Light-driven Molecular Motors on Surfaces for Single Molecular Imaging

This protocol provides a first example of visualizing the rotation of a man-made light-driven molecular motor at the single molecular level. The synthetic technique used here is designed to allow the synthesis of a complex molecular machine with several functional groups. First, under an argon atmosphere, place 640 milligrams of the rotor precursor compound two, 219 milligrams of copper iodide, and 3.44 grams of sodium iodide in a 100-milliliter Schlenk tube equipped with a stir bar.

Connect the sealed tube to a Schlenk line and add 50 milliliters of 1, 4-dioxane and 263 milligrams of trans-1, 2-Diaminocyclohexane. Stir the mixture at 140 degrees Celsius for 24 hours to exchange the bromine substituent for iodine. Then, let the mixture cool to room temperature and evaporate the solvent under vacuum.

Purify the compound by silica gel flash chromatography and remove the volatiles to obtain the iodine-substituted compound three as a sticky, yellow oil. Next, place 415 milligrams of Lawesson's reagent and 219 milligrams of compound three in a Schlenk flask equipped with a stir bar. Connect the flask to a Schlenk line via a condenser and purge it with argon three times.

Add 10 milliliters of toluene and reflux the mixture for two hours to convert compound three to a thioketone. Evaporate the solvent and purify the thioketone by flash chromatography. Remove volatiles from the pure fraction and dissolve the isolated thioketone in 20 milliliters of tetrahydrofuran.

Next, dissolve 476 milligrams of freshly-prepared compound 4, which is the stator diazo precursor, in another 20 milliliters of THF. Add the solution of compound 4 to the thioketone solution and reflux the mixture under argon for 16 hours while stirring to form the double bond between the rotor and the stator. Evaporate excess solvent, purify the crude product by flash chromatography, and remove the volatiles to obtain motor compound 5 as a red solid.

Next, add 165 milligrams of motor 5, 4.56 milligrams of bis(triphenylphosphine)palladium chloride, and 2.48 milligrams of copper iodide to a 20-milliliter Schlenk tube equipped with a stir bar. Seal the tube and connect it to a Schlenk line. Combine 10 milliliters of THF and two milliliters of diisopropylamine and bubble argon through the mixture for 10 minutes.

Then, transfer the mixture to the Schlenk tube and stir the reaction mixture under argon at room temperature for 10 minutes. Add 42 milligrams of triisopropylsilyl acetylene and continue stirring for 15 to 16 hours to replace the iodine with TIPS acetylene. Then, pour the product mixture into 25 milliliters of saturated aqueous ammonium chloride.

Extract the product into three 20-milliliter portions of dichloromethane and wash the combined organic layers once with 50 milliliters of saturated brine. Dry the washed organic layers over sodium sulfate. Filter out the desiccant and remove excess solvent.

Purify the residue by flash chromatography and remove the volatiles under vacuum to obtain motor six as a brown oil. In a 50-milliliter flask equipped with a stir bar, combine 90 milligrams of the PBI-labeled motor 12, five milliliters of THF, five milliliters of methanol, and five milliliters of one-molar aqueous sodium hydroxide. Stir the mixture at 70 degrees Celsius for six hours to hydrolyze the esters on the stator.

Then, cool the mixture to room temperature while stirring. Add five milliliters of doubly-distilled water and remove the volatile solvents by rotary evaporation. Add aqueous one-molar hydraulic acid until the mixture reaches pH one, at which point motor 1b will precipitate from solution as a brown solid.

Recover the solid by filtration, wash it with 10 milliliters of cool water and dry it under vacuum. Next, soak quartz slides in piranha solution at 90 degrees Celsius for one hour. Rinse the slides with five milliliters of doubly-distilled water three times and with methanol once.

Dry the slides with nitrogen gas. Then, prepare a one-millimolar solution of 3-aminopropyl(diethoxy)methylsilane in freshly-distilled toluene. Soak the slides in this solution for 12 hours at room temperature and then rinse the silanized slides with five milliliters each of toluene and methanol.

Immerse the slides in toluene and methanol in sequence for two minutes each, and then dry them under a stream of argon gas. Next, prepare five milliliters of a 0.1-millimolar solution of motor 1b in dimethylformamide for each slide. Soak the slides in the 1b solution at room temperature for 12 hours to functionalize the quartz surfaces with a monolayer of 1b.

Wash the functionalized slides with DMF, water, and methanol in sequence. Dry the slides with argon gas and store them in a sealed container under argon. Molecular motor 1b was synthesized in moderate yield, with a rigid, phenyl-ethynylene tetramer arm connecting the core of the rotor to the fluorescent tag.

The proton NMR spectrum showed no significant vicinal coupling between Ha and Hc, which is consistent with Ha and Hc both being in pseudoequatorial orientations. Axial equatorial vicinal coupling was observed between Hb and Hc.Irradiation with 365-nanometer light induced isomerization around the central double bond to this unstable isomer. The downfield shift of the methyl signal and the development of vicinal coupling between Ha and Hc both indicated that the methyl group was pseudoequatorial.

When the compound was kept in the dark at room temperature, thermal helix inversion released the strain on the molecule with the naphthalene slipping past the fluorene. This returned the molecule to its original configuration because of the symmetric fluorene stator. UV/vis spectroscopy of the stable and unstable isomers showed modest differences in the characteristic absorption regions for the rigid arm and the fluorescent tag.

The successful assembly of a monolayer of motor 1b on quartz was confirmed by UV/vis spectroscopy. The monolayer required only 15 minutes of irradiation to reach the unstable isomer in the photo stationary state. It is important to make sure the diazo and thioketone compounds are freshly made to ensure the successful synthesis of the motor 5.

The research field of molecular machines can benefit from this method, as it provides an important guideline to designing, synthesizing, and visualizing complex molecular machines. Piranha solution is used to clean the slides. This solution is highly acidic, and should be used with caution.