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Busch J, Paschek D. Computing Accurate True Self-Diffusion Coefficients and Shear Viscosities Using the OrthoBoXY Approach. J Phys Chem B 2024; 128:1040-1052. [PMID: 38240259 DOI: 10.1021/acs.jpcb.3c07540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
In a recent paper [Busch, J.; Paschek, D. J. Phys. Chem. B 2023, 127, 7983-7987], we have shown that for molecular dynamics (MD) simulations using orthorhombic periodic boundary conditions with "magic" box length ratios of Lz/Lx = Lz/Ly = 2.7933596497, the self-diffusion coefficients Dx and Dy in x- and y-directions are independent of the system size. They both represent the true self-diffusion coefficient D0 = (Dx + Dy)/2, while the shear viscosity can be calculated from diffusion coefficients in x-, y-, and z-directions, using η = kBT·8.1711245653/[3πLz(Dx + Dy - 2Dz)]. In this contribution, we test this "OrthoBoXY" approach by its application to a variety of different systems: liquid water, dimethyl ether, methanol, triglyme, water/methanol mixtures, water/triglyme mixtures, and imidazolium-based ionic liquids. The chosen systems range from small-sized molecular liquids to complex mixtures and ionic liquids, while spanning a viscosity range of almost 3 orders of magnitude. We assess the efficiency of the method for computing true self-diffusion and viscosity data and provide simple formulas for estimating the required MD simulation lengths and sizes for delivering reliable data with targeted uncertainty levels. Our analysis of the system size dependence of statistical uncertainties for both the viscosity and the self-diffusion coefficient leads us to the conclusion that it is preferable to extend the simulation length instead of increasing the system size. MD simulations consisting of 768 molecules or ion pairs seem to be perfectly adequate.
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Affiliation(s)
- Johanna Busch
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
| | - Dietmar Paschek
- Institut für Chemie, Abteilung Physikalische und Theoretische Chemie, Universität Rostock, Albert-Einstein-Str. 27, D-18059 Rostock, Germany
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Hu Y, Xing Y, Yue H, Chen T, Diao Y, Wei W, Zhang S. Ionic liquids revolutionizing biomedicine: recent advances and emerging opportunities. Chem Soc Rev 2023; 52:7262-7293. [PMID: 37751298 DOI: 10.1039/d3cs00510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Ionic liquids (ILs), due to their inherent structural tunability, outstanding miscibility behavior, and excellent electrochemical properties, have attracted significant research attention in the biomedical field. As the application of ILs in biomedicine is a rapidly emerging field, there is still a need for systematic analyses and summaries to further advance their development. This review presents a comprehensive survey on the utilization of ILs in the biomedical field. It specifically emphasizes the diverse structures and properties of ILs with their relevance in various biomedical applications. Subsequently, we summarize the mechanisms of ILs as potential drug candidates, exploring their effects on various organisms ranging from cell membranes to organelles, proteins, and nucleic acids. Furthermore, the application of ILs as extractants and catalysts in pharmaceutical engineering is introduced. In addition, we thoroughly review and analyze the applications of ILs in disease diagnosis and delivery systems. By offering an extensive analysis of recent research, our objective is to inspire new ideas and pathways for the design of innovative biomedical technologies based on ILs.
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Affiliation(s)
- Yanhui Hu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yuyuan Xing
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Yue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Chen
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yanyan Diao
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wei
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemical and Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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Xu S, Liu Y, Li X, Yue B, Huo F, He H, Zhang S. Quantitative Relation between Ionic Diffusivity and Ionic Association in Ionic Liquid-Water Mixtures. J Phys Chem Lett 2023; 14:2708-2714. [PMID: 36892821 DOI: 10.1021/acs.jpclett.2c03610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular dynamic simulations of aqueous mixtures of imidazolium ionic liquids (ILs) were performed to elucidate the dependence of the ionic diffusivity on the microscopic structures changed by water. Two distinct regimes of the average ionic diffusivity (Dave) were identified with the increased water concentrations: the jam regime with slowly increased Dave and the exponential regime with rapidly increased Dave, which are found to be directly correlated to the ionic association. Further analysis leads to two general relationships independent of IL species between Dave and the degree of ionic association: (i) a consistent linear relationship between Dave and the inverse of ion-pair lifetimes (1/τIP) in the two regimes and (ii) an exponential relationship between normalized diffusivities (D̃ave) and short-ranged interactions between cations and anions (Ẽions), with different interdependent strengths in the two regimes. These findings revealed and quantified the direct correlation between dynamic properties and ionic association in IL-water mixtures.
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Affiliation(s)
- Shuting Xu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of the Chinese Academy of Sciences School of Chemical Engineering, Beijing 100049, P. R. China
| | - Yawei Liu
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xuefu Li
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Bowen Yue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Feng Huo
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Zhengzhou Institute of Emerging Industrial Technology, Zhengzhou 450000, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, P. R. China
| | - Hongyan He
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of the Chinese Academy of Sciences School of Chemical Engineering, Beijing 100049, P. R. China
| | - Suojiang Zhang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of the Chinese Academy of Sciences School of Chemical Engineering, Beijing 100049, P. R. China
- Zhengzhou Institute of Emerging Industrial Technology, Zhengzhou 450000, China
- Longzihu New Energy Laboratory, Zhengzhou Institute of Emerging Industrial Technology, Henan University, Zhengzhou 450000, P. R. China
- College of Chemistry and Chemical Engineering, Henan University, Zhengzhou 451460, China
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Assessing the impact of increase in the number of hydroxyl groups on the microscopic behaviors of ammonium-based room temperature ionic liquids: A combined fluorescence up-conversion, fluorescence correlation and NMR spectroscopic study. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Bodo E. Perspectives in the Computational Modeling of New Generation, Biocompatible Ionic Liquids. J Phys Chem B 2022; 126:3-13. [PMID: 34978449 PMCID: PMC8762658 DOI: 10.1021/acs.jpcb.1c09476] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/15/2021] [Indexed: 12/11/2022]
Abstract
In this Perspective, I review the current state of computational simulations on ionic liquids with an emphasis on the recent biocompatible variants. These materials are used here as an example of relatively complex systems that highlights the limits of some of the approaches commonly used to study their structure and dynamics. The source of these limits consists of the coexistence of nontrivial electrostatic, many-body quantum effects, strong hydrogen bonds, and chemical processes affecting the mutual protonation state of the constituent molecular ions. I also provide examples on how it is possible to overcome these problems using suitable simulation paradigms and recently improved techniques that, I expect, will be gradually introduced in the state-of-the-art of computational simulations of ionic liquids.
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Affiliation(s)
- Enrico Bodo
- Chemistry Department, University of Rome “La Sapienza”, P. A. Moro 5, 00185 Rome, Italy
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Al-Sheakh L, Fritsch S, Appelhagen A, Villinger A, Ludwig R. Thermodynamically Stable Cationic Dimers in Carboxyl-Functionalized Ionic Liquids: The Paradoxical Case of "Anti-Electrostatic" Hydrogen Bonding. Molecules 2022; 27:molecules27020366. [PMID: 35056680 PMCID: PMC8778807 DOI: 10.3390/molecules27020366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 11/18/2022] Open
Abstract
We show that carboxyl-functionalized ionic liquids (ILs) form doubly hydrogen-bonded cationic dimers (c+=c+) despite the repulsive forces between ions of like charge and competing hydrogen bonds between cation and anion (c+–a−). This structural motif as known for formic acid, the archetype of double hydrogen bridges, is present in the solid state of the IL 1−(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC−CH2−py][NTf2]. By means of quantum chemical calculations, we explored different hydrogen-bonded isomers of neutral (HOOC–(CH2)n–py+)2(NTf2−)2, single-charged (HOOC–(CH2)n–py+)2(NTf2−), and double-charged (HOOC– (CH2)n−py+)2 complexes for demonstrating the paradoxical case of “anti-electrostatic” hydrogen bonding (AEHB) between ions of like charge. For the pure doubly hydrogen-bonded cationic dimers (HOOC– (CH2)n−py+)2, we report robust kinetic stability for n = 1–4. At n = 5, hydrogen bonding and dispersion fully compensate for the repulsive Coulomb forces between the cations, allowing for the quantification of the two equivalent hydrogen bonds and dispersion interaction in the order of 58.5 and 11 kJmol−1, respectively. For n = 6–8, we calculated negative free energies for temperatures below 47, 80, and 114 K, respectively. Quantum cluster equilibrium (QCE) theory predicts the equilibria between cationic monomers and dimers by considering the intermolecular interaction between the species, leading to thermodynamic stability at even higher temperatures. We rationalize the H-bond characteristics of the cationic dimers by the natural bond orbital (NBO) approach, emphasizing the strong correlation between NBO-based and spectroscopic descriptors, such as NMR chemical shifts and vibrational frequencies.
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Affiliation(s)
- Loai Al-Sheakh
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
| | - Sebastian Fritsch
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
| | - Andreas Appelhagen
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
| | - Alexander Villinger
- Institut für Chemie, Abteilung für Anorganische Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany;
| | - Ralf Ludwig
- Institut für Chemie, Abteilung für Physikalische Chemie, Universität Rostock, Dr.-Lorenz-Weg 2, 18059 Rostock, Germany; (L.A.-S.); (S.F.); (A.A.)
- Department LL&M, University of Rostock, Albert-Einstein−Str. 25, 18059 Rostock, Germany
- Leibniz−Institut für Katalyse an der Universität Rostock e.V., Albert-Einstein−Str. 29a, 18059 Rostock, Germany
- Correspondence:
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