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. Here, we review the state of the art in simulations of self-assembling bio-inspired supramolecular systems. We will first discuss progress in force fields, simulation protocols and enhanced sampling techniques using recent examples. Secondly, we will focus on efforts to enable the comparison of experimentally accessible observables and computational results. Experimental quantities that can be measured by microscopy, spectroscopy and scattering can be linked to simulation output either directly or indirectly, via quantum mechanical or semi-empirical techniques. Overall, we aim to provide an overview of the various computational approaches to understand not only the molecular architecture of nanostructures, but also the mechanism of their formation.

Multiscale modeling resolves the molecular structure of a synthetic light-harvesting complex, unraveling the microscopic origin of its photophysical properties.

Natural light-harvesting antennae employ a dense array of chromophores to optimize energy transport via formation of delocalized excited states (excitons), which are critically sensitive to spatio-energetic variations of the molecular structure. Identifying the origin and impact of such variations is highly desirable for understanding and predicting functional properties, yet hard to achieve due to averaging of many overlapping responses from individual systems. Here, we overcome this problem by measuring the heterogeneity of synthetic analogues of natural antennae – self-assembled molecular nanotubes – by two complementary approaches: single-nanotube photoluminescence spectroscopy and ultrafast 2D correlation spectroscopy in the bulk. We demonstrate remarkable homogeneity of the nanotube ensemble and reveal that ultrafast (~50 fs) modulation of the exciton frequencies governs spectral broadening. Using multiscale exciton modeling, we show that the dominance of homogeneous broadening at the exciton level results from exchange narrowing of strong static disorder found for individual molecules within the nanotube. The detailed characterization of static and dynamic disorder at the exciton as well as the molecular level presented here, opens new avenues in analyzing and predicting dynamic exciton properties, such as excitation energy transport.

Self-assembled nanostructures arise when building blocks spontaneously organize into ordered aggregates that exhibit different properties compared to the disorganized monomers.

Molecular self-assembly is a fundamental process in nature that can be used to develop novel functional materials for medical and engineering applications. However, their complex mechanisms make the short-lived stages of self-assembly processes extremely hard to reveal. In this article, we track the self-assembly process of a benchmark system, double-walled molecular nanotubes, whose structure is similar to that found in biological and synthetic systems. We selectively dissolved the outer wall of the double-walled system and used the inner wall as a template for the self-reassembly of the outer wall. The reassembly kinetics were followed in real time using a combination of microfluidics, spectroscopy, cryogenic transmission electron microscopy, molecular dynamics simulations, and exciton modeling. We found that the outer wall self-assembles through a transient disordered patchwork structure: first, several patches of different orientations are formed, and only on a longer time scale will the patches interact with each other and assume their final preferred global orientation. The understanding of patch formation and patch reorientation marks a crucial step toward steering self-assembly processes and subsequent material engineering.