Surface assembly of porphyrin nanorods with one-dimensional zinc-oxygen spinal cords

Article abstract of DOI:10.1039/c1ce05494e

We have built long-range ordered, one-dimensional (1D) nanorods by self-assembly of zinc porphyrin derivatives through axial coordination with oxygenated ligands on different noble-metal surfaces. The structures were studied by a combination of Variable-Temperature Scanning-Tunnelling Microscopy (VT-STM), X-Ray Photoelectron Spectroscopy (XPS) and Density Functional Theory (DFT) calculations. The combined morphological, chemical and theoretical results demonstrate that the zinc atoms at neighbouring porphyrin molecules are coordinatively linked through oxygen-containing species, most probably water, leading to an adsorption geometry in which the porphyrin planes are perpendicular to the substrate plane, and the polymers are lying parallel to the surface.

Full text of DOI:10.1039/c1ce05494e

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Other articles published in this issue include:
Nanopatterning the graphite surface with ordered macrocyclic or ribbon-like
assemblies of isocytosine derivatives: an STM study
Artur Ciesielski, Silvia Colella, Leszek Zalewski, Bernd Bruchmann and Paolo Samorì
CrystEngComm, 2011, DOI: 10.1039/C1CE05521F
Engineering homologous molecular organization in 2D and 3D. Cocrystallization of
aminoazines and alkanecarboxylic acids
Adam Duong, Thierry Maris and James D. Wuest
CrystEngComm, 2011, DOI: 10.1039/C1CE05445G
Chiral non-periodic surface-confined molecular nanopatterns revealed by scanning
tunnelling microscopy
Wojciech J. Saletra, Hong Xu, Tom Vosch, Steven De Feyter and David B. Amabilino
CrystEngComm, 2011, DOI: 10.1039/C1CE05403A
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PAPER
Surface assembly of porphyrin nanorods with one-dimensional zinc–oxygen
spinal cords†
Marta Trelka,a Christian Urban,a Celia Rogero,bc Paula de Mendoza,d Eva Mateo-Marti,b Yang Wang,e
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Inaki Silanes, David Ecija, Manuel Alcamı, Felix Yndurain, Andres Arnau, Fernando Martın,
ei
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Antonio M. Echavarren, Jose Angel Martın-Gago, Jose Marıa Gallego, Roberto Otero
and Rodolfo Mirandaai
Received 26th April 2011, Accepted 22nd June 2011
DOI: 10.1039/c1ce05494e
We have built long-range ordered, one-dimensional (1D) nanorods by self-assembly of zinc porphyrin
derivatives through axial coordination with oxygenated ligands on different noble-metal surfaces. The
structures were studied by a combination of Variable-Temperature Scanning-Tunnelling Microscopy
(VT-STM), X-Ray Photoelectron Spectroscopy (XPS) and Density Functional Theory (DFT)
calculations. The combined morphological, chemical and theoretical results demonstrate that the zinc
atoms at neighbouring porphyrin molecules are coordinatively linked through oxygen-containing
species, most probably water, leading to an adsorption geometry in which the porphyrin planes are
perpendicular to the substrate plane, and the polymers are lying parallel to the surface.
through the metal atoms along their spinal cords. This is a rather
high value for organic-based materials even though most of the
experimental measurements were carried out in powder form,
where inter-grain barriers might significantly lower the conduc-
tivity of the material with respect to their intrinsic value.1,3,4
1D and 2D coordination polymers and networks have also
been obtained on solid surfaces by codeposition of organic linkers
and metal atoms,10,11 where the organic linkers are planar mole-
cules that adsorb parallel to the surface binding to neighbouring
metal centres. Thus, in this case, all the coordination bonds in the
network are coplanar and parallel to the surface, a geometry not
compatible with the coordination geometry of the polymers
described above.1,3–5,7,9 For such compounds, all the bonds of the
metal centre with the macrocycle are coplanar, but the axial
coordination bond is oriented perpendicular to the macrocycle
plane. Assembling shish-kebab coordination polymers made of
phthalocyanines or porphyrins on solid surfaces implies, thus,
one of the two following approaches: (a) if the macrocycle ring is
adsorbed parallel to the surface, axial coordination must occur
out of the plane, so that the polymers will grow perpendicular to
the surface, or (b) if the macrocycle ring is perpendicular to the
surface, axial coordination can occur parallel to the surface, and
the polymers will grow parallel to the substrate.
Introduction
One-dimensional (1D) coordination polymers have attracted
much attention due to its potential impact on the development of
organic-based conductors.1,2 In particular, metalated macro-
cycles such as porphyrins and phthalocyanines have been shown
to polymerize into well-ordered, conductive 1D structures via
axial coordination of polytopic ligands to the metal centres in
neighbouring
macrocycles
(the
so-called
shish-kebab
approach).1,3–9 Such materials have shown conductivities up to
10ꢀ1 S cmꢀ1, which are attributed to conduction channels
aDep. De Fꢀısica de la Materia Condensada, Universidad Autoꢀnoma de
Madrid, 28049 Madrid, Spain. E-mail: roberto.otero@uam.es
bCentro de Astrobiologꢀıa, CSIC-INTA, 28850 Madrid, Spain
cCentro de Fisica de Materiales CSIC-UPV/EHU, Materials Physics
Center MPC, San Sebastian, Spain
dInstitute of Chemical Research of Catalonia (ICIQ), Av. Pa€ısos Catalans
16, 43007 Tarragona, Spain
eDep. de Quꢀımica, Facultad de Ciencias, Universidad Autoꢀnoma de Madrid,
28049 Madrid, Spain
fDonostia International Physics Center (DIPC), 20018 San Sebastian,
Spain
gInstituto de Hidraꢀulica Industrial de Cantabria (IH), 39005 Santander,
Spain
In this paper we show Variable-Temperature Scanning
Tunnelling Microscopy (VT-STM) experiments demonstrating
that zinc meso-tetramesitylporphyrin (ZnTMP, see Fig. 1)
molecules self-assemble on Cu(100) and Au(111) by forming long
nanorods that are only one-molecule wide, in which the
porphyrin core is not lying flat on the surface, but it is perpen-
dicular to it. X-Ray Photoelectron Spectroscopy (XPS) reveals
hDepto. Fisica de Materiales UPV/EHU, Facultad de Quimica, San
Sebastian, Spain
iInstituto Madrilen~o de Estudios Avanzados en Nanociencia (IMDEA-
NANO), Campus de Cantoblanco, 28049 Madrid, Spain
jInstituto de Ciencia de Materiales de Madrid—CSIC, Cantoblanco, 28049
Madrid, Spain
† Electronic supplementary information (ESI) available. See DOI:
10.1039/c1ce05494e.
This journal is ª The Royal Society of Chemistry 2011
CrystEngComm, 2011, 13, 5591–5595 | 5591

obtained with an Aarhus-SPECS STM both at low and room
temperature. XPS experiments were carried out at room
temperature in a separate chamber (base pressure 5 ꢁ 10ꢀ10
Torr). This system is equipped with a hemispherical electron
energy analyser and spectra were measured using Al Ka X-rays
as excitation source. The overall energy resolution was estimated
to be around 0.9 eV. RT STM images recorded at the XPS
chamber were used to check the reproducibility of the results in
both independent experimental chambers.
DFT calculations of the ZnTMP–molecule–ZnTMP complex
in gas phase have been performed with the Gaussian 03
package.13 The Perdew–Burke–Ernzerhof (PBE)14 formula has
been applied for correlation and exchange functional. The
lanl2dz basis set15–17 with an effective core potential (ECP) for
inner shell electrons has been employed for Zn atoms. The 6-31G
(d) basis set has been used for N atoms and the central molecule
to get a good description of the interaction between the ZnTMP
and the small central molecule. The 3-21G basis set has been
employed for the rest of the atoms.
Calculations on the periodic system were carried out within the
Density Functional Theory (DFT) framework using the SIESTA
code.18 The Perdew–Burke–Ernzerhof (PBE) functional was
used, with a double-z plus polarization basis set, a 50 meV energy
shift, and a 300 Ry cutoff for the spatial grid. Total energy
minimization was performed, relaxing all internal degrees of
freedom of the unit cell geometry subject to the only constrain
that the metalomacrocycle be planar.
Fig. 1 Space-fill model of the ZnTMP molecule with a water molecule
coordinated to the Zn atom.
the presence of oxygenated species that turn out to be necessary
for nanorod formation, i.e. for all these situations in which the
oxygen signal is not present, a planar adsorption geometry is
found for the TMP molecules. The origin of such oxygenated
species might be water or other small molecules present during
the synthetic process or during the transportation to the UHV
chamber where deposition is made. Actually, Density Functional
Theory (DFT) calculations confirm the stability and geometry of
ZnTMP linked axially by means of a variety of oxygen con-
taining ligands, most prominently water or carbon monoxide,
both for cluster models and extended periodic systems. The
picture that emerges from the combination of these studies is that
axial coordination is the driving force for nanorod assembly,
providing a strong enough bond so as to keep porphyrin cores
perpendicular to the surface in spite of the considerable decrease
in adsorption energy.
Results and discussion
Fig. 2a and b show STM images recorded at 150 K of the
molecular structures formed upon deposition of ZnTMP
Experimental and theoretical methods
ZnTMP molecules were synthesized from free-base tetramesi-
tylporphyrin (TMP) following standard metalation methodology
with Zn(OAc)2.12 The resulting metaloporphyin was character-
1
ized by H NMR, mass spectrometry, IR and UV/vis spectros-
copy (see ESI†).
Au(111) and Cu(100) surfaces were prepared under Ultra-
High Vacuum (UHV) conditions by standard cleaning cycles of
sputtering (Ar+, 1 kV) and annealing (800 K). This preparation
resulted in atomically flat terraces about 150 nm wide separated
by monoatomic steps. ZnTMP molecules were deposited by
sublimation from a glass crucible at 450 K onto the metals
surfaces kept at room temperature. The STM images were
Fig. 2 (a) 104 ꢁ 96.5 nm2 STM image (It ¼ 0.5 nA, Vbias ¼ ꢀ1.9 V) of
the nanorods formed on the Au(111) surface upon ZnTMP deposition.
(b) 104.5 ꢁ 126 nm2 STM image of the nanorods on Cu(100).
5592 | CrystEngComm, 2011, 13, 5591–5595
This journal is ª The Royal Society of Chemistry 2011

molecules on Au(111) and Cu(100) respectively. The formation
of long (hundreds of nm) 1D rod-looking structures is clearly
observed on both surfaces, independent of the substrate’s
chemical nature and structural symmetry, a clear indication that
intermolecular interactions must be the main driving force for
nanorod self-assembly. High-resolution images of the porphyrin
nanorods reveal an ordered array of protrusions with a typical
diameter of about 0.6 nm (significantly smaller than the size of
a single molecule) distributed helicoidally over the extension of
the tube with a periodicity of four units per turn, and a typical
height of about 0.9 nm. A planar adsorption geometry, in which
the porphyrin ring is placed parallel to the surface, seems to be
inconsistent with these observations. On the contrary, as it will
become clear later, such observation can be explained by
assuming that each protrusion corresponds to a single mesityl
group, each porphyrin showing two mesityl groups (see Fig. 4).
STM images recorded at higher temperatures do not reveal any
structure that can be attributed to molecular adsorption, so the
nanorod structures are not stable at higher temperatures. High-
resolution STM images reveal a periodic corrugation along the
tube direction which is identical for both metal surfaces, showing
that the substrate’s influence on nanorod formation is negligible.
A non-planar adsorption geometry for macrocyclic molecules
on metal surfaces is not expected at all on the basis of previous
studies.19–24 Standing-up geometries have been reported for the
adsorption of porphyrins functionalized with polar groups on
insulating surfaces, due to the reduced dispersive interactions (p–
p, vdW) between surface and macrocycle, and the strong elec-
trostatic interactions between the polar groups and ions at the
surface.25 In our case, however, neither the substrate is insu-
lating, so the interactions between the porphyrin core and the
substrate are not expected to be weak, nor the peripheral func-
tional groups are polar to mediate new molecule substrate
interaction. Such argument directly points towards strong
Fig. 3 Correlation between XPS spectra on self-assembled tetramesitylporphyrin (TMP) derivatives on Cu(100) and characteristic STM images. Upon
deposition of ZnTMP a clear oxygen peak can be found in the XPS spectra (black curve), a situation in which STM images reveal nanorod formation
(left inset). Deposition of base-free H2TMP, however, does not show either oxygen in the XPS spectra (blue curve) or nanorod formation (top inset).
Similarly, water detachment achieved by annealing to 525 K (see red curve in the XPS spectra) also lead to nanorod dissociation (bottom inset).
This journal is ª The Royal Society of Chemistry 2011
CrystEngComm, 2011, 13, 5591–5595 | 5593

intermolecular interactions stabilizing the non-planar adsorption
geometry. Since the electronic polarizability of a metal surface is
necessarily larger than the polarizability of the p-clouds in the
macrocycles, dispersive interactions alone cannot account for the
preference of the molecular units to bind to each other instead of
binding to the substrate. On the other hand, it is well known that
columnar structures in metallic macrocycles are very often
stabilized by coordination between neighbouring metal centres
through an organic ligand.1,3–6,8,9 It seems thus natural to attri-
bute this strong intermolecular interaction to axial coordination
to yield shish-kebab polymers such as those described in previous
works.1,3,4
an annealing procedure.24,29,30 The molecules can be imaged by
STM even at room temperature, but they cannot be pushed away
from their adsorption positions. The enhanced stability in the
adsorbed porphyrins after a thermal treatment could possibly be
explained by the formation of a covalent bond by dehydroge-
nation of the methyl groups at the mesityl legs, as previously
suggested.24
The possible effect of oxygen-containing axial ligands in
bridging two neighbouring ZnTMP molecules has also been
investigated by Density Functional Theory calculations for water
and other small molecules present in the atmosphere. A stable
structure corresponding to a minimum in the ZnTMP–water–
ZnTMP potential energy surface was found in which a water
molecule is sandwiched between two ZnTMP molecules rotated
45ꢂ around their C4 axis, in such a way that the lone pairs in the
oxygen atom of the water molecule can interact with both Zn
centres (see sketch in Fig. 4a, and ESI†). The calculated binding
energy is about 0.6 eV, indicating that the formation of the
ZnTMP–water–ZnTMP complex is significantly exothermic.
This interaction leads to a deformation of the porphyrin ring to
allow the Zn atoms to approach the encaged water molecule.
This deformation might raise the question on whether it is
possible or not to continue the structure beyond the dimer.
However, periodic arrangements of stacked Zn porphyrin rings
(without the mesityl groups) can also bind to each other through
a water molecule in a similar fashion (see ESI†). The calculations
yield binding energies in the range of 0.4–0.6 eV per dimer.
In order to check the presence of axial ligands in the observed
nanorods, we have carried out X-ray Photoemission Spectros-
copy (XPS) experiments on samples grown under the same
conditions and the same dosing system as those investigated by
STM. Apart from the expected C 1s, N 1s and Zn 2p core level
peaks, at about 284.8 eV, 398.3 eV and 1021 eV binding energies,
respectively, we clearly detect an oxygen signal (O 1s centred at
531.4 eV binding energy, see black curves in Fig. 3) which is not
present before deposition, i.e. it cannot be attributed to surface
contamination. Oxygen is not present in the chemical structure of
ZnTMP, but X-Ray Diffraction studies carried out with crystals
of ZnTMP showed a water molecule axially coordinated to the
Zn atom.26
If the nanorods were hold together by intermolecular inter-
actions such as p-stacking, they should also be observed for free-
base tetramesitylporphyrin (H2-TMP) molecules, something that
can be ruled out if the interaction is mediated by coordination
with axial linkers. Our experiments indeed show that H2-TMP
molecules do not form tubes (see top STM image in Fig. 3). On
the contrary, they adsorb on Cu(100) with the porphyrin ring
parallel to the surface, and the mesityl groups acting as ‘‘spacer
legs’’ lifting the molecular board from the substrate.20 For high
enough coverage, close-packed 2D islands appear on the surface.
The height of both individual molecules and self-assembled 2D
islands is about 0.32 nm, i.e. about three times smaller than the
height of the nanorods. Their XPS spectra show no measurable
traces of oxygen, while two components in the N1s core level are
observed, corresponding to the two chemically different nitrogen
species, –NH (400.3 eV) and ]N– (398.2 eV), on the non-met-
allated porphyrin ring (see blue spectra in Fig. 3). Similar results
have been found for other porphyrins on a variety of metal
surfaces.20,21,27,28
Moreover, ligand detachment from the adsorbed nanorods
can be achieved by annealing the surface up to 575 K (higher
than the ZnTMP sublimation temperature), as supported by the
absence of the oxygen peak in XPS spectra (see red curves in
Fig. 3). At the same time the N1s and Zn2p core levels slightly
shift to the reported values for other Zn porphyrins (398.5 eV
and 1021.7 eV, respectively).21 STM images reveal that, upon
annealing to 575 K the nanorods no longer exist on the surface.
Instead, the molecules are imaged as rings with four little
protrusions at 90ꢂ from each other. Superimposing a stick-and-
ball model for the ZnTMP molecules on the experimental STM
images, we can ascribe the central ring to the porphyrin ring and
the four protrusions to the peripheral mesityl groups. The STM
images in the bottom inset of Fig. 3 are very similar to the results
for other metalated and free-base porphyrins on a surface after
Fig. 4 Schematic diagram showing the proposed structure for the
nanorods. Each ZnTMP molecule is rotated by 45ꢂ with respect to their
common C4 axis, in such a way that the mesityl groups (orange spheres)
fit between the neighbouring mesityl groups of the adjacent ZnTMP
molecule. The Zn atoms are bound to each other through a bridging
water molecule (blue ellipsoid). (b) Comparison with STM images reveals
that the brightest central protrusions in the nanorods can be ascribed to
the uppermost methyl groups whereas the lighter bumps correspond to
the methyl groups pointing sideways.
5594 | CrystEngComm, 2011, 13, 5591–5595
This journal is ª The Royal Society of Chemistry 2011

3 J. P. Collman, J. T. McDevitt, G. T. Yee, C. R. Leidner,
L. G. McCullough, W. A. Little and J. B. Torrance, Proc. Natl.
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Similar results were obtained for CO, but not for O2, which is not
able to bridge neighbouring porphyrin molecules in a stable way,
while CO2 forces a non-linear geometry that is not compatible
with our observations. Finally, although CO shows a similar
behaviour as that shown by water, its scarcity in the atmosphere
renders it an unlikely candidate to explain our observations.
Moreover, the presence of CO can usually be recognized by
a characteristic peak in the C1s spectra at about 286.7 eV, which
is absent in our measurements.
ꢁ
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Based upon the theoretical models described above we propose
the structure depicted in Fig. 4a for the observed nanorods. Each
porphyrin molecule is rotated by 45ꢂ around its C4 axis with
respect to its neighbours. The ZnTMP molecules are linked to
each other through coordination with bridging water molecules.
Similar structures are known to occur in solution for a variety of
metaloporphyrins and phthalocyanines with different ligands
acting as linkers. An STM image of such a tube can be expected
to show bright protrusions at the position of the topmost mesityl
groups, and lighter protrusions for the remaining mesityl groups
pointing towards the top of the tube. This description fits well
with the observed STM images (Fig. 4b).
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Conclusions
In this paper we describe the synthesis of shish-kebab type
coordination polymers of porphyrin derivatives on solid
surfaces. The polymers have a straight conformation for over
hundreds of nanometres. We suggest that the axial ligands that
bridge the Zn atoms are water molecules that can bind to the
upper and lower Zn atoms via the lone pairs at the oxygen atom,
but other possibilities cannot be excluded. The synthesis of
individual molecular wires on solid surfaces also opens up the
possibility of probing their conductivity one by one, obtaining
thereby information about the real internal conduction mecha-
nisms along the rod spinal cord, not mixed up with grain
boundary resistance. Moreover, a purely 1D sequence of zinc
and oxygen atoms might show fascinating photovoltaic
behaviour.
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Acknowledgements
This work has been supported by the MICINN of Spain
(MAT2009-13488, FIS2010-18847, FIS2010-15127, FIS2010-
19609-C02-01, ACI2008-0777, CTQ2010-17006 MAT2010-
17720), Comunidad de Madrid (Nanobiomagnet S2009/MAT-
1726), Gobierno vasco (IT-366-07), CONSOLIDER-INGENIO
2010 on Molecular Nanoscience (CSD2007-00010) and Nano-
select (CSD2007-41); and European Union (SMALL PITN-GA-
2009-23884 and MONET MEST-CT-2005-020908). R.O. thanks
the Spanish Ministry for Science and Innovation for salary
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Science Lab at Universidad Autónoma de Madrid
(Prof. Roberto Otero).
Title: Surface assembly of porphyrin nanorods with
one-dimensional zinc–oxygen spinal cords
1D metalloporphyrin nanorods have been grown on solid surfaces.
A combination of Scanning Tunnelling Microscopy (STM), X-ray
Photoelectron Spectroscopy (XPS) and Density Functional Theory
calculations has been used to demonstrate that the nanorods
are held together by axial coordination of the metal atoms with
polytopic linkers.
See Otero et al.,
CrystEngComm, 2011, 13, 5591.
www.rsc.org/crystengcomm
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