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• W3081187148 abstract "•Identifying conformational isomers of cyclohexane at room temperature•The attached electrodes retard the interconversion of conformational isomers•The confinement effect stabilizes the twist-boat intermediate of cyclohexane Conformational isomer is a fundamental concept in chemistry, providing the essential view to understand their unique role in molecular biology, medicine, and supramolecular chemistry. However, the interconversion between conformational isomers of the flexible molecule is fast at room temperature, and ensemble methods could only reflect the average contribution from all the conformational isomers, suggesting a significant challenge to distinguish corresponding isomers individually. In this work, we develop a single-molecule method to quantificationally identify the chair isomers of cyclohexane at room temperature beyond ensemble methods. We also demonstrate that the confinement effect of the attaching of electrodes to molecules could help in stabilizing and characterizing the twist-boat intermediate of cyclohexane. Our study provides a promising strategy to study the conformational isomers of flexible molecules and offers an insight into the fields, where flexible molecules play a role. Isomerism reflects the ubiquitous nature that molecules with the same molecular formula show different structures. The interconversion between conformational isomers of flexible molecules is quite fast owing to the low barriers of around 10 kcal mol−1, leading to average signal contributed by all the possible isomers characterized by ensemble methods. On this account, identifying the conformational isomers of flexible molecules at room temperature has a substantial challenge. Here, we develop a single-molecule approach to identify the conformational isomers of cyclohexane at room temperature through the single-molecule electrical characterization. By noise analysis and feature extraction of the conductance of single-molecule junctions, we quantificationally identified two chair isomers of cyclohexane at room temperature, while such identification is only feasible at low temperatures by ensemble characterization. The strategy to apply the single-molecule approach to identify conformational isomers paves the avenue to investigate the isomerization of flexible molecules beyond the ensemble methods. Isomerism reflects the ubiquitous nature that molecules with the same molecular formula show different structures. The interconversion between conformational isomers of flexible molecules is quite fast owing to the low barriers of around 10 kcal mol−1, leading to average signal contributed by all the possible isomers characterized by ensemble methods. On this account, identifying the conformational isomers of flexible molecules at room temperature has a substantial challenge. Here, we develop a single-molecule approach to identify the conformational isomers of cyclohexane at room temperature through the single-molecule electrical characterization. By noise analysis and feature extraction of the conductance of single-molecule junctions, we quantificationally identified two chair isomers of cyclohexane at room temperature, while such identification is only feasible at low temperatures by ensemble characterization. The strategy to apply the single-molecule approach to identify conformational isomers paves the avenue to investigate the isomerization of flexible molecules beyond the ensemble methods. Conformational isomer is essential to understand the properties of molecules made up of the same atoms but in a different arrangement.1Canfield P.J. Blake I.M. Cai Z.L. Luck I.J. Krausz E. Kobayashi R. Reimers J.R. Crossley M.J. 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USA. 1999; 96: 7894-7898Crossref PubMed Scopus (140) Google Scholar which could restrict the degree of freedom of molecular components when the electrodes are attached,47Reisner W. Beech J.P. Larsen N.B. Flyvbjerg H. Kristensen A. Tegenfeldt J.O. Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment.Phys. Rev. Lett. 2007; 99: 058302Crossref PubMed Scopus (152) Google Scholar providing another opportunity to enhance the distinguishability. Benefiting from the data discreteness, high sensitivity, and confinement effect of the single-molecule technique, the conformational isomers of flexible molecules could be identified even at room temperature beyond thermodynamic averaging in ensemble methods. In this work, we characterize the charge transport through single-molecule junctions of cyclohexane formed between the two gold electrodes using the scanning tunneling microscopic break junction (STMBJ) technique. We find that the flicker noise of the single-molecule conductance of cyclohexane shows a bimodal distribution, which is associated with the different conformational isomers of cyclohexane. The identification of the conformational isomers of cyclohexane is achieved at room temperature with good distinguishability, showing a ratio consistent with the thermokinetic experiment of NMR characterization below the temperature of 233 K. Moreover, owing to the confinement effect applied to the cyclohexane bridging with two electrodes, we have the opportunity to stabilize and characterize the twist-boat intermediate of cyclohexane. To form the single-molecule junctions between the two gold electrodes, we introduced anchor groups –SMe or –SAc in cyclohexane cySMe and cySAc (shown in Figure 2A) with two distinct chair isomers ee and aa, named by their anchor groups in axial (abbreviated to “a”) or equatorial (abbreviated to “e”) positions. The synthesis and characterization of target molecules are shown in Figures S15–S22. The NMR characterization of cySMe at room temperature only shows one pattern of signals (Figure 2B, 298 K), contributed by the average of all the conformational isomers that are in rapid interconversion, which is the challenge to identify such kind of conformational isomers at room temperature by NMR and corresponding ensemble methods. When the temperature decreases to 253 K, we first observed a broadening of the NMR signal, suggesting that the interconversion rate between conformational isomers is slowing down and has become comparable to the time scale of the NMR spectrum. Further reducing the temperature from 253 to 233 K leads to a splitting of the broad signals, which are attributed to the two chair isomers of cySMe with the ratio between cySMe-aa (both anchor group in axial position) and cySMe-ee (both anchor group in equatorial position) to be 60: 40. The attribution of NMR signals is shown in Supplemental Information (Figure S13). The ratio indicates that the free energy of cySMe-aa is 0.18 kcal mol−1 lower than cySMe-ee, suggesting a ratio of 54:46 between cySMe-aa and cySMe-ee at room temperature (298 K). For molecule cySAc, we also observe a similar phenomenon (Figure S22), and determine the ratio between cySAc-aa and cySAc-ee of about 56:44 at room temperature. It is worth noting that the distinguishability for both molecules by NMR is only feasible at the temperature below 233 K (Figures S21 and S22). To characterize the charge transport through single-molecule junctions of cySMe and cySAc, we carry out the STMBJ experiments in the solution of 0.1 mM target molecules, with 0.1 V bias applied between the gold tip and substrate at room temperature. Through retracting the gold tip connected with the substrate, the plateaus around G0 firstly form (symbol G0 is the quantized unit of quantum conductance), which is associated with the formation of gold-gold atomic contact (Figure 2C).48Yanson A.I. Bollinger G.R. van den Brom H.E. Agraït N. van Ruitenbeek J.M. Formation and manipulation of a metallic wire of single gold atoms.Nature. 1998; 395: 783-785Crossref Scopus (926) Google Scholar,49Agraït N. Yeyati A.L. van Ruitenbeek J.M. Quantum properties of atomic-sized conductors.Phys. Rep. 2003; 377: 81-279Crossref Scopus (1297) Google Scholar Further retracting the tip breaks the atomic contacts with another type of plateaus formed in the range from 10−5.0 to 10−6.0 G0, which is the conductance signals of the formed single-molecule junctions. We collected thousands of such conductance traces of cySMe (6,370 traces) and cySAc (4,031 traces) to construct the one-dimensional (1D) conductance histogram. As shown in Figure 2C, both cySMe and cySAc have a mono peak centered at 10−5.9 G0. The superimposition of conductance traces of cySMe leads to the two-dimensional (2D) conductance histogram shown in Figure 2D, which shows about 1.4 nm stretching distance. By adding 0.5 nm gold-gold snap-back distance to the stretching distance,50Hong W. Manrique D.Z. Moreno-García P. Gulcur M. Mishchenko A. Lambert C.J. Bryce M.R. Wandlowski T. Single molecular conductance of tolanes: experimental and theoretical study on the junction evolution dependent on the anchoring group.J. Am. Chem. Soc. 2012; 134: 2292-2304Crossref PubMed Scopus (307) Google Scholar the corrected junction length of cySMe is 1.9 nm, which agrees well with the sulfur-to-sulfur distance of cySMe. Meanwhile, cySAc shows the similar junction lengths to cySMe (1.8 nm, Figure 2E), suggesting that the single-molecule junctions of cySMe and cySAc are formed between two sulfur atoms. The binding strength between the used anchor groups and gold electrodes is reported to be stronger than 0.5 nN,51Aradhya S.V. Meisner J.S. Krikorian M. Ahn S. Parameswaran R. Steigerwald M.L. Nuckolls C. Venkataraman L. Dissecting contact mechanics from quantum interference in single-molecule junctions of stilbene derivatives.Nano Lett. 2012; 12: 1643-1647Crossref PubMed Scopus (144) Google Scholar, 52Frei M. Aradhya S.V. Hybertsen M.S. Venkataraman L. Linker dependent bond rupture force measurements in single-molecule junctions.J. Am. Chem. Soc. 2012; 134: 4003-4006Crossref PubMed Scopus (99) Google Scholar, 53Leary E. La Rosa A. González M.T. Rubio-Bollinger G. Agraït N. Martín N. Incorporating single molecules into electrical circuits. The role of the chemical anchoring group.Chem. Soc. Rev. 2015; 44: 920-942Crossref PubMed Google Scholar, 54Huang Z. Chen F. Bennett P.A. Tao N. Single molecule junctions formed via Au-thiol contact: stability and breakdown mechanism.J. Am. Chem. Soc. 2007; 129: 13225-13231Crossref PubMed Scopus (143) Google Scholar, 55Xu B. Xiao X. Tao N.J. Measurements of single-molecule electromechanical properties.J. Am. Chem. Soc. 2003; 125: 16164-16165Crossref PubMed Scopus (305) Google Scholar which is strong enough to overcome the interconversion barriers between two chair isomers of cyclohexane during the break junction process, leading to the dominant distributions of the stabilized structure during the stretching of junctions. Nevertheless, the discreteness of single-molecule characterization provides the opportunity to extract more information than conductance. First, we analyze the variance distributions of break junction traces of the conductance plateaus (Supplemental Experimental Procedures, Section 4). As shown in Figure 3A, we find that the variance distributions of the conductance plateaus of cySMe and cySAc show bimodal distributions, which are significantly different from a series of control molecules with rigid backbones (Figure S8). Second, we perform a flicker noise analysis of cySMe. The flicker noise of single-molecule junctions contains the information of the electrode-molecule interactions,27Adak O. Rosenthal E. Meisner J. Andrade E.F. Pasupathy A.N. Nuckolls C. Hybertsen M.S. Venkataraman L. Flicker noise as a probe of electronic interaction at metal-single molecule interfaces.Nano Lett. 2015; 15: 4143-4149Crossref PubMed Scopus (65) Google Scholar,28Inkpen M.S. Liu Z.F. Li H. Campos L.M. Neaton J.B. Venkataraman L. Non-chemisorbed gold–sulfur binding prevails in self-assembled monolayers.Nat. Chem. 2019; 11: 351-358Crossref PubMed Scopus (123) Google Scholar,31Garner M.H. Li H. Chen Y. Su T.A. Shangguan Z. Paley D.W. Liu T. Ng F. Li H. Xiao S. et al.Comprehensive suppression of single-molecule conductance using destructive σ-interference.Nature. 2018; 558: 415-419Crossref PubMed Scopus (180) Google Scholar providing the extra dimension to make such statistical enhancement to distinguish the conformation isomers of cyclohexane. To extract the noise of single-molecule junctions, we suspend the retracting process of the tip for 150 ms once a plateau of the molecular junctions is observed. As shown in Figure 3B, we cut out the data in the region when the tip is suspended. Then, as shown in the inset of Figure 3B, Fourier transformation is applied to the region with the integration from 100 to 1,000 Hz to extract the flicker noise power spectral density (PSD), which is further normalized by the average conductance of the conductance plateau (Supplemental Experimental Procedures, Section 4). The blue and red traces in Figure 3B are two types of typical traces in the experiment of flicker noise analysis, showing a low (10−7.5) and high (10−6.1) noise PSD, respectively. We could also observe a high-conductance plateau around 10−4.5 for the trace (red trace in Figure 3B) with high-noise PSD. We further construct the 2D flicker noise distribution of cySMe (7,652 traces). In the 2D flicker noise distribution, each sampling trace is represented by one point in the intensity graph. As shown in Figure 3C, we observe a bimodal distribution in better distinguishability than the variance distributions. We divide the two distributions of flicker noise by the common chord of the boundaries of the two distributions, leading to the ratio between the more dominant one and the other one of ~63:37, which is consistent with the ratio between the two chair isomers of cySMe (54:46 between cySMe-aa and cySMe-ee) at room temperature (Figure 2B). Since the flicker noise of single-molecule junctions highly depends on the electrode-molecule interaction,27Adak O. Rosenthal E. Meisner J. Andrade E.F. Pasupathy A.N. Nuckolls C. Hybertsen M.S. Venkataraman L. Flicker noise as a probe of electronic interaction at metal-single molecule interfaces.Nano Lett. 2015; 15: 4143-4149Crossref PubMed Scopus (65) Google Scholar,31Garner M.H. Li H. Chen Y. Su T.A. Shangguan Z. Paley D.W. Liu T. Ng F. Li H. Xiao S. et al.Comprehensive suppression of single-molecule conductance using destructive σ-interference.Nature. 2018; 558: 415-419Crossref PubMed Scopus (180) Google Scholar we used another type of anchor group –SAc, to test whether such statistical enhancement facilitated by flicker noise still exist. As shown in Figure 3D, we find that such enhanced distinguishability is also observed in cySAc. The flicker noise of cySAc also shows a bimodal distribution with a ratio of about 66:34, which is also consistent with the ratio between the two chair isomers of cySAc (56: 44 between cySAc-aa and cySAc-ee, Figure S22). Both cySMe and cySAc show similar noise distributions, suggesting that the bimodal flicker noise distributions are not from the coupling between electrodes and anchor groups, but mainly contributed by the molecular backbones. Meanwhile, we find that the traces with different noise distributions (Figure 3) show distinct features. As shown in Figure 3B, the traces (red trace) with a high-conductance plateau around 10−4.3 G0, show more substantial fluctuations than the other type of traces (blue trace) without the high-conductance plateaus. We further analyze the flicker noise distribution (Figure 3C) to classify the high-noise and low-noise traces and plot corresponding 2D conductance histogram (Figure S6), showing that the high-noise traces show a distinct plateau around 10−4.3 G0. As a control, we perform the same experiment to a series of molecules with a more rigid backbone (Figure S11), only the mono distributions of flicker noise are observed, suggesting that such bimodal distribution of flicker noise for cyclohexane is associated with its conformational isomers. From the above result, we think the dominant flicker noise distribution with high-noise PSD is associated with conformation “aa,” while the other distribution is associated with conformation “ee.” We further carry out the theoretical calculation to understand the single-molecule data of cyclohexane isomers. As shown in Figure 4A, the free energy of cySMe-ee is 0.1 kcal mol−1 higher than that of cySMe-aa, which is consistent with the variable temperature NMR (VTNMR) result that the distribution of cySMe-aa is more dominated. Also, the interconversion between cySMe-ee and cySMe-aa is via the intermediate Int, a twist-boat geometry, which is about 5.0 kcal mol−1 higher than both chair conformations, suggesting that the distribution of Int is negligible in comparison with the two chair isomers. The barriers for the interconversion between cySMe-ee and cySMe-aa are similarly low (12.1 and 13.6 kcal mol−1, respectively), reflecting the rapid interconversion between the two chair isomers. From the sulfur-to-sulfur distances in each component, we find that the theoretical junction lengths are in the following trend: cySMe-ee > Int > cySMe-aa. According to the junction lengths, cySMe-ee or cySMe-aa would be the stabilized structure during the stretching or compressing of single-molecule junctions, respectively. From the calculated transmission coefficients of the two chair conformations, we find that the transmission probability of cySMe-aa is lower than that of cySMe-ee in a broad range of energy choices (Figure 4B). Meanwhile, Int shows a higher transmission probability than both chair isomers. From the above results, we expect that the conductance of cySMe-aa would be lower than 10−7 G0, which is below the detection limit of our current amplifier. Meanwhile, during the formation of single-molecule junctions of cySMe, there are two situations, the cySMe-ee or cySMe-aa is first captured. If cySMe-ee is captured first, since cySMe-ee is fully extended, further stretching of the junction of cySMe-ee will not induce the switch of its conformations. On the contrary, if" @default.
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• W3081187148 date "2020-10-01" @default.
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• W3081187148 title "Identifying the Conformational Isomers of Single-Molecule Cyclohexane at Room Temperature" @default.
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