1. Mapping: The first step of the CG model preparation was selecting a mapping for the aromatic core that would be rigid enough to maintain the flat surface of the benzimidazole rings and, at the same time, flexible enough to adopt different orientations of the side chains. The mapping of the cyanine aromatic core and C8S3 tails is presented in Figure . The benzimidazole rings are mapped with 4 tiny beads and 1 virtual site at their centre of geometry, following the suggested mapping of small ring-containing molecules with Martini 3 . Additionally, there is a dummy particle (black sphere) that does not interact with other beads, but it allows the definition of the axis (dashed line) around which the benzimidazole ring is able to rotate. The substituents of the aromatic core are mostly represented by small beads, as commonly used for chemical fragments consisting of three heavy atoms or four heavy atoms in a branched configuration . There are also two tiny beads that connect the aromatic core with the aliphatic tails of C8S3. C8S3 has eight carbon atoms in each aliphatic tail that could be also mapped with two regular beads. We decided to use a mapping with tiny and small beads, in order to have a smoother transition to the aromatic core that is mapped mainly with tiny beads. 2. Bead types: Martini 3 offers a wide variety of bead types covering a vast number of chemical groups . The selection of the bead types for the aromatic core of the cyanine dyes and each substituent is shown in Figure . Default Martini 3 bead types were used for the majority of the C8S3 chemical group, apart from the beads of the tails that are adjacent to the aromatic core. The main reason for this modification is the high polarisability of the aromatic core that should affect the atoms of the tails. Consequently, the first beads of the hydrophobic tails were changed by two interaction levels (TC2 was changed to TC4), and the beads of the hydrophilic tails were changed by four interaction levels (TC2 to TC6v) to capture the inductive effects from the SO3-group. Finally, the aromatic core of these cyanine dyes is positively charged (+1) (see Figure ). The extra charge was equally divided among the beads that include atoms of the polymethine chain (4xTN1q and TC4).