Helical Conformation Tunability via Hydrogen Bonding in Supramolecular Frameworks

Open AccessCCS ChemistryRESEARCH ARTICLE15 Jun 2021Helical Conformation Tunability via Hydrogen Bonding in Supramolecular Frameworks Zhijie Xue†, Fuwei Gan†, Hong Liu†, Chengshuo Shen, Huibin Qiu, Bo Yang and Ping Yu Zhijie Xue† School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai , Fuwei Gan† School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 200240 Shanghai , Hong Liu† School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai , Chengshuo Shen School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 200240 Shanghai , Huibin Qiu *Corresponding authors: E-mail Address: email protected E-mail Address: email protected E-mail Address: email protected School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 200240 Shanghai , Bo Yang *Corresponding authors: E-mail Address: email protected E-mail Address: email protected E-mail Address: email protected School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai and Ping Yu *Corresponding authors: E-mail Address: email protected E-mail Address: email protected E-mail Address: email protected School of Physical Science and Technology, ShanghaiTech University, 201210 Shanghai https://doi.org/10.31635/ccschem.021.202100784 SectionsSupplemental MaterialAboutAbstractPDF ToolsAdd to favoritesTrack Citations ShareFacebookTwitterLinked InEmail Hydrogen-bonded molecules and their dynamics are significantly important in chemistry and biology due to their widespread functionality. Besides their natural abundance and diversity, applications of molecules with dynamic conformations in artificial networks allow information storage and molecular motor design on the nanometer scale. Here, we report hydrogen-bonded molecular networks with tunable helical conformation on metal surfaces. The dynamics of helical conformation in two-dimensional hydrogen-bond networks are triggered and resolved by scanning probe microscopy at the single-molecule level. In combination with theoretical calculations, the surface-specific hydrogen bonds are identified as the origin of the dynamic helical conformation. Our results provide a distinctive access to molecular architecture with tunable helical conformation driven by hydrogen-bond interaction on surfaces. Download figure Download PowerPoint Introduction Hydrogen-bonded molecular structures are essential in nature and play a vital role in numerous biological processes.1,2 As inspired by nature, molecular self-assemblies on surfaces directed by noncovalent interactions, for example hydrogen bonding,3–6 metal–organic coordination,7–9 and van der Waals (vdW) forces,10,11 offer a great potential to fabricate supramolecular architectures with tailored functionalities through the design and synthesis of desired molecular building blocks. Among them, hydrogen bonding is one of the most employed noncovalent interaction in supramolecular structures because of its directionality, robust energy range, and biological relevance.12–17 Understanding how hydrogen bonding influences the molecular self-assembly is a key step to realize the controllable fabrication and manipulation of functionalized molecules into complex architectures and is crucial for the potential applications such as molecular electronic devices.18–20 With the development of scanning-probe microscopy techniques, high-resolution imaging provides the possibility to characterize the molecular structures directly,21,22 which delivers an appealing hotbed for investigating the role of hydrogen bonds in molecular self-assembly. Here, we used specifically designed molecules with dynamical molecular conformation as building blocks for self-assembly fabrication, which furnishes a model system for investigating the rich relationships between hydrogen bonding and molecular self-assembly, including the emergent tunable molecular conformation in the molecular framework. In this study, the helical molecule anthra(1,2-f:5,6-f′)diquinoline ( 2N-S7) is designed and synthesized for building the molecular networks ( Supporting Information Schemes S1–S2 and Figures S1–S9). This aromatic molecule has an S-shaped geometric structure (Figure 1a) and exhibits nonplanar molecular conformation due to the hydrogen repulsion between the terminal and the central phenyl ring ( Supporting Information Figure S10 and Tables S1–S2). The nitrogen substitutes in the two terminal rings of 2N-S7 are responsible for forming the intermolecular hydrogen bonds.23–25 Moreover, the helical structure of 2N-S7 allows three possible configurations (Figure 1b). By considering the central benzene ring of 2N-S7 as a reference, high-high (HH)/low-low (LL) configurations can be defined with the two terminal rings being located higher and lower than the central ring. In contrast, the high-low (HL) configuration is composed of a terminal ring above the central ring while the other terminal ring is positioned below. By taking advantage of noncontact atomic force microscopy (nc-AFM) with submolecular resolution,26–29 the helical conformation of each 2N-S7 molecule on the surface can be directly visualized. Figure 1 | Molecular model of 2N-S7 and structure characterization of monomer on surface. (a) Molecular model of 2N-S7. (b) Models for helical conformation HH, HL, and LL; gradient red color in the molecular sketches indicates the height increment. (c and d) STM and AFM images for 2N-S7 monomer on Ag(111). (e) Simulated AFM image based on DFT optimized geometry (tip-sample distance 7.5 Å). Set point: (c) Vs = 300 mV and I = 10 pA; (d) Δz = 1.2 Å. Scale bars: 5 Å. Download figure Download PowerPoint Experimental Methods All the scanning tunneling microscopy (STM) and AFM experiments were performed at 5K with commercial Createc LT-STM/qPlus AFM (CreaTec Fischer (c and d) Δz = 1 Å; (e) tip-sample distance 7 Å. Scale bars: (a) 50 Å; (b–d) 10 Å. Download figure Download PowerPoint That hydrogen bonding in the molecular framework can tune the helical conformation of the molecular building block can be further supported by a tip-manipulation experiment,30,31 where a trimer is separated into isolated monomers. As shown in Figures 3a–3g, the CO-tungsten tip is located at one of the molecules in the trimer, and then lateral manipulation is employed by setting the tip to the molecule to be separated under the bias of 5 mV with 6 nA current. Then, the trimer is separated into isolated monomers step by step. Upon the AFM measurements, the helical structure can be determined after each manual separation. The AFM images clearly show that once the hydrogen bonds surrounding a monomer are removed, its helical conformation is switched from HL to HH conformation, unambiguously indicating that hydrogen bonding, instead of the influence of adsorption, is the most important factor for determining the helical conformation of 2N-S7 molecular networks. Figure 3 | Manual separation of a trimer on Ag(111). (a–c) STM images measured after each manual separation step. (d–f) AFM images measured after each manual separation step. (g) Molecular models for the separation process. Set point: (a–c) Vs = 300 mV and I = 10 pA; (d–f) Δz = 1 Å. Scale bars: 5 Å. Download figure Download PowerPoint Moreover, the switching of molecular conformations in the framework can be triggered by the electron tunneling process. As some fluctuating features indicated in the STM images (Figure 4a), the STM tip can be placed above the molecular end position (Figure 4a, red and green dots) and the tunneling currents are recorded with disabled STM feedback. Figure 4b shows the temporal evolution of the tunneling currents displaying two distinct current levels on the red dot position, which are assigned to the high and low positions of the molecular end directly underneath the tip, whereas the tunneling current displays only one stable current level on the green dot position, suggesting that the molecular end measured at the green dot is stabilized at the high position as resolved by the AFM. Thus, the molecular conformation in the framework can switch between HH and HL molecular configurations as demonstrated by the right panel in Figure 4b. The occupation probabilities for the HH and HL configurations are also revealed by the histogram (Figure 4b, middle panel), indicating that although the HL configuration is the dominant conformation, the HH configuration can be triggered in the tunneling process. The switching rate between HH and HL conformations is obtained from the current versus time spectra by fitting the residence time distribution ( Supporting Information Figure S13). The voltage- and current-dependent switching rates are summarized in Figures 4c and 4d. Regarding the voltage dependence, we found that the slope of the switching rate changes obviously as a function of voltage. The switching rate approaches nearly zero at approximately 50 meV, suggesting the energy barrier between HH and HL conformations, which is also in good agreement with the binding energy difference between HH and HL conformations obtained by DFT calculations ( Supporting Information Table S4). For the current dependence, the power law fitting to the experimental data using R∼IN gives N = 0.79 ± 0.04, which is close to 1, indicating a major contribution from the one-electron tunneling processes. The adsorption site analysis also suggests that the dynamic conformation is mainly determined by the hydrogen-bonding interactions in the molecular network instead of the adsorption site on the substrate ( Supporting Information Figure S12).32,33 Figure 4 | The analysis of molecular switching behavior. (a and e) STM images of a trimer structure and fivefold vertex of 2N-S7. (b and f) Left panel: time-resolved tunneling current measured at the molecular end as marked by red and green dots in (a and e); set point: V = 150 mV, I = 50 pA. Middle panel: histogram; right panel: schematics of the HH and the HL configurations for (b) and the two long-lived HL configurations for (f). (c, d, g, and h) The voltage and current dependence of trimer and fivefold vertex. Set point: (a and b) Vs = 300 mV and I = 10 pA. Scale bars: 10 Å. Download figure Download PowerPoint In addition, the hydrogen-bond interaction strongly depends on the coordination number of the molecule, which further tunes the molecular conformation framework and dynamics. As Figure 4e shows, once the molecule is shared by two nearby trimers, its molecular conformation can become frustrated considering both trimers prefer HL conformation, which will require the molecular conformation to adopt the LL configuration. However, the LL configuration is a completely unfavorable conformation for the molecule, thus forcing interchange of the low and high positions between molecular terminals. Indeed, Figure 4f shows a different time-resolved tunneling current as a function of time. Both the currents measured at two molecular end positions show different current levels. The lowest and highest current levels should correspond to the two mirror-symmetric HL configurations with swapped end points (Figure 4f, right panel). The origin of the intermediate current level may be due to the tip-induced structural change34 and will be studied in the future. We also investigated the current- and voltage-dependent switching rates between the two HL conformations (Figures 4g and 4h). A linear current dependence and the power fitting N of 0.83 is observed, also suggesting the one-electron tunneling processes. Upon tuning the strength of the surrounding hydrogen bond, the dynamic molecular conformation can be transformed into a single stable helical conformation. According to previous pioneering studies of hydrogen-bonded molecules at surfaces,35,36 the strength of the hydrogen bond can be significantly influenced by the underlying substrate. Similar to the 2N-S7 network on Ag(111), a honeycomb structure of 2N-S7 forms on Au(111), as shown in Figure 5a. A closer look in Figures 5b–5d reveals each molecule has an HH configuration. This configuration is the preferred and only helical configuration observed on Au(111). Moreover, the simulated AFM image of 2N-S7 trimer on Au(111) (Figure 5e) agrees well with the experimental AFM image, supporting that the preferred helical conformation of the 2N-S7 network on Au(111) becomes the HH conformation with both ends pointing upward. In addition, 2N-S7 molecules can form stable chain-like structures on Cu(111) and each molecule shows HH configuration ( Supporting Information Figure S15). Figure 5 | Hydrogen-bond network of 2N-S7 on Au(111). (a) STM image of 2N-S7 on Au(111). (b–d) AFM images of networks, six-member ring, and threefold vertex. (e) Simulated AFM images of threefold vertex. Set point: (a) Vs = 300 mV and I = 10 pA; (b) Δz = 1.8 Å; (c) Δz = 2.6 Å; (d) Δz = 2 Å; (e) tip-sample distance 7 Å. Scale bars: (a) 50 Å; (b–d) 10 Å. Download figure Download PowerPoint The mechanism of molecular conformation tuned according to the strength of hydrogen bonds on surfaces is further investigated by DFT calculations. In the DFT calculations, we constructed and optimized the structure of the threefold vertices on the surfaces per the molecular model shown in Figure 6a. The optimized molecular structures and detailed calculations can be found in Supporting Information Table S3 and Figure S14. According to our DFT calculations, the hydrogen-bonding interaction in the threefold vertices on Ag and Au can be analyzed by three aspects: (1) the geometrical distortion induced by the hydrogen bonds, (2) the corresponding charge redistribution, and (3) the hydrogen-bond length. To quantitatively estimate the geometrical distortion, we introduce Δhc as the change of height difference between the nitrogen atom on one end of the 2N-S7 molecule (N) and its second nearest hydrogen atom (H2) due to the formation of the hydrogen bonds (Figure 6b). As shown by the calculated values listed in the table of Figure 6c, on Ag(111) a threefold vertex with the HL configurations has a 12.1 pm smaller distortion than the HH configurations. In stark contrast, on Au(111) the HL configurations result in a 35.3 pm larger distortion than the HH configurations. Since a larger value of Δhc indicates a higher energy cost for the helical conformation switching, the much larger difference between the Δhc of HH and HL on Au than that on Ag indicates the helical conformation HH is more stable on Au(111) substrate. Figure 6 | Theoretical calculations of conformation-dependent energy landscapes. (a) Molecular models of 2N-S7 network on Au(111) and Ag(111). (b) Molecular models for illustrating the height difference between the N and H2 atoms of 2N-S7 to its threefold vertex. (c) The change of height difference between the N and H2 atoms from monomer (Δhm) to threefold vertex (Δht), where hN and hH2 are the height from the surface layer to the N and H2 atom, respectively. (d) Differential charge density Δρ for HH and HL configurations on Ag and Au, per the equation Δρ = ρ(sur + 3 mol) − ρ(sur + mol) − ρ(2 mol). Red and blue contours represent charge depletion and accumulation. Download figure Download PowerPoint The charge redistribution upon the formation of the hydrogen bonds can be revealed by the differential charge density Δρ = ρ(sur + 3 mol) − ρ(sur + mol) − ρ(2 mol), where ρ(sur + 3 mol) is the total charge density of a threefold vertex on the surface, ρ(sub + mol) the charge density of the surface with one single 2N-S7 molecule, and ρ(2 mol) the charge density of the other two 2N-S7 molecules. Here, Δρ represents the influence from the other two 2N-S7 molecules on the charge distribution of one 2N-S7 monomer and indicates qualitatively the strength of the hydrogen bond.37,38 The calculated Δρ in the marked area (rectangle in Figure 6d) is shown for threefold vertices with HH and HL configurations. On Ag(111), Δρ is comparable for both HH and HL configurations. However, on Au(111), there is pronounced change of Δρ as indicated by the larger contour of the charge depletion (red) in the N–H bonding area for the HH configurations. Finally, the strength of the hydrogen bond can also be reflected by its bond length. As marked by the dashed lines, the calculated N–H distance of the hydrogen bonding in the threefold vertices with the HL configurations on Ag is 1.7 pm shorter than that of the HH configurations. In contrast, in the case of Au the N–H distance of the vertex with the HH configurations is 9.5 pm shorter than that of the HL. These values suggest that the hydrogen bonding is very strong in the vertices with the HH conformation on Au substrate so that no helical conformation switching is observed on it. While on Ag(111), although the hydrogen bonding of HL conformation is a little bit stronger than that of the HH conformation, they are almost comparable with each other and neither helical conformation is overwhelming. This is the reason why we can observe the helical conformation switching between HH and HL configurations on Ag(111) surface. Conclusion The dynamics of 2D molecular networks are revealed by STM and nc-AFM measurements with submolecular spatial resolution. In combination with the theoretical calculations, the role of hydrogen bonds for the molecular conformation dynamics in the molecular networks is unveiled. The observed helical conformation tuning in our study can be applied as a possible route to realize molecular switches in a 2D hydrogen-bond network. In future, it will be of great interest to employ molecules with dynamic conformation in their molecular architecture, whose various molecular conformations can be employed as storage bits, and the stored information can be inputted and extracted by controlling and detecting the conformation in the molecular network. Supporting Information Supporting Information is available and includes details for the synthesis of S7 and 2N-S7 molecules, X-ray crystallographic data of S7 and 2N-S7, conformations of S7 and 2N-S7 monomers on the surfaces, theoretical details, adsorption site analysis of 2N-S7 network on Ag(111), the analysis of switching rates, calculated trimers with different conformations on surfaces, and 2N-S7 molecules on Cu(111) surface. Conflict of Interest There are no conflicts to declare. Acknowledgments The author P.Y. gratefully acknowledges the financial support from the Science and Technology Commission of Shanghai Municipality (no. 20ZR1436900) and ShanghaiTech start-up funding. References 1. He Y.; Ye T.; Su M.; Zhang C.; Ribbe A. E.; Jiang W.; Mao C.Hierarchical Self-Assembly of DNA into Symmetric Supramolecular Polyhedra.Nature2008, 452, 198–201. Google Scholar 2. Rappas M.; Schumacher J.; Beuron F.; Niwa H.; Bordes P.; Wigneshweraraj S.; Keetch C. A.; Robinson C. 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A.; W.; M.; of by Google Scholar Information & Chemical probe author P.Y. gratefully acknowledges the financial support from the Science and Technology Commission of Shanghai Municipality (no. 20ZR1436900) and ShanghaiTech start-up funding.