Formation of Highly Ordered Molecular Porous 2D Networks from Cyano-Functionalized Porphyrins on Cu(111)

Article abstract of DOI:10.1002/chem.202001980

We investigated the adsorption of three related cyano-functionalized tetraphenyl porphyrin derivatives on Cu(111) by scanning tunneling microscopy (STM) in ultra-high vacuum (UHV) with the goal to identify the role of the cyano group and the central Cu atom for the intermolecular and supramolecular arrangement. The porphyrin derivatives studied were Cu-TCNPP, Cu-cisDCNPP, and 2H-cisDCNPP, that is, Cu-5,10,15,20-tetrakis-(p-cyano)-phenylporphyrin, Cu-meso-cis-di(p-cyano)-phenylporphyrin and 2H-meso-cis-di(p-cyano)-phenylporphyrin, respectively. Starting from different structures obtained after deposition at room temperature, all three molecules form the same long-range ordered hexagonal honeycomb-type structure with triangular pores and three molecules per unit cell. For the metal-free 2H-cisDCNPP, this occurs only after self-metalation upon heating. The structure-forming elements are pores with a distance of 3.1 nm, formed by triangles of porphyrins fused together by cyano-Cu-cyano interactions with Cu adatoms. This finding leads us to suggest that two cyano-phenyl groups in the “cis” position is the minimum prerequisite to form a highly ordered 2D porous molecular pattern. The experimental findings are supported by detailed density functional theory calculations to analyze the driving forces that lead to the formation of the porous hexagonal honeycomb-type structure.

Full text of DOI:10.1002/chem.202001980

Accepted Article
Accepted Article
Title: Formation of highly ordered molecular porous 2D networks from
cyano-functionalized porphyrins on Cu(111)
Authors: Hans-Peter Steinrück, Rajan Adhikari, Gretel Siglreithmaier,
Martin Gurrath, Manuel Meusel, Jan Kuliga, Michael Lepper,
Helen Hölzel, Norbert Jux, Bernd Meyer, and Hubertus
Marbach
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to ensure accuracy of information. The authors are responsible for the
content of this Accepted Article.
To be cited as: Chem. Eur. J. 10.1002/chem.202001980
Link to VoR: https://doi.org/10.1002/chem.202001980
01/2020

10.1002/chem.202001980
Chemistry - A European Journal
Formation of highly ordered molecular porous 2D networks from
cyano-functionalized porphyrins on Cu(111)
Rajan Adhikari1, Gretel Siglreithmaier1, Martin Gurrath2, Manuel Meusel1, Jan Kuliga1,
Michael Lepper1, Helen Hölzel3, Norbert Jux3, Bernd Meyer2,*, Hans-Peter Steinrück1,* and
Hubertus Marbach1
______________________________________________________________________
[1]
Rajan Adhikari, Gretel Siglreithmaier, Manuel Meusel, Jan Kuliga,
Dr. Michael Lepper, Prof. Dr. Hans-Peter Steinrück*, Dr. Hubertus Marbach
Lehrstuhl für Physikalische Chemie II,
Friedrich-Alexander-Universität Erlangen-Nürnberg,
Egerlandstr. 3,
D-91058 Erlangen, Germany
Email: hans-peter.steinrueck@fau.de
[2]
Martin Gurrath, Prof. Dr. Bernd Meyer*,
Interdisciplinary Center for Molecular Materials (ICMM) and Computer-Chemistry-
Center (CCC), Friedrich-Alexander-Universität Erlangen-Nürnberg,
Nägelsbachstr. 25,
D-91052 Erlangen, Germany
Email: bernd.meyer@fau.de
[3]
Helen Hölzel, Prof. Dr. Norbert Jux
Lehrstuhl für Organische Chemie II,
Friedrich-Alexander-Universität Erlangen-Nürnberg,
Nikolaus-Fiebiger-Str. 10,
D-91058 Erlangen, Germany
Supporting information for this article is given via a link at the end of the document.
*) corresponding authors
1
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10.1002/chem.202001980
Chemistry - A European Journal
Abstract
We investigated the adsorption of three related cyano-functionalized tetraphenyl porphyrin
derivatives on Cu(111) by scanning tunneling microscopy (STM) in ultra-high vacuum (UHV)
with the goal to identify the role of the cyano group and the central Cu atom for the
intermolecular and supramolecular arrangement. The porphyrin derivatives studied were Cu-
TCNPP, Cu-cisDCNPP, and 2H-cisDCNPP, that is, Cu-5,10,15,20-tetrakis-(p-cyano)-phenyl-
porphyrin, Cu-meso-cis-di(p-cyano)-phenyl-porphyrin and 2H-meso-cis-di(p-cyano)-phenyl-
porphyrin, respectively. Starting from different structures obtained after deposition at room
temperature, all three molecules form the same long-range ordered hexagonal honeycomb-type
structure with triangular pores and three molecules per unit cell. For the metal-free 2H-
cisDCNPP, this occurs only after self-metalation upon heating. The structure-forming elements
are pores with a distance of 3.1 nm, formed by triangles of porphyrins fused together by cyano-
Cu-cyano interactions with Cu adatoms. This finding leads us to suggest that two cyano-phenyl
groups in the “cis” position is the minimum prerequisite to form a highly ordered 2D porous
molecular pattern. The experimental findings are supported by detailed density functional
theory calculations to analyze the driving forces that lead to the formation of the porous
hexagonal honeycomb-type structure.
2
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Introduction
It is still an ongoing challenge to organize matter on the molecular or even atomic scale. In this
regard, the topic of self-assembled supramolecular networks of organic molecules on noble-
metal surfaces developed as a vivid research field over the last two decades. Molecular self-
[1]
assembly, based on molecular recognition concepts in supramolecular chemistry, aims at
design, synthesis, and understanding of the assembly of a discrete number of molecular entities
into larger ensembles. In the new supramolecular entities with larger shapes and sizes, the
spatial organization of the functional building blocks is controlled by intermolecular forces
such as hydrogen bonding, [2] π-π stacking, [3] dipolar coupling, [4] metal coordination, [5] and
dispersion forces, all of which are weaker than covalent bonding. Molecular self-assemblies
and their properties on surfaces not only depend on the intermolecular interactions but also on
the adsorbate−substrate interactions; therefore they can be tuned by modifications within the
molecules [6] and by the choice of the underlying substrate. [7]
If it comes to the directed self-assembly toward functional molecular architectures,
porphyrins [8] appear to be a particularly suitable class of molecules, since they are omnipresent
[9]
[10]
in nature, for example in chlorophyll (Mg-center)
and heme (Fe-center).
Porphyrins
consist of a tetrapyrrolic macrocycle with a central cavity, which can coordinate a variety of
metal atoms. [9-11] Owing to these properties, porphyrins adsorbed at metal surfaces offer a rich
playground for the detailed investigation and manipulation of desired systems. Recently, the
attachment of one or more cyano-functionalized groups to porphyrins turned out to be
particularly interesting, because the negatively charged N-atoms can interact through different
bonding motifs with neighboring molecules. Notably, cyano groups cannot only contribute in
[4,
hydrogen bonding and dipolar coupling, but also can coordinate to different noble-metals.
12]
Furthermore, it was shown that the electron withdrawing effect of the peripheral cyano
groups significantly influences the self-metalation of corresponding metal-free porphyrin
derivatives on Cu(111). [12a]
In addition to the already reported individual molecules (0D) [12d] and molecular chains
(1D) [12b] of cyano-functionalized porphyrins, we herein report the formation of peculiar porous
networks (2D), which is again triggered by the functional cyano groups. Previously, 2D
molecular porous networks were reported using different classes of organic molecules on single
crystal metal surfaces. [13] These 2D molecular porous networks are especially interesting, since
they have a high potential as “host template” for functional guest molecules, e.g., to study the
dynamics of guest binding within the pore or to localize them even at elevated temperatures
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10.1002/chem.202001980
Chemistry - A European Journal
for the manipulation by an STM tip. Moreover, the pores may also serve as nanoreactors. [14]
Generally, the self-assembly of ordered supramolecular networks depends on the nature
and functionality of the corresponding molecular building blocks, the choice of the substrate
and the applied conditions. For example, the porous networks formed by trimesic acid (TMA)
and its larger relative 1,3,5-benzene-tribenzoic acid (BTB) have been studied on surfaces like
[15]
[16]
HOPG
and Au(111).
Moreover, the porous networks stabilized by metal coordination
captured increasing attention due to metal-ligand bonding, and thus its stability is stronger than
[17]
usual hydrogen-bonded porous networks.
More often, for the formation of metal-organic
networks Fe, Co, Ni, or Cu atoms are introduced as linker metals for co-adsorbed organic
molecules. Aside from directly introduced transition metal atoms, adatoms from the surface,
onto which molecules are deposited, can be used as metal-organic coordination. Recently,
examples for this type of interactions have been reported by Lepper et al. on Cu(111) [12b] and
by Gottardi et al. on Au(111). [18]
Figure 1 depicts the chemical structures of Cu-TCNPP, Cu-cisDCNPP, and 2H-
cisDCNPP, in which fourfold and twofold (cis)-cyano-phenyl groups are attached to the meso-
position of the porphyrin core. In this contribution, we will show that the depicted metalated
species tend to self-assemble into a peculiar well-ordered porous commensurate array, which
is stable at RT. We will discuss the importance of the cyano-cis conformation as a prerequisite
for the latter structure as well as the role of the metalated center.
The adsorption of the different molecules was studied by scanning tunneling microscopy
(STM) and density functional theory (DFT) calculations. The DFT calculations are based on a
modified dispersion correction scheme, which gave very accurate results for binding energies
and structures of aromatic molecules on Cu and Ag surfaces in a recent benchmark study. [17,
19]
Details of the methods and the synthesis of the molecules are provided in the Supporting
Information (SI).
Figure 1. Chemical structure of different cyano-functionalized porphyrins: (a) Cu-TCNPP, (b)
Cu-cisDCNPP, and (c) 2H-cisDCNPP.
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Results and Discussion
Cu-TCNPP on Cu(111):
Figure 2a depicts an STM image of Cu-TCNPP deposited on Cu(111) at RT, with an average
coverage of 0.0084 ML (1 ML refers to the one adsorbate molecule per surface atom). One can
clearly distinguish two prominent molecular ordering patterns, namely a 2D hexagonal
honeycomb-type motif and a 1D linear double-row motif. The self-assembled supramolecular
ordered islands are often connected to step edges, which indicates that the steps are
energetically favored adsorption sites, which act as nucleation centers. [11e] While no isolated
Cu-TCNPP species could be imaged at RT, we observe clear indications for the existence of
very mobile molecules on the surface, e.g., attaching and detaching molecules and noisy streaks
appearing in the fast scanning direction of the STM. The latter observation is attributed to fast
Cu-TCNPP moving molecules, which can be interpreted as two-dimensional (2D) gas phase.
[11a] Similar observations have been reported for copper(II)-tetraphenylporphyrin (Cu-TPP) on
Cu(111) at RT. [11a] In addition to the described behavior, we observe an individual molecule
diffusing towards and away from the hexagonal honeycomb-type pattern in Figure 2a (indicted
by an arrow; see also Figure S1 in the SI). This molecule moves along one of the high-
symmetry crystallographic directions of the Cu(111) surface and is identified as 2H-TCNPP,
[12b] which is a residue stemming from the synthesis of Cu-TCNPP. The 2H-TCNPP molecule
appears as four bright lobes in the periphery and two dominating protrusions in the center. The
diffusion of individual isolated metal-free porphyrins along high-symmetry crystallographic
directions at RT is a common observation on Cu(111). [11b, e]
In the following, we will discuss the appearance of individual Cu-TCNPP molecules in the
two motifs. The molecules in the 1D linear double-row motif are shown in Figure 2b and 2c on
enlarged scales; they appear as six distinguishable, clearly recognizable protrusions, which are
arranged in two parallel groups of three. By comparison with the chemical structure (c.f.
[8-11]
Figure 1a) and STM reports concerning metallo-porphyrins in literature,
the outer four
protrusions are assigned to the peripheral phenyl substituents, and the two central ones to the
slightly bent up pyrrole groups; this is evident from Figure 2d, where the STM image from
Figure 2c is overlaid with a scaled molecule model. The overall intramolecular conformation
can be described as saddle-shape conformation with the pyrrole groups tilted out of the
[20]
macrocyclic plane.
The elongated depression (dark line) between two parallel groups of
three protrusions is referred to as molecular axis; it is aligned to one of the high-symmetry
crystallographic directions of the Cu(111) substrate.
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Figure 2. (a) Average frame of an STM movie (15 consecutively recorded images) of Cu-
TCNPP, deposited and measured at RT, showing a 1D linear parallel motif and a 2D porous
hexagonal honeycomb-type motif (30 × 30 nm2, Ubias = -1 V, Iset = 28.8 pA). (b) Short 1D
parallel molecular chains (5 × 5 nm2, Ubias = -1 V, Iset = 28.8 pA). (c) High resolution STM
image of a single Cu-TCNPP molecule with six protrusions, which are ascribed to the two
iminic pyrrole groups (center) and the 4 phenyl (peripheral) groups (1.5 × 1.5 nm2, Ubias = -1
V, Iset = 28.8 pA). (d) Single Cu-TCNPP molecule overlaid with molecule models
(1.5 × 1.5 nm2, Ubias = -1 V, Iset = 28.8 pA). (e) STM image of the highly ordered 2D porous
honeycomb-type pattern with the lattice vectors of the unit cell indicated as dashed yellow
lines, respectively (10 × 10 nm2, Ubias = -1 V, Iset = 29 pA). (f) STM image of (e) is overlaid
with scaled models of Cu-TCNPP molecules.
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Generally, the intramolecular conformation of TPPs on a surface is determined by a subtle
balance between molecule−surface and molecule−molecule interactions as well as steric forces
within the molecule. The saddle-shape conformation is common for TPPs and slightly modified
TPPs on a variety of surfaces. In contrast, metal-free 2H-TPP [21] and the corresponding cyano-
functionalized species 2H-(5-mono-(p-cyanophenyl))-(10,15,20-triphenyl)-porphyrin (2H-
MCNPP), 2H-cisDCNPP, and 2H-TCNPP [12a, b] exhibit a very peculiar “inverted” structure on
Cu(111), which is characterized by direct N−Cu bonds and two nearly upright pyrrole groups.
[22]
Next, we analyze the supramolecular arrangement in the 2D hexagonal honeycomb-type
motif in detail. Figure 2e shows a high resolution image clearly resolving the sub-molecular
features and the highly ordered network with regular triangular pores. The structure can be
described with a primitive hexagonal unit cell (γ = 60° ± 2°) containing 3 molecules and lattice
vectors of 3.0 ± 0.15 nm. In order to further elucidate the supramolecular structure and the
intermolecular network, the STM image is overlaid with scaled models of Cu-TCNPP in
Figure 2f. From this comparison, it is evident that neighboring cyano groups face each other at
the corners of the triangular pores. Notably, the molecules enclosing the triangular pores are
aligned along the three high-symmetry crystallographic directions of the Cu(111) surface.
The arrangement of the cyano groups at the corners of the triangular pores indicates that
the observed supramolecular network of Cu-TCNPP on Cu(111) is not due to the mutual
stabilization via attractive intermolecular interactions, which was proposed for the metal-free
[12b]
2H-TCNPP on Ag(111).
Considering the polarity of the cyano groups, a direct CN-NC
coordination is not expected to be energetically favorable. Furthermore, we interpret that the
commonly observed T-type and π-π intermolecular stacking of porphyrin derivatives are not in
line with the relatively large distance of peripheral cyano groups. [3-4, 23] For the same reasons,
we also rule out the known binding interaction for cyano groups, namely, via hydrogen bonds
and dipolar coupling. [4, 12d, e, 18]
We rather propose that the terminating C−N groups are linked via native Cu adatoms.
Indeed, the lone pair electrons provided by the N atoms of the functionalized cyano end groups
possess high binding affinity towards transition metals. [24] This mechanism has been reported
frequently for N-terminated organic molecules for metal-organic network formation, since the
Cu(111) surface is known to offer adequate native adatoms. [12d, 25] We suggest that the native
adatoms at the corners of the triangles fuse together two porphyrins via cyano-Cu-cyano
interactions, and thereby stabilize the ordered 2D porous honeycomb-type networks (for details
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see DFT calculations below). Three Cu-TCNPP molecules are rotated by 60° with each other
forming the regular triangular pores. The fact that the adatoms located at the corners of the
triangular cavities are not visible in the STM images has been reported before for 3d-block
transition metals within 2D porous networks on metal surfaces. [12b, d, 24, 26]
After analyzing the appearance of individual Cu-TCNPPs and their supramolecular
arrangement, we performed annealing experiments to probe the stability of the different phases.
Figure 3a shows the STM image acquired at RT after annealing at 400 K. Interestingly we find
a complete transformation to the monomodal appearance of the 2D hexagonal honeycomb-type
pattern, with no 1D linear double-row motifs left.
Figure 3. (a) A 100 × 100 nm2 STM image depicts the full monomodal transformation of Cu-
TCNPP after annealing at 400 K (Ubias = -1 V, Iset = 30 pA); the high-symmetry crystallo-
graphic <110> substrate directions are indicated as white double arrows. (b) DFT-optimized
structure of the porous honeycomb-type network showing a hexagonal (7√3×7√3)R30°
superstructure, where the molecules are linked via Cu adatoms on Cu(111).
The observation of the extended long-range ordered structure, which is perfectly aligned
along the high symmetry directions of the substrate allows for further insights. The perfect
alignment and the absence of any moiré pattern is a strong indication that the superstructure is
commensurate with the underlying substrate. The driving force likely is that the linking Cu
adatoms have a well-defined adsorption site on the Cu(111) surface. In Figure 3b, we depicted
a structural model, which is based on the STM image in Figure 3a, and on the detailed DFT
calculations presented below. Note that while we are not able to determine the exact positions
of the Cu-TCNPP molecules on the Cu(111) lattice from our STM images, this information
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solely stems from the calculations. The primitive hexagonal unit cell corresponds to a
(7√3×7√3)R30° superstructure, with a length of the lattice vector of 3.09 nm. In this structure,
the porphyrins adsorb on bridge sites and the connecting Cu adatoms occupy threefold hollow
sites (see below).
Further annealing to 450 K results in a loss of the long-ranged ordered structure, and the
observation of randomly oriented individual molecules, which display four pronounced
protrusions; see Figure S2 in the SI. We tentatively assign our observations to the formation of
intramolecular C-C bonds between the phenyl groups and the porphyrin core, after
dehydrogenation of the corresponding carbon atoms.[11a] Similar reactions have been proposed
for 2H-TPP on Ag(111) after heating to above 525 K, [6b, 27], for 2H-TPP on Cu(111) [28] and
for 2H-TCNPP on Pd/Cu(111). [29] Moreover, from STM, we find that there is no long range
order any more, but most of the reacted molecules are still aligned along one of the high
symmetry substrate directions. This likely is due to specific interactions of the cyano groups
with the substrate Cu atoms.
Cu-cisDCNPP on Cu(111):
In order to gain deeper insight into the formation of 2D porous networks and in particular into
the role of the cyano-functionalized phenyl groups, we varied the number of cyano-functio-
nalized substitutions from four to two in cis-configuration. Figure 4a depicts an STM image of
Cu-cisDCNPP deposited and measured at RT on Cu(111) with an average coverage of 0.0067
ML. We observe characteristic structures with one or more pores, which show a large similarity
to the 2D hexagonal honeycomb-type motif observed Cu-TCNPP (see above). We distinguish
triangular “monoflakes” with one pore, “biflakes” with two pores and “multiflakes” with more
than 2 pores. The molecularly resolved image of a monoflake in Figure 4b shows that the
individual molecules within the flakes are characterized by two parallel elongated protrusions,
[21b]
which indicates a saddle-shape conformation,
identical to that proposed for Cu-TCNPP.
Notably, also a small number of monomers and dimers are visible, which are assigned to metal-
free 2H-cisDCNPP molecules, which are most likely present in the Cu-cisDCNPP material as
residues of the synthesis process.
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Figure 4. (a) A 80 × 80 nm2 STM image showing Cu-cisDCNPP deposited and measured at
RT (Ubias = -1.02 V, Iset = 28.8 pA). (b & c) High resolution STM image showing a monoflake
with molecular model superimposed (7.5 × 7.5 nm2, Ubias = -1.02 V, Iset = 28.8 pA). (d) A
100 × 100 nm2 STM image depicts 2D porous network formation after a 400 K annealing step
(Ubias = -1.01 V, Iset = 29.5 pA). (e & f) Close-up STM image with unit cell and tentative
molecule model overlayed (10 × 10 nm2, Ubias = -1.02 V, Iset = 28.8 pA).
In Figure 4c, the STM image of the monoflake in Figure 4b is superimposed with scaled
models of Cu-cisDCNPP. Three molecules rotated to each other by 60° to form the central
triangular pore of the monoflake. From the tentative overlay, it becomes apparent that the
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neighboring cyano groups face each other at the corners of the triangular pore, which is the
identical arrangement as for Cu-TCNPP (see above). Again, the three sides of the triangular
pores reflect the three main high-symmetry crystallographic directions of Cu(111). Along the
lines discussed for Cu-TCNPP, we propose that native Cu adatoms from the substrate stabilize
the structure via a local CN-Cu-NC motifs.
As a next step, we annealed the adsorbed layer to 400 K for 60 min. Figure 4d depicts the
STM image acquired at RT after annealing. Interestingly, the triangular porous “monoflakes”,
“biflakes” and “multiflakes” are not observed anymore, but instead have undergone a transfor-
mation towards a long range-ordered 2D porous hexagonal honeycomb-type pattern. Its
structure is within the margins of error identical to the one observed for Cu-TCNPP. The
comparison to Figure 3a shows smaller domains, with areas of uncovered substrate in between.
This observation is likely due to the low mobility of the larger flakes, which serve as nucleation
centers for the larger long range-ordered domains. Interestingly, all pores in Figure 4d and 4e
are empty, which is in contrast to Figure 3a, where some of the pores are filled by unidentified
contaminations, which could originate from the synthesis process.
2H-cisDCNPP on Cu(111):
To obtain further information on the formation of the observed long-range ordered porous
networks and in particular to evaluate the role of the central Cu atom, we also studied the
adsorption of the metal-free 2H-cisDCNPP on Cu(111) at RT with an average coverage of
0.0168 ML. Figure 5a depicts an STM image of 2H-cisDCNPP deposited and measured at RT
on Cu(111). The molecules do not form any long-range ordered network, but are adsorbed as
individual species. Each molecule appears as four bright lobes in the periphery, and two
dominating protrusions in the center; the latter are hardly resolved and mostly appear as one
longish protrusion. The molecular appearance and the general adsorption behavior is very
[12b]
similar to that of 2H-TCNPP on Cu(111),
where the intramolecular conformation is
described by the so-called “inverted” structure. [21b] In this structure, two opposite pyrrole rings
are oriented perpendicular to the Cu surface, yielding the two bright central protrusions in the
sub-molecularly resolved STM image, similar as seen in Figure 5a. The molecules are aligned
along one of the high-symmetry crystallographic directions of the substrate, which is due to a
strong attractive site-specific interaction between the iminic nitrogens of the macrocycle and
the Cu atoms of the Cu(111) surface. [21] In a previous study of 2H-cisDCNPP on Cu(111) at
much lower coverages, but otherwise similar conditions, the formation of dimers connected via
native Cu adatoms was reported, along with self-metalation at 400 K. [12a] At the high coverage
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studied here, we do observe some dimers, but neither extended 1D chains nor 2D porous
networks are evident.
Figure 5. (a) A 40 × 40 nm2 STM image showing 2H-cisDCNPP deposited and measured at
RT (Ubias = -1 V, Iset = 30.3 pA). (b) Annealing at 400 K results in conversion of 2H-cisDCNPP
into Cu-cisDCNPP (30 × 30 nm2, Ubias = -1.22 V, Iset = 29.4 pA). (c & d) Close-up STM image
with unit cell and tentative molecule model overlayed (10 × 10 nm2, Ubias = -1.22 V,
Iset = 29.4 pA).
As a next step, we annealed the adsorbed layer to 400 K for 300 min. After heating, we
observe almost complete transformation of the individually adsorbed molecules into a perfectly
ordered 2D hexagonal honeycomb-type porous structure, as depicted in Figure 5b. Obviously,
the prolonged heating step leads to the formation of this thermodynamically more favorable
long-range ordered structure. Notably, within the islands no single defect or adsorbed
contaminations are observed. In the sub-molecularly resolved image in Figure 5c, the
molecules appear as six clearly distinguishable protrusions, which are arranged in two parallel
rows of three protrusions. This appearance is identical to that observed for Cu-TCNPP (see
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Chemistry - A European Journal
Figure 2), which is a strong indication that upon heating self-metalation of 2H-cisDCNPP with
Cu atoms from the Cu(111) surface occurred, yielding Cu-cisDCNPP. [11a, e, 30]
The detailed analysis of the molecularly resolved STM images in Figure 5c reveals that
the ordered 2D network has the identical structure with triangular pores as described above for
Cu-cisDCNPP and Cu-TCNPP, within the margin of error. The STM image overlaid with
scaled models of Cu-cisDCNPP molecules in Figure 5d shows that neighboring cyano groups
face each other at the corners of the triangular pore. Again, three molecules rotated by 60° to
each other and oriented along the three main high-symmetry crystallographic directions of
Cu(111) form the triangular pores. In analogy to the observations for Cu-cisDCNPP and Cu-
TCNPP, we propose that the driving force for the formation of the observed porous pattern is
a linking via native adatoms at the corners of the triangular pore, that is, the Cu-cisDCNPP
molecules fuse together via CN-Cu-NC interactions as illustrated in Figure 5d.
[12b]
Notably, 2H-TCNPP on Cu(111)
did not show the transition to the porous structure
upon annealing at elevated temperatures, which was observed here for 2H-cisDCNPP. This
behavior is attributed to the significantly larger activation barrier for metalation for 2H-
TCNPP.[12a]
Theoretical calculations
To analyze the driving forces that lead to the formation of the porous hexagonal honeycomb-
type structure of the adsorbed porphyrins, we performed extensive density functional theory
(DFT) calculations. In a first series of calculations, we determined the preferred adsorption site
of the CN-functionalized Cu porphyrins on the Cu(111) surface. The corrugation of the energy
landscape, which is obtained when a Cu porphyrin is translated over the surface, is rather weak
(about 0.35 eV in the case of Cu-TPP, see Figure S5b in the SI), which leads to fast diffusion
on Cu(111), as observed by STM. Nevertheless, there is one single site, which is clearly
preferred by the porphyrins, independent of a CN functionalization. This site is determined by
the interaction of the N atoms of the porphyrin core with Cu atoms of the substrate. The central
porphyrin Cu atom is in a bridging position and the N atoms are roughly on-top of surface Cu
atoms (see Figure 6). This position of the porphyrin core simultaneously guarantees that
terminal CN groups point to on-top sites of the Cu(111) surface (see Figure 6b,c and
Figure S6a,b). Only the on-top sites show an attractive interaction with the CN groups, the
[12b]
hollow and the bridge sites are repulsive.
Furthermore, Figures S6c,d and S7b,c
demonstrate that the terminal CN groups can easily incorporate Cu adatoms, which sit
preferentially in fcc or hcp hollow sites.
13
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Chemistry - A European Journal
All Cu porphyrins with and without CN functionalization maintain their gas-phase saddle-
shape configuration upon adsorption on Cu(111). The downward-tilted pyrrole rings give rise
to a dark line in the STM contrast. The calculations predict that in the preferred orientation of
the Cu porphyrins the dark line is aligned with the densely-packed Cu rows, which is in
agreement with the experimental STM observation (see Figure 2c).
Figure 6. Side and top view of the relaxed structure of (a) Cu-TPP, (b) Cu-TCNPP and (c) Cu-
cisDCNPP molecules on Cu(111) at their most favorable adsorption sites. In all cases, the
saddle shape of the porphyrin is visible. The downward-tilted pyrrole rings (with slightly higher
N atoms) are oriented along the densely-packed Cu rows. Cu, C, N and H atoms are shown in
yellow, black, blue and white, respectively. The same color code is used in all figures.
Next we performed a detailed analysis of the molecule−molecule interactions of the
porphyrin molecules on the Cu(111) surface. Six configurations of Cu porphyrin molecules
with and without CN functionalization as well as with and without Cu adatoms were
considered, which will be discussed in the following step-by-step. All were done with a
(7√3×7√3)R30° surface unit cell containing three Cu porphyrin molecules. The experimentally
observed honeycomb-type structure is characterized by two different types of molecular
contacts: three molecules form a triangle with a large pore in the middle and CN groups facing
each other at the corners. Subsequently, the triangles are densely packed and their outer rim
connect in another triangular motif, in which the phenyl rings are roughly oriented in a T-
shaped stacking (see Figure S8 in the SI). In the following we will refer to these two types of
molecule−molecule interactions as the "pore" and the triangular "rim" contact.
The first important observation is that three porphyrin molecules can be arranged in a
(7√3×7√3)R30° unit cell in such a way that (1) the pore and rim contacts proposed by the
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10.1002/chem.202001980
Chemistry - A European Journal
analysis of the STM images can be established, (2) the structure maintains a 3-fold symmetry
and, most important, (3) all porphyrins adopt their preferred adsorption site, thereby gaining
the largest possible adsorption energy.
We start by building this structure with the non-functionalized Cu-TPP porphyrins
without CN groups (Figure 7a,c, structure 1; this structure is calculated as a hypothetical
reference to evaluate the contributions of the different interactions). The centers of the pore
and the triangular rim contact are hollow sites on the Cu(111) surface (see Figure 7a,c and
Figure S8 in the SI). Without the terminal CN, the pore is "open", i.e., the phenyl rings are far
enough apart that they do not interact. On the other hand, the rim contact is fully "closed" (see
Figure 7a,c), i.e., the distance between the Cu-TPPs on Cu(111) (measured between the central
Cu atoms) of 16.265 Å is close to the gas-phase value of 15.385 Å, which was obtained by a
structure optimization of the Cu-TPP triangle without substrate (note that in the gas-phase
calculation the phenyl rings are more upright-oriented with respect to the porphyrin plane than
on the surface, which allows the molecules to come closer together).
Table 1. Calculated binding energy ꢀblayer per molecule of Cu porphyrins on Cu(111) for the
6 porous honeycomb-type structures discussed in the text. All calculations were done with a
(7√3×7√3)R30° unit cell containing three porphyrin molecules. ꢀbsingle is the binding energy
of a single, well-separated porphyrin molecule as given in Table S1. The difference ∆ꢀb
between the two binding energies describes the on-surface molecule−molecule interaction.
ꢀblayer(ꢁꢂ)
ꢀbsingle(ꢁꢂ)
Porphyrin
∆ꢀb(ꢁꢂ)
1: Cu-TPP
3.50
3.39
+0.11
2: Cu-cisDCNPP
3: Cu-cisDCNPP
4: Cu-TCNPP
3.61
3.68
3.67
3.60
3.60
3.79
+0.01
+0.08
−0.12
5: Cu-cisDCNPP + Cuad
6: Cu-TCNPP + Cuad
4.06
4.17
3.44
3.69
+0.62
+0.48
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Figure 7. Atomic structure of the triangular contact at the rim, (a) without and (b) with terminal
CN groups. (c) Open pore structure, (d) with terminal CN groups interacting with neighboring
Cu atoms of the substrate, and (e) with terminal CN groups connected by Cu adatoms.
By comparing the binding energy per molecule of this structure with the value for the
single, well-separated molecule we can determine the strength of the molecule−molecule
rim
int
rim
int
interaction ꢀ
for the rim contact. Since no "pore interaction" is present, ꢀ
is given by
the difference ∆ꢀb of the two binding energies. The rim interaction is attractive with about
0.11 eV per molecule (see Table 1). Since we do not observe that the Cu-TPP molecules are
pulled out of their bridge position, the dispersion interaction across the rim is close to its
optimum and cannot be increased further by bringing the Cu-TPP molecules closer together.
The next three structures 2−4 were obtained by adding CN groups to structure 1 (see
Figure S9). Structure 2 consists of Cu-cisDCNPPs with CN groups in the rim area while still
maintaining an "open" pore (see Figure 7b). The N atoms of the terminal CN groups coordinate
to surface Cu atoms as in the case of well-separated adsorbates (see Figure 6b) and do not
establish hydrogen bonds with the neighboring pyrrole rings. The lower-lying CN groups
basically do not interact with the higher-lying pyrrole rings of the neighboring molecules.
Consequently, the binding energy per molecule in the network structure is basically unchanged
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10.1002/chem.202001980
Chemistry - A European Journal
rim
int
compared to the isolated adsorbate (i.e. ꢀ
is almost zero, see Table 1). This shows that the
same packing of "pore triangles" can be achieved with and without CN groups at the outer rim.
Structure 3 is also built of Cu-cisDCNPPs, but now the CN groups are pointing to the pore
(see Figure 7d and Figure S9). These CN groups connect to neighboring Cu atoms on the
Cu(111) surface. In previous studies, it was speculated that such an adsorption on neighboring
sites could lead to an attractive interaction induced by a small lift of the Cu atoms out of the
surface plane. [31] However, in our previous calculations [12b] we could not confirm the presence
of an attractive interaction but found a small repulsion instead. Also here, the inspection of the
binding energies points toward the absence of a significant attractive interaction between
neighboring CN−Cu sites. Structure 3 exhibits the same rim contact as structure 1 together with
a pore contact consisting of terminal CN groups interacting with neighboring substrate Cu sites.
The rim contact should give at least the same gain in binding energy ∆ꢀb of 0.11 eV as
observed in structure 1. However, for structure 3 we only observe a gain of 0.08 eV (see
Table 1). The difference of 0.03 eV per Cu-cisDCNPP molecule stems from the pore
interaction and is repulsive.
The absence of a significant attractive interaction of CN−Cu contacts involving
neighboring Cu surface sites is furthermore demonstrated by repeating the calculations of the
structural motif 3 with a larger (8√3×8√3)R30° unit cell, in which we can systematically open
and close the pore and the rim contact (see Figure S10). No significant change in energy is
observed when the CN−Cu sites are pulled apart by one Cu−Cu distance.
Also structure 4 (Figure S9d) of the porphyrins with four terminal CN groups (Cu-
TCNPP) indicates a repulsive interaction for the core contact. The binding energy per molecule
is reduced with respect to the separated molecules. In the first place, the rim contact has become
slightly repulsive since the porphyrins cannot be displaced anymore from their bridge sites
(compare to structure 2 in Figure 7b and 7d), but obviously this is not compensated by a strong
attractive pore interaction.
In summary, in the triangular pore motif, a strong repulsion between facing CN groups
of neighboring porphyrin molecules is avoided by a bending-down of the CN groups and the
formation of CN−Cu contacts with neighboring Cu surface atoms. However, this binding motif
does not lead to a significant attractive interaction between the porphyrins. The experimentally
observed dominant formation of the triangular pore structure and its thermal stability therefore
cannot be explained by this binding motif.
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On the other hand, Cu adatoms can mediate a strong attraction. If Cu adatoms are added
to structure 3 (the result is structure 5, see Figure 7e and Figure S11), the binding energy per
molecule increases by 0.65 eV compared to separated molecules (see Table 1). Subtracting the
contribution of the rim contact of 0.11 eV (see structure 1), we find a strong attractive pore
interaction of 0.54 eV per molecule. The origin of the attraction is that now two instead of only
one CN group connect to a Cu adatom (or, in other words, less Cu adatoms for a given number
of CN groups have to be created). The strong attractive pore interaction is also confirmed by
adding Cu adatoms to structure 4 (giving structure 6; see Figure 3b), where we find a value of
0.48 eV for the molecule−molecule interaction in the pore (assuming that the rim interaction is
about zero, see structure 2).
The overall larger binding energy for the network structures with Cu adatoms also
implies that they are the thermodynamic ground state. This is in contrast to single molecules,
where the DFT calculations predict a decomposition of adatom structures into molecules
adsorbed on the terrace and a condensation of the Cu atoms at zero temperature (see SI).
Summary and Conclusion
We investigated the adsorption of three related cyano-functionalized tetraphenyl porphyrin
derivatives on Cu(111) by scanning tunneling microscopy (STM) in ultra-high vacuum (UHV)
combined with detailed DFT calculations. The goal was to identify the role of the cyano group
and the central Cu atom for the intermolecular and supramolecular arrangement. The porphyrin
derivatives studied were Cu-TCNPP, Cu-cisDCNPP, and 2H-cisDCNPP. Cu-TCNPP, with
four cyano groups, forms a hexagonal honeycomb-type pattern with triangular pores, which
coexists with 1D molecular double chains at room temperature (RT). Annealing to 400 K yields
a complete transformation to a hexagonal honeycomb-type structure with pronounced long
range order. Cu-cisDCNPP, with two cyano groups in “cis” position, forms monoflakes with
a triangular pore, along with bi- and multiflakes at RT, which all transform in the hexagonal
honeycomb-type structure at 400 K. The metal-free 2H-cisDCNPP shows no order at RT, but
selfmetalates upon heating to 400 K and transforms into the same perfectly ordered hexagonal
honeycomb-type structure as the other two porphyrins. The ordered flakes and the hexagonal
honeycomb-type structures all contain the same structure-forming element, namely triangles
of porphyrins fused together by cyano-Cu-cyano interactions with native Cu adatoms. These
three molecules are rotated to each other by 60° and are aligned parallel to the substrate high-
symmetry directions; this alignment is enforced by the preferential adsorption arrangement of
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Chemistry - A European Journal
the porphyrins and it is stabilized by the linking Cu adatoms at threefold sites at the corners of
the pores. These site-specific interactions with the Cu surface also make the long-range ordered
structure commensurate. The DFT calculations provide detailed insights into the various
energetic contributions that lead to the observed long-range ordered hexagonal honeycomb-
type structure with triangular pores. Looking at the internal structure of the unit cell, one gets
the impression that interactions of the other two porphyrin ligands (with CN groups for Cu-
TCNPP, and without CN ligands for Cu-cisDCNPP and 2H-cisDCNPP) do not play a major
role for the formation of the long-range order. This finding leads us to suggest that the twofold
cyano-functionalized porphyrin with “cis” conformation is the minimum prerequisite to form
a highly ordered 2D porous molecular pattern that might grant protocols as a nanoscaled
template. To conclude, our findings suggest that the cyano groups as functional groups
participate in directed attractive interactions, which will allow for the rational design and
construction of a wide range of nano-scaled supramolecular architectures adsorbed to surfaces.
Notes
The author declares no competing financial interest.
Acknowledgements
The authors gratefully acknowledge funding by the German Research Foundation (DFG)
through Research Unit FOR 1878 (funCOS) and the Collaborative Research Center SFB 953
(project number 182849149) at the Friedrich-Alexander-Universität Erlangen-Nürnberg.
Keywords
Porphyrins, coordinated networks, cyano functionalization, scanning tunneling microscopy
(STM), density-functional theory (DFT) calculations.
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TOC:
Twelve doubly cyano-functionalized Cu-tetraphenylporphyrins form a snowflake-like structure around
a macropore, as observed by scanning tunneling microscopy at room temperature.
22
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