Unravelling the Mechanism of Glaser Coupling Reaction on Ag(111

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

Unravelling the Mechanism of Glaser Coupling Reaction on Ag(111) and Cu(111) Surfaces: a Case for Halogen Substituted Terminal Alkyne Tao Wang, Haifeng Lv, Lin Feng, Zhijie Tao, Jianmin Huang, Qitang Fan, Xiaojun Wu, and Junfa Zhu J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b02893 • Publication Date (Web): 11 Jun 2018 Downloaded from http://pubs.acs.org on June 11, 2018

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The Journal of Physical Chemistry

Unravelling the Mechanism of Glaser Coupling Reaction on Ag(111) and Cu(111) Surfaces: a Case for Halogen Substituted Terminal Alkyne Tao Wang1#, Haifeng Lv2,3#, Lin Feng1, Zhijie Tao1, Jianmin Huang1, Qitang Fan1†, Xiaojun Wu2,3*, and Junfa Zhu1* 1

National Synchrotron Radiation Laboratory and Department of Chemical Physics, University of

Science and Technology of China, Hefei 230029, P.R. China, [email protected] 2

Hefei National Laboratory of Physical Sciences at the Microscale, School of Chemistry and

Materials Science, CAS Key Laboratory of Materials for Energy Conversion, and CAS Center for Excellence in Nanoscience, University of Science and Technology of China, Hefei 230026, P.R. China, [email protected] 3

Synergetic Innovation of Quantum Information & Quantum Technology, University of Science

and Technology of China.

ABSTRACT: The mechanisms of Glaser coupling reaction on metal surfaces have been poorly understood. Herein, we propose a reaction pathway towards surface-confined Glaser coupling which is initiated by single-molecule dehydrogenation of terminal alkyne. This is inspired by our

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experimental observations of alkynyl-Ag-alkynyl and alkynyl-Cu-alkynyl type organometallic intermediates in the coupling reaction of 1,1’-biphenyl,4-bromo-4’-ethynyl (BPBE) on Ag(111) and Cu(111), respectively. Theoretical calculations reveal that the dehydrogenation process of terminal ethynyl of BPBE is most likely catalyzed by a stray H adatom on Ag(111) while by a Cu adatom on Cu(111), followed by the formation of the organometallic intermediates. After the release of interstitial metal adatoms, the final C-C coupling occurs easily on Ag(111), but shows extremely low efficiency on Cu(111) due to the too strong interaction between ethynylene and the Cu(111) substrate.

INTRODUCTION Ullman and Glaser homo-couplings are the two most well-studied coupling reactions on surfaces, which have been successfully utilized to fabricate porous graphenes,1 graphene nanoribbons2 and graphdiynes.3 For Ullman reaction, the high-symmetry surfaces of coinage metals (Au, Ag and Cu) were reported to be efficient catalysts because of the compromise between sufficient activity and high molecular mobility.4 The widely acceptable mechanism towards surface-confined Ullman coupling was established as a two-step process: 1) dehalogenation of the precursor molecule, immediately followed by the formation of organometallic intermediate; 2) ejection of the interstitial metal adatoms, forming C-C covalent bond.5-8 For Glaser coupling, Ag(111) surface was reported as an efficient substrate with less side reactions9,10 than Au(111) where cyclization of terminal alkyne is easy to be activated.11-13 However, the mechanism of Glaser coupling on Ag(111) has been poorly understood until now.


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Bjork et al. proposed a multistep reaction pathway: Glaser reaction on Ag(111) is initiated by covalent coupling between two terminal alkyne-type molecules rather than by single-molecule dehydrogenation. This leads to the formation of a nonlinear covalent dimer intermediate which binds to the substrate. Such intermediate further undergoes a stepwise dehydrogenation process to afford the conjugated diyne.14,15 In their studies, however, only the final products but no intermediate states were observed in the STM data. Recently, a few alkynyl-Ag-alkynyl type organometallic intermediates were reported in studies toward reactions of terminal alkynes: Wu et al. studied the reaction of 2,5-diethynyl-1,4bis(phenylethynyl)-benzene on Ag(111), Ag(110) and Ag(100) in which organometallic chains were formed on all the three surfaces and further C-C coupling was activated on Ag(111);16 We investigated the reaction of 1,1’-biphenyl,4-bromo-4’-ethynyl (BPBE) on Ag(111) and found that BPBE could couple into alkynyl-Ag-alkynyl type organometallic dimer at 285 K17 and conjugated diyne at 330 K.18 Incompatible with the mechanism proposed by Bjork et al.,14,15 Glaser reactions in these examples should be initiated by single-molecule dehydrogenation, followed by the formation of organometallic intermediate and then covalent product finally. On the basis of these experimental results, a mechanism similar as on-surface Ullman reaction should be taken into serious reconsideration for Glaser coupling on Ag(111) and an exploration of comprehensive picture of the reaction mechanism is of urgency and significance. Surprisingly, Cu(111) has been reported having extremely low efficiency for on-surface Glaser coupling,9,13,19 in contrast with the high catalytic activity of Cu ions towards Glaser reaction occurred in solution.9 Moreover, the widely existed Cu-acetylide organometallic intermediates in wet chemistry have been rarely reported on Cu surfaces, which was only observed in the reaction


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of simple ethyne molecule.20 Challenges remain to understand the behavior of terminal alkyne on a Cu(111) surface. Herein, with the interplay of scanning tunneling microscopy (STM), X-ray photoemission spectroscopy (XPS) and density functional theory (DFT) calculations, we have explored the detailed reaction pathways of Glaser coupling reaction of BPBE molecules on both Ag(111) and Cu(111). Similar as the case on Ag(111), alkynyl-Cu-alkynyl type intermediate have been also observed on Cu(111). Interestingly, the related single-molecule dehydrogenation process of sp C-H seems to be catalyzed differently on the two surfaces. Further C-C coupling between alkynyls can easily occur on Ag(111), while on Cu(111) the strong interaction between ethynylene and the substrate restricts the final C-C coupling. The detailed reaction mechanisms on both surfaces are discussed. EXPERIMENTAL AND THERETICAL METHODS The experiments were performed in a two-chamber UHV system, which has been described previously21, at a background pressure with 2×10-10 mbar. The scanning tunneling microscope is a SPECS STM 150 Aarhus with SPECS 260 electronics. All voltages refer to the sample and the images were recorded in constant current mode. The Ag(111) and Cu(111) single crystals with an alignment of better than 0.1° relative to the nominal orientation were purchased from MaTecK, Germany. Preparation of clean and well-ordered surfaces was achieved by cycles of bombardment with Ar+ ions and annealing at 750 K for Ag(111) and 800 K for Cu(111), respectively. 1, 1’-Biphenyl, 4-bromo-4’-ethynyl (BPBE) was purchased from commercial companies and used without further purification. They were vapor-deposited from a commercial Kentax evaporator with a Ta crucible held at 323 K. The evaporator is cut off from the two-


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chamber UHV system with a vacuum valve which was only opened during the molecular deposition. The vapor pressure of the UHV system is typically about 7×10-10 mbar in the deposition process. Molecular coverages were derived from STM images. All the samples were subsequently cooled down to 85 K for STM imaging. The XPS measurements were performed on the Catalysis and Surface Science Endstation located in National Synchrotron Radiation Laboratory (NSRL), Hefei, China. The detailed description of the endstation can be found elsewhere.22 The XPS spectra were collected at an emission angle of 45° with respect to the surface normal. All first-principle calculations were performed based on the periodic density functional theory (DFT) methodology implemented with the Vienna Ab-initio Simulation Package (VASP) package23-24. The projector augmented wave (PAW)25-26 pseudopotential was employed to describe the interactions between ions and electrons and the exchange-correlation interaction was considered using the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional.27 The van der Waals density functional (vdW-DF)28 introduced by Hamada29 which was denoted as evvdWDF2 was used. The cutoff energy for plane-wave functions were set to be 400 eV. The convergence tolerance of force on each atom was smaller than 0.02 eV and the energy convergence criteria is 10-5 eV. The reduced Brillouin zone is sampled with a gamma-center 3×3×1 k-mesh. In order to reduce the layer interactions, the vacuum spacing in the z axis, which is perpendicular to cleaved surfaces, is at least 15 Å. Transition states were calculated employing the Climbing Image Nudged-Elastic Band (CI-NEB) method30 and was optimized until the forces acting perpendicular to the path were converged typically to below 0.05 eV/Å. STM simulations were carried out with the Tersoff-Hamann approximation31 using the implementation by Lorente and Persson32.


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RESULTS AND DISCUSSIONS Coupling reaction on Ag(111). Supramolecular structure assembled by intact BPBE molecules on Ag(111) held at 93 K was reported previously.18 The large-area rhombic supramolecular structure can be formed at different molecular coverages (0.6 ML and 0.3 ML), implying the sufficient mobility of BPBE on Ag(111) at these conditions (See details in Figure S1, Supporting information). Deposition of BPBE onto Ag(111) held at 285 K and 330 K leads to the formation of organometallic and covalent dimer, respectively, as stated above. Specifically, the C-Br bonds keep intact at 285 K and the formed organometallic dimer unexpectedly assemble into Kagome lattice via intermolecular C-Br···π bonds and π-π stacking.17 The complete dissociation of C-Br bonds occur at 330 K, accompanied by the generation of phenyl-Ag-alkynyl type organometallics and conjugated diynes18 (See details in Figure S2). The alkynyl-Ag-alkynyl and phenyl-Ag-alkynyl type organometallic species observed in the experiments unambiguously demonstrate that the Glaser reaction of BPBE is initiated by single-molecule dehydrogenation, followed by the alkynyl-Ag connection.


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Figure 1. a), b) Typical STM images of two types of molecular islands upon deposition of BPBE on Ag(111) held at 313 K. Type A is shown in a) and Type B is shown in b). The molecular models of the formed dimeric structures are attached to the inset of a) and b), which are the zoom-in STM image of the circled dimers. Color code: C, grey; H, white; Br, red; Ag, silver. Tunneling parameters: a), b) U= -1.5 V, I= -0.3 nA. c) Br 3p XPS recorded after depositing BPBE molecules onto the Ag(111) surface held at 93 K, 313 K, 330 K, respectively. d) Typical reaction pathway of Glaser coupling of BPBE on Ag(111). The length of the scale bars of all the insets is 5 Å.


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To explore the complete reaction pathway of Glaser coupling of BPBE molecules on Ag(111), the BPBE molecules were deposited onto the surface held at 313 K. This leads to the partial dissociation of C-Br bonds of BPBE, as evidenced by Br 3p XPS shown in Figure 1c. The Br 3p spectrum at 313 K can be fitted with two different components in a ratio of 2:1. The binding energy (BE) of Br 3p3/2 of the minority signal is located at 184.4 eV, identical to that at 93 K, implying that this signal should be attributed to the Br in intact C-Br bond33. On the other hand, the majority signal of Br 3p3/2 at 182.1 eV should be assigned to chemisorbed Br adatoms on metal surface,33 generated from the dissociation of C-Br bond. The complete dissociation of CBr occurs at 330 K, because only a single signal of Br 3p3/2 at 182.1 eV is involved at these conditions. Figure 1a and Figure 1b show the two different types of the molecular islands assembled by the reaction products of BPBE at 313 K, denoted as type A and type B. The dominant dimeric species in type A exhibits a one-dot and two-rod feature (marked as yellow dotted circle), suggesting the formation of organometallic dimer. Similar to the previous works,17,34-37 the bright dot in the central of the dimer should be Ag interstitial adatom, and the rods are assigned to BPBE monomers. A biphenyl group can be identified as two protrusions and the center-to-center distance between the two biphenyl groups in a dimer is measured to be 16.5±0.5 Å, as shown by AB in Figure 1a. This implies that the organometallic dimer should be connected via a alkynyl-Ag-alkynyl bond,16,17 as revealed by the molecular model in the inset 1. The slight bend of C-Ag σ-bond is most possibly caused by the steric effect of the close-packed island and π-π stacking may be involved between two back-to-back dimers.17 Note that several smaller and dimmer dots (marked by yellow arrows) than Ag adatoms are inlayed in the island of Type A and the stoichiometric ratio of such dot to organometallic dimer is estimated to be about 2:1. Thus these dots should be attributed to the chemisorbed Br adatoms because two Br adatoms


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are produced by forming one organometallic dimer. This is in agreement with the XPS analysis above that the majority of C-Br bonds are dissociated at 313 K. Therefore, the dominant product in type A is confirmed to be organometallic dimer anchored to the surface. Apart from the main products, a few smoothly connected dimers can be also observed in Type A, as marked by blue dotted circle. The dimer here is most likely 1,3-conjugated diyne, because of its identical morphology and dimension to the same species reported previously.13,18,38 In addition, the molecular model of the conjugated diyne can match perfectly with the STM result, as revealed by the inset 2 in Figure 1a. Interestingly, as shown in Figure 1b, some BPBE monomers in type B feature bright ends, while others show uniform brightness in their ends similar as the case of type A. According to previous works39-41 and also the result of 93 K, these bright ends are most possibly assigned to the intact C-Br bonds, which is further supported by XPS result that 1/3 C-Br bonds stay intact at 313 K. Two kinds of dots inlayed in the island can be recognized in Figure 1b. The brighter dots pointed by green and white arrows should be assigned to Ag adatoms and the dimmer dots pointed by yellow arrows can be attributed to chemisorbed Br adatoms. These assignments are supported by the similar features in Figure 1a and many previous works.34-36 Some Ag adatoms bind to two BPBE monomers (pointed by green arrows), forming organometallic dimers with and without C-Br ends, as shown by blue and white dotted circles respectively. The wellmatching between their molecular models and the STM images further support this point, as can be seen in the inset 3 and 4 in Figure 1b. Other Ag atoms (pointed by white arrows) are typically very near to the intact C-Br ends of the BPBE monomers as circled by yellow dots and the BPBE parts in organometallic dimers as circled by blue dots, which are most possibly stabilized by


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Coulomb attraction of Ag···Br, as reported by many similar previous works.42-45 The Ag···Br distance is measured to be about 4.0±0.4 Å. Further annealing the organometallic dimers covered sample shown in Figure 1 to 345 K leads to the formation of conjugated diyne type dimers, accompanied with a few organometallic species, as exhibited in Figure S3. This strongly implies that the alkynyl-Ag-alkynyl organometallic state should be the intermediate of Glaser coupling of BPBE on Ag(111). In addition, a comparative experiment was performed by using 4-bromoethynyl-biphenyl (BEBP) as the precursor (Figure S4). Deposition of BEBP on Ag(111) held at 270 K leads to the formation of organometallic dimers and annealing of this sample to 310 K gives rise to the generation of conjugated diynes. Note that both the organometallic and conjugated dimers in this system have almost 100% yield under the corresponding conditions, thus the organometallic dimers must be the precursor state of the formation of conjugated diynes. Similar phenomenon was reported very recently.46 Owing to the observations and analyses of various intermediate species of Glaser coupling reaction of BPBE on Ag(111), the reaction pathway can be depicted as follows: 1) dehydrogenation of terminal alkyne, followed by the formation of organometallic dimer via alkynyl-Ag-alkynyl bond; 2) dissociation of C-Br bond, generating organometallic dimer anchored to the surface; 3) ejection of interstitial Ag adatoms in the organometallics, leading to the formation of 1,3-conjugated diyne. The whole reaction process is visually presented in Figure 1d.


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Figure 2. a), b) Overview and magnified STM image of the sample prepared by deposition of 0.3 ML BPBE on Cu(111) held at 93 K. Three high-symmetry directions [011], [110], [101] of the substrate are overlaid in both a) and b). DFT-based simulated STM image and corresponding molecular models are attached in b). Color code: C, grey; H, white; Br, red. Tunneling parameters: a), b) U=-1.7 V, I=-0.2 nA. c) Br 3p XPS of 0.3 ML BPBE on Cu(111) deposited at 93 K, followed by annealing to 245 K and 285 K. Coupling reaction on Cu(111). Different from the case on Ag(111), BPBE molecules on Cu(111) held at 93 K exhibit a scattered distribution, as shown in Figure 2a. The magnified STM image in Figure 2b reveals the coexistence of separate molecules and triangular molecular aggregates at these conditions. These molecules typically have a bright end as marked by yellow arrows, which should be attributed to intact C-Br bonds, similar to the case on Ag(111) and supported by the XPS result as shown in Figure 2c: the BE of Br 3p3/2 is located in 184.2 eV, implying the C-Br bonds are intact.33 Therefore, the triangular aggregate is probably stabilized by intermolecular Br···H bonds, as reflected by the attached molecular model (marked as white dotted circles). This is further supported by the excellent matching between the DFT-simulated STM image (marked as blue circle) and the experiment result. Interestingly, these BPBE molecules only orientate along three directions, marked as the yellow triangle in Figure 2b,


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exhibiting a 30° deviation with the high-symmetry directions [011], [110], [101] of the substrate lattice. Note that no large-area ordered molecular assemblies are formed on Cu(111) at 93 K, implying that BPBE molecules interact much stronger with Cu(111) than Ag(111). The strong interaction between BPBE and Cu(111) may be introduced by alkynyl group, because large-area close-packed islands can be typically formed on Cu(111) at similar conditions by using Br substituted aromatics as precursors.7,47 Annealing the sample to 215 K leads to the formation of large-area close-packed islands as shown in Figure 3a (low-coverage regions are shown in Figure S5). The sub-molecular resolution STM image in Figure 3b and 3c reveals details of the islands consisting of rods and dots. Figure 3b shows the major phase 1 (~70%) where the rods are crosswise arranged. The rods should be assigned to BPBE molecules because of their similar morphologies and dimensions with intact BPBE shown in Figure 2b. This assertion is also supported by the perfect matching between molecular models and STM results. Note that the C-Br bond must keep intact below 245 K on Cu(111), proved by XPS shown in Figure 2c, where the BE of Br 3p3/2 is located at 184.2 eV, identical to the value of 93 K. Thus no chemisorbed Br adatoms exists on the surface and the dots must be attributed to Cu adatoms with a stoichiometric ratio of 1:1 to BPBEs. According to the similar previous works,42-45 the supramolecular networks here are most probably stabilized by weak Coulomb attractions between Cu adatoms and BPBEs. According to a previous work of Gottfried et al., the dissociation of C-Br bonds of 4,4’-dibromo-para-terphenyl on Cu(111) occurs within a temperature range 170 K< T< 240 K,33 thus the existence of alkynyl groups, as proved by XPS results, indicates that the energy barrier of C-Br dissociation of a Brominated aromatic on Cu(111) may be increased, which will be further discussed in the section of theoretical calculations. Except for the major phase 1 of Cu-BPBE coordinated aggregate, minor


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phase 2 (~20%, other 10% is sparsely distributed) can be also observed on the sample, as shown in Figure 3c (marked with white circles). In phase 2, BPBE molecules are parallelly arranged.

Figure 3. a) Overview STM image recorded after annealing the sample in Figure 2a to 215 K. b) Magnified STM image of the major phase 1 of the molecular aggregate at 215 K. c) Magnified STM image showing the coexistence of major phase 1 and minor phase 2 of the molecular aggregate at 215 K. d) Overview STM image recorded by annealing the sample in a) to 245 K. e), f) High-resolution STM image of two regions in d) where the molecules show scattered distribution. g), h) Typical STM images recorded after annealing the sample shown in d) to 285 K and 360 K, respectively. Three high-symmetry directions [011], [110], [101] of Cu(111) are attached to all the magnified STM images above. Corresponding molecular models are overlaid in b), c), f), g), h). The insets in g) and h) are the zoom-in STM images of the white dot marked regions. The length of the scale bars of all the insets is 5 Å. Tunneling parameters: a) U=-1.2 V, I=-0.2 A; b) U=-1.5 V, I=-0.2 nA; c) U=-1.0 V, I=-0.3 nA; d) U=-1.4 V, I=-0.1 nA; e) U=-1.4 V, I=-0.2 nA; f) U=-1.1 V, I=-0.3 nA; g) U=-2.6 V, I= -0.2 nA; h) U=-1.1 V, I=-0.2 nA.


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The interactions between Cu and BPBE most likely involve weak Coulomb attraction of Cu···Br and Cu···alkynyl, as revealed by the molecular models. Similar weak interactions were reported by many previous works.42-45 A higher annealing temperature of 245 K largely breaks the above-mentioned large-area ordered islands and leads to the sparsely distribution of molecules, as exhibited by the overview STM image in Figure 3d, accompanied with only a few small-area molecular aggregates (white circles). Magnified STM images in Figure 3e and 3f show the separate arranged molecules. Interestingly, except for some single BPBE monomers, a few dimeric species can be occasionally observed, as marked by white dashed circles. Their one-dot and two-rod feature implies the formation of organometallic dimer, similar to the case shown in Figure 1a and 1b. The center-to-center distance between the two biphenyl groups in a dimer, as shown by AB in Figure 3e is measured to be 16.3±0.4 Å, suggesting that the dimer should be formed via an alkynyl-Cu-alkynyl bond.20 Because the C-Br bonds stay intact at these conditions, which is confirmed by the XPS results shown in Figure 2c and the fact that no dot-like species is observed in areas where molecules are sparsely distributed, the structure of the dimeric species can be determined and the corresponding molecular models are shown in Figure 3f. The alkynyl-Cu species, to our knowledge, is reported for the first time in the on-surface reactions of aromatic terminal alkynes. The minor molecular aggregate as marked by white circles in Figure 3d is identical to phase 2 at 215 K (See details in Figure S6). Thus it is reasonable to infer that the molecular aggregate at 245 K is the unbroken phase 2 after the sample annealing. We deduce that the coordination-unsaturated Cu adatoms in Figure 3b and Figure 3c should be of high activity and may play an important role in the dissociation of sp C-H bonds of BPBE, which will be discussed in detail in the section of theoretical calculations below.


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After further annealing the sample shown in Figure 3d to 285 K, large-area 1D chains are formed (Overview STM image is shown in Figure S7), implying the complete dehydrogenation and debromination of BPBE molecules. The complete cleavage of C-Br bonds is further confirmed by Br 3p XPS result in Figure 2c where the Br 3p3/2 peak locating at 182.1 eV appears at 285 K.33 The chemisorbed Br adatoms on Cu(111) can be identified as dim dots inlayed between the formed chains, as shown by the magnified STM image in Figure 3g. Three types of nodes in these nanowires are recognized, marked as type I, II, III, and type II is the dominant connection. Based on the distinctly different distances between Cu adatoms and their neighboring two BPBEs, the three types can be deduced as alkynyl-Cu-alkynyl, alkynyl-Cuphenyl and phenyl-Cu-phenyl, respectively. This assertion is supported by the well-matching between the overlaid molecular models and STM results, revealed by the inset in Figure 3g. An even higher annealing treatment of 360 K towards this sample leads to a significant decrease of the length of the 1D chains (Overview STM image is shown in Figure S7). This should be attributed to the cleavage of alkynyl-Cu-alkynyl, because no such species is observed on the sample, typically revealed by the high-resolution STM image in Figure 3h. The main connection type here is still alkynyl-Cu-phenyl, as marked by the white dotted circle in Figure 3h. It is worthy to note that no conjugated diyne species is generated at these conditions after the dissociation of alkynyl-Cu-alkynyl. Similar results were also observed when BPBE molecules were directly deposited on a hot Cu(111) held at 360 K, where neither alkynyl-Cu-alkynyl nor alkynyl-alkynyl connections were generated (See details in Figure S8). These experimental facts demonstrate that although alkynyl-Cu-alkynyl type organometallics can be formed followed by the dehydrogenation of ethynyl of BPBE, the further C-C coupling after ejection of the interstitial Cu adatom should involves a high energy barrier. Moreover, in fact, the C-C coupling


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reactions between BPBEs on Cu(111) are still of low efficiency when BPBE molecules were deposited on Cu(111) held at 470 K, because uncoupled BPBE monomers are dominating at these conditions, accompanied with only a few covalent oligomers (See Figure S9).

Figure 4. Optimal adsorption geometries of single BPBE molecule on a) Cu(111) surface and b) Ag(111) surface from top view and cross view. Color code: Cu, light orange; Ag, silver; C, grey; H, white; Br, brown. Theoretical calculations and discussion. First-principles calculations were performed to gain further insight into the Glaser coupling reactions of BPBE on the Cu(111) and Ag(111) surfaces. Figure 4 displays the most stable configurations of the adsorption of BPBE on both Cu(111) and Ag(111) surfaces. The molecular orientations are perfectly compatible with that observed in experiments. On Cu(111), the terminal ethynyl is coordinated with four surface Cu atoms. The Cu-C bonding length is about 2.13 Å and the other end, the Br terminal is 3.31 Å away from the surface. On Ag(111), the BPBE molecule is almost lying flat and the terminal ethynyl is slightly attracted to the surface. The distance between the outmost carbon atom and surface is 2.43 Å and the Br terminal is 3.28 Å away from the surface. The optimized adsorption configuration is consistent with the calculated adsorption energies, where the calculated adsorption energies of


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BPBE on the Cu(111) and Ag(111) surfaces are 1.95 and 1.54 eV, respectively. Therefore, the adsorption of BPBE molecule on Cu(111) is stronger than that on Ag(111). These results well explained why BPBE molecules can assemble into large-area supramolecular network on Ag(111) while sparsely distributed on Cu(111) at 93 K. Moreover, based on the Bader charge analysis, 0.61 electron is transferred from the Cu(111) substrate to BPBE and 0.06 electron is transferred from BPBE to the Ag(111) substrate, showing a same trend with the binding energy. The following reactions are studied based on above models. For the dehydrogenation process of terminal ethynyl on Cu(111), we considered two reaction pathways: 1) direct C-H dissociation on the flat surface, and 2) with the aid of the Cu adatom inspired by the experimental findings in Figure 3. The direct dehydrogenation is endothermic (0.32 eV) with an activation barrier of 1.12 eV. In the Cu adatom-catalyzed process, Cu adatom is modeled as an isolated Cu atom adsorbed on the surface closely to the alkyne termini (Figure 5a). Interestingly, the dissociation barrier of C-H bond is reduced to 0.88 eV and the reaction is endothermic with a reduced reaction heat of only 0.08 eV. This result indicates that the aggregates composed by Cu adatoms and BPBE molecules shown in Figure 3b and Figure 3c might be precursor phases of the dehydrogenation process on Cu(111). On Ag(111), the direct dissociation is endothermic (0.76 eV) with an energy barrier of 1.88 eV and the Ag adatom-catalyzed process is also endothermic (0.54 eV) with the barrier of 1.62 eV, which makes the dehydrogenation difficult to be activated with the presence of Ag adatom. Therefore, it is possible that there are some other species of adatoms exist on Ag(111) to catalyze the dehydrogenation. Two most possible catalysts are Br and H adatoms on surface. The Br adatom can be ruled out because the C-Br bonds keep intact at the reaction temperature of 285 K.17 Thus we considered the possibility that the dehydrogenation process is catalyzed with a stray H adatom on Ag(111) by forming a H2 molecule after the C-H


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dissociation. The formed H2 can be desorbed from the Ag(111) surface above 200 K, as reported by previous studies.48-50 As a result, the activation barrier is lowered to 1.21 eV with reaction heat of 0.41 eV (Figure 5b), agreeing well with the experimental conditions (~285 K). According to previous studies, stray H adatoms should be abundant on the Au(111), Ag(111) and Cu(111) surfaces in a UHV-chamber: 1) Talirz et al. concluded that the termini of graphene nanoribbons on Au(111) and Ag(111) is most likely passivated by diffusing atomic H atoms,51 although recombinative desorption of H from Au and Ag surfaces occurs already below room temperature;48-50 2) Kawai et al. observed the H-passivation of the radicals generated from the debrominations of 3,3’-dibromo-2,2’-binaphthalene on Ag(111) at 406 K.52 Considering no H atoms are released from the molecules, the H atoms should be from UHV-background, Ag substrate or hot filaments as they stated;

Figure 5. The potential pathway for the dehydrogenation of the terminal ethynyl of a BPBE molecule on a) Cu(111) with the presence of a Cu adatom and b) Ag(111) with the presence of a H adatom. Top and side views of initial state (IS), transition state (TS), and final state (FS) for splitting off a hydrogen atom are depicted.


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3) The addition reactions of terminal alkynyl bromides were observed on both Ag(111) and Au(111) surfaces (~420 K) after its debromination, as reported by us and Xu et al. respectively,18,38 but there are also no H atoms released from the precursor molecules; 4) The addition reaction of triangular dehydrobenzo annulene occurs on Cu(111) held at 150 K,53 with no H or H2 dosing, reported by Kawai et al. Nevertheless, it is necessary to mention that the role of the proposed stray hydrogen atoms is rather hypothetic with no direct experimental evidence here, thus further experimental explorations are looked forwarded to be held in the future. Other mechanisms initiating the Glaser reactions like the direct coupling of two BPBE molecules without dehydrogenation proposed by Bjork et al.14,15 are not considered here since no related intermediates were observed in experiments. We note that the energy barrier of 1.21 eV in our study is higher than that in Bjork’s work (0.86 eV).14 However, a prerequisite of the direct coupling mechanism proposed by Bjork et al. is that the two terminal alkynes need to meet with an appropriate molecular orientation. This process, however, might be hindered by the steric effect caused by the close-packed self-assembly of BPBE molecules, which was not considered in their theoretical calculations. Therefore, it is very possible that the single-molecule dehydrogenation catalyzed by H atom occurs prior to the direct coupling process, because it involves much weaker steric limits. As a result, the priority of single-molecule dehydrogenation leads to the formation of organometallic species, as observed in the experiments. Similar kinetics-regulated thermal selectivity of intermolecular versus intramolecular reactions were reported by Ecija et al..54 In their studies, only intramolecular reaction occurs when depositing the precursor molecules on a hot Au(111) surface (~573 K), although its energy barrier (1.82 eV) is much higher than that of intermolecular reaction (1.04 eV). In summary, the most possible


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dehydrogenation process of BPBE is Cu adatom-catalyzed on Cu(111) and H adatom-catalyzed on Ag(111). After the dissociation of C-H bond, an Ag or Cu adatom is adsorbed close to the terminal ethynylene and the migration barrier of this kind of unit is 0.71 eV on the Cu(111) surface and 0.16 eV on the Ag(111) surface along with the growth direction. The low migration barrier guarantees the formation of organometallic dimers on the two surfaces. Then, the dissociation barrier of C-Br bond on Cu is 1.16 eV with the adsorbed energy of 0.09 eV and that on Ag is 0.86 eV with the released energy of 0.64 eV (Figure S10). The energy barrier of 1.16 eV on Cu is higher than that of Br substituted aromatics as reported previously,55 which can be attributed to the larger distance between Br and the substrate in this system induced by the strong binding of ethynyl on Cu(111) (Figure S10). On the other hand, the barrier of 0.86 eV on Ag(111) is in consistence with previous work,55 but slightly deviates the experimental results that dissociations of C-Br bonds typically start near RT either in this system or previous studies.36,45 Note that steric hindrance introduced by dense molecular islands is not considered in both previous and current calculations, thus the energy barriers of the debromination might be underestimated. The direct experimental evidences that steric effect can influence the energy barrier of on-surface reactions have been reported previously. In our previous work,18 because of the steric hindrance caused by Br···H hydrogen bond in the close-packed cis-enediyne island, the highly active cisenediynes are protected from further reactions. Comparative experiments and DFT-calculations corroborate such steric effect. According to the calculation, the energy barrier of addition reaction of cis-enediyne is much larger when a Br atom is placed near the cis-enediyne, compared to the single-molecule case. Wu et al. also reported similar studies toward the onsurface reactions steered by molecular self-assemblies.41,56 In their studies, both molecular


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coverage and the type of supramolecular network can greatly influence the reaction pathways and energy barriers. They all come from the steric effect (or intermolecular interaction). Although steric hindrance effect is also applicable to the calculated barrier for dehydrogenation, the interaction of halogen bonds and even Ag···Br coordination bonds are much stronger than the Van de Waals interactions between alkynyl groups. This can be confirmed by the much larger length of alkynyl···alkynyl (~5 Å)17 than the other two (3.6 Å for Br···Br17 and 4 Å for Ag···Br). Therefore, the steric hindrance effect during the debromination should be much stronger than the dehydrogenation process. Consequently, the contradiction between the calculated debromination barrier and the experimental observations in previous studies36,45 may be also attributed to the strong steric hindrance caused by Br···Br halogen bonds. Once the dehydrogenation of terminal alkyne occur, the alkynyl radical may attach to a surface Ag adatom immediately, which makes the BPBE tilting, thus the distance from the C-Br end to the surface should increase. This may further increase the difficulty of C-Br dissociation. Overall, the influence of steric effect of molecular self-assembly is the most reasonable interpretation toward the fact that the dehydrogenation is prior to debromination of BPBE on Ag(111), which typically occurs above 285 K.


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Figure 6. The potential pathway of C-C coupling by the ejection of a interstitial Cu or Ag adatom from an organometallic dimer on a) Cu (111) and b) Ag (111). Top and side views of initial state (IS), transition state (TS), and final state (FS) are depicted. Next, the reason of the high efficiency of Glaser coupling of BPBE on Ag(111) while low efficiency of that on Cu(111) is discussed. On Ag(111), the ejection of interstitial Ag atom from the organometallic dimer anchored to the surface is exothermic (0.80 eV) and the activation barrier is 1.54 eV, which completes the Glaser coupling, as shown in Figure 6b. The energy barrier of 1.54 eV seems a little large under such experimental conditions (~330 K). However, considering only the 0 K potential energy is included here, the neglected vibrational enthalpy and entropy may lower the reaction barrier. The energy barrier of C-C coupling between alkynyls after the release of interstitial Cu atom on Cu(111) is 2.47 eV with adsorption heat of 1.14 eV, which is difficult to overcome, as depicted in Figure 6a. We note that C-C coupling process on two metal surfaces is thermodynamically dominated. It shows that the process of Glaser reaction is favorable on Ag(111) since the formation of dimeric conjugated diyne involves the release of heat. However, on Cu(111), the strong interaction between the substrate and ethynylene makes


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the Glaser reaction an endothermal process, thus the ethynylenes prefer to bind with Cu substrate rather than couple into conjugated diynes. Conclusion In summary, we have explored the reaction pathways of BPBE molecules on the Ag(111) and Cu(111) surfaces with the combined STM, XPS and DFT-calculations. The formed alkynyl-Agalkynyl and alkynyl-Cu-alkynyl type organometallic intermediates imply a single-molecule dehydrogenation of terminal alkyne on the two surfaces. The dehydrogenation process is most likely H adatom-catalyzed on Ag(111) and Cu adatom-catalyzed on Cu(111). Further C-C coupling between alkynyls on Ag(111) is an exothermic process with a relative low energy barrier, forming conjugated diyne-type product. However, Glaser-type C-C coupling exhibits extremely low efficiency on Cu(111). This is attributed to the strong interaction between alkynyl and Cu substrate, which makes the C-C coupling an endothermic process with considerable high energy barrier. Our findings not only comprehensively unraveled the mechanism of Glaser coupling of 1,1’-biphenyl,4-bromo-4’-ethynyl on Ag(111) and Cu(111) surfaces but also demonstrate that the adsorbate-substrate interaction should play a decisive role in some onsurface reactions. ASSOCIATED CONTENT Supporting Information. The following files are available free of charge. Additional STM results and debromination process derived by DFT-study. (file type, i.e., PDF) AUTHOR INFORMATION Corresponding Author


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* J. F. Zhu, [email protected]. * X. J. Wu, [email protected]. Present Addresses † Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str., 35032 Marburg, Germany. Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript. #These authors contributed equally. Notes The authors declare no conflict of interest. ACKNOWLEDGMENT This work was financially supported by the National Natural Science Foundation of China (21473178, 21773222, 21573204), the National Key R&D Program of China (2017YFA0403402, 2016YFA0200602), CAS Interdisciplinary Innovation Team, Collaborative Innovation Center of Suzhou Nano Science and Technology and by Supercomputer Center of USTCSCC and SCCAS. REFERENCES (1) Bieri, M.; Treier, M.; Cai, J.; Ait-Mansour, K.; Ruffieux, P.; Groning, O.; Groning, P.; Kastler, M.; Rieger, R.; Feng, X. et al. Porous Graphenes: Two-Dimensional Polymer Synthesis with Atomic Precision. Chem. Commun. 2009, 45, 6919-6912.


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Unravelling the Mechanism of Glaser Coupling Reaction on Ag(111

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