Self-assembly of covalently linked porphyrin dimers at the solid-liquid interface

Article abstract of DOI:10.3390/molecules24163018

The synthesis and surface self-assembly behavior of two types of metal-porphyrin dimers is described. The first dimer type consists of two porphyrins linked via a rigid conjugated spacer, and the second type has an alkyne linker, which allows rotation of

Full text of DOI:10.3390/molecules24163018

molecules
Article
Self-Assembly of Covalently Linked Porphyrin
Dimers at the Solid–Liquid Interface
Thomas Habets 1,†, Dennis Lensen 1,†, Sylvia Speller 2,3 and Johannes A.A.W. Elemans 1,
*
1
Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135,
6525 AJ Nijmegen, The Netherlands
Institute of Physics, University of Rostock, Albert-Einstein-Straße 23, 18059 Rostock, Germany
Department Life, Light & Matter—University of Rostock, 18051 Rostock, Germany
2
3
*
Correspondence: j.elemans@science.ru.nl; Tel.: +31-24-3653099; Fax: +31-24-3652929
†
These authors contributed equally.
ꢀꢁꢂꢀꢃꢄꢅꢆꢇ
Academic Editors: Nathalie Solladié and Regis Rein
Received: 31 July 2019; Accepted: 17 August 2019; Published: 20 August 2019
ꢀꢁꢂꢃꢄꢅꢆ
Abstract: The synthesis and surface self-assembly behavior of two types of metal-porphyrin dimers
is described. The first dimer type consists of two porphyrins linked via a rigid conjugated spacer,
and the second type has an alkyne linker, which allows rotation of the porphyrin moieties with
respect to each other. The conjugated dimers were equipped with two copper or two manganese
centers, while the flexible dimers allowed a modular built-up that also made the incorporation of two
different metal centers possible. The self-assembly of the new porphyrin dimers at a solid–liquid
interface was investigated at the single-molecule scale using scanning tunneling microscopy (STM).
All dimers formed monolayers, of which the stability and the internal degree of ordering of the
molecules depended on the metal centers in the porphyrins. While in all monolayers the dimers were
oriented coplanar with respect to the underlying surface (‘face-on’), the flexible dimer containing
a manganese and a copper center could be induced, via the application of a voltage pulse in the
STM setup, to self-assemble into monolayers in which the porphyrin dimers adopted a non-common
perpendicular (‘edge-on’) geometry with respect to the surface.
Keywords: porphyrins; self-assembly; scanning tunneling microscopy; surfaces
1. Introduction
Metal-porphyrins occur ubiquitously in nature, e.g., as magnesium porphyrin pigments in the light
harvesting system [
enzyme cytochrome P450 [
developed with the aim to approach the efficient functional properties of their natural counterparts,
for instance in areas of molecular electronics [ ] and catalysis [ 11]. In the past decades, our
group has extensively investigated the catalytic properties of Mn(III) porphyrins in the epoxidation of
alkenes [12 16]. The majority of these studies have been carried out using supramolecular systems
1,
2] and as iron porphyrins in the blood protein hemoglobin [3] and the oxidation
4,5]. In biomimetic chemistry, many artificial porphyrin systems have been
6–
8
9–
–
in solution, and in order to obtain more detailed information about the reaction mechanisms during
catalysis, we have also investigated the behavior of single porphyrin molecules adsorbed at a surface.
To this end, we constructed self-assembled monolayers of metal-porphyrins at a solid–liquid interface
and investigated their properties with scanning tunneling microscopy (STM) [17–20]. This technique
does not only enable the probing of structural properties of single molecules but also provides electronic
information, e.g., about changes in the redox state of the porphyrin metal center during a chemical
reaction. Furthermore, a solid–liquid interface environment closely resembles the reaction conditions
encountered in laboratory-scale chemical reactions: Room temperature, atmospheric pressure, and the
presence of a liquid to which reagents can easily be added and products withdrawn. For these reasons,
Molecules 2019, 24, 3018; doi:10.3390/molecules24163018
www.mdpi.com/journal/molecules

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STM at a solid–liquid interface has evolved as a tool to analyze chemical reactions at single-molecule
scale, which is complementary to conventional ensemble techniques such as NMR spectroscopy and
mass spectrometry [21].
In previous work, we had constructed a variety of supramolecular assemblies of (metal-) porphyrins
at solid–liquid interfaces and imaged their spatial organization with the help of liquid-STM [7]. By
applying specific molecular design, we were able to precisely control the two-dimensional (2D)
polymorphic behavior of these assemblies by varying the nature or the concentration of the solution
in the STM experiments [22
porphyrins and investigated their reactivity with oxygen and the epoxidation of alkenes at the
single-molecule scale [25 26]. While these porphyrins are inert in solution, their adsorption to a
–24]. We also constructed 2D assemblies of catalytically active Mn(III)
,
negatively biased surface in the STM setup (or the application of a voltage pulse [27]) induced the
reduction of the metal centers from Mn(III) to Mn(II), which was accompanied by a topographic
signature change of the molecules in the STM images and which resulted in the emergence of reactivity
towards molecular oxygen (O2). Interestingly, STM revealed that O2 reacted in a cooperative fashion
with the manganese porphyrins, in the sense that the adsorbed catalysts were able to coordinate O2
to the metal center, dissociate the oxygen-oxygen bond, and subsequently distribute the two oxygen
atoms over two adjacent metal-porphyrins at the surface, generating Mn(IV)-oxo complexes [25,26].
These complexes appeared in the STM images as signatures with a significantly increased apparent
height compared to the signatures attributed to the Mn(III) and Mn(II) porphyrins, highlighting the
ability of the technique to map both structural and electronic changes during chemical reactions.
Intrigued by the cooperative reactivity of manganese porphyrins adsorbed at adjacent locations at
the solid–liquid interface, we decided to design and synthesize covalently connected metal-porphyrins,
with the ultimate aim to investigate with STM the possible cooperativity between two metal centers in
the same molecule. Several examples of covalently linked porphyrin dimers have been described [28
and some have been imaged with STM in an ultra-high vacuum environment or at a solid–liquid
interface [33 37]. Our intention to adsorb porphyrin dimers as immobilized assemblies at a solid–liquid
–32]
–
interface required the attachment of long aliphatic chains, which are known to aid assembly as a result
of van der Waals interactions with the surface and intermolecular alkane chain interdigitation [38].
We have designed two types of porphyrin dimers (Figure 1), either connected via a rigid conjugated
system (compounds 1) or via a relatively flexible alkyne linker (compounds 2). We had inserted Mn(III)
centers into the dimers because of their potential redox and catalytic properties, and Cu(II) centers that
did not show redox or catalytic behavior and may thus serve as a reference. It should be noted that,
unlike copper porphyrins, manganese porphyrins carry a counter anion, which in our case is an inner
shell axial chloride. In a previous communication, we had already reported the synthesis of flexible
dimers H42, Cu2, and MnCu2 [39]. While STM revealed that Cu2 formed highly ordered monolayers
at a solid–liquid interface, MnCu2 turned out to be able to self-assemble into stacked bilayers in which
the porphyrin dimers in the two layers were ordered in a specific geometry with respect to each other.
In this paper, we present the synthesis of Mn22 and of the rigid conjugated dimers H41, Cu21, and
Mn21, and STM studies of the self-assembly behavior of the metal-porphyrin dimers at the solid–liquid
interface. We are particularly interested in the effect of the presence of the axial chloride ligands at
the manganese porphyrin dimers on the ability of the dimers to form stable adlayers, since these
ions may inhibit favorable cofacial adsorption of the porphyrin planes with respect to the underlying
surface. Finally, we report an unexpected change in two-dimensional (2D) surface polymorphism of
MnCu2 upon the application of mild voltage pulses to the solid–liquid interface, which caused the
orientation of the porphyrin planes to switch from a ‘face-on’ to an ‘edge-on’ geometry with respect to
the underlying graphite surface.

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Figure 1. Molecular structures of porphyrin dimers with a rigid conjugated linker (top) and with a
freely rotatable alkyne linker (bottom).
2. Results and Discussion
2.1. Synthesis
Conjugated porphyrin dimer H41 was synthesized in five steps, starting from
4-hydroxybenzaldehyde, which was alkylated with 1-bromooctadecane to give
(Scheme 1). This compound was subsequently condensed with pyrrole to give porphyrin
38% yield. Using a modified previously reported protocol [40], was regioselectively dihydroxylated
at one of its -pyrrole moieties using osmium tetraoxide to give diol in 41% yield. This compound
was oxidized with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) to diketone in 38% yield.
Finally, two equivalents of were condensed with one equivalent of 1,2,4,5-tetraaminobenzene to
3
in 78% yield
4
in
4
β
5
6
6
give the desired bis-porphyrin H41 in 38% yield. Compound H41 could be readily converted into
Cu21 by reacting it with copper(II) acetate, and into Mn22 by reacting it with manganese(II) acetate
tetrahydrate followed by aerobic oxidation in brine (both in nearly quantitative yields). The synthesis
of acetylene-linked porphyrin dimer H42 and its metal complexes Cu22 and MnCu2 has been reported
by us previously [39]. Bis-manganese dimer Mn22 was synthesized in nearly quantitative yield from
H42 following the same procedure as for the synthesis of Mn21. The progress of all-metal insertion
reactions was monitored by UV-vis spectroscopy, in which chloroform solutions of the reaction mixtures
were acidified with concentrated aqueous HCl; as soon as absorptions correlated to protonated free
base porphyrins remained absent, the metallation was considered complete and the reaction stopped
(see Supplementary Materials for spectral data of all new compounds).

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Scheme 1. Synthesis of porphyrin dimers with a rigid conjugated linker, and their metal derivatives.
2.2. Self-Assembly of Conjugated Porphyrin Dimers Cu21 and Mn21 at a Solid–Liquid Interface
In Figure 2, STM images of self-assembled monolayers of Cu21 and Mn21 at the highly oriented
pyrolytic graphite (HOPG)/1-octanoic acid interface are shown. Droplets of 3–5 L with concentrations
µ
of ~10−5 M of the compounds in 1-octanoic acid were applied to a freshly cleaved HOPG surface. Only
in approximately 20% of the attempts, monolayers could be successfully imaged at (sub)molecular
resolution. In all other cases, typically poorly resolved structures were found revealing at best the
presence of vague lamellar arrays. This is probably due to incomplete assembly of the molecules in a
fully packed layer, or to fast adsorption/desorption kinetics [41–43] of the molecules at the solid–liquid
interface, preventing the formation of a layer that is immobilized enough to be resolvable by STM.
The orientation of the dimers of Cu21 within the self-assembled monolayer can be derived from
the image in Figure 2A. Based on their shape and size, and taking into account the arrangement of
the side-groups, each of the bright-appearing (i.e., elevated) spots is assigned to a porphyrin moiety
that is oriented with its aromatic plane in a largely coplanar geometry with respect to the surface.
Consequently, two of such signatures may constitute one porphyrin dimer molecule. The dimers
are aligned with their long axis along the lamellae, as is shown in the proposed structural model
in Figure 2E. This organization was concluded by considering the distances between the porphyrin
moieties along and perpendicular to the lamella, respectively, especially the observation of alternating
small and large spacings. The unit cell of the monolayer (drawn in Figure 2A) is defined by vectors
a = 3.5 ± 0.2 and
b
= 3.9
±
0.2 nm, with an angle of 79
±
8◦ between them. Based on the distance
between the lamellae, the C18-alkyl chains of adjacent porphyrin dimers have to be interdigitated.
In some parts of the image, these chains are discernable in the darker regions between the bright
signatures (inset in Figure 2A), and careful analysis revealed that they are fully adsorbed on the HOPG
surface in an interdigitated geometry. They are, however, not always ordered alternately, i.e., one chain
originating from a dimer in a lamellar array is not necessarily followed on the surface by a chain of a
dimer from an adjacent lamella. This irregular distribution is also shown in the model in Figure 2E. The
chains are organized in pairs as a result of the limited spacing between the porphyrin moieties within
one dimer, which does not allow interdigitation of a chain from a dimer in an adjacent lamella. Based

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on the orientation of the dimers, one would expect to observe an even number of bright signatures
along each lamella within a monolayer domain. Overall, this is indeed observed in the monolayer of
Cu21, for example when the lamella along line 1 in Figure 2A is considered. However, the lamella
along line 2 reveals an odd number of bright signatures. The cross-sections of both lines are shown in
Figure 2C. Cross-section 1 shows the apparent height profile of six dimers, which show up as twelve
protrusions, each corresponding to a porphyrin moiety within the dimers. The gray boxes indicate the
separate dimers. The cross-section furthermore shows that the depression in apparent height between
the porphyrin moieties in a dimer is less deep than the depression between the porphyrin moieties of
two adjacent dimers, which is the basis of our assignment. If we now consider cross-section 2, dimers
can also be assigned based on the apparent height of the porphyrin moieties. Again the gray boxes
indicate which of the protrusions form a dimer. Based on this analysis, the 5th protrusion from the
left, with a width of about 1.8 nm, is not a fragment of a dimer. We, therefore, assign this feature to a
vacant site, although the small protrusion may be caused by one or more trapped and poorly resolved
solvent molecules [44,45]. The model in Figure 2E also shows such a vacancy. Since the alkyl chains
are not ordered in an alternating fashion, the next bright signature available is at a distance half a
dimer distance further, at 12 a = 1.75
vacancy feature.
±
0.1 nm, which is in agreement with the width of the described
Figure 2.
at the highly oriented pyrolytic graphite (HOPG)/1-octanoic acid interface. The unit cell is indicated
by vectors and . The inset shows a magnification. The black lines represent two cross-sections
which are shown in panel ( ). Tunneling parameters: Vbias 350 mV, It = 5.5 pA. ( ) STM image of a
self-assembled monolayer of Mn21 at the HOPG/1-octanoic acid interface. The unit cell is indicated by
vectors a’ and b’. The black line represents the cross-section shown in panel ( ). Tunneling parameters:
Vbias 450 mV, It = 3.2 pA. ( ) Proposed molecular model of the organization of both porphyrin
dimers at the interface. ( ) Molecular models of the aromatic framework of Mn21 (side view) in which
the two axial chloride ligands are either oriented syn (top) or anti (bottom) with respect to each other.
(A) Scanning tunneling microscopy (STM) image of a self-assembled monolayer of Cu21
a
b
C
=
−
B
D
=
−
E
F

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Figure 2B shows an STM image of a self-assembled monolayer of Mn21 at the HOPG/1-octanoic
acid interface. Although the resolution is not as good as that of the monolayer of Cu21, it is clear that
also Mn21 self-assembles into a lamellar structure, with unit cell vectors a0 = 3.4
±
0.4 and b0 = 3.9
±
0.3 nm, under an angle of 80◦
±
10◦. Within experimental error, these values are the same as those of
the unit cell of Cu21, indicating that the substitution of the metal centers does not change the spatial
ordering of the dimers on the HOPG surface. The difference in resolution between the monolayers
of Cu21 and Mn21 may be explained by the presence of the axial chloride ligand at the manganese
centers of Mn21. This ligand may hinder the adsorption of the dimers at the surface, or alter the
tunneling pathway between the surface and the tip. The self-assembled monolayers of Mn21 appeared
to be not very stable. They only persisted when the tunnel current was maintained below 10 pA, and
even then they typically disappeared after about 30 min of scanning. Although the resolution is not
optimal, the signatures of some of the manganese porphyrin moieties appear to differ in brightness.
The cross-section in Figure 2D shows an apparent height difference of 0.1 nm between bright and less
bright appearing porphyrins. The brighter signatures have a radius of 1.2 nm, and thus span only one
manganese porphyrin, not the whole dimer structure. Due to the lack of sub-molecular resolution, it is
not possible to determine whether more than two different signatures are present in the monolayer. So
far, the origin of the different signatures is unclear. They might be the result of redox reactions occurring
at the manganese centers. Unlike the Cu(II) centers of Cu21, the Mn(III) centers of Mn21 may undergo
reduction to Mn(II), or oxidation to Mn(IV) upon reaction with oxygen, as has been demonstrated in
our previous STM work on monomeric manganese porphyrins [25,26]. Such reactions would most
certainly lead to a difference in the appearance of the porphyrins in the STM images. An alternative
explanation would be that the two porphyrins within an Mn21 dimer adsorb in a different geometry
to the underlying surface. Since the manganese centers have an axially coordinated chloride ligand,
Mn21 can exist in two isomeric forms, at least in principle. Assuming kinetically stable coordination
of the inner shell chloride ligand to the metal center, a molecule of Mn21 can have both chloride
ligands coordinated at the same (syn-isomer) or at the opposite face (anti-isomer) of a porphyrin dimer
(Figure 2F). Due to the paramagnetic nature of the manganese centers, the existence or abundance of
these isomers could not be investigated with the help of NMR spectroscopy. The rigid, conjugated
linker between the porphyrin moieties furthermore inhibits isomerization, via rotation, from the syn-
to the anti-isomer and vice versa. Assuming the existence of both isomers, one can envisage that they
will adsorb in different geometries at the solid–liquid interface. While the conjugated porphyrin plane
of the syn-isomer can adsorb in a cofacial geometry with respect to the surface, this is impossible for
the anti-isomer since one axial chloride ligand will always inhibit this geometry. In the latter case,
the dimer may be adsorbed in a geometry in which it is lifted on the side where the chloride ligand
points in the direction of the surface. As a result of this tilted geometry, the amount of π−π stacking
and van der Waals interactions between the surface and the molecules is not ideal, which may be an
explanation for the limited stability of the monolayer structure in time.
2.3. Self-Assembly of the Non-Conjugated Porphyrin Dimers Cu22, Mn22, and MnCu2 at a Solid–Liquid
Interface
In a previous paper [39] we reported the self-assembly properties of Cu22 and MnCu2 at the
solid–liquid interface. Both compounds formed stable and highly organized monolayers, and in some
cases, bilayer formation was observed for MnCu2, in which the dimers were stacked in two 2D layers
on top of each other. The top 2D layer was found to be able to laterally move stepwise with respect
to the bottom 2D layer, which was strongly immobilized to the HOPG surface. The fact that the
molecules of MnCu2 formed stable and extended uniform 2D layers of molecules that were oriented
with their porphyrin planes coplanar with the underlying HOPG substrate, indicates that the single
axial chloride ligand at the manganese centers of these molecules does not hinder such an adsorption
geometry. It was therefore of interest to investigate the assembly behavior of Mn22, which has two of
these chloride ligands.

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It turned out to be very difficult to obtain assemblies of Mn22 at the HOPG/1-octanoic acid
interface that were stable enough to be imaged with STM. In most cases, only vague and very dynamic
structures were observed and no reliable unit cell could be determined. Only sparingly, small patches
(<30
×
30 nm2) emerged, which were not as close-packed as those of Cu22 or MnCu2 (Figure 3).
The layers were even more unstable than those of the rigid conjugated dimer Mn21 and typically
disappeared within several minutes. Like Mn21, also Mn22 can exist as isomers in which the two
chloride ligands are oriented in different directions with respect to each other. However, unlike in
the case of Mn21, the isomers of Mn22 can interconvert since the two porphyrin moieties can freely
rotate with respect to each other about the alkyne linker. The fact that MnCu2 forms extended and
stable assemblies and Mn22 does not, and the fact that also layers of Mn21 are unstable, suggests that
the presence of two axial chloride ligands within a given manganese porphyrin dimer inhibits the
formation of stable layers at a surface. This may be the result of a higher stability of dimers with an
anti-configuration of the two ligands compared to those with a syn-configuration, which in turn may
be governed by a lower dipole moment in the former isomers.
Figure 3. STM image and magnification of a self-assembled monolayer of Mn22 at the HOPG/1-octanoic
acid interface. A schematic dimer of Mn22 is superimposed in red in the magnification. Tunneling
parameters: Vbias = −500 mV, It = 2.5 pA.
2.4. 2D Polymorphism of Porphyrin Dimer MnCu2
During the STM measurements of porphyrin dimer MnCu2, we observed an interesting case of 2D
polymorphism. In less than 10% of the attempts to image a self-assembled structure of this compound,
no structures were observed at all at the HOPG surface. It is then common practice to induce monolayer
formation by electric polarization, applying one or more mild voltage pulses to the tunnel junction, in
this case between +1 and +2 V with a duration of 900 µs. In about 5% of these attempts, within 5 min
a monolayer structure as shown in the STM images in Figure 4A–B grew over the whole scan area.
After the other attempts, no structure emerged or the STM tip became too blunt to be used for further
imaging. Although the STM images are inconclusive about the precise orientation of the dimers, it is
plausible that they are oriented with their porphyrin planes perpendicular (‘edge-on’) to the surface,
as is drawn in the schematic representation in Figure 4C, in which each rectangle corresponds to one
porphyrin moiety within a dimer. 2D polymorphic changes upon the application of a voltage pulse
have been reported previously for other types of disk-shaped molecules adsorbed at a solid–liquid
interface [46,47].
Similar as was observed in the other STM images of the porphyrin dimers, we propose that the
bright lamellae correspond to the aromatic parts of MnCu2 and the darker regions to the alkyl chains.
Similar ‘edge-on’ orientation geometries at the solid–liquid interface have previously been observed
for porphyrin oligomers containing six [17] and twelve porphyrin moieties [18
derivatives [48], and other planar molecules with extended aromatic surfaces [49
of the ‘edge-on’ assemblies of MnCu2 is most likely governed by stabilizing
,19], phthalocyanine
–53]. The formation
π
-stacking between

Molecules 2019, 24, 3018
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the aromatic porphyrin planes of the dimers. Despite the fact that individual dimers can be hardly
discerned in Figure 4A–B, in the darker parts between the lamellae signatures are visible, which we
propose to be the alkyl chains of the dimer molecules. Based on this assumption, a unit cell was
determined with vectors
c
= 6.2
±
0.3 and
d
= 0:53
±
0.2 nm, under an angle of 48◦
±
5◦. These unit cell
dimensions give no clue as to whether the alkyl chains of dimers in adjacent lamella are interdigitated
or not. The unit cell parameters correspond to an orientation of the dimers as drawn in Figure 4C, i.e.,
in which the porphyrin rings are oriented in an off-set geometry, which is typical for π−π stacking of
small molecules. From the parameters, a porphyrin stacking distance of about 4 Å can be calculated,
which is a realistic value for stacked aromatic surfaces. Remarkably, the bright parts of the lamellae all
show a brighter side and a less bright side, which can also be discerned in the cross-section drawn in
Figure 4A,D. These differences in brightness may be explained by the presence of different metal centers
in the two halves of the porphyrin dimers, and a unidirectional orientation within the lamellae. In the
schematic drawing in Figure 4E, the squares representing the porphyrin moieties are shown either
filled or empty, corresponding to porphyrin moieties with a manganese or a copper center, respectively.
A unidirectional orientation would mean that in a given stack of porphyrin dimers the same metal
centers are always aligned behind each other, resulting in an apparent height difference between the
two halves of the lamella. Such an ordering might be governed by favorable dipole–dipole interactions
between the Mn-Cl metal-ligand pairs of adjacent dimers. However, similar internal differences in
lamellar brightness have previously been observed in STM images of porphyrin hexamers [17] and
dodecamers [18,19] which contained no or identical metal centers. Another, and probably more likely
explanation for the contrast differences in the lamellae of MnCu2 may, therefore, be variations in the
orientation of the stacks of the dimers with respect to the atomic ordering of the underlying solid
surface. The ordering of the stacks may not be fully commensurate with the ordering of the underlying
graphite, leading to the observed differences in the sub-lamellar signature.
Figure 4.
the unit cell vectors
pA, ( ) Vbias = 450 mV, It = 50 pA. (
orientation of the molecules of MnCu2 on HOPG. (
drawn in panel ( ); the small black arrows point in the direction of the brighter parts of the lamellae.
) Schematic representation of one of the proposed orientations of the molecules of MnCu2; the filling
(A
) and (
B
c
): STM images of a monolayer of MnCu2 at the HOPG/1-phenyloctane interface;
and are drawn in panel ( ); tunneling parameters: ( ) Vbias 550 mV, It = 50
) Schematic representation (top view) of the proposed ‘edge-on’
) Cross-section corresponding to the black line
d
B
A
=
−
B
C
D
A
(E
of the squares represent the different metal porphyrin moieties and the small black arrows a possible
directionality within the stacks.

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The assemblies of ‘edge-on’-orientated dimers of MnCu2 were exclusively observed after the
application of a voltage pulse to the tunnel junction, which strongly indicates that the pulse plays
a decisive role in their formation. A first explanation for this may be that the pulse removes the
axial chloride ligands from the manganese porphyrin moieties, as has been proposed before for the
dissociation of the same ligand from a single manganese porphyrin upon application of a voltage pulse
to the interface of HOPG and a 1-octanoic acid solution of that compound [27]. Alternatively, or perhaps
also concomitantly, the strong electric field involved with the pulse might align the dimers already
in solution and induce the deposition a small seed of ‘edge-on’ oriented dimers at the solid–liquid
interface. Subsequently, other porphyrin dimers can attach to this seed resulting in the growth of
extended ‘edge-on’ patterns over the whole scanning area. The ‘edge-on’ patterns remained stable over
time and no porphyrin dimers that were adsorbed coplanar (‘face-on’) to the surface were observed.
Remarkably, the scanning by the STM tip seemed to play a role in the growth of the edge-on
domains of MnCu2. In the STM image in Figure 5A an area with edge-on oriented assemblies of
MnCu2 is shown, directly after scanning it after the application of a voltage pulse. The next STM image
(Figure 5B) is a zoom-out in which the scanning area was enlarged from 150
×
150 to 300 × 300 nm2
.
The square drawn in this image corresponds with the scanning area of Figure 5A. It can be clearly
seen that the edge-on assemblies are predominantly present in the confined area of the previous scan.
The STM image in Figure 5C shows the same area as in Figure 5B, but now after 20 min of continuous
scanning. A large part of the scanning area is now covered with the ‘edge-on’ assemblies, which
indeed indicates that the STM tip plays an active role in their growth and that the domains are formed
from a seed of ‘edge-on’ oriented molecules, as described above. The precise mechanism by which
the tip assists in the domain growth is as yet unknown. With the applied tunneling parameters (Vbias
= 450 mV, It = 5 pA) the tip is relatively far removed from the surface, minimizing direct physical
−
contact with the monolayer. The porphyrins are not very polar, but to some extent polarizable along
their planar axes. The electric field in the tip-sample junction is rather high (in the regime of 109 V/m).
Polar and polarizable species may form bridges in electric fields, which can act as nuclei for further
growth with a molecular orientation of the most polarizable direction along the field direction, i.e., in
this case, perpendicular to the surface. This effect is best known for water molecules [54], which are
polar, however, a static polarization during the pulse duration may suffice to initiate growth nuclei
of polarizable species of such an ‘upright’ configuration. Furthermore, the movement of the tip may
perturb the supernatant solution containing molecules or assemblies of MnCu2 and thereby provide
them with energy to self-assemble into ordered arrays at the solid–liquid interface.
Figure 5.
HOPG/1-phenyloctane interface. (
pulse. ( ) Zoom-out, the black square corresponds with the scan area of the STM image in (
STM images showing the growth of an ‘edge-on’ domain of MnCu2 at the
) The pattern formed directly after the application of a voltage
). (
450 mV,
A
B
A
C)
STM image of the same area as in (
B
) after 20 min of scanning. Tunneling parameters: Vbias
=
−
It = 5 pA.

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3. Materials and Methods
3.1. General Materials and Methods
All commercially obtained chemicals were used without further purification unless stated
otherwise. CHCl3 (Merck, Burlington, MA, USA) was distilled under nitrogen from calcium
chloride. Toluene (Merck, Burlington, MA, USA) was distilled under nitrogen from sodium. Pyrrole
(Sigma-Aldrich Co. St. Louis, MO, USA) was freshly distilled before use. For TLC analysis, TLC Silicagel
60 F254 (Merck, Burlington, MA, USA) and for column chromatography Silica gel 0.035–0.070 mm, 60A
1
(Acros, Branchburg, N.J., USA) or Alumina 0.050–0.200 mm 60A activity I (Acros) were used. H and
13C-NMR spectra were recorded on Varian Inova 400 MHz or Bruker Avance 500 MHz spectrometers
at 25 ◦C. Chemical shifts are reported in parts per million (ppm) relative to tetramethylsilane (TMS,
0.00 ppm) as the internal reference. Multiplicities used are: s = singlet, bs = broad singlet, d =
doublet, dd = doublet of doublets, bd = broad doublet, t = triplet, q = quartet, m = multiplet and/or
multiple overlapping resonances). Phase and baseline correction was applied to all NMR spectra
(Bruker, Billerica, MA, USA). MALDI-TOF mass spectra were measured in reflective mode with
dithranol as a matrix on a Bruker Microflex LRF MALDI-TOF mass spectrometer (Bruker, Billerica, MA,
USA). All chemical reactions were carried out under an argon atmosphere. Computational studies
were performed by using the molecular modeling program Spartan14 and the energy minimization
calculations were performed using the semi-empirical PM3 method.
3.2. Syntheses
4-Octadecyloxy-benzaldehyde
(3
)
.
A mixture of 1-bromooctadecane (24.5 g, 73.4 mmol,
4-hydroxybenzaldehyde (8.15 g, 66.7 mmol, and K2CO3 (27.7 g, 200 mmol) in DMF (100 mL) was stirred
under argon at 60 ◦C for 4 h. After cooling, the solvent was evaporated and the residue dissolved in
CHCl3 (150 mL). This solution was washed with aqueous 0.1 N HCl (2 ) and water and evaporated to
×
dryness. The crude product was recrystallized from methanol to yield 4-octadecyloxy-benzaldehyde
1
as a white solid (19.5 g, 78%). H-NMR (400 MHz, CDCl3)
δ
9.88 (s, 1H), 7.83 (d, 2H, J = 8.8 Hz), 6.99
(d, 2H, J = 8.8 Hz), 4.40 (t, 2H, J = 6.8 Hz), 1.85–1.77 (m, 2H), 1.49–1.41 (m, 2H), 1.41–1.19 (m, 30H),
0.88 (t, 3H, J = 7.0 Hz) ppm. 13C-NMR (100 MHz, CDCl3)
δ 190.78, 164.25, 131.97, 129.73, 114.73, 68.43,
31.92, 29.68, 29.35, 29.05, 25.95, 22.69, 14.11 ppm.
5,10,15,20-Tetrakis-(4-octadecyloxy-phenyl)-porphyrin (4). Compound 3 (5.107 g, 13.63 mmol) and
pyrrole (915 mg, 13.63 mmol) were dissolved in propionic acid (100 mL). The mixtures were stirred
at reflux for 4.5 h) After cooling, the solvent was evaporated and the crude product was purified by
column chromatography (alumina, eluent: CHCl3). The resulting product was recrystallized 3 times
1
from methanol to yield
4
as a purple solid (2.17 g, 38%). H-NMR (500 MHz, CDCl3)
δ
8.86 (s, 8H),
8.10 (d, 8H, J = 9.0 Hz), 7.27 (d, 8H, J = 9.0 Hz), 4.25 (t, 8H, J = 6.5 Hz), 2.03–1.93 (m, 8H), 1.67–1.57 (m,
8H), 1.55–1.19 (m, 112H), 0.87 (t, 12H, J = 7.0 Hz),
2.75 (bs, 2H) ppm. 13C-NMR (125 MHz, CDCl3)
−
δ
158.95, 135.58, 134.45, 119.79, 112.69, 68.36, 31.93, 29.72, 29.69, 29.66, 29.55, 29.36, 26.26, 22.69, 14.12
ppm. MALDI-TOF calculated for C116H174N4O4: m/z 1688.7; measured: 1688.1 (M)+. UV-vis (CHCl3)
λ/nm 423, 519, 557, 593, 650.
5,10,15,20-Tetrakis-(4-octadecoxy-phenyl)-2,3,21,23-tetrahydro-porphine-2,3-diol
(5). To a stirred
solution of (2.39 g, 1.41 mmol) in a mixture of CHCl3 (180 mL) and pyridine (20 mL), osmium
4
tetroxide solution (1.11 mL, 3.54 mmol) was added, and the mixture was stirred in the dark for 5
days at room temperature. The reaction was quenched by adding a solution of sodium bisulfite (1.62
g, 15.6 mmol) in water (800 mL) and the resulting mixture was stirred for an additional 1.5 h. The
organic layer was separated and washed with 1N aqueous HCl, with water, with a saturated aqueous
NaHCO3 solution, dried over MgSO4, and evaporated to dryness. The product was purified by column
chromatography (Silica, eluent: gradient, CHCl3 to 3% MeOH in CHCl3 (v/v). Compound
5 was
1
obtained as a red/purple solid (1.0 g, 0.58 mmol, 41%). H-NMR (400 MHz, CDCl3)
δ 8.62 (bd, 4H, J =

Molecules 2019, 24, 3018
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4.8 Hz), 8.58 (d, 2H, J = 4.8 Hz), 8.46 (s, 2H), 8.29 (d, 2H, J = 4.8 Hz), 7.99 (bd, 4H, J = 6.4 Hz), 7.94
(bd, 1H, J = 7.7 Hz), 7.86 (bd, 1H, J = 6.8 Hz), 7.82–7.75 (m, 2H), 7.41–7.33 (m, 4H), 7.20 (d, 4H, J = 8.9
Hz), 7.14–7.07 (m, 1H), 6.99 (s, 2H), 6.91–6.85 (m, 1H), 4.21 (t, 4H, J = 6.5 Hz), 4.13 (t, 4H, J = 6.7 Hz),
2.00–1.87 (m, 8H), 1.65–1.20 (m, 120H), 0.88 (t, 12H, J = 6.7 Hz),
calculated for C116H176N4O6: m/z 1722.7; measured: 1723.2 (M + H)+, 1704.2 (M – OH + H)+, 1689.2
(M /nm (log(
2OH + H)+. UV-vis (CHCl3) /M−1cm−1) 424 (5.02), 525 (3.93), 555 (3.98), 596 (3.73),
648 (3.98).
−
1.73 (bs, 2H) ppm. MALDI-TOF
−
λ
ε
5,10,15,20-Tetrakis-(4-octadecoxy-phenyl)-porphyrin-2,3-dione
(
6
).
Compound
5
(1.0 g, 0.58 mmol) was dissolved in distilled toluene and dry pyridine.
4,5-Dichloro-3,6-dioxocyclohexa-1,4-diene-1,2-dicarbonitrile (DDQ) (0.546 g, 2.41 mmol) was
added and the mixture was stirred at reflux for 24 h. After cooling, the mixture was evaporated to
dryness and taken up in dichloromethane, which was filtered through celite. The resulting filtrate
was evaporated to dryness and the product was purified by column chromatography (Silica, eluent:
1
CH2Cl2: n-heptane 1:1, v/v), yielding
CDCl3)
(m, 4H), 7.80–7.74 (m, 4H), 7.27–7.22 (m, 4H), 7.22–7.16 (m, 4H), 4.25–4.16 (m, 8H), 2.01–1.89 (m, 8H),
1.66–1.55 (m, 8H), 1.52–1.18 (m, 112H), 0.87 (s, 12H, J = 6.8 Hz),
1.96 (bs, 2H) ppm. 13C NMR (125
MHz, CDCl3) 188.18, 159.35, 159.18, 155.74, 140.83, 140.20, 138.34, 135.34, 134.25, 133.79, 133.36,
6
as a brown/yellow solid (0.38 g, 38%). H NMR (400 MHz,
δ
8.76 (dd, 2H, J = 5.0 Hz, J = 1.0 Hz), 8.62 (dd, 2H, J = 5.0 Hz, J = 1.0 Hz), 8.58 (s, 2H), 8.03–7.98
−
δ
131.42, 128.42, 128.07, 124.01, 113.53, 113.23, 113.02, 68.39, 68.20, 31.93, 29.73, 29.68, 29.55, 29.48, 29.37,
26.25, 22.70, 14.12 ppm. MALDI-TOF calculated for C116H172N4O6: m/z 1718.6; measured: 1719.4 (M +
H)+. UV-vis (CHCl3) λ/nm (log(ε/M−1cm−1) 410 (5.26), 479 (4.28).
Porphyrin dimer H41
.
Compound 6 (105 mg, 0.061 mmol) and benzene-1,2,4,5-tetraamine
tetrahydrochloride (8.25 mg, 0.029 mmol) were dissolved in pyridine (35 mL) and the solution
was refluxed with solvent running back through a soxhlet condenser containing mol sieves (4 Å).
After 60 h, the mixture was allowed to cool and subsequently evaporated to dryness. The product
was purified by column chromatography (Silica, eluent: CH2Cl2:n-heptane 1:1, v/v), followed by
purification by size-exclusion chromatography (BioBeads, eluent: toluene). The first fraction contained
the desired product, which was redissolved in a minimal amount of CHCl3. This solution was added
to an excess of stirred methanol, which caused the product to precipitate. After filtration, H41 was
1
obtained as a red/brown solid (13.4 mg, 13%). H NMR (500 MHz, CDCl3)
δ
9.00 (d, 2H, J = 4.9 Hz),
8.94 (d, 2H, J = 4.9 Hz), 8.77 (s, 2H), 8.74 (s, 4H), 8.20–8.12 (m, 16H), 7.41 (d, 8H, J = 8.5 Hz), 7.31 (d, 8H,
J = 8.6 Hz), 4.50 (t, 8H, J = 6.2 Hz), 4.27 (t, 8H, J = 6.4 Hz), 2.32–2.23 (m, 8H), 2.05–1.96 (m, 8H), 1.88–1.78
(m, 8H), 1.69–1.57 (m, 16H), 1.54–1.46 (m, 8H), 1.46–1.14 (m, 200H), 0.88 (t, 12H, J = 6.8 Hz), 0.84 (t,
12H, J = 6.9 Hz), δ 159.52, 159.15, 155.30, 153.35,
2.31 (bs, 4H) ppm. 13C NMR (125 MHz, CDCl3)
−
145.85, 140.21, 139.50, 135.63, 135.21, 134.05, 133.94, 127.96, 121.74, 116.35, 113.06, 112.88, 68.54, 68.38,
31.93, 29.94, 29.73, 29.68, 29.55, 29.37, 29.33, 26.56, 26.27, 22.70, 14.13 ppm. MALDI-TOF calculated for
C238H346N12O8: m/z 3503.4; measured: 3504.1 (M + H)+. UV-vis (CHCl3) /M−1cm−1) 431
λ/nm (log(ε
(5.61), 462 (5.56), 631 (4.42).
Copper porphyrin dimer Cu21. Porphyrin dimer H41 (2.3 mg, 0.66 µmol) was dissolved in a mixture
of CHCl3 (20 mL) and MeOH (5 mL). Copper acetate monohydrate (1.33 mg, 6.66 mmol) was added
and the mixture was heated at reflux for 15 h. After cooling, the solvent was evaporated and the
product was purified by column chromatography (Silica, eluent: CHCl3/n-heptane 1:2, v/v, Rf = 0.025)
to yield Cu21 as an orange/red solid (2.3 mg, 97%). MALDI-TOF calculated for C238H342N12O8Cu2:
λ/nm (log(ε
m/z 3626.4; measured: 3627.4 (M + H)+. UV-vis (CHCl3) /M−1cm−1) 428 (5.50), 457 (5.39),
517 (4.88), 543 (4.84), 675 (4.38).
Manganese porphyrin dimer Mn21. Porphyrin dimer H41 (3.0 mg, 0.9
mixture of CHCl3 (3 mL) and MeOH (3 mL). Manganese diacetate tetrahydrate (2.1 mg, 8.6
added and the mixture was heated at reflux for 16 h. After cooling, brine (10 mL) was added and the
µmol) was dissolved in a
µmol) was

Molecules 2019, 24, 3018
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mixture was vigorously stirred for 8 h. The layers were separated and the organic layer was washed
with water, dried over MgSO4 and evaporated to dryness. The product was purified by column
chromatography (Silica, eluent: 5% MeOH in CHCl3, v/v, Rf = 0.55) to yield Mn21 as a green/brown
solid (3.1 mg, 98%). MALDI-TOF calculated for C238H342Cl2N12O8Mn2: m/z 3678.5; measured: 3610.2
(M − 2Cl + H)+. UV-vis (CHCl3) λ/nm (log(ε/M−1cm−1) 432 (5.50), 500 (5.32), 655 (4.69).
Manganese porphyrin dimer Mn22. Porphyrin dimer H42 (3.0 mg, 0.9
µmol) was dissolved in a
mixture of CHCl3 (3 mL) and MeOH (3 mL). Manganese diacetate tetrahydrate (2.1 mg, 8.6
µmol) was
added and the mixture was heated at reflux for 16 h. After cooling, brine (10 mL) was added and the
mixture was vigorously stirred for 8 h. The layers were separated and the organic layer was washed
with water, dried over MgSO4 and evaporated to dryness. The product was purified by column
chromatography (Silica, eluent: 5% MeOH in CHCl3, v/v, Rf = 0.7) to yield Mn21 as a dark green solid
(3.1 mg, 98%). MALDI-TOF calculated for C198H270Cl2N8O6Mn2: m/z 3037.9; measured: 2967.7 (M
−
2Cl)+, 3002.5 (M Cl)+. UV-vis (CHCl3) /M−1cm−1) 339 (4.85), 382 (5.02), 406 (5.00), 482
−
λ/nm (log(
ε
(5.34), 584 (4.28), 625 (4.46).
3.3. STM Experiments
Approximately 10
applied to a freshly cleaved HOPG substrate (10
µ
L droplet of a solution of a porphyrin dimer (concentration ~10−4 M) was
10 mm2, NT-MDT, ZYB) which was mounted into a
×
home-built liquid-STM setup [25]. The STM-tip (mechanically cut from Pt0.8Ir0.2 wire, diameter 0.5 mm)
was immersed in the droplet and the surface was scanned at a rate of 300 nm/s. To minimize thermal
drift effects, the STM setup was mounted and left to equilibrate for several hours before the solution
containing the compound was added. The STM measurements were performed in constant-current
mode using an Omicron Scala SPM controller. The images shown were only corrected for background
and no additional filters were applied to the raw data. All STM measurements were performed in the
thermostatted environment (21.5 ± 0.5 ◦C) of the NanoLab Nijmegen.
4. Conclusions
A porphyrin dimer with a rigid aromatic linker was readily synthesized in five steps, and its
bis-copper and bis-manganese complexes were obtained nearly quantitatively from the free base
precursor. The bis-copper dimer self-assembled into stable monolayers at a solid–liquid interface. The
bis-manganese dimer formed monolayers with a similar structure, but these were much less stable
than the layers of the bis-copper dimers. Similar unstable layers were observed for bis-manganese
porphyrin dimers in which the porphyrins are linked by a less-rigid alkyne spacer. The instability of
both layers is attributed to the presence of inner shell axial chloride ligands at the manganese centers,
which are believed to hinder a cofacial orientation of the porphyrin planes with respect to the surface.
The application of a mild voltage pulse induced the emergence of an adlayer of a copper-manganese
porphyrin dimer with an alkyne spacer, in which the dimer molecules were exclusively oriented with
their porphyrin planes perpendicular to the surface. The formation of this surface polymorph was
attributed to (i) dissociation of the axial chloride ligand from the manganese center allowing cofacial
intermolecular stacking, and/or (ii) electric field-induced preorganization of small stacks in solution
which, after adsorption to the surface, serve as seeds for further growth of the edge-on polymorph.
Future research will be directed to investigating the (cooperative) reactivity of the bis-manganese
dimers towards molecular oxygen. In addition, these dimers will be equipped with non-coordinating
anions (e.g., PF6− or BPh4−) via ion-exchange reactions, to improve their adsorption at a solid–liquid
interface into more stable adlayers.
Supplementary Materials: The following are available online: 1H and 13C-NMR, mass, and UV-vis spectra of all
new compounds.
Author Contributions: J.A.A.W.E. conceived the ideas and designed the experiments. T.H. and D.L. designed
and performed STM experiments and carried out data analyses. D.L. synthesized the compounds. T.H. and

Molecules 2019, 24, 3018
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J.A.A.W.E. co-wrote the paper. All authors (J.A.A.W.E., T.H., D.L., and S.S.) analyzed and discussed the results
and commented on the manuscript.
Funding: This research was funded by the Council for the Chemical Sciences of The Netherlands Organisation for
Scientific Research (ECHO grant 700.57.023 and VIDI grant 700.58.423) and the European Research Council (ERC
Starting Grant NANOCAT–259064). S.S. acknowledges collaborative network centers 652 and 1270 of the German
Physical Society.
Conflicts of Interest: The authors declare no conflict of interest.
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Sample Availability: Samples of the compounds are not available from the authors.
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