# Self-assembly of large nanographene into ordered structures on Au(111)

Hamza El Kari, Van Binh Vu, Xiao Zhang, Azzedine Bendounan, Hanna

Enriquez, Andrew J Mayne, Yannick J Dappe, Hamid Oughaddou

► To cite this version:

Hamza El Kari, Van Binh Vu, Xiao Zhang, Azzedine Bendounan, Hanna Enriquez, et al. Self-assembly of large nanographene into ordered structures on Au(111). Advanced Materials Interfaces, 2025, 2025, pp.e00725. 10.1002/admi.202500725. hal-05391429

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Submitted on 1 Dec 2025

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RESEARCH ARTICLE

OPEN ACCESS

# Self-Assembly of Large Nanographene Into Ordered Structures on Au(111)

Hamza El Kari<fnref n="1" /> | Van Binh Vu² | Xiao Zhang<fnref n="1" /> | Azzedine Bendounan<fnref n="3" /> | Hanna Enriquez<fnref n="1" /> | Andrew J. Mayne<fnref n="1" /> |
Yannick J. Dappe⁴ | Hamid Oughaddou<fnref n="1" />,⁵,⁶

**Correspondence:** Hamid Oughaddou (Hamid.Oughaddou@universite-paris-saclay.fr)

**Received:** 7 August 2025 | **Revised:** 15 November 2025 | **Accepted:** 16 November 2025

**Keywords:** 2D materials | DFT | polycyclic aromatic molecules | self-assembling | STM

## ABSTRACT

Polycyclic aromatic hydrocarbons (PAHs) offer a unique platform for bridging molecular design and nanoscale functionality owing to their tunable structures. Beyond their intrinsic electronic properties, PAHs exhibit significant potential for directed self-assembly, enabling the formation of ordered nanostructures with tailored functionalities. Here, we report the on-surface self-assembly of quantum dot-like nanostructures and nanoribbons from two closely related PAH molecules, $C_{96}H_{24}(C_{12}H_{25})_6$ (C96-A) and $C_{96}H_{30}$ (C96), deposited on Au(111) via molecular beam epitaxy. Scanning tunneling microscopy and spectroscopy (STM/STS) reveal a structural evolution from ordered single molecules to extended nanoribbons, with the latter exhibiting a narrow electronic bandgap of 0.8 eV. X-ray photoelectron spectroscopy (XPS) indicates a single carbon chemical environment, while near-edge X-ray absorption fine structure (NEXAFS) spectroscopy confirms a flat-lying molecular orientation. Density functional theory (DFT) calculations corroborate the experimental findings and provide insight into the self-assembly mechanisms. These results highlight the potential of engineered PAHs for the bottom-up fabrication of nanoscale electronic materials.

## 1 | Introduction

Graphene is a material of considerable interest due to its exceptional electronic [1, 2], optoelectronic [3], and optical properties [4]. However, its semi-metallic nature limits its applicability in technologies that require well-defined semiconducting behavior. Consequently, extensive efforts have been directed toward engineering semiconducting nanostructures derived from graphene [5]. In this context, quasi-1D graphene nanoribbons (GNRs) and quasi-0D graphene quantum dots (GQDs) have attracted significant attention for their potential in a wide range of applications [6, 7], including optical gain media [8], single-photon emitters [9], and photovoltaic devices [10].

The most widely employed strategy for fabricating these nanostructures is the top-down approach, which includes chemical treatments [11], lithographic patterning [12], and etching techniques [13]. While these methods can yield large quantities of graphene-based nanostructures, they generally lack precise control over size and edge structure [14, 15]; critical parameters governing the intrinsic properties of the material. This lack of structural control presents a major challenge for systematically investigating and tuning the relationship between structure and function in graphene nanostructures [16, 17].

Recently, bottom-up approaches have emerged as powerful alternatives to overcome the limitations of top-down fabrication of

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

© 2025 The Author(s). *Advanced Materials Interfaces* published by Wiley-VCH GmbH

<footnote n="1">¹Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, Orsay, France | ²SPEC, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France |</footnote>

<footnote n="3">³Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France | ⁴Université Paris-Saclay, CNRS, Centre De Nanosciences et De Nanotechnologies, Palaiseau, France | ⁵Département de Physique, CY, Cergy Paris Université, Cergy-Pontoise, France | ⁶Laboratory of Condensed Matter and Interdisciplinary Sciences (LaMCSci), B.P. 1014, Faculty of Science, Mohammed V University, Rabat, Morocco</footnote>
graphene nanostructures. These methods enable the synthesis
of molecular building blocks with precisely defined sizes and
structures, allowing for controlled growth of graphene-based
nanostructures and facilitating rigorous investigation of their
intrinsic properties [18, 19].

Graphene nanoribbons (GNRs) have been extensively
synthesized via on-surface synthesis, a bottom-up technique
that typically involves Ullmann coupling followed by cyclo-
dehydrogenation [20]. This process can be summarized in four
key steps: (1) deposition of halogenated aromatic precursors onto
a catalytic surface; (2) thermal activation to induce dissociation of
the halogen substituents; (3) surface-assisted Ullmann coupling
to form polymeric chains or intermediate structures; and (4)
cyclo-dehydrogenation to yield structurally well-defined GNRs
[20]. Using this approach, Dimas G. de Oteyza et al. demonstrated
the successful synthesis of chiral (3,1)-GNRs on various metallic
substrates, including Ag(111), Cu(111), and Au(111), using
this on-surface synthesis method [21]. Similarly, Yen-Chia
Chen et al. reported the fabrication of atomically precise 13-
armchair graphene nanoribbons (13-AGNRs) on Au(111), with
an experimentally measured bandgap of approximately 1.4 eV
[22].

On the other hand, organic synthesis enables the preparation of
large polycyclic aromatic hydrocarbon (PAH) molecules, com-
monly referred to as nanographenes [23, 24]. These well-defined
molecular building blocks enable the fabrication of graphene
nanoribbons (GNRs) on substrates in a precise, modular, and
highly controlled manner, tailored to specific structures. To
date, liquid-phase techniques have been primarily employed
to deposit nanographenes onto substrates. These methods typ-
ically involve dispersing nanographenes in a solvent, followed
by deposition via drop-casting, spin-coating, or zone-casting
[18, 25]. However, the practical application of this approach is
hindered by the poor solubility of large nanographenes and
their strong tendency to aggregate in solution, which com-
plicates both handling and uniform deposition [26, 27]. An
alternative strategy is thermal sublimation, in which specific
nanographene molecules are loaded into a Knudsen cell, ther-
mally sublimated, and subsequently deposited onto various
substrates. While the deposition of larger nanographenes by
this technique is generally limited by thermal cracking [28], it
has proven effective for smaller PAH molecules, such as hex-
abenzocoronene [29] and hexa-peri-hexabenzocoronene (HBC,
C42H18), which has a molecular diameter of approximately 1.2 nm
[30, 31].

In this article, we report on the molecular self-assembly of large
nanographenes on an Au(111) surface using molecular beam
epitaxy (MBE). Two polycyclic aromatic hydrocarbon molecules,
C96-A, and C96 are investigated in this work (Figure 1). Scan-
ning Tunneling Microscopy and Spectroscopy (STM/STS) reveal
that these molecules undergo self-assembly, forming striped
structures with a uniform size of several tens of nanometers
and a bandgap of 0.8 eV. X-ray photoelectron spectroscopy
(XPS) and near-edge X-ray absorption fine structure (NEXAFS)
measurements indicate a single carbon chemical environment,
consistent with a nearly flat molecular orientation on the
surface.

<figure><img src="image_2.png" /><figcaption>**FIGURE 1** | Molecular structures of (a) C<sub>96</sub>H<sub>30</sub> (C96) and (b) C<sub>96</sub>H<sub>24</sub>(C<sub>12</sub>H<sub>25</sub>)<sub>6</sub> (C96-A). For clarity, peripheral hydrogen atoms are omitted.</figcaption></figure>

2 | Growth and Characterization of C96-A

Figure 2a displays an STM image of the bare Au(111) surface. The well-known herringbone reconstruction is clearly visible. The atomically resolved surface is shown in the inset. Figure 2b presents an STM image of a large surface area after the deposition of 0.2 monolayers (ML) of C96-A molecules. The deposition rate, approximately 0.2 ML per minute, was calibrated using the Knudsen cell flux and confirmed by STM coverage analysis. C96-A molecules are adsorbed preferentially on the elbows of the herringbone structures, as also highlighted by the inset in Figure 2b. An individual C96-A is presented in Figure 2c. Three spots in a triangular shape are clearly observed. Surprisingly, the molecule appears only as a triangular shape without any apparent evidence of the C<sub>12</sub>H<sub>25</sub> alkyl chains groups. There is neither any tip-instability around the molecule [32], nor any bright protrusions around the molecules [33]. The line scan (L1) shown in Figure 2d, measured across the molecule in Figure 2c gives a value around 1.6 nm consistent with the expected size for this molecule (1.72 nm).

As the coverage increases, molecules start to grow and self-assemble to form dense island-shaped structures (Figure 2e–g). Figure 2h is a zoom of Figure 2g. The internal structure of the islands shows a striped structure and three orientations corresponding to the directions of the substrate are observed.

Interestingly, annealing the striped structures induces molecular
desorption from the surface. Figure 3 displays three STM images
recorded after covering the entire surface, followed by annealing
at 150°C for progressively longer durations. A clear desorption
process is observed, and after prolonged annealing, only isolated
molecules remain on the surface (Figure 3c). These results
suggest that during growth, the molecules adsorb first at the
elbows of the Au(111) herringbone reconstruction, where they act
as nucleation sites from which self-assembly proceeds, eventually
leading to the formation of striped structures.

Let us now analyze the structure of these stripes in more detail.
Figure 4a shows an atomically resolved STM image of the stripes,
where periodic protrusions are clearly visible. The line scan (L1)
in Figure 4b, taking along a stripe, gives a periodicity of 1.7 nm,
while the average distance between neighboring protrusions
within a stripe is 0.22 nm. The latter value corresponds exactly
<figure><img src="image_3.png" /></figure>

**FIGURE 2** | (a) Large-scale STM image showing the herringbone reconstruction of Au(111). Inset: atomic resolution of the clean surface. (b) Large-scale STM image of the surface after deposition of 0.2 ML of C96-A (U = 3 V, I = 0.01 nA), showing self-assembled molecules. The inset highlights the elbow adsorption sites. (c) STM image of an individual molecule (U = 1.7 V, I = 0.01 nA). (d) Line scan (L1) measured across the molecule in Figure 2c. (e–g) STM images recorded for increasing molecular coverages. (h) Zoom of (g) showing the formation of striped structures.

<figure><img src="image_4.png" /></figure>

**FIGURE 3** | (a) STM image recorded after a 1 ML exposure, showing that the molecules cover the entire surface. (b) After annealing at 150°C for 30 min. (c) After annealing at 150°C for 1 h.

to the second-nearest-neighbor distance of carbon atoms in graphene. The line scan (L2) in Figure 4c, measured across adjacent stripes, yields an inter-stripe spacing of 0.4 nm.

STS measurements were performed to probe the electronic structure of these striped structures. The differential conductivity (dI/dV) spectrum recorded at random positions on the stripes is shown in Figure 4d. The data unambiguously demonstrate the existence of a semiconducting bandgap of 0.8 eV.

### 3 | Growth and Characterization of C96 Molecule

We have also studied the deposition of the same molecular core C96 on Au(111) but without alkyl chains groups (Figure 1a) in order to observe how the absence of the alkyl chains influences the self-assembling process.

The STM image of the surface after deposition of 0.2 ML of C96 is shown in Figure 5a. As was the case for the C96-A molecule, C96 molecules preferentially adsorb on the elbows of the herringbone structure. An individual C96 is presented in Figure 5b, resembling the configuration observed for the C96-A molecules with alkyl chains. The line scan (L1) shown in Figure 5c, measured across the molecule in Figure 5b gives a size of 1.6 nm, the same size as observed for the C96-A molecule.

As the coverage increases, self-assembled striped structures are observed (Figure 5d). The line scan (L2) in Figure 5e measured along the stripes in Figure 5d gives lengths around 0.4 nm similar to the stripes obtained for the C96 molecule with alkyl chains. Figure 5f displays an STM image of these stripes. The line scan (L3) in Figure 5g measured across the stripes in Figure 5f gives lengths around 1.7 nm and an average distance between the neighboring protrusions within each stripe of 0.22 nm, respectively. These values are also identical to those observed for the C96-A
<figure><img src="image_5.png" /></figure>

**FIGURE 4** | (a) STM images showing stripes formed by the molecules, (U = 1.60 V, I = 0.3 nA). (b) Line scan (L1) measured across the stripes in Figure 2a. (c) Line scan (L2) measured along the stripes in Figure 2(a). (d) STS dI/dV curve acquired on stripes showing an energy bandgap of 0.8 eV.

<figure><img src="image_6.png" /></figure>

**FIGURE 5** | (a) STM image showing self-assembled individual C96 molecules on Au(111), (U = 3.6 V, I = 0.01 nA). (b) STM image showing individual molecule (U = -2.1 V, I = 0.01 nA). (c) line scan (L1) measured across the molecule in Figure 5b. (d) STM image showing individual molecules and stripes formed by C96 molecules (U = -2.1 V, I = 0.01 nA). (e) line scan (L2) measured along the stripes in Figure 5d. (f) STM image showing stripes with atomic resolution. (g) Line scan (L3) measured across the stripes in Figure 5f. (h) STS dI/dV curve acquired on stripes indicating an energy gap of 0.8 eV.
<figure><img src="image_7.png" /><figcaption>**FIGURE 6** | (a) The C K-edge NEXAFS spectra of a C96 film grown on Au(111), measured at normal incidence $\theta = 90^\circ$ (blue line) and grazing incidence $\theta = 20^\circ$ (red line). (b) Drawing illustrating the measurement geometry.</figcaption></figure>

molecules with alkyl chains. Finally, in order to probe the local electronic structure, we have recorded STS data on these stripes (Figure 5h). The spectra indicate a semiconducting character with an energy bandgap of 0.8 eV. These investigations point to the similarity of the results obtained by molecular beam epitaxy on both molecules, C96 and C96-A, which suggests that alkyl chains are dissociated from C96-A during the evaporation process, hence giving rise to the deposition of molecules composed of the C96 core. Initially, the alkyl separation was thought to occur during the deposition on the surface, but this hypothesis is rejected by the non-observation of alkyl islands on the surface.

Near-edge X-ray absorption fine structure (NEXAFS) is a powerful technique for gaining insights into the bonding environment and local structural configuration. It has been used to study the Carbon K-edge adsorption characteristics of many materials, including graphene [34], carbon nanotubes [35], and various organic molecules [36, 37]. Figure 6a shows NEXAFS data for a C96 film grown on Au(111), measured at normal ($90^\circ$) and grazing incidence ($20^\circ$) geometries, respectively. The measurement geometry used is illustrated in Figure 6b, which shows the orientation of the electric field relative to the incident plane (p-polarization). The spectra exhibit numerous spectroscopic features, arising from transitions of the Cls orbital to various empty final states. A strong absorption resonance, indicated by the sharp narrow peak (A), appears around 285 eV, which corresponds to the $C 1s \rightarrow \pi^*$ transition, while the $\sigma^*$ resonance is generally located at a higher photon energy (above 290 eV). Note that two other features labeled B and C with low intensity occur at 287 and 288.5 eV, respectively. They may also be associated with $\pi^*$ resonances of different chemical environments, including out-of-plane carbon atoms due to bending or tilting of the periphery of the molecules. Depending on the incident angle of the photon, an intensity balance is observed between the $\pi^*$ and $\sigma^*$ resonances. By varying the angle $\theta$ from $20^\circ$ to $90^\circ$, all $\pi^*$ resonances undergo significant attenuation, whereas the $\sigma^*$ intensity increases, indicating in this case that the $\pi$ orbitals, formed from the $p_z$ orbitals, are oriented perpendicular to the

surface. This is characteristic of benzene rings lying flat on the surface similar to monolayer graphene [38, 39]. However, at normal incidence, their intensity is not completely absent. The NEXAFS results answer the question that was raised in the initial study by Shen et al. [9], namely whether the molecules were oriented perpendicular to the surface, or did they lie flat on the surface? From our results, it is clear that most molecules lie flat, but we do not exclude that some of them are present on the surface at an angle, probably those that appear individually on the surface.

In the STM images, the molecules appear only 0.1 nm high because through-bond tunnelling reduces the apparent height [40], so only the NEXAFS results could resolve the uncertainty, showing clearly that most molecules are flat (or nearly flat) on the surface.

We have also performed X-ray photoelectron spectroscopy (XPS) to check the carbon chemical environments. Figure 7a,b displays the Cls core level spectra recorded after deposition of the C96 molecule on the Au(111) surface, measured at normal emission and at $60^\circ$ off-normal emission for surface-sensitive detection, respectively. The spectra are fitted using the Doniach-Sunjic line shape [41]. The best fit was obtained with a Gaussian profile width of 0.32 eV and a Lorentzian profile width of 0.14 meV. The experimental data are represented by black dots, while the fitted curves are the solid black lines.

The $Cl_s$ core-level spectra in both figures show only one component, located at 283.67 eV, indicating the existence of only one chemical environment. In general, as the emission angle increases, XPS surface sensitivity improves, allowing selective detection of surface contributions, increasing the relative intensities of the surface component peak. Therefore, comparing Figure 7a,b, the peaks remain unchanged, suggesting that this component originates from molecules lying in the same plane on the surface, in good agreement with STM and NEXAFS results.
<figure><img src="image_8.png" /><figcaption>**FIGURE 7** | XPS spectra recorded after deposition of C96 on an Au(111) substrate. (a) C1s core-level spectrum recorded at normal emission. (b) C1s core-level spectrum recorded at grazing emission (60° off-normal).</figcaption></figure>

To better understand the experimental results, we employed the second-nearest-neighbor tight-binding (2NN TB) method and the FIREBALL DFT formalism (see Computational Method). From the experimental STM images (Figures 2c and 5b), it is evident that the alkyl chains were effectively separated from the central part of the C96-A molecule on the gold surface. Accordingly, we modeled the system by adsorbing a C96 molecule onto a five-layer Au(111) slab with a periodicity of 26.09 × 25.85 Å² (Figure 8a). The gold surface was compressed by 1.19% and 0.39% along the in-plane lattice vectors of the Au(111) surface. Notably, this level of compression does not significantly affect the density of states within the compression range of [-5%, +5%] compared to the pristine surface (see Figure S1). The resulting surfaces remain stable under compressive, tensile, or combined strain conditions within the [-5%, +5%] strain range compared to the pristine surface.

The corresponding FIREBALL-STM simulated images, based on the unit cell shown in Figure 8a, are shown in Figure 8b,c. The simulations successfully reproduce the characteristic three-lobe signature of the C96-A observed in the experimental STM images (Figures 2c and 5b). The origin of this signature is

further elucidated by the local density of states (LDOS) maps in Figure 8d,e, obtained using the 2NN TB method.

Figure 9a shows an atomically resolved STM image of two groups of three C96 molecules on the gold surface. This image reveals that the C96 molecules self-assemble and strongly confirms that the alkyl chains were separated from the central part of the C96-A. Figure 9b presents the corresponding simulated STM image of three C96 adsorbed on a five-layer Au(111) slab with a periodicity of 43.48 × 43.09 Å². This simulation was performed using the FIREBALL-STM method, considering only the C96 and four apex atoms of the gold tip, while neglecting the contribution of the gold surface. The corresponding atomic model is shown in Figure 9c. A good agreement is observed between the experimental and simulated STM images.

In addition, we simulated a 2D network of C96 by investigating two hexagonal arrangements, labeled M1 and M2 (Figure 10a,b). The M1 model consists of a single C96 molecule in the primitive cell, with all molecules oriented in the same direction (Figure 10a). The corresponding simulated STM image is shown in Figure 10c, where a striped pattern is observed. These stripes also appear along the armchair edges of the C96 and are highlighted by blue continuous lines.

In contrast, the M2 model contains two C96 molecules in a rectangular primitive cell, oriented in opposite directions (Figure 10b). The simulated STM image for this configuration is shown in Figure 10d, where a similar striped pattern is observed and again highlighted by blue lines.

Both models show good agreement with the experimental STM images. Distinct empty spaces separating the stripes are clearly visible, with an inter-stripe distance of approximately 0.38 nm, which is consistent with the experimental value of 0.4 nm. The projected density of states (PDOS) for the M1 and M2 models are shown in Figure 10e,f, respectively. Both exhibit semiconducting behavior, with an experimental bandgap of 0.8 eV, which is reasonably close to the density functional theory (DFT) calculated value of about 1.2 eV. The slight difference between the experimental and calculated values arises from substrate screening and many-body effects that are not fully accounted for in the DFT formalism.

Because of the scale of the system, it is computationally impractical to incorporate the herringbone reconstruction of the Au(111) surface into the STM simulations. This reconstruction significantly affects the molecular stripe arrangement. While explicitly modeling it would demand simulating a prohibitively large number of atoms beyond our current computational resources, our simulations still successfully replicate the experimental findings.

In conclusion, in this article, we have studied the adsorption and self-assembly of PAH nanographene molecules on the Au(111) surface using STM, NEXAFS, and XPS techniques. At low coverage, individual molecules are mainly located at the elbows of the Au(111) herringbone reconstruction, while higher coverage leads to the formation of nanometer-sized striped islands with a bandgap of about 0.8 eV. XPS and NEXAFS data indicate a largely homogeneous carbon environment and suggest that
<figure><img src="image_9.png" /><figcaption>**FIGURE 8** | (a) Optimized C96 on a five-layer slab of 26.09 × 25.85 Å² Au(111) surface. (b,c) Constant-height STM images calculated using FIREBALL-STM simulations. (d,e) Constant-height current calculated STM images achieved using the 2NN TB method.</figcaption></figure>

<figure><img src="image_10.png" /><figcaption>**FIGURE 9** | (a) Experimental STM image of two groups of three C96 on the gold surface ((U = -2 V, I = 0.01 nA). (b) corresponding STM simulation. (c) corresponding atomic model.</figcaption></figure>

most molecules adopt a flat orientation on the surface. However, the remaining $\pi^*$ intensity at normal incidence indicates the presence of an average molecular tilt, likely due to molecules that are individually oriented on the surface. These findings, supported by TB and DFT calculations, demonstrate the self-assembly capability of these molecules on Au(111) and open the way for further studies on different substrates to better assess their reactivity and intrinsic electronic and optical properties.

## 4 | Experimental Method

All experiments were carried out in an ultrahigh vacuum system where the base pressure was better than $3.0 \times 10^{-10}$ mbar. The single-crystal Au(111) substrate (99.999%) was cleaned by several cycles of Ar+ sputtering with a beam energy of 2 keV at $5 \times 10^{-6}$ mbar. The substrate was then annealed at 500°C for 40 min to obtain a high-quality surface as attested by low-energy electron diffraction (LEED) and STM topography measurements.

Two PAH molecules, C96 and C96-A (Figure 1) [42], were deposited on the Au(111) substrate. Two separate Knudsen cells loaded with these PAH molecules were used to avoid any cross-contamination. The temperature of evaporation of C96 and C96-A was 120°C and 110°C, respectively. These temperatures give a deposition rate of approximately 0.2 ML/min. 1 ML corresponds

to a molecular coverage where one layer of C96 (or C96-A) molecules uniformly covers the Au(111) surface.

The chemical composition was monitored by Auger electron spectroscopy (AES) by observing the appearance of a peak at 272 eV corresponding to the carbon of the molecules. The morphology of the surface was characterized in situ by LT-STM, operated at 77 K, while the electronic structure was probed by STS also at 77K using a standard lock-in technique. Tungsten tips were prepared by electrochemical etching, degassed in situ at 200°C, and cleaned by applying voltage pulses until atomic resolution of the clean metal surface was obtained, and the STS spectrum exhibited a peak at 400 mV, characteristic of the surface state of clean Au [43]. All STM measurements were recorded in the constant current mode. The Nanotec WSxM software [44] was used for processing and analyzing the data. The NEXAFS and XPS experiments were performed at the TEMPO beamline of the Synchrotron SOLEIL-France. The measurements were performed using linear horizontal polarization of the light. The energy resolution of the XPS data was estimated to be approximately 80 meV for the photon energy used of 390 eV (mainly limited by the resolving power of the beamline) and the meusurments were recored at normal incidence (90° with respect to the surface plan of the sample) and grazing geometry (60° with respect to the surface plan of the sample).
<figure><img src="image_11.png" /><figcaption>**FIGURE 10** | (a,c) M1 atomic model with its corresponding simulated STM image, respectively. (b,d) M2 atomic model with its corresponding calculated STM image respectively. The stripes are highlighted by blue continuous lines. (e,f) PDOS for the M1 and M2 models, respectively.</figcaption></figure>

For NEXAFS, the normal incidence corresponds to 90° with respect to the surface plan of the sample, and the grazing geometry corresponds to 20°.

**4.1 | Computational Method**

Numerical calculations to model these molecules on surfaces were performed using parametrized Tight-binding (TB) model (for big systems) or density functional theory (DFT) approach (for smaller systems).

**Tight-Binding calculations:** we have used the second-nearest-neighbor tight-binding (2NN TB) Hamiltonian, which only considers the 2p_z orbitals of the carbon atoms. As such, we set the on-site energy to 0 eV, the nearest-neighbor hopping energy to -2.7 eV, and the next-nearest-neighbor hopping energy to 0.27 eV.

After diagonalization, the resulting eigenvalues and eigenstates were used to calculate the local density of states (LDOS). This approach can be considered as the constant-height STM current in the Tersoff-Hamman approximation [45].

**DFT calculations:** we have used the localized-orbital basis set DFT FIREBALL code [46]. Using a local density approximation (LDA)-like for the exchange and correlation functional through the McWeda approach [47] and a combination of atomic-like orbitals as a basis set [48], the FIREBALL code is a very efficient DFT tool to speed up the calculations. One of the most important advantages of FIREBALL is that it provides a great approach to the STM experiments by using a combined non-equilibrium Green function technique [49, 50]. In this case, the tip and sample were separately calculated with the FIREBALL code [46] using the same cutoff radius as set in Ref. [51]. In this article, the PAH molecules have been studied on a five-layer slab of the fcc
gold Au(111). Because of the large size of the systems, we have chosen to set effortless convergence criteria as less than 10⁻⁴ eV for the total energy difference and 0.1 eV/Å for the force tolerance. Moreover, we used 99 Å of vacuum thickness along the z-axis. The systems without gold surface have also been studied and in this case, we reduced the force tolerance to 0.05 eV/Å to improve the accuracy. All these structures studied in vacuum were performed at the Γ point. Additionally, all the other structures on the gold surface were calculated at the Γ point. The two bottom layers of the gold surface were fixed in the geometry relaxation process in order to keep the bulk parameters on the bottom of the slab.

## 4.2 | Statistical Analysis

### 4.2.1 | Scope and Rationale

This study focuses on the structural and electronic characterization of self-assembled large nanographenes using scanning probe and synchrotron-based spectroscopies. Classical inferential statistics (e.g., *t*-tests, ANOVA) were not applicable, as conclusions were drawn from reproducible physical phenomena rather than comparative hypothesis testing.

### 4.2.2 | Data Acquisition and Replication

All STM, STS, XPS, and NEXAFS measurements were repeated across independently prepared samples and multiple surface regions to ensure consistency.

Observed phenomena reflect intrinsic properties of the system and were not artifacts of specific measurement locations or preparation runs.

### 4.2.3 | Sample Size (n)

STS curves were collected at ≥ 15 random locations per sample. Representative dI/dV spectra were averages of these curves, confirming reproducibility and consistent bandgap values (~0.8 eV).

XPS and NEXAFS spectra were acquired in multiple independent runs to validate the chemical environment and molecular orientation.

### 4.2.4 | Data Pre-Processing and Presentation

STS spectra were processed using standard lock-in amplification; smoothed for clarity while preserving spectral features.

STM images were plane-corrected and flattened using WSxM [44]; molecular dimensions and inter-row distances were confirmed on raw images.

XPS spectra were fitted using Doniach-Sunjić line shapes convoluted with a Gaussian profile; C 1s binding energies and FWHM were consistent across measurements.

Data were presented as representative spectra or images; quantitative values were reported as consistent averages with estimated uncertainties (±0.05 eV for STS, ±0.1 nm for STM).

### 4.2.5 | Software

WSxM [44] (STM/STS), Igor Pro (XPS/NEXAFS) were used for data processing.

FIREBALL DFT and in-house tight-binding routines were employed for theoretical modeling and simulations.

## Author Contributions

H.O. conceived and conducted the research project. H.E.-K., X.Z., A.B., A.J.M., and H.O. performed the experiments. V.-B.V. and Y.D. performed the calculations. H.E.-K., V-B.V., X.Z., H.E., A.B., Y.D., A.J.M., and H.O. analyzed the results and contributed to the scientific discussions. All the authors contributed to the manuscript preparation.

## Acknowledgements

This work was supported by a public grant overseen by the French National Research Agency (ANR), reference: ANR-11-IDEX-0003-002. H.O. thanks Dr. Stéphane Campidelli for providing the C₉₆H₂₄(C₁₂H₂₅)₆ and C₉₆H₃₀ molecules. H.O. would also like to thank the Moroccan FINCOME PROGRAM 2025 for funding.

## Conflicts of Interest

The authors declare no conflicts of interest.

## Data Availability Statement

All data needed to evaluate the conclusions of this study are available in the main text or the supporting materials. Any additional data pertaining to this study can be made available, pending approval, by contacting the corresponding author.

## References

1. J.-H. Chen, C. Jang, S. Xiao, M. Ishigami, and M. S. Fuhrer, "Intrinsic and Extrinsic Performance Limits of Graphene Devices on SiO₂," *Nature Nanotechnology* 3 (2008): 206–209.

2. K. I. Bolotin, K. J. Sikes, Z. Jiang, et al., "Ultrahigh Electron Mobility in Suspended Graphene," *Solid State Communications* 146 (2008): 351–355.

3. T. V. Cuong, V. H. Pham, Q. T. Tran, et al., "Optoelectronic Properties of Graphene Thin Films Prepared by Thermal Reduction of Graphene Oxide," *Materials Letters* 64 (2010): 765–767.

4. R. R. Nair, P. Blake, A. N. Grigorenko, et al., "Fine Structure Constant Defines Visual Transparency of Graphene," *Science* 320 (2008): 1308.

5. Y. Zhang, T.-T. Tang, C. Girit, et al., "Direct Observation of a Widely Tunable Bandgap in Bilayer Graphene," *Nature* 459 (2009): 820–823.

6. K. Müllen, "Evolution of Graphene Molecules: Structural and Functional Complexity as Driving Forces behind Nanoscience," *ACS Nano* 8 (2014): 6531–6541.

7. X. Zhang, H. El Kari, H. Enriquez, et al., "Synthesis and Properties of Phosphorus Nanostructures on Au(110)," *Nanoscale* 16, no. 45 (2024): 21088–21095.

8. G. M. Paternò, Q. Chen, X. Y. Wang, et al., "Synthesis of Dibenzo[hi,st]Ovalene and Its Amplified Spontaneous Emission in
a polystyrene Matrix,” *Angewandte Chemie International Edition* 56 (2017): 6753–6757.

9. S. Zhao, J. Lavie, L. Rondin, et al., “Single Photon Emission from Graphene Quantum Dots at Room Temperature,” *Nature Communications* 9 (2018): 3470.

10. X. Yan, X. Cui, B. Li, and L. S. Li, “Large, Solution-processable Graphene Quantum Dots as Light Absorbers for Photovoltaics,” *Nano Letters* 10 (2010): 1869–1873.

11. L. Liu, Y. Zhang, W. Wang, C. Gu, X. Bai, and E. Wang, “Nanosphere Lithography for the Fabrication of Ultranarrow Graphene Nanoribbons and on-Chip Bandgap Tuning of Graphene,” *Advanced Materials* 23 (2011): 1246–1251.

12. B. Song, G. F. Schneider, Q. Xu, G. Pandraud, C. Dekker, and H. Zandbergen, “Atomic-scale Electron-beam Sculpting of near-defect-free Graphene Nanostructures,” *Nano Letters* 11 (2011): 2247–2250.

13. M. Y. Han, B. Ozyilmaz, Y. Zhang, and P. Kim, “Energy Band-gap Engineering of Graphene Nanoribbons,” *Physical Review Letters* 98 (2007): 206805.

14. D. V. Kosynkin, A. L. Higginbotham, A. Sinitskii, et al., “Longitudinal Unzipping of Carbon Nanotubes to Form Graphene Nanoribbons,” *Nature* 458 (2009): 872–876.

15. L. Jiao, L. Zhang, X. Wang, G. Diankov, and H. Dai, “Narrow Graphene Nanoribbons from Carbon Nanotubes,” *Nature* 458 (2009): 877.

16. L. Li, G. Wu, G. Yang, J. Peng, J. Zhao, and J. J. Zhu, “Focusing on Luminescent Graphene Quantum Dots: Current Status and Future Perspectives,” *Nanoscale* 5 (2013): 4015–4039.

17. Q. Xu, Q. Zhou, Z. Hua, et al., “Single-particle Spectroscopic Measurements of Fluorescent Graphene Quantum Dots,” *ACS Nano* 7 (2013): 10654–10661.

18. A. Narita, X. Feng, Y. Hernandez, et al., “Synthesis of Structurally Well-defined and Liquid-phase-processable Graphene Nanoribbons,” *Nature Chemistry* 6 (2014): 126–132.

19. A. Narita, I. A. Verzhbitskiy, W. Frederickx, et al., “Bottom-up Synthesis of Liquid-phase-processable Graphene Nanoribbons with near-infrared Absorption,” *ACS Nano* 8 (2014): 11622–11630.

20. J. Cai, P. Ruffieux, R. Jaafar, et al., “Atomically Precise Bottom-up Fabrication of Graphene Nanoribbons,” *Nature* 466, no. 7305 (2010): 470–473.

21. D. G. de Oteyza, A. García-Lekue, M. Vilas-Varela, et al., “Substrate-Independent Growth of Atomically Precise Chiral Graphene Nanoribbons,” *ACS Nano* 10 (2016): 9000–9008.

22. Y.-C. Chen, D. G. de Oteyza, Z. Pedramrazi, C. Chen, F. R. Fischer, and M. F. Crommie, “Bottom-Up Synthesis of N = 13 Sulfur-Doped Graphene Nanoribbons,” *ACS Nano* 10 (2016): 6123–6128.

23. Y. Yamamoto, G. Zhang, W. Jin, et al., “Ambipolar-Transporting Coaxial Nanotubes with a Tailored Molecular Graphene–fullerene Heterojunction,” *Proceedings of the National Academy of Sciences USA* 106 (2009): 21051–21056.

24. S. Lei and S. De Feyter, “STM, STS and Bias-Dependent Imaging on Organic Monolayers at the Solid–Liquid Interface,” *Topics in Current Chemistry* 285 (2008): 269–312.

25. W. Pisula, A. Menon, M. Stepputat, et al., “A Zone-Casting Technique for Device Fabrication of Field-Effect Transistors Based on Discotic Hexa-Peri-Hexabenzocoronene,” *Advanced Materials* 17 (2005): 684–689.

26. A. N. Abbas, G. Liu, A. Narita, et al., “Deposition, Characterization, and Thin-film-based Chemical Sensing of Ultra-long Chemically Synthesized Graphene Nanoribbons,” *Journal of the American Chemical Society* 136 (2014): 7555–7558.

27. H. J. Rader, A. Rouhanipour, A. M. Talarico, V. Palermo, P. Samori, and K. Müllen, “Processing of Giant Graphene Molecules by Soft-landing Mass Spectrometry,” *Nature Materials* 5 (2006): 276–280.

28. C. Wagner, D. Kasemann, C. Golnik, et al., “Repulsion between Molecules on a Metal: Monolayers and Submonolayers of Hexa-peri-hexabenzocoronene on Au(111),” *Physical Review B* 81 (2010): 035423.

29. P. Sonnet, L. Stauffer, M. Gille, et al., “Molecular Dissociation on the SiC (0001) 3×3 Surface,” *ChemPhysChem* 17 (2016): 3900–3906.

30. Y. Zhang, Y. Zhang, G. Li, et al., “Construction of Single-crystalline Supramolecular Networks of Perchlorinated Hexa-peri-hexabenzocoronene on Au (111),” *The Journal of Chemical Physics* 142 (2015): 101911.

31. F. Vonau, D. Suhr, D. Aubel, L. Bouteiller, G. Reiter, and L. Simon, “Evolution of Multilevel Order in Supramolecular Assemblies,” *Physical Review Letters* 94 (2005): 066103.

32. G. Schull, L. Douillar, C. Fiorinei-Debuisschert, et al., “Single-molecule Dynamics in a Self-assembled 2D Molecular Sieve,” *Nano Letters* 6 (2006): 1360.

33. F. Moresco, L. Gross, M. Alemani, et al., “Probing the Different Stages in Contacting a Single Molecular Wire,” *Physical Review Letters* 91 (2003): 036601.

34. D. Pacilé, M. Papagno, A. Fraile Rodríguez, et al., “Near-edge X-ray Absorption Fine-structure Investigation of Graphene,” *Physical Review Letter* 101 (2008): 066806.

35. R. Eba Medjo, B. Thiodjio Sendja, J. Mane Mane, and P. Owono Ateba, “A Study of Carbon Nanotube Contamination by XANES Spectroscopy,” *Physica Scripta* 80 (2009): 045601.

36. L. Soukiassian, A. J. Mayne, G. Comtet, L. Hellner, G. Dujardin, and A. Gourdon, “Selective Internal Manipulation of a Single Molecule by Scanning Tunneling Microscopy,” *The Journal of Chemical Physics* 122 (2005): 134704.

37. Y. Tong, F. Nicolas, S. Kubsky, et al., “Interplay between Structural and Electronic Properties in 1, 4, 5, 8-Naphthalenetetracarboxylic Dianhydride Films on Cu (100),” *The Journal of Physical Chemistry C* 121 (2017): 5050–5057.

38. J. B. Neaton, M. S. Hybertson, and S. G. Louie, “Renormalization of Molecular Electronic Levels at Metal-molecule Interfaces,” *Physical Review Letters* 97 (2006): 216405.

39. H. Yang, G. Baffou, A. J. Mayne, G. Comtet, G. Dujardin, and Y. Kuk, “Topology and Electron Scattering Properties of the Electronic Interfaces in Epitaxial Graphene Probed by Resonant Tunneling Spectroscopy,” *Physical Review B* 78 (2008): 041408.

40. A. J. Mayne, T. R. I. Cataldi, J. Knall, et al., “Chemisopttion of Organic Adsorbates on Silicon and Gold Studied by Scanning Tunnelling Microscopy,” *Faraday Discussions* 92 (1992): 199–207.

41. S. Doniach and M. Sunjic, “Many-Electron Singularity in X-ray Photoemission and X-ray Line Spectra from Metals,” *Journal of Physics C: Solid State Physics* 3 (1970): 285.

42. J. Lavie, V. B. Vu, D. Medina-Lopez, et al., “Bottom-Up Synthesis, Dispersion and Properties of Rectangular-Shaped Graphene Quantum Dots,” *Helvetica Chimica Acta* 106 (2023): 00034.

43. M. El Gemayel, A. Narita, L. F. Dossel, et al., “Graphene Nanoribbon Blends with P3HT for Organic Electronics,” *Nanoscale* 6 (2014): 6301–6314.

44. I. Horcas, R. Fernández, J. M. Gómez-Rodríguez, J. Colchero, J. Gómez-Herrero, and A. M. Baro, “WSXM: A Software for Scanning Probe Microscopy and a Tool for Nanotechnology,” *Review of Scientific Instruments* 78 (2007): 013705.

45. J. Tersoff and D. R. Hamann, “Theory of the Scanning Tunneling Microscope,” *Physical Review B* 31 (1985): 805–813.

46. J. Lewis, P. Jelinek, J. Ortega, et al., “Advances and Applications in the FIREBALL Ab Initio Tight-Binding Molecular-Dynamics Formalism,” *Physica Status Solidi B* 248 (2011): 1989–2007.

47. M. A. Basanta, Y. J. Dappe, P. Jelinek, and J. Ortega, “Optimized Atomic-Like Orbitals for First-principles Tight-binding Molecular Dynamics,” *Computational Materials Science* 39 (2007): 759–766.
48. O. F. Sankey and D. J. Niklewski, "Ab Initio Multicenter Tight-binding Model for Molecular-dynamics Simulations and Other Applications in Covalent Systems," *Physical Review B* 40 (1989): 3979-3995.

49. N. Mingo, L. Jurczyszyn, F. J. Garcia-Vidal, et al., "Theory of the Scanning Tunneling Microscope: Xe on Ni and Al," *Physical Review B* 54 (1996): 2225-2235.

50. L. V. Keldysh, "JEPT" Ionization in the Field of a Strong Electromagnetic Wave," *Soviet Physics* 47, no. 1515 (1965): 1018.

51. C. Gonzalez, E. Abad, Y. J. Dappe, and J. C. Cuevas, "Theoretical Study of Carbon-Based Tips for Scanning Tunnelling Microscopy," *Nanotechnology* 27 (2016): 105201.

**Supporting Information**

Additional supporting information can be found online in the Supporting Information section.

**Supporting file:** admi70319-sup-0001-SuppMat.docx