Real-Time Fluctuations in Single-Molecule Rotaxane Experiments Reveal an Intermediate Weak Binding State during Shuttling

Abstract

We report on the use of atomic force microscopy (AFM) to identify and characterize an intermediate state in macrocycle shuttling in a hydrogen bonded amide-based molecular shuttle. The [2]rotaxane consists of a benzylic amide macrocycle mechanically locked onto a thread that bears both fumaramide and succinic amide-ester sites, each of which can bind to the macrocycle through up to four intercomponent hydrogen bonds. Using AFM-based single-molecule force spectroscopy, we mechanically triggered the translocation of the ring between the two principal binding sites ("stations") on the axle. Equilibrium fluctuations reveal another interacting site involving the two oxygen atoms in the middle of the thread. We characterized the ring occupancy distribution over time, which confirms the intermediate in both shuttling directions. The study provides evidence of weak hydrogen bonds that are difficult to detect using other methods and shows how the composition of the thread can significantly influence the shuttling dynamics by slowing down the ring motion between the principal binding sites. More generally, the study illustrates the utility that single-molecule experiments, such as force spectroscopy, can offer for elucidating the structure and dynamics of synthetic molecular machines.

Molecularly Engineered Black Phosphorus Heterostructures with Improved Ambient Stability and Enhanced Charge Carrier Mobility

“…However, this strategy largely compromises their electronic properties due to the direct breaking of PP bonds. In contrast, non‐covalent functionalization (or surface coordination) using 1,2‐benzenedithiol on BP/Al 3+ , [ 16 ] Group 13 Lewis acids [ 17 ] (i.e., AlCl 3 and AlBr 3 ) or Pd–Pd units [ 18 ] can preserve or modify the intrinsic properties of BP sheets to a large extent. However, it is generally less effective to regulate electronic properties of BP because of the weak interfacial coupling.…”

Side chain interactions govern the response of polypeptide alpha-helices under mechanical stress and prevent the formation of beta-sheets

“…We previously showed that this approach, based on the physisorption of caught PEG tethers onto the tip, provides a sufficiently strong and stable attachment of the molecule onto the tip to obtain reliable information on the system grafted on the surface. [14][15][16][17][18][19] As a result of the different side chains (Figure 1), the ahelices form under opposite pH conditions, pH > 11 for PLys and pH < 4 for PGA. Immediately prior to performing single-molecule force spectroscopy experiments, the gold substrates were dipped in a diluted solution of the molecules and a passivating agent PEG6-SH was added, to enable single molecules to be individually distributed and immobilized onto the cleaned surface (see Methods section).…”

“…This approach, combined with the small size of the molecules, also prevents the unspecific adsorption of the polymer chains onto the surface and gives rise to very clean force curves without unspecific peaks. 14,16,[18][19][20][21] Poly(L-lysine) mechanical unfolding. The typical forceextension profile for PLys in a-helix conformation at pH 12 shows a plateau at 34 ± 4 pN (Figure 2).…”

Real-time observation of the dynamics of an individual rotaxane molecular shuttle using a single-molecule junction

“…The dynamics of molecular shuttles has generally been studied in solution, using a range of techniques that interrogate the average behavior of many molecules, such as NMR, IR, and electrochemistry. [9][10][11][12][13][14][15][16] Although most rotaxanes are far smaller than typical motor proteins, the first accounts of the use of single-molecule force spectroscopies [17][18][19][20][21][22][23][24] (SMFS) and optical tweezers 25 to probe such systems have been described. Nevertheless, the real-time measurement of the kinetics and thermodynamics of individual molecular shuttles, particularly temperature-dependent behavior that can be hard to obtain using single-molecule force spectroscopy, remains a significant technical and scientific challenge.…”