Molecular modelling of ionic liquids: Physical properties of species with extremely long aliphatic chains from a near-optimal regime

Sun, Zhaoxi; Kayal, Abhijit; Gong, Zhihao; Zheng, Lei; He, Qiaole

doi:10.1016/j.molliq.2022.120492

Cited by 13 publications

(16 citation statements)

References 111 publications

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“…The model construction follows the previously accumulated near-optimal protocol reported in our series papers. [31][32][33] Specifically, the chemical structures of ions downloaded from PubChem database are optimized at B3LYP [48][49][50] /6-31G*, after which atomic charges are derived with the restrained electrostatic potential (RESP) regime 51 based on molecular ESP scanned at HF/6-31G*. The atomic charges of ions forming ILs are scaled down to account for charge transfer and polarization effects, while the charges of solutes remain untouched.…”

Section: Computational Setupmentioning

confidence: 99%

“…Such observation is similar to our previous benchmarks on other ions forming ILs, indicating the generality of this behavior. [31][32][33] Another criticism in charge generation is the use of gas-phase data, which should be augmented with implicit solvent models to incorporate the solvent effects. To benchmark this point, we re-perform the ab initio calculations with the integral-equation-formalism polarizable continuum model (IEFPCM) 92 implicit solvent and recompute the ESP RRMSE for the HF/6-31G* RESP charges in Fig.…”

Section: Charge Generationmentioning

confidence: 99%

“…31,32 Aside from the benchmark set used to derive these conclusions, this modelling regime has been proven to be successful also for species with significantly different structural features. 33 Aside from the charge scaling issue, another critical point in the parametrization of ILs species validated in our series works is the ab initio level in the ESP scan. The traditional HF/6-31G* level is often criticized to produce lowquality data and should be replaced with higher-level methods.…”

Section: Introductionmentioning

confidence: 96%

“…1. Compared with anionic species investigated in our previous works, [31][32][33] replaced with -C2F5. This chemical modification could incur variations in various properties of ILs, e.g., molar volume, viscosity, thermal stability and gas permeability.…”

Section: Introductionmentioning

confidence: 99%

“…However, this 'cheap' option is validated to generate satisfactory atom-centered charges that accurately reproduce the higher-level ESP. [31][32][33] Despite the diversity in chemical and structural space covered in our series works, there are still many ILs species with special properties that are not considered, especially for large anions with a large number of fluorine substitutions. In this work, we consider two new ILs formed by imidazolium cations and perfluorinated organic anions, the 2D chemical structures of which are depicted in Fig.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Modelling of Ionic Liquids: Perfluorinated Anionic Species with Enlarged Halogen Substitutions

Sun

Zheng

Zhang

et al. 2022

Preprint

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Ionic liquids as promising green solvents are widely applied in laboratory and industrial applications. Despite the massive experimental efforts on various applications, accurate computational modelling of such complex solution remains challenging. Our previous extensive numerical experiences on bulk properties, solvation and partition of external drug-like molecules between water and ionic-liquids phases lead to the recommended modelling regime of 0.8-scaled RESP charges and the GAFF2 parameter set. Such a protocol has been found to be effective in reproducing the experimental thermodynamic properties that require balanced descriptions of solute-solvent and solvent-solvent interactions. A deficiency in the previous benchmark set is the lack of voluminous and highly halogen-substituted anions. Therefore, in this work, we explore the calculation of ionic liquids involving large voluminous perfluorinated anionic species. Also, the ESP analysis confirms the similarity of the ESP produced by the gas-phase HF/6-31G* generated atomic charges and the higher-level implicit-solvent calculations. The quality of the HF/6-31G*-targeted charges is further validated by a direct face-to-face comparison of the bulk density estimated from molecular simulation under different charge sets, consolidating the protocol for model construction.

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Section: Computational Setupmentioning

confidence: 99%

Section: Charge Generationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Molecular Modelling of Ionic Liquids: Perfluorinated Anionic Species with Enlarged Halogen Substitutions

Sun

Zheng

Zhang

et al. 2022

Preprint

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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Liu

Zheng

Cong

et al. 2022

J Comput Aided Mol Des

Self Cite

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End-point free energy calculations as a powerful tool have been widely applied in protein-ligand and protein-protein interactions. It is often recognized that these end-point techniques serve as an option of intermediate accuracy and computational cost compared with more rigorous statistical mechanic models (e.g., alchemical transformation) and coarser molecular docking. However, it is observed that this intermediate level of accuracy does not hold in relatively simple and prototypical host-guest systems. Specifically, in our previous work investigating a set of carboxylated-pillar[6]arene host-guest complexes, end-point methods provide free energy estimates deviating significantly from the experimental reference, and the rank of binding affinities is also incorrectly computed. These observations suggest the unsuitability and inapplicability of standard end-point free energy techniques in host-guest systems, and alteration and 2 / 41 development are required to make them practically usable. In this work, we consider two ways to improve the performance of end-point techniques. The first one is the PBSA_E regression that varies the weights of different free energy terms in the end-point calculation procedure, while the second one is considering the interior dielectric constant as an additional variable in the end-point equation. By detailed investigation of the calculation procedure and the simulation outcome, we prove that these two treatments (i.e., regression and dielectric constant) are manipulating the end-point equation in a somehow similar way, i.e., weakening the electrostatic contribution and strengthening the non-polar terms, although there are still many detailed differences between these two methods. With the trained end-point scheme, the RMSE of the computed affinities is improved from the standard ~12 kcal/mol to ~2.4 kcal/mol, which is comparable to another altered end-point method (ELIE) trained with system-specific data. This phenomenon along with the extremely efficient optimized-structure computation procedure suggests the regression (i.e., PBSA_E as well as its GBSA_E extension) as a practically applicable solution that brings end-point methods back into the library of usable tools for host-guest binding. However, the dielectric-constant-variable scheme cannot effectively minimize the experiment-calculation discrepancy for absolute binding affinities, but is able to improve the calculation of affinity ranks. This phenomenon is somehow different from the protein-ligand case and suggests the difference between host-guest and biomacromolecular (protein-ligand and proteinprotein) cases. Therefore, the spectrum of tools usable in protein-ligand cases could be unsuitable for hostguest binding, and numerical validations are necessary to screen out really workable solutions in these 'prototypical' situations.

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Molecular modelling of ionic liquids: Perfluorinated anionic species with enlarged halogen substitutions

Sun

Zheng

Zhang

et al. 2023

Journal of Molecular Liquids

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Molecular modelling of ionic liquids: Physical properties of species with extremely long aliphatic chains from a near-optimal regime

Cited by 13 publications

References 111 publications

Molecular Modelling of Ionic Liquids: Perfluorinated Anionic Species with Enlarged Halogen Substitutions

Molecular Modelling of Ionic Liquids: Perfluorinated Anionic Species with Enlarged Halogen Substitutions

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Molecular modelling of ionic liquids: Perfluorinated anionic species with enlarged halogen substitutions

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