A molecular dynamics study on aminoacid-based ionic liquids

Herrera, Cesar; García, Gregorio; Aparício, Santiago

doi:10.1016/j.molliq.2015.10.056

Cited by 35 publications

(32 citation statements)

References 83 publications

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“…This may due to anion from the amino acid (glycinate) which can form strong and stable H‐bonds with the enzyme polypeptide backbone and may dissociate the H‐bonds that maintain the structural integrity of the alpha‐helices and beta‐sheets, causing the protein to unfold partially. This conclusion can also be supported by various studies …”

Section: Discussionsupporting

confidence: 81%

Comprehensive Evaluation of Biomolecular Interactions between Protein and Amino Acid Based‐Ionic Liquids: A Comparable Study between [Bmim][Br] and [Bmim][Gly] Ionic Liquids

2016

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Protein is one of the most intricate and overriding biological system. Over the past years, there is an increased demand to consider ionic liquids (ILs) as novel biocompatible co-solvents for proteins.The overwhelming attention grabbed by new-generation ''amino acid ionic liquids (AAILs)''among various fields of modern chemistry and biology, has been attributed to their unique and designer nature. However, the stability of proteins in such AAILs is still untouched. Therefore, we have synthesized 1-butyl-3-methylimidazolium glycine ([Bmim][Gly]) in which anion is directly derived from natural amino acid and characterized to improve the stability of stem bromelain (BM). Since, it is speculated that replacement of cation/anion with the amino acids (AAs) will improve the stability of protein. Therefore, the main aim of present work is to highlight the influence of [Bmim][Gly] on the conformational stability and activity of BM. Furthermore, enzyme's stability and activity arecompared with the conventional imidazolium-based ionic liquid i. e. 1-butyl-3methylimidazolium bromide [Bmim][Br] by using spectroscopic techniques, enzyme assay and molecular docking. Our study shows that both studied ILs interact with functional groups of BM. As a result, in contrast to our expectation it appears that [Bmim] [Br] stabilizes BM more than [Bmim] [Gly]. We believe that present study will provide new insights into the interactions between enzyme and AAILs in the field of protein stabilization.

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Section: Discussionsupporting

confidence: 81%

Comprehensive Evaluation of Biomolecular Interactions between Protein and Amino Acid Based‐Ionic Liquids: A Comparable Study between [Bmim][Br] and [Bmim][Gly] Ionic Liquids

2016

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“…They reported a very good enhancement of the enzymatic hydrolysis of microcrystalline cellulose and rice straw after pretreatment using the [Cho][Gly] IL. The structural and dynamical properties of some [Cho][AA] ILs have been reported based on molecular dynamics (MD) simulations and quantum chemistry calculations during 2014–2019. − …”

Section: Introductionmentioning

confidence: 99%

Tracing Local Nanostructure of the Aqueous Solutions of the Biocompatible [Cho][Gly] Ionic Liquid: Importance of Hydrogen Bond Attraction between Like-Charged Ions

Khorrami

Kowsari

2020

J. Phys. Chem. B

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The neat and aqueous solutions of the cholinium glycinate ionic liquid (IL), [Cho][Gly], at different water mole fractions, x ws, are studied by molecular dynamics simulations. The changes in the local nanostructure of systems with composition have been determined by calculation of various structural distribution functions. Hydrogen bond (H-bond) attractions determine the major relative orientations of the oppositely and like charged nearest neighbors. The cation–anion H-bonds mainly form between the hydrogen of the hydroxyl or methyl groups of the cation and the carboxylate oxygen of the anion. A preferred (antiparallel) arrangement between adjacent [Cho]+ cations is due to the effective H-bond between the hydroxyl oxygen and the methyl hydrogen sites that promotes the like-charge cluster formation. Adding water decreases the occurrence probability of the [Cho]+···[Gly]−···[Cho]+ bridge structure in the aqueous solutions due to the formation of the [Gly]−···HOH···[Gly]− structure via H-bonding. Observed density trend versus x w is interpreted based on an interstice model and investigating the water cluster size distribution. Finally, the effect of x w on the infrared (IR) vibrational spectra were studied and blue and red shifts were observed for the stretching and bending vibrational modes of the hydroxyl group of [Cho]+, respectively. Current findings will improve the efficient engineering design and task-specific applications of aqueous solutions of bio-ILs consist of [Cho]+ and amino acid anions.

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“…With ILs being seen as designer solvents, the task of screening such a large collection is indeed formidable. Computational approaches based on density functional theory [10][11][12] and molecular dynamics [13,14] have generally been used to provide a mechanistic understanding of the working of ILs but are restricted by the time complexity of the modelling. Faster alternatives have relied on quantitative structure property relationship (QSPR) models wherein physicochemical descriptors derived from the molecular structure are correlated with the property of interest using chemometric and machine learning tools.…”

Section: Introductionmentioning

confidence: 99%

In silico prediction and experimental verification of ionic liquid refractive indices

Venkatraman

Raj

Evjen

et al. 2018

Journal of Molecular Liquids

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Ionic liquids (ILs) have seen increasing use as environmentally friendly solvents in a wide array of applications from energy to pharmaceuticals. Among the many properties of interest, the refractive index, is of considerable importance since several related properties can be estimated once the refractive index of a material is known. Furthermore, high refractive index ILs are also used as reference solutions to determine properties of optical materials. However, with a large collection of cation-anion combinations to choose from, the task of finding suitable ionic liquids is far from trivial. In this article, machine learning models have been used to estimate the temperature-dependent refractive index over 450 diverse ILs using cheap to compute semi-empirically derived structure descriptors. In addition to using independent test sets for evaluating the predictive ability of the models, the efficacy of the models was further evaluated using 14 new ionic liquids that were synthesized. Overall, ensemble decision tree-based approaches gave the best results with mean absolute errors < 0.01 and squared correlations > 0.85 across both calibration and test data.

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A molecular dynamics study on aminoacid-based ionic liquids

Cited by 35 publications

References 83 publications

Comprehensive Evaluation of Biomolecular Interactions between Protein and Amino Acid Based‐Ionic Liquids: A Comparable Study between [Bmim][Br] and [Bmim][Gly] Ionic Liquids

Comprehensive Evaluation of Biomolecular Interactions between Protein and Amino Acid Based‐Ionic Liquids: A Comparable Study between [Bmim][Br] and [Bmim][Gly] Ionic Liquids

Tracing Local Nanostructure of the Aqueous Solutions of the Biocompatible [Cho][Gly] Ionic Liquid: Importance of Hydrogen Bond Attraction between Like-Charged Ions

In silico prediction and experimental verification of ionic liquid refractive indices

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