The development of instruments and techniques that allow the manipulation of single-molecules, such as atomic force microscopy (AFM) and scanning tunneling microscopy (STM), has made it possible to apply external stimuli (e.g. mechanical forces and bias voltages) to single-molecules to trigger chemical reactions. Here, we computationally evaluate the ability of conductance measurements and force signatures to inform about these processes when mechanical forces are exerted on previously formed molecular junctions and on separated molecular pieces to form junctions. Specifically, we first simulated the force–conductance profile of cyclopropane oligomers connected to graphene nanoribbon electrodes that undergo a cis-to-trans isomerization during mechanical elongation. This was done using a combination of classical molecular dynamics simulation of the pulling using a reactive force field, and Landauer transport computations of the conductance with nonequilibrium Green's function methods. The isomerization events can be distinguished in both force and conductance profiles. However, the conductance profile during the mechanical elongation distinguishes between reaction intermediates that cannot be resolved using force. In turn, the force signals non-reactive deformations in the molecular backbone which are not visible in the conductance profile. Then, we simulated a Diels-Alder cycloaddition between a diene (cyclopentadiene) and a dienophile (cyanoethylene) that are initially attached to separated gold electrodes. This kind of association reactions in molecular junctions has been challenging to realize experimentally. Here, we explore how the thermodynamics of these reactions is modified due to the spatial confinement of the junction and suggest approaches to overcome thermodynamic penalties (high entropic barriers) that prevent the occurrence of such reactions in the junction setting. These computations exemplify the potential of the integration of covalent mechanochemistry with molecular conductance to investigate chemical reactivity at the single-entity limit and provide useful insights into the underlying mechanisms that govern such processes.

Computational insights into chemical reactivity in molecular junctions: Force-conductance signatures and thermodynamic constraints

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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