Simulations of optically switchable molecular machines for particle transport

Abstract

A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first-generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene-derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on-the-fly photodynamics, excited-state surface-hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating-occupation configuration interaction as the QM part and the OPLSAA-L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi-molecule arrangements. Our results provide valuable design guidelines for cilia-driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium-target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc.

Exploring self‐organization of molecular tether molecules on a gold surface by global structure optimization

“…Finally, to move yet another step toward the intended applications, we have also done a few global optimization runs in which we replaced the centrally mounted methyl group with a phenyl group, attached via an ethynyl spacer. Sterically, this corresponds fairly well to the lower part of an artificial cilium mounted onto the TATA platform, and this and very similar further substituents were also employed experimentally . For the tris‐methyl‐case of this setup, we encountered a new phenomenon never seen in our other runs: the formation of persistent, well‐ordered bilayers (Fig.…”

“…A central design idea of the TATA platforms with lateral alkyl chains was that by varying these chain lengths it should be possible to change the TATA–TATA distances in surface‐adsorbed TATA monolayers. This idea was expressed and repeated in all TATA papers and was seen as a welcome tool to control these TATA–TATA distances, to accommodate the spatial needs of different functionalities mounted at the TATA centers. However, only in a few of these papers, these TATA–TATA distances were systematically measured for several different chain lengths (by STM).…”

“…Therefore, we resorted to a force‐field description. In earlier work of our group, we had already employed a quantum‐mechanical/molecular‐mechanical description, with the TATA unit described by the optimized potential for liquid simulations, all‐atom local (OPLS‐AA‐L) Møller–Plesset perturbation theory of second order force field, with missing parameters taken from OPLS‐AA . For the present proof‐of‐principle work, we simply reused this OPLS‐AA(‐L) setting.…”

“…TATA platforms were investigated in many experimental studies, demonstrating the formation of regular superstructures on Au(111) with room‐temperature STM. Further work employed TATA platforms to mount photoswitchable molecules to surfaces. For this goal, some control over TATA–TATA distances is available by varying the lateral alkyl chain lengths.…”

Repurposing Existing Molecular Machines through Accurate Regulation of Cooperative Motions

“…To fully grasp the working principles of artificial molecular machines, experimentalists have collected a host of information on how the latter respond to external stimuli. − However, predicting the property of a molecular machine prior to its synthesis remains difficult. Because they offer atomic insights into the structure and dynamics of molecular objects, computational approaches have been broadly utilized to investigate the mechanisms underlying complex relative movements between components of nanomachines. − Many such artificial molecular machines, controlled by pH, − solvent, , ion, , and light, have been studied by molecular simulations. There is, however, a significant gap between the molecular assemblies investigated in experiments and in simulations, namely that a molecular machine may be affected concomitantly by various external stimuli in experiment, − while a single stimulus is usually considered in theoretical calculations.…”