Controlling Growth to One Dimension in Nanoislands of Ferrocene

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Controlling Growth to One Dimension in Nanoislands of Ferrocene-Sugar Derivatives Prithwidip Saha, Khushboo Yadav , Shibin Chacko, Anijamol T Philip, Ramesh Ramapanicker, and Thiruvancheril G. Gopakumar J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.6b00774 • Publication Date (Web): 11 Apr 2016 Downloaded from http://pubs.acs.org on April 16, 2016

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The Journal of Physical Chemistry

Controlling Growth to One Dimension in Nanoislands of Ferrocene-Sugar Derivatives Prithwidip Saha,† Khushboo Yadav,† Shibin Chacko,†,‡ Anijamol T. Philip,† Ramesh Ramapanicker,† and Thiruvancheril G. Gopakumar∗,† Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India E-mail: [email protected] Phone: +91 5122596830. Fax: +91 5122596806

Abstract Ferrocenyl-Alkyl-Protected Sugar (Fc-Sug) and Ferrocenyl-Oxo-Alkyl-Protected Sugar (Fc-Oxo-Sug) were deposited on the basal plane of Highly Oriented Pyrolytic Graphite (HOPG) using a drop casting method. Ultra-thin films of these molecules were investigated using Atomic Force Microscopy to understand the growth at low coverage. Both molecules are forming highly ordered one dimensional molecular islands, which are growing from a dimer building block. The dimer and inter-dimer interactions (along the length of islands) are stabilized by –C2 O.... H–C hydrogen bonding. Unlike for FcSug, the islands of Fc-Oxo-Sug are extended to tens of micrometers and the growth is only limited by terrace edges or other islands on surface. This exceptional growth of islands are understood in terms of an additional –C=O.... H–C– hydrogen bonding leading to stronger inter-dimer interactions along the length of the islands compared to Fc-Sug. ∗

To whom correspondence should be addressed Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India ‡ Current Address: Department of Bio-Chemistry, Brandeis University, Boston, USA †

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Introduction Right from its discovery ferrocene (Fc) and its derivatives are well known for their catalytic applications. 1 Recently, derivatives of Fc have attracted interest in molecular thin film based electronic applications due to the redox activities of Fc. 2–5 The electrochemical potential of Fc is highly sensitive to the group attached to cyclopentadienyl (Cp) rings. 4 Thin film transistors based on Fc derivatives have been realized recently. 6,7 Adsorption induced modifications in the electronics structures of few Fc derivatives have been investigated and the electronic properties are showing their potential applicability in molecular electronics. 8–10 The quality (defect free) and structure of such molecular two dimensional adlayers on surface are decisive in their applications. The adlayer patterns, which in turn are controlled by intermolecular interactions, influence their electronic structure. 11–13 Molecules with electronic functions – diodes, switches – show strong dependency between molecular adlayer patterns and their electronic functions. 6,14–16 Several Fc derivatives have been studied on surface and show excellent two dimensional patterns. 17–23 The stability and symmetry of these patterns are controlled by the chemical nature of groups attached to Fc. Here, we present one dimensional growth of a Fc derivative – controlled by selective hydrogen bonding – over the expected 2D growth. Ultra-thin films of Ferrocenyl-Alkyl-Protected Sugar (Fc-Sug) and Ferrocenyl-Oxo-Alkyl-Protected Sugar (Fc-Oxo-Sug) molecules (cf. Figures 1a and 2a ) on the basal plane of highly oriented pyrolytic graphite (HOPG) were investigated using an Atomic Force Microscopy (AFM). Due to high diffusion rate, metallocenes (Mc) form ordered patterns on surface only at low temperatures. 9,17 To reduce the diffusion anchoring groups are attached to Mc and these derivatives show ordered adlayer at room temperature. 18,21 Ferrocenyl Alkyl-Protected Sugar molecules are chosen here due to its long-term chemical inertness at ambient conditions over molecule with unprotected sugar and are offering reasonable number of oxygen atoms for hydrogen bonding. Fc-Sug molecules grow into very regular islands with well defined growth facets at sub-monolayer coverage. The growth is unidirectional and forms long nanoscale islands aligned along a lattice di2 ACS Paragon Plus Environment

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rection of graphite. Fc-Oxo-Sug shows similar unidirectional growth as Fc-Sug. Strikingly, the islands are growing exceptionally long and the growth is limited only by terrace edges and other islands. Typical scan areas of 10 µm is revealing islands whose length extending to tens of micrometers. The width of islands (typically 200 nm) increases only with high surface coverage of molecules suggesting a high preference for the growth along the length of islands. Using density functional theory (DFT) calculations and high resolution images, a microscopic structural model is proposed. A –C=O.... H–C– inter-dimer interaction seems to be at the origin of the unexceptional length of Fc-Oxo-Sug islands.

Experiment All measurements were performed using Agilent 5500 Scanning Probe Microscope in soft tapping mode. PPP-NCH silicon cantilevers from Nanosensors were used as AFM probes. The resonance frequency of cantilever during the imaging was ≈ 300 kHz and the typical force constant at this frequency range is around 30 − 34 N/m. Processing of images were carried out using WSxM from Nanotec. Ultra-thin films were prepared by drop casting methanolic (Fisher Scientific) solution of Fc derivatives to freshly cleaved HOPG (ZYB grade from µmasch). Typical concentration of methanolic solution was in the order of 10−6 M. Methanol with purity > 99.9 % was used for the preparation of all solution and no further purification was employed. 3–4 µL of the methanolic solutions of ferrocene derivatives were drop casted on freshly cleaved HOPG surface and dried (few minutes) in ambient condition and performed AFM studies. Relative humidity (≈ 50 %) and temperature (22–25 0 C) of the room was controlled by air conditioning. While drop casting, the sample was kept ≈ 300 to ensure a smooth flow of the solvent over the substrate. Pure methanol was studied on freshly cleaved HOPG surface (drop casted and dried in ambient condition as mentioned above) and no ordered patterns of solvent was observed. Freshly cleaved HOPG was also characterized prior for comparison of the contrast of clean terraces and terrace edges in both phase and



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topography. Fc-Sug and Fc-Oxo-Sug were synthesized from 2-ferrocenyl-1,3-dithiane 24 and the details are provided in SI.

Results and Discussion DFT (B3LYP/6-311G) optimized geometry of Fc-Sug is depicted in Figure 1a using a ball and stick model. Figures 1b and c display typical AFM phase images of drop-casted ultrathin film of Fc-Sug molecules on HOPG(0001) plane. 25 The coverage in Figures 1b and c is ≈ 0.1 and ≈ 0.5, respectively. 25 Few terrace edges are marked with green dashed lines in the images for visibility, which are appearing bright in phase image. Two types of molecular islands are visible in the images: 1. Islands with irregular boundary (few islands are marked with white line), which are appearing bright (positive phase shift with respect to set-point) in the phase images. These islands are assigned as amorphous due to its irregular boundaries and height distribution; 2. Islands with well defined boundaries (few islands are marked with magenta dashed parallelograms), which are appearing dark (negative phase shift) in the phase images. 26 These islands are identified as crystalline due to the following reasons. They have well defined growth facets (cf. Figures 1d and 3a) and the long edge of islands are aligned along three typical directions on surface (indicated by arrows). A statistical analysis (provided in SI) indicates that these directions are related to the symmetry of the surface. In addition, high resolution images (Figures 1d and 3) show periodic pattern within the islands and is suggesting a molecular level ordering. The apparent height of islands is 0.6 ± 0.1 nm and is typical for monolayer. The striking observation is that the islands are growing along one direction. The typical width of the islands is ranging between 150–200 nm where as the length is reaching to a maximum of 700 nm within the observed coverage. This width has a clear correlation with the surface coverage of molecules, that is, islands grow one dimensionally (1D) at lower coverage. It is to be noted that in addition to amorphous and crystalline islands small clusters (few encircled) are also observed.


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b

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ter

ste

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Figure 1: (a) shows the ball and stick model of DFT optimized geometry of Fc-Sug. (b) and (c) are constant-force AFM phase images of islands of Fc-Sug on HOPG (0001). Graphite step edges appear white in phase image and few are marked with green dashed lines. Crystalline molecular islands show negative phase shift (dark) and few are indicated with magenta dashed parallelograms. Three arrows are indicating the growth directions of molecular islands. Amorphous islands shows high phase shift (bright), which are either small clusters (encircled) or large irregular islands (marked with white boundary). (d) Constant-force AFM topography of two crystalline monolayer islands on a single terrace. θ marks angle between the long edges of islands and α marks the facet angle (angle between the growing faces of island). The indicated θ and α are ≈ 600 and ≈ 1000 in the image. Molecular rows are visible within the crystalline islands (see text for details).



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a Fe C

O

H

Fc-Oxo-Sug

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d

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2 mm

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Figure 2: (a) shows the ball and stick model of DFT optimized geometry of Fc-Oxo-Sug. (b) and (c) are constant-force AFM phase images of islands of Fc-Sug on HOPG (0001). Graphite step edges are marked with green dashed lines. Crystalline molecular islands shows negative phase shift (dark) and few are indicated with magenta dashed polygons. Three arrow pairs (white and magenta; rotated by ≈ 60 ) are indicating the growth directions of molecular islands. Amorphous islands show high phase shift (bright), which are either small clusters (encircled) or large irregular islands (marked with white boundary). (d) Constant-force AFM topography of marked region in (c). Long edges of two islands (not parallel) are marked with dashed magenta and white lines and are rotated with respect to each other by ≈ 60 . The indicated islands are mirror domains, which are observed in addition to rotational domains.


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The striking preference for growth in one direction for Fc-Sug islands triggered us to perform the study with slightly modified Fc-Sug molecules. We have introduced an oxo group adjacent to Ferrocene unit in the alkyl chain (cf. Figure 2a, Fc-Oxo-Sug). Typical constant-force AFM phase images of sub-monolayer coverage of Fc-Oxo-Sug from different regions are shown in Figures 2b and c. The coverage in Figures 2b and c is ≈ 0.5 and ≈ 0.6, respectively. Interestingly, the crystalline islands are growing in one dimension but the length of islands are limited only by step edges (green dashed lines) or by other islands. The islands are growing as long as 10 µm at the given coverage (0.5). For Fc-Sug at 0.5 ML coverage the maximum length of islands is ≈ 700 nm. This indicates a very high preference for one dimensional growth for Fc-Oxo-Sug compared to Fc-Sug. Since the coverage of molecules on the surface is comparable in both cases, we assume that the extended growth of one dimensional islands are due to additional interaction from oxo group. The typical growth directions of islands are depicted in Figure 2c using white and magenta arrows. Figure 2d is a constant-force AFM topography and it shows the height variations of crystalline and amorphous islands. Notably the apparent height of the crystalline islands are slightly larger (0.7 ± 0.1 nm) than that of Fc-Sug. For non-planar molecules, the observed height is consistent to monolayer formation. To understand the relative orientation of islands of Fc-Sug and Fc-Oxo-Sug further with respect to the basal plane of graphite, we have analyzed the angle between long edge of each islands with respect to all other islands in a given AFM image, which is depicted as θ in Figures 1d and 3a. This angle indicates the rotational orientation of islands with respect to each other. 10 AFM images with 4 × 4 µm size were used in both cases for the analysis. The analysis is included in SI, which shows a narrow distribution of rotational angles between the islands for Fc-Sug and peaks at 2 ± 2.50 , 60 ± 50 and124 ± 50 . These angles indicate that the majority of the islands are rotational domains and are growing along a graphite lattice direction. In addition to these major rotational angles, there are minor but significant angles observed in the distribution, at ≈ 27.50 , 900 and1450 . It is surprising that molecules with



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bulky groups (protected sugar in this case) are aligning along a graphite lattice direction. Molecules containing long alkyl chains are known to order with its along the zig-zag carbon chain along the graphite compact directions. 27–29 Several examples of Ferrocene attached to alkyl chains were also shown forming ordered patterns on HOPG surfaces. 30–34 Therefore we assume that the alkyl chain of molecules is aligned along the graphite compact directions ([01¯10], [1¯100] and [¯1010]). 27,30 Interestingly the analysis of θ performed for Fc-Oxo-Sug is showing a broader distribution compared to Fc-Sug (0 ± 150 , 60 ± 100 and120 ± 150 ). Unlike Fc-Sug, the islands of Fc-OxoSug are growing along six directions on surface. Two nonparallel islands are indicated in Figure 2d using magenta and white dashed lines and are rotated by ≈ 60 . This shows that in addition to three rotational domains, each rotational domain is mirrored over a preferred graphite lattice direction giving a total of six domains (broad distribution of θ) Presumably the introduction of oxo group in the alkyl-chain is interrupting the interaction between alkyl chain and graphite and causing such verity of adsorption.

a

b a q

200 nm 0.0 nm

0.0

0.1 nm 4.2 nm 0.0 nm

40 nm 0.6 nm

Figure 3: Constant-force AFM topography of Fc-Sug on HOPG. (a) Islands on adjacent HOPG terraces; α and θ are facet angle and angle between domains, respectively. Both the indicated angles in the image are ≈ 1200 . Inset shows high resolution image of an island; thick and thin arrows depicts adjacent molecular rows. (b) High resolution images of defects in Fc-Sug islands. A missing less-bright row is indicated by a thin red arrow. Terminating bright and less-bright rows are indicated by red arrows, which are facing to each other. A typical high resolution image obtained from an island of Fc-Sug molecule is shown in 8 ACS Paragon Plus Environment

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the inset of Figure 3a. It shows that the islands consist of bright rows which are extending along the length of islands. Thick arrows in the image mark these bright rows. It is to be noted that the height variation is only 0.1 nm between the bright rows (thick arrows) and the less-bright region in between the bright rows (thin arrow). This indicates that the less bright regions (in the following text we refer to it as less-bright row) are not missing molecular rows. To understand this further, we have analyzed high resolution images of regions with spontaneous defects (Figure 3b). The defects are forming either by missing bright or less-bright rows and are extended along the length of the islands. A missing lessbright row is depicted by a red thin arrow. A terminating bright and less-bright rows are indicated by a thick and a thin red arrows pointing against each other. This is suggesting that the adjacent molecular rows vary their apparent height and are appearing as bright and less-bright in the images. We further analyzed the typical distance (perpendicular to the length of island) between adjacent rows of molecules (between bright and less-bright rows) in several molecular islands and found two favorable distances, 2.9± 0.1 and 3.4± 0.1 nm (see SI for statistical analysis). The obtained distance between the rows is approximately double the length of a single Fc-Sug molecule. This is suggesting a dimer based growth and the observed bright and less-bright contrasts are dimer rows. The symmetry of dimer (2-fold) thus tentatively justifies the one dimensional growth of islands. To understand the molecular level growth within the islands further, we have optimized the geometry of free dimers (no surface) with protected sugar group facing against each other. DFT with dispersion correction (DFT-D) was used for the optimization (see details of calculations and dimer geometry in SI). The optimized dimer shows the possible hydrogen bonding between the protected sugar groups and is observed that – C2 O.... H–C– hydrogen bonds are stabilizing the dimers. We used this understanding to propose a tentative model for the one dimensional growth of islands. Two tentative models are proposed and depicted in Figures 4a and b. Optimized isolated molecules were used and the – C2 O.... H–C– hydrogen bonding distance is fixed to 2.5 Å according to the calculations and the Fc-Fc dimer



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a

A B

a

b

A a

B

A

c B a

Figure 4: Tentative model for the observed patterns of Fc-Sug (a, b) and Fc-Oxo-Sug (c). ~ and B ~ as unit vectors. α is the angle Unit cell is marked with a parallelogram with A ~ and B, ~ which is equivalent to the facet angle between adjacent edges of islands. between A Red dashed lines depict the possible hydrogen bonds. Single molecule geometry is optimized using DFT calculations.


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distances (5.9 Å) are fixed according to literature. 35 Hydrogen bonds are indicated using red dashed lines in Figures 4a and b. We refer to the models in Figures 4a and b as oblique and quasi-rectangular patterns, respectively. The major difference between the oblique and quasi-rectangular patterns are the relative orientation of dimers within the molecular dimer rows and the orientation of –O–Me group (marked with oval in Figure 4b) with respect to neighboring molecules. Four hydrogen bonds are feasible in the predicted patterns per unit ~ and B. ~ A ~ is directly correlated to the dimer cell. The lattice vectors are marked as A length, which is 3.17 and 3.21 nm for quasi rectangular and oblique patterns respectively and the perpendicular distance between dimer rows are 2.8 and 3.1 nm. These distances are comparable with the experimentally observed inter dimer-row distance measured perpendicular to the dimer rows. The predicted models clearly show the growth motif and that the inter-dimer hydrogen bonding is most likely the cause for preferred one dimensional growth of Fc-Sug. The angle between the lattice vectors, α in the model may be compared with the experimentally observed α (cf. Figure 3a). Analysis of several islands with well defined growth facets provides two typical α values, 99 ± 20 and 121 ± 1.50 (details of analysis in SI). This experimental parameter was also fixed while generating the models. In the experiment we observed quasi-rectangular pattern as the most abundant. However, the reason for the abundance is not clear at the moment. Unlike Fc-Sug, we could not observe any perfect facets for the islands of Fc-Oxo-Sug since the growth of islands were terminated at terrace edges. However, we have observed detailed fine structure within islands (see SI) as observed for Fc-Sug. The spacing between bright and less bright rows is 3.1 ± 2 nm (see SI for statistical analysis). This observation suggests that Fc-Oxo-Sug is following a dimer based growth as described in the case of Fc-Sug. Figure 4c shows a tentative model obtained for Fc-Oxo-Sug by the same procedure as above. In the case of Fc-Oxo-Sug, the optimized geometry shows that the Cp rings of Fc is facing away from the alkyl chain (cf. Figure 2a). This allows the Cp ring of Fcs to lay parallel to the surface.



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a Fe C

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Figure 5: (a) shows the ball and stick model of DFT optimized geometry of Fc-Oxo-Boc. (b) and (c) are constant-force AFM phase images of islands of Fc-Oxo-Boc on HOPG (0001). Graphite step edges are marked with green dashed polygons. Crystalline molecular islands shows positive phase shift (bright) and few are indicated with magenta dashed polygons. Few of small clusters of molecules are encircled.


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The dimer is stabilized by – C2 O.... H–C– hydrogen bonds as in Fc-Sug. Strikingly, along the dimer rows the molecules are stabilized by additional – C=O.... H–C– hydrogen bonding, giving a total of 6 hydrogen bonds per unit cell (2 for Fc-Sug) along the length of islands. In addition, –C=O is a stronger hydrogen bond acceptor than –C2 O. Therefore the observed difference in the structure for Fc-Sug and Fc-Oxo-Sug, especially the extended growth in one direction is concluded due to the inter-dimer hydrogen bonding interactions along the length of islands mediated by oxo group (the only difference between these molecules). Comparing the rotational domains, molecular raw spacing, growth facets etc. it can be concluded that both molecules undergo similar adsorption geometry with the underlying graphite. We note that in the islands of Fc-Oxo-Sug no spontaneous defects are observed as in the previous case (cf. Figure 3b). The strong inter-dimer hydrogen bonding proposed in the model along the length of the islands is supporting this observation. To prove the above hypothesis of –C=O driven one dimensional growth, we have studied ultra-thin film growth of another Fc derivative (Fc-Oxo-Boc) with one oxo group adjacent to Fc and a different end group (cf. Figure 5a). 24 The end group is chosen in such a way that there are strong hydrogen bond acceptors for forming dimers than the protected sugar group. Typical AFM phase images (at different resolutions) of drop-casted Fc-Oxo-Boc molecular film on HOPG(0001) plane are shown in Figures 5b and c. Long one dimensional islands growing as wide as HOPG terraces are visible. Few monolayer islands are marked with magenta polygons. The islands are growing along three directions (see analysis in SI) as in the previous cases. The growth of these islands is hindered only by terrace edges and other island edges. High resolution images of islands (a typical image is included in SI) show linear rows of molecules similar as in Fc-Oxo-Sug. The spacing between the rows of molecules are 3.2 ± 2 nm , which is approximately double the length of a molecule and indicating that the building blocks of linear islands are dimers. These observations therefore suggest a similar structural pattern and growth for Fc-Oxo-Boc as in the case of Fc-Oxo-Sug. A tentative model is presented in SI. We note here that no amorphous islands are observed



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in this case. This is presumably due to strong hydrogen bond acceptors (-C=O) in the end group of Fc-Oxo-Boc, which offers more thermodynamically stable dimers than those formed by protected sugar derivatives.

Conclusion We have investigated the microscopic growth of two alkyl ferrocenyl derivatives with protected sugar groups. Both molecules show a one dimensional growth at monolayer coverage. Analysis show that the building blocks of these islands are dimers and inter-dimer hydrogen bonding along the island length plays a crucial role in controlling the growth into one dimension. The Fc derivative with oxo group is showing exceptionally long one dimensional islands whose length is only limited by the terrace edges. The 1D growth in this case is aided by a – C=O.... H–C– hydrogen bonding. We further proved this observation with the help of another Fc derivative containing an oxo group. The study is suggesting that the introduction of hydrogen bonding acceptor groups like –C=O in the alkyl chain connected to Fc will facilitate additional interaction along a preferred direction. Such directionality in inter-molecular interactions may allow one dimensional growth in molecular islands. These type of long 1D molecular islands on surfaces may find interest in transferring energy or electron over distances in the order of micrometers.

Acknowledgments The authors would like to thank Science and Engineering Research Board (SERB), Department of Science and Technology (DST), India and Indian Institute of Technology Kanpur for funding. PS, KY, SC and ATP would like to thank DST (INSPIRE fellowship), IIT Kanpur (GATE fellowship), Council of Scientific and Industrial Research (CSIR) (Senior Research Fellowship) and University Grant Commission (UGC) (Senior Research Fellowship), respectively. 14 ACS Paragon Plus Environment

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Supporting Information Available (S1) Statistical analysis of angle between domains and spacing between molecular rows of islands of Fc-Sug and Fc-Oxo-Sug, (S2) High resolution and large area AFM topography of Fc-Oxo-Sug film, (S3) Details of theoretical calculations for dimers of Fc-Sug and FcOxo-Sug, (S4) High resolution image of an island of Fc-Oxo-Boc and (S5) Synthetic details of Fc-Sug and Fc-Oxo-Sug.

This material is available free of charge via the Internet at

http://pubs.acs.org/.

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Graphical TOC Entry

500 nm

20 nm


Controlling Growth to One Dimension in Nanoislands of Ferrocene

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