Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction

Vazquez-Salazar, Luis Itzá; Selle, Michele; Vries, Alex H. de; Marrink, Siewert J.; Souza, Paulo C. T.

doi:10.1039/d0gc01823f

Cited by 51 publications

(65 citation statements)

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“…We demonstrate the accuracy of the model by reproducing the salt dependent coacervation of poly-L-lysine / poly-L-glutamate (pLys / pGlu) systems, which have been studied extensively by Tirrell, Perry and coworkers 17,20,30,36,37 , and show the potential of the model by simulating the partitioning of ions and small nucleotides between the condensate and surrounding solvent phase. The advantage of the Martini model over other CG approaches, in addition to the chemical specificity, is the building block approach offering immediate compatibility of polyelectrolytes with other molecules parameterized using the Martini philosophy, such as lipids, 38 proteins 39 , sugars 40 , nucleotides 41,42 , ionic liquids 43 and polymers 44 . This provides a quick route to the simulation of extraction of valuable compounds in biotechnological applications, as well as to study prebiotic cell precursors and biomolecular condensates in current cells with realistic composition.…”

Section: Introductionmentioning

confidence: 99%

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

et al. 2021

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Section: Introductionmentioning

confidence: 99%

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

et al. 2021

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“…Vazquez-Salazar et al 30 parameterized and consequently studied ionic liquids with the Martini 3 open beta scheme. Finally, Srinivasan et al 31 evaluated Martini 3 efficiency in studying peripheral protein-membrane interactions.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

Lamprakis

Andreadelis

Manchester³

et al. 2021

J. Chem. Theory Comput.

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Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could ultimately lead to new approaches in designing novel therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we use parallel tempering metadynamics simulations in the well-tempered ensemble to evaluate the performance of Martini 2.2P and Martini open-beta 3 (Martini 3) force fields in reproducing the structure and energetics of the dimerization process of membrane proteins and proteins in an aqueous solution in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association by estimating large barriers in distinct areas, which likely leads to overaggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results in a systematic underestimation of the free energy of association for proteins in solution, while it performs well in describing the association of membrane proteins. In all cases the near-native dimer complexes are identified as minima in the free energy surface albeit not always as the lowest minima. In the case of Martini 3 we find that the spurious supramolecular protein aggregation present in Martini 2.2P multimer simulations is alleviated and thus this force field may be more suitable for the study of protein oligomerization. We propose that the use of enhanced sampling simulations with a refined coarse-grained force field and appropriately defined collective variables is a robust approach for studying the protein dimerization process, although one should be cautious of the ranking of energy minima. File list (2) download file view on ChemRxiv Protein-Dimerization-MARTINI.pdf (3.46 MiB) download file view on ChemRxiv SUPPORTING INFORMATION_martini-dimerization.pdf (8.58 MiB)

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“…[ 35,83,113,278–283 ] Recently, interest in surfactants has renewed as ionic liquids (ILs) have attracted much attention for their use as biocompatible and green solvents and co‐solvents. This has led several authors to use Martini to simulate the self‐assembly of IL mesophases, [ 284,285 ] the process of IL‐mediated extractions, [ 285,286 ] as well as to guide the design of de novo molecules. [ 286 ]…”

Section: Example Applicationsmentioning

confidence: 99%

The Martini Model in Materials Science

2021

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The Martini model, a coarse‐grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

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Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction

Abstract: Ionic liquids (IL) are remarkable green solvents, which find applications in many areas of nano- and biotechnology including extraction and purification of value-added compounds or fine chemicals. These liquid salts...

Cited by 51 publications

References 74 publications

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments

The Martini Model in Materials Science

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