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Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium

One of the most investigated properties of porous crystalline metal-organic frameworks (MOFs) is their potential flexibility to undergo large changes in unit cell size upon guest adsorption or other stimuli, referred to as “breathing”. Computationally, such phase transitions are usually investigated...

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Autores principales: Schaper, Larissa, Keupp, Julian, Schmid, Rochus
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8575409/
https://www.ncbi.nlm.nih.gov/pubmed/34760871
http://dx.doi.org/10.3389/fchem.2021.757680
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author Schaper, Larissa
Keupp, Julian
Schmid, Rochus
author_facet Schaper, Larissa
Keupp, Julian
Schmid, Rochus
author_sort Schaper, Larissa
collection PubMed
description One of the most investigated properties of porous crystalline metal-organic frameworks (MOFs) is their potential flexibility to undergo large changes in unit cell size upon guest adsorption or other stimuli, referred to as “breathing”. Computationally, such phase transitions are usually investigated using periodic boundary conditions, where the system’s volume can be controlled directly. However, we have recently shown that important aspects like the formation of a moving interface between the open and the closed pore form or the free energy barrier of the first-order phase transition and its size effects can best be investigated using non-periodic nanocrystallite (NC) models [Keupp et al. (Adv. Theory Simul., 2019, 2, 1900117)]. In this case, the application of pressure is not straightforward, and a distance constraint was used to mimic a mechanical strain enforcing the reaction coordinate. In contrast to this prior work, a mediating particle bath is used here to exert an isotropic hydrostatic pressure on the MOF nanocrystallites. The approach is inspired by the mercury nanoporosimetry used to compress flexible MOF powders. For such a mediating medium, parameters are presented that require a reasonable additional numerical effort and avoid unwanted diffusion of bath particles into the MOF pores. As a proof-of-concept, NCs of pillared-layer MOFs with different linkers and sizes are studied concerning their response to external pressure exerted by the bath. By this approach, an isotropic pressure on the NC can be applied in analogy to corresponding periodic simulations, without any bias for a specific mechanism. This allows a more realistic investigation of the breathing phase transformation of a MOF NC and further bridges the gap between experiment and simulation.
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spelling pubmed-85754092021-11-09 Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium Schaper, Larissa Keupp, Julian Schmid, Rochus Front Chem Chemistry One of the most investigated properties of porous crystalline metal-organic frameworks (MOFs) is their potential flexibility to undergo large changes in unit cell size upon guest adsorption or other stimuli, referred to as “breathing”. Computationally, such phase transitions are usually investigated using periodic boundary conditions, where the system’s volume can be controlled directly. However, we have recently shown that important aspects like the formation of a moving interface between the open and the closed pore form or the free energy barrier of the first-order phase transition and its size effects can best be investigated using non-periodic nanocrystallite (NC) models [Keupp et al. (Adv. Theory Simul., 2019, 2, 1900117)]. In this case, the application of pressure is not straightforward, and a distance constraint was used to mimic a mechanical strain enforcing the reaction coordinate. In contrast to this prior work, a mediating particle bath is used here to exert an isotropic hydrostatic pressure on the MOF nanocrystallites. The approach is inspired by the mercury nanoporosimetry used to compress flexible MOF powders. For such a mediating medium, parameters are presented that require a reasonable additional numerical effort and avoid unwanted diffusion of bath particles into the MOF pores. As a proof-of-concept, NCs of pillared-layer MOFs with different linkers and sizes are studied concerning their response to external pressure exerted by the bath. By this approach, an isotropic pressure on the NC can be applied in analogy to corresponding periodic simulations, without any bias for a specific mechanism. This allows a more realistic investigation of the breathing phase transformation of a MOF NC and further bridges the gap between experiment and simulation. Frontiers Media S.A. 2021-10-25 /pmc/articles/PMC8575409/ /pubmed/34760871 http://dx.doi.org/10.3389/fchem.2021.757680 Text en Copyright © 2021 Schaper, Keupp and Schmid. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Chemistry
Schaper, Larissa
Keupp, Julian
Schmid, Rochus
Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
title Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
title_full Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
title_fullStr Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
title_full_unstemmed Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
title_short Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
title_sort molecular dynamics simulations of the breathing phase transition of mof nanocrystallites ii: explicitly modeling the pressure medium
topic Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8575409/
https://www.ncbi.nlm.nih.gov/pubmed/34760871
http://dx.doi.org/10.3389/fchem.2021.757680
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