Direct Imaging of Photoswitching Molecular Conformations Using

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Direct Imaging of Photo-Switching Molecular Conformations Using Individual Metal Atom Markers Mihael A. Gerkman, Sapna Sinha, Jamie H. Warner, and Grace G. D. Han ACS Nano, Just Accepted Manuscript • DOI: 10.1021/acsnano.8b08441 • Publication Date (Web): 06 Dec 2018 Downloaded from http://pubs.acs.org on December 6, 2018

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Direct Imaging of Photo-Switching Molecular Conformations Using Individual Metal Atom Markers Mihael A. Gerkman1, Sapna Sinha2, Jamie H. Warner2, Grace G. D. Han1* 1Department

of Chemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA

2Department

of Materials, University of Oxford, 16 Parks Road, Oxford, OX1 3PH, United Kingdom

Email: [email protected]

Abstract Photo-switching behavior of individual organic molecules was imaged by annular dark-field scanning transmission electron microscopy (ADF-STEM) using a highly electron beam transparent graphene support. Photo-switching azobenzene derivatives with ligands at each ends containing single transition metal atoms (Pt) were designed (Pt-complex), and the distance between the strong ADF-STEM contrast from the two Pt atoms in each Pt-complex is used to track molecular length changes. UV irradiation was used to induce photo-switching of the Pt complex on graphene, and we show that the measured Pt-Pt distances within isolated molecules decreases from ~2.1 nm to ~1.4 nm, indicative of a trans-to-cis isomerization. Light illumination of the Pt-complex on the graphene support also caused their diffusion out from initial clusters to the surrounding area of graphene, indicating that the light-activated mobilization overcomes the inter-molecular van der Waals interactions. This approach shows how individual isolated heavy metal atoms can be included as markers

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into complex molecules to track their structural changes using ADF-STEM on graphene supports, providing an effective method to study a diverse range of complex organic materials at the single molecule level.

Keywords: photo-switch, azobenzene, heavy atom marker, annular dark-field scanning transmission electron microscopy, direct imaging, graphene support

Photo-switching molecules, which reversibly isomerize under irradiation of light, have been of interest to diverse applications including liquid crystal assembly,1-3 sensing,4-7 surface functionalization for controlling hydrophilicity,8-10 drug delivery,11 and modulation of porous materials12 due to their reversible change in various properties such as polarity, reactivity, and molecular length. Many photo-switching systems, such as spiropyran,13 diarylethene,14 azobenzene,10,12,15 donor-acceptor Stenhouse adduct,16 norbornadiene,17 and diruthenium fulvalene complex,18 have been widely investigated for the fundamental understanding of their photophysics and for practical applications, and mostly optical methods and NMR studies19-21 were employed to verify the quantitative change of population between their photoisomers. Based on the different UV-Vis spectrum of isomers and chemical shifts that are indicative of respective isomers, we can predict the molecular structure changes that occur in dilute solutions. In rare cases, some molecules such as perfluorinated azobenzene can be crystallized after light-activation,22 which allows us to elucidate the structure of well-aligned metastable isomer, i.e. cis conformation of such molecule. Despite the direct and clear visualization of photoisomeric structures, crystallography often requires slow sample preparation which relies on molecular self-assembly


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and generally fails to capture metastable isomers due to their non-planar structures and relaxation to ground-state isomers. In the last two decades techniques for imaging individual small molecules have advanced significantly with scanning tunneling microscopy (STM),23-26 non-contact atomic force microscopy (nc-AFM),27-30 and aberration-corrected transmission electron microscopy (ACTEM),31 as the leading approaches. Despite being widely used for imaging broad shapes of small molecules as well as polymers, STM is generally limited by its resolution which is insufficient for imaging individual atoms. In contrast, nc-AFM offers higher resolution which can distinguish atoms and bonds in a given molecule using atomically sharp tips such as a carbon monoxide molecule.32,33 However, long acquisition time (e.g. 15 to 30 minutes)30 required for imaging a small molecule by nc-AFM makes it challenging to analyze many molecules for statistical studies and to capture transient molecules such as metastable photoisomers of molecular switches. AC-TEM offers the highest spatial resolution out of these techniques, but faces the challenge of obtaining sufficient contrast from small carbon molecules against the supporting substrate during phase-contrast TEM, which is often amorphous carbon. Graphene supports offer an improvement to this by their monolayer nature, but always contain surface carbon residues that can originate from the TEM vacuum chamber and from the specimen.34 The carbon residue acts to bind deposited molecules due to their higher surface affinity and dangling bonds. Annular darkfield scanning transmission electron microscopy (ADF-STEM) offers non-linear contrast with atomic number, but has the challenge of low scattering cross sections of light carbon elements on graphene supports. ADF-STEM has been used effectively to image a wide range of low dimensional materials such as graphene,35 hBN,36 2D transition metal dichalcogenides37 and quantum dots,38,39 and also for organic materials that are decorated with heavy atoms.40 It also has 3 ACS Paragon Plus Environment

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been used to locate the positions of heavier metal atoms on supports that act as single atom catalysts.41 In complex small molecules, the ability to incorporate multiple single heavy metal atoms at sites spread out across the molecule will provide marker points that can be rapidly detected using high angle ADF-STEM (HAADF-STEM). Furthermore, if the molecules exhibit conformation changes, then the positions of the heavy metal marker atoms will also shift and can be captured to reveal the structural changes. Here, we explore how ADF-STEM can be used to track the structure and photo-switching behavior of heavy metal atom-decorated molecular switches, which can shed light on understanding solid-state transient molecular movement of individual photo-switches as well as those as a group. We use graphene as the substrate and design shape-changing molecular switches based on an azobenzene moiety connected to terpyridine ligands for binding heavy atoms such as Pt. The significant molecular length change between linear trans isomers and bent cis isomers can be detected by ADF-STEM due to the presence of Pt atoms that are easily distinguished from graphene substrate. Image simulations of various conformations, orientations, and packing structures of molecules allows us to identify the states of molecules. The direct imaging of photoswitching induced changes is captured, providing significant confirmation of molecular-level interactions among photo-switches and light-activated diffusion, which were suggested from prior studies of bulk materials under light illumination.


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Results and Discussion

Design and Synthesis of Photo-Switches with Metal Atom Markers

Figure 1. (a) Synthetic scheme for azobenzene-bridged bis(terpyridine) Pt(II) complex (compound 2). Insets show the photos of respective compound. (b) Expected structures of compound 2 in two isomeric states (trans and cis) and intramolecular distance between Pt atoms for each structure. The trans-to-cis isomerization of molecule is triggered by UV irradiation, and the reverse direction is thermally triggered in our study. Visible light irradiation can also induce cis-to-trans isomerization. (c) UV-Vis spectra of compound 1 in CH2Cl2 before (black curve) and after (red curve) UV irradiation for 40 min. The original spectrum was recovered after leaving the UV-charged solution in dark at 20 oC overnight. (d) UV-Vis 5 ACS Paragon Plus Environment

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spectra of compound 2 in DMSO before (black curve) and after (red curve) UV irradiation for 10 hrs. The original spectrum was recovered after leaving the UV-charged solution in dark at 20 oC for 5 hrs. (e) Powder X-ray diffraction pattern of 2 trans which shows the crystalline nature of as-produced compound.

We designed an azobenzene derivative consisting of terpyridine groups and transition metal complexes on each end of molecule (Figure 1(a)), inspired by the work of Nishihara and others who explored the metal-chelating azobenzene ligands and their photo-physical properties. We synthesized bisplatinum compound 2, following a procedure that was used for a similar compound42,43 (Supporting Scheme S1) which possesses asymmetric structure with a terpyridine group and a platinum complex. The synthesis successfully yielded trans isomers of azobenzenebridged bis(terpyridine) Pt(II) complex which is expected to have approximately 2.1 nm distance between two platinum atoms within a molecule, based on the molecular model (Figure 1(b)). Upon UV absorption, the compound 2 is expected to switch to its cis conformation, if the photoswitching is successful. The suggested structure of cis compound 2 has two platinum atoms that are approximately 1.4 nm apart. The relaxed structures presented here follow general photoswitching dynamics of azobenzene derivatives which have relatively planar structure in the ground state (trans isomer) and twisted structure in the metastable state (cis isomer).21 The photo-switching dynamics of pristine ligands and platinum complexes in solution state were first measured by UV-Vis spectroscopy while irradiating the samples by an external UV source (365 nm, 100 W), using a 4-side open cell which is temperature- and stirring-controlled. The comparative absorption spectra of trans and cis isomers are shown in Figure 1(c) and 1(d), which mainly indicates the decrease of π-π* transition band of each compound around 350-400 nm during UV charging. Although the complete conversion of trans isomers was challenging, due to the low solubility of highly symmetric molecules in most of organic solvents, we were able to 6 ACS Paragon Plus Environment

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identify the trans-to-cis isomerization occurring in solutions under UV irradiation and cis-to-trans reversion during thermal treatment in dark. The powder X-ray diffraction patterns (Figure 1(e)) show the crystalline nature of trans compound 2 as synthesized, and the significant peaks at 2θ of ~30 o correspond to d spacing of ~3 Å. The schematic crystal models of compound 2 are shown in Supporting Figure S1 to help illustrate the molecular packing through π-π interaction, based on a crystal structure of a similar Pt-bearing azobenzene derivative.42

Direct Imaging of Photo-Switching Molecules

Figure 2. (a) Top view of atomic models of compound 2 in cis and trans isomeric states on a monolayer graphene substrate which is used for TEM studies. (b) Side view of the models in (a) showing relatively planar structure of trans and twisted structure of cis. Blue arrow in (a) indicates viewing direction. (c) 3D view of the models in (a) showing the trans structure that has a larger contact area with the underlying graphene substrate and the cis structure that has minimal contact area with graphene. (d) Multislice HAADF image simulation based on the atomic model in (a) showing high contrast from the heavy Pt atoms in the 7 ACS Paragon Plus Environment

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molecules. (e) Line profile from the yellow boxed area in (d), as indicated with red line, of compound 2 in cis form and (f) Line profile from the yellow boxed area in (d), as indicated with red line, of trans form, indicating Pt-Pt distances measurable at high resolution. (g-l) Side and top views of 2 cis for a range of different orientations relative to the graphene support and the respective HAADF image simulation below. The numbers indicate various Pt-Pt distances obtainable from cis isomers by line profile measurements.

In order to understand the contrast expected for these molecules on a graphene support using HAADF-STEM imaging, we first conducted a series of multislice image simulations with different orientations and configurations relative to graphene (Figure 2). Figure 2(a)-(c) show the configurations of trans and cis compound 2 on a monolayer graphene support. Relatively planar trans isomers will have significant π-π interaction with the underlying graphene support due to the large contact area, while twisted cis isomers will have decreased interaction due to smaller contact area. One potential configuration of cis isomer which has minimal interaction with graphene is shown in Figure 2(c). The multislice simulated HAADF-STEM images of the representative isomers are shown in Figure 2(d) which shows strong contrast from Pt atom pairs that are used to identify a single molecule. Figure 2(e)-(f) show the line profiles across each molecule, and the measured distance between two Pt atoms contrast feature in each molecule matches with the molecular models in Figure 1(b). While the trans molecule is presumed to be present in the suggested conformation on graphene, there are various feasible configurations of cis isomer due to its non-planar structure. Figure 2(g)-(l) provide possible orientations of cis isomers on graphene with increasing degree of π-π interaction towards graphene. The simulated HAADF-STEM images suggest that Pt-Pt distance can vary between 0.99 and 1.4 nm in the depicted cases, and we predict that slightly broader range of Pt-Pt distances will be shown in experiments due to the freedom of rotation around single bonds in the molecular structure. 8 ACS Paragon Plus Environment

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Figure 3. (a) Low magnification HAADF-STEM image of compound 2 deposited on monolayer graphene showing clusters of molecules. (b) Magnified view of the yellow square box from (a), showing highly dense areas and relatively empty space. (c) Magnified view of the yellow rectangular box from (b) where an isolated molecule bearing two Pt atoms was found. The distance between two bright dots is 2.3 nm. (d) High magnification HAADF-STEM image of graphene substrate where darker area (marked by yellow dot) is composed of pristine graphene with hexagonal carbon lattice and lighter area (marked by green dot) is 9 ACS Paragon Plus Environment

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covered by amorphous carbon. (e) Image showing another area with high coverage by amorphous carbon (marked by green dot), central graphene area (marked by yellow dot) and Pt-containing species preferentially stuck on amorphous carbon (marked by red box). (f) An area containing many isolated molecules. (g-k) Line profiles measured on each molecule in (f) and the corresponding distances between two Pt atoms in each color-coded molecule. The distance ranges from 1.8 nm to 2.4 nm, similar to the expected distance of 2.1 nm for trans isomer.

As-prepared compound 2 was dissolved in MeOH, and a dilute solution was dropcast to a TEM grid containing monolayer graphene suspended across lacey carbon mesh Cu TEM grid. After evaporating the solvent at 60 oC, the sample was observed by HAADF-STEM using a low accelerating voltage of 80 kV to reduce electron beam induced knock-on damage. Low magnification HAADF-STEM imaging of the sample, Figure 3(a), showed bright round particles visible on graphene as a result of clustering of compound 2. A magnified view, Figure 3(b), shows particles with various size and density as well as a dark area where the chance of finding isolated molecule is higher. In regions away from the dense clusters, we commonly found two Pt atoms isolated from other bright features (Figure 3(c)), indicating the presence of a single molecule of compound 2. The distance between two Pt atoms was measured to be 2.3 nm which is slightly larger than the predicted value of 2.1 nm. We conducted an elemental analysis in the form of large area EDX (Supporting Figure S2) which confirms the significant Pt content along with carbon and Cu signals from the TEM grid as well as minor Cr impurity. In order to further support the identification of Pt atoms by their strong contrast relative to graphene support and light element impurities such as Cu, Cr and Si atoms, we compared the ADF-STEM signal of those elements (Supporting Figure S3) and also provided multislice image simulations (Supporting Figure S4), which shows significantly higher contrast from the Pt atoms than others due to the high z number 10 ACS Paragon Plus Environment

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of Pt. A control experiment of ADF-STEM imaging which investigates Rh-containing azobenzene derivatives (Supporting Figure S3 and S4) instead of compound 2 shows the weaker distinction between Rh atoms and other impurities, reinforcing the benefit of incorporating high z number atomic markers such as Pt. The HAADF-STEM image contains low contrast regions associated with clean monolayer graphene (yellow spots in Figure 3(d) and 3(e)), and higher contrast regions where thin amorphous carbon is adhered to the graphene surface (green spots in Figure 3(d) and 3(e)). The amorphous carbon substance can be generally seen in high-resolution TEM studies on graphene or 2D materials, and complete removal of the amorphous feature is very challenging even after high temperature annealing under H2 condition.44,45 It comes initially from the polymer used to transfer the graphene to the TEM grid, but even after complete removal of the surface carbon at high temperature, it will redeposit from exposure to the atmosphere and is an inevitable part of graphene that must be considered when studying surface interactions. Deposited organic molecules prefer adhesion to amorphous carbon than graphene (Figure 3(f)) as previously shown in other studies that also included metal deposition.44,46 The isolated molecules found in various areas away from the clusters had an average measured distance between nearest Pt atoms of ~1.8 nm, which is slightly reduced from the image simulation results for the planar trans conformation (Figure 2(d)). The slight variation of distance is considered to be inherent in TEM studies of organic molecules, as the electron beam can fragment organic substances containing weak bonds,47 N=N bond in this case, and the fragmented pieces can translate over time (Supporting Figure S5). The uneven substrate of amorphous carbon substance can also contribute to outer-plane distortion of molecules, resulting in the reduced molecular lengths. Furthermore, in ADF-STEM imaging sample scan drift can also lead to broadening of the distribution of measured distances. The Pt11 ACS Paragon Plus Environment

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containing molecules can be stationary or mobile depending on their local environment, and the movement of individual Pt atoms was seen during the analysis of consecutively taken images on the identical location. The split azobenzene molecules can exhibit two Pt atoms that are shifted either closer or more separated, as compared to intact molecules, after brief moment (45-50 sec) in dark between consecutive imaging. Care was taken to perform ADF-STEM imaging under lowdose conditions to minimize damage and to only use measured data from the first images taken of an area. More isolated trans compound 2 were found and analyzed (Supporting Figure S6), and the identification of isolated molecules was carefully conducted in order to prevent false assignment of Pt atoms that belong to one molecule. Inevitably, most of areas with low population of molecules still possess many Pt atoms that are closely located in nm scale, which makes multiple interpretations possible for the identical set of Pt atoms. Therefore, we excluded any area that locally contains more than two Pt atoms from the molecule assignments. Single isolated Pt atoms that are away from the nearest Pt atom by >2.5 nm were considered to be mono-Pt-containing fragment and excluded from analysis as well. Unambiguously assigned molecules (Supporting Figure S6) from moderately populated areas have a distribution of Pt-Pt distance ranging from 1.0 nm to 2.2 nm, which indicates flexible molecular structures which can adapt to local environment and the impact of electron beam-induced damage on organic molecules. However, more welldefined areas as shown in Figure 3(c) and 3(f) represent ideal imaging of isolated molecules in trans conformation.


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Figure 4. (a) ADF-STEM image of an isolated molecule found after photo-activation on graphene substrate. (b) Line profile across the molecule, showing the distance between two Pt atoms to be 1.4 nm. (c) Isolated molecules found near a crystalline particle. (inset) Magnified view of yellow box area and distances measured for each molecule. (d) An area showing two isolated molecules clearly. (e) Distance measured per molecule is displayed. (f) An area where isolated Pt atoms are found but clear identification of each molecule is challenging due to the close proximity of multiple Pt atoms (upper part of image). Distance was measured only for clear molecules while upper part is excluded from interpretation due to the multiple 13 ACS Paragon Plus Environment

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possibilities. (g) Histogram of Pt-Pt distances measured for 28 isolated molecules found before light activation. The average and standard deviation of the distribution is shown. (h) Histogram of Pt-Pt distances measured for 28 isolated molecules found after light activation. The average and standard deviation of the distribution is shown.

The photo-response of isolated molecules on a TEM grid to UV light (365nm) exposure was examined by directly illuminating the grid for 10 min and then loading it immediate into the TEM for HAADF-STEM imaging (Figure 4). Overall, we found the average distance between Pt atom pairs had reduced compared to beforehand (Figure 4(g) and 4(h)). Figure 4(a) shows a typical HAADF-STEM image of an isolated compound 2 after photo-activation, and the measured distance between Pt atoms corresponds to 1.4 nm (Figure 4(b)), consistent to one of the cis isomer configurations on graphene as shown in Figure 2(f). Other examples of isolated molecules found near a molecular cluster (Figure 4(c)) shows a few molecules bearing Pt-Pt distances between 0.9 nm and 1.5 nm (inset) indicating shorter Pt-Pt distances compared to initial trans isomers. Another area containing two isolated molecules (Figure 4(d)) also presents Pt-Pt distance of 1.4 nm (Figure 4(e)), matching with the expected values for a cis conformation from image simulation in Figure 2. We note that there are still uncharged compound 2 found after photo-switching process, as shown in Figure 4(f) where isolated molecules with Pt-Pt distances of 2.1 nm and 1.8 nm are indicative of remaining trans isomers. The photo-switching process of azobenzene molecules in solution by the excitation of π-π* band (near 365 nm) is known to have low quantum yields (ca. 10%).48,49 While the saturation % of cis isomers upon UV absorption varies depending on molecular designs, solvents, concentrations, duration of illumination, and so on,15 it is generally known that over 90% of cis population in azobenzene isomeric mixtures can be achieved upon extended irradiation, with negligible degradation even after tens of hours of continuous exposure 14 ACS Paragon Plus Environment

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to UV light.19,21,22 Given the extremely low concentration of molecules on the TEM grid and the absence of solvent, which may interfere with photo-switching by absorbing incident light, we illuminated the grid for 10-15 min in proximity to UV source (~ 5cm). Figure 4(g) and 4(h) display histograms of Pt-Pt distances measured for total 20 and 21 isolated molecules (Supporting Figure S6 and S7) before and after photo-excitation, respectively. Both show broad distribution of Pt-Pt distances inferring the presence of mixed isomeric states (trans and cis) as a result of intrinsic equilibrium between isomers and incomplete light activation. The statistical average of each distribution is shifted, however, from 1.8 nm to 1.4 nm after light illumination. Even though the electron beam-induced degradation of molecules can contribute to further broadening of distribution, the overall decrease of Pt-Pt distances can point towards the impact of light activation. The photo-switching of azobenzene derivatives, both organic and transition metal complexes, have been extensively studied in solution and in solid state due to the effective switching and stability of molecules.50-53 The static imaging of individual molecules and the switching behavior can provide fundamental support to the previous observation of photoactivated physical property changes in bulk.


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Imaging of Molecular Diffusion and Ordering

Figure 5. (a) ADF-STEM image of initial clusters of compound 2 showing broadly distributed Pt atoms around the clusters of molecules. (b) ADF-STEM image of clusters found shortly after light illumination. 16 ACS Paragon Plus Environment

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The Pt atoms show linear and square orders among them near the clusters. (c) Magnified view of the yellow square box from (b) showing ordered atoms. (d) Line profile measured between two atoms indicated by yellow line in (c). (e) Distances between nearest Pt atoms from (c) surveyed and averaged. (f) Top view of atomic models of compound 2 in cis isomeric states that are packed into anti-parallel fashion maximizing π-π interaction between terpyridine groups. Monolayer graphene substrate which is used for TEM studies is shown. (g) Side view of the models in (f) showing the twisted structure of cis isomers and the packing between them. Blue arrow in (f) indicates viewing direction. (h) Simplified view of (g) showing the first layer of molecules from the side view. (i) Multislice HAADF image simulation based on the atomic model in (f) showing high contrast from the heavy Pt atoms in the molecules and the square order between them. The distance between two Pt atoms marked by yellow line is measured to be 0.5 nm. (j) 3D view of the models in (f) showing the overall arrangement of cis isomers that have strong intermolecular interaction between themselves. (k) Top view of atomic models of compound 2 in cis isomeric states that are packed into parallel fashion. (l) Multislice HAADF image simulation based on the atomic model in (k) showing linear order among the nearby Pt atoms. The distance between two Pt atoms marked by yellow line is measured to be 0.5 nm.

Another interesting feature found near molecular clusters after light activation is dense packing of Pt atoms and some linear/square orders among them as compared to initial images before exposure to light (Figure 5(a) and 5(b)). We believe that the concentrated Pt atoms found near the clusters originate from the diffusion of compound 2 induced by light activation. Prior reports by Norikane, et al.54 describe the mobility of azobenzene derivatives in bulk forms, such as solid-state powder, which translates on water surface as activated by UV. The macroscale experiments infer that azobenzene molecules on the surface of powder convert their structures and polarities and diffuse from the clusters. Our TEM imaging which sheds light on sub-nm scale movement of molecules can support the previous finding. A magnified image of the yellow box in 17 ACS Paragon Plus Environment

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Figure 5(b) is shown in Figure 5(c), emphasizing linear and square packing among Pt atoms, and a line profile between nearest Pt atoms was generated in Figure 5(d). The Pt-Pt distance of 0.45 nm suggests the presence of close-packing between cis isomers and π-π stacking between aromatic moieties. If the individual bright dots were either Pt atoms without organic ligands or those bound to fragmented ligands, the ordered structures and spacing of ~5 Å on average (Figure 5(e)) would not be achieved. Individual metal atoms on graphene or amorphous carbon are prone to aggregate and form larger metallic clusters,55,56 and the metal atoms with short ligands will also form tighter aggregates with less order. The suggested molecular packing structures and simulated TEM images for square and linear packing are shown in Figure 5(f)-(j) and 5(k)-(l), respectively. Atomic models in Figure 5(f) are generated by mostly anti-parallel packing of multiple cis molecules and those in Figure 5(k) reflect parallel packing of three cis isomers, as illustrated in recent work of Barrett, Friscic, and the team.57 We created the models based on the reported crystal structures of parallel and antiparallel-stacked cis azobenzenes, adopting the reported distances between nearest atoms (such as N=N group and the nearest carbon of a phenyl group on the neighboring molecule) in crystal structures and preferred alignment among cis structures. The simulated HAADF images (Figure 5(i) and 5(l)) exhibit short square and linear ordering among Pt atoms found in multiple areas of Figure 5(b). The Pt-Pt distances among 10 pairs of nearest atoms are measured to be 0.54 ± 0.04 nm from Figure 5(i), and those measured for 4 pairs in Figure 5(l) are 0.52 ± 0.01 nm, revealing similarity to the experimental values. More images of densely packed and ordered Pt atoms near clusters following light exposure are displayed in Supporting Figure S8. The impact of amorphous carbon residue on the ADF-STEM imaging of photo-switching organic molecule was studied by generating multislice HAADF simulation of compound 2


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deposited on amorphous carbon substance (Supporting Figure S9). Due to the high affinity of molecules to amorphous carbon compared to pristine graphene surface, the preferential adsorption of compound 2 onto amorphous substance is observed in experiments. As thicker layers of amorphous carbon is present, the distinction of organic backbones from the background becomes challenging, as a result of similar atomic composition and mass between two entities. We note that, therefore, the strategy to place heavy atom markers on organic molecules is essential for the clear observation of subtle photo-switching behavior of azobenzene derivatives.

Conclusions In summary, the design of Pt-decorated azobenzene molecules enables the visualization of small organic molecules by ADF-STEM using monolayer graphene support, which illuminates the subtle structural change of such molecules in response to light. Imaging of the photo-switching behavior can support previous findings on bulk-level solid-state photo-mechanics that operate by collective movement of organic photo-switching molecules. Based on this approach that can distinguish photo-isomeric states, further visualization of nano-scale device operation involving photo-switching nano-mechanical-switches will be feasible. The application of our molecular design and ADF-STEM imaging will particularly support the integration of organic photo-switches and 2D materials and the direct imaging of the dynamically changing device structures for nextgeneration transparent and flexible electronics.


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Experimental Section Methods 1H

NMR spectra were recorded on a Varian instrument 400 MHz and internally referenced to

tetramethylsilane signal or residual protio-solvent signal. Data for 1H NMR are recorded as follows: chemical shift (δ, ppm), multiplicity (s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet), integration, coupling constant (J, Hz). Matrix-assisted laser desorption/ionization timeof-flight mass spectrometry (MALDI-TOF MS) analysis was carried out on Bruker microflex LT instrument. Mass spectrum (MS) of the compound 2 was captured using positive ionization and Dithranol was used as the matrix.

UV-Vis Absorption Spectroscopy UV-Vis adsorption spectra were obtained with a Cary 50 Bio UV-Vis Spectrophotometer in a UV Quartz cuvette with a pathlength of 10 mm. Compounds were dissolved in chloroform (Compound 1) or DMSO (Compound 2). The UV-Vis absorption was first recorded in dark for 10 minutes, then samples were irradiated with a UV lamp (365 nm, 100 W) until no change in their absorbance was observed. After the UV lamp was turned off, the samples were monitored in dark until the original spectra were obtained.

Annular Dark Field Scanning Transmission Electron Microscopy Room-temperature ADF-STEM imaging was performed using a JEOL ARM200F at 80 kV located at the David Cockayne Centre for Electron Microscopy (DCCEM) within the Department of Materials at the University of Oxford. Imaging conditions used were a 30 μm CL aperture with a


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convergence semiangle of 22.5 mrad and a beam current of 35pA. The acquisition angles for these images were 72.8–271 mrad.

TEM Sample Preparation and Measurement Graphene was grown by chemical vapor deposition (CVD) on a copper foil catalyst substrate. The copper foil was sonicated in a hydrochloric acid solution (HCl, 1 mol/L) to remove oxides on the surface and then sonicated in DI water, acetone, and isopropanol (IPA) for 5 min each to remove organic residues. 1% Methane in argon (CH4), 25% hydrogen in argon (H2), and 100% argon (Ar) were used for graphene growth. The system was first purged with 1000 sccm Ar, 500 sccm H2, and 100 sccm CH4 for 30 min. The furnace was then heated to 1060 °C with a ramp rate of 50 °C/min accompanied by a flow of 500 sccm Ar and 100 sccm H2. When the temperature reached 1060 °C, the copper was annealed with the same flow rate for 1 h. Following the annealing process, the synthesis was carried out at 1060 °C for 1 h with a flow of 500 sccm Ar, 100 sccm H2, and 5 sccm CH4. The furnace was moved to enable rapid cooling of the sample to room temperature. For TEM grid preparation, the as-grown CVD graphene on copper substrate was spin-coated with PMMA. The copper was subsequently etched by using APS solution. Graphene was then transferred onto a lacey carbon 400 mesh Cu TEM grid using the PMMA support. It was then heated in vacuum at 160 oC for a few hours. PMMA was removed by using acetone and then the leftover residues were cleaned by using Ar/H2 and vacuum annealing. Compound 2 in MeOH (1 mg /mL) was dropcast onto the graphene, and the TEM holder was baked in vacuum at 60 °C to remove all the solvents from the surface. For UV charging, a UV lamp with 365 nm LEDs was used, and the irradiation was conducted for 10-15 min directly onto the TEM grid.


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Energy dispersive x-ray spectroscopy (EDX) EDX was taken using a JEOL 2100 TEM operated at 200kV in bright field mode from an area of ~200nm in diameter. Pt molecules were deposited on graphene that was transferred on lacey carbon Cu mesh TEM grids, as mentioned before.

Associated Content Supporting Information The Supporting Information is available free of charge on the ACS Publications website. Notes The authors declare no competing financial interest Acknowledgements J. H.W. thanks the support from Royal Society.


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ToC graphic


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