Research ArticleChemistry

Direct single-molecule dynamic detection of chemical reactions

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Science Advances  09 Feb 2018:
Vol. 4, no. 2, eaar2177
DOI: 10.1126/sciadv.aar2177
  • Fig. 1 Device structure and electrical characterization of GMG-SMJs.

    (A) Schematic representation of the device structure that highlights a reversible nucleophilic addition reaction of hydroxylamine to a carbonyl group. (B) I-V curves of open circuits with graphene point contacts (black) and single-molecule junctions after molecular connection (red). (C) Schematic diagram of real-time measurement setup with a home-made microchannel for single-molecule dynamics characterization.

  • Fig. 2 Real-time current recordings and mechanism analysis.

    (A) Real-time current recordings of single-molecule reaction dynamics during 1 s measured in a mixed EtOH/H2O (1:4) solution with NH2OH (10 μM) and NaOH (10 μM) at 298 K. VD = 300 mV. (B) Corresponding histogram of current values, showing a bimodal current distribution. (C) Reaction mechanism and energy profile of 9-fluorenone reacting with NH2OH. Energies are shown in kcal/mol. (D) Transmission spectra of GMG-SMJs with the RS and the IS. The red and blue rectangles mark the transmission peaks of p-HOMO and p-LUMO for both states.

  • Fig. 3 Solvent-dependent measurements.

    I-t curves, corresponding enlarged I-t curves marked in orange, and corresponding histograms of a working GMG-SMJ device measured in the reaction solutions with 0% (A), 20% (B), 40% (C), 60% (D), 80% (E), and 100% (F) water in EtOH at 298 K. VD = 300 mV.

  • Fig. 4 Kinetic analyses of single-molecule reaction dynamics.

    (A) I-t curve (black) of GMG-SMJs immersed in the reactive solution (Vwater = 60%) at 298 K and the idealized fit (red) obtained from a segmental k-means method based on hidden Markov model analysis by using a QUB software. (B and C) Plots of time intervals of the low-current (B) and high-current (C) states in the idealized fit in (A). Single-exponential fittings derive the lifetimes of each state (τlow and τhigh). (D) Lifetime changes of the low (black) and the high states (red) with different proportions of water.

  • Table 1 Energy barriers and reaction rates of each step during the reaction.

    Theoretical calculations are only performed under pure EtOH and water conditions, which are good enough to confirm the experimental results. Lifetimes of the low and high states during the first-step reaction with different proportions of water are summarized. The second step is not observed in single-molecule experiments because of a high-energy barrier. NA, not applicable.

    Solvent (EtOH/water)100% EtOH80%/20%60%/40%40%/60%20%/80%100% water
    Energy barriersCalculation resultsFirst stepForward12.2 kcal/molNANANANA10.5 kcal/mol
    Backward11.1 kcal/molNANANANA10.8 kcal/mol
    Second stepForward16.0 kcal/molNANANANA18.7 kcal/mol
    Backward28.8 kcal/molNANANANA30.4 kcal/mol
    Experiment resultsFirst stepForward13.0 kcal/mol12.9 kcal/mol12.5 kcal/mol12.5 kcal/mol12.4 kcal/mol11.9 kcal/mol
    Backward12.1 kcal/mol12.0 kcal/mol12.6 kcal/mol12.6 kcal/mol12.7 kcal/mol12.8 kcal/mol
    Second stepForwardNANANANANANA
    BackwardNANANANANANA
    Reaction ratesCalculation resultsFirst stepForward138.53 μsNANANANA7.88 μs
    Backward21.68 μsNANANANA13.07 μs
    Second stepForward84.03 msNANANANA7,976.09 ms
    Backward55,229.7 hoursNANANANA844,695.89 hours
    Experiment resultsFirst stepForward557 μs466 μs230 μs228 μs207 μs86 μs
    Backward127 μs98.2 μs261 μs268 μs298 μs369 μs
    Second stepForwardNANANANANANA
    BackwardNANANANANANA

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/4/2/eaar2177/DC1

    Supplementary Materials and Methods

    scheme S1. Synthetic routes to the carbonyl molecule (compound 4) with a 9-fluorenone functional center and −NH2-terminal groups.

    fig. S1. Schematic of fabricating graphene FET arrays.

    fig. S2. Schematic of fabricating graphene point contact arrays.

    fig. S3. Electrical measurements of single-molecule junctions.

    fig. S4. I-t curves and corresponding histograms of current values for a typical GMG-SMJ in different environments at 298 K.

    fig. S5. Representative I-V and dI/dV-V curves of a control device.

    fig. S6. I-t curves and corresponding histograms of current values for a control device in different environments at 298 K.

    fig. S7. MPSH spectra of the molecule in the RS and IS.

    fig. S8. LC-MS characterizations of the two-step reaction.

    fig. S9. Plots of time intervals.

    fig. S10. Additional solvent-dependent experiments.

    Reference (40)

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • scheme S1. Synthetic routes to the carbonyl molecule (compound 4) with a 9-fluorenone functional center and −NH2-terminal groups.
    • fig. S1. Schematic of fabricating graphene FET arrays.
    • fig. S2. Schematic of fabricating graphene point contact arrays.
    • fig. S3. Electrical measurements of single-molecule junctions.
    • fig. S4. I-t curves and corresponding histograms of current values for a typical GMG-SMJ in different environments at 298 K.
    • fig. S5. Representative I-V and dI/dV-V curves of a control device.
    • fig. S6. I-t curves and corresponding histograms of current values for a control device in different environments at 298 K.
    • fig. S7. MPSH spectra of the molecule in the RS and IS.
    • fig. S8. LC-MS characterizations of the two-step reaction.
    • fig. S9. Plots of time intervals.
    • fig. S10. Additional solvent-dependent experiments.
    • Reference (40)

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