Coarse-grained molecular dynamics simulations are employed to obtain a detailed view of the formation of long-range ordered lamellar structures of physisorbed self-assembling long functionalized alkanes on graphite. During the self-assembly, two processes take place: Langmuir preferential adsorption and rearrangement on the surface. The rearrangement starts with nucleation, in which molecules create an ordered domain. The nucleation mechanism is temperature dependent. At lower temperature independent, small and stable nuclei seed the emergence of long-range ordered domains. In contrast, at a higher temperature, molecules adsorb on the surface, and only when a certain level of surface coverage by the adsorbent is reached, the whole structure undergoes a transition from a liquid-like structure to an ordered structure. After this step, relatively slow corrections of the structure take place by Ostwald ripening.

Reversible control over the functionality of biological systems via external triggers may be used in future medicine to reduce the need for invasive procedures. Additionally, externally regulated biomacromolecules are now considered as particularly attractive tools in nanoscience and the design of smart materials, due to their highly programmable nature and complex functionality. Incorporation of photoswitches into biomolecules, such as peptides, antibiotics, and nucleic acids, has generated exciting results in the past few years. Molecular motors offer the potential for new and more precise methods of photoregulation, due to their multistate switching cycle, unidirectionality of rotation, and helicity inversion during the rotational steps. Aided by computational studies, we designed and synthesized a photoswitchable DNA hairpin, in which a molecular motor serves as the bridgehead unit. After it was determined that motor function was not affected by the rigid arms of the linker, solid-phase synthesis was employed to incorporate the motor into an 8-base-pair self-complementary DNA strand. With the photoswitchable bridgehead in place, hairpin formation was unimpaired, while the motor part of this advanced biohybrid system retains excellent photochemical properties. Rotation of the motor generates large changes in structure, and as a consequence the duplex stability of the oligonucleotide could be regulated by UV light irradiation. Additionally, Molecular Dynamics computations were employed to rationalize the observed behavior of the motor-DNA hybrid. The results presented herein establish molecular motors as powerful multistate switches for application in biological environments.

Ostwald ripening can improve the long-range order of self-assembled monolayers by the growth of large domains and disassembly of smaller ones. Here, coarse-grained molecular dynamics simulations are used to study the dynamics of the stable assembly and the coarsening of defects of physisorbed monolayers of long-chain functionalized alkanes. Our results show that the partial desorption from the surface of one or more adsorbent molecules is the essential process that allows other adsorbent molecules to rearrange on the surface and thereby improve alignment. We also show that the ripening process is faster at higher temperature because the rate of partial desorption is higher.