Simulating a Molecular Machine in Action

A computational study of a light-driven artificial device: a third generation rotational photo-molecular motor in dilute solutions

A third-generation artificial photo-molecular motor, featuring two photo-switchable rotating moieties in connection with a pseudoasymmetric molecular centre, is investigated by combining quantum-mechanics (QM) algorithms with classical molecular dynamics (MD) propagators. In particular, in the present contribution we have addressed such a molecular motor in different rotational isomers following the experimental observations arising from the application of multiple spectroscopic techniques in dilute solutions. At first, we focused our attention on the reproduction of the UV/Vis absorption spectrum in two solvents (acetonitrile and cyclohexane) with different gradient-corrected density functional theory (B3LYP, Cam-B3LYP, PBE, PBE0) functionals in conjunction with the conductor-like and polarizable continuum model (C-PCM). Furthermore, we refined the absorption signals by combining a classical MD sampling at room-temperature with DFT-based electronic degrees of freedom to compute perturbed excitation wavelengths driven by thermal fluctuation and solvation effects. In this respect, we have modelled the investigated artificial motor within solution nanodroplets with solvent molecules treated contextually at atomistic level and via a dielectric and polarizable continuum model.

Full-Dimensional Photodynamics of Bistable Proton Transfer Switches

Excited-state intramolecular proton transfers (ESIPT) are one of the fastest reactions in chemistry (<100 fs) which – among other features like high photostability – makes them an important reaction class for molecular switches. ESIPTs can be coupled with double bond rotation/isomerization, so that molecules can act as “molecular cranes”, facilitating long-range proton transfer. A versatile model system is 7-hydroxy-4-methylquinoline-8-carbaldehyde (HMQCA): it features two proton-accepting sites, two stable ground-state isomers and should allow for easy derivatization. There is also experimental and theoretical reference data available, however, only for static properties, e.g. ground-state IR spectra or potential energy surface scans. In this contribution we show the results of full-dimensional surface-hopping molecular dynamics (MD) of HMQCA after photo-excitation, employing semiempirical quantum mechanics coupled to floating-occupation configuration interaction. The results support the potential of HMQCA as prototype system for directed proton transport by ESIPT.

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

We employ nondeterministic global cluster structure optimization, based on the evolutionary algorithms paradigm, to model the self-assembly of complex molecules on a surface. As a real-life application example directly related to many recent experiments, we use this approach for the assembly of triazatriangulene "platform" molecules on the Au(111) surface. Without additional restrictions like spatial discretizations, coarse-graining or precalculated adsorption poses, and despite the proof-of-principle character of this study, we achieve satisfactory qualitative agreement with several experimental observations and can provide answers to questions that experiments on these species had left open so far. © 2019 Wiley Periodicals, Inc.

Simulations of optically switchable molecular machines for particle transport

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.

Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis

In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.