J. Phys. Chem. C 2009, 113, 19601–19608
19601
Scanning Tunneling Microscopic Observation of Adatom-Mediated Motifs on Gold-Thiol
Self-Assembled Monolayers at High Coverage
Yun Wang,† Qijin Chi,‡ Noel S. Hush,†,§ Jeffrey R. Reimers,*,† Jingdong Zhang,‡ and
Jens Ulstrup*,‡
School of Chemistry, The UniVersity of Sydney, Australia, Department of Chemistry and NanoDTU, Technical
UniVersity of Denmark, DK-2800 Lyngby, Denmark, and School of Molecular and Microbial Biosciences, The
UniVersity of Sydney, Australia
ReceiVed: July 2, 2009; ReVised Manuscript ReceiVed: September 9, 2009
Self-assembled monolayers (SAMs) formed by chemisorption of a branched-chain alkanethiol, 2-methyl-1propanethiol, on Au(111) surfaces were studied by in situ scanning tunneling microscopy (STM) under
electrochemical potential control and analyzed using extensive density functional theory (DFT) calculations.
The SAM forms in the unusual (8 × 3)-4 superlattice, producing a very complex STM image. Seventy
possible structures were considered for the SAM, with the calculated lowest-energy configuration in fact
predicting the details of the unusual observed STM image. The most stable structure involves two
R-S-Au-S-R adatom-mediated motifs per surface cell, with steric-induced variations in the adsorbate
alignment inducing the observed STM image contrasts. Observed pits covering 5.6 ( 0.5% of the SAM
surface are consistent with this structure. These results provide the missing link from the structural motifs
observed on surfaces at low coverage and on gold nanoparticles to the observed spectroscopic properties of
high-coverage SAMs formed by methanethiol. However, the significant role attributed to intermolecular steric
packing effects suggests a lack of generality for the adatom-mediated motif at high coverage.
1. Introduction
Self-assembled monolayers (SAMs) have been of great
interest both experimentally and theoretically as potential
applications range from molecular devices to biorecognition to
nanotechnology.1 Among all the SAMs studied, alkanethiol
monolayers on Au(111) are the most comprehensively investigated due to their strong S-Au interaction and ease of
production.2,3 Although numerous studies on thiol-gold SAMs
have been performed, some fundamental details of electronic
structures and formation processes remain to be clarified, such
as the precise atomic-level details of structures adopted at the
thiol-gold interface and the factors that control them, factors
including both the headgroup interaction and the role of the
aliphatic spacer.3
The sulfur-gold (S-Au) junctions that connect the substrate
surface to the organic molecules are among the most important
aspects of the SAM, with, e.g., the conductance of alkanethiol
molecules sandwiched between two gold electrodes depending
strongly on the structure.4 While thiol-gold SAMs are usually
produced by exposing gold surfaces to alkanethiol or dialkanedisulfide solutions, many studies have demonstrated that
the active adsorbates are in fact alkanethiyl radicals formed
following loss of the thiol protons or cleavage of disulfide
bonds.5-8 The purely physical interactions between alkanethiol
molecules and the gold surface are too weak to form stable
monolayers,9,10 while the gold surface possesses insufficient
reducing power to drive thiolate formation.11
* To whom correspondence should be addressed. E-mail: [email protected]
(J.U.); [email protected] (J.R.R.).
†
School of Chemistry, The University of Sydney.
‡
Technical University of Denmark.
§
School of Molecular and Microbial Biosciences, The University of
Sydney.
Early insight into the nature of the interface between Au(111)
and chemisorbed thiol monolayers came from theoretical studies
of binding to regular bulk-like (111) surfaces; these suggest that
sulfur atoms preferentially locate in the region between the
classic fcc and bridge adsorption sites.5,9 However, preferential
adsorption to irregular surfaces containing vacancies and/or
adatoms has also been predicted.12-17 Much progress has been
made experimentally in recent years concerning the structure
of SAMs made from alkanethiols. Groundbreaking detailed
structural studies on methanethiol SAMs using normal incidence
X-ray standing wave (NIXSW) analysis by Roper et al., as well
as the scanned-energy and scanned-angle S 2p photoelectron
diffraction experiments by Kondoh et al., show that sulfur atoms
occupy atop sites,18,19 but insufficient information was obtained
to fully identify the interface structure. Some studies proposed
that sulfur atoms may be associated with gold adatoms,12-14,20,21
and later this motif was observed in X-ray structures of gold
nanoparticles.22 A recent scanning tunneling microscopy (STM)
study on thiol-gold SAMs before and after reaction with atomic
hydrogen by Kautz et al. also demonstrated that there is one
additional gold adatom for every two alkanethiol adsorbate
molecules,23 consistent with the adatom-mediated model, and
it has also been shown that these adatoms can be liberated to
form islands.21 The success of these studies raises the possibility
that the adatom-mediated motif is produced in general during
SAM formation between gold and alkanethiols. A very similar
adatom-mediated motif has been observed for SAMs formed
from the bidentate ligand 1,10-phenanthroline,24 but small
changes in conditions for these SAMs lead to monolayers above
the regular flat surface, and the structure is strongly coverage
dependent. Direct observation of the adatom-mediated motif
within SAMs formed from thiols has been achieved only at low
thiol coverage,13 leaving partially answered the important
question of the nature of the interface on surfaces at high
10.1021/jp906216k CCC: $40.75  2009 American Chemical Society
Published on Web 10/12/2009
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J. Phys. Chem. C, Vol. 113, No. 45, 2009
coverage and hence the interconnection between the lowcoverage, high-coverage, and nanoparticle-coverage scenarios.
The gross structural properties at high coverage of gold SAMs
formed using linear alkanethiols are well known, these forming
in the (3 × 23)-4 superlattice (also termed the c(4 × 2)
superlattice), The (3 × 23)-4 superlattice means that there
are four adsorbates in each surface cell, with lattice lengths of
3 or 23 times to the shortest Au-Au distance in bulk,
respectively. Wang et al. proposed that the four adsorbate
molecules in this unit cell attach with two connected in an
adatom-mediated motif while two more attach directly to the
surface gold layer.16 Alternatively, Grönbeck et al. propose that
adatom-bound motifs alone can account for the structure,
possibly with or without local surface gold vacancies.17 Finally,
Cossaro et al. suggested that the structure of the c(4 × 2)
superlattice is quite complex involving directly attached adsorbate molecules, local vacancies, and one-dimensional adatommediated -(S-Au)n- zigzag chains.15 In principle, the observed
density of pits on the gold surface3 provides significant
information that could be used to assess these differing models,
but their concentration is difficult to quantify. Also, while
observed STM images do provide critical information, their
interpretation is not always unambiguous. Many specific questions thus remain unanswered, and new probes are required.
Progress has been made by considering the analogous
properties of branched-chain alkanethiol monolayers. Indeed,
a recent scanning tunnelling microscopy (STM) study found
that a branched alkanethiol chemisorbate on the Au(111) surface
formed quite different structural patterns compared to those for
linear alkanethiols.25 In the report by Chi et al., the selfassembled monolayer formed from 2-methyl-2-propanethiol is
found to adopt the (27 × 7)R19.1°-2 lattice, with two
inequivalent radicals in a (27 × 7)R19.1° surface cell.11,25
This structure is strikingly different from the (3 × 23)-4 and
similar (e.g., (3 × 3)R30°) structures found for most SAMs
formed from straight-chain alkanethiols.3 In particular, there is
no surface pitting involved in the SAM formation, and DFT
calculations indicate that no adatom-mediated motifs are
involved in the binding at all, with the appearance of the unusual
double-occupied surface cell attributed to steric repulsions
between the aliphatic chains.11 Hence, small changes in the steric
interactions between adsorbate molecules can control SAM
structure.
In this work, we employ electrochemical STM technology
(in situ STM) and plane-wave-based density-functional theory
(DFT) to investigate the SAMs formed from a systematically
chosen molecule, 2-methyl-1-propanethiol, on Au(111). This
isomer of 2-methyl-2-propanethiol contains a longer chain
section and a secondary carbon rather than the fully branched
tertiary isomer studied previously and is intermediary with
respect to the well-studied straight-chain alkanethiols. This
modification illustrates the extent to which further interchain
steric interactions could modify the SAM structure.
2. Methods
2.1. Experimental Measurements. 2-Methyl-1-propanethiol
((CH3)2CHCH2SH, 98%) was obtained from Sigma. The NH4Ac
buffer (5 mM, pH 4.6) was prepared from 5 M stock solution
(Fluka, ultrapure) and solution pH was adjusted by acetic acid
(Aldrich, 99.7%). NaOH (0.1 or 0.5 M) solutions were prepared
from 30% stock solution (Merck, ultrapure) and used for
voltammetric measurements of reductive desorption. Absolute
ethanol (ultrapure) was from Merck. Milli-Q purified water (18.2
MΩ cm) was used throughout. The Au(111) electrodes used in
Wang et al.
both electrochemical and STM measurements were homemade
and pretreated before use as described.23
The SAMs were prepared by soaking freshly quenched
Au(111) electrodes in ethanol solution containing 2-methyl-1propanethiol (1-5 mM) overnight, followed by thorough rinsing
with pure ethanol and Milli-Q water before measurements. To
observe the dynamic processes of the SAM formation, 2-methyl1-propanethiol was directly added to the electrochemical STM
cell. The details were similar to that for 1-propanethiol.24
Electrochemical measurements were performed using an Autolab system (Eco Chemie, Netherlands), with a three-electrode
system containing a Pt counter electrode, a reversible hydrogen
electrode (RHE) as the reference electrode, and an Au(111)
working electrode. STM imaging was carried out in the
electrochemical in situ mode using a PicoSPM system (Molecular Imaging Co.) equipped with a bipotentiostat for potential
control of both the substrate and tip. The STM tips were
prepared from Pt/Ir (80:20) wire by electrochemical etching and
covered with Apiezon wax to reduce or eliminate Faradaic
currents.
2.2. Computational Modeling. All the computations were
conducted using periodic density functional theory (DFT)
methods with the Vienna ab initio simulation package (VASP).26
For the electron-electron exchange and correlation interactions,
the functional of Perdew and Wang (PW91),27 a form of the
general gradient approximation (GGA), was used throughout.
Electron-ion interactions were described using the optimized
relativistic Vanderbilt-type ultrasoft pseudopotentials.28,29 A
plane-wave basis set was employed to expand the smooth part
of the wave functions with a kinetic energy cutoff of 300 eV,
required to properly describe the carbon atoms. VASP utilized
an iterative scheme to solve self-consistently the Kohn-Sham
equations using residuum-minimization techniques. The geometric structure was optimized with the conjugated-gradient
method. The broadening approach proposed by Methfessel and
Paxton with an electronic temperature of 0.2 eV was used for
the calculation of orbital occupancies.
The Au(111) surface was modeled by a supercell consisting
of a four-layer slab separated by a vacuum region equivalent to
a six-layer thickness. When the geometry was optimized, the
top two atomic layers and the adsorbates were allowed to relax,
while the lower two layers were fixed at the ideal bulk-like
position (using the lattice constant a0 ) 4.18 Å obtained at the
same level of theory30). It has been demonstrated that the fourlayer slab is thick enough to obtain reliable results.11 The
methods proposed by Neugebauer and Makov et al. were used
to correct the error for the surface with a large dipole
moment,31,32 when the energy converges slowly with respect to
the z axis of the supercell. All the calculations of the alkanethiyl/
Au(111) systems were performed by ignoring spin polarization
as studies33 on similar systems indicate that the adsorbatesubstrate interaction is strong and the effects of spin polarization
are small. The Brillouin-zone integrations were performed using
Monkhorst-Pack grids of special points, with (1 × 6 × 1) and
(4 × 4 × 1) k-points meshes used for the (8 × 3) and (3 ×
23) surface cells, respectively. These k-points meshes have
been demonstrated to be sufficient for our purposes.33 STM
images were simulated using the Tersoff-Hamann approximation34 with a bias voltage of 1.0 V.
While the clean Au(111) surface undergoes a (22 × 3)
reconstruction,35,36 thiol chemisorption lifts the reconstruction,3,12
and in these equilibrium studies binding only to the unreconstructed surface is considered. Even though experimental results
for this system have been obtained in aqueous solution, we
Adatom-Mediated Motifs on Gold-Thiol SAMs
Figure 1. In situ STM images of the 2-methyl-1-propanethiol SAM
assembled on a Au(111) surface obtained in 5 mM NH4Ac (pH 4.6),
with the substrate lattice vectors (black) and (3 × 23)-4 substrate
lattice (blue) indicated. (a) 100 nm × 100 nm, (b) 36 nm × 36 nm, (c)
7.3 nm × 7.3 nm; the blue rectangle also indicates the part of the image
that is reproduced in Figure 6. STM imaging conditions: tunnel current
(It) 0.25 nA, bias voltage (Vb) -0.60 V, and substrate potential (Ew)
0.26 V (vs SCE).
model only monolayers under vacuum conditions. Since the
alkanethiol tail groups are hydrophobic, solvent interactions are
most likely of only minor importance, in contrast to the SAMs
containing ionic tail groups (such as cysteamine) in which
solvation of the charged tail groups is critical.37 The thiyl rather
than thiolate nature of the headgroup means that the actual
surface charge transfer is small, and so once again solvent effects
are not of great significance.11
3. Results and Discussion
3.1. Experimental Observations. In situ STM images
observed over different scanned areas are shown in Figure 1.
The surface unit cell is rectangular with dimensions of 23.3 Å
× 4.8 Å (Figure 1c). Observation of the reconstruction lines of
the bare single-crystal gold surface before addition of the
J. Phys. Chem. C, Vol. 113, No. 45, 2009 19603
adsorbate allows the absolute orientation of the surface-cell
vectors to be determined, indicating that the SAM forms in the
(8 × 3) lattice and contains 16 gold atoms per regular surface
layer in the unit cell. Electrochemical measurements of the
surface coverage using reductive desorption (Supporting Information) give a density of 5.9 ( 0.4 × 10-10 mol cm-2, indicating
a surface coverage (denoted in the number of adsorbate
molecules per Au(111) regular-surface gold atom) of Θ ) 0.26
( 0.02 ∼ 1/4. As expected, this coverage is intermediate
between those found for the 2-methyl-2-propanethiol and
1-propanethiol SAMs of 0.14 and 0.33, respectively. Four
adsorbate molecules thus occupy each surface unit cell, possibly
with four different internal structures. Indeed, four regions in
each unit cell are observed in the in situ STM image (Figure
1c) with strongly varying contrast. Some of these features are
widely spaced while others are spaced less than the minimumpossible S-S intra-adsorbate distance, suggesting that each
adsorbate can produce more than one STM feature. Hence, very
many adsorbate configurations could, in principle, generate this
image. The most striking features of the image are two bright
spots very close to each other and two dimer spots separated
by a large dark region; also, the spots are not collinear.
3.2. Computational Modeling of the Monolayer Structures. Full details of all 70 computed structures for Au(111)
SAMs made from 2-methyl-1-propanethiol are provided in the
Supporting Information, including calculated STM images for
11 structures. Owing to the multitude of possible structures,
we perform systematic investigations, starting with the nature
of adsorption of noninteracting or partially interacting molecules
on the flat surface (i.e., low to medium coverage). Then we
increase the coverage and investigate SAM formation on the
regular flat surface Au(111). Structures are then considered in
which the gold atoms can rearrange within the unit cell, forming
adatoms and vacancies, but transport of gold atoms to or from
the unit cell is not allowed. Finally, the number of gold atoms
in each surface unit cell is varied, allowing for gold adatoms
above regular surfaces and possible associated pit formation.
In this way, a range of low-energy structures can be identified
and their suitability is further characterized in terms of their
relative energy and ensuing STM images.
3.2.1. General Features of Chemisorptions on a Flat
Au(111) Surface with Low to Medium CoWerage. On a regular
Au(111) surface, there are four kinds of high-symmetry adsorption sites: atop, bridge, fcc, and hcp sites. Previous computational studies have demonstrated that sulfur atoms of chemisorbed alkanethiols prefer low-symmetry locations either between
the bridge and fcc sites, termed FB, or between the bridge and
hcp sites, termed HB.11 Hence, we calculate the adsorption
energy at atop, HB, and FB sites only. Initially we consider
adsorbates with similar alkane-chain conformations at sufficiently low coverage, Θ ) 1/12 ) 0.083, to avoid intermolecular steric interactions on the (3 × 23) supersurface lattice.
For comparison we also consider an alternate lattice, (8 × 3),
that gives a slightly lower coverage of Θ ) 1/16 but, because
of its short unit-cell length in the [112j] direction, does actually
display significant intermolecular steric interactions.
The energy of adsorption (∆E) is determined from
∆E ) Etot - Esurf - Ead
(1)
where Etot and Esurf are the optimized total energies of the
systems with and without adsorbate, respectively, and Ead
represents the energy of the optimized isolated 2-methyl-1propanethiyl radical calculated allowing for spin polarization.
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J. Phys. Chem. C, Vol. 113, No. 45, 2009
Wang et al.
Figure 2. Elevation view of four DFT-optimized configurations A-D
for the 2-methyl-1-propanethiyl radical adsorbed on the regular Au(111)
surface obtained at the low coverage of Θ ) 0.083 using the (3 ×
23) substrate lattice: gold, Au; green, S; gray, C; white, H.
TABLE 1: Adsorption Energies ∆E and Geometrical
Properties for Single 2-Methyl-1-propanethiyl Radicals
Adsorbed on (3 × 23)R30o or (8 × 3)R30o Au(111)
Supersurface Lattices in Different Configurations (see
Figure 2)a
surface cell structure ∆E (eV)
dS-Au (Å)
(3 × 23)
2.46,
2.47,
2.45,
2.47,
2.47,
2.46,
2.48,
2.47,
(8 × 3)
A
B
C
D
A
B
C
D
-1.70
-1.65
-1.71
-1.71
-1.62
-1.58
-1.78
-1.72
2.59
2.52
2.56
2.53
2.59
2.56
2.58
2.62
dS-C (Å) θ (degree)
1.87
1.86
1.86
1.87
1.88
1.86
1.87
1.87
21
7
9
21
23
10
7
19
a
dS-Au is the shortest distance from a sulfur atom to the surface
gold atom, ds-c is the C-S bond length, and θ is the tilt angle of
S-C bond to the surface normal.
The most stable site is predicted to be the FB site, this being
0.16 eV more stable than the HB site and 0.34 eV more stable
than the atop site, similar to the results obtained in previous
theoretical studies of chemisorbed alkanethiol monolayers on
regular Au(111) surfaces.9,12,38
A range of possible conformations are available at each
adsorption site of the flat Au(111) surface for the adsorbate
molecules, originating from the degrees of freedom afforded
by the rotation and tilt angles of the aliphatic chain. However,
the energy differences associated with these conformational
variations are calculated to be much smaller than those associated with the variations in the surface binding sites. Four lowenergy structures, A-D, are shown in Figure 2 above the FB
site on the (3 × 23) and (8 × 3) surface cells; their energetic
and structural properties are listed in Table 1, while full details
are provided in the Supporting Information. For the (3 × 23)
surface cell, structures A, C, and D differ in energy by only
0.01 eV at ∆E ≈ -1.71 eV per adsorbate molecule, while
structure B is just 0.06 eV (2 kT at room temperature) less stable.
Hence, we see that at low coverage the substrate surface to
headgroup interaction does not fully govern the conformations
of the adsorbate molecules on the flat surface, and so other
factors such as intermolecular interactions and solvation effects
should affect the SAM conformations more significantly. The
results provided for the lower-coverage (3 × 23) surface cell
confirm this analysis, with configurations C and D showing
enhanced binding (∆E ) -1.78 eV per adsorbate molecule for
C and -1.72 eV for D) owing to improved substrate relaxation.
Configurations A and B are destabilized by steric interactions
in the short [112j] direction (∆E ) -1.62 eV per adsorbate
molecule for A and -1.58 eV for B). For 2-methyl-1propanethiol chemisorbates, steric interactions also destabilize
the (3 × 23)-4 and similar lattices in which the SAMs of
most straight-chain alkanethiols form, with the calculated energy
of adsorption on e.g. the (3 × 3)R30° lattice being calculated
to be just -1.32 eV. These results show the importance of
substrate and steric interactions at low to medium coverage,
effects that are expected to become more significant when four
adsorbate molecules are crammed into the (8 × 3) surface
cell at the high coverage (Θ ) 0.25) actually observed for stable
SAMs.
Considering the calculated structural properties in detail
(Table 1), we see that those for 2-methyl-1-propanethiol
chemisorbed monolayers directly parallel those for related
molecules such as methanethiol and 2-methyl-2-propanethiol.11
After adsorption, the Au-Au bond lengths at the adsorption
site increase from their optimized bulk value of 2.96 Å to over
3.50 Å while the calculated S-Au bond lengths of 2.47 Å also
indicate a strong metal-molecule interaction. Applying the
Bader method which decomposes the space charge density into
atomic contributions to our system,39,40 it is found that only 0.07e
is transferred from the substrate to the adsorbate when 2-methyl1-propanethiol chemisorbs at the FB site, where e is the
magnitude of the charge on the electron. Changes of ca. 0.2e
have been found in experimental studies41-43 of thiol chemisorption. While in general the significant band lineup error that
occurs in DFT for molecular adsorbates on metal surfaces results
in an underestimation of calculated charge flows,33 the results
again clearly indicate that ionic thiolate states are not involved
in the chemisorption. Thus, the adsorbate forms as a thiyl species
identified as the 2-methyl-1-propanethiyl radical.
3.2.2. High-CoWerage Adsorption on the Flat Au(111)
Surface. Here we consider the possibility that dense SAMs made
from 2-methyl-1-propanethiol form on the flat Au(111) surface,
as has been observed by STM for related SAMs.2 The most
significant aspect of the observed STM images of 2-methyl-1propanethiol SAMs (Figure 1) is the starkly different separations
and contrasts of the features. A similar scenario was also found
for chemisorbed monolayers of 2-methyl-2-propanethiol on
Au(111), a SAM for which more than one molecule per surface
cell was observed to form on the flat Au(111) surface.25 For
that molecule, variations in the tilt angles of S-C bonds on the
surface were found to account for the STM-image topology;11
our initial computational studies of the high-coverage monolayer
test the hypothesis that similar variations also account for the
observed STM images for 2-methyl-1-propanethiol SAMs. A
wide variety of DFT geometry optimizations were performed
starting with conformations similar to C or D from Figure 2,
the only conformations shown feasible in the low-density studies
on the observed (8 × 3) lattice; full details of the results are
provided in the Supporting Information. All of the stable
structures found are of similar energy, with ∆E varying by less
than 0.05 eV. However, the energy of adsorption per radical is
-1.46 eV for the most stable case, this being 0.32 eV less stable
than that at the lower coverage reported in Table 1. The
repulsion between the adsorbates at high coverage is therefore
rather strong and could be manifest through either direct steric
interactions or significant distortions induced in the substrate
lattice.
Adatom-Mediated Motifs on Gold-Thiol SAMs
Figure 3. DFT-optimized structure for the SAM of 2-methyl-1propanethiol chemisorbed to the regular Au(111) surface (configuration
b from Figure 4) at the observed coverage of Θ ) 0.25 in the (8 ×
3)-4 substrate lattice. Top, elevation view highlighting the configuration (see Figure 2) of each adsorbate molecule (gold, Au; green, S;
gray, C; white, H); middle, plan view with vectors indicating the regular
Au(111) surface with the location of the adsorbate S atoms (green)
superimposed; bottom, simulated STM image.
The simulated STM image of the most stable configuration
found is shown in Figure 3; of its four adsorbate molecules,
one adopts configuration C while the others adopt configuration
D. All the bright spots in the calculated STM image originate
from the vertically aligned terminal methyl groups; thermally
induced changes in the conformational angles will induce some
variation in the calculated image, but the main features are
expected to be preserved. Since the tilt angles of the S-C bond
are different, the heights of the terminal methyl groups vary
(see Figure 3), and therefore, the STM image contrast is
modulated. However, the simulated STM image is significantly
different from the observed in situ image shown in Figure 1c,
with just three resolved features per cell and no large intense
closely spaced image pair. Furthermore, owing to the steric
interactions associated with the dimensions of the branched
chain, no alternate configuration can be envisaged in which
vertically aligned chains from two molecules are separated by
the observed short distance between the spots of the bright pair.
Thus, the hypothesis that four adsorbate molecules assemble
on a regular Au(111) surface, akin to the binding observed
following chemisorptions of the isomer 2-methyl-2-propanethiol,
cannot be supported.
3.2.3. High-CoWerage Adsorption with Adatom-MediatedBonding Motifs aboWe the Au(111) Surface. Recently, several
groups have found, both experimentally and theoretically, that
the chemisorption of linear alkanethiols occurs at supersurface
gold adatoms12-17 that may or may not be associated with
surface-layer vacancies; in this binding motif, two adsorbate
molecules are always attached to one gold adatom. As four
adsorbate chains occupy the unit cell for 2-methyl-1-propanethiol SAMs, either zero, one, or two of these motifs may
be formed, and as there exists many sites for each adatom and
possible vacancy, a large number of configurations are possible.
As a starting point we consider only the structures in which
the number of adatoms equals the number of vacancies; for
these structures, the number of gold atoms per simulation cell
is the same as that for adsorption on the flat Au(111) surface
considered previously and so the results may be directly
compared. We have examined 18 possible new configurations,
J. Phys. Chem. C, Vol. 113, No. 45, 2009 19605
Figure 4. DFT-optimized structures and relative energies for the SAM
of 2-methyl-1-propanethiol chemisorbed to the regular and irregular
Au(111) surfaces at the observed coverage of Θ ) 0.25 in the (8 ×
3)-4 substrate lattice. The lines indicate interatomic vectors on the
clean (111) surface, while white circles indicate surface vacancies, gold
indicate supersurface gold adatoms, and green indicates the S atoms
of the adsorbate molecules. For configuration j, some adsorbate features
are reproduced in the neighboring unit cell to accentuate the linearity
of the structure; only the lower-energy all-trans adatom-mediated
structures are shown. All energies are expressed with respect to that
for configuration a (total interaction energy ∆E ) -7.15 eV per cell).
optimizing the energy of each structure using DFT; the results
for 10 illustrative examples, named configurations a-j, are
sketched in Figure 4, while all results are reported in the
Supporting Information. Configuration a is the lowest-energy
structure found, and the energies for the remaining (8 × 3)-4
lattices are expressed relative to its energy. This configuration
has two adatom motifs and therefore two vacancies that are
found to be located nearly underneath the adatoms. Some
variants of this structure are shown in configurations d-i
containing different locations for the adatom sites and different
arrangements of the vacancies. As some of these configurations
are less than 0.3 eV higher in energy than configuration a, the
adsorbed molecules and the vacancies may be quite mobile on
the surface.
The lowest energy configuration involving no adatoms or
vacancies (previously detailed in Figure 3) is also sketched in
Figure 4 for comparison with configuration b. Its average energy
of adsorption per adsorbed molecule is -1.46 eV, much less
than the single configuration energies reported in Table 1, owing
to the significant steric interactions between the four adsorbate
molecules. This unit-cell configuration is 1.33 eV per cell less
stable than configuration a, indicating that adsorption on a flat
Au(111) surface will spontaneously induce rearrangement of
the surface gold atoms. Much of the strain energy apparent in
b is relieved through the formation of just a single adatomvacancy pair in the surface cell, with configuration c being only
0.24 eV per cell less stable than the double adatom-vacancy
structure, configuration a. The possibility that mixed configurations of this type are also important for linear alkanethiol SAMs
has been raised by Wang et al.16
Recently, Cossaro et al. proposed that one-dimensional
-S-Au-S-Au-S- chains form the SAMs of long-chain
linear alkanethiol SAMs on gold with the (3 × 23) surface
cell.15 This precise structure is not feasible on the (8 × 3)
surface cell owing to the considerably different unit-cell
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J. Phys. Chem. C, Vol. 113, No. 45, 2009
Wang et al.
Figure 5. Atomic structures for two adatom-mediated-bonding motifs adsorbed on flat Au(111) in the configuration a from Figure 4: all-trans
isomer; right, all-cis isomer.
parameters, but a somewhat analogous structure is reported as
configuration j. This configuration involves three adatom/
vacancy pairs per unit cell but is 1.44 eV per cell less stable
than configuration a and hence should not be favored within
2-methyl-1-propanethiol SAMs.
In general, an important feature of the adatom-bound
adsorbate structure is whether the S-C bonds are located cis
or trans with respect to each other. In a previous study of this
adatom motif within methanethiol SAMs, the cis structure has
been found to have the lowest energy.17 However, in the present
case all structures reported in Figure 4 have lower-energy trans
configurations; Figure 5 compares the atomic positions and
relative energies for the cis and trans variants of configuration
a. The alternative result for 2-methyl-1-propanethiyl adsorbate
could arise from the different interadduct steric interactions; the
trans configuration was also observed in the adatom-mediated
motifs in a p-mercaptobenzoic acid (p-MBA)-protected gold
nanoparticle22 and hence may in general be preferred for bulkier
adsorbate molecules.
The adatom-mediated structures have their Au-S bonds
orientated nearly parallel to the surface, with the S-adatom-S
angle being 173° for the lowest-energy structure, configuration
a. However, the C-S-Au angles show significant variations
between 109° and 116° for configuration a. Hence the C-S
vectors rise at 52°-62° to the surface normal, quite different
to the nearly parallel and nearly vertical orientations apparent
in Figure 2 for molecules bound directly to Au(111). The
variation in the angles is caused by the steric interactions which
force the two adatom-mediated motifs to adopt slightly different
structures, giving rise to a variation in height of terminal carbon
atoms of 0.25 Å. Figure 6 shows a simulated STM image for
this structure where it is compared to an extract of the observed
in situ STM image from Figure 1c: all major qualitative features
of the experimental image are reproduced. Also shown in Figure
6 are side and top views of configuration a, with the adsorbate
chains numbered i-iv. This reveals that all of the bright spots
originate from the terminal methyl groups, with the major factor
controlling their relative brightness being the height of the
carbon atoms above the surface. As each adsorbed molecule
orients with two methyl groups upward, a total of eight spots
of this type could in principle be found in the simulated STM
images. The large central bright region of the computed STM
image is assigned to the two methyl groups from molecule (ii),
with the close proximity of the two groups emphasizing their
significance. Two nearby resolved features arise from methyl
groups of molecules (iii) and (i), while a further weak feature
arises from molecule (iv). Together, these results account for
all of the features in the observed in situ STM image.
In addition, STM images for five alternative configurations
have been simulated. Of these only the image for configuration
c is in realistic agreement with the observed STM image (see
the Supporting Information). Further, as the relative energy of
Figure 6. DFT-optimized structures (top panels, configuration a plan
and elevation) and STM images (lower panels, configurations a, a′,
and a′′ and experiment extracted from Figure 1c) for the SAM of
2-methyl-1-propanethiol chemisorbed to the regular and irregular
Au(111) surfaces at the observed coverage of Θ ) 0.25 in the (8 ×
3)-4 substrate lattice. The lines on the plan view indicate interatomic
vectors on the clean (111) surface while white circles indicate surface
vacancies, gold indicate supersurface gold adatoms, and green indicates
the S atoms of the adsorbate molecules. Configurations a′ and a′′ differ
from a only in that either one (a′) or two (a′′) of the surface gold
vacancies are filled from an external atom source.
this structure is only 0.24 eV more than that for configuration
a, it warrants further consideration. The lowest-energy alternative
configuration, configuration f generates a much poorer STM
image but is also retained at this stage as a possible option. All
the structures considered so far contain the same number of
gold atoms in each unit cell as does a flat Au(111) surface.
However, Figure 4 indicates that the gold atoms may be quite
mobile, requiring further refinements to be made to the
optimized structures.
Indeed, the clean gold surface to which the adsorbate
molecules initially bind is not flat Au(111) but instead is a
reconstructed surface in which 46 surface gold atoms (in two
Adatom-Mediated Motifs on Gold-Thiol SAMs
rows of 23 atoms along the [110] direction) occupy only 44
(rather than 46) bulk-like positions.36,44 After formation of the
SAM, this reconstruction is lifted, releasing 4.5% of the atoms
in a gold layer. These excess gold atoms must either be
consumed as adatoms or else merge generating new surface
terraces. While terrace growth is difficult to positively identify,
the opposing process of pit formation is often observed as a
common feature in many thiol-gold SAMs including the present
case.3 Specifically, the coverage of pits on the surface for the
SAMs made from 2-methyl-1-propanethiol is estimated to be
5.6% ( 0.5% of the total surface. This value is slightly larger
than that observed for linear 1-propanethiol SAMs, 4.0% (
0.4%.35 If the gold atoms liberated by lifting of the reconstruction combine with those atoms mined from the pits, then the
number of total gold atoms available as adatoms above a
vacancy-free surface would increase to 10.1% ( 0.5% for the
2-methyl-1-propanethiol case, close to the adatom coverage of
configuration a, 12.5%. In addition, gold atoms mined from
terrace edges could also form adatoms, but this effect is difficult
to quantify.
We have also calculated an additional 43 configurations
containing either one or no vacancies in the topmost gold layer.
They include all possible variants of configurations a, c, and f,
i.e., the configurations previously identified as the ones of
greatest interest. All results are given in the Supporting
Information, while the four lowest-energy structures found are
shown in Figure 4; these four structures are those obtained by
adding one Au atom (configuration a′) or two Au atoms
(configuration a′′) to configuration a, one Au atom (configuration
c′) to configuration c, and two Au atoms (configuration f′′) to
configuration f. In these calculations, the average energy of a
surface gold atom taken from a pit is estimated as one-quarter
of the energy difference between a flat surface and that obtained
by removing two adjacent rows (4 atoms) from the original 8
rows in the (8 × 3) surface layer, as described in the
Supporting Information; the cost is expected to be slightly less
if the filling atom originates from the lifting of the gold
reconstruction rather than from surface mining. Filling the vacant
atoms is thus found to be an exothermic process, with
configurations a′′ being 0.10 eV, more stable than configuration
a. Shown in Figure 6 are the simulated STM images for
configurations a′ and a′′, the images that are almost identical to
that for configuration a considered earlier. STM images are thus
insensitive to local pitting under the SAM, and the predicted
image for configuration a′′ is in excellent agreement with
experimental observation. The calculated image for the nextlowest energy structure, configuration f′′, is in poor agreement
with the observed image (see Supporting Information).
4. Conclusions
The structure of the SAM formed by chemisorption of
2-methyl-1-propanethiol on the Au(111) surface has been
investigated comprehensively both by electrochemical in situ
STM measurements and by a priori DFT calculations. In
addition to providing visualization of the SAM at the singlemolecule level in situ, STM establishes a means for selection
from among the large number of surface-molecule and intermolecular adsorbate interactions conceived by the computations.
This complementary approach resembles the complementary
information offered jointly by in situ STM and electrochemistry
at single-crystal electrode surfaces, with, for example, the
adsorbate coverage measured by electrochemical reductive
desorption significantly supporting the interpretation of the in
situ STM image.37,45
J. Phys. Chem. C, Vol. 113, No. 45, 2009 19607
For 2-methyl-1-propanethiol on the Au(111) surface, an
adatom-mediated binding motif is deduced. This adatommediated motif is now well established for SAMs at low
coverage12-14 and for nanoparticles,22 but this is in fact the first
positive identification of such a structure on a flat surface at
high coverage. As key aspects of this structure have also been
observed for methanethiol SAMs,18,19 the adatom motif may
indeed be common. However, our results also show clearly that
a wide range of alternate structures are possible in the sense of
showing only very small energy differences. Steric interactions
between molecules and adsorbate relaxation thus provide
significant influences. STM cannot resolve variations of the basic
motif involving surface-layer vacancies, but the density of
surface pits can be mapped through careful measurements. This
may also call for reconsideration of the effects of the solvent
environment even though these effects are likely to be small
for the alkanethiol systems. In any case, we see that the
monolayer structure adopts the common adatom-mediated motif
not because of some inherent stability but rather as a result of
competition between many opposing forces.
Taken together with the comprehensive STM/DFT/electrochemical approach used in our previous studies,25,35,37,45-47 a
highly diverse pattern in both Au-S binding modes and surface
packing of short linear and branched similar-size alkanethiols
actually emerges. The straight-chain alkanethiol, 1-propanethiol,
was shown to bind on a flat Au(111)-electrode surface and pack
into a (3 × 3)R30° surface lattice. Extensive Au-atom
surface dynamics and pitting accompanies this surface adlayer
formation.35 The fully branched 2-methyl-2-propanethiol (tertbutanethiol) instead adopt a strikingly different (27 ×
7)R19.1° surface cell with no surface pitting. Finally, 2-methyl-1-propanethiol (secondary butanethiol) addressed here adopts
a third thiol binding and packing mode at high coverage, i.e., a
(8 × 3)-4 surface lattice with two gold-atom-mediated surface
entities per unit cell as a dominating binding motif. Chemically
very similar adsorbates can thus produce strikingly different
SAMs.
Acknowledgment. We thank the Australian Research Council
for funding this work under the Discovery Grant program. The
use of the supercomputer facilities at the Australia Partnership
for Advanced Computing (APAC) is gratefully acknowledged.
Financial support from the Danish Research Council for
Technology and Production Sciences (Contract No. 274-070272) and the NABIIT programme of the Danish Strategic
Research Council (Contract No. 2106-04-0039) is acknowledged.
Supporting Information Available: Optimized coordinates
for 70 SAMs, 4 substrate lattices, the adsorbate radical along
with 11 simulated STM images of SMAs, and a linear
voltammogram to show reductive desorption of 2-methyl-1propanethiol. This material is available free of charge via the
Internet at http://pubs.acs.org.
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