“This document is the Accepted Manuscript version of a Published Work that appeared in final
form in ACS Nano 2017, 11, 9321-9329, copyright © American Chemical Society after peer
review and technical editing by the publisher. To access the final edited and published work see
10.1021/acsnano.7b04728”

Nonacene generated by on-surface dehydrogenation
Rafal Zuzak1, Ruth Dorel2, Mariusz Krawiec3, Bartosz Such1, Marek Kolmer1, Marek
Szymonski1, Antonio M. Echavarren2,4, Szymon Godlewski1,*
1

Centre for Nanometer-Scale Science and Advanced Materials, NANOSAM, Faculty of Physics,
Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, PL 30-348
Krakow, Poland
2

Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and
Technology, Av. Països Catalans 16, 43007 Tarragona, Spain
3

Institute of Physics, M. Curie-Sklodowska University, Pl. M. Curie-Skłodowskiej 1, 20-031
Lublin, Poland
4

Departament de Química Orgànica i Analítica, Universitat Rovira i Virgili, C/ Marcel·lí
Domingo s/n, 43007 Tarragona, Spain
*

e-mail: szymon.godlewski@uj.edu.pl

The on-surface synthesis of nonacene has been accomplished by dehydrogenation of an air-stable
partially saturated precursor, which could be aromatized by using a combined scanning tunnelling
and atomic force microscope (STM/AFM) tip as well as by on-surface annealing. This
transformation allowed the in-detail analysis of the electronic properties of nonacene molecules
physisorbed on Au(111) by scanning tunnelling spectroscopy (STS) measurements, which were
corroborated by density theory functional (DFT) calculations thus confirming the spatial mapping
of its molecular orbitals. Furthermore, the thermally-induced dehydrogenation uncovered the
isomerisation of intermediate dihydrononacene species, which allowed for their in-depth
structural and electronic characterization.

Acenes are an important class of polycyclic aromatic hydrocarbons constituted by linearly fused
benzene rings and are considered to be central to the development of the future generation of
(opto)electronic devices. These molecules have been the subject of extensive study due to their
unique electronic and magnetic properties1-5, which make them promising candidates to be
implemented as low bandgap semiconducting materials in molecular electronic devices such as
field-effect transistors6, photovoltaic devices7, or light emitting diodes8. The electronic properties
of acenes have been predicted to be improved for higher acenes anticipating narrower HOMOLUMO (highest occupied molecular orbital – lowest unoccupied molecular orbital) gaps as well
as lower reorganization energies as the number of annealed rings grows9-12. At the same time,
acenes could be regarded as the narrowest graphene nanoribbons (GNR) with zig-zag edge

	

1	

topology suggesting potential applicability in spintronics13 and plasmonics14. Nevertheless, both
the preparation and the fundamental study of extended acenes are limited by their intrinsic
instability and low solubility, which has prompted the development of a variety of synthetic
methods and stabilization strategies that allow gaining access to acenes longer than pentacene1519

.

Despite initial reports dating from the 1940s and 1950s20-21, it was not until recently that the
Strating-Zwanenburg reaction of stable a-(diketo)precursors combined with low-temperature
matrix-isolation techniques allowed the first unambiguous generation and spectroscopic
characterization of hexacene22 and heptacene23, which could also later be synthesized and isolated
in bulk in the solid state24-26. Octacene and nonacene were likewise generated through the photoinduced decarbonylation of the corresponding bis(a-diketo)precursors in a cryogenic argon
matrix27, which constitutes the sole evidence for the existence of nonacene reported to date.
However, despite kinetically stabilized nonacene derivatives have been successfully isolated28-29,
the detailed electronic structure of the parent nonacene has not yet been established.
In recent years, on-surface synthesis has attracted much attention from the scientific community,
offering a breakthrough in the atomically precise assembly of molecular nano-architectures30-32.
The enormous progress in scanning probe techniques has boosted the planar molecule
manipulation and tip-induced chemical reactions to an unprecedented level of precision33-39.
Moreover, the combination of ultra-high vacuum conditions with cryogenic temperatures and
application of chemically inert substrates has also made feasible the synthesis and detailed
characterization of molecules otherwise too reactive and therefore unstable under ambient
conditions40-41. The ability of tip functionalized non-contact atomic force microscopy (NC-AFM)
to

resolve

chemical

structures42-46

is

complementary

to

microscopy/spectroscopy (STM/STS) electronic orbital imaging

the

scanning

47-50

tunnelling

toward detailed and

complete molecule description. In the last two years the on-surface chemistry approach has also
been applied for the generation of middle-sized acenes such as tetracene51 and hexacene52 by
deoxygenation of stable molecular precursors. We have recently developed a method for the
preparation of hydroacenes, which can be considered as stable ‘hydrogen protected acenes’53,
based on the gold(I)-catalyzed cyclization of aryl-tethered 1,7-enynes54. Thus, we envisioned that
the hydroacenes accessed through our method could be suitable precursors for the generation of
otherwise elusive higher acenes.
Herein we present the on-surface generation of nonacene as well as the detailed study of its
electronic structure on a Au(111) surface. Our method is based on the atomically precise step-bystep dehydrogenation of a stable and easily handled tetrahydrononacene precursor Nn-4H
(6,10,17,21-tetrahydrononacene)54 with the application of the tip of combined STM/AFM setup
(Scheme 1a). High resolution NC-AFM imaging is applied for the detailed visualization of the

	

2	

internal structure of generated long acenes. Details on the electronic structure of the generated
nonacene molecules, as well as the intermediate 6,21-dihydrononacene (Nn-2H-3), are revealed
using high resolution dI/dV mapping, which allows to visualize spatially the electron density
cloud. Our measurements showed that not only frontier molecular orbitals (i.e. HOMO and
LUMO), but also deeper lying ones (i.e. HOMO-1 and LUMO+1) could be imaged with
submolecular resolution. Additionally, we demonstrated that the surface assisted dehydrogenation
process that leads to the generation of nonacene could also be induced thermally, constituting a
highly efficient method for the preparation of increased amounts of this long acene. We observed
that in this case the hydrogen abstraction process was accompanied by a series of 1,3-hydrogen
shifts over the dihydrononacene species resulting in a variety of Nn-2H isomers with the nonaromatic ring located at different positions within the internal structure of the molecule, which
therefore allowed the electronic characterization of a range of Nn-2H isomers (Scheme 1b).
a)

b)
H H

H H

H H

Nn-4H

H H

H H

H H

Nn-2H-3
H H

Au(111)
Δ or STM tip

on-surface
dehydrogenation
H H
Nn-2H-4
H H

			

nonacene

H H

Nn-2H-5

	

Scheme	1.	On-surface	synthesis	of	nonacene;	(a)	Nonacene	generated	from	6,10,17,21-tetrahydononacene	(Nn4H)	precursor;	(b)	Dihydrononacene	intermediates	(Nn-2H)	observed	on	Au(111).

Results
Tip-induced on-surface generation of nonacene. For the experiments reported here we
sublimed molecules on the Au(111) surface at room temperature. The starting material for our
research was Nn-4H, a molecule with two non-aromatic rings bearing each two methylene groups
susceptible of being dehydrogenated54. After deposition, the molecules preferentially physisorbed
at the corners of the herringbone surface (red contours in Figure 1a,b) patterning similarly to
pentacene molecules, as reported by Soe et al48. When the amount of molecules increased they
tended to follow the herringbone reconstruction pattern as shown in Figure 1a,b. However, the
molecules located at reconstruction elbows were ultimately more stable and were therefore used
for the detailed characterization in this study. The presence of the two non-aromatic rings was
discernible in filled- and especially empty-state STM topographies (Figure 1c), as well as in the

	

3	

high resolution constant height NC-AFM image (Figure 1d), proving that the thermal evaporation
of the material does not lead in general to molecule defragmentation. Nevertheless, we noted that
a small fraction of molecules underwent hydrogen abstraction spontaneously and were found as
Nn-2H-3, marked by white contours in Figure 1b. A deeper analysis of the STM appearance of
Nn-4H indicated that the enhanced contrast over the methylene moieties in the non-aromatic rings
was recorded for voltages exceeding +1.95 V. This correlates with the STS resonance recorded
over the non-aromatic rings pointing to the increased empty state density cloud (see
Supplementary Information Figure S4). The presence of the characteristic large lobes located
above the non-aromatic rings in the empty state STM images provided a hint to discriminate the
planar and aromatic board of molecules fabricated by atom manipulation from the non-planar
starting molecules. Tip-induced cleavage of one of the Csp3-H bonds within the non-aromatic ring
occurred when the apex was located over the methylene selected for manipulation and the
tunneling current was increased to several hundreds of pA with the feedback loop turned off. The
sudden drop of the current was a signature of hydrogen abstraction (see Supplementary
Information Figure S5). We found in our experiments that within the time resolution of the
STM/AFM apparatus two hydrogen atoms of the initially non-aromatic ring, one from each
methylene moiety, were extracted leading to its aromatization. The application of the STM/AFM
setup did not allow to determine the details of the abstraction reaction and consequently did not
allow to discern whether both hydrogen atoms were abstracted in a concerted or a stepwise
process. Nonetheless, the straight removal of the two hydrogen atoms associated with
planarization and aromatization of the ring was not surprising as the cleavage of one of the
benzylic C-H bonds would result in a highly reactive radical intermediate that should rapidly lead
to aromatization upon loss of a second hydrogen atom. In our experiments, we noted that the
dehydrogenation of Nn-4H only occurred for voltages higher than +1.95 V. This threshold
corresponds to the resonant tunneling through the recorded state (see Supplementary Information
Figure S4) and is much lower than the C-H bond dissociation energy39,55, which indicates that the
energy dissipated from vibronic excitations cleaves the bonds. We note here that the Csp3-H bonds
in the methylene groups are the anticipated breaking points, since their bond-dissociation energy
(3.4 eV for 9,10-dihydroanthracene39,55) is lower compared to Csp2-H bonds in the aromatic rings
(e.g. 4.8 eV for benzene39,56). The observed reaction is reminiscent to the recently reported C-H
bond cleavage that leads to triangulene40. The STM appearance of the intermediate Nn-2H-3
generated using the above described approach is shown in Figure 1e. Upon aromatization of one
of the initially non-aromatic rings we clearly noticed the enhancement of the intramolecular
ladder contrast characteristic for the acene filled-state images and the disappearance of the
pronounced empty-state lobes associated with the presence of the methylene groups in the starting
material. Importantly, the remaining two CH2 groups exhibit the characteristic empty-state twoside-lobe appearance at significantly lower voltages compared to Nn-4H, i.e. starting from +1.2

	

4	

V, which correlates with the STS measured resonance (see Supplementary Information Figure
S1) resulting from extension of the central aromatic backbone of the molecule to a hexacene-like
moiety upon aromatization. This is even better visualized in NC-AFM images, shown in Figure
1f, in which the six fused benzene rings are clearly discernible. The final target nonacene
molecule was fabricated by application of the same dehydrogenation procedure to the second nonaromatic ring. However, we found an important difference in the process responsible for the
transformation of Nn-2H-3 into nonacene, compared to the first dehydrogenation of Nn-4H into
Nn-2H-3. The efficient dehydrogenation was already recorded at voltages starting from +1.2 V,
which correlates with the significantly lower energy of the delocalized LUMO orbital of Nn-2H3 (recorded in STS at 1.12 V, see Supplementary Information Figure S1) compared with the
energy of Nn-4H LUMO orbital. This finding further corroborates the extraction mechanism
based on vibronic excitation. The filled state STM image (Figure 1g) of the final product –
nonacene – clearly shows the ladder internal contrast with the expected nine lobes along the
molecule, whereas in the empty state image the bright lobes related to the presence of CH2 groups
are obviously absent. High-resolution NC-AFM image displayed in Figure 1h clearly shows
presence of linearly fused nine benzene rings, doubtlessly proving generation of the nonacene
molecule.

	

5	

	
Figure	1.	(a)	Filled	and	(b)	empty	state	STM	topographies	of	Au(111)	sample	after	Nn-4H	deposition.	Red-dashed	
contours	 mark	 Nn-4H	 physisorbed	 at	 herringbone	 reconstruction	 elbows,	 white-dashed	 contours	 indicate	
molecules	that	spontaneously	underwent	dehydrogenation	into	Nn-2H-3.	High	resolution	empty-	and	filled-state	
STM	constant	current	topographies	with	corresponding	Laplace	filtered	NC-AFM	constant	height	images	of	Nn-4H	
(c,d),	 Nn-2H-3	 (e,f)	 and	 nonacene	 (g,h).	 Molecules	 shown	 in	 (e,f)	 and	 (g,h)	 were	 generated	 by	 tip-induced	
dehydrogenation;	tunnelling	current:	50	pA	(a),	30	pA	(b),	100	pA	(c,	upper	image),	25	pA	(c,	lower	image),	35	pA	
(e),	50	pA	(g,	upper	image),	45	pA	(g,	lower	image);	NC-AFM	oscillation	amplitude:	113	pm	(d,f),	57	pm	(h).

Nonacene electronic properties. In order to confirm the on-surface generation of nonacene and
to provide its detailed electronic structure characterization we performed STS measurements and
dI/dV mapping of its molecular orbitals using a lock-in amplifier. For STS measurements only
tips allowing for clear identification of the Au(111) surface state resonance at approximately -0.5
V were used. Taking into account that the electron cloud is spatially distributed over the molecule
and in order to avoid measurements at positions that correspond to nodal planes of monoelectronic
orbitals, which would lead to suppression of the dI/dV STS signal corresponding to these orbitals,
we performed point STS measurements at several different horizontal locations of the tip apex.
Based on previous reports for shorter acenes, namely pentacene47-48 and hexacene52, we expected
the most prominent signal to be recorded at the corners of the molecule (marked by a circle in
Figure 2a left inset) for filled-states spectroscopy and at the ends (indicated by a circle in Figure
2a right inset) for empty states measurements. Therefore, for point spectroscopy measurements
we positioned the tip in the above mentioned different locations, as indicated by blue dots in the
insets in Figure 2a. The recorded differential conductance spectra contain strong filled-state

	

6	

resonances at -1.00 V and -0.34 V and slightly broader resonances in the empty state regime at
+0.85 V and +1.70 V. Additionally, a plain shoulder can also be noticed positioned within filled
states at around -1.65 V. In order to determine if the recorded peaks could be attributed to the
measurements of the molecular orbitals in a mono-electronic approximation we performed spatial
dI/dV mapping at the voltages corresponding to these resonances and compared those results with
the simulated dI/dV maps obtained on the basis of the simple Tersoff-Hamann approximation
(Figure 2b-e)57. The calculations were performed for the gas phase molecule configuration due to
the weak interaction of the molecule with the substrate and expected insignificant influence on
the orbital distribution. The maps recorded at -1.00 V and -0.34 V showed two rows containing 8
and 9 lobes, respectively, and a nodal plane along the molecule. These maps correspond to the
spatial distribution of the HOMO-1 and HOMO electronic orbitals of the free nonacene molecule
as corroborated by the simulated images. This is in line with the expected single electron wave
function signature of the linearly fused benzene rings, for which it is expected to record 2n (2n2) lobes separated by a nodal plane along the molecule backbone for HOMO (HOMO-1) of the
n-acene molecule. This allowed us to unambiguously assign the peaks recorded at -1.00 V and 0.34 V as the signature of HOMO-1 (Figure 2b) and HOMO (Figure 2c) single electron orbitals,
respectively. We did not map the spatial distribution of the dI/dV signal at the voltage
corresponding to the lowest lying peak recorded at -1.65 V, which for consistency, we denote as
HOMO-2, although in previous reports for shorter acenes it became clear that the recorded dI/dV
maps largely deviated from expected for spatial mapping of purely mono-electronic HOMO-2
orbital for pentacene48 and hexacene52. Comparison of the dI/dV maps recorded at voltages
corresponding to the peaks at +0.85 V and +1.70 V with the ones simulated for LUMO (Figure
2d) and LUMO+1 (Figure 2e) monoelectronic wavefunctions showed striking agreement thus
confirming the assignment of these peaks. The only minor discrepancy for both maps was the
experimental missing of the faintest, banana-shape features located in the closest proximity to the
large, oval end-lobes. This is, however, in agreement with the results obtained for pentacene and
hexacene physisorbed on Au(111) and assigned to limited spatial tip resolution52. Despite it has
been theoretically predicted58-61 and experimentally evidenced27 that nonacene might be
characterized by an antiferromagnetic ground state structure with open-shell singlet state, it is
important to note that we have obtained the excellent agreement between computed and
experimental dI/dV maps for the non-magnetic structure of nonacene corresponding to the closedshell ground state configuration. This can be easily rationalized taking into account that it is
expected for the magnetic anisotropy to be suppressed for molecules interacting with a Au(111)
surface. Hence, we conclude that for the longest acene known to date, namely nonacene, we have
successfully mapped spatially not only the frontier molecular orbitals, i.e. HOMO and LUMO,
but also deeper lying HOMO-1 and LUMO+1 ones.

	

7	

	
Figure	2.	(a)	Single	point	STS	data	recorded	over	a	nonacene	molecule.	Insets	show	the	lateral	tip	position	during	
filled	(left	panel,	100	pA)	and	empty	(right	panel,	50	pA)	state	spectroscopy	data	acquisition.	(b-e)	Experimental	
dI/dV	spatial	maps	recorded	at	energies	corresponding	to	resonances	shown	in	(a)	complemented	by	theoretically	
calculated	 maps,	 cross-sections	 along	 experimental	 maps	 are	 displayed	 to	 guide	 the	 eye	 in	 symmetry	 analysis;	
tunnelling	current:	100	pA	(b,c),	50	pA	(d,e).	

Having assigned the STS recorded resonances, we infer that the STS recorded transport gap of
nonacene equals approximately 1.2 eV, which follows the expected reduction of gap with
increased length of the fused benzene rings system and is in good agreement with the optical gap
determination of photochemically-generated nonacene, which needed to be performed by
irradiation in a solid Ar matrix27 and in which, from the UV-Vis spectrum, a HOMO-LUMO gap
of 1.4 eV could be estimated.
Thermally-induced on-surface generation of nonacene. The above reported procedure for the
on-surface generation of nonacene based on atomic manipulation is very precise, although not
efficient for the preparation of increased amounts of molecules of this long acene. Therefore, we
decided to adapt an alternative approach based on the surface-assisted thermally-induced
dehydrogenation of Nn-4H, which would allow for the efficient parallel preparation of a whole

	

8	

array of nonacene species by annealing after molecule deposition. The empty state STM image
recorded for the sample heated at 150 °C clearly indicated that the majority of Nn-4H molecules
underwent a transition (Figure 3a). Hence, whereas a small fraction of them stayed intact and
exhibited the characteristic STM appearance for the starting material with 4 pronounced lobes
(see the molecules marked by red dashed contours in Figure 3a), the vast majority was found as
Nn-2H species with clearly visible markers of the two remaining CH2 groups. However, a detailed
inspection revealed that the dihydrononacenes present on the surface were not identical since the
bright lobe corresponding to the non-aromatic ring was found at different positions. This is
documented in high resolution STM images shown in Figure 3c-e, which present the different
Nn-2H isomers obtained after thermal treatment. We found that the most abundant isomer was
the symmetric 8,19-dihydrononacene (Nn-2H-5) (Figure 3e). The sample contained also 7,20dihydrononacenes (Nn-2H-4, Figure 3d) and already described in the first section Nn-2H-3
(Figure 3c), the latter being formed directly from Nn-4H by hydrogen removal without
subsequent hydrogen migration. Our experiments demonstrated that upon dehydrogenation of the
starting material, which leads to Nn-2H-3, the hydrogen atoms in the remaining methylene
moieties migrate along the molecule with a preference to be located within the central ring. The
overall transformation is similar to the thermally-induced 1,3-hydrogen migration sequence
reported for the conversion of 5,14-dihydropentacene into thermodynamically more stable 6,13dihydropentacene62. Furthermore, this transformation is in agreement with our gas phase DFT
calculations, which show that the Nn-2H-4 and Nn-2H-5 are characterized by an energy lowering
of 85 meV and 100 meV, respectively, with respect to Nn-2H-3.

	

9	

	
Figure	3.	Empty	state	STM	topographies	showing	the	sample	after	annealing	to	150	°C	(a)	and	210	°C	(b),	the	white	
contour	 marks	 the	 nonacene	 molecule,	 whereas	 the	 red	 ones	 point	 the	 Nn-4H.	 The	 streaky	 pattern	 clearly	
discernible	above	molecules	in	panel	(b)	results	from	high	mobility	of	nonacene	species,	which	are	not	located	in	
the	 herringbone	 reconstruction	 elbows;	 (c),	 (d)	 and	 (e)	 high	 resolution	 filled	 and	 empty	 state	 STM	 images	 of	
different	Nn-2H	isomers	generated	by	thermal	hydrogen	removal	and	on-surface	isomerisation;	red	dashed	line	
indicates	the	position	of	the	non-aromatic	ring,	tunnelling	current:	30	pA	(a,b),	35	pA	(c),	100	pA	(d,	upper	image),	
50	pA	(d,	lower	image),	100	pA	(e,	upper	image),	30	pA	(e,	lower	image).

Our experiments showed that thermal treatment at a higher temperature of 210 °C results in the
complete dehydrogenation of all the starting Nn-4H species leading to an on-surface generated
array of well separated fully aromatic nonacene molecules, as documented in Figure 3b.
Discussion
Our results demonstrate that partially saturated acene derivatives – hydroacenes – are indeed
‘hydrogen protected’ acenes and can therefore be used as suitable precursors for the synthesis of
the corresponding parent acenes. We have successfully generated nonacene on the Au(111)
surface by atomically precise step-by-step hydrogen desorption performed with the application
of combined STM/AFM setup. The detailed analysis of the hydrogen abstraction process revealed
that it is efficiently initiated when the STM tip is placed over the methylene groups and the bias
voltage is raised above the value corresponding to the LUMO energy. Importantly, the threshold

	

10	

voltage was found to differ between dihydrononacene and tetrahydronoancene species, which
follows the decrease of the LUMO orbital energy associated to an extended aromatic backbone.
This demonstrates that the desorption occurs during resonant tunneling, which indicates on the
vibronic mechanism of hydrogen removal. Furthermore, we have applied point STS
measurements and dI/dV mapping to record spatial distribution of frontier, i.e. HOMO and
LUMO, as well as deeper lying HOMO-1, and LUMO+1 molecular orbitals. Spectroscopic
measurements revealed that the STS recorded transport gap reaches 1.19 eV, which is in
reasonable agreement with optical gap measurements reported by Tönshoff et al27.
We have proven that annealing of the sample provides an efficient approach to generate a larger
amount of nonacene molecules. Additionally, we have found that the thermally induced
dehydrogenation is associated with isomerisation of the dihydrononacene intermediates by
migration of hydrogen atoms located in methylene moieties toward the central ring of the
molecule. The generation of different Nn-2H isomers boosted additional experiments toward the
detailed analysis of their electronic properties. The non-aromatic ring divides the backbone of the
species into two aromatic platforms. By STS measurements complemented with dI/dV spatial
mapping we found that the electronic properties are determined by the orbitals, which are
separately localized over the aromatic skeletons. In other words, e.g., HOMO (LUMO) orbital of
Nn-2H-4 and Nn-2H-3 is spatially extended only over the pentacene or hexacene moiety of the
dihydrononacene, respectively (see Supplementary Information Figure S2 and S1). The STS
resonances recorded over the shorter aromatic platforms, i.e., anthracene and naphthalene
moieties, are found at much higher energies as expected for short acenes. The detailed analysis
revealed that the energies of HOMO and LUMO resonances of Nn-2H-3, which correspond to 0.65V and +1.25V, respectively, perfectly match the values from STS measurements for hexacene
on Au(111) reported by Krüger et al52. Similarly, the data obtained for Nn-2H-4 are in good
agreement with the resonances recorded for pentacene by Soe et al48. These findings suggest that
the frontier electronic levels delocalized over the longest aromatic moiety are not impaired
significantly by the presence of the second aromatic backbone separated by the non-aromatic ring.
However, the spatial distribution of the electronic cloud is modified at internal peripheries of the
aromatic cores (see Supplementary Information Figure S1-S3). In particular, by analyzing the
projected density of states, we found that the projection of delocalized orbitals at the states of
hydrogen atoms within the methylene groups exhibits an important contribution. This finding
explains the appearance of pronounced lobes associated with the presence of non-aromatic rings
in STM topographies of dihydro- and tetrahydrononacene molecules.
In summary, our experiments demonstrated that the on-surface generation of nonacene can be
achieved by dehydrogenation of partially saturated molecular precursors. This opens up new
opportunities for the synthesis and study of even higher acenes by selecting properly designed

	

11	

molecular hydroacene precursors and gives perspectives for fine tuning of their electronic and
magnetic properties by atomically precise substitutional doping. Furthermore, the use of partially
saturated acene precursors equipped with reactive functionalities may also allow for further onsurface processing, which could lead to more complex functional materials based on covalently
linked acene substructures.
Methods
Sample preparation & STM/AFM experiments. The experiments were performed in a ultrahigh vacuum multi-chamber system with the low-temperature scanning probe microscope that
could operate in a scanning tunneling and non-contact atomic force microscopy mode. The
microscope was manufactured by Omicron GmbH. The Au(111) sample was prepared in a
standard procedure of thermal annealing at 450 °C and subsequent Ar+ ion bombardment. The
molecules were evaporated thermally from a water-cooled Knudsen cell manufactured by Kentax
GmbH on a sample kept at room temperature. The sublimation temperature was established at
260 °C with the application of a quartz microbalance giving a flux of approximately 0.05
monolayer/minute. After molecule deposition the sample was inserted into the microscope at
liquid helium (4.5 K) temperature and subsequently measurements were performed. In all STM
and STS experiments electrochemically etched Pt-Ir tips were applied as probes. All dI/dV maps
and STS spectra were collected using lock-in amplifier (Zurich Instruments MFLI) with
frequency of 610 Hz and amplitude of 23 mV (rms). NC-AFM measurements were performed
with the setup based on a qPlus sensor63 operated in frequency modulation mode with the bias
voltage V set to 0 V. To obtain higher spatial resolution in AFM measurements, carbon monoxide
molecules were deposited onto the gold surface and then picked up by the AFM tip using
procedure described by Gross et al42. Sample annealing leading to thermally driven
dehydrogenation was performed in a preparation chamber using resistive heater. The samples
were heated for 15 minutes at temperatures ranging from 150 °C up to 300 °C. The temperature
of the samples during annealing was controlled by the thermocouple.
DFT calculations. First-principles calculations of gas-phase nonacene molecules and their diand tetrahydroderivatives were performed using density functional theory (DFT) with the
projector augmented waves (PAW)64 and van der Waals corrected exchange-correlation
functional (vdW-DF) available in VASP (Vienna ab-initio simulation package)65-67. The optPBEvdW implementation of the vdW-DF method was used in all the calculations68-70.
The plane wave basis set was restricted by an energy cutoff of 700 eV. Only the Γ point was used
in the Brillouin zone sampling. The total energy convergence criterion was chosen to be 10-6 eV.
The atomic positions were fully relaxed by a conjugate gradient method until the maximum force
in any direction was less than 0.01 eV/Å. The local density of states maps have been calculated
according to the Tersoff-Hamann approach in the constant-current mode57.

	

12	

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Acknowledgements
The research was supported by the National Science Center, Poland (2014/15/D/ST3/02975)
European Research Council (Advanced Grant No. 321066), MINECO/FEDER, UE (CTQ201675960-P), MINECO-Severo Ochoa Excellence Acreditation 2014-2018, SEV-2013-0319), and

	

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CERCA Program / Generalitat de Catalunya. MK acknowledges the support of the National
Science Centre (Poland), project No. DEC-2014/15/B/ST5/04244. The STM experiments were
carried out using equipment purchased with financial support from the European Regional
Development Fund within the framework of the Polish Innovation Economy Operational Program
(contract no. POIG.02.01.00-12-023/08). RZ acknowledges support received from KNOW
(scholarship KNOW/59/SS/RZ/2016).
Author contributions
R.Z. performed all the STM/AFM experiments under the guidance of S.G., M.S., M.Ko.
(STM/STS) and B.S. (AFM). R.D. synthesized the precursor molecules. M.Kr. performed the
DFT calculations and image simulations. A.M.E initiated the work, oversaw and directed the
synthesis of the acene precursors. S.G. supervised the research, conceived the experiments and
prepared the interpretation of the STM/STS results. R.D. interpreted the isomerization of the
intermediates. The manuscript was written by S.G. and R.D. All the authors discussed the results.
Additional information
Supplementary information is available in the online version of the paper. Reprints and
permissions information is available online at www.nature.com/reprints. Correspondence and
requests for materials should be addressed to S.G.
Competing financial interests
The authors declare no competing financial interests.
Graphical abstract

	

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