scholarly journals Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length, Part I

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 116
Author(s):  
Fatemeh Fadaei ◽  
Michelle Seifert ◽  
Joshua R. Raymond ◽  
David Řeha ◽  
Natalia Kulik ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Alkyl Chain ◽  
Hydrophobic Interactions ◽  
Fluorescence Emission ◽  
Md Simulations ◽  
Distribution Functions ◽  
Dna Duplex ◽  
Groove Binding ◽  
Imidazolium Chloride ◽  
Time Constants

Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Imn,1]+) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T×A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500–1000 cm−1, spectral broadening (~1000 cm−1), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL. Fluorescence lifetimes for DAPI/IL solutions yielded two time constants 0.15 ns (~80% to 60% contribution) and 2.36–2.71 ns for IL up to 250 mM. With DNA, three time constants were required that varied with added IL (0.33–0.15 ns (1–58% contribution), ~1.7–1.0 ns (~5% contribution), and 3.8–3.6 ns (94–39% contribution)). MD radial distribution functions revealed that π-π stacking interactions between the imidazolium ring were dominant at lower IL concentration and that electrostatic and hydrophobic interactions become more prominent as IL concentration increased. Alkyl chain alignment with DNA and IL-IL interactions also varied with IL. Collectively, our data showed that, at low IL concentration, IL was primarily bound to the DNA minor groove and with increased IL concentration the phosphate regions and major groove binding sites were also important contributors to the complete set of IL-DNA duplex interactions.

Hydration Behavior Study of Imidazolium Based ILs in Water

2014 ◽  
Vol 625 ◽  
pp. 553-556 ◽  
Author(s):  
Bhajan Lal
Keyword(s):  
Ionic Liquids ◽  
Structural Changes ◽  
Alkyl Chain ◽  
Hydrophobic Interactions ◽  
Hydrophobic Hydration ◽  
Alkyl Chain Length ◽  
Apparent Molar Volumes ◽  
Volumetric Properties ◽  
Molar Volumes ◽  
Behavior Study

These ILs were chosen to provide an understanding of the influence of the cation alkyl chain length, and the anion influence on the volumetric properties. Densities for aqueous solutions of ionic liquids having 1-butyl-3-methylimidazolium as cation and chloride, bromide, iodide and acetate as anions were accurately measured at various concentrations and temperature, (288.15, 293.15, 298.15, 303.15 and 308.15) K. The results have been discussed in terms of hydrophobic hydration, hydrophobic interactions, and water structural changes in aqueous medium. The data were used in evaluating thermodynamic properties as apparent molar volumes, and apparent molar expansions. Apparent molar volumes were found to increase with temperature.

scholarly journals A Molecular Model of PEMFC Catalyst Layer: Simulation on Reactant Transport and Thermal Conduction

Membranes ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 148
Author(s):  
Wenkai Wang ◽  
Zhiguo Qu ◽  
Xueliang Wang ◽  
Jianfei Zhang
Keyword(s):  
Thermal Conductivity ◽  
Proton Exchange Membrane ◽  
Molecular Model ◽  
Phase Interface ◽  
Catalyst Layer ◽  
Md Simulations ◽  
Distribution Functions ◽  
Proton Exchange ◽  
Pt Catalyst ◽  
Reaction Efficiency

Minimizing platinum (Pt) loading while reserving high reaction efficiency in the catalyst layer (CL) has been confirmed as one of the key issues in improving the performance and application of proton exchange membrane fuel cells (PEMFCs). To enhance the reaction efficiency of Pt catalyst in CL, the interfacial interactions in the three-phase interface, i.e., carbon, Pt, and ionomer should be first clarified. In this study, a molecular model containing carbon, Pt, and ionomer compositions is built and the radial distribution functions (RDFs), diffusion coefficient, water cluster morphology, and thermal conductivity are investigated after the equilibrium molecular dynamics (MD) and nonequilibrium MD simulations. The results indicate that increasing water content improves water aggregation and cluster interconnection, both of which benefit the transport of oxygen and proton in the CL. The growing amount of ionomer promotes proton transport but generates additional resistance to oxygen. Both the increase of water and ionomer improve the thermal conductivity of the C. The above-mentioned findings are expected to help design catalyst layers with optimized Pt content and enhanced reaction efficiency, and further improve the performance of PEMFCs.

Spectroscopic Study on Imidazolium-Based Ionic Liquids: Effect of Alkyl Chain Length and Anion

2012 ◽  
Vol 116 (11) ◽  
pp. 3512-3518 ◽  
Author(s):  
Enrico Binetti ◽  
Annamaria Panniello ◽  
Leonardo Triggiani ◽  
Raffaele Tommasi ◽  
Angela Agostiano ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Spectroscopic Study ◽  
Chain Length ◽  
Alkyl Chain ◽  
Alkyl Chain Length

Relationship between mesoscale dynamics and shear relaxation of ionic liquids with long alkyl chain

2012 ◽  
Vol 137 (10) ◽  
pp. 104511 ◽  
Author(s):  
Tsuyoshi Yamaguchi ◽  
Ken-ichi Mikawa ◽  
Shinobu Koda ◽  
Kenta Fujii ◽  
Hitoshi Endo ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Alkyl Chain ◽  
Mesoscale Dynamics ◽  
Shear Relaxation ◽  
Long Alkyl Chain

Aggregation Behaviours of Surface-Active Ionic Liquids 1-Alkyl-3-methylimidazolium Bis(2-ethylhexyl)sulfosuccinate

2016 ◽  
Vol 69 (11) ◽  
pp. 1254 ◽  
Author(s):  
Jiequn Wu ◽  
Tianxiang Yin ◽  
Shaoxiong Shi ◽  
Weiguo Shen
Keyword(s):  
Ionic Liquids ◽  
Self Assembly ◽  
Alkyl Chain ◽  
Systematic Investigation ◽  
Bulk Solution ◽  
Free Energies ◽  
Imidazolium Cation ◽  
Structure Transition ◽  
Surface Active ◽  
Counter Ion Binding

The systematic investigation of the aggregation behaviours of newly synthesised surface-active ionic liquids 1-alkyl-3-methylimidazolium bis(2-ethylhexyl)sulfosuccinate ([Cnmim][AOT], n = 2, 3, 5, 6, 7) by various techniques is reported. The critical aggregation concentrations (CACs) and the standard Gibbs free energies of aggregation () were determined from measurements on conductivity, fluorescence, and surface tension, which suggested a stronger self-assembly ability in the bulk solution for [Cnmim][AOT] surfactants with longer alkyl chain cations. An interesting structure transition driven by the penetration of the imidazolium cation into the aggregate when n > 4 was found by analysis of the variations of the values of CAC, , the degree of counter ion binding (β), and the micropolarity (I1/I3) immediately after the CAC with changing alkyl chain length of the imidazolium cation, which was further confirmed by 1H NMR measurements.

Long alkyl chain quaternary ammonium-based ionic liquids and potential applications

2006 ◽  
Vol 8 (9) ◽  
pp. 798 ◽  
Author(s):  
Juliusz Pernak ◽  
Marcin Smiglak ◽  
Scott T. Griffin ◽  
Whitney L. Hough ◽  
Timothy B. Wilson ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Quaternary Ammonium ◽  
Alkyl Chain ◽  
Potential Applications ◽  
Long Alkyl Chain

scholarly journals Exploration of Novel Xanthine Oxidase Inhibitors Based on 1,6-Dihydropyrimidine-5-Carboxylic Acids by an Integrated in Silico Study

2021 ◽  
Vol 22 (15) ◽  
pp. 8122
Author(s):  
Na Zhai ◽  
Chenchen Wang ◽  
Fengshou Wu ◽  
Liwei Xiong ◽  
Xiaogang Luo ◽  
...  
Keyword(s):  
Xanthine Oxidase ◽  
Carboxylic Acids ◽  
Hydrophobic Interactions ◽  
Pharmacophore Model ◽  
3D Qsar ◽  
Md Simulations ◽  
Pharmacophore Modeling ◽  
Binding Modes ◽  
Comfa Model ◽  
Validation Parameters

Xanthine oxidase (XO) is an important target for the effective treatment of hyperuricemia-associated diseases. A series of novel 2-substituted 6-oxo-1,6-dihydropyrimidine-5-carboxylic acids (ODCs) as XO inhibitors (XOIs) with remarkable activities have been reported recently. To better understand the key pharmacological characteristics of these XOIs and explore more hit compounds, in the present study, the three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) studies were performed on 46 ODCs. The constructed 3D-QSAR models exhibited reliable predictability with satisfactory validation parameters, including q2 = 0.897, R2 = 0.983, rpred2 = 0.948 in a CoMFA model, and q2 = 0.922, R2 = 0.990, rpred2 = 0.840 in a CoMSIA model. Docking and MD simulations further gave insights into the binding modes of these ODCs with the XO protein. The results indicated that key residues Glu802, Arg880, Asn768, Thr1010, Phe914, and Phe1009 could interact with ODCs by hydrogen bonds, π-π stackings, or hydrophobic interactions, which might be significant for the activity of these XOIs. Four potential hits were virtually screened out using the constructed pharmacophore model in combination with molecular dockings and ADME predictions. The four hits were also found to be relatively stable in the binding pocket by MD simulations. The results in this study might provide effective information for the design and development of novel XOIs.

Thermo-physical and tribological characteristics of ionic liquid-based rice bran oil as green cutting fluid

2021 ◽  
pp. 135065012110461
Author(s):  
Aswani K Singh ◽  
Varun Sharma
Keyword(s):  
Ionic Liquid ◽  
Ionic Liquids ◽  
Coefficient Of Friction ◽  
Rice Bran ◽  
Alkyl Chain ◽  
Rice Bran Oil ◽  
Alkyl Chain Length ◽  
Cutting Fluid ◽  
Cutting Fluids ◽  
Base Oil

During machining, the cutting fluids play an essential role in cooling and lubrication. In order to reduce the friction forces, the excessive amount of the cutting fluids are generally used. This, in turn, leads to wastage of the cutting fluids which results in a serious impact on the environment, health and cost of production. Therefore, the judicious use of lubricants is the foremost concern in the manufacturing industry. In order to mitigate these drawbacks, various alternatives have been developed in the last decade. In the present paper, ionic liquids have been proved as favourable sustainable alternative additives in the base oil. The effect of alkyl chain length of ionic liquids with base oil on the thermo-physical and tribological characteristics of cutting fluids including viscosity, wettability, anticorrosion behaviour, thermal stability, and coefficient of friction have been analysed. In the present study, pyrrolidinium and hexafluoro-phosphate (PF6) have been used as cation and anion, respectively, with rice bran oil as base oil. The five different ionic liquids have been dispersed in base oil by 1.0 wt%. It has been found that longer alkyl chain length showed the favourable results as compared to the shorter one. Results indicated that ionic liquid based cutting fluid attained ample enhanced thermophysical and tribological properties as compared to the neat rice bran oil. There has been 5.08% and 4.29% improvement in viscosity and thermal conductivity for IL4 + RBO in comparison to neat RBO. In addition, the wettability, coefficient of friction, and wear volume have been reduced by 20.34%, 53.79% and 57.87% correspondingly.

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