Supplemental Material
On Sulfur Core Level Binding Energies in Thiol Self-Assembly and
Alternative Adsorption Sites: an Experimental and Theoretical Study
Juanjuan Jia†‡, Abdelkader Kara*, Luca Pasquali§,+,#, Azzedine Bendounan$, Fausto Sirotti$,
and Vladimir A. Esaulov†‡*+
†Institut des Sciences Moléculaires d’Orsay, Université-Paris Sud, 91405 Orsay, France
‡CNRS, UMR 8214, Institut des Sciences Moléculaires d’Orsay, Orsay ISMO, Bâtiment 351,
Université Paris Sud, 91405 Orsay, France
§Dipartimento di Ingegneria ‘E. Ferrari’, Università di Modena e Reggio Emilia, Via Vignolese
905, 41125 Modena, Italy
+IOM-CNR, s.s. 14, Km. 163.5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
#Department of Physics, University of Johannesburg, PO Box 524, Auckland Park, 2006, (South
Africa)
$Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48, F-91192 Gif-sur-Yvette
Cedex, France
The supporting information provides some details on the experimental and theoretical parts of
the paper.
1. Experimental Details
1.1 Peak Areas
The relative intensities of the different doublet components in the fitted spectra for the
room temperature (RT normal and grazing) and heated sample (60°)are given below. On the
heated sample the relative intensity of the 161eV to 162eV component decreases from 0.91 to
0.63 when the deposition is done on the heated sample.
Spectrum
RT –N fig 2a
RT-G fig 2b
60° fig 2c
161eV
0.74
0.37
0.475
162eV
0.82
0.53
0.75
163eV
1
1
1
163.6eV
0.53
0.47
0.49
1.2 X ray irradiation effects
X ray radiation can induce damage to SAMs and lead to modification of the S 2p spectra.
As noted in the main text of the paper, earlier studies show that in aromatic SAMs this leads to
cross linking in the SAM due to C-H bond cleavage but no atomic S is observed and spectral
shapes are not modified.
Here we investigated the effect of radiation by scan-by-scan measurements as a function of time
on the same sample spot and exploration of different sample regions. Fig S2a shows a color map
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in the scan-by-scan diagram of the intensities in the S2p spectrum where no significant changes
can be observed when going from the first to last scan. This is further illustrated by comparing
the spectra from the first and last scans in fig S2b.
Figure S2c shows measurements in two points on the sample and again statistically significant
major variations are not observed. Small variations may be expected because of inhomogeneities
in the sample on a macroscopic scale. The data has a poorer statistics since it corresponds to the
first few scans in these measurements.
From these measurements we conclude that the S2p spectra were not affected by X ray damage.
(a)
(b)
(c)
Figure S1 X ray damage assessment. (a) Intensity maps of the S 2p spectra taken scan by scan
(b) S2p spectra corresponding to first two and last two spectra in the 12 scans of the colour map.
(c) S2p spectra in two points of the surface.
1.3 NEXAFS measurements
NEXAFS measurements for the evaporated BDMT layer for different angles between the
surface plane and the electric field vector. The first clear narrow peak at 285.5 eV is associated
with the C=C/π* resonance involving the C atoms of the aromatic ring. Its intensity evolution as
a function of the angle show that either the molecules are strongly tilted away from the normal
or else there is a mixed phase of lying down and standing up molecules.
2
Figure S2. NEXAFS spectra for
some angles between the surface
plane and the electric field vector
as indicated.
2. Computational Details
In order to further understand the adsorption characteristics of BDMT molecules on
Au(111), we have performed a series of calculations of sulfur on Au(111) at different coverages
and adsorption sites.
2.1 Sulfur adsorption on Au(111): (√3x√3)
Let us start with the high coverage calculations using the (√3x√3) configuration.
Figure S3 shows the adsorption of a single S atom in the hollow (fcc), bridge and atop sites. The
adsorption energy of the atomic sulfur was found to be 4.51 eV, 4.09 eV and 3.13 eV for hollow,
bridge and atop sites, respectively. The corresponding S(2p) CLBEs are 164.06 eV, 163.65 eV
and 162.61 eV for hollow, bridge and atop sites, respectively. The trend in the CLBEs is
correlated to the binding energy of the sulfur atom on Au(111), which in turn is correlated to the
coordination of the S atom (3 for hollow, 2 for bridge and 1 for atop). The binding energy and
the core level energy are stronger for higher coordination. The change in CLBE when going from
coordination 3 (hollow) to coordination 2 (bridge) is -0.41 eV as compared to a change of -1.04
eV, when going from coordination 2 to coordination 1 (atop).
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Figure S3: Adsorption geometry of a S atom
adsorbed on Au(111) in the (√3x√3)
configuration with: a) hollow-fcc site, b)
bridge site c) atop site
2.2 Sulfur adsorption on Au(111): (√7x√7)
The second set of calculations is done using a (√7x√7) structure for Au(111) with 7
atoms per layer and 6 layers. We have performed calculations of the S(2p) core level energy for
one and two sulfur atoms in different situations. For a single S atom, we have explored the same
adsorption sites as for the (√3x√3), namely the hollow, bridge and atop sites. The corresponding
adsorption/CLB energies are: 4.62/164.35 eV, 4.14/164.07 eV and 3.19/162.68 eV for hollow,
bridge and atop sites, respectively. Note that the coverage changes from 1/3 to 1/7 when going
from (√3x√3) to (√7x√7) for a single adatom. As a consequence, the core level energy is changed
by +0.29 eV, +0.42 eV and +0.07 eV for hollow, bridge and atop sites respectively. The change
in the core level energy when, changing coordination, is -0.28 eV and -1.39 eV for the cases of
coordination 3 to 2 and coordination 2 to 1, respectively. We note that for both (√3x√3) and
(√7x√7) structures, the largest change in the core level energy occurs when the sulfur atom is
moved from a bridge to an atop site. Since the binding energy of a sulfur atom is more than 1 eV
lower than for the bridge and the hollow site, we conclude that the peak corresponding to an
adsorption at the atop site would be smaller than that corresponding to adsorption at the hollow
and bridge sites. The calculated energies are summarized in Table S1.
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TABLE S1: CLBEs and adsorption energies (in parenthesis) for a sulfur atom on
Au(111). The different configurations are discussed in the text. All energies are given in eV.
Atop
Bridge
Hollow
S/(√3x√3)
162.61(3.13) 163.65(4.09)
164.06(4.51)
S/(√7x√7)
162.68(3.19) 164.07(4.14)
164.35(4.62)
We have also performed calculations with two sulfur atoms on the (√7x√7) structure,
corresponding to a 2/7 coverage (close to the 1/3 of the (√3x√3) structure) (Table S2). When two
sulfur atoms are occupying neighboring hollow sites, the core level energy is 164.13 eV very
close to the 164.06 eV for a single sulfur atom on the (√3x√3) structure, and down from the
164.35 eV corresponding to a single sulfur atom on the (√7x√7) structure. When one sulfur atom
is occupying an fcc site, and another is occupying a neighboring hcp site (note that in this case,
the S-S bond is shorter than that when two S atoms occupy neighboring fcc sites), the core level
energy is 165.12 eV (for both S atoms), an almost 1 eV increase, pointing to the importance of
the S-S interactions at very short distances. For the situation where a S atom occupies an fcc site
and another occupies a neighboring bridge site, the core level energy is 164.66 eV for both sulfur
atoms. Finally, when a sulfur atom occupies an fcc site and another occupies a neighboring atop
site, the core level energies are 165.28 eV and 164.25 eV for fcc and atop respectively. In
summary, increasing the coverage of S atoms increases the core level energy. The same trend is
also found when the S-S distance is decreased.
TABLE S2: CLBEs for two sulfur atoms on (√7x√7)Au(111). The different
configurations are discussed in the text. All energies are given in eV.
Atop
Bridge
Hollow
(fcc+fcc)
-
-
164.13
(fcc+hcp)
-
-
165.12
(fcc+bridge)
-
164.66
164.66
(fcc+atop)
164.25
-
165.28
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The Au(111) real surface presents a large number of steps and kinks that are sources for
adatoms diffusing on the surface. Often, sulfur atoms adsorb on or near these adatoms and they
have been considered important in thiol self-assembly. It is hence important to study the effect of
adatoms on the core level energies of neighboring sulfur atoms. We have explored three
situations when two sulfur atoms are adsorbed “around” an adatom on the (√3x√3) structure. In
Figure S4, we show the top and side views of these three configurations. The calculated energies
are summarized in Table S3.
Figure S4. : Top and side view of two sulfur atoms (yellow) around a gold adatom
(grey) with, from left to right, the two sulfur atoms located: a) both on fcc sites, b) both on bridge
site and c) one on fcc and the other on hcp site.
For these configurations, the atomic binding energy of the pairs of sulfur atoms was
found to be 3.60 eV/S for the first configuration, where the two S atoms occupy neighboring fcc
site, followed by that where the S atoms are on bridge site (4.08 eV/S), with the most stable one
is when the S atoms are occupying neighboring fcc and hcp sites with a binding energy of 4.42
eV/S. Note that for this configuration, the two S atoms occupy positions with different heights.
Though atoms in this configuration and the one where S atoms occupy bridge sites are far from
the substrate, as compared to the first one with S atoms very close to the substrate, the binding
energy per sulfur atom for the former configurations is the highest, pointing to the fact that S
atoms bind more strongly to gold adatoms (with the lowest coordination) than to the gold surface
atoms. This strong binding to low coordinated surface atoms (adatoms in this case, with
coordination 3) affects also the core level energies. For the three cases at hand (2fcc, 2 bridge
and fcc-hcp) we find the corresponding S(2p) core level energy to be 163.96 eV, 164.08 eV and
(164.41 eV (fcc), 164.34 eV (hcp)), respectively. Note that the presence of an adatom affects the
2p core level energy for all configurations. The 163.96 eV corresponding to two fcc sites was
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164.06 for S at fcc site on the clean Au(111) surface, pointing to the role of defects in shifting
core level energies.
TABLE S3: CLBEs and adsorption energies (in parenthesis) for two sulfur atoms on
(√3x√3)Au(111) with the presence of an adatom on an fcc hollow site. The different
configurations are discussed in the text. All energies are given in eV.
Atop
Bridge
fcc+fcc
bridge+bridge
fcc+hcp
Hollow
163.96(3.60)
164.08(4.08)
164.41f+164.34h(4.42)
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