Advanced search
2 files | 5.36 MB

A comparison of barostats for the mechanical characterization of metal-organic frameworks

Sven Rogge (UGent) , Louis Vanduyfhuys (UGent) , An Ghysels (UGent) , Michel Waroquier (UGent) , Toon Verstraelen (UGent) , G Maurin and Veronique Van Speybroeck (UGent)
Author
Organization
Abstract
In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterize closed pore the rigid MOF-5 and flexible MIL-53(Al) metal organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-Tobias-Klein (MTTK), and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behavior in isothermal isobaric simulations. A thermodynamic integration method is used to construct the free energy profiles as a function of volume at finite temperature. It is observed that the aforementioned static properties are well-reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure fluctuations more drastically. Finally, dynamic properties, which are directly related to the fluctuations of the cell, such as the time to transition from the large-pore to the closed-pore phase, cannot be well-reproduced by any of the coupling schemes.
Keywords
MOLECULAR-DYNAMICS SIMULATIONS, ELASTIC NEUTRON-SCATTERING, STATISTICAL-MECHANICS, COORDINATION POLYMERS, CANONICAL ENSEMBLE, COMPUTATIONAL EXPLORATION, STRUCTURAL TRANSITIONS, FLEXIBLE MIL-53(CR), INFORMATION-THEORY, ISORETICULAR MOFS

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 2.02 MB
  • 7024350.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 3.34 MB

Citation

Please use this url to cite or link to this publication:

Chicago
Rogge, Sven, Louis Vanduyfhuys, An Ghysels, Michel Waroquier, Toon Verstraelen, G Maurin, and Veronique Van Speybroeck. 2015. “A Comparison of Barostats for the Mechanical Characterization of Metal-organic Frameworks.” Journal of Chemical Theory and Computation 11 (12): 5583–5597.
APA
Rogge, S., Vanduyfhuys, L., Ghysels, A., Waroquier, M., Verstraelen, T., Maurin, G., & Van Speybroeck, V. (2015). A comparison of barostats for the mechanical characterization of metal-organic frameworks. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11(12), 5583–5597.
Vancouver
1.
Rogge S, Vanduyfhuys L, Ghysels A, Waroquier M, Verstraelen T, Maurin G, et al. A comparison of barostats for the mechanical characterization of metal-organic frameworks. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. 2015;11(12):5583–97.
MLA
Rogge, Sven, Louis Vanduyfhuys, An Ghysels, et al. “A Comparison of Barostats for the Mechanical Characterization of Metal-organic Frameworks.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11.12 (2015): 5583–5597. Print.
@article{7024350,
  abstract     = {In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterize closed pore the rigid MOF-5 and flexible MIL-53(Al) metal organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-Tobias-Klein (MTTK), and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behavior in isothermal isobaric simulations. A thermodynamic integration method is used to construct the free energy profiles as a function of volume at finite temperature. It is observed that the aforementioned static properties are well-reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure fluctuations more drastically. Finally, dynamic properties, which are directly related to the fluctuations of the cell, such as the time to transition from the large-pore to the closed-pore phase, cannot be well-reproduced by any of the coupling schemes.},
  author       = {Rogge, Sven and Vanduyfhuys, Louis and Ghysels, An and Waroquier, Michel and Verstraelen, Toon and Maurin, G and Van Speybroeck, Veronique},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  keyword      = {MOLECULAR-DYNAMICS SIMULATIONS,ELASTIC NEUTRON-SCATTERING,STATISTICAL-MECHANICS,COORDINATION POLYMERS,CANONICAL ENSEMBLE,COMPUTATIONAL EXPLORATION,STRUCTURAL TRANSITIONS,FLEXIBLE MIL-53(CR),INFORMATION-THEORY,ISORETICULAR MOFS},
  language     = {eng},
  number       = {12},
  pages        = {5583--5597},
  title        = {A comparison of barostats for the mechanical characterization of metal-organic frameworks},
  url          = {http://dx.doi.org/10.1021/acs.jctc.5b00748},
  volume       = {11},
  year         = {2015},
}

Altmetric
View in Altmetric
Web of Science
Times cited: