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Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks

Ruben Demuynck (UGent) , Jelle Wieme (UGent) , Sven Rogge (UGent) , Karen Dedecker (UGent) , Louis Vanduyfhuys (UGent) , Michel Waroquier (UGent) and Veronique Van Speybroeck (UGent)
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Abstract
Various kinds of flexibility have been observed in metal-organic frameworks, which may originate from the topology of the material or the presence of flexible ligands. The construction of free energy profiles describing the full dynamical behavior along the phase transition path is challenging since it is not trivial to identify collective variables able to identify all metastable states along the reaction path. In this work, a systematic three-step protocol to uniquely identify the dominant order parameters for structural transformations in flexible metal-organic frameworks and subsequently construct accurate free energy profiles is presented. Methodologically, this protocol is rooted in the time-structure based independent component analysis (tICA), a well-established statistical modeling technique embedded in the Markov state model methodology and often employed to study protein folding, that allows for the identification of the slowest order parameters characterizing the structural transformation. To ensure an unbiased and systematic identification of these order parameters, the tICA decomposition is performed based on information from a prior replica exchange (RE) simulation, as this technique enhances the sampling along all degrees of freedom of the system simultaneously. From this simulation, the tICA procedure extracts the order parameters-often structural parameters-that characterize the slowest transformations in the material. Subsequently, these order parameters are adopted in traditional enhanced sampling methods such as umbrella sampling, thermodynamic integration, and variationally enhanced sampling to construct accurate free energy profiles capturing the flexibility in these nanoporous materials. In this work, the applicability of this tICA-RE protocol is demonstrated by determining the slowest order parameters in both MIL-53(Al) and CAU-13, which exhibit a strongly different type of flexibility. The obtained free energy profiles as a function of this extracted order parameter are furthermore compared to the profiles obtained when adopting less-suited collective variables, indicating the importance of systematically selecting the relevant order parameters to construct accurate free energy profiles for flexible metal-organic frameworks, which is in correspondence with experimental findings. The method succeeds in mapping the full free energy surface in terms of appropriate collective variables for MOFs exhibiting linker flexibility. For CAU-13, we show the decreased stability of the closed pore phase by systematically adding adsorbed xylene molecules in the framework.
Keywords
Physical and Theoretical Chemistry, Computer Science Applications

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Chicago
Demuynck, Ruben, Jelle Wieme, Sven Rogge, Karen Dedecker, Louis Vanduyfhuys, Michel Waroquier, and Veronique Van Speybroeck. 2018. “Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks.” Journal of Chemical Theory and Computation 14 (11): 5511–5526.
APA
Demuynck, R., Wieme, J., Rogge, S., Dedecker, K., Vanduyfhuys, L., Waroquier, M., & Van Speybroeck, V. (2018). Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks. Journal of Chemical Theory and Computation, 14(11), 5511–5526.
Vancouver
1.
Demuynck R, Wieme J, Rogge S, Dedecker K, Vanduyfhuys L, Waroquier M, et al. Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks. Journal of Chemical Theory and Computation. American Chemical Society (ACS); 2018;14(11):5511–26.
MLA
Demuynck, Ruben, Jelle Wieme, Sven Rogge, et al. “Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks.” Journal of Chemical Theory and Computation 14.11 (2018): 5511–5526. Print.
@article{8588446,
  abstract     = {Various kinds of flexibility have been observed in metal-organic frameworks, which may originate from the topology of the material or the presence of flexible ligands. The construction of free energy profiles describing the full dynamical behavior along the phase transition path is challenging since it is not trivial to identify collective variables able to identify all metastable states along the reaction path. In this work, a systematic three-step protocol to uniquely identify the dominant order parameters for structural transformations in flexible metal-organic frameworks and subsequently construct accurate free energy profiles is presented. Methodologically, this protocol is rooted in the time-structure based independent component analysis (tICA), a well-established statistical modeling technique embedded in the Markov state model methodology and often employed to study protein folding, that allows for the identification of the slowest order parameters characterizing the structural transformation. To ensure an unbiased and systematic identification of these order parameters, the tICA decomposition is performed based on information from a prior replica exchange (RE) simulation, as this technique enhances the sampling along all degrees of freedom of the system simultaneously. From this simulation, the tICA procedure extracts the order parameters-often structural parameters-that characterize the slowest transformations in the material. Subsequently, these order parameters are adopted in traditional enhanced sampling methods such as umbrella sampling, thermodynamic integration, and variationally enhanced sampling to construct accurate free energy profiles capturing the flexibility in these nanoporous materials. In this work, the applicability of this tICA-RE protocol is demonstrated by determining the slowest order parameters in both MIL-53(Al) and CAU-13, which exhibit a strongly different type of flexibility. The obtained free energy profiles as a function of this extracted order parameter are furthermore compared to the profiles obtained when adopting less-suited collective variables, indicating the importance of systematically selecting the relevant order parameters to construct accurate free energy profiles for flexible metal-organic frameworks, which is in correspondence with experimental findings. The method succeeds in mapping the full free energy surface in terms of appropriate collective variables for MOFs exhibiting linker flexibility. For CAU-13, we show the decreased stability of the closed pore phase by systematically adding adsorbed xylene molecules in the framework.},
  author       = {Demuynck, Ruben and Wieme, Jelle and Rogge, Sven and Dedecker, Karen and Vanduyfhuys, Louis and Waroquier, Michel and Van Speybroeck, Veronique},
  issn         = {1549-9618},
  journal      = {Journal of Chemical Theory and Computation},
  keyword      = {Physical and Theoretical Chemistry,Computer Science Applications},
  number       = {11},
  pages        = {5511--5526},
  publisher    = {American Chemical Society (ACS)},
  title        = {Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal--Organic Frameworks},
  url          = {http://dx.doi.org/10.1021/acs.jctc.8b00725},
  volume       = {14},
  year         = {2018},
}

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