Coordination Reactions of 5-(2-(4-Bromophenyl)ethynyl)pyrimidine in

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

Coordination Reactions of 5-(2-(4bromophenyl)ethynyl)pyrimidine in On-Surface Synthesis Qian Shen, Eugene J Larkin, Colm Delaney, Yingchun Cheng, Chunyang Miao, Xiong Zhou, Lacheng Liu, Wei Huang, Hong-Ying Gao, Sylvia Mary Draper, and Harald Fuchs J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b00696 • Publication Date (Web): 05 Apr 2018 Downloaded from http://pubs.acs.org on April 7, 2018

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The Journal of Physical Chemistry

Coordination Reactions 5-(2-(4-bromophenyl)ethynyl)pyrimidine On-Surface Synthesis

of in

Qian Shen,a,b,c Eugene J. Larkin,d Colm Delaney,d Yingchun Cheng,a Chunyang Miao, a

Xiong Zhou,e Lacheng Liu,b,c Wei Huang,a Hongying Gao,*b,c Sylvia M. Draper,*d

and Harald Fuchs*a,b,c

a

Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials

(IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, China b

Physikalisches Institut, Westfälische Wilhelms-Universität, Wilhelm-Klemm-Straße

10, 48149 Münster, Germany c

Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany

d

School of Chemistry, Trinity College Dublin, the University of Dublin, Dublin 2,

Ireland e

SynCat@Beijing, Synfuels China Technology Co., Ltd, Huairou, Beijing 101407,

China

1 ACS Paragon Plus Environment

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ABSTRACT

The molecule 5-(2-(4-bromophenyl)ethynyl)pyrimidine (PEPmBr) on Ag(111) was studied by low-temperature scanning tunneling microscopy (LT-STM). First, vapor deposition of PEPmBr molecules onto Ag(111) at room temperature leads to the formation of large scale pin wheel like self-assembly structure. Then, hierarchical coordination reactions are employed to synthesize organometallic dimers and tetramers on Ag(111) surface. In contrast to the releasing of the coordinated Ag atoms and forming covalent bonds, it is found herein that further thermal activation induces the rotation of the C-Ag-C and N-Ag-N coordination bonds, resulting in various organometallic nanoteris with triangle, rectangle and zigzag structures.


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INTRODUCTION

Bottom-up nanotechnology requires the controllable fabrication and arrangement of molecular building blocks into smart complex systems with atomic precision. Flowing from this idea, on-surface synthesis has developed from an advanced concept to a viable synthetic strategy in the past decade. Up to now, numerous reactions have been realized on surfaces, including Ullmann coupling,1-8 Glaser coupling,9-12 Bergman reaction,13,14

decarboxylative

polymerization,15

cycloaddition,16,17

dehydrogenation,18-22 and many others. Within these surface-mediated reactions, covalent or coordination bonds are built-up between different organic molecular building blocks. Strong covalent bonds ensure structural and thermal stability, and efficient electronic charge transport, but they also serve to restrict the self-repair ability and consequent regularity in the resulting two-dimensional architectures. In contrast, metal coordination bonds can serve to preserve both the structural thermal stability and the self-repair ability, which have been used to build zero-dimensional (0D) organometallic clusters,23 one-dimensional (1D) organometallic chains3,24 and two-dimensional (2D) metal-organic networks.25 Furthermore, their topology, composition and properties can be finely tuned (for example by the substrate23), and open-up specific and targeted applications such as carbon capture,26,27 quantum box,28,29 and catalysis.30 In recent years, pyridyl–metal–pyridyl (N-metal-N) coordination has been utilized by the Lin group to synthesize 1D and 2D organometallic polymers.31,32 Their studies demonstrate the contributions made by pyridyl-Cu-pyridyl coordination and Ullman 3 ACS Paragon Plus Environment


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covalent coupling in the synthesis of 2D narrow organometallic/covalent polymers.6 In addition, the role of carbon-metal-carbon (C-metal-C) coordination in the organometallic intermediate stage of Ullman coupling is well understood3 and exploited in the on-surface synthesis of organometallic structures. Good examples are the organometallic macrocycles (meta-terphenyl-Cu)n and zigzag-shaped 1D organometallic polymers reported by Gottfried et al.24 Given the above, this work describes our investigation into the hierarchical formation of N-metal-N and C-metal-C coordination modes on metallic surfaces, using 5-(2-(4-bromophenyl)ethynyl)pyrimidine (PEPmBr) as a potential source of pyrimidyl-M and benzyl-M sites (Scheme 1). The study was performed using low-temperature scanning tunnelling microscopy (LT-STM) on a range of different substrates. Our results show that the C-Ag-C and N-Ag-N bond formation can be hierarchically triggered by a simple thermal treatment, to generate organometallic dimers and tetramers. Subsequent annealing of the above organometallic structures gives rise to various triangular, rectangular and zigzag-shaped nanotetris. An outline of the entire reaction process involving PEPmBr on Ag(111) is shown in Scheme 1.


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Scheme 1 Chemical scheme of thermally-induced hierarchical coordination of 5-(2-(4-bromophenyl)ethynyl)pyrimidine (PEPmBr) on Ag(111).

EXPERIMENTAL SECTION

STM measurements were performed with a Createc LT-STM housing in ultra-high vacuum (UHV) chambers with base pressures of 10-10 mbar or below. Electrochemical etched polycrystalline tungsten tips were used and all STM images were acquired at 77 K. Bias voltages were applied to the sample. WSxM software was used for the STM image data processing and analysis.33 Ag(111), Au(111) and Cu(111) single crystals were cleaned by cycles of Ar+ sputtering and thermal annealing at 800 K. The 5 ACS Paragon Plus Environment


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precursor, 5-(2-(4-bromophenyl)ethynyl)pyrimidine, which has a high vapour pressure at room temperature, was evaporated to the single crystal surfaces by room temperature diffusion. The coverage can be controlled by the diffusion time. XPS experiments were performed in a SPECS system with base pressure of 5 × 10-10 mbar. A Ag(111) crystal was cleaned by cycles of 5 × 10-5 mbar Ar+ sputtering at 1.5 keV for 20 minutes and then annealed in UHV at 800 K for 15 minutes. The cleaning cycles were repeated until no carbon contaminations could be detected in XPS. All spectra were collected at normal emission with the X-rays impinging onto the sample at an angle of 45° with respect to the plane of the sample. PEPmBr molecules were dosed onto the substrate at RT for 10 seconds. Then the XPS spectra were collected in situ with a temperature rising from RT to 600 K. C 1s curves were fitted with Voigt profiles, since the peak shapes are typically determined by a Lorentzian contribution due to the limited lifetime of the core hole state and a Gaussian broadening. The simulations for the structure optimization were carried out by using first-principles density functional theory (DFT) calculations, which employed the the Quantum-ESPRESSO package34 and DMol3 module of Material Studio package35. The generalized gradient approximation (GGA) with the Perdew–Burke–Ernzerhof (PBE) functional was utilized as the exchange-correlation potential. While DFT provides a many-particle framework that, in principle, incorporates both local and non-local interactions, the standard semi-local approximation used in DFT neglects long-range attractive contribution (London dispersion forces). In order to consider the 6 ACS Paragon Plus Environment

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dispersion interaction, a DFT-D semi-empirical correction with Tkatchenko-Scheffler (TS) method was applied with the PBE functional. The STM images were simulated by using the Tersoff-Hamann approach for a relaxed atomic structure.

RESULTS AND DISCUSSION

Figure 1a shows the representative high resolution STM image of the self-assembled structures of PEPmBr molecules on Ag(111) after room temperature deposition. An overview STM image can be found in the supporting information, Figure S1. A large-scale pin wheel like self-assembly structure is observed on Ag(111) with few defects. A similar structure is found on Au(111) at room temperature (see supporting information, Figure S2). The measured length of a single molecule represented by one of the lobes is 1.25 nm, in good agreement with the calculated result (12.543 Å). In the STM images, one end of the molecule is slightly brighter than the other. (This is more obvious on Au(111) (see supporting information, Figure S2)). The brighter portion is assigned to the bromine terminus which has a higher electronic density of state. The intermolecular Br…N halogen bonds are responsible for stabilizing the observed structures. Similar halogen bonds between N atoms and halogen atoms (Br, I) have been used to build binary supramolecular structures.36-38 The DFT-optimized structure model for the self-assembled structure is shown in Figure 1b. The calculation were performed with a supercell size of 2.5nm×2.3nm×3.4nm with 328 atoms, which includes three layers of Ag substrate with (111) orientation and four PEPmBr molecules. In order to reduce the computational cost, structures similar to 7 ACS Paragon Plus Environment


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the STM images are chosen as initial configurations. After the geometry optimization, the energetically most favourable arrangement for these PEPmBr molecules also presents a pin wheel like morphologies, matches well with the STM result. The calculated Br…N halogen bond length is 2.98 Å and the bond angle is 176.8°. The unit cell is superimposed on top of the STM image with periodic parameters of a=2.07 nm, b=2.31 nm.

Figure. 1 (a) STM image of the pin wheel-like self-assembly structure of PEPmBr on Ag(111) at 300 K (V=-1.201 V, I=0.057 nA). Its unit cell (illustrated by the white square) is shown superimposed on the STM image. The insert in (a) shows the molecular structure and calculated length of PEPmBr. (b) The DFT-optimized molecular arrangement of PEPmBr on Ag(111). Carbon atoms are shown in grey, hydrogen atoms in white, bromine atoms in red, and nitrogen atoms in blue.

After annealing to 450 K, the dehalogenation is triggered and the residual 5-(2-phenylethynyl)pyrimidine segments are bridged by Ag adatoms. Similar events have been reported previously in the literature and the structures of the formed organometallic states have been clearly proved by STM and XPS expermients.39,40 8 ACS Paragon Plus Environment

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The resulting organometallic dimers self-assemble into two different phases on Ag(111), the chevron phase (Figure 2a and b) and the parallel phase (Figure 2c and d). Similar self-assembly structures of organometallic compounds were also reported by Zhou et al.41 Cu-coordinated organometallic intermediates show a chevron structure on Cu(111), while on Cu(100) a brick-like structure is observed. The periodic parameters of the unit cells for the chevron structure and the parallel structure are a1=1.70 nm, b1=2.02 nm, a2=0.92 nm, b2=2.32 nm. The organometallic dimers show 5 spots in an alternate bright and dim manner in the STM images. The middle bright one is assigned to the bridging Ag atom, which connects two benzene rings that are less intense in the image. The outer bright spots are the pyrimidine rings which are brighter than the benzene rings indicating relatively higher electronic density. The proposed molecular models are superimposed on top of the high resolution STM image shown in Figure 2b and d. The dot-like features between the molecules are detached Br atoms, highlighted by white cycles in Figure 2b and d. The detached Br atoms are stabilized by Br…H hydrogen bonds with the neighboring molecules, similar to those previously reported in the literature.3,24



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Figure. 2 STM images of two different phases of self-assembly structures of the organometallic dimers on Ag(111) after annealing to 450 K. (a) Overview and (b) high resolution of the chevron self-assembly structure of the organometallic dimers on Ag(111). Both were acquired at V = -0.198 V, I = 0.048 nA. (c) Overview and (d) high resolution STM images of the parallel self-assembly structure of the organometallic dimers on Ag(111) (V = -0.100 V, I = 0.067 nA). The unit cells are represented by white boxes in (a) and (c), while the molecular arrangements are superimposed in (b) and (d) respectively. Br atoms in between the dimers are highlighted by white cycles in (b) and (d).

Further annealing at 470 K, the coordination reactions between the N atoms of the pyrimidine and Ag adatoms are triggered. Organometallic tetramers are synthesized


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on Ag(111) and self-assembled into 1D chains with over 20 nm length. Large-scale and high-resolution STM images can be found in the supporting information, Figure S3. The STM result shown in Figure 3a indicates that organometallic dimers are connected to each other by N-Ag-N coordination involving the pyrimidine ends. The electronic density of states of the pyrimidines have been increased on coordination to the Ag adatoms. The DFT simulation confirms this structural motif (Figure 3b and Figure S4). The unit cell is shown as a white box in Figure 3a, with periodic parameters a=1.12 nm and b=4.61 nm. Coordination is only observed at one end of the molecule probably due to steric hindrance. If the coordination happened at both sides of the molecules, the backbone of PEPmBr has to be slightly bent, about 10 degrees, as proved by DFT simulation (Figure S4c). The N-Ag-N coordination is not strong enough to trigger this configuration change, therefore, the coordination was only observed at one end. Br atoms are observed between the coordinated dimers. We also performed STS measurements along the organometallic tetramer (Figure S5), which show prominent peaks at +700 mV at different positions for the lowest unoccupied molecular orbital, agree with previous reports.3,8



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Figure. 3 (a) STM image of 1D self-assembly organometallic tetramer chains. The unit cell is marked by a white box. Tunnelling parameters: V = -0.298 V, I = 0.077 nA. (b) DFT simulation of the self-assembly structure of organometallic tetramers on Ag(111).

Surprisingly, further annealing at higher temperatures (>480 K) did not release the Ag atoms from the organometallic dimers to form C-C covalent bonds, as has been reported for on-surface Ullmann coupling process.3,5 Instead, the C-Ag-C bond angle changes, forming nanotetris with various structural motifs, including triangle, rectangle and zigzag structures (as shown in Figure 4). Similar zigzag- and rectangle-shaped organometallic polymers and tetramers have been reported by depositing 1,4-diaminonaphthalene on Cu substrates with different crystallographic planes,23 but the size of the rectangles formed were small. In comparison, our structures are significantly larger with Br atoms hosted inside the supramolecular rectangles. To better understand this structure, we did DFT simulations, as shown in


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Figure S6. The first model is simply the bond rotation of C-Ag-C, but due to the steric hindrance between the H atoms on the adjacent benzene rings, the optimized bond angle is about 150°, much larger than the STM experimental result. The second model assumes that the H atoms on the adjacent benzene rings are activated and detached from the benzene rings, while the segments are bridged by Ag adatoms. The simulated structure is more like an ellipse, not a rectangle, doesn’t match with the STM result. In the third model, the C atoms are connected by C-C bond directly, which shows a rectangle structure. Therefore, we believe that along with the rotation of the C-Ag-C coordination bond, the C-H activation also take place, together resulting the rectangle structure observed.

Figure. 4 Overview (a) and high resolution (b) STM images of the various nanotetris synthesized by the rotation changes in the C-Ag-C and N-Ag-N coordination. Tunnelling parameters: V = -0.150 V, I = 0.046 nA.

To support our result, we performed XPS experiment. After dosing at room temperature, three types of C 1s signals were detected, C-C, C-N and C-Br, which 13 ACS Paragon Plus Environment


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were fitted at the positions of 284.4 eV, 285.8 eV and 285.2 eV (Figure 5). The intensities of these peaks have an 8 : 3 : 1 intensity ratio, in agreement with the stoichiometry of PEPmBr. Then the sample was heated to 420 K. The C-Br signal disappeared, indicating the detachment of bromine. At the same time, the whole C 1s signal shifted to lower binding energy (BE) (0.2 eV), which agrees with the proposition that the molecules bond to the electropositive (Ag) species. C-Ag-C 1s signal is located at 283.3 eV. These changes in BE indicate that PEPm- species generated by the Br detachment instead couple to Ag atoms. Then heated the sample to higher temperatures (460 K, 520 K, 600 K), we only observed the decrease of the intensities of C 1s signals which is due to the thermal effect and partially molecular desorption. However, the shape and BE position of C 1s curves keep almost the same as the C 1s curve at 420 K. That supported the proposition that the organometallic dimers did not change any more. Unfortunately, in the area of Br 3d and N 1s signals, the background of Ag(111) is not blank, thus the week signals of Br 3d and N 1s can’t be properly detected (see supporting information, Figure S7).


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Figure. 5 C 1s signals during the in situ heating of adsorbed PEPmBr molecules on Ag(111).

We also examined the thermally induced reactions of PEPmBr molecules on Au(111) and Cu(111). On Au(111), the molecules desorb from the surface before coordination can occur. On Cu(111), the molecules self-assemble into complex structures at room temperature, as shown in Figure S8a. This is due to the fact that the dehalogenation is triggered at room temperature on Cu(111) and the residues are not lying flat on the surface. After annealing to 400 K, C-Cu-C organometallic intermediates are found on Cu(111), (see Figure S8b and c). From the high-resolution STM images, middle Cu atoms can be distinguished. The N-Cu-N coordination occurs at both ends of the molecules, but only small 2D islands are formed.

CONCLUSIONS



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In conclusion, we have studied the self-assembly and hierarchical coordination processes of PEPmBr molecules on Ag(111), Au(111) and Cu(111). Large-scale pin wheel like self-assembled structures are formed on Ag(111) after room temperature deposition. Thermal treatment at 450 K causes dehalogenation and C-Ag-C bond formation. The organometallic dimers form two different self-assembled structural phases. Further annealing to 470 K triggers the coordination reaction between the N atoms in the pyrimidine rings with Ag adatoms, tetramers are formed and self-assembled into 1D organometallic chains with over 20 nm length on Ag(111). The C-Ag-C as well as the N-Ag-N coordination angles are temperature dependent. At 480 K, various nanotetris are produced. This is the first observation of such changes in coordination bonds, offering a new route for the construction of smart complex nanoarchitectures.

ASSOCIATED CONTENT

Supporting Information.

The following files are available free of charge on the ACS Publications website.

Synthetic procedure and NMR Spectra for PEPmBr molecules, supplementary STM images of the self-assembly structures of PEPmBr on Ag(111) and Au(111) , high resolution STM images of the two phases of organometallic dimers on Ag(111), supplementary STM images of 1D self-assembly organometallic tetramer chains, self-assembly and reaction process of PEPmBr on Cu(111), DFT simulations of the 16 ACS Paragon Plus Environment

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self-assembly structures of organometallic dimers with and without N-Ag-N coordination, DFT simulation of three possible structures for nanotetris, Br 3d and N 1s XPS spectra. (PDF)

AUTHOR INFORMATION

Corresponding Author * E-mail: [email protected].

* E-mail: [email protected].

* E-mail: [email protected].

Notes The authors declare no competing financial interest.

ACKNOWLEDGMENT

This study was supported by National Natural Science Foundation of China (21673118, 11504169, 61575094, 61704080), the Deutsche Forschungsgemeinschaft, TRR 61 and SFB 858, Science Foundation Ireland (SFI/15/1A/3046 and 15/IACA/3413), Natural Science Foundation of the Jiangsu Higher Education Institutions of China (16KJB150018) and the China Scholarship Council (201608320070).

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(26) Feng, M.; Petek, H.; Shi, Y.; Sun, H.; Zhao, J.; Calaza, F.; Sterrer, M.; Freund, H.-J. Cooperative Chemisorption-Induced Physisorption of CO2 Molecules by Metal–Organic Chains. ACS Nano 2015, 9, 12124-12136. (27) Čechal, J.; Kley, C. S.; Pétuya, R.; Schramm, F.; Ruben, M.; Stepanow, S.; Arnau, A.; Kern, K. CO2 Binding and Induced Structural Collapse of a Surface-Supported Metal–Organic Network. J. Phys. Chem. C 2016, 120, 18622-18630. (28) Pivetta, M.; Pacchioni, G. E.; Schlickum, U.; Barth, J. V.; Brune, H. Formation of Fe Cluster Superlattice in a Metal-Organic Quantum-Box Network. Phys. Rev. Lett. 2013, 110, 086102. (29)

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(39) Di Giovannantonio, M.; El Garah, M.; Lipton-Duffin, J.; Meunier, V.; Cardenas, L.; Fagot Revurat, Y.; Cossaro, A.; Verdini, A.; Perepichka, D. F.; Rosei, F.; et al. Insight into Organometallic Intermediate and Its Evolution to Covalent Bonding in Surface-Confined Ullmann Polymerization. ACS Nano 2013, 7, 8190-8198. (40) Chen, M.; Xiao, J.; Steinrück, H.-P.; Wang, S.; Wang, W.; Lin, N.; Hieringer, W.; Gottfried, J. M. Combined Photoemission and Scanning Tunneling Microscopy Study of the Surface-Assisted Ullmann Coupling Reaction. J. Phys. Chem. C 2014, 118, 6820-6830. (41) Zhou, X.; Wang, C.; Zhang, Y.; Cheng, F.; He, Y.; Shen, Q.; Shang, J.; Shao, X.; Ji, W.; Chen, W.; Xu, G.; Wu, K. Steering Surface Reaction Dynamics with a Self-Assembly Strategy: Ullmann Coupling on Metal Surfaces. Angew. Chem., Int. Ed. 2017, 56, 12852-12856.


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Coordination Reactions of 5-(2-(4-Bromophenyl)ethynyl)pyrimidine in

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