A spectroscopic study of self-assembled monolayer of porphyrin- functionalized oligo(phenyleneethynylene)s on gold: The influence of the anchor moiety

Article abstract of DOI:10.1039/b802914h

Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for molecular electronics applications. Three such molecules (1-3) with the common structure P-OPE-AG (P and AG are a porphyrin and anchor group, respectively) and different anchor groups, viz. an acetyl protected thiol, -S-COCH₃ (1), an acetyl protected thiol with methylene linker, -CH₂-S-COCH₃ (2), and a trimethylsilylethynyl group, -C≡C-Si(CH₃)₃ (3) have been synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have been prepared. The integrity and structural properties of these films were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The results suggest that the films formed from 1 have a high orientational order with an almost upright orientation and dense packing of the molecular constituents, i.e. represent a high quality SAM. In contrast, molecule 2 formed disordered molecular layers on Au, even though the molecule-surface bonding (thiolate) is the same as in the case of molecule 1. This suggests that the methylene linker in molecule 2 has a strong impact on the quality of the resulting film, so that a well-ordered SAM cannot be formed. The silane system, 3, is also able to bind to the gold surface but the resulting SAM has a poor quality, being significantly disordered and/or comprised of strongly inclined molecules. The above results suggest that the nature of the anchor group along with a possible linker is an important parameter which, to a high extent, predetermines the entire quality of OPE-based molecular layers.

Full text of DOI:10.1039/b802914h

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PAPER
www.rsc.org/pccp | Physical Chemistry Chemical Physics
A spectroscopic study of self-assembled monolayer
of porphyrin-functionalized oligo(phenyleneethynylene)s on gold: the
influence of the anchor moiety
Somsakul Watcharinyanon,*a Daniel Nilsson,b Ellen Moons,a Andrey Shaporenko,c
˚
Michael Zharnikov, Bo Albinsson, Jerker Martensson and Lars S. O. Johansson
c
b
b
a
Received 19th February 2008, Accepted 3rd June 2008
First published as an Advance Article on the web 1st July 2008
DOI: 10.1039/b802914h
Porphyrin-functionalized oligo(phenyleneethynylene)s (OPE) are promising molecules for
molecular electronics applications. Three such molecules (1–3) with the common structure
P–OPE–AG (P and AG are a porphyrin and anchor group, respectively) and different anchor
groups, viz. an acetyl protected thiol, –S–COCH3 (1), an acetyl protected thiol with methylene
linker, –CH2–S–COCH3 (2), and a trimethylsilylethynyl group, –CRC–Si(CH3)3 (3) have been
synthesized and the corresponding self-assembled monolayers (SAMs) on Au(111) substrates have
been prepared. The integrity and structural properties of these films were studied by X-ray
photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The
results suggest that the films formed from 1 have a high orientational order with an almost
upright orientation and dense packing of the molecular constituents, i.e. represent a high quality
SAM. In contrast, molecule 2 formed disordered molecular layers on Au, even though the
molecule–surface bonding (thiolate) is the same as in the case of molecule 1. This suggests that
the methylene linker in molecule 2 has a strong impact on the quality of the resulting film, so that
a well-ordered SAM cannot be formed. The silane system, 3, is also able to bind to the gold
surface but the resulting SAM has a poor quality, being significantly disordered and/or comprised
of strongly inclined molecules. The above results suggest that the nature of the anchor group
along with a possible linker is an important parameter which, to a high extent, predetermines the
entire quality of OPE-based molecular layers.
porphyrin tailgroups have been reported.20–29 In many cases,
thiolate (S-) was used as an anchor which chemically binds the
molecule to the gold surface. This anchoring is frequently used
for the fabrication of SAMs on coinage metal and semicon-
ductor substrates.30 However, thiolate is not the only head-
group suitable for formation of SAMs on these substrates.
Several other groups are available as well. In addition, the
structural parameters of SAMs can be improved by introduc-
tion of a linker between the molecular spacer and the head-
group. In particular, a short aliphatic chain of a proper length
was found to be a suitable linker for oligophenyl SAMs with
thiolate and selenolate headgroups.31–35
1. Introduction
The idea of molecular electronics has recently received much
attention in connection with the ongoing feature size reduction
of electronic devices. In order to operate such an electronic,
the electron transport through the molecular devices is
essential. Oligo(phenyleneethynylene) (OPE) derivatives have
attracted special interest due to their largely delocalized
p-conjugated systems, resulting in a relatively high electrical
conductivity along the molecular backbone.1–9 By introducing
a porphyrin as the tail group onto the OPE molecules, a wire-
like molecule with optical and redox properties can be created
and be of potential interest for application in solar cells,10,11
sensors12–14 and other optoelectronic devices.15–18 The immo-
bilization of the molecules on the electrode, e.g. gold, can be
achieved by self-assembly, by which molecules organize them-
selves on the surface19 in so-called self-assembled monolayers
(SAMs). In recent years, a variety of studies on SAMs with
In this study, we prepared and characterized SAMs formed
on Au(111) from newly synthesized free-base porphyrin-
functionalized OPE (1–3), Scheme 1, with the common struc-
ture P–OPE–AG (P and AG are porphyrin and anchor group,
respectively) and three different AGs, viz. an acetyl protected
thiol, –S–COCH3 (1), an acetyl protected thiol with methylene
linker, –CH2–S–COCH3 (2), and
a trimethylsilylethynyl
group, –CRC–Si(CH3)3 (3). For the first two anchor moi-
eties, the acetyl protecting groups are used to avoid the
problem associated with oxidation, disulfide formation and a
multitude of possible side reactions during synthesis.36,37 The
acetyl groups are expected to be removed upon the adsorption,
resulting in the formation of a thiolate–gold bond.36 In the
a Department of Physics, Karlstad University, S-65188 Karlstad,
Sweden. E-mail: somsakul@kau.se; Fax: 46 54 700-1829;
Tel: 46 54 700-1546
b Department of Chemical and Biological Engineering, Chalmers
University of Technology, S-41296 Goteborg, Sweden
¨
¨
c Angewandte Physikalische Chemie, Universitat Heidelberg,
Im Neuenheimer Feld 253, D69120 Heidelberg, Germany
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Scheme 1 (i) Pd2(dba)3, triphenylphosphine, diisopropylethylamine, THF, 40 1C, 12 h; (ii) Pd2(dba)3, triphenylarsine, TEA, CH2Cl2, MeOH, 40 1C, 12 h.
case of 2, by inserting a methylene linker in-between the sulfur
and the OPE moiety, we intended to achieve an improvement
of orientational order and increase of the packing density, as
occurring in oligophenyl-substituted alkanethiol and alkane-
selenol SAMs on gold.31–35,38,39 The above adsorbates with the
linker consisting of an odd number of the methylene groups
were found to be densely packed and less inclined on Au than
the respective oligophenylthiol SAMs themselves.33,38,39 In the
case of 3, we took into account that the high reactivity
displayed by the acetyl group in thiophenolesters can compli-
cate or even make the syntheses of complex molecules im-
possible. A less labile group, still suitable for the SAM
formation, would therefore be of vital importance for the
successful construction of functionalized molecules of the
complexity necessary for future applications. One such group
might be the trimethylsilyl (TMS) group, a well established
protective group in organic synthesis with a desirable reactiv-
ity pattern, which has been shown to be suitable for the
formation of SAMs when attached to alkynes. However, the
interaction of the trimethylsilyl with the gold surface is still
unknown. For that reason, we have chosen to explore the
TMS-ethynyl group as the molecular anchor. Our recent
experiments on a series of OPEs with the different TMS-based
anchors showed that the TMS-ethynyl group supports the
formation of SAMs on Au(111).37
The headgroup–substrate interface in the films of this study
was characterized by high resolution X-ray photoelectron
spectroscopy (HRXPS). This technique was also used to
determine the composition and effective thickness of the films.
The chemical and structural information on the systems under
consideration was provided by near-edge X-ray absorption
fine structure (NEXAFS) spectroscopy; this technique pro-
vides an information which is complementary to HRXPS. The
structure, packing density, and the orientation of the films
comprised of porphyrin-functionalized OPEs were analyzed
and compared with those for OPE SAMs without a porphyrin
tailgroup.
2. Experimental
2.1 Synthesis
5-(3, 5-Di-tert-Butylphenyl)-2, 8, 12, 18-tetraethyl-3,7,13,17-tetra-
methyl-15-{4- [4- (4 -acetylthiophenylethynyl) phenylethynyl]phenyl}-
porphyrin (1). To 1-Acetylthio-4(40-ethynyl)phenylethynyl)benzene
(9.0 mg, 33 mmol), 5-(3,5-di-tert-butylphenyl)-2,8,12,18-tetraethyl-
3,7,13,17-tetramethyl-15-p-iodophenylporphyrin (21 mg, 24 mmol)
and triphenylphosphine (15 mg, 55 mmol) put under an argon
atmosphere and dry toluene (10 ml) and diisopropylethylamine (2
ml) were added, followed by bubbling with argon for 20 min.
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Pd2(dba)3 (9.9 mg, 9.6 mmol) was added and the reaction mixture
was stirred at 40 1C for 12 h and then concentrated to give a red
solid. The solid was dissolved in CH2Cl2 and added to a short
silica pad, washed with CH2Cl2, and eluted with diethylether.
Evaporation of the solvent gave a red solid which was purified by
column chromatography (pentane/diethylether, 10 : 1 followed by
pentane/diethylether, 1 : 1) followed by SEC (toluene) to give 1 as
a red solid (7 mg, 6.9 mmol, 29%); 1H-NMR (CDCl3) d ꢁ2.44 (br
s, 2H), 1.50 (s, 18H), 1.77 (m, 12H), 2.45 (m, 9H), 2.55 (s, 6H),
3.97–4.06 (m, 8H), 7.43 (d, 2H), 7.58–7.62 (m, 4H), 7.69 (d, 2H),
7.80 (m, 1H), 7.90 (d, 2H), 7.93 (d, 2H), 8.10 (d, 2H), 10.23 (s, 2H);
HRMS (FAB) calculated for [C70H73N4OS] + 1017.5506, found
1017.5504.
concentrated to give the desired product as a yellowish solid.
Flash chromatography (hexane/DCM, 2 : 3) yielded a solid
which was recrystallized in hexane to afford 5 as a light red
solid (12 mg, 33 mmol, 25%); 1H-NMR (CDCl3) d 0.28 (s, 9H),
7.36 (m, 3H), 7.50–7.57 (m, 10H). Elemental analysis calcd
(%) for C25H18OS C: 81.93 H: 4.95, found C: 81.75 H: 4.86.
Materials. Reagents and solvents were purchased from
Acros and Aldrich and used without further purification.
Tetramethylsilane was used as reference for the chemical shifts
(dH = 0 ppm) in NMR experiments. Solvents were dried by
distillation under nitrogen, triethylamine (TEA) from calcium
hydride and toluene and tetrahydrofurane (THF) from
sodium/benzophenone. Inert argon atmosphere was applied
by three repetitive vacuum-argon cycles that replaced the
atmosphere above the reactants. Solvents were removed using
a rotary evaporator at reduced pressure unless stated other-
wise. Reference compounds 443 and 644 (Fig. 1) were prepared
according to published procedures.
5-(3,5-Di-tert-Butylphenyl)-2,8,12,18-tetraethyl-3,7,13,17-tet-
ramethyl-15-{4-[4-(4-acetylthiomethylphenylethynyl)phenylethy-
nyl]phenyl}porphyrin (2). Using the same reaction conditions
as for 1, with the exception that the quota toluene/diiso-
propylethylamine was 10 : 3, 5-(3,5-di-tert-butylphenyl)-2,
8, 12, 18-tetraethyl-3, 7, 13, 17-tetramethyl-15-para-iodophenyl-
porphyrin (21 mg, 24 mmol) and 1-acetylthiomethyl(-4-(4-ethy-
nyl)-phenylethynyl)benzene (10 mg, 33 mmol) was coupled. The
crude product was purified to give 2 as a red solid (18 mg, 17
Gold substrates were purchased from Georg Albert PVD-
Beschichtungen (Heidelberg Germany). They were prepared by
thermal evaporation of 300 nm of gold onto mica. Then the gold
films were flame-annealed with a butane torch in air until they
reached the point where the orange glow was visible. After that
the samples were immediately quenched and stored in argon.45–47
This resulted in a polycrystalline film with (111) orientation of the
individual crystallites.45,47 The substrates were stored under argon
before film preparation and used without further cleaning.
1
mmol, 61%); H-NMR (CDCl3) d ꢁ2.43 (br s, 2H), 1.51 (s,
18H), 1.78 (m, 12H), 2.39 (s, 3H), 2.46 (s, 6H), 2.55 (s, 6H),
3.98–4.06 (m, 8H), 4.15 (s, 2H), 7.31 (d, 2H), 7.50 (d, 2H), 7.60
(d, 2H), 7.68 (d, 2H), 7.81 (m, 1H), 7.90–7.96 (m, 4H), 8.11 (d,
2H), 10.24 (s, 2H)); HRMS (FAB) calculated for
[C71H75N4OS] + 1031.5662, found 1031.5675.
Methods. Column chromatography was performed on silica
gel (Matrex, normal phase, LC60A/35–70 mm). The porphyrin
systems were purified using size exclusion chromatography
(SEC) (Bio-Rad, Bio-beads S-X3, 200–400 mesh). Proton
(400 MHz) NMR spectroscopy was performed on a Varian
UNITY-400 NMR spectrometer, while carbon (100.6 MHz)
NMR was performed on a JEOL Eclipse 400 apparatus, both
at ambient temperature in CDCl3.
5-(3,5-Di-tert-butylphenyl)-2,8,12,18-tetraethyl-3,7,13,17-tet-
ramethyl-15-{4-[4-(4-trimethylsilylethynylphenylethynyl)phenyl-
ethynyl]phenyl}porphyrin (3). 1-Iodo(-4(40-trimethylsilylethynyl)
phenylethynyl)benzene (3.5 mg, 8.7 mmol), Pd2(dba)3 (0.74 mg,
0.71 mmol) and triphenylarsine (1.3 mg, 4.2 mmol) were put
under an argon atmosphere. To the mixture, a solution of P2
(0.67 ml, 10 mmol) in CH2Cl2 and CH2Cl2 (2.33 ml) was added,
followed by addition of MeOH (3 ml) and TEA (80 ml). The
reaction mixture was stirred at ambient temperature overnight
and then concentrated affording a brownish solid. The solid
was dissolved in CH2Cl2 and added to a silica pad, washed
with CH2Cl2, and eluted with diethylether. Subsequent eva-
poration and SEC (toluene) gave 3 as a red solid (4.7 mg, 4.5
2.2 SAM preparation
The target compounds 1–3 were dissolved in THF to give a
1 mM solution. The gold substrate was immersed into 1–2 ml
of this solution for 20 h; the reaction vessels were kept in
argon, at room temperature, and in the dark. In the case of
compounds 1 and 2, an excess (2–3 drops) of a 1% ammonium
hydroxide solution in THF (prepared from ammonium hydro-
xide, 25–30% NH3) was added to the reaction vessels to
remove the acetyl protective group and form the free thiol.
Later, the assembly formed the thiolate upon exposure to the
gold surface. For the silane, 3, no such additional activation
was needed. After the immersion, the samples were thoroughly
rinsed with THF (several times), dried with nitrogen and
stored under argon in the absence of light to avoid oxidation
1
mmol, 52%); H-NMR (CDCl3) d ꢁ2.43 (br s, 2H), 0.26 (s,
9H), 1.50 (s, 18H), 1.78 (m, 12H), 2.46 (m, 6H), 2.56 (s, 6H),
3.97–4.07 (m, 8H), 7.46–7.53 (m, 4H), 7.60 (d, 2H), 7.69 (d,
2H), 7.81 (m, 1H), 7.91 (d, 2H), 7.94 (d, 2H), 8.11 (d, 2H),
10.24 (s, 2H) HRMS (FAB) calculated for [C73H79N4Si] +
1039.6075, found 1039.6061.
1-(S-Acetylthiomethyl)-4-[4-(4-phenylethynyl)phenylethynyl]-
benzene (5). 1-Ethynyl-4-(phenylethynyl)benzene40,41 (26 mg,
0.13 mmol), 1-acetylthiomethyl-4-iodobenzene42 (48 mg,
0.17 mmol), Pd2(dba)3 (5.1 mg, 4.9 mmol), triphenylphosphine
(7.9 mg, 30 mmol), and CuI (2.0 mg, 11 mmol) were dissolved in
THF (5 ml) and diisopropylethylamine (5 ml) under argon.
The solution was stirred for 20 h at ambient temperature,
filtered, and concentrated to afford a brown solid. The solid
was dissolved in boiling hexane/DCM (4 : 1), and after cooling,
a dark brown precipitate was filtered off. The filtrate was
Fig. 1 Reference OPE-based systems.
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and photoinduced degradation.48,49 Additional cleaning of the
samples using sonication was regretfully not possible due to
flaking of the gold substrate. As discussed below, it is un-
certain whether all three molecular layers can be regarded as
true SAMs. However, for simplicity, we use the notation SAM
1, SAM 2 and SAM 3 for molecular layers formed from
compound 1, 2, and 3, respectively.
901 (E-vector in the surface plane) to 201 (E-vector near
surface normal) to monitor the molecular orientation. The
NEXAFS spectra were normalized to the incident photon flux
by dividing the raw spectrum by a spectrum of a clean, freshly
sputtered gold substrate. The spectra were then reduced to the
standard form by setting the pre-edge region to zero and
normalization to the height of the absorption edge.
2.3 High-resolution X-ray photoelectron spectroscopy
(HRXPS)
3. Results
3.1 Synthesis
The SAMs were characterized by synchrotron-based HRXPS.
The measurements were carried out at the synchrotron storage
ring MAX II at MAX-lab in Lund, Sweden, using the beam-
line D1011. The beamline is equipped with a Zeiss SX-700
plane-grating monochromator and a two-chamber ultrahigh
vacuum experiment station with a SCIENTA type analyzer.
The spectra were acquired in normal emission geometry. The
Au 4f and C 1s spectra were collected at photon energies of
350 and 580 eV. The photon energies of 350 and 160 eV were
used to probe the S 2p and Si 2p core level regions, respec-
tively. The N 1s region was also monitored with photon energy
580 eV. The binding energy (BE) scale of every spectrum was
calibrated using the Au 4f7/2 emission line of a dodecanethiol
SAM on an Au substrate at 83.95 eV.50 The energy resolution
of the spectrometer was better than 100 meV. The HRXPS
spectra were fitted by a symmetric Voigt function with a
variable Lorentz–Gauss ratio,51 and a Shirley background.52
The S 2p3/2,1/2 doublets were fitted by using a 1.2 eV spin–orbit
splitting and a branching ratio (S 2p3/2/S 2p1/2) of 2. The Si
2p3/2,1/2 doublets were fitted by using a spin–orbit splitting of
0.6 eV. Both 2p3/2,1/2 components were fitted with the same full
width at half-maximum (fwhm). If there were several different
species in a particular spectrum, the same fwhm was used for
all individual emissions related to the same core level. The
effective film thicknesses were estimated using the intensity
ratio of the C 1s and Au 4f signals and standard attenuation
lengths.53,54
Three free-base porphyrin systems were synthesized
(Scheme 1). These systems are characterized by different
groups responsible for the attachment of the SAM-constituent
to the gold substrate, viz. an acetyl protected thiophenol,
benzylic thiol, and a TMS-ethynyl group. The syntheses of
the OPE building blocks 1B, 2B and 3B (see Scheme 1) and the
porphyrins P1 and P2 have been reported elsewhere.56–58
Terminal alkynes and aryl halides are normally cross-coupled
by palladium catalysis in the presence of cuprous salts. How-
ever, since copper can be readily inserted into the porphyrin
cavity, copper-free conditions had to be used for the prepara-
tion of compounds 1–3. Compound 3 was prepared in a
satisfactory yield by a cross-coupling of the acetylene functio-
nalized porphyrine P2 with the bridge-building block 3B using
the conditions optimized for couplings of substrates of this
kind.41,59 Due to the high reactivity of the acetyl protection
group towards nucleophiles, other coupling conditions were
necessary for the preparation of compounds 1 and 2.60 The
sterically hindered and less nucleophilic diisopropylethylamine
had to be used as the base instead of more favourable bases
with higher nucleophilicity. Also triphenylarsine, a preferred
ligand under copper-free conditions, interfered with the acetyl
protective group and the less efficient triphenylphosphine had
to be used.61 The substantial difference in obtained yields of
compounds 1 and 2 reflects the difference in stability of the two
different acetyl-protected thiols towards nucleophiles. In con-
trast to the high lability of the acetyl-protected thiols, the
TMS-ethynyl group is stable under a large variety of reaction
conditions. This would make it an attractive anchor group if it
supports the formation of high-quality SAMs.
2.4 Near-edge X-ray absorption fine structure (NEXAFS)
spectroscopy
This technique can give information about the electronic and
structural properties of molecular films by probing electron
transitions from core-levels to unoccupied molecular orbitals
which are characteristic of specific bonds or functional
groups.55 Furthermore, the average molecular orientation
can be determined by monitoring the intensity variation of
the absorption resonances in the spectra when the X-ray
incidence angle is varied. The NEXAFS measurements of
SAM 1–3 were performed at the same beamline and experi-
mental station as in the case of HRXPS. In addition, the
NEXAFS spectra of the building blocks of molecules 1–3, viz.
three reference OPE systems with corresponding anchor moi-
eties but without the porphyrin tailgroup (Fig. 1), were
measured at the HE-SGM beamline of the synchrotron sto-
rage ring BESSY II in Berlin (Germany). Both the MAX-lab
and BESSY II spectra were acquired at the C K-edge in the
partial electron yield mode with a retarding voltage of
–150 eV. The incidence angle of the light was varied from
3.2 HRXPS measurements
The S 2p, Si 2p, and Au 4f HRXPS spectra were examined to
characterize the binding motif of the molecules 1–3 to the Au
surface. The S 2p spectra of both thiol-derived porphyrin
SAMs are shown in Fig. 2. Both spectra show a relatively
poor signal-to-noise ratio, which mostly results from the
attenuation of the initially weak S 2p signal (there is just 1
monolayer of S) by the thick hydrocarbon overlayer. The
quality of the spectra further deteriorated due to a very intense
inelastic background at the position of the S 2p emission; this
background originates from the Au 4f emission of the gold
substrate. Note that the spectra acquisition time was limited
by possible X-ray induced damage, so that the spectra statis-
tics could not be improved significantly.
In spite of the poor signal-to-noise ratio, one can clearly see
that the S 2p spectrum of SAM 1 does not represent a single S
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between bound and unbound sulfur was estimated to be 98 : 2
for SAM 1. (If the lack of attenuation is not taken into
account, the ratio between bound and unbound sulfur will be
62 : 38.) Although these values are not exact because of the
poor signal-to-noise ratio of the S 2p spectra and the possible
effect of a partial intercalation, they clearly indicate, never-
theless, that most of the molecules in the films are attached to
the substrate by the thiolate–gold bond.
The intensity of the S 2p features for SAM 2 is lower than
that for SAM 1, but the form of this spectrum is quite similar,
so that it can also be tentatively described as a superposition of
two components assigned to the bound (by thiolate anchor)
and unbound molecules. Whereas a spectra decomposition is
even less reliable than that for the case of SAM 1, it is clearly
seen that the major spectra weight is at about 162.0 eV, which
is characteristic of the thiolate–gold bond. Therefore, it can be
assumed that the majority of the molecules in SAM 2 were
bonded to the substrate by the respective anchor.
For SAM 3, the interaction of TMS–acetylene,
R–CRC–Si(CH3)3, with the gold substrate being investigated
by probing the Si 2p core levels. The respective spectrum is
shown in Fig. 3. Note that at the same packing density in films
1–3, the total intensity of the Si 2p signal is expected to be
higher than that of the S 2p signal by a factor of 3 due to the
photoionization cross section difference for the given photon
energies and core levels.68
Fig. 2 S 2p HRXPS spectra of SAMs 1 and 2 (the respective target
molecules contain a sulfur headgroup). The spectrum of SAM 1 was
decomposed into two components (thin solid line). The background is
shown by dotted lines. The BE of the S 2p3/2 peak in the thiolate-
related doublet is indicated.
Due to the small spin–orbit splitting of both components,
the Si 2p3/2,1/2 doublet looks like a single slightly asymmetric
peak. There is only one such peak in the Si 2p spectrum of
SAM 3. The BE of this peak is 101.9 eV, which is characteristic
of the Si–C bond in the TMS group.69,70 The fwhm of this
peak is 1.2 eV. In recent studies of the alkylsilane (CnH2nꢁ1
SiH3) SAMs on Au, the Si 2p3/2,1/2 peak was observed at a BE
of 99.8 eV and with fwhm of 0.4 eV.71,72 It was proposed that
three Si–H bonds are cleaved during the SAM formation, and
then Si atoms form three covalent bonds to the gold sur-
face.71,72 In the case of the TMS–ethynyl system of this study,
2p3/2,1/2 doublet with a characteristic branching ratio of 2 : 1.
At the same time, this spectrum can be tentatively described as
a superposition of two doublets (see the respective spectrum
decomposition in Fig. 2). The BE position of the first doublet is
B162 eV (S 2p3/2). This energy is characteristic of the thiolate-
type sulfur bound to the metal surface62–66 indicating that a
significant part of the molecules 1 bind to the gold substrate
through the thiolate anchor. Another doublet at a BE of
B163.5 eV (S 2p3/2) is usually associated with a disulfide or
unbound sulfur.67 This doublet can presumably indicate the
occurrence of residual physisorbed molecules at the SAM-
ambient interface, which could not be removed in spite of the
extensive washing of the samples. Alternatively, this doublet
could arise from an intercalation of the unbound molecules
with the bound ones due to the p–p interaction between the
OPE moieties and the porphyrin groups. However, we consider
this second scenario as less probable or, at least, occurring to a
minor extent, since such an intercalation will presumably
destroy the orientational order in the film, which is not the
case (see below). The relative contributions of the chemi- and
physisorbed species were estimated from the ratio between the
intensity of the respective doublets and the total intensity of the
S 2p signal. However, for the physisorbed species, the mole-
cules were assumed to reside at the SAM-ambient interface,
which is, in our opinion, the most probable scenario. There-
fore, the intensity of the peak related to the physisorbed
molecules has to be scaled down to correct for the lack of
attenuation of the respective S 2p signal. For this correction,
the film thicknesses obtained from the intensity ratio of the C
1s and Au 4f signals (see below) and the attenuation length
given by Lamont et al.54 were used. As a result, the ratio
Fig. 3 Si 2p HRXPS spectrum of SAM 3. The Si 2p3/2 and Si 2p1/2
components are merged in an asymmetric peak. The BE and fwhm of
this peak are indicated.
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Fig. 4 Au 4f7/2 HRXPS spectra of a clean Au and SAMs 1–3. The BE
and fwhm of the Au 4f7/2 peaks and their components are indicated.
the observed BE position of the Si 2p peak (101.9 eV) is higher,
which indicates that not all Si–CH3 bonds are cleaved upon
the film formation. This suggests that the binding of molecules
3 to the Au surface is different from the alkylsilane case.
Importantly, the Si 2p signal for SAM 3 is quite intense which
would not be the case if the respective molecule did not bind to
the Au surface, since all (or almost all) physisorbed species
should be removed when the samples were thoroughly rinsed
with the solvent during the SAM preparation.
Fig. 5 C 1s HRXPS spectra of SAMs 1–3. The BE and fwhm of the
individual peaks are indicated. The spectra were acquired at a photon
energy of 350 eV.
systems (0.86 eV).77 For SAMs 2 and 3, the main C 1s peak is
accompanied by
a small shoulder at a higher BE of
285.6–286.0 eV. This shoulder is most probably related to
contamination, although analogous features have previously
been observed for different aromatic SAMs and were alter-
natively assigned to either the carbon atom bound to the sulfur
headgroup or a shake-up process.78–81
The Au 4f7/2 spectra of clean gold substrate and SAM 1–3
acquired at a photon energy of 350 eV are presented in Fig. 4.
The spectrum of the clean gold substrate shows two compo-
nents at BEs of 83.95 and 83.62 eV (with fwhm of 0.40 eV).
They are assigned to gold atoms in the bulk and in the topmost
layer, respectively.73–76 In contrast, the spectra of all SAMs of
this study exhibit just a single peak. We interpret this peak as
the result of the adsorbate-induced shift of the Au 4f7/2 surface
component to higher BE, so that it overlaps with the bulk
component.73,74,76 Note that the relatively low Au 4f signal
intensity for SAM 1 indicates a thicker film as compared to
SAMs 2 and 3.
In Fig. 6, N 1s HRXPS spectra of SAMs 1–3 are presented.
For SAM 1, two N 1s emissions at BEs of 396.7 and 398.7 eV
were observed (with a fwhm of 1.0 eV). They can be assigned
to two chemically different nitrogen atoms present in the free-
base porphyrin, i.e. N and NH, respectively. In this case, the
intensity ratio of these two peaks (N : NH = 43 : 57) is close to
the expected stoichiometric value (1 : 1). Also, the BE differ-
ence between the peaks (2.0 eV) agrees well with the values
typically observed in free-base porphyrins (2.1 ꢂ 0.1 eV).82–84
At the same time, the absolute BE positions of these peaks are
lower by B1.0 eV compared to those for free-base octaethyl-
porphyrins.82,85 This is presumably related to the difference in
substitution patterns between topical porphyrin and octaethyl-
porphyrin. The N 1s electrons in a macrocycle are very
sensitive to perturbations.82,86 Compared to octaethylpor-
phyrin, which has hydrogen atoms in the 5 and 15 positions,
the topical porphyrins are substituted with a phenyl ring and
an OPE moiety on two opposite meso positions. Consequently,
nitrogen atoms gain an additional electron density from the
The C 1s spectra of SAMs 1–3 are shown in Fig. 5. The total
C1s intensity for SAM 1 is significantly higher than that for
SAM 2, which, in its turn, is much higher than that for SAM 3.
The main emission peaks were observed at BEs of 284.7, 284.4,
and 284.3 eV for SAMs 1, 2, and 3, respectively. These peaks
are composed of the C 1s emissions originated from both OPE
moiety and porphyrin group. However, these different con-
tributions merge and cannot be unequivocally resolved by
curve fitting, but are just reflected in a rather large fwhms
(B1.2–1.3 eV) of the joint peak as compared to porphyrin-free
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the film. The k value was determined using the reference
system of hexadecanethiolate SAM on Au(111). lC and lAu
were obtained using the expression l = 0.3Ekin0.64 for alkane-
thiolate SAMs.54 The resulting values of the effective thickness
obtained for SAMs 1, 2, and 3 are 2.9, 1.2, and 1.1 nm,
respectively.
3.3 NEXAFS measurements
The C K-edge NEXAFS spectra of SAMs 1–3 acquired at an
X-ray incidence angle of 551 are shown in Fig. 7 (top curves)
along with the spectra of the reference OPE SAMs with
corresponding anchor moieties but without the porphyrin
group (bottom curves). The positions of the observed absorp-
tion resonances and those for the porphyrin endgroup88,89
(as a reference) are indicated. Note that at this particular
geometry (close to magic angle of X-ray incidence, y = 54.71,
see eqn (2) below) the spectra are exclusively representative of
the electronic structure of the target systems and are unaf-
fected by molecular orientation.55
The spectra of all SAMs comprised of the non-substituted
molecules in Fig. 7 (bottom curves) exhibit a dominant peak at
B285.0 eV assigned to the p1* resonance of the phenyl rings in
*
OPE moiety. This peak is accompanied by a weaker p2
resonance at B288.6 eV and broad s* resonances at higher
photon energies of 293.5 and B303 eV. The C K-edge NEX-
AFS spectrum of porphyrin (from ref. 86 and 87) exhibits a p*
resonance at 285.2 eV, a s* resonance at 287.3 eV (assigned to
the C–H moieties in the alkyl groups surrounding the
porphyrin), a further p* resonance at 288.3 eV, and broad
s* resonances at about 294 and 303 eV.88,89
Fig. 6 N 1s HRXPS spectra of SAMs 1–3. Peak positions are
indicated. The spectra were acquired at a photon energy of 580 eV.
The NEXAFS spectra of SAMs 1–3 (Fig. 7 top curve) can
be fairly described as a superposition of the spectrum of the
respective reference OPE SAM and the spectrum of porphyrin
with a clear dominance of the contribution from the porphyrin
moiety. At the same time, whereas the shapes of the spectra for
SAMs 1 and 2 are quite similar, they differ to some extent from
meso substituents, which results in a downward shift of the
respective emissions.
In contrast to SAM 1, the N 1s spectra of SAMs 2 and 3
show only a single peak at 398.7 and 398.6 eV, respectively
(with a similar fwhm of 1.0 eV). This result is unexpected for a
free-base porphyrin, and the origin of this phenomenon is not
completely clear (see below). Note that a single N 1s peak is
commonly observed in metalloporphyrins, in which all four
nitrogen atoms become equivalent.82,87 In particular, Yasseri
et al. have observed a single N 1s peak at BE of 398.2 ꢂ 0.1 eV
in the SAM bearing the OPE bridge, zinc porphyrin as a
tailgroup, and the same anchor moiety as 2.22
*
that for SAM 3. The latter spectrum exhibits a weak p1
resonance structure and a clear signature of contamination,
e.g. a p* resonance related to CQO moiety at 288.6 eV.
The average orientation of the molecules in the target SAMs
can be estimated by monitoring the linear dichroism of the
NEXAFS spectra, i.e. dependence of the absorption resonance
intensity on the X-ray incidence angle. Generally, the intensity
of a NEXAFS resonance depends on the orientation of the
electric field vector (E-vector) of the incidence light with
respect to the transition dipole moment (TDM) of the probed
transition.55 The intensity is maximal if the E-vector direction
and the TDM are parallel to each other and is equal to zero if
they are orthogonal. Furthermore, a pronouced linear dichro-
ism in the NEXAFS spectra implies an orientational order in
the film. These linear dichroism effects disappear when the
molecules are randomly oriented or when the TDM of the
molecules is oriented with a tilt angle a = 54.71 (magic angle)
with respect to surface normal (see eqn (2) below).
The effective thickness of films 1–3 was estimated on the
basis of the Au 4f and the C 1s XPS spectra acquired at a
photon energy of 580 eV and the standard attenuation lengths
for the Au 4f and C 1s emission.53
h
i
ꢁðdeffꢁdSðor SiÞÞ
1 ꢁ exp
IC
lC
h
i
¼ k
ð1Þ
ꢁdeff
IAu
exp
lAu
where IC and IAu are the total intensity of the C 1s and Au 4f
signals, respectively, k is an instrument-specific constant for a
given photon energy, lC and lAu are the attenuation lengths
for the C 1s and Au 4f photoelectrons, respectively, at the
given kinetic energy, ds(or Si) is the S–Au or Si–Au distance,
both assumed to be 1.8 A and deff is the effective thickness of
The C K-edge NEXAFS spectra of SAMs 1–3 acquired at
X-ray incidence angles of 20, 55, and 901 are shown in Fig. 8,
along with the respective differences between the 90 and
201 spectra. For SAM 1, the p* resonances are more intense
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Fig. 7 The C K-edge NEXAFS spectra of SAM 1 (a), 2 (b), and 3 (c) (top curves) in comparison with the spectra of the reference OPE SAMs on
Au with corresponding anchor moieties but without the porphyrin tailgroup (bottom curves); the positions of the characteristic absorption
resonances are indicated by dotted lines. All spectra were acquired at an X-ray incidence of 551. The positions of the characteristic absorption
resonances of the porphyrin tailgroup88,89 are indicated by the solid lines.
at normal than at grazing incidence while the s* features
exhibit the opposite behavior. Considering that the TDMs
for the transition to the p* and s* orbitals are oriented
perpendicular to and along the molecular axis, respectively,
the observed linear dichroism suggests that, on average, the
constituents of SAM 1 have an almost upright orientation and
the SAM is well-ordered. Since the orientational order results
from intermolecular interaction, SAM 1 can be assumed to be
densely packed as well. The film thickness derived from XPS
data corresponds well with these results for SAM 1 (see
below). In contrast, for SAM 2, the intensity of p* resonances
decreases with increasing X-ray incidence angle, which means
that its constituents are significantly inclined. Also, XPS-
derived thickness is very low for SAM 2, supporting a large
inclination of the molecules with a low packing density in this
film. Finally, the NEXAFS spectra of SAM 3 exhibit almost
no linear dichroism. This can either indicate that the film has a
low orientational order or the molecules are strongly inclined
with the average tilt angle of the TDM close to the magic angle
(a = 54.71). At this particular angle, the NEXAFS intensity
does not depend on the angle of light incidence (see eqn (2)). It
is principally not possible to distinguish between these two
possibilities on the basis of the NEXAFS data alone. How-
ever, a comparison between the film thickness derived from
*
NEXAFS and XPS data (see below) and a very weak p1
resonance, which is characteristic of both OPE moiety and
Fig. 8 The C K-edge NEXAFS spectra of SAMs 1–3 acquired at X-ray incidence angles of 90, 55, and 201, along with the difference between the
90 and 201 spectra. The dashed line corresponds to zero.
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porphyrin tailgroup, suggested that SAM 3 has a poorly
defined orientational order.
where I(y,a) is the intensity of the selected absorption
resonance and y is the X-ray incidence angle. The TDM
tilt angle a is related to the average tilt angle of the molecular
axis j and the twist angle g of the molecule with respect to
the plane spanned by the surface normal and molecular axis
by
We have previously found, in accordance with the literature
data, that reference compound 4 (same as 1, but without the
porphyrin tailgroup) forms a highly oriented and a densely
packed SAM, with the SAM constituents being almost up-
right.77,90–92 Along with the above results for SAM 1, this
suggests that the anchor group 1 (R-S-) is suitable for the SAM
formation. In contrast, the NEXAFS spectra of the film
formed from the reference compound 5 (same as 2, but with-
out the porphyrin tailgroup), in Fig. 9 show a similar ‘‘nega-
tive’’ dichroism as the spectra of SAM 2, suggesting that it is
not the porphyrin tailgroup but the CH2 linker that is respon-
sible for the low quality of the film.
cos a = cos g sin j
(3)
*
For the evaluation, the p1 resonance at photon energy
B285.0 eV has been selected as the most pronouced absorp-
tion feature in the spectra, and the intensity ratios I(y)/I(201)
were used instead of the absolute intensities to avoid normal-
ization problems. The average tilt angles a of the p1* TDM for
SAMs 1, 2 and 3 were determined to be 61, 49, and 551,
respectively. Assuming the twist angle to be 321, as found from
the prior experimental results of thioaromatic SAMs (e.g.
oligo(phenyleneethynylene)),32,90,93 the average tilt angles of
the molecular axis j were estimated to be B 35, 50 and 421 for
SAMs 1, 2 and 3, respectively. However, it is likely that the
OPE moiety and porphyrin tailgroup are not in-plane, but are
rotated with respect to each other by 901 around the molecular
axis.94 This makes the estimated values of the average tilt
angles somewhat uncertain.
Apart from the above qualitative considerations, the aver-
age tilt angle of the SAM constituents can be determined from
numerical analysis of the NEXAFS data.55 The average tilt
angle a of the respective TDM with respect to the surface
normal is given by
2
2
1
2
I(y,a) p 1 + (3 cos y ꢁ 1)(3 cos a ꢁ 1)
(2)
NEXAFS data can be used to estimate the effective thick-
ness on the basis of the derived average tilt angles. Taking a
theoretical length of the molecule dtheo, spacing dS (or Si) =
1.8 A for S–Au or Si–Au distances and the NEXAFS-derived
average tilt angle j, the effective thickness deff of the film can
be calculated by
deff = dtheo cos j + ds
(4)
Assuming SAMs 1, 2, and 3 are well ordered with the
respective average molecular tilt angle derived by NEXAFS,
the NEXAFS-estimated thicknesses will be 2.9 nm for SAM
1, 2.3 nm for SAM 2 and 2.8 nm for SAM 3. The NEXAFS-
derived thickness for SAM 1 is in good agreement with
the thickness obtained by XPS. This supports an ordered
layer with a molecular tilt angle of 351 for SAM 1, as shown
by the angular dependence in the NEXAFS spectra. In con-
trast, the NEXAFS-derived thicknesses for SAM 2 and 3 give
a much higher value compared to the XPS results. This
discrepancy suggests a low orientational order in those two
SAMs.
4. Discussion
Monomolecular layers were prepared from the porphyrin
decorated oligo(phenyleneethynylene) molecules with three
different anchor moieties. The HRXPS and NEXAFS data
for all three films under study correlate well with each other.
Both techniques consistently reveal that all the molecules form
SAM-like layers on the Au substrate, but with different
molecular orientation, structural order, and packing density.
The C K-edge NEXAFS spectra of all molecular layers show
the absorption resonance features which are characteristic of
both OPE moiety and porphyrin tailgroup.
Fig. 9 The C K-edge NEXAFS spectra of the reference SAM formed
from compound 5 (same as 2, but without the porphyrin tailgroup)
acquired at X-ray incidence angles of 90, 55, and 201, along with the
difference between the 90 and 201 spectra. The dashed line corresponds
to zero.
Both molecules 1 and 2 are bound to the substrate via a
gold–thiolate bond as evidenced by the characteristic doublet
in the S 2p XPS spectra. The molecule without the methylene
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linker between the OPE moiety and the sulfur (molecule 1) was
found to form SAMs of significantly higher quality than the
one with the linker (molecule 2). This conclusion can be drawn
on the basis of both HRXPS and NEXAFS data, which
suggest severe differences in the packing density and molecular
inclination between SAMs 1 and 2: whereas SAM 1 has a high
packing density and is comprised of almost upright standing
molecules, SAM 2 exhibits a low packing density, a poor
orientational order, and strongly inclined molecules. Along
with the qualitative results, this conclusion is supported by
clear numerical parameters such as the effective film thickness
and average tilt angle of the SAM constituents. In addition,
there is a subtle observation: a lower BE of the major C1s
emission for SAM 2 as compared to SAM 1, implying a
difference in the packing density and molecular orientation.
Furthermore, the N 1s HRXPS spectrum of SAM 1 exhibits
two emission peaks, as expected for the two different nitrogen
species (N and NH) in the free-base porphyrin tailgroup, while
the N 1s spectrum of SAMs 2 and 3 shows a single emission
peak, indicating a significant disturbance or decomposition of
the porphyrin units. Since both the chemical structure of the
target molecules 1–3 and preparation conditions of the respec-
tive SAMs were quite similar, we do not believe in the
decomposition scenario. This belief is further supported by
the observation of the characteristic absorption resonances of
porphyrin in the NEXAFS spectra of SAMs 2 and 3. So, we
are only left with the disturbance hypothesis. Whatever the
reason for such a disturbance, it presumably resulted in the
equivalency of all N atoms in the porphyrin unit as it occurs in
metalloporphyrins.86,87 In the present case, one may speculate
that the interaction of the strongly inclined molecules with the
Au substrate could lead to metal-coordinated porphyrins and
be thereby responsible for the single N 1s peak. An Au
coordination of the porphyrin has previously been proposed
by Katsonis et al., who performed STM and XPS studies on
SAM of meso-tetradodecylporphyrin on Au(111).95 However,
the respective N 1s XPS spectra were quite complex and
contained several peaks, even though one of them was clearly
dominating.95
linker (the reference compound 5) does not form a well-
ordered and densely packed SAMs. This result for the OPE
molecules with the methylene spacer is remarkably different
from the reported behavior of oligo(phenylene)-substitued
alkanethiolate and -selenolate SAMs on Au, in which well-
ordered and upright standing SAM constituents were ob-
served in the films formed from the molecules with the
methylene linked systems.31–35,38,79,99 Also, it has been re-
ported that methylthioacetate terminated tolane, an analogous
compound to our reference 5, formed well-ordered SAMs after
incubation in vacuum at room temperature for 10 days.100
In the case of SAM 3, the respective molecules are likely to
adsorb on the Au surface as indicated by an intense Si 2p
doublet and the shift of the surface component of the Au 4f
emission (compared to the clean Au substrate) in the HRXPS
spectra. The BE position of the Si 2p emission (101.9 eV)
suggests that not all the Si–CH3 bonds are broken upon the
adsorption. The above results are in accordance with recently
reported studies which show that molecules with the same
binding group, R–CRC–Si(CH3)3, form SAMs on Au sur-
faces.101,102 The reported STM images showed a densely
packed arrangement with an intermolecular distance equal
to the diameter of the trimethylsilyl group, Si–(CH3)3, which is
about 5.0 A.101,102 However, the nature of the bonding
between the trimethylsilyl group and Au surface is still not
well understood. It has been proposed that Si becomes penta-
valent and binds to the Au surface in an axial position.101–103
The bound Si should have a higher binding energy compared
to a clean Si sample (99.3 eV).71 The observed Si 2p peak at
101.9 eV in our HRXPS spectra is consistent with this model.
A very small, negative linear dichroism observed in the
NEXAFS spectra of SAM 3 suggests either a large molecular
inclination or/and a poorly defined monolayer consisting of
randomly oriented molecules (we favor the latter model). It is
reasonable to assume that the interaction between the tri-
methylsilyl and Au substrate is not strong enough to enable
the self-assembly of such large molecules, as our OPE–
porphyrin moieties, which makes them strongly inclined and
oriented randomly on the surface, resulting in a loosely packed
film.
Another possibility of the porphyrin disturbance is the
intermolecular interaction between these moieties and phenyl
rings in the OPE moiety. Due to the strong molecular inclina-
tion in SAMs 2 and 3, porphyrin moieties can move suffi-
ciently close to the phenyl rings in the OPE chains of the
neighbor molecules and build complexes, kept together by the
p–p interaction, as observed for porphyrin and phenyl rings
before.83,96–98 This interaction can affect the charge distribu-
tion at the nitrogen atoms, even though it is not clear whether
it can result in their equivalency. In particular, Sarno et al.
reported that free-base porphyrins exhibit two N 1s XPS peaks
regardless of any intermolecular interaction.83
Conclusions
Porphyrin-functionalized OPEs with the same molecular
structure but three different binding moieties, viz. acetyl-
protected sulfur with and without methylene linker and
trimethylsilylethynyl were synthesized and used for the pre-
paration of monomolecular films on polycrystalline Au(111)
substrate. The resulting films were characterized by synchro-
tron-based HRXPS and NEXAFS spectroscopy. We demon-
strated that molecule 1, containing the thiophenolate structure
(without the methylene linker between the sulfur and the OPE
moiety) forms the best quality SAMs of all three precursor
molecules. According to the HRXPS and NEXAFS data,
SAM 1 has a high packing density and high orientational
order with a small inclination angle (351) of the molecular
adsorbates. In contrast, molecule 2, containing the methylene
linker between the sulfur and the OPE moiety, which was
expected to form a highly ordered and densely packed SAMs
In the case of molecule 2, a methylene group was inserted in-
between the sulfur and OPE moiety with the purpose of
enabling the molecule to orient more upright on the surface
and thereby improve the packing density in the molecular
layer. Surprisingly, SAM 2 exhibits the opposite features such
as strongly inclined molecules and low packing density, which
correspond to a poor quality layer. Furthermore, we found
that even the non-substituted OPE molecule with methylene
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on Au, with an upright orientation of the individual constitu-
ents, shows the opposite result. Although it binds to the gold
surface through the thiolate anchor similarly to SAM 1, it
forms a low packing density film with poor orientational order
and large inclination of the molecular adsorbates. Also, even if
Si seems to bind to the gold surface, the trimethylsilyl-ethynyl
group gives a low-quality molecular layer comprised of in-
clined and randomly oriented species. Thus, among the three
porphyrin-functionalized OPEs with different anchor moieties,
only the anchor group 1 is suitable for the SAM formation,
even in the case of such a large tailgroup as porphyrin used in
this study, while anchor moieties 2 and 3 are less suitable for
the fabrication of high-quality SAMs.
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