Thermodynamic and Transport Properties of Crown-Ethers: Force Field Development and Molecular Simulations

Jamali, Seyed Hossein; Ramdin, Mahinder; Becker, Tim M.; Rinwa, Shwet Kumar; Buijs, Wim; Vlugt, Thijs J. H.

doi:10.1021/acs.jpcb.7b06547

Cited by 15 publications

(10 citation statements)

References 72 publications

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“…The past few decades, Equilibrium Molecular Dynamics (EMD) simulation has emerged as a powerful tool for computing diffusion coefficients of pure components and multicomponent mixtures. − Typically, system sizes in the order of hundreds to a few thousands molecules are used, combined with periodic boundary conditions. , As shown in the pioneering work by Dünweg and Kremer almost 30 years ago, the choice of the system size strongly affects computed self-diffusivities, which scale linearly with the inverse of the simulation box size. In early 2000s, Yeh and Hummer (YH) derived an analytic hydrodynamic correction which should be added to self-diffusivities computed from EMD, to obtain diffusivities at the thermodynamic limit, i.e., the quantity measured in experiments.…”

Section: Introductionmentioning

confidence: 99%

Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation

Jamali

Bardow

Vlugt

et al. 2020

J. Chem. Theory Comput.

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The system-size dependence of computed mutual diffusion coefficients of multicomponent mixtures is investigated, and a generalized correction term is derived. The generalized finite-size correction term was validated for the ternary molecular mixture chloroform/acetone/methanol as well as 28 ternary LJ systems. It is shown that only the diagonal elements of the Fick matrix show system-size dependency. The finite-size effects of these elements can be corrected by adding the term derived by Yeh and Hummer (J. Phys. Chem. B 2004, 108, 15873–15879). By performing an eigenvalue analysis of the finite-size effects of the matrix of Fick diffusivities we show that the eigenvector matrix of Fick diffusivities does not depend on the size of the simulation box. Only eigenvalues, which describe the speed of diffusion, depend on the size of the system. An analytic relation for finite-size effects of the matrix of Maxwell–Stefan diffusivities was developed. All Maxwell–Stefan diffusivities depend on the system size, and the required correction depends on the matrix of thermodynamic factors.

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Section: Introductionmentioning

confidence: 99%

Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation

Jamali

Bardow

Vlugt

et al. 2020

J. Chem. Theory Comput.

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“…The exponential increase in computational power in the past few decades, along with the development of robust open-source packages, such as LAMMPS, GROMACS, and NAMD, allows for the efficient use of MD as a part of the design and optimization of various industrial processes (Figure ). Typical examples are gas treatment, , carbon capture and sequestration, − and desalination using nanoporous membranes. , Since there is a continuous demand for the prediction of transport coefficients, computational tools that are both accurate and easy-to-use are urgently needed. , …”

Section: Introductionmentioning

confidence: 99%

OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order-nAlgorithm in LAMMPS

Jamali

Wolff

Becker

et al. 2019

J. Chem. Inf. Model.

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103

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We present a new plugin for LAMMPS for on-the-fly computation of transport properties (OCTP) in equilibrium molecular dynamics. OCTP computes the self- and Maxwell–Stefan diffusivities, bulk and shear viscosities, and thermal conductivities of pure fluids and mixtures in a single simulation. OCTP is the first implementation in LAMMPS that uses the Einstein relations combined with the order-n algorithm for the efficient sampling of dynamic variables. OCTP has low computational requirements and is easy to use because it follows the native input file format of LAMMPS. A tool for calculating the radial distribution function (RDF) of the fluid beyond the cutoff radius, while taking into account the system size effects, is also part of the new plugin. The RDFs computed from OCTP are needed to obtain the thermodynamic factor, which relates Maxwell–Stefan and Fick diffusivities. To demonstrate the efficiency of the new plugin, the transport properties of an equimolar mixture of water–methanol were computed at 298 K and 1 bar.

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“…The first purely simulation study of PLs appeared in 2017. In this work, [151] the thermodynamic and transport properties of various crown-ethers were investigated by Vlugt and coworkers. Specifically, the viscosity, density, and self-diffusion coefficients of crown-ethers were analyzed using the MD simulation.…”

Section: Theoretical Simulation Of Plsmentioning

confidence: 99%

Shining Light on Porous Liquids: From Fundamentals to Syntheses, Applications and Future Challenges

Wang

Xin

Yao

et al. 2021

Adv Funct Materials

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Porous liquids (PLs), an emerging type of flowing liquid materials that combine the merits of porous solids and flowing liquids, have garnered immense attention since the concept of PLs was proposed in 2007. Meanwhile, PLs have witnessed growing success in versatile synthesis strategies and emerging applications, especially since 2017. Given the lack of a timely comprehensive review, developing a prompt summary with a comprehensive understanding is undoubtedly urgent. Thus, this critical review offers a comprehensive summary of the progress in fundamental chemistry, developmental history, synthetic strategies, and emerging applications of PLs. First, the fundamental chemistry and developmental history are reviewed. Then, the synthesis strategies of PLs are highlighted. Additionally, crosscutting studies of pure theoretical simulations are reviewed. Meanwhile, the daunting characterization issues of PLs are analyzed. Next, the state-of-the-art of PLs applications is reviewed in detail. In the end, perspectives regarding the remaining challenges and future directions for PLs are presented. It is speculated that this critical comprehensive review of PLs could inspire scientific communities who focus on the taskspecific materials for various applications, such as gas sorption, membrane separation, catalytic conversion, chiral separation, thermal management and electrolyte, and so on.

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Thermodynamic and Transport Properties of Crown-Ethers: Force Field Development and Molecular Simulations

Cited by 15 publications

References 72 publications

Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation

Generalized Form for Finite-Size Corrections in Mutual Diffusion Coefficients of Multicomponent Mixtures Obtained from Equilibrium Molecular Dynamics Simulation

OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order-nAlgorithm in LAMMPS

Shining Light on Porous Liquids: From Fundamentals to Syntheses, Applications and Future Challenges

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