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Efficient construction of free energy profiles of breathing metal–organic frameworks using advanced molecular dynamics simulations

Ruben Demuynck (UGent), Sven Rogge (UGent), Louis Vanduyfhuys (UGent), Jelle Wieme (UGent), Michel Waroquier (UGent) and Veronique Van Speybroeck (UGent)
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Abstract
In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.
Keywords
INDUCED STRUCTURAL TRANSITIONS, NEGATIVE GAS-ADSORPTION, MONTE-CARLO, RARE EVENTS, FORCE-FIELD, BASIS-SET, MIL-53, FLEXIBILITY, TEMPERATURE, PRESSURE

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Chicago
Demuynck, Ruben, Sven Rogge, Louis Vanduyfhuys, Jelle Wieme, Michel Waroquier, and Veronique Van Speybroeck. 2017. “Efficient Construction of Free Energy Profiles of Breathing Metal–organic Frameworks Using Advanced Molecular Dynamics Simulations.” Journal of Chemical Theory and Computation 13 (12): 5861–5873.
APA
Demuynck, R., Rogge, S., Vanduyfhuys, L., Wieme, J., Waroquier, M., & Van Speybroeck, V. (2017). Efficient construction of free energy profiles of breathing metal–organic frameworks using advanced molecular dynamics simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13(12), 5861–5873.
Vancouver
1.
Demuynck R, Rogge S, Vanduyfhuys L, Wieme J, Waroquier M, Van Speybroeck V. Efficient construction of free energy profiles of breathing metal–organic frameworks using advanced molecular dynamics simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION. American Chemical Society (ACS); 2017;13(12):5861–73.
MLA
Demuynck, Ruben, Sven Rogge, Louis Vanduyfhuys, et al. “Efficient Construction of Free Energy Profiles of Breathing Metal–organic Frameworks Using Advanced Molecular Dynamics Simulations.” JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13.12 (2017): 5861–5873. Print.
@article{8545220,
  abstract     = {In order to reliably predict and understand the breathing behavior of highly flexible metal--organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.},
  author       = {Demuynck, Ruben and Rogge, Sven and Vanduyfhuys, Louis and Wieme, Jelle and Waroquier, Michel and Van Speybroeck, Veronique},
  issn         = {1549-9618},
  journal      = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION},
  keyword      = {INDUCED STRUCTURAL TRANSITIONS,NEGATIVE GAS-ADSORPTION,MONTE-CARLO,RARE EVENTS,FORCE-FIELD,BASIS-SET,MIL-53,FLEXIBILITY,TEMPERATURE,PRESSURE},
  language     = {eng},
  number       = {12},
  pages        = {5861--5873},
  publisher    = {American Chemical Society (ACS)},
  title        = {Efficient construction of free energy profiles of breathing metal--organic frameworks using advanced molecular dynamics simulations},
  url          = {http://dx.doi.org/10.1021/acs.jctc.7b01014},
  volume       = {13},
  year         = {2017},
}

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