Engineering Long-Range Order in Supramolecular Assemblies on Surfaces: The Paramount Role of Internal Double Bonds in Discrete Long-Chain Naphthalenediimides

Article abstract of DOI:10.1021/jacs.0c00765

Achieving long-range order with surface-supported supramolecular assemblies is one of the pressing challenges in the prospering field of non-covalent surface functionalization. Having access to defect-free on-surface molecular assemblies will pave the way for various nanotechnology applications. Here we report the synthesis of two libraries of naphthalenediimides (NDIs) symmetrically functionalized with long aliphatic chains (C₂₈ and C₃₃) and their self-assembly at the 1-phenyloctane/highly oriented pyrolytic graphite (1-PO/HOPG) interface. The two NDI libraries differ by the presence/absence of an internal double bond in each aliphatic chain (unsaturated and saturated compounds, respectively). All molecules assemble into lamellar arrangements, with the NDI cores lying flat and forming 1D rows on the surface, while the carbon chains separate the 1D rows from each other. Importantly, the presence of the unsaturation plays a dominant role in the arrangement of the aliphatic chains, as it exclusively favors interdigitation. The fully saturated tails, instead, self-assemble into a combination of either interdigitated or non-interdigitated diagonal arrangements. This difference in packing is spectacularly amplified at the whole surface level and results in almost defect-free self-assembled monolayers for the unsaturated compounds. In contrast, the monolayers of the saturated counterparts are globally disordered, even though they locally preserve the lamellar arrangements. The experimental observations are supported by computational studies and are rationalized in terms of stronger van der Waals interactions in the case of the unsaturated compounds. Our investigation reveals the paramount role played by internal double bonds on the self-assembly of discrete large molecules at the liquid/solid interface.

Full text of DOI:10.1021/jacs.0c00765

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Article
Engineering long-range order in supramolecular assemblies
on sur-faces: the paramount role of internal double
bonds in discrete long chain-naphthalenediimides
Jose Augusto Berrocal, G Henrieke Heideman, Bas F.M. de Waal, Mihaela Enache,
Remco W. A. Havenith, Meike Stöhr, Egbert Willem Meijer, and Ben L. Feringa
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.0c00765 • Publication Date (Web): 23 Jan 2020
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Engineering long-range order in supramolecular assemblies on
surfaces: the paramount role of internal double bonds in discrete
long chain-naphthalenediimides
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José Augusto Berrocal,a,b,†,‡ G. Henrieke Heideman,a‡ Bas F. M. de Waal,b Mihaela Enache,c Remco W.
A. Havenith,c Meike Stöhr,c E. W. Meijer,b* Ben L. Feringaa,c*
a Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
b Institute for Complex Molecular Systems and Laboratory of Macromolecular and Organic Chemistry, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
c Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
KEYWORDS. Naphthalenediimides, van der Waals interactions, long-range order, internal double bonds, liquid-solid
interface, scanning tunneling microscopy.
ABSTRACT: Achieving long-range order with surface-supported supramolecular assemblies is one of the pressing challenges in the
prospering field of non-covalent surface functionalization. Having access to defect-free on-surface molecular assemblies will pave
the way for various nanotechnology applications. Here we report the synthesis of two libraries of naphthalenediimides (NDIs)
symmetrically functionalized with long aliphatic chains (C28 and C33) and their self-assembly at the 1-phenyloctane/Highly Oriented
Pyrolytic Graphite (1-PO/HOPG) interface. The two NDI libraries differ by the presence/absence of an internal double bond in each
aliphatic chain (unsaturated and saturated compounds, respectively). All molecules assemble into lamellar arrangements with the
NDI cores lying flat and forming 1D rows on the surface, while the carbon chains separate the 1D rows from each other. Importantly,
the presence of the unsaturation plays a dominant role in the arrangement of the aliphatic chains, as it exclusively favors
interdigitation. The fully saturated tails, instead, self-assemble into a combination of either interdigitated or non-interdigitated
diagonal arrangements. This difference in packing is spectacularly amplified at the whole surface level and results in almost defect-
free self-assembled monolayers for the unsaturated compounds. In contrast, the monolayers of the saturated counterparts are globally
disordered, even though they locally preserve the lamellar arrangements. The experimental observations are supported by
computational studies and are rationalized in terms of stronger van der Waals interactions in the case of the unsaturated compounds.
Our investigation reveals the paramount role played by internal double bonds on the self-assembly of discrete large molecules at the
liquid/solid interface.
aliphatic tails to form thermodynamically stable self-assembled
INTRODUCTION
monolayers. Moreover, a number of studies have highlighted
the role played by the alkyl chains in the 2D structure.18–23
While a favorable interaction between the molecules and the
substrate is certainly necessary, the structure and extent of order
of the assemblies generated are mostly the manifestation of the
The non-covalent functionalization of surfaces has become
one of the pillars of nanotechnology in the last twenty years.1–4
Achieving exact control over the formation of monolayers
allows to modulate the properties of surfaces in a predictable
manner,5 which holds promise for relevant technological
breakthroughs.6–8 For instance, controlling the density of
nitrogen-based n-dopants on graphene via monolayer formation
has proved to play a pivotal role on tuning the charge carrier
concentration of the modified 2D material.9
Surface-supported supramolecular assemblies rely on
stabilizing interactions between the adsorbed molecules and the
surface, as well as favorable intermolecular interactions
between the adsorbed compounds.10,11 Given the significant
epitaxial stabilization of 64 meV (1.5 kcal/mol) per methylene
unit that highly oriented pyrolytic graphite (HOPG) exerts at the
liquid/HOPG interface, the molecular designs typically adopted
in the field feature long alkyl chains - usually up to 18 carbon
atoms - to favor adsorption to the substrate.12,13 Previous work
on long-chain alkanes14–17 highlighted the tendency of long
intermolecular
interactions
between
the
adsorbed
molecules.10,13 On-surface supramolecular assemblies are
typically created by resorting to noncovalent forces, such as van
der Waals (vdW) interactions,24 hydrogen bonding (HB),25–32
coordination chemistries,33–36 and halogen bonding.37,38 So far,
various approaches focused on limiting the number of domain
boundaries and/or molecular defects to improve the
organization and quality of the 2D architectures generated.39–41
More recently, spatially confining the self-assembly process
into nanocorrals created on HOPG afforded impressive results
in terms of order.42 However, the defect-free engineering of
surface-supported supramolecular assemblies on unconfined
HOPG remains a major challenge for the whole field.43
Given the high commercial availability of alkylating reagents
in the C1-C22 range, a large body of work has been carried out
using alkyl chain-functionalized compounds. To the best of our
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knowledge the attention dedicated to their unsaturated present) is highlighted by the letter u. The key synthetic
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analogues featuring internal double bonds has been very
limited. Deng et al. compared the assemblies of E-oleic acid and
Z-oleyamine at the 1-phenyloctane (1-PO)/HOPG interface.44
Monolayers obtained from E-oleic acid at the 1-PO/HOPG
interface were characterized by a high stability, while those
deriving from the amine with Z-configuration were poorly
stable.44 This comparative study44 was consistent in terms of
chain length (oleyl = C18) and double bond position (between
carbon atoms 9 and 10), but the two structures investigated
differed in double bond configurations (E vs Z) and end-group
functionalities (carboxylic vs amino). The hypothesis that
various parameters could play a role in the overall stability of
the on-surface assemblies could not be ruled out. More recently,
Shokri et al. suggested that the introduction of a Z-configured
double bond in the side chains of bis(urea) molecules leads to
the formation of long-range ordered polymers on graphite.45
However, the study was conducted with one chain length only
(C18) and the influence of the internal double bond was visible
only after storing the modified surface for one year.45 Although
both studies independently posed the question of the influence
of internal double bonds on on-surface self-assembly processes,
no further investigations followed in this direction.
intermediates in the preparation of the final compounds were
the unsaturated amines uC28NH2 and uC33NH2, also shown in
Chart 1. We discover that the self-assembled monolayers
obtained at the 1-PO/HOPG interface from the unsaturated
compounds are characterized by a significantly higher degree
of organization compared to their saturated counterparts, with a
size difference for ordered domains corresponding to thousands
of squared nanometers. The experimental results are supported
by computational studies. Our results point to the establishment
of the internal double bond as a counterintuitive, yet key
structural element for obtaining long-range order in self-
assembled monolayers at the liquid/solid interface. Finally, the
highly adaptive character of supramolecular assemblies at the
liquid/solid interface49 allows for the use of mixtures of EE, EZ
and ZZ isomers of the unsaturated NDIs, as the system selects
the most stable pattern created (almost exclusively) by one
stereoisomer.
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Intrigued by the chance to unravel the possible influence of
internal double bonds on surface-supported supramolecular
assemblies, we envisioned a system based on long carbon
chains featuring internal double bonds symmetrically bound at
the periphery of naphthalendiimides46 (NDIs). NDIs are
electron poor46 and have a pronounced tendency to be deposited
at the liquid/HOPG interface due to a highly favorable enthalpy
of interaction.47,48 Symmetrical NDIs functionalized with fully
hydrogenated, linear alkyl chains (Cn-NDI-Cn design) with a
number of carbon atoms in the 3-18 range were previously
investigated at the 1-tetradecane/HOPG interface.47 Particularly
relevant for the present work, alkyl chains with a number of
carbon atoms equal to or longer than 13 units consistently
afforded lamellar arrangements in which both the long carbon
chains and aromatic cores lie flat on the surface, as visualized
with scanning tunneling microscopy (STM).47 The morphology
of the obtained monolayers was explained (lamellar), but the
larger long-range ordered areas obtained represented only a
limited part of the surface (50 nm × 50 nm). In order to exploit
the potential of supramolecular assemblies on surfaces, ordered
areas larger than 100 nm × 100 nm (at least) are highly
desirable.43 Relying on the consistency of the Cn-NDI-Cn design
with n>13 (lamellar arrangement), we hypothesized that
extending the carbon chain length in the Cn-NDI-Cn design
would be beneficial for expanding the order extent. Moreover,
to answer the key question on the role of the internal double
bonds, we envisioned a Cn-NDI-Cn system that features internal
unsaturations in the carbon chain. Reducing these double bonds
by catalytic hydrogenation should offer the possibility to
compare compounds that belong to a very consistent molecular
platform (long chain-NDIs) but that differ by a subtle structural
modification (formally two hydrogen molecules).
Chart 1. Fully extended chemical structures of uC28-NDI-
uC28, uC33-NDI-uC33, C28-NDI-C28, C33-NDI-C33, and key
synthetic intermediates uC28-NH2 and uC33-NH2.
RESULTS AND DISCUSSION
Synthesis and characterization. Compounds uC28NH2 and
uC33NH2 (Chart 1) were the key intermediates in the
preparation of the target NDIs. They were synthesized from
building blocks 1,50 2 and 3 in 67% and 40% yield, respectively,
applying a strategy based on Wittig olefination (Scheme 1).
Details on the preparation of 2 and 3 are presented in the
Supporting Information (SI). The amines were obtained as ~
84:16 mixture of non separable Z and E isomers, respectively
(assigned by integration of the 13C NMR spectra, see SI). The
preference of the Z-configuration of the double bond is in line
with the Wittig olefination conditions adopted, especially with
the use of non-stabilized phosphonium ylides.51 The position of
the unsaturation along the two carbon chains (between C6 and
C7 in uC28, and C11 and C12 in uC33) was exactly engineered, as
it will be corroborated by our STM study (vide infra). The
choice of the base-induced Wittig reaction as elongation step
implied a careful choice of protecting groups for the amino
moieties on the phosphonium salts. We opted for tert-
Butyloxycarbonyl- (Boc) and Phthalimide- (Phth) protected 2
and 3 for uC28NH2 and uC33NH2, respectively, after an initial
screening of the reaction conditions. A related approach for
obtaining discrete oligoethylenes (Cn ≤ 400) was previously
reported in the effort to build model compounds to study the
crystallization of polyethylene. 52,53 Being complementary, our
We present the synthesis and on-surface investigation of
uC28-NDI-uC28 and uC33-NDI-uC33 (unsaturated NDIs), and
compare it to their hydrogenated counterparts C28-NDI-C28 and
C33-NDI-C33 (saturated NDIs). The fully extended chemical
structures are shown in Chart 1. The studied NDIs feature either
28 or 33 carbon atoms in the linear chain (C28 and C33,
respectively) and only differ by the presence/absence of one
unsaturation in each carbon chain. The unsaturation (when
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synthesis allows for the introduction of functional groups in the straight and parallel to each other and modulate the distance
between the NDI cores (Figure 1a and 1c).47 The arrangement
of the individual alkyl chains was determined from high
resolution STM images. We could identify two different
packing modes for the aliphatic chains of C28-NDI-C28 (Figure
1b) and C33-NDI-C33 (Figure 1d): an interdigitated-mode,
hereby defined as ˮlamellar phase Aˮ, and a non-interdigitated
diagonal mode, denominated ˮlamellar phase Bˮ. A pictorial
representation of both lamellar phases A and B is given in
Figure 1e. The lamellae are rotated by 60° with respect to each
another. The observation of the two different packing modes of
the aliphatic chains is in line with previous reports on Cn-NDI-
Cn, with 13≤n≤18.47 In this respect, extending the length of the
alkyl chains did not result in significant differences compared
to previous studies.
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linear moieties, expanding the applicability of these long
aliphatic chains. The cleavage of the -Boc and -Phth protecting
groups was carried out with trifluoroacetic acid (TFA) and
methylamine solution in ethanol (33 wt%), respectively
(experimental details in SI).
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The unit cell parameters determined for C28-NDI-C28 and
C33-NDI-C33 are listed in Table 1, while for a visualization of
the unit cell we refer to Figure 5 and the discussion further on.
Although the two lamellar assemblies differ in the orientation
of the aliphatic chains, the unit cell parameters do not differ for
a fixed alkyl chain length. The measured value are a=4.45 ±
0.24 nm, b=0.88 ± 0.08 nm and γ=85.21 ± 3.39° for C28-NDI-
C28, and a=5.29 ± 0.49 nm, b=0.99 ± 0.10 nm and γ=84.10 ±
5.28° for C33-NDI-C33.
Scheme 1: Synthesis of uC28NH2 and uC33NH2.
The unsaturated amines were subsequently coupled to
commercially available naphthalenedianhydride (NDA) via a
modified microwave assisted protocol (Scheme 2).54–56 The
unsaturated NDIs uC28-NDI-uC28 and uC33-NDI-uC33 were
obtained in 71% and 80% yield, respectively, as non resolvable
mixtures of ZZ:ZE:EE isomers (~ 70.5:27:2.5, based on the
possible combinations of the two reacting amines) after
chromatographic purification. The fully saturated analogs C28-
NDI-C28 and C33-NDI-C33 were prepared from their alkenyl
counterparts by palladium on carbon (Pd/C)-catalyzed
hydrogenation in ethyl valerate at 100 ˚C (Scheme 1), and
purified by Soxhlet extraction (see SI).
Scheme 2: Synthesis of uC28-NDI-uC28, uC33-NDI-uC33, C28-
NDI-C28 and C33-NDI-C33.
Self-assembly on HOPG. We started our investigation by
studying the self-assembly of saturated C28-NDI-C28 and C33-
NDI-C33 at the 1-PO/HOPG interface. Solutions of the two
NDIs (0.4 mg/mL in 1-PO) were drop cast at 100 °C onto
freshly cleaved HOPG substrates and subsequently imaged. The
saturated compounds spontaneously self-assembled into
ordered lamellae immediately after deposition. In the STM
images, the aromatic cores appear as bright protrusions and the
alkyl chains as dark regions (Figure 1a-d). The lamellar
packings are consistent with the aromatic cores lying flat and
next to each other on the surface, while the alkyl chains are
Figure 1: Self-assembly of C28-NDI-C28 and C33-NDI-C33 at the
1-phenyloctane/HOPG interface. a) STM image of C28-NDI-C28
(40 nm × 40 nm, Vtip = 1 V, Iset = 50 pA); b) STM image of C28-
NDI-C28 showing the two arrangements of alkyl chains (phase
A and phase B) (10 nm × 10 nm, Vtip = 1 V, Iset = 50 pA); c) STM
image of C33-NDI-C33 (40 nm × 40 nm, Vtip = -0.6 V, Iset = 50 pA)
d) STM image of C33-NDI-C33 showing the two arrangements
of alkyl chains (phase A and phase B); (10 nm × 10 nm, Vtip
=
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0.6 V, Iset = 150 pA); e) schematic representation of lamellar
indicative example, the carbon chain of Z-oleylamine shows
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phase A (with interdigitation of the alkyl chain) and phase B
(no interdigitation, diagonal organization of the alkyl chains).
this bending as a consequence of the fixed configuration of the
double bond.44 The deposition of mainly EE-isomer is
remarkable, since this isomer is calculated to be roughly 2.5%
of the whole population of unsaturated NDIs (based on the 13C-
NMR analysis of uC28NH2 and uC33NH2 and the binomial
distributions of the two amines). The remaining 97.5% of the
material, which accounts for the EZ- and ZZ-isomers, remains
in the overlying liquid phase and is not imaged. We conclude
that our long-chain NDIs system at the 1-PO/HOPG interface is
highly dynamic and adaptive. Such characteristic allows for the
use of EE-, EZ- and ZZ-isomers mixtures because the system
autonomously selects the isomer that forms the most stable
pattern on the surface – the EE-isomer in this case. A similar
concept has been recently reported by Samorì, Lehn et al. with
on-surface bisimine formation.49 It should be noted that some
Z-configured double bonds were present in the monolayer and
we speculate that these are responsible for the tiny defects and
irregularities observed in the monolayers.
Next, we focused on unsaturated uC28-NDI-uC28 and uC33-
NDI-uC33 at the 1-PO/HOPG interface under similar
experimental conditions. Exemplary images are shown in
Figure 2. Assemblies similar to the ones obtained for the
saturated NDIs were observed with uC28-NDI-uC28 and uC33-
NDI-uC33. The lamellar arrangements correspond to parallel
NDI cores flat on the surface (bright protrusions) and the
interdigitating aliphatic chains that tune the distance between
them (dark regions) (Figure 2a for uC28-NDI-uC28, and Figure
2b for uC33-NDI-uC33). In stark contrast with the saturated
NDIs, additional bright protrusions were observed in the STM
images of uC28-NDI-uC28 and uC33-NDI-uC33 (orange arrows
in Figure 2a and 2b). They appeared symmetrically with respect
to the aromatic cores, and their distance to the aromatic cores
changed upon extending the chain length. These features were
less evident in the case of uC28-NDI-uC28 (Figure 2a), while
they appeared more separated and resolved in the case of uC33-
NDI-uC33 (Figure 2b). We attribute these additional bright
protrusions to the double bonds present in the unsaturated
chains. As a general remark, the imaging of the double bonds
was in general easier for uC33-NDI-uC33 than uC28-NDI-uC28.
Such behavior is attributed to the structural differences between
the two molecules and corroborates the more remote position of
the double bond with respect to the NDI core in uC33-NDI-uC33
(between C11 and C12) compared to uC28-NDI-uC28 (between
C6 and C7).
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Pivotal role of the internal double bonds in the 2D-
crystallization. The results presented so far have apparently
revealed only minor differences in the self-assembly of both
saturated and unsaturated NDIs at the 1-PO/HOPG interface.
However, a very important difference arises in the organization
of the aliphatic chains: the fully saturated ones simultaneously
arrange in either phase A or B, while the unsaturated chains
only pack in the phase A fashion. This difference does not alter
the local ordering of the self-assembled monolayer, but has
dramatic repercussions on the global ordering of the 2D
architectures. The presence of just one type of self-assembly
arrangement (phase A) for the carbon chains of uC28-NDI-uC28
and uC33-NDI-uC33 results in considerably increased domain
sizes and thus, in a reduction of the number of domains per area
compared to those created by their saturated counterparts. The
contrast is striking: for large scale images, very large domains
and significantly less defects are observed in the STM images
of uC28-NDI-uC28 and uC33-NDI-uC33 (Figure 3b and 3d,
respectively) compared to those of C28-NDI-C28 and C33-NDI-
C33 (Figure 3a and 3c, respectively).
Figure 2: Self-assembly of uC28-NDI-uC28 and uC33-NDI-uC33
at the 1-phenyloctane/HOPG interface. a) STM image of uC28-
NDI-uC28 (20 nm × 20 nm, Vtip = 1 V, Iset = 100 pA); b) STM
image of uC33-NDI-uC33 (20 nm × 20 nm, Vtip = 1 V, Iset = 90
pA). The double bonds appear as bright protrusions next to the
bright NDI cores (orange arrows). Both unsaturated molecules
assemble in an interdigitated fashion (phase A).
The determined unit cell parameters for uC28-NDI-uC28 and
uC33-NDI-uC33 are reported in Table 1. The values are very
similar to those obtained for the saturated counterparts, pointing
to an apparent similarity between the assemblies of saturated
and unsaturated NDIs. The close resemblance of the unit cell
parameters of the NDIs with the same chain length (C28 or C33)
strongly suggests that the self-assembled monolayers are
mostly formed by all-E-configured molecules. The E-
configured carbon chains are expected to assume zigzag
conformations on HOPG in a very similar fashion to alkyl
chains and hence cover distances comparable to their saturated
counterparts (C28 and C33). The Z-configured chains, instead,
should differ in distance, as the Z-configuration forces a
bending of the carbon which cannot be compensated by a
rotation around the double bond (forbidden in this case). As an
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Figure 3: Large scale STM images (300 nm × 300 nm) of
Figure 4. Domain size distribution for (a) C28-NDI-C28 (blue)
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different NDIs at the 1-PO/HOPG interface. a) C28-NDI-C28
(Vtip = 1 V, Iset = 100 pA); b) uC28-NDI-uC28 (Vtip = 1 V, Iset = 80
pA); c) C33-NDI-C33 (Vtip = 1 V, Iset = 100 pA); d) uC33-NDI-uC33
(Vtip = 1 V, Iset = 100 pA).
and uC28-NDI-uC28 (orange); (b) C33-NDI-C33 (blue) and uC33-
NDI-uC33 (orange). Y-axis: percentage of ordered domains (%
of domains); X-axis: domain size (103 nm2).
The experimental results were rationalized by means of a
computational study (for computational details see SI). For
consistency with our experimental observations on the self-
assembled monolayers, we studied only alkenes with E-
configurations. Our working hypothesis focused on the
increasing strength of van der Waals inter-chain interactions
upon introducing internal double bonds in the carbon chains.
Initial studies on shorter carbon chains (C6) in the gas phase
showed a promising trend in this respect (see SI). Periodic
energy decomposition analysis (PEDA)57 revealed that the
interaction energy between neighboring chains becomes more
favorable upon introducing the internal double bonds (Figure
S41 and Table S1). Encouraged by these results, we focused on
both C28-NDI-C28 and uC28-NDI-uC28 in the lamellar A
organization. In the calculated molecular arrangements, the
NDI cores lay flat and next to each other while the carbon
chains interdigitate, in line with the experimental observations
(Figure 5a for C28-NDI-C28, and 5b for uC28-NDI-uC28). The
distance between the hydrogen atoms of the aromatic C-H and
the oxygen atoms of the neighboring imide moieties amounts to
2.5 Å for both C28-NDI-C28 and uC28-NDI-uC28, in line with
the literature.47 This allows for unconventional hydrogen
bonding interactions between adjacent NDI cores, which
stabilize the molecular arrangement. Unconventional hydrogen
bonding may additionally occur between the oxygen atoms of
the imide moieties and the terminal methyl groups of the
interdigitating chains from the adjacent row of NDIs for both
C28-NDI-C28 and uC28-NDI-uC28. The H-O distance varies in
the 2.6-3 Å range in this case. The calculated unit cell values
are a = 44.8 Å, b = 8.5 Å and γ = 90º for C28-NDI-C28, and a =
44.5 Å, b = 8.5 Å and γ = 90º for uC28-NDI-uC28, nicely
matching with the experimental values (Table 1). This further
confirmed the accuracy of the computational study. Finally, we
compared the adsorption energies for both C28-NDI-C28 and
uC28-NDI-uC28 in the lamellar phase A arrangement on
graphene. Assemblies of C28-NDI-C28 adsorbed on graphene
were 0.166 eV (3.83 kcal/mol) per molecule energetically more
favorable than those of uC28-NDI-uC28. However, the
experimental observation of improved long-range order with
uC28-NDI-uC28 compared to C28-NDI-C28 and the stronger van
der Waals interchain interactions between unsaturated C6
carbon chains (Figure S41 and Table S1) clearly point to more
favorable intermolecular interactions in the case of uC28-NDI-
uC28. Considering that the unconventional hydrogen bonding
occurring in the calculated lamellar phases of C28-NDI-C28 and
uC28-NDI-uC28 should be very similar, if not identical, from the
energetic point of view, we can only ascribe such “more
favorable intermolecular interactions” to van der Waals forces.
We simulated an STM image for an individual molecule at a
bias voltage of -1V from the calculated lamellar phases of both
C28-NDI-C28 and uC28-NDI-uC28. The individual molecules, as
well as the corresponding simulated STM images at bias -1V
for C28-NDI-C28 and uC28-NDI-uC28, are shown in Figure 5c
and 5d, respectively. Both C28-NDI-C28 and uC28-NDI-uC28
showed some level of distortion from a linear geometry of the
carbon chains (Figure 5c and 5d, top part). Interestingly, the two
E-configured double bonds (encircled by an orange ellipse in
Figure 5d) were rotated by almost 90º with respect to the
imaginary line that connects the nitrogen atoms of the NDI core
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The different position of the double bonds in uC28-NDI-uC28
and uC33-NDI-uC33 does not seem to play a role, considering
the very similar behavior (Figure 3b and 3d). Results obtained
on a positional isomer of uC28-NDI-uC28 with the double bond
located between carbon atoms 11 and 12 also rule out a
positional influence of the unsaturation (see SI). In contrast, the
overview STM images of the saturated NDIs are characterized
by relatively small domains accompanied by disordered areas.
The lack of a clear preference for either lamellar phase A or B
arrangements seems to cause the existence of disordered
regions and welter areas (Figure 3a and 3c; see SI for the
assignment of disordered areas).
We conducted a statistical analysis on the domain sizes for
the different NDIs to support the qualititative observation on the
dramatic influence of the internal double bonds. For a detailed
description on the assignment of the domain size and further
experimental observations upon scanning see the SI. The results
on the domain size distributions for C28-NDI-C28 and uC28-
NDI-uC28, and C33-NDI-C33 and uC33-NDI-uC33 are
summarized by the two histograms shown in Figure 4. The
saturated NDIs mainly arrange in relatively small domains (≤
1000 nm2) (Figure 4a and 4b, blue columns). Moreover, on
roughly 24% of the surface, the molecules do not arrange in an
ordered way resulting in disordered areas. On the other hand,
the images of the unsaturated NDIs show only a marginal
amount of disordered areas. The observed domains reach much
larger extensions, with a significant population larger than
15000 nm2 (Figure 4a and 4b, orange columns).
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in uC28-NDI-uC28 (Figure 5d, top part). As expected, the
simulated STM images of C28-NDI-C28 and uC28-NDI-uC28 are
almost identical with respect to the aromatic cores (Figure 5c
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4
Table 1. Unit cell parameters for the supramolecular arrangements of C28-NDI-C28, uC28-NDI-uC28, C33-NDI-C33 and uC33-
NDI-uC33 at the 1-PO/HOPG interface. The lengths of the unit cell vectors are labelled a and b and the internal angle is
specified by  (see also Figure 5 and b).
5
6
7
8
Lamellar
phase
Domain size
Domain size
Disordered areas
[%]
Compound
a[nm]
b [nm]
γ [deg]
average [nm2]
median [nm2]
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C28-NDI-C28
4.45 ±
0.24
0.88 ±
0.08
85.21 ±
3.39
A and B
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949
737
2923
540
26±5
uC28-NDI-
uC28
4.53 ±
0.08
0.86 ±
0.10
87.33 ±
1.78
A
6764
1268
8026
-
24 ± 8
-
C33-NDI-C33
5.29 ±
0.49
0.99 ±
0.10
84.10 ±
5.28
A and B
uC33-NDI-
uC33
5.27 ±
0.08
0.94 ±
0.06
84.93 ±
1.80
A
3684
Figure 5. (a) Optimized geometries for Phase A of (a) C28-NDI-C28 and (b) uC28-NDI-uC28 adsorbed on a graphene surface. The black
rectangle shows the unit cells. The orange ellipses show the positions of the double bonds within the NDIs. Hydrogen, carbon, oxygen
and nitrogen atoms are shown in white, grey, red and blue, respectively. The graphene layer is shown in cyan. The unit cell
parameters a, b and  are marked in magenta. (c) Single molecule in lamellar phase A geometry (top) and simulated STM image
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(bottom, black and white image) at -1 V for C28-NDI-C28. (d) Single molecule in lamellar phase A geometry (top) and simulated STM
image (bottom, black and white image) at -1 V for uC28-NDI-uC28.
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and 5d, top parts). The main difference concerns the long
carbon chains, with the clear presence of the internal double
bonds in uC28-NDI-uC28 (Figure 5d). The two internal double
bonds appear as bright spots, suggesting the presence of two
localized areas of higher electronic densities along the carbon
chains (Figure 5d). In stark contrast, the distribution of the
electronic density along the carbon chains of C28-NDI-C28 is
more homogeneous and points to a discrete series of single
bonds (Figure 5c). Consistently with the on-graphene optimized
structure of uC28-NDI-uC28, the internal double bonds are
rotated by almost 90º, also in the simulated STM image (Figure
5d). This peculiar feature may account for a different
visualization of the internal double bond by STM. Such
hypothesis seems to be consistent with the experimental STM
images reported in Figure 2, in which one of the two double
bonds appears more visible than the other one for both uC28-
NDI-uC28 and uC33-NDI-uC33. This difference is more evident
in the case of uC33-NDI-uC33 and it is probably due to an
increased distance for the internal double bonds from the NDI
core, which ultimately facilitates the imaging. Hence, the
gratifying agreement between the calculations on uC28-NDI-
uC28 and the experimental STM images on both uC28-NDI-uC28
and uC33-NDI-uC33 allowed us to generalize the conclusions to
both unsaturated molecular systems.
functionalized surfaces and highly dynamic and smart
functional substrates.
ASSOCIATED CONTENT
Supporting Information. Synthetic details, characterization of the
new isolated compounds, in situ STM imaging at the liquid/solid
interface, computational details.
This material is available free of charge via the Internet at
http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Authors
* e.w.meijer@tue.nl
* b.l.feringa@rug.nl
Present Addresses
†Adolphe Merkle Institute, University of Fribourg, Chemin des
Verdiers 4, CH-1700 Fribourg, Switzerland.
Author Contributions
The manuscript was written through contributions of all authors.
All authors have given approval to the final version of the
manuscript. ‡These authors contributed equally.
Funding Sources
CONCLUSIONS
This work was supported financially by the European Research
Council (ERC, advanced grant no. 694345 to B.L.F.), and the
Ministry of Education, Culture and Science (Gravitation Program
We presented the synthesis and self-assembly at the 1-
PO/HOPG interface of C28-NDI-C28, C33-NDI-C33, uC28-NDI-
uC28 and uC33-NDI-uC33. The molecular structures only differ
by the presence/absence of precisely positioned internal double
bonds in their molecular skeletons. These compounds self-
assembled into lamellar arrangements characterized by parallel
aromatic cores that lay flat on the surface, and aliphatic chains
that modulate the distance between such cores. The longer the
chain, the larger the distance, implying that the entire molecular
system lays flat on the surface. The packing of the long carbon
chains results into two different arrangements: one, in which the
tails are interdigitated (lamellar phase A), and a second one,
where the long tails arrange diagonally, without interdigitation
(lamellar phase B). We find the presence/absence of the simple
double bonds to be the critical parameter for the selection of the
chain arrangements. The fully saturated compounds present a
combination of both self-assembly motifs, whereas the
unsaturated molecules are capable of selecting the fully
interdigitated arrangement. Such difference is magnified and
reflected on the long-range order of the generated monolayers,
with the unsaturated compounds forming much larger domains
(in some cases larger than 15000 nm2). This contrasts starkly
with the locally ordered, yet globally disordered, monolayers of
the saturated compounds. The experimental results were also
corroborated by computational studies, which suggest stronger
van der Waals interactions between unsaturated carbon chains
as possible explanation. Showing the paramount role played by
internal double bonds in the self-assembly of long carbon chain-
derivatives on surfaces, our results point to the use of “simple”
internal double bonds as a critical structural parameter for
no.
024.001.035).
Acknowledgment
Mr Ralf Bovee (TU Eindhoven) is acknowledged for MALDI-TOF
measurements. The authors thank Pieter van der Meulen
(University of Groningen) for assistance during some NMR
experiments.
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