In this contribution, the well-known MARTINI particle-based coarse graining approach is tested for its ability to model the ZIF-8 metal-organic framework. Its capability to describe structure, lattice parameters, thermal expansion, elastic constants and amorphization is evaluated. Additionally, the less coarsened models were evaluated for reproducing the swing effect and the host-guest interaction energies were analyzed. We find that MARTINI force fields successfully capture the structure of the Metal-Organic Framework (MOF) for different degrees of coarsening, with the exception of the MARTINI 2.0 models for the less coarse mapping. MARTINI 2.0 models predict more accurate values of C11 and C12, while MARTINI 3.0 has a tendency to underestimate them. Among the possibilities tested, the choice of bead flavors within a particular MARTINI version appears to have a less critical impact in the simulated properties of the empty framework. None of the coarse-grained (CG) models investigated were able to capture the amorphization nor the swing effect within the scope of MD simulations. A perspective on the importance of having a proper Lennard-Jones (LJ) parametrization for modeling guest-MOF and MOF-MOF interactions is highlighted.
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http://dx.doi.org/10.1063/5.0145924 | DOI Listing |
J Chem Inf Model
January 2025
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
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IBiTech - BioMMedA Group, Ghent University, Corneel Heymanslaan 10, Entrance 98, 9000 Gent, Belgium.
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View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
Understanding the molecular mechanisms of pore formation is crucial for elucidating fundamental biological processes and developing therapeutic strategies, such as the design of drug delivery systems and antimicrobial agents. Although experimental methods can provide valuable information, they often lack the temporal and spatial resolution necessary to fully capture the dynamic stages of pore formation. In this study, we present two novel collective variables (CVs) designed to characterize membrane pore behavior, particularly its energetics, through molecular dynamics (MD) simulations.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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View Article and Find Full Text PDFJ Phys Chem A
January 2025
Computer Modelling Group, 3710 33 St NW, Calgary, Alberta T2L 2M1, Canada.
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