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Label-Free Dynamic Detection of SingleMolecule Nucleophilic Substitution Reaction Chunhui Gu, Chen Hu, Ying Wei, Dongqing Lin, Chuancheng Jia, Mingzhi Li, Dingkai Su, Jianxin Guan, Andong Xia, Linghai Xie, Abraham Nitzan, Hong Guo, and Xuefeng Guo Nano Lett., Just Accepted Manuscript • DOI: 10.1021/acs.nanolett.8b00949 • Publication Date (Web): 06 Jun 2018 Downloaded from http://pubs.acs.org on June 6, 2018
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Nano Letters
Label-Free Dynamic Detection of Single-Molecule Nucleophilic Substitution Reaction Chunhui Gu,1† Chen Hu,2† Ying Wei,3 Dongqing Lin,3 Chuancheng Jia,1 Mingzhi Li,1 Dingkai Su,1 Jianxin Guan,1 Andong Xia,4 Linghai Xie,3 Abraham Nitzan,5 Hong Guo,2* Xuefeng Guo 1* 1
Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural
Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China; 2
Center for the Physics of Materials and Department of Physics, McGill University,
Montreal, Quebec H3A 2T8, Canada; 3
Center for Molecular Systems and Organic Devices, Key Laboratory for Organic
Electronics & Information Displays and Institute of Advanced Materials, Nanjing University of Posts & Telecommunications, Nanjing 210023, P. R. China; 4
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China;
5
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323,
USA;
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ABSTRACT: The mechanisms of chemical reactions, including the transformation pathways of the electronic and geometric structures of molecules, are crucial for comprehending the essence and developing new chemistry. However, it is extremely hard to realize at the single-molecule level. Here we report a single-molecule approach capable of electrically probing stochastic fluctuations under equilibrium conditions and elucidating time trajectories of single species in nonequilibrated systems. Through molecular engineering, a single molecular wire containing a functional center of 9-phenyl-9-fluorenol was covalently wired into nanogapped graphene electrodes to form stable single-molecule junctions. Both experimental and theoretical studies consistently demonstrate and interpret direct measurement of the formation dynamics of individual carbocation intermediates with a strong solvent dependence in a nucleophilic substitution reaction. We also show the kinetic process of competitive transitions between acetate and bromide species, which is inevitably through a carbocation intermediate, confirming the classical mechanism. This unique method opens up plenty of opportunities to carry out single-molecule dynamics or biophysics investigations in broad fields beyond reaction chemistry through molecular design and engineering. 1 2
KEYWORDS: Single-molecule detection, reaction dynamics, molecular electronics,
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nucleophilic substitution
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Revealing the dynamic processes of detailed molecular transformations of chemical
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reactions is crucial for comprehending the essence and developing new chemistry.13
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Previous reports proved that the pathway of chemical reactions seemed to be more complex
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than we imagine. For instance, even for a simple bimolecular nucleophilic substitution (SN2)
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reaction, the mechanism is complicated and not fully understood.2,3 In general, it is
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extremely hard to access the detailed reaction pathways in macroscopic experiments
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because the ensemble always shows thermodynamic quasi-equilibrium conditions. In
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contrast, single-molecule analysis of chemical reactions can effectively avoid ensemble-
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average effects, discover new phenomena/species and reveal the chronological reaction
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processes.4 To date, discrete single-molecule detection technologies, including optical
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methods57 and nanopores,810 have been developed to achieve the dynamic investigation
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of biological macromolecules. However, these techniques seem to be unsuitable for the
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detection of general organic molecules and their reaction trajectories, mainly limited by the
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challenges including the lack of precise molecular immobilization, the requirement of
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fluorescent labelling and low temporal resolution. Therefore, the development of robust
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single-molecule detection platforms with label-free capability is invaluable to offer plenty
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of room for probing molecular mechanisms of basic chemical reactions.
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In this regard, the electrical approach may be a suitable choice.11,12 In particular,
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electrical platforms based on single-molecule junctions (SMJs) are potentially attractive
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because these platforms might overcome the major challenges mentioned above. In the past
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two decades, different approaches to build SMJs,13 particularly mechanically controllable
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break junction14 and conductive scanning probe microscope,1517 were developed, which
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have made remarkable contributions to investigate the electronic properties of particular 3 ACS Paragon Plus Environment
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molecules. In our previous studies, we developed a reliable methodology to build a new
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type of SMJs based on graphene electrodes,18 where amine-terminated molecular wires can
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be immobilized in the nanogap between carboxylic acid-terminated graphene electrodes
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through covalent amide bonds. Such molecular nanocircuits benefit from the unique
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coupling modes and robust contacts at the electrode-molecule interface, resulting in the
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strong stability during long-term conductance measurements. As a single molecule
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sandwiched between source and drain electrodes is the key contributor to the device
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conductance, the conductance of SMJs is generally ultrasensitive to the electronic
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structures of molecules. Through molecular engineering, specially-designed molecules
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were integrated into SMJs to construct molecular electronic devices with specific functions
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such as rectifiers,1921 field-effect transistors,22 switches23 and memories.24 These examples
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demonstrate the capacity for in-situ modulating the electronic structure (and thus the
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conductance) of SMJs by external stimuli, where the rearrangement of the molecular
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electronic structures caused by chemical reactions can be deemed as possible external
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stimuli.25 On the basis of this strategy, SMJs have been specially designed through
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structure-function relationships and have successfully detected chemical reactions such as
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complex formation26 and nucleophilic addition.27
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In the present study, for the first time we test the potential of the utilization of SMJs
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as an electrical platform for direct dynamic measurement of a reversible unimolecular
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nucleophilic substitution (SN1) reaction at the single-molecule level. As a well-known
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organic reaction, the classical pathway of a SN1 reaction involves two steps: (i) Heterolysis:
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A leaving group separates from the reactant to form a carbocation intermediate. (ii)
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Recombination: The carbocation intermediate combines with a nucleophile to form a 4 ACS Paragon Plus Environment
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product. The reaction potential energy surface is shown in Figure 1 (up-right). Thereinto,
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carbocation, as a short-lived but common intermediate, has attarcted great interest in the
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field of organic chemistry, in which, especially, Olah, G. A. made great contributions.28,29
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We expect that the carbocation intermediate can be distinguished from the reactant/product
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electrically due to the conductance increase caused by the transition from sp3 to sp2
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hybridization, which has been reported previously.30 By real-time monitoring SMJs with a
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9-phenyl-9-fluorenol center, we found that the conductance of SMJs was faithfully
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synchronous to the chemical reaction, through which we observed the reversible SN1
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reaction and its closely-following competitive reactions, respectively. Statistical analyses
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in time domain further revealed significant information about the reaction kinetics, which
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also provides the useful guidance to other chemical reactions.
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Specially, 9-phenyl-9-fluorenol was applied as a reactant to investigate the acid-
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catalyzed SN1 reaction in the mixed solution of acetic acid (HAc) and trifluoroacetic acid
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(TFA). Such a mixed acid solution can provide the high proton environment to stabilize
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the carbocation intermediate, which is favorable to further detection. This particular
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reaction was first investigated by a series of macroscopic experiments. GC-MS confirmed
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the complete consumption of the reagent and observed a reversible transition between a 9-
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phenyl-9-fluorenyl cation and a 9-phenyl-9-fluorenyl acetate in the solution. The kinetic
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and thermodynamic properties of the reaction were determined by UV-Vis experiments
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and flash photolysis (see Supporting Information, Section 1). Through molecular
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engineering, we covalently integrated a molecular wire with a functional center of 9-
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phenyl-9-fluorenol into nanogapped graphene electrodes to form stable graphene-
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molecule-graphene single-molecule junctions (GMG-SMJs) (Figure 1). The details of 5 ACS Paragon Plus Environment
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molecular synthesis are provided in the Supporting Information (Section 2). To confirm
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the formation of GMG-SMJs, the current-voltage (IV) curves of the devices at different
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stages were measured as shown in Figure S9a. We found that the current decreased to zero
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after precise oxygen plasma etching and recovered to some extent after molecular
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immobilization, indicating the success of the device fabrication. Under optimized
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conditions, the connection yield was found to be ~15%, that is, 25 of 169 devices on the
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same silicon chip showed the increased conductance. These working devices showed
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similar electrical properties in the following experiments, demonstrating the
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reproducibility. On the basis of these data, statistical analysis demonstrated that charge
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transport through the junction mainly resulted from single-molecule connection (see
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Supporting Information, Section 3).
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Figure 1. Schematic of a graphene-molecule-graphene single-molecule junction that shows the formation dynamics of a 9-phenyl-9-fluorenyl cation in a SN1 reaction. 6 ACS Paragon Plus Environment
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High temporal resolution electrical characterization was carried out to monitor the
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conductance of GMG-SMJs in real time (Figure 2. Constant bias voltage: 0.3 V; Sampling
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rate: 57.6 kSa/s). GMG-SMJs were initially measured in the air and then anhydrous
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HAc/TFA solutions with different proportions were gradually added to GMG-SMJs with
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the aid of a polydimethylsiloxane (PDMS) solvent reservoir (Figure S9b). Figures 2a and
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2b show the representative current-time (It) trajectories. In comparison with the It
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trajectory in the air, which was dominated by the flicker (1/f) noise, random telegraph
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signals (RTSs) appeared when acid solutions were added. Correspondingly, in the current
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distribution histograms (Figure 2c), we observed large-amplitude two-level conductance
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states: a large numbered, narrowly broadened low conductance state (shown in blue) and a
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less numbered, widely broadened high conductance state (shown in red). This observation
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demonstrated that GMG-SMJs had two stable states in acid solutions. A previous report
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demonstrated that the current itself might lead to the reconnection of graphene electrodes
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at high bias voltages (~1.2 V for ~3 nm nanogaps, similar to the condition in this work).31
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To rule out this possibility, we fixed an optimized bias voltage at 0.3 V (much lower than
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1.2 V used in the literature) to maintain a stable conductance as well as a high signal-noise
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ratio. Under such a condition, we proved that the RTS did not appear in the air and the RTS
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behavior was highly related to the acid solution, demonstrating that RTS signals are
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solvent-dependent, rather than the behavior of graphene electrodes. To further rule out
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other potential artifacts, three different charge-transporting systems were established as
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control devices: (i) Macroscopic uncut graphene ribbons,(ii) Partially-cleaved graphene
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nanoconstrictions and (iii) SMJs bridged by a molecular wire containing an acid-inert
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sexiphenyl core, which has the similar molecular length and conductance with the 97 ACS Paragon Plus Environment
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phenyl-9-fluorenol core, were applied to exclude the possibility of conformation-induced
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switching or the other systemic interference between the solvent and SMJs. Under the same
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testing conditions used in Figure 2, RTS fluctuations did not appear in all the It trajectories
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(see Supporting Information, Section 4), proving that the observed RTSs only originated
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from the chemical reaction happening on the 9-phenyl-9-fluorenol core.
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0.075 Time (s)
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Figure 2. Real-time conductance measurements of a representative GMG-SMJ among 5 different devices. (a) Representative It trajectories in different conditions (from top to bottom: in the air, pure HAc, 25% TFA/75% HAc, 50% TFA/50% HAc, and 75% TFA/25% HAc (vol/vol)). (b) Partial It curves of the corresponding parts in (a). Insets show the enlarged views of the peaks as indicated by white arrows. (c) The corresponding histograms of (a). The blue and red lines show the gauss-shaped fit for the low and high 8 ACS Paragon Plus Environment
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conductance states, respectively. Insets show the enlarged views in the high conductance regions. Source-drain bias voltage (VD): 0.3 V; Gate voltage (VG): 0 V; Sampling rate: 57.6 kSa/s.
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To attribute the conductance states to the corresponding molecular forms, the
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molecular electronic structures and quantum transport properties were theoretically
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analyzed. As shown in Figures 3a and 3b, the first-principles calculations performed by
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Gaussian package (See Supporting Information, Section 5) showed totally different
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electronic structures between acetate and carbocation forms, due to the variation of the
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hybridization types of the central carbon atom: sp3 hybridization in the former and sp2
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hybridization in the latter. As a result, the valence electrons are much more conjugated in
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the carbocation, yielding the fact that the energy gap between the frontier molecular
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orbitals (FMOs) is significantly decreased to ~1.34 eV (Figure 3a). Different energy gaps
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and orbital distributions can be verified by the different UV-Vis spectroscopic behaviors
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in Figure S15. According to the transition voltage spectroscopy (TVS) model and the
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theoretical approach by Bâldea et al.,3234 the decreased FMO gap of the carbocation form
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can largely lower the tunneling barrier height and increase the tunneling current, leading
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to a higher conductance. We further calculated the charge transport properties of these
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molecules in combination with graphene probes by using the density functional theory
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(DFT) within the nonequilibrium Green’s function (NEGF) technique (See Supporting
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Information, Section 5). As shown in Figure 3c, in comparison with the acetate form, for
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the carbocation form the perturbed lowest unoccupied molecular orbital (p-LUMO) and
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perturbed highest occupied molecular orbital (p-HOMO) have transmission peaks with
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energy much closer to the unbiased electrode chemical potentials (EF). In the resonant 9 ACS Paragon Plus Environment
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tunneling mechanism described by the Landauer-Büttiker formalism, the energy gap
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between the p-FMOs and the EF plays a crucial role in the current calculation under a low
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bias voltage: The smaller the gap is, the more electrons can enter the Fermi window in the
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bias range explored.23,35,36 In addition to the p-FMOs, we also notice that for the
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carbocation form the p-HOMO-1 is also close to the EF with a distinguished transmission
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peak, which can contribute to a large conductance. Therefore, with the same results
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analyzed by the above-mentioned two methods and the quantum transport calculations, we
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can conclude that the carbocation form should have a higher conductance than the acetate
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form under a low bias voltage. The calculated scattering states of these critical transmission
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p-FMOs are consistent with the FMOs (Figure 3b), indicating that the transmission
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channels are mainly derived from the electronic orbitals of the molecules (Figure S16). It
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was found that carbocation conductance varied along with solution conditions. Recent
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studies reported that the dipole-dipole interaction between the measured molecule and
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solution molecules might affect molecular conductance.21,37 Considering the fact that HAc
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and TFA have the big difference in dielectric constant (~6 for acetic acid and ~39 for TFA),
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the different polar intermolecular interactions should affect electron transport of molecular
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junctions to some extent, thus causing the conductance variation. Another possibility is that
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different solutions could influence the lifetime of carbocation. Due to the measurement
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limit of the instruments used, the transition between the carbocation and acetate forms
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could be too fast to follow without fully reaching the conductance platform of carbocation,
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as demonstrated in Figure 2 in mixed solutions (pure HAc and 25% TFA/75% HAc).
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a
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0 –1
–1.71
–1.66
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Ac
Br
–2
E (eV)
–3
LUMO
–3.64
–4 –5 –6
HOMO –4.98
R = (+)
–7 R = (+)
c Transmission
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p-HOMO
R = Br p-LUMO p-LUMO
p-HOMO
10 0
p-HOMO-1 p-HOMO
10 –4
p-LUMO
10 –8 R= (+) R= Ac R= Br
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R = Ac
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Figure 3. Theoretical simulations of GMG-SMJs. (a) Calculated energy levels of the molecular wire in the three forms: R = (+) (Carbocation, red), R = Ac (acetate, blue) and R = Br (Bromide, orange). The dash line shows the Fermi level of graphene electrodes: EF = –4.8 eV. (b) Corresponding calculated frontier molecular orbitals (FMOs) of the molecular wire in the three forms. (c) Transmission spectra of GMG-SMJs in the three forms around the Fermi level of graphene at a zero-bias voltage.
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To analyze the reaction dynamics, RTSs in It trajectories were idealized into a two-
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level interconversion by using a QuB software (Figure 4a). In this analysis, the lifetimes
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(τlow/τhigh) of the acetate/carbocation forms are derived from the probability distributions of
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the dwell times (Tlow/Thigh) of the low/high conductance states. By taking the device in
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Figure 2 as an example, both of the probability distributions of Tlow and Thigh in the solution
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of 75% TFA/25% HAc (vol/vol) were well fit by a single exponential decay function as
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shown in Figures 4b and 4c, which produce the values of τlow = 5320 ± 790 μs and τhigh =
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2540 ± 200 μs, respectively, according to a hidden Markov chain model. On the basis of
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this fact, we initially assumed that the reversible reaction could be regarded as a simple
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Poisson process. Their rate constants (kd and kc), corresponding to the heterolytic 11 ACS Paragon Plus Environment
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dissociation of the acetate form (kd = 1/τlow) and the combination of the carbocation form
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with acetic acid (kc = 1/τhigh) (insets in Figures 4b and 4c), were derived to be (1.88 ±0.28)
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× 102 s–1 and (3.94 ± 0.29) × 102 s–1, respectively. More data in different conditions are
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shown in the Supporting Information (Section 6). Figure 4d (solid lines) shows the
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corresponding activation energies (Ed and Ec) calculated from the Eyring equation E =
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RTln(kBT/hk), where R = 8.314 J/(mol·K), T is the temperature, kB is the Boltzmann
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constant, and h is the plank constant. These values show the same tendency in comparison
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with the macroscopic results measured by UV-Vis experiments and flash photolysis (dash
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lines). It was worthy to notice that these statistics were proceeded from a long-term
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observation of one molecule rather than the observation of the ensemble, and thus the
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results were defined in a time domain, which should be comparable to the macroscopic
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results due to the equivalence between time average and ensemble average.
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Figure 4. Statistical analyses of the GMG-SMJ device used in Figure 2. (a) Measured It trajectories (black dots) of a GMG-SMJ in the solution of HAc-TFA (25%/75%, vol/vol). The red line shows the idealised two-level interconversion by using a QUB software. (b,c) Plots of time intervals of the low (b) and high (c) states derived from It trajectories of a GMG-SMJ in the solution of HAc-TFA (25%/75%, vol/vol). The distributions were well fitted by a single-exponential decay function (blue lines). Insets show the corresponding reaction pathways. (d) Activation energies of the symmetric SN1 reaction derived from macroscopic (dash lines) and single-molecule (solid lines) experiments. (e) Combination constants of carbocation (pKR+). Column: pKR+ values derived from GMG-SMJs. Solid columns represent the respective pK values; Striped columns represent the generalized acid function J0 in the corresponding solutions. The blue and black dash lines show the J0TFA% relationship and the pKR+ values derived from bulk experiments, respectively.
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Single-molecule “thermodynamic functions” should be redefined based on kinetic
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constants derived from GMG-SMJ experiments. The equilibrium constant (K) is defined
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as the division of the rate constants of the dissociation/combination reactions (K = kd/kc).
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In the solution containing TFA proportions from 0% to 75%, the pK values (p means the
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minus denary logarithm) were calculated to be 3.57 ± 0.11 (0% TFA), 2.55 ± 0.21 (25% 13 ACS Paragon Plus Environment
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TFA), 1.73 ±0.06 (50% TFA) and 0.32 ±0.20 (75% TFA), respectively. The combination
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constants (KR+) between the carbocation form and acetic acid were derived from the pK
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values normalized by a carbocation-based generalized acid function (J0) (Figure 4e, blue
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line and striped columns), which was measured by an indicator overlap method: pKR+ = J0
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+ pK. The pKR+ values were calculated as −4.10 ± 0.11 (0% TFA), −8.11 ± 0.21 (25%
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TFA), −9.46 ± 0.06 (50% TFA) and −9.72 ± 0.20 (75% TFA) (Figure 4e, solid columns),
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respectively. In comparison with the macroscopic results pKR+ = ~10.50 (see Supporting
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Information, Section 1), it seems that GMG-SMJs may improve the stability of the
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carbocation state more or less. Two possibilities could explain this finding: (i) In
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comparison with isolated molecules, graphene electrodes extend the conjugation range of
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carbocation, which obviously lower the Columbic potential of carbocation; (ii)
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Electrostatic catalysis may take effect in GMG-SMJs, that is, the strong electro-static field
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between graphene electrodes (Es = ~0.3 V/nm) increases the stability of charge-separated
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intermediates. In brief, the dipole (μ) of molecules is more likely to array parallel to the
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electrostatic field, thus generating a field-induced stabilization energy μ × Es.38,39 As the
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carbocation-anion pair is charge separated and much more polar than the acetate, it is no
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doubt that the electrostatic field generates more stabilization energy in the carbocation
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intermediate. Considering that the external electric field can be “counteracted” by the
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directional alignment of solution molecules, the effect of electrostatic catalysis depends on
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the polarity of solution. Since TFA is much more polar than HAc, it is reasonable that the
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effect of electrostatic catalysis becomes stronger along with the decrease of TFA
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proportion (Figure 4e), thus leading to the higher pKR+ value at 0% TFA.
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We further investigated the feasibility of observing the competitive reactions between
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different nucleophiles (Figure 5a). To do this, bromide anions were introduced to the
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solution to act as another nucleophile. Specifically, 10 μmol/L cetyltrimethylammonium
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bromide was introduced to a HAc/TFA solution (25%/75%, vol/vol). We measured the
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conductance changes of functioning GMG-SMJs in the HAc/Br−/TFA ternary solution in
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real time. In addition to RTSs observed previously, a third conductance state was
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occasionally detected in the It trajectory (Figures 5b5e), which did not exist before. The
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appearance of this novel conductance state is probably related to a new competitive product:
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the bromide form (Figure 5a). To understand its origin, in Figure 3 we compared the
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electronic structures and transport properties of the bromide form with the formers (the
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carbocation form and the acetate form). The calculated results showed that the bromide
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and acetate forms have much more similarity in comparison with the carbocation form.
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This is mainly because both bromide and acetate forms have an identical sp3 hybridization
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type in the central carbon atom, leading to the close FMOs energy values in Figure 3a and
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similar conjugated orbital distribution in Figure 3b. The transmission spectrum in Figure
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3c also shows that the transmission peaks (p-FMOs) of these two sp3-hybridized structures
258
are close, while much further away from EF, in comparison with the sp2-hybridized
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carbocation form. Furthermore, we noticed that there is a minor transmission difference
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between these two structures as shown in Figure 3c and the p-HOMO (which dominates
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the conductance) of the bromide form is a bit closer to EF in comparison with the acetate
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form. According to the models and the quantum transport analysis discussed above, it is
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reasonable to conclude that the bromide form and the acetate form should correspond to
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the experimentally-observed two similar low conductance states, and the conductance of
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the bromide form is slightly higher than the acetate form.
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Figure 5. Competitive reactions between carbocation and different nucleophiles. (a) Schematic representation of competitive reactions of carbocation with Ac− and Br−. (b-e) Representative It trajectories and corresponding enlarged views of a GMG-SMJ, which was submerged into a HAc/Br−/TFA ternary solution (25% HAc/75% TFA (vol/vol); Br−: 10 μmol/L). Ac, Br and C+ represent the acetate form, the bromide form and the carbocation form, respectively.
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carbocation form (C+, red), the bromide form (Br, orange) and the acetate form (Ac, blue),
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respectively. On the basis of the attribution, we can elucidate the reaction pathway of
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individual molecules in GMG-SMJs from real-time conductance recordings, which are
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faithfully synchronous to the chemical reaction. By taking Figure 5e as an example, we
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witnessed
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Ac−(C+)−Br−(C+)−Ac−(C+)−Br−(C+)−Br−(C+)−Ac, which nicely includes the similar
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reaction
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Ac−(C+)−Ac−(C+)−Br−(C+)−Ac in Figure 5d. Reproducibly, the fact we found is that the
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carbocation form is an inevitable intermediate in the transition between the bromide and
Therefore, we attribute these three conductance states (from high to low) to the
the
processes
transformation
of
Ac−(C+)−Br−(C+)−Ac
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pathway
in
Figure
of
5c
and
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acetate forms, which confirms the classical SN1 mechanism. It should be mentioned that
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the carbocation form was less populated when the bromide anion was added, which is
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consistent with the bulk experiments (Figure S6). In addition, the kinetics of competitive
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reactions were analyzed according to the statistical approach used above. The rate constants,
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involving the heterolytic dissociation process of the acetate/bromide forms (kd) and the
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combination process of the carbocation form with acetic acid/bromide (kc), were calculated
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as kd = (1.16 ± 0.18) × 102 s1 and kc = (2.73 ±0.16) ×103 s1 (Figure S18), respectively.
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In comparison with the condition without the addition of the bromide anion, the rate of
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heterolytic dissociation barely changed while the rate of combination increased. Such
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results also confirm the classical SN1 mechanism, that is, the heterolytic dissociation
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process (first step) is only related to the reactant and the combination process (second step)
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is related to both the reactant and the nucleophile at the same time.
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In conclusion, this work demonstrates a single-molecule way to overcome the
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difficulty of realizing label-free, real-time electrical measurements of fast reaction
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dynamics with single-event sensitivity and high temporal resolution, and reveal molecular
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mechanisms of classical chemical reactions. Both experimental and theoretical results
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demonstrated the reversible acid-catalyzed SN1 reactions at the single-molecule level,
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including acidity dependence and nucleophilic competitive reactions. On the basis of these
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results, more details in SN1 reactions, such as racemization and intramolecular
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rearrangement reactions, are feasible to investigate in the future. By rationally integrating
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target functional groups into molecular bridges via molecular engineering, this approach
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offers a promising tool for revealing fundamental mechanisms of general chemical 17 ACS Paragon Plus Environment
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reactions as well as deeply understanding the basic processes of life at the molecular level
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and developing accurate molecular diagnostics.
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ASSOCIATED CONTENT
309
Supporting Information
310
The Supporting Information is available free of charge on the ACS Publications website at
311
DOI: 10.1021/acs.nanoletter.xxxxxxx.
312
Macroscopic experiments, molecular synthesis, device characterization and analysis,
313
characterization of control devices, detailed theoretical analysis, dynamic analysis, and
314
additional experimental results (PDF)
315
AUTHOR INFORMATION
316
Corresponding Author
317
*E-mail:
[email protected] 318
*E-mail:
[email protected] 319
ORCID
320
Chunhui Gu: 0000-0002-2332-4513
321
Xuefeng Guo: 0000-0001-5723-8528
322
Author contributions
323
†
324
Notes
325
The authors declare no competing financial interests
326
ACKNOWLEDGMENTS
C.G. and C.H. contributed equally to the work.
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We acknowledge primary financial supports from National Key R&D Program of China
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(2017YFA0204901), the National Natural Science Foundation of China (grant 21727806),
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the Natural Science Foundation of Beijing (Z181100004418003) and NSERC of Canada.
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We thank the CalculQuebec and Compute Canada for computational facility where the
331
calculations were carried out. We are particularly grateful to Prof. Andrew M. Rappe from
332
University of Pennsylvania, Prof. K. N. Houk in University of California, Los Angeles,
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Prof. Zhenfeng Xi from Peking University and Prof. Yiqin Gao from Peking University for
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helpful discussions.
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Figure Legends
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Figure 1. Schematic of a graphene-molecule-graphene single-molecule junction that
407
shows the formation dynamics of a 9-phenyl-9-fluorenyl cation in a SN1 reaction.
408
Figure 2. Real-time conductance measurements of a representative GMG-SMJ among 5
409
different devices. (a) Representative It trajectories in different conditions (from top to
410
bottom: in the air, pure HAc, 25% TFA/75% HAc, 50% TFA/50% HAc, and 75% TFA/25%
411
HAc (vol/vol)). (b) Partial It curves of the corresponding parts in (a). Insets show the
412
enlarged views of the peaks as indicated by white arrows. (c)
413
histograms of (a). The blue and red lines show the gauss-shaped fit for the low and high
414
conductance states, respectively. Insets show the enlarged views in the high conductance
415
regions. Source-drain bias voltage (VD): 0.3 V; Gate voltage (VG): 0 V; Sampling rate: 57.6
416
kSa/s.
417
Figure 3. Theoretical simulations of GMG-SMJs. (a) Calculated energy levels of the
418
molecular wire in the three forms: R = (+) (Carbocation, red), R = Ac (acetate, blue) and
419
R = Br (Bromide, orange). The dash line shows the Fermi level of graphene electrodes: EF
420
= –4.8 eV. (b) Corresponding calculated frontier molecular orbitals (FMOs) of the
421
molecular wire in the three forms. (c) Transmission spectra of GMG-SMJs in the three
422
forms around the Fermi level of graphene at a zero-bias voltage.
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The corresponding
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426
Figure 4. Statistical analyses of the GMG-SMJ device used in Figure 2. (a) Measured It
427
trajectories (black dots) of a GMG-SMJ in the solution of HAc-TFA (25%/75%, vol/vol).
428
The red line shows the idealised two-level interconversion by using a QUB software. (b,c)
429
Plots of time intervals of the low (b) and high (c) states derived from It trajectories of a
430
GMG-SMJ in the solution of HAc-TFA (25%/75%, vol/vol). The distributions were well
431
fitted by a single-exponential decay function (blue lines). Insets show the corresponding
432
reaction pathways. (d) Activation energies of the symmetric SN1 reaction derived from
433
macroscopic (dash lines) and single-molecule (solid lines) experiments. (e) Combination
434
constants of carbocation (pKR+). Column: pKR+ values derived from GMG-SMJs. Solid
435
columns represent the respective pK values; Striped columns represent the generalized acid
436
function J0 in the corresponding solutions. The blue and black dash lines show the J0TFA%
437
relationship and the pKR+ values derived from bulk experiments, respectively.
438
Figure 5. Competitive reactions between carbocation and different nucleophiles. (a)
439
Schematic representation of competitive reactions of carbocation with Ac− and Br−. (b-e)
440
Representative It trajectories and corresponding enlarged views of a GMG-SMJ, which
441
was submerged into a HAc/Br−/TFA ternary solution (25% HAc/75% TFA (vol/vol); Br−:
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10 μmol/L). Ac, Br and C+ represent the acetate form, the bromide form and the
443
carbocation form, respectively.
444 445 446
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Figure 1
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Nano Letters
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Figure 2 a
b
Current (nA)
Air
Current (nA)
0
0.2
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Figure 3
a
b
0 –1
–1.71
–1.66
–5.50
–5.42
Ac
Br
–2
E (eV)
–3
LUMO
–3.64
–4 –5 –6
HOMO –4.98
R = (+)
–7 R = (+)
c Transmission
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
Nano Letters
p-HOMO
R = Ac p-LUMO p-LUMO
p-HOMO
10 0
R = Br
p-HOMO-1 p-HOMO
10 –4
p-LUMO
10 –8 R= (+) R= Ac R= Br
10 –12
10 –16 –2.0
–1.5
–1.0
–0.5
471
0 0.5 E–EF (eV)
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1.0
1.5
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Figure 4
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Keywords: Single-molecule detection, reaction dynamics, molecular electronics, nucleophilic substitution
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TOC Graphic: Through molecular engineering, a single molecular wire containing a functional center of 9-phenyl-9-fluorenol was covalently wired into nanogapped graphene electrodes to form stable single-molecule junctions. Both experimental and theoretical studies consistently demonstrate and interpret direct measurements of the dynamic processes of detailed molecular transformations of a SN1 reaction at the singlemolecule/single-event level.
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