Chemistry of 4-[(4-bromophenyl)ethynyl]pyridine at metal surfaces studied by STM

Article abstract of DOI:10.1039/c8cc03986k

Molecular architectures (Kagome networks, coordinated/covalent dimers and branched coordination chains) via self-assembly, Ullmann reaction and pyridine coordination of 4-[(4-bromophenyl)ethynyl]pyridine are found to be sensitive to the underlying metallic surfaces. The molecular species were characterised on the surface by low-temperature scanning tunnelling microscopy (LT-STM) at sub-molecular level.

Full text of DOI:10.1039/c8cc03986k

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Chemistry of 4-[(4-bromophenyl)ethynyl]pyridine at metal
surfaces studied by STM
Received 00th January 20xx,
Accepted 00th January 20xx
a,b
c
c
d
d
a,b
Jindong Ren, Eugene Larkin, Colm Delaney, Yang Song, Xin Jin, Saeed Amirjalayer, Anne
a,b
d
* a,b
* d
c
Bakker, Shixuan Du, Hongying Gao,
Yu-Yang Zhang, Sylvia M. Draper, * and Harald
*a,b
DOI: 10.1039/x0xx00000x
Fuchs
www.rsc.org/
Molecular architectures (Kagome networks, coordinated/covalent
dimers and branched coordination chains) via self-assembly or
Ullmann
reaction,
pyridine
coordination
of
4-[(4-
bromophenyl)ethynyl]pyridine are found to be sensitive to the
underying metallic surfaces. The molecular species were
characterised on the surface by low-temperature scanning
tunnelling microscopy (LT-STM) at sub-molecular level.
Scheme 1: Schematic diagram of the DFT optimized orientation of 44BEP on
metal (M) surfaces. The different distances (dBr_sub and dN_sub) on different
surfaces will bring different configurations and self-assembling behaviours.
An understanding of heterogeneous catalysis at the sub- N-metal-N and C-metal-C coordination modes on metallic
nanometer scale is important, both for investigating surface surfaces by using 5-(2-(4-bromophenyl)ethynyl)pyrimidine
reaction mechanisms and building advanced molecular (BPPA). Given that the on-surface chemistry of these species
1
devices. Versatility in the synthesis of complex architectures revolves around the reactivity of the N-atoms of the
2
requires the control of the on-surface reactivity and metal- pyrimidine ring, the pyridine molecule is expected to show
3
4
directed self-assembly. The Ullmann reaction , a well-known different self-assembly behaviours as well as subsequent
organic reaction mediated by metal catalysts, has been used to coordination/covalent chemistry (Scheme S1). The origin is a
link aromatic units through C-C bonds and to further construct subtle balance between the distances from the substrate to
regular chains or complex porous networks. Furthermore, the N- and Br-atoms respectively, which is dependent on the
noble metal atoms involved in coordination and adatom bonds type of metal substrate. Synthetic procedure and NMR Spectra
also take-on specific roles in building supramolecular for 44BEP are listed in the Supporting Information. Au(111),
5
quasicrystalline materials. The judicious choice and Ag(111) and Cu(111) were chosen to study the roles played by
application of these various types of reactivity, therefore, offer the metallic catalysts in surface chemistry. All STM images
opportunities for the formation of organic frameworks with were acquired with the same parameter (I = - 0.1 nA, V = - 2.0
b
6
9
targeted applications in future molecular devices.
Here, we have investigated the self-assembly, Ullmann on the interaction between 44BEP and various metal surfaces
reaction and pyridine coordination of 4-[(4- demonstrates that the different distances between two side
V). Similar to Björk et al. , DFT calculations (Table S4) focusing
bromophenyl)ethynyl]pyridine (44BEP) on sublimation under groups (pyridine N and bromide) and substrates will cause
ultrahigh vacuum onto various crystalline metallic surfaces and different self-assembly behaviours and chemical reactions. In
7
in line with density-functional-theory (DFT) calculations. contrast to the disordered networks on Au(111), self-assembly
8
Recently, Shen et al. reported on the hierarchical formation of architectures of closely stacked Kagome lattices were observed
on the Ag(111) surface at room temperature. Ullmann reaction
intermediates in two different phases were found on the
Ag(111) substrate after thermal annealing. Novel branched
coordinated chains were identified on the Cu(111) surface.
These observations demonstrate the decisive catalytic role
played by the metal atoms in surface assembly behaviour and
in the following chemical reactions of the 44BEP molecule.
Fig. 1 displays a series of images of Au(111) surfaces with
a low coverage of molecules scanned at 77 K. The molecules
are seen to self-assemble into several structures after
1
0
adsorbing onto the substrate. The STM tip could be used to
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Fig.1 STM images of 44BEP on Au(111). (a) and (b) show subsequent
images of the same scanning area of a low-coverage sample where the
island’s position has changed. (c) Close-up image of the dimer and trimer
on Au(111). Brightness contrast of the lobes and I-t spectra (inset, 0.1 nA,
Fig.2 STM images of self-assembled molecules on a Ag(111) surface. (a)
The delicate interaction between the Br and H leads to the formation of a
Kagome lattice at low coverage. (b) The close packed structure found on
increasing the molecular coverage.
-
2.0 V.) show the swing of the dimer and the rotation of the trimer. The
lobe rotates into the tunnelling gap, a much higher tunnelling
current is detected. Therefore, the high and low current states
correspond to the molecular lobes moving inside and outside
of the tunnelling junction, and demonstrate the rotation of the
molecules. By checking the calculated dBr-sub and dN-sub (see
Table S4), we found that there is no chemical bond between
purple sphere in the centre of the trimer is an additional Au adatom. The
vibration angles (30° and 150°) are shown in a). (d) At high coverage, the
dimers and trimers are connected to form disordered networks.
move the densely packed islands of intact molecules, thus
indicating a weak coupling between Au(111) surface and
molecules. Dimers and trimers are the main constructions on
the surface and act as nuclear seeds for the growth of the
larger molecular networks. The dimer, appearing as four lobes
due to its swinging motion at 77 K, only adsorbs at the elbow
sites of the Au(111) herringbone template. Each dimer is
constructed by two 44BEP molecules connected through a 150°
angle. The dimer can swing between two stable sites at 30°
from the focal point, leading to the observed four lobes in the
STM image, see Fig. 1a. The stable sites are determined by the
underlying symmetric arrangement of Au atoms. As for the
trimer, the central bright sphere indicates an additional Au
atom is present. Furthermore, the molecular orientations
inferred from the models presented in Fig. 1c suggest that
there is N-Au coupling in the trimer.
4
4BEP and Au(111). The largest binding energy is 1.85 eV. It is
also found that the energy difference between different
16
binding sites is very small (less than 0.1 eV), indicating a
small diffusion and rotation barrier, which explains the fast
rotation of 44BEP molecules. Details of the DFT calculations
can be found in the supporting information.
Further deposition of the molecules on the Au(111)
surface gives rise to disordered networks that nucleate around
the existing dimers and trimers, see Fig. 1d. The swing and the
rotation of the molecules are hindered by increasing proximity
of neighbouring molecules. Unlike the regular and robust
structures observed on the Ag(111) and Cu(111) crystals, the
networks generated on the Au(111) surface are easily removed
by the STM tip demonstrating that they are weakly coupled to
the Au(111) surface. Gradual annealing of the sample leads
only to the desorption of molecules from the Au(111) surface.
To determine the role of the supporting substrate in the
chemical reactivity, we changed the crystalline substrate to
Ag(111). After evaporation of ~0.5 ML 44BEP molecules onto
To prove the postulated swing and rotation behaviours,
1-14
1
I-t spectra
were performed. As reported, Stipe et al.
demonstrated the direct monitoring of single molecular
motion by recording the tunnelling current as a function of
1
5
time. After placing the STM tip above a certain pre-selected
position, the feedback loop is switched off, leading to a fixed
tip height in the succeeding measurements. Dynamical
behaviours such as molecular motion under the tip will lead to
an abrupt change in the tunnelling current. Fig. 1c (inset)
displays the spectra detected above and between the lobes
indicated in Fig. 1c. Taking the blue spectrum as an example,
the measured absolute value of the current is high when first
fixing the tip upon molecule. Since the rotation of the
molecule moves the molecular lobe out of the tunnelling gap,
it results in a larger tunnelling gap distance and lower
tunnelling current (absolute value) between the tip and
sample. The tunnelling current reverts back to a high value
when the rotation moves the molecule back into the tunnelling
gap. Similarly, for the green spectrum, when the molecular
17
Ag(111) at 300 K, a regular Kagome lattice was formed. The
typical size of the unit length in the Kagome networks is
5.00±0.05 nm. Fig. 2a displays a high resolution image of the
Kagome lattice super-imposed by the optimized molecular
model. Each 44BEP molecule is imaged as an assembly of
bright ellipsoids and dim spheres. The combination of the Br
atom and the benzene ring enhances the topography intensity
and results in the bright protrusion observed.
It is easy to discern from the images that each four-
branch joint in the Kagome lattice contains two Br ended
branches and two pyridine N ended branches. The Br
terminated branches are arranged in a straight line while a
displacement of 0.42 ± 0.05 nm is observed for the N
terminated parallel branches. Although the molecules are not
2
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Fig.3 STM topography images of the densely packed molecular layer on a
Ag(111) surface at different stages during the annealing process. (a)-(d)
Two different phases (described as parallel (a)-(b) and chevron phases
(c)-(d)) of the organometallic dimers were found after annealing sample
to 410 K. (e) and (f) both Ullmann reaction and N induced activation give
rise to the formation of chain structures after annealing.
Fig.4 STM topography images of molecules on the Cu (111) surface. (a), (b)
connected to each other at 77 K, the lattice is stabilized by organometallic chains were found after depositing molecule at room
some Br…H–C hydrogen bonds indicated by the molecular temperature. (c) and (d) statistic of each configurations of dimer(c) and
modelling. The distance between the Br and the nearest H is trimer (d) in the chain on Cu(111) surface. Purple ball represents Cu atom.
1
8
0
.28
±
0.05 nm, which is reasonable for hydrogen bonds.
Fig. 2c demonstrates both a porous Kagome lattice and a brighter with respect to the molecule and there is no sphere
close-packed molecular layer. Due to the Br protrusion in attached at the end. We attributed this contrasting
4BEP molecule, there is a large displacement between each modulation, i.e. dim and bright centres for the Ag adatoms, to
the bar. For the chevron phase, the central Ag adatom appears
4
molecules and its closest molecule and the delicate Br…H–C the different adsorption configurations in relation to the
interaction is disturbed, to give a quasi-regular structure at surface. For the parallel phase with the Ag adatom at each
high coverage, see Fig. 2b. This is different from the BPPA termination, the central Ag adatom will be lifted by the linked
19
tetramers held by C-H…N hydrogen bonds. DFT calculations molecules. Thus, the vertical displacement with respect to the
show that by forming this quasi-regular structure with Br…H–C, substrate will cause a poor conduction during STM scanning
the binding energy of one 44BEP molecule on a Ag(111) and result in a dimmer feature in the centre of the bars.
substrate increased from 1.72 eV to 1.97 eV per molecule.
On further annealing the sample to 480 K for 10 min, the
Furthermore, desorption of the molecule leads to the release of the coordinating Ag atoms in C-Ag-C bonds induces
2
1
appearance of a Kagome lattice for the high coverage sample if covalent C-C coupling between the aromatic species. The
the sample is held at 380 K for 10 min.
remaining adjacent benzene rings twist and are no longer
To investigate the possibility of on-surface coupling parallel with respect to the substrate surface. They are
reactions, we annealed the sample gradually and observed therefore imaged as two bright protrusions in the new bar
two different phases of the intermediate caused by an centre. The C-H bonds adjacent to the N atom in the pyridine
Ullmann reaction around 410 K (see Fig. 3a and 3c). Here, the ring are activated and form a covalent bond with the Ullmann
4
4BEP molecules are completely debrominated by the Ag free radical of another 44BEP molecule, leading to the
surface, resulting in such Ag-bridged organometallic formation of some short zigzag chains on the surface, see Fig.
intermediates. The length of the main uniform bars which are 3e and 3f. Due to desorption of the molecule during annealing,
constructed by one Ag adatom and two molecules is 2.20 ± these products mainly assemble at the step edge sites.
0.05 nm. The Ag atoms are either extracted from the terraces
We also took measurements on a Cu(111) crystal which is
or originated from the free Ag gas on the surface during the more active than Au(111) and Ag(111). Our calculations also
4
previous annealing process . As for the intermediates, the Ag show that 44BEP has a larger binding energy on Cu(111). Fig.
adatom can be easily distinguished in the middle of the bars. 4a depicts a large-scale STM image of a Cu(111) surface
The split-off Br adatoms, also appear as spheres between the covered by one dimensional (1D) chains after depositing the
2
2
bars. We labelled the bars according to their different molecules at 300 K. The chains show a preference for 1D
orientations, as a parallel (Fig. 3a) or a chevron phase (Fig. 3c). growth with three-branch junctions at high coverage. To probe
Further high-resolution images are presented in Fig. 3b and Fig. the specific sites of the complexation in each chain, a high-
3
d. These provided sub-molecular resolution images of the resolution image with dim-bright contrast is shown in Fig. 4b
two phases, and enabled us to construct molecular models. and superimposed with the fitted molecular structures. The
The spherical protrusion in the centre of the dimer can be repeating unit of 1.20 ± 0.05 nm unit length, corresponds to
easily discerned and is attributed to a single Ag adatom based one 44BEP molecule. The higher intensity observed here is
4
, 20
on previously published results.
attributed to the Br atom. This is helpful to the identification of
In the case of the parallel phase, each bar is terminated the molecular position in the chain. The molecular orientation
by one Ag adatom, which is observed as a sphere at the end of at each site in the chain is either parallel or antiparallel with
respect to the neighbouring molecules. This results in three
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different dimer configurations, i.e. Br-Br, Br-N and N-Cu-N (see 14/IA/3046, SFI 15/IACA/3413), CAS Pioneer Hundred Talents
Fig. 4c) after considering the measured centre-to-centre Program and Beijing Nova Program (No. Z181100006218023).
distances. As for the last N-Cu-N connection, it is well known
that Cu adatoms form a two-dimensional gas on the surface
4
during the annealing process . The reactive Cu adatom can
Notes and references
then participate in the formation of an organometallic chain 1. Y.-Q. Zhang, M. Paszkiewicz, P. Du, L. Zhang, T. Lin, Z. Chen, S.
and cause the dim sphere apparent between each N-N
Klyatskaya, M. Ruben, A. P. Seitsonen, J. V. Barth and F.
connection. This is apparent from the high-resolution images
Klappenberger, Nat. Chem., 2018,10,2924.
and the lateral distance measurements in Fig. 4c. Indeed, each 2. H. Kong, S. Yang, H. Gao, A. Timmer, J. P. Hill, O. Diaz Arado, H.
Monig, X. Huang, Q. Tang, Q. Ji, W. Liu and H. Fuchs, J. Am.
molecule in the dimer is stabilized by hydrogen bonding or N-
Chem. Soc., 2017, 139, 3669-3675.
Cu-N coupling. A statistical analysis of the dimer in the chain,
3
4
5
. A. Dmitriev, H. Spillmann, N. Lin, J. V. Barth and K. Kern,
Angew.Chem., Int. Ed., 2003, 42, 2670-2673.
. W. Wang, X. Shi, S. Wang, M. A. Van Hove and N. Lin, J. Am.
Chem. Soc., 2011, 133, 13264-13267.
. M. Knor, H. Y. Gao, S. Amirjalayer, A. Studer, H. Gao, S. Du and H.
Fuchs, Chem. Commun., 2015, 51, 10854-10857.
based on several hundreds of connections obtained from STM
images (10 nm 10 nm), determined that the ratios of the Br-Br,
×
Br-N and N-Cu-N connections are 25%, 47% and 28%
respectively (Fig. 4c). The random nature of the connections
demonstrates that the Br and N atoms in the molecule play a
similar role in the 1D chain formation.
6. X. Zhang, N. Li, H. Wang, C. Yuan, G. Gu, Y. Zhang, D. Nieckarz, P.
Szabelski, S. Hou, B. K. Teo and Y. Wang, ACS Nano, 2017, 11,
8511-8518.
For the three-branch junctions (Fig. 4d), only three types
of junction, classified by the number of Br terminated
branches, were found on the surface. In fact, no three-branch 7. R. Gutzler, H. Walch, G. Eder, S. Kloft, W. M. Heckl and M.
Lackinger, Chem. Commun., 2009, 4456-4458.
junctions originated from three N terminated branches in our
8
. Q. Shen, E. J. Larkin, C. Delaney, Y. Cheng, C. Miao, X. Zhou, L.
Liu, W. Huang, H. Gao, S. M. Draper and H. Fuchs, J. Phys. Chem.
C, 2018,122(16),8954.
experiment. The proportions of the three-branch junctions
involving three, two or one Br atoms were 46%, 42% and 12%
respectively. The high ratios of the three and two Br type
junctions, probably indicates the preferential formation of the
three-branch junction at Br-Br sites when two chains touch
each other at high coverage. Furthermore, a dim sphere
9
1
. J. Bjork, F. Hanke and S. Stafstrom, J. Am. Chem. Soc., 2013, 135,
5
768-5775.
0.T. A. Pham, F. Song, M. T. Nguyen and M. Stohr, Chem. Commun.,
014, 50, 14089-14092.
2
attributed to a Cu adatom appears in the centre of every 11.T. Kudernac, N. Ruangsupapichat, M. Parschau, B. Macia, N.
three-branch junction. This suggests that a Cu adatom is
critical to the construction of such junctions in the molecular
networks. We also gradually annealed the sample. Neither
regular C-Cu-C organometallic products nor covalent dimer
products were observed on the Cu(111) surface.
Katsonis, S. R. Harutyunyan, K. H. Ernst and B. L. Feringa, Nature,
2011, 479, 208-211.
1
1
2.Y. Zhang, H. Kersell, R. Stefak, J. Echeverria, V. Iancu, U. G.
Perera, Y. Li, A. Deshpande, K. F. Braun, C. Joachim, G. Rapenne
and S. W. Hla, Nat. Nanotechnol., 2016, 11, 706-712.
3.U. G. Perera, F. Ample, H. Kersell, Y. Zhang, G. Vives, J.
Echeverria, M. Grisolia, G. Rapenne, C. Joachim and S. W. Hla,
Nat. Nanotechnol., 2013, 8, 46-51.
4.T. Jasper-Toennies, M. Gruber, S. Karan, H. Jacob, F. Tuczek and
R. Berndt, Nano Lett., 2017, 17, 6613-6619.
5.B. C. Stipe, M. A. Rezaei and W. Ho, Science, 1998, 279, 1907-
1909.
In conclusion we have demonstrated both the self-
assembly and dehalogenation of 44BEP molecules on different
crystal surfaces at sub-molecular level. We have shown that
the molecular architectures formed are sensitive to the
underlying crystalline metal surfaces due to distance-induced
effects. This reveals the important role of noble metal species
1
1
in the construction of large scale regular molecular lattices and 16.N. Jiang, Y. Y. Zhang, Q. Liu, Z. H. Cheng, Z. T. Deng, S. X. Du, H. J.
in catalysing the C-Br bond dissociation. For Au(111), both
swinging and rotational motions of the dimer and trimer
indicate a high mobility and weak surface coupling with the
surface. Kagome lattices stabilized by Br…H–C and N…H-C
hydrogen bonds are produced on Ag(111) surfaces resulting in
regular self-assembled architectures. C-C bonds formed by
Ullmann reactions and pyridine induced C-H activations, reveal
a way to potentially build large scale chains in a controlled
manner. While for the Cu(111) surface, the random connection
between two neighbouring molecules in linear chains and
Gao, M. J. Beck and S. T. Pantelides, Nano Lett., 2010, 10, 1184-
188.
7.J. Mao, H. Zhang, Y. Jiang, Y. Pan, M. Gao, W. Xiao and H. J. Gao,
J. Am. Chem. Soc., 2009, 131, 14136-14137.
8.J. V. Barth, Annu. Rev. Phys. Chem., 2007, vol. 58, pp. 375-407.
9.S. K. Hämäläinen, N. van der Heijden, J. van der Lit, S. den
Hartog, P. Liljeroth and I. Swart, Phys. Rev. Lett., 2014, 113,
1
1
1
1
186102.
2
0.X. Zhou, C. G. Wang, Y. J. Zhang, F. Cheng, Y. He, Q. Shen, J.
Shang, X. Shao, W. Ji, W. Chen, G. Q. Xu and K. Wu, Angew.
Chem. Int. Ed., 2017, 56, 12852-12856.
selective three-branch junctions at Br…Br sites offer 21.Q. T. Fan, C. C. Wang, Y. Han, J. F. Zhu, J. Kuttner, G. Hilt and J.
opportunities to design tailored molecular architectures.
These results shed new light on how to fabricate
supramolecular devices using a bottom-up approach.
M. Gottfried, ACS Nano, 2014, 8, 709-718.
2.H. Y. Gao, P. A. Held, M. Knor, C. Muck-Lichtenfeld, J.
Neugebauer, A. Studer and H. Fuchs, J. Am. Chem. Soc., 2014,
2
136, 9658-9663.
The authors acknowledge financial support from the
Deutsche Forschungsgemeinschaft (SFB 858, TRR 61, GA
2430/1-1, AM 460/2-1), Science Foundation Ireland (SFI
4
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