Yu, Yu Chen, Ruifen Shi, Fengyi Zhou, Tiancheng Mu
Summary: This paper introduces the evaluation method of thermal stability of deep eutectic solvents (DESs). Traditional thermogravimetric analysis (TGA) has issues such as decomposition overlap and low resolution, while high-resolution TGA (HR-TGA) can more accurately evaluate the thermal stability of DESs.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2022)
Article
Thermodynamics
Reza Haghbakhsh, Ana Rita C. Duarte, Sona Raeissi
Summary: This study measured and analyzed the viscosity behavior of two phenolic DES mixtures, showing negative viscosity deviations for both mixtures at different compositions and temperatures. The Preferential Solvation and Jouyban-Acree models achieved more reliable results compared to other models, suggesting stronger interactions among the DESs and water molecules in the mixtures.
FLUID PHASE EQUILIBRIA
(2022)
Article
Multidisciplinary Sciences
Abbeha Malik, Muhammad Nasir Iqbal, Sidrah Ashraf, Muhammad Saleem Khan, Samar Shahzadi, Muhammad Farhan Shafique, Zureesha Sajid, Muhammad Sajid, Sheikh Arslan Sehgal
Summary: A study found that the deficiency of calcium regulatory protein (CaM) leads to dysfunction of the cGMP signaling pathway, which is associated with various diseases. Through high-throughput virtual screening and comparative molecular docking, two compounds with strong binding affinity to eNOS were identified, which may be helpful in designing therapeutic targets against eNOS.
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
Polymer Science
Yeasmin Nahar, James Horne, Vinh Truong, Alex C. Bissember, Stuart C. Thickett
Summary: Thermoresponsive poly(N-isopropylacrylamide) (polyNIPAM) hydrogels were prepared via free radical polymerization in deep eutectic monomer solvents (DEMs) for the first time, where NIPAM served as a polymerizable hydrogen bond donor. The hydrogels prepared with DEMs showed increased cross-linking density and mechanical strength compared to those prepared in aqueous polymerization, exhibiting unique thermoresponsive swelling behavior.
Article
Biochemistry & Molecular Biology
Harshita Tiwari, Diksha Raina, Monika Gupta, Manas Ranjan Barik, Inshad Ali Khan, Farrah Khan, Amit Nargotra
Summary: UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is an important enzyme involved in bacterial cell wall synthesis. This study identified two potent inhibitors of MurA through virtual screening and validated their efficacy through in vitro assays. The study also discovered a novel binding site and revealed the mechanism of enzyme inhibition through conformational changes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Multidisciplinary Sciences
Ryosuke Matsuzaki, Yusuke Chisaka, Tomohiro Tajiri
Summary: This study uses molecular dynamics simulations to investigate the high permeability of water flow in CNT-based nanomaterials. It was found that the permeability coefficient increases with higher CNT content and with smaller intermolecular forces between water and CNTs. Additionally, changes in the arrangement structure of water molecules also contribute to the increase in permeability.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Physical
Elizabeth A. Recker, David Hardy, Grace I. Anderson, Arsalan Mirjafari, Durgesh V. Wagle
Summary: This study investigated the impact of a covalent link between hydrogen bond donor species on the behavior of deep eutectic solvents (DES). The presence of a glycosidic bond in trehalose limited the movement of sugar units, resulting in fewer interactions with choline chloride in DES(t). This limitation influenced the physical state of DES(t), making it behave more like a semi-solid material compared to the liquid-like behavior of DES(g).
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Ahmed Said Mohamed, Abdirahman Elmi, Rosella Spina, Maha A. Y. Kordofani, Dominique Laurain-Mattar, Hassan Nour, Oussama Abchir, Samir Chtita
Summary: The study aimed to investigate the phytochemical composition and antioxidant capacity of Avicennia marina extracts. The leaves had high levels of total flavonoid content, while the fruits showed the highest total phenolic content. Fat-soluble pigments such as beta-carotene, lycopene, chlorophyll a, and chlorophyll b were abundant in the leaves. The crude methanolic flower extracts exhibited strong DPPH and ABTS radical scavenging activity, with the ethyl acetate fraction showing the best antioxidant activity. HR-LCMS/MS analysis identified 13 compounds, including flavonoids and iridoid glycosides, in different parts of the plant. A bioinformatics study revealed the antioxidant activity and toxicity profiles of the major iridoid glycosides.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Pharmacology & Pharmacy
Juqin Peng, Xiaoxiao Chen, Min Hou, Kuo Yang, Bing Yang, Pan Wang, Yang Du, Qingyuan Yu, Junguo Ren, Jianxun Liu
Summary: The Feilike mixture (FLKM) was found to improve clinical symptoms, regulate immune inflammation response, and ameliorate pulmonary function in pneumonia treatment. Various active components interacted with pneumonia-related targets, mainly enriched in immune-related pathways. In vivo experiments showed that FLKM reduced lung injury and neutrophil infiltration in rats with pneumonia. Molecular docking tests revealed tight binding between active compounds and targeted proteins. This study identified core compositions and targets for FLKM in pneumonia treatment and provided pharmacological evidence supporting its clinical efficacy.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lei Wang, Xianying Fang, Yang Hu, Yiwei Zhang, Zhipeng Qi, Jie Li, Linguo Zhao
Summary: Deep eutectic solvent (DES) has shown significant advantages in the extraction of natural products, particularly flavonoids from Celtis sinensis. By comparing and optimizing the extraction conditions of six different DESs, the extraction yields have been significantly improved. Furthermore, purification using macroporous resin D-101 and evaluation of anti-inflammatory activity have demonstrated the potential medicinal value of DES extracts.
Article
Chemistry, Multidisciplinary
Meena Bisht, Margarida Martins, Ana C. R. Dias, Sonia P. M. Ventura, Joao A. P. Coutinho
Summary: Marine fish industries generate significant amounts of fish waste annually, with a majority being discarded in the form of skins, bones, fins, heads, guts, and scales, containing high levels of collagen type I. This study investigates the extraction of collagen from waste using deep eutectic solvents (DES) to develop a more efficient, cost-effective, and biocompatible process.
Article
Biochemistry & Molecular Biology
Priya Sundararajan, Darjily Dharmaraj Rajaselvi, Suseela Vivekananthan, Shanmuga Priya Ramasamy
Summary: In this study, the potential of prodigiosin as a PARP-1 inhibitor was virtually evaluated using molecular docking and molecular dynamics simulation. The results showed that prodigiosin exhibited good structural stability and high binding affinity with the PARP-1 protein, and demonstrated significant anticancer activity in TNBC cells. Therefore, prodigiosin could be a potential candidate for the treatment of TNBC.
BIOORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jameel M. Abduljalil, Abdo A. Elfiky, El-Sayed T. A. Sayed, Maha M. AlKhazindar
Summary: This study predicted the structure of the L protein of Nipah virus and identified potential inhibitors for the RNA-dependent RNA polymerase. Norov-29 showed the highest binding affinity and purine nucleotide analogs were found to be a potential scaffold for effective antiviral drugs against Nipah virus.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Rajiblochan Sahoo, Ligesh Theeyancheri, Rajarshi Chakrabarti
Summary: This study computationally investigates the transport of an active tracer through a polymer grafted cylindrical channel. The results show that passive tracers exhibit subdiffusion with increasing stickiness, while repulsive tracers prefer to diffuse through pore-like space along the channel axis. In contrast, active tracers show faster dynamics and intermediate superdiffusion, despite staying close to the dense polymeric region.
Article
Biochemistry & Molecular Biology
Asha Rani Choudhury, Atanu Maity, Sayantani Chakraborty, Rajarshi Chakrabarti
Summary: This article discusses the mechanism of SARS-CoV-2 virus binding to host cells and proposes using the RBD as a therapeutic target to design drugs. Computer simulation was used to estimate the thermodynamics of binding between six stapled peptides and RBD, and one of the peptides showed high binding affinity.
Article
Chemistry, Physical
Pooja Nanavare, Asha Rani Choudhury, Soham Sarkar, Atanu Maity, Rajarshi Chakrabarti
Summary: Recent studies have shown the industrial applications of aqueous choline chloride (ChCl) solution as an alternative solvent, and its role as a protecting co-solvent for proteins. The presence of ChCl affects the microscopic arrangement and hydrogen bonding structure of water molecules around methane, leading to disruption of the tetrahedral geometry of water and a decrease in hydrogen bonds with increasing ChCl concentration.
Review
Physics, Multidisciplinary
Koushik Goswami, Subhasish Chaki, Rajarshi Chakrabarti
Summary: This topical review provides an overview of the structure and dynamics of a single polymer chain in active baths, discussing the effects of Gaussian or non-Gaussian noises. The study reveals that the active noise leads to slower reconfiguration dynamics of the chain and causes swelling, as well as superdiffusive or ballistic motion of the tagged monomer. The review mainly focuses on the analytically exact or almost exact results obtained from the authors' group, while briefly mentioning important works from other groups and presenting some new results.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Chemistry, Multidisciplinary
Ligesh Theeyancheri, Rajiblochan Sahoo, Praveen Kumar, Rajarshi Chakrabarti
Summary: This paper reviews computer simulation studies on the dynamics of single active probes in crowded media. The research shows that active systems are out of equilibrium and cannot be described by equilibrium statistical mechanics. The motion of individual particles in crowded media is of prime importance for understanding the transport of bacteria, single cells, and synthetic active agents.
Article
Mechanics
R. Kailasham, Rajarshi Chakrabarti, J. Ravi Prakash, J. Ravi Prakash
Summary: An approach to solve the coupling problem in coarse-grained polymer models with fluctuating internal friction and hydrodynamic interactions is proposed. The governing stochastic differential equations are numerically integrated using Brownian dynamics simulations. The effects of finite extensibility, internal friction, and hydrodynamic interactions on shear viscosity are studied, revealing that shear-thickening induced by internal friction is more pronounced than that due to hydrodynamic interactions.
JOURNAL OF RHEOLOGY
(2023)
Article
Chemistry, Physical
Praveen Kumar, Rajarshi Chakrabarti
Summary: This study investigates the dynamics of tracer particles in mesh-like environments and finds that the size of the particles and the stiffness of the network affect their motion. Larger particles experience more confinement from the network particles, resulting in intermediate-time subdiffusion, while smaller particles or those with high self-propulsion velocities can easily escape from the cages, showing intermediate-time superdiffusion. The stiffness of the network slows down the dynamics of the tracer particles, with larger particles exhibiting longer-lived intermediate time superdiffusion. Active tracer particles exhibit more pronounced non-Gaussian behavior at the intermediate time scale.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Subhasish Chaki, Ligesh Theeyancheri, Rajarshi Chakrabarti
Summary: A living cell is affected by different forms of activity, which leads to the subdiffusive motion of loci and the coherent motion of chromatin. A study using a bead-spring polymer chain with dipolar active forces shows that the dynamics and organization of active chains differ from the passive chain. The dipolar active forces modify the elasticity of the chain.
Article
Chemistry, Physical
Ramanand Singh Yadav, Chintu Das, Rajarshi Chakrabarti
Summary: We used computer simulations to study the dynamics of a self-propelled spherical tracer particle in a viscoelastic medium. The interplay between viscoelasticity, stickiness, and activity brings additional complexity to the tracer dynamics. Our simulations reveal that increasing stickiness slows down the tracer particle's dynamics, while increasing self-propulsion velocity enhances it.
Article
Chemistry, Physical
Pooja Nanavare, Ligesh Theeyancheri, Soham Sarkar, Rajarshi Chakrabarti
Summary: The motion of hydrophobic moieties in a solvent is crucial for biomolecular functioning and is influenced by the surrounding environment. We simulated the dynamics of a methane molecule in different concentrations of aqueous choline chloride (ChCl) solution to understand the molecular-level behavior. Our findings show slower translational dynamics of methane and the emergence of spatio-temporal heterogeneity, leading to non-Gaussian behavior, which becomes more pronounced with higher ChCl concentration. This indicates more confined motion of methane in smaller and closely spaced cages, with an increase in jump percentage and a decrease in jump length. However, residual diffusion contributes the most to total diffusion, accounting for caging and small step displacements.
CHEMICAL PHYSICS IMPACT
(2023)
Article
Chemistry, Physical
Ligesh Theeyancheri, Subhasish Chaki, Tapomoy Bhattacharjee, Rajarshi Chakrabarti
Summary: To study the behavior of deformable active agents in porous media, we computationally investigate the dynamics of linear chains and rings made of active Brownian monomers. We find that flexible linear chains and rings migrate smoothly and undergo swelling, while semiflexible linear chains shrink at lower activities and swell at higher activities. Semiflexible rings, on the other hand, shrink and get trapped at lower activities, but escape at higher activities. This demonstrates the interplay between activity and topology in controlling the structure and dynamics of linear chains and rings in porous media.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Rajiblochan Sahoo, Rajarshi Chakrabarti
Summary: We use computer simulations to investigate the complex dynamics of a polymer, made of active Brownian particles, inside a channel grafted internally with passive polymer chains. We find that the structure and dynamics of the polymer are influenced by the interaction between the active polymer and the passive grafted chains. The activity of the polymer allows it to escape from local traps caused by the grafted chains, resulting in structural changes and enhanced diffusion.
Article
Chemistry, Physical
Praveen Kumar, Rajarshi Chakrabarti
Summary: We perform computer simulations to study the escape dynamics of a self-propelled nanorod from confinements. Our results demonstrate that the persistent and directed motion of the nanorod is crucial for its escape. We quantify the escape dynamics using the radial probability density function and mean first escape time, and show that the activity of the nanorod leads to a bimodal radial probability density function, which is absent in passive nanorods.
Article
Chemistry, Physical
Praveen Kumar, Rajarshi Chakrabarti
Summary: This study utilizes computer simulations to investigate the escape dynamics of a self-propelled nanorod from circular confinements with narrow openings. The results demonstrate the importance of persistent and directed motion in the escape process and the impact of the nanorod's activity on various escape parameters.