Supramolecular Aggregates

In bionanotechnology, the field of creating functional materials consisting of bio-inspired molecules, the function and shape of a nanostructure only appear through the assembly of many small molecules together. The large number of building blocks required to define a nanostructure combined with the many degrees of freedom in packing small molecules has long precluded molecular simulations, but recent advances in computational hardware as well as software have made classical simulations available to this strongly expanding field, reviewed in [1].

The Martini model is increasingly contributing to this field, as the neglect of atomistic degrees of freedom allows to study supramolecular assemblies at spatiotemporal scales not accessible with all-atom models [2]. Key examples include the Martini simulations of self-assembly of (functionalized) peptide hydrogels [3,4], supramolecular polymers [5,6], self-replicating nanorings [7], and light harvesting nanotubes [8].

[1] P.W.J.M. Frederix, I. Patmanidis, S.J. Marrink. Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments. Chem. Soc. Review, 47:3470 - 3489, 2018. doi:10.1039/C8CS00040A

[2] R. Alessandri, F. Grünewald, S.J. Marrink. Martini Perspective in Materials Science, Adv. Materials 2021.

[3] P.W.J.M. Frederix, G.G. Scott, Y.M. Abul-Haija, D. Kalafatovic, C.G. Pappas, .et al. Exploring the sequence space for (tri-) peptide self-assembly to design and discover new hydrogels. Nature Chemistry 7:30, 2015.

[4] E.R. Draper, B. Dietrich, K. McAulay, C. Brasnett, H. Abdizadeh, I. Patmanidis, et al. Using Small-Angle Scattering and Contrast Matching to Understand Molecular Packing in Low Molecular Weight Gels. Matter 2:764-778, 2020.

[5] D. Bochicchio, G.M. Pavan. From cooperative self-assembly to water-soluble supramolecular polymers using coarse-grained simulations. ACS nano 11:1000-1011, 2017.

[6] A. Sarkar, R. Sasmal, C. Empereur-Mot, D. Bochicchio, S.V.K. Kompella, et al. Self-Sorted, Random, and Block Supramolecular Copolymers via Sequence Controlled, Multicomponent Self-Assembly. J. Amer. Chem. Soc. 142:7606-7617, 2020.

[7] S. Maity, J. Ottelé, G.M. Santiago, P.W.J.M. Frederix, P. Kroon, O. Markovitch, M.C.A. Stuart, S.J. Marrink, S. Otto, W.H Roos. Caught in the act: mechanistic insight into supramolecular polymerization-driven self-replication from real-time visualization. J. Amer. Chem. Soc. 142:13709–13717, 2020. doi:org/10.1021/jacs.0c02635

[8] I. Patmanidis, in preparation, 2021.