Thermally Induced Transformation of Non-Hexagonal Carbon Rings in

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Thermally Induced Transformation of Non-Hexagonal Carbon Rings in Graphene-like Nanoribbons Meizhuang Liu, Mengxi Liu, Zeqi Zha, Jinliang Pan, Xiaohui Qiu, Tao Li, Jiaobing Wang, Yue Zheng, and Dingyong Zhong J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.8b02565 • Publication Date (Web): 19 Apr 2018 Downloaded from http://pubs.acs.org on April 19, 2018

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The Journal of Physical Chemistry

Thermally Induced Transformation of Non-hexagonal Carbon Rings in Graphene-like Nanoribbons ⊥

⊥

Meizhuang Liu†, , Mengxi Liu‡, , Zeqi Zha‡, Jinliang Pan‡, Xiaohui Qiu‡, Tao Li§, Jiaobing Wang§, Yue Zheng†, and Dingyong Zhong*,† †

School of Physics and State Key Laboratory for Optoelectronic Materials and Technologies, Sun Yat-sen University, 510275 Guangzhou, China

‡

CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China §

School of Chemistry, Sun Yat-sen University, 510275 Guangzhou, China

Abstract Exploring the structural transformation of non-hexagonal rings is of fundamental

importance

for

understanding

the

thermal

stability

of

non-hexagonal rings and revealing the structure-property relationships. Here, we report on the thermally induced transformation from the fused tetragon-hexagon (4-6) carbon rings to a pair of pentagon (5-5) rings in the graphene-like nanoribbons periodically embedded with tetragon and octagon (4-8-4) carbon rings. A distinct contrast among tetragon, pentagon, hexagon and octagon carbon rings is provided by non-contact atomic force microscopy with atomic resolution. The thermally activated bond rotation with the dissociation of the shared carbon dimer between the 4-6 carbon rings is the key step for the 4-6 to 5-5 transformation. The energy barrier of the bond rotation, which results in the formation of an irregular octagon ring in the transition state, is calculated to be 1.13 eV. The 5-5 defects markedly change the electronic local density of states of the graphene-like nanoribbon, as observed by scanning tunneling microscopy. Our density functional theory calculations indicate that the introduction of periodically embedded 5-5 rings will significantly narrow the electronic band gap of the graphene-like nanoribbons. 1 / 17

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Introduction Non-hexagonal defects as a topological modification play an important role in altering the physical and chemical properties of low-dimensional graphenic structures.1,2 In graphene, the topological defects can be spontaneously formed during the growth process.3-5 The extended line defects composed of alternative pentagon-heptagon (5-7) rings or pentagon pair and octagon rings (5-8-5) have been observed by scanning tunneling microscopy (STM) at grain boundaries in graphene grown by chemical vapor deposition. The 5-8-5 line defects have been predicted to have a metallic character in graphene-based nanodevices.6 As for graphene nanoribbons (GNRs), which has attracted extensive attention as promising materials for nanoelectronic devices,7-12 the non-hexagonal carbon rings have also been embedded through surface-assisted chemical synthesis.13,14 Specific non-hexagonal defects can be obtained by utilizing predefined precursor molecules.15-17 The tetragon and octagon rings (4-8-4) have been confirmed to have prominent influences on the distribution of localized electronic states and markedly change the electronic structure of the nanoribbons.14 The transformation of non-hexagonal rings usually requires sufficient energy to surmount the activation barrier of atom migration and bond rotation. For instance, Stone-Wales (SW) transformation, in which four hexagons are converted into an arrangement of two pentagons and two heptagons by a 90° rotation of a pair of atoms, has a high kinetic barrier which obstructs the occurrence of the SW transformation at a temperature below 1000 °C.18 Similar to SW transformation, the divacancy defects can be converted from the configuration of two pentagons and one octagon into three pentagons and three heptagons, which has the barriers of 5-6 eV for the bond rotations.19 The transformation of non-hexagonal rings can be induced by electron beam irradiation, which has been directly observed in graphene by transmission electron microscope (TEM).20-22 The high-energy electron beam irradiation drives the atom migration and bond rotation resulting in the local reorganization of graphene lattice. In on-surface synthesis, thermal activation is applied for promoting covalent 2 / 17


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bond dissociation and formation and has been employed to induce, for example, dehalogenation,

dehydrogenation

and

radical

cyclization.23-27

However,

the

transformation of non-hexagonal rings induced by thermal activation was rarely observed due to the relatively high energy barriers. Herein, we report the thermally induced transformation from tetragon-hexagon (4-6) carbon rings to a pair of pentagon (5-5) rings in the graphene-like nanoribbons periodically embedded with tetragon and octagon (4-8-4) carbon rings. The embedded tetragon carbon rings have a strong ring strain due to the C-C-C bond angles of 90°.16 Thermally activated bond rotation takes place in the 4-6 rings with the formation of 5-5 rings. Non-contact atomic force microscopy (nc-AFM) with a CO-functionalized tip allows us to unambiguously distinguish the intramolecular structures, confirming the existence of tetragon, pentagon, hexagon and octagon carbon rings in the GNRs. The effect of 5-5 defects on the local density of states has been revealed by scanning tunneling microscopy (STM), consistent with our density functional theory (DFT) calculations.

Experimental and Theoretical Methods STM measurements were performed on an Omicron low-temperature STM operated in ultrahigh vacuum (base pressure of 1× 10 mbar) at 78 K. Single crystalline Au(111) surfaces were cleaned by cycles of Ar+ sputtering and annealing. 1,6,7,12-tetrabromo-3,4,9,10-perylene-tetracarboxylic-dianhydride

(Br4-PTCDA)

molecules were synthesized following a reported method.28 4, 4"-dibromo-p-terphenyl (DBTP) and Br4-PTCDA molecules were evaporated onto the Au(111) substrate from quartz crucibles at the temperatures of 423 K and 528 K, respectively. A direct current tungsten filament located on the back side of the sample holder was used to heat the samples. Electrochemically etched tungsten tips were used for STM measurements. The STM images were taken in the constant-current mode and the voltages refer to the bias on samples with respect to the tip. The nc-AFM measurement was carried out at LHe temperature in constant-height frequency modulation mode with a CO-functionalized tip (resonance frequency f0 ~ 40.7 kHz, oscillation amplitude A ~ 3 / 17



100 pm, quality factor Q ~ 5.6×104). Spin polarized DFT calculations were conducted with the Vienna ab-initio Simulation Package (VASP) code.29,30 For geometry optimizations and electronic structure calculations, the Perdew-Burke-Ernzerhof (PBE) functional31 was applied. The valence-core interactions are described using the Projector Augmented Wave (PAW) method.32 The plane-wave energy cutoff used for all calculations is 400 eV. The convergence criterion for the forces of structure relaxations is 0.01 eV Å. A supercell arrangement was used with a 15 Å vacuum layer to avoid spurious interactions between the nanoribbons and periodic images. The electronic structure calculations were performed using a k-point grid of 6×1×1. We employed the climbing image nudged elastic band method (CINEB)33,34 using 6 images to calculate the energy barrier of transition state for the transformation process. The convergence criterion for the forces during seeking for the transition state is set to 0.01 eV/ Å. The structural relaxation is carried out with the Fast Inertial Relaxation Engine (FIRE) optimizer.35

Results and Discussion

Figure 1.Schematic diagram of the thermally induced transformation from 4-6 to 5-5 rings. (a) 1,6,7,12-tetrabromo-3,4,9,10-perylene-tetracarboxylic-dianhydride (Br4-PTCDA) precursor; (b) Linear PTCDA-Au polymers formed at 220 °C. (c) Graphene-like nanoribbons comprising 4-8-4 carbon rings. (d) The transformation from tetragon-hexagon carbon rings to a pair of pentagon rings after the removal of side anhydride groups.

4 / 17


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Graphene-like nanoribbons comprising 4-8-4 rings were fabricated by using the Br4-PTCDA molecule on Au(111) surfaces through surface-assisted dehalogenation and cyclodehydrogenation. As sketched in Figure 1, after annealing to 220 °C, Br4-PTCDA molecules (Figure 1a) are dehalogenated and bound with gold atoms, resulting in the formation of gold-organic polymers (Figure 1b). Au-C bond cleavage and simultaneous cyclodehydrogenation leads to the formation of 4-8-4 rings between adjacent perylene backbones by annealing at 360 °C (Figure 1c).14 By further annealing at 380 °C for 20 min, the side anhydride groups are partially dissociated from the perylene backbones. Due to the existence of the tetragon ring, the graphenic structure will undergo a structural evolution, resulting in the transformation from the fused 4-6 ring to the 5-5 ring (Figure 1d). The radical sites formed by the removal of a dianhydride group are saturated with hydrogen atoms which can be provided by the dehydrogenation in the formation of four-membered rings and the fusion of poly(para-phenylene) (PPP) nanowires.

Figure 2. Bottom-up fabrication of the graphene-like nanoribbons periodically embedded with 4-8-4 rings. (a) High-resolution STM image of the PPP polymers and PTCDA-Au polymers alternatively aligned on Au(111) prepared at 220 °C (V = −1.8 V, I = 1.4 nA). (b) STM image obtained at positive bias voltage (V = 0.6 V, I = 1.0 nA). (c, d) Charge density plots related to the highest occupied and lowest unoccupied ribbon states of the PTCDA-Au polymer. (e, f) STM images of the highest occupied (e) and lowest unoccupied (f) ribbon states of graphene-like nanoribbons (dashed regions) comprising 5 / 17



4-8-4 carbon rings acquired at negative bias voltage (V = −1.0 V, I = 0.5 nA) and positive bias voltage (V = 0.6 V, I = 0.5 nA).

One-dimensional constraint assisted by the PPP polymers was employed to synthesize the nanoribbons with a better structural quality. The PPP polymers were obtained from the DBTP molecules after dehalogenation at 160 °C on the Au(111) surface. After annealing at 220 °C, the formed PTCDA-Au polymers and PPP polymers were alternatively aligned on the surface through the hydrogen-bond interactions. The high-resolution STM images (acquired at 78 K) of both PPP and PTCDA-Au polymers were obtained by using the molecule-functionalized tip, as shown in Figure 2. The molecular orbitals can be directly imaged in the constant-current mode owing to the enhanced spatial resolution and the electronic states at the tip apex (see supporting information Figure S1).36,37 The distinct electronic states of PTCDA-Au polymers were clearly revealed in the STM images (Figure 2a and b), even if the metal-organic polymers have relatively strong interactions with the gold substrate as verified by the relief of the herringbone reconstruction (see supporting information Figure S2).38,39 With a negative sample bias (−1.8 V), the occupied states consisting of eight maxima for each PTCDA intermediate were displayed (Figure 2a),40 consistent with the calculated result shown in Figure 2c. However, only a blurred image of the unoccupied states of the hybrid intermediate was acquired when a positive bias voltage (0.6 V) was applied (Figure 2b). As the substrate temperature was elevated, 4-8-4 rings started to emerge between adjacent perylene backbones (dashed regions), coexisting with the unreacted PTCDA-Au hybrids (Figure 2e and 2f). The spatial distribution of the highest occupied (HO) and lowest unoccupied (LU) ribbon states, which are identified as four and two bright protrusions located symmetrically around the octagon and tetragon rings, respectively, is much different from that of the PTCDA-Au hybrids.

6 / 17


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Figure 3. High-resolution STM images of the 5-5 defect states. (a, c) High-resolution STM images of

the graphene-like nanoribbon with one 5-5 defect located at one side (dashed regions) of the nanoribbon at negative bias voltage (V = −1.0 V, I = 1.2 nA) and positive bias voltage (V = 0.6 V, I = 1.0 nA). (b, d) Density plots related to the highest occupied (b) and lowest unoccupied (d) ribbon states of the graphene-like nanoribbon with one 5-5 defect. (e,g) High-resolution STM images of the axisymmetric defect states (dashed regions) with two 5-5 defect on both sides of the ribbon at different bias voltages (V = −1.0 V, I = 1.0 nA; V = 0.6 V, I = 0.8 nA). (f, h) Density plots of the highest occupied (f) and lowest unoccupied (h) ribbon states of the nanoribbon with two pairs of 5-5 defects.

By further annealing to 380 °C for 20 min, a portion of the side anhydride groups were dissociated from the perylene backbones accompanied with the transformation from tetragon carbon rings to more stable pentagon rings. The high temperature simultaneously resulted in the disorder of polymer arrays and the occurrence of side reactions (see supporting information Figure S3). PTCDA molecules adsorbed on a Cu(111) surface also undergo decarboxylation at much lower temperatures, as reported elsewhere.41 We believe that the formation of the pentagon carbon rings leads to the release of the strain arising from the four-membered cyclic structure with a large angular distortion from the ideal sp2-hybridization. The insertion of pentagon rings dramatically alters the local electronic states of the nanoribbons. The high-resolution STM images revealed two types of defect states in the nanoribbons, which correspond to one and two pairs of pentagon carbon rings, respectively (see 7 / 17



supporting information Figure S4)42. The STM images (Figure 3a and e) acquired at −1 V exhibit two bright protrusions located at two opposite edges of the octagon carbon rings. As the bias voltage was set at 0.6 V, the localized defect states (Figure 3c and g) have an obvious enhancement around the octagon rings. The defect states shown in Figure 3c are lack of 2-fold rotational symmetry because there is only one pair of 5-5 rings located at one side (right) of the nanoribbon. In contrast, the symmetric location of the two pairs of pentagon rings on both sides of the ribbons results in the symmetric distribution of the defect states in Figure 3e and g. The same defect states can be repeatedly observed in the experiments (see supporting information Figure S5). The spatial distribution of the defect states in the high-resolution STM images agrees with the density plots related to the highest occupied (Figure 3b and f) and lowest unoccupied (Figure 3d and h) ribbon states of graphene-like nanoribbons with 5-5 defects.

Figure 4. Experimental and simulated AFM images of the nanoribbon with 5-5 rings. (a)

Constant-height nc-AFM frequency shift image of graphene-like nanoribbon resolving the non-hexagonal carbon rings taken with a CO-functionalized tip (Oscillation amplitude AOSC = 1 Å, V = 0 V, z offset −2 Å below STM setpoint: −0.6 V, 20 pA ). (b, c) Zoomed AFM images of the nonhexagonal carbon rings. (d) AFM image with overlaid molecular structure optimized by DFT calculations. (e) Simulated constant-height AFM images. A flexible CO tip (AOSC=1 Å; ktip=0.5 N/m) at the heights of 800 pm is used in the simulation.

Non-contact atomic force microscopy (nc-AFM), which is a unique way to directly observe the atomic structures of single molecules or on-surface synthesized 8 / 17


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products,43-45 was employed to verify the bonding configurations of non-hexagonal carbon rings in the graphene-like nanoribbons (Figure 4). Besides the tetragon and hexagon rings, three pairs of pentagon rings were observed surrounding the central octagon rings in Figure 4a. Figure 4b and c are the zoomed AFM images showing the details of the hexagonal and nonhexagonal rings. Among them, the tetragon ring exhibits the highest contrast probably due to the proximity of the four carbon atoms. The transformation from the 4-6 to 5-5 rings results in a non-axisymmetric feature and leads to a geometric distortion of the graphene-like nanoribbon, which coincides with the optimized geometric structure by DFT calculations (Figure 4d). Furthermore, the simulated AFM image (Figure 4e) shows very good agreement with the main features obtained in the AFM experiments.46,47

Figure 5. DFT calculations. (a) Top views of initial state (IS), transition state (TS), and final state (FS)

of the transformation from 4-6 to 5-5 rings. (b) Transformation energy barrier. (c, d) Optimized atomic structures of graphene nanoribbons embedded with different concentrations of pentagon carbon rings and the corresponding band structures calculated by DFT.

DFT calculations have been carried out to get insight into the kinetics of the thermally induced transformation from 4-6 to 5-5 rings. In our model system, the initial state contains the 4-8-4 rings between two perylenes. One hydrogen atom neighboring a tetragon ring is removed, mimicking the removal of the anhydride group of PTCDA in our experiment. The 4-6 to 5-5 transformation is related to the rotation of a pair of carbon atoms (green colored in Figure 5a) by about 35°. At the 9 / 17



same time, the C-C bond shared by the 4-6 rings is dissociated, leading to an irregular flattened eight-membered carbon ring in the transition state. The flattened eight-membered ring are divided into two five-membered rings by further rotation of the carbon pair by about 40° followed by the bonding of carbon atoms. The activation barrier for the transformation is calculated to be 1.13 eV which can be surmounted on the Au(111) surface at the temperature of 380 °C (Figure 5b). The final state with a pair of pentagon rings is energetically favorable than the initial state comprising tetragon rings (Figure 5b), implying the transformation is thermodynamically favorable. The embedding of non-hexagonal carbon rings has been theoretically proven to markedly change the electronic structure and magnetic properties of GNRs.48-50 The calculated geometric configurations of GNRs embedded with different concentrations of pentagon and octagon rings and the corresponding electronic structures are displayed in Figure 5c and 5d. As shown in Figure 5c, the GNR embedded with lower concentration of pentagon and octagon rings has a direct band gap of 0.23 eV. As the concentration of pentagon carbon rings increases, the conduction band minimum deviates from the X point and the band gap turns to be indirect (Figure 5d). The band gap of 0.10 eV is smaller than that of the pristine 6-ZGNR (0.58 eV) due to the introduction of non-hexagonal carbon rings. For both cases, the spin-polarized edge states are quenched owing to the local rehybridization of σ- and π-orbitals around the non-hexagonal carbon rings.

Conclusions In summary, we have studied the thermally induced transformation of non-hexagonal carbon rings in the graphene-like nanoribbons on the Au(111) surface. Under the thermal activation, the 4-6 rings were transformed to 5-5 rings after the removal of anhydride groups in the nanoribbons. Non-contact atomic force microscopy with a CO-functionalized tip provided the atomic resolution to allow us to investigate the difference among the tetragon, pentagon, heptagon and octagon carbon rings. Based on a combined STM and DFT calculations, the existence of 5-5 defects 10 / 17


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was confirmed to have a great influence on the local density of states of the nanoribbons. The energy barrier for the bond rotation in the transformation was calculated to be 1.13 eV. The different embedding concentrations of pentagon and octagon rings can determine the direct or indirect band gap type and the magnitude of the band gap, which would be an effective approach to modulate the electronic properties of carbon-based nanostructures for achieving desired functionalities.

AUTHOR INFORMATION Corresponding Author *E-mail: [email protected] Author Contributions ⊥

Meizhuang Liu and Mengxi Liu contributed to the work equally.

Notes The authors declare no competing financail interest.

Acknowledgments This work was financially supported by NSFC (project 11374374, 11574403, 21425310, 21603045) and the computation part of the work was supported by National Super-computer Center in Guangzhou.

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Thermally Induced Transformation of Non-Hexagonal Carbon Rings in

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