The role of gold adatoms and stereochemistry in self-assembly of methylthiolate on Au(111).

The Role of Gold Adatoms and Stereochemistry in
Self-Assembly of Methylthiolate on Au(111)
Oleksandr Voznyy,*,† Jan J. Dubowski,† J. T. Yates, Jr.,‡,§ and
Peter Maksymovych*,§,|
Department of Electrical and Computer Engineering, Centre of Excellence for Information
Engineering (CEGI), UniVersite´ de Sherbrooke, Sherbrooke, Que´bec J1K 2R1, Canada,
Department of Chemistry, UniVersity of Virginia, CharlottesVille, Virginia 22904, Department of
Chemistry, UniVersity of Pittsburgh, Pittsburgh, PennsylVania 15217, and Center for Nanophase
Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
Received April 2, 2009; E-mail: o.voznyy@usherbrooke.ca; 5 nm@ornl.gov
Abstract: On the basis of high resolution STM images and DFT modeling, we have resolved low- and
high-coverage structures of methylthiolate (CH3S) self-assembled on the Au(111) surface. The key new
finding is that the building block of all these structures has the same stoichiometry of two thiolate species
joined by a gold adatom. The self-arrangement of the methylthiolate-adatom complexes on the surface
depends critically on their stereochemical properties. Variations of the latter can produce local ordering of
adatom complexes with either (3 × 4) or (3 × 4�3) periodicity. A possible structural connection between
the (3 × 4�3) structure and commonly observed (�3 × �3)R30° phase in methylthiolate self-assembled
monolayers is developed by taking into account the reduction in the long-range order and stereochemical
isomerization at high coverage. We also suggest how the observed self-arrangements of methylthiolate
may be related to the c(4 × 2) phase of its longer homologues.
1. Introduction
Molecular self-assembly is a quickly developing field of
nanoscience that aims to tailor self-recognizing and self-
organizing properties of molecules for the bottom-up construc-
tion of complex molecular systems and implementation of the
designer molecular functionality. The greatest attention has been
devoted to the self-assembly of alkylthiolates (general formula
CnH2n+1S) on gold surfaces, which yields three-dimensional
crystalline monolayers with molecular tails decoupled from the
metal substrate.1 These unique properties have enabled a great
variety of alkanethiol-based applications, including molecular
electronics, immobilization of biomolecules, surface magnetism,
passivation of nanoparticles and so forth (see ref 2 and
references therein). However, despite the apparent simplicity
of the self-assembly process, commonly regarded as an evolution
of the packing order upon increasing surface coverage of the
adsorbate, almost every aspect of alkanethiol self-assembly on
Au(111) remains controversial.3
Until only recently, the gold surface has been considered a
passive template which provides a series of high-symmetry
adsorption sites for the alkylthiolate species.1,4-8 However, it
is now well-established that the bonding of the sulfur headgroup
to the Au(111) surface involves Au-adatoms.9-12 The Au-
adatoms are supplied by lifting the herringbone reconstruction
of the Au(111) surface,9 as well as etching of the monatomic
steps and terraces7 upon thiolate self-assembly. In our recent
publication based on scanning probe imaging,9 it was found
that the elementary building block of the self-assembled
methylthiolate phase at low coverage is a CH3S-Au(adatom)--
SCH3 species. A similar motif was subsequently found in the
self-assembly of benzenethiolate on Au(111)13 as well as in the
bonding of arenethiolates to gold nanoparticles.14 Au-adatoms
provide a significant contribution to the energy of the
anchor-bond,9,15,16 and it is therefore very likely that they will
influence the self-assembly process at all coverages and stability
† Universite´ de Sherbrooke.
‡ University of Virginia.
§ University of Pittsburgh.
| Oak Ridge National Laboratory.
(1) Schreiber, F. Prog. Surf. Sci. 2000, 65, 151–256.
(2) Love, J. C.; Estroff, L. A.; Kriebel, J. K.; Nuzzo, R. G.; Whitesides,
G. M. Chem. ReV. 2005, 105, 1103–1169.
(3) Woodruff, D. P. Phys. Chem. Chem. Phys. 2008, 10, 7211–7221.
(4) Poirier, G. E.; Pylant, E. D. Science 1996, 272, 1145–1148.
(5) Kondoh, H.; Iwasaki, M.; Shimada, T.; Amemiya, K.; Yokoyama, T.;
Ohta, T.; Shimomura, M.; Kono, S. Phys. ReV. Lett. 2003, 90, 066102–
066105.
(6) Gronbeck, H.; Curioni, A.; Andreoni, W. J. Am. Chem. Soc. 2000,
122, 3839–3842.
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(8) Torrelles, X.; Barrena, E.; Munuera, C.; Rius, J.; Ferrer, S.; Ocal, C.
Langmuir 2004, 20, 9396–9402.
(9) Maksymovych, P.; Sorescu, D. C.; Yates, J. T. Phys. ReV. Lett. 2006,
97, 146103–146106.
(10) Mazzarello, R.; Cossaro, A.; Verdini, A.; Rousseau, R.; Casalis, L.;
Danisman, M. F.; Floreano, L.; Scandolo, S.; Morgante, A.; Scoles,
G. Phys. ReV. Lett. 2007, 98, 016102–016105.
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Milligan, P. K.; Jones, R. G.; Woodruff, D. P.; Dhanak, V. Phys. ReV.
Lett. 2006, 97, 166102–166105.
(12) Kautz, N. A.; Kandel, S. A. J. Am. Chem. Soc. 2008, 130, 6908–
6909.
(13) Maksymovych, P.; Yates, J. T., Jr. J. Am. Chem. Soc. 2008, 130, 7518–
7519.
(14) Jadzinsky, P. D.; Calero, G.; Ackerson, C. J.; Bushnell, D. A.;
Kornberg, R. D. Science 2007, 318, 430–433.
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112, 15940–15942.
Published on Web 08/19/2009
10.1021/ja902629y CCC: $40.75  2009 American Chemical Society J. AM. CHEM. SOC. 2009, 131, 12989–12993 9 12989

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The Role of Gold Adatoms and Stereochemistry in Self-Assembly of
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of thiolate species against desorption. So far, very little direct
evidence has been obtained as to what role Au-adatoms play in
the intermediate 2D-monolayers, the so-called striped phases,1,4
and whether the sulfur-gold bonding changes as the coverage
of thiolates on gold surfaces approaches saturation. For the
saturation coverage, several models have been proposed, involv-
ing thiolate species bonded atop Au-adatoms,11 thiolate-adatom-
thiolate complexes akin those observed at low coverage,15
polymer-like adatom-thiolate complexes17,18 or a dynamic
equilibrium between adatom-bonded and bridge-bonded alky-
lthiolates adjacent to vacancy.10,19 In addition, at least three
kinds of symmetry were reported in alkanethiolate SAMs,
depending on the length of the hydrocarbon chains:1 (�3 ×
�3)R30°, (3 × 2�3) (which is a c(4 × 2) superstructure of the
�3 symmetry) and (3 × 4). The mechanism of self-assembly
leading to this variety of structures remains unresolved and
demands further exploration.
In this paper, we present a combined study of the intermediate
and high coverage structures of short-chain alkylthiolates on
Au(111) using scanning tunneling microscopy (STM) and
density-functional theory (DFT). We describe underappreciated
inherent chirality of the low coverage (striped) phase and
observe how it manifests in the structure evolution at higher
coverages. We develop a unified picture where the methylthi-
olate SAMs at all coverages are built of compositionally the
same unit (CH3S-Au-SCH3), while its stereochemical proper-
ties play a critical role in determining the order within the self-
assembled structure.
2. Methods
The experiments were conducted with a low-temperature STM
(Omicron) operating in an ultrahigh vacuum (UHV) chamber
(background pressure <5.0 × 10-11 Torr). The Au(111) surface (in
our case a facet of a single crystal at the end of a gold wire20) was
cleaned by Ar+ sputtering and annealing to 773 K. The clean gold
surfaces exhibited a terrace size of 1-2 µm and a (22 × �3)
herringbone reconstruction with no surface impurity adsorbates
visible in the elbow sites.21 The CH3SSCH3, CH3SH and C3H7SH
were purified using several freeze-pump-thaw cycles. Each
compound was deposited on the surface through an effusive beam
doser while the crystal was in the STM imaging position at <10 K.
The surface was subsequently heated to higher temperatures where
molecular dissociation and self-assembly occurred, as described
further in text. All the STM images presented here were taken at
a temperature of 5K.
The DFT calculations were performed using scalar-relativistic
pseudopotentials with nonlinear core corrections, within the gen-
eralized gradient approximation (GGA) as implemented in the
SIESTA code.22 The surface slab was modeled with 5 Au layers
and a vacuum region of 30 Å. A (4 × 5) Monkhorst-Pack k-grid
was used for Brillouin zone sampling. More calculation details can
be found in previous works.23
3. Results and Discussion
Methylthiolate species was previously found to chemisorb
on the Au(111) surface in the form of the CH3S-Au-
(adatom)-SCH3 complex at temperatures above ∼200 K
(hereafter (CH3S)2Au or adatom complex) with the S-atom
forming three covalent bonds:9 S-C to the methyl group, S-Au
to the adatom and S-Au to the gold atom in the surface, as
shown in Figure 1. The S-atom is positioned beside the Au-
adatom and atop the surface Au-atom (Figure 1d,e), providing
for an agreement with the original findings of the atop bonding
by the spectroscopic measurements using photoelectron dif-
fraction (PED)5 and normal incidence X-ray standing wave
(NIXSW).3,11 For the purpose of the following discussion, it is
convenient to consider sp3-like hybridization of the S-atoms in
the adatom complex,24 where three orbitals participate in the
bonding and the fourth one contains a lone electron pair. The
S-atom is thus formally chiral and can be designated as being
R- or S-type using the standard stereochemical nomenclature
(16) Wang, Y.; Hush, N. S.; Reimers, J. R. J. Am. Chem. Soc. 2007, 129,
14532–14533.
(17) Gronbeck, H.; Hakkinen, H. J. Phys. Chem. B 2007, 111, 3325–3327.
(18) Chaudhuri, A.; Lerotholi, T. J.; Jackson, D. C.; Woodruff, D. P.;
Dhanak, V. Phys. ReV. Lett. 2009, 102, 126101–126104.
(19) Cossaro, A.; Mazzarello, R.; Rousseau, R.; Casalis, L.; Verdini, A.;
Kohlmeyer, A.; Floreano, L.; Scandolo, S.; Morgante, A.; Klein, M. L.;
Scoles, G. Science 2008, 321, 943–946.
(20) Clavilier, J.; Faure, R.; Guinet, G.; Durand, R. J. Electroanal. Chem.
1979, 107, 205–209.
(21) Maksymovych, P.; Sorescu, D. C.; Dougherty, D.; Yates, J. T., Jr. J.
Phys. Chem. B 2005, 109, 22463–22468.
(22) Soler, J. M.; Artacho, E.; Gale, J. D.; Garcia, A.; Junquera, J.; Ordejon,
P.; Sanchez-Portal, D. J. Phys.: Condens. Mater. 2002, 14, 2745–
2779.
(23) Voznyy, O.; Dubowski, J. J. Langmuir 2009, 25, 7353–7358.
(24) Sellers, H.; Ulman, A.; Shnidman, Y.; Eilers, J. E. J. Am. Chem. Soc.
1993, 115, 9389–9401.
Figure 1. STM images of self-assembled structures of methylthiolate at low coverage on Au(111), produced by heating the gold crystal predosed with
CH3SSCH3 above 200 K for ∼10 min (a). Triangulation of two trans-(CH3S)2Au complexes (b) and adjacent cis- and trans-adatom complexes (c), and their
schematic models (d) and (e), respectively. The known adsorption sites of the adatom-complexes9 and the orientation of the 1D-stripes were used to derive
the relative location of the surface lattice (hexagonal mesh). DFT-optimized structures of (R,R)-trans (f) and (R,S)-cis (g) configurations. The formal
R-configuration of sulfur is assigned based on the following order: lone electron pair, CH3, surface Au atom (other surface atoms are not considered), Au
adatom (connected to the other CH3S fragment).
12990 J. AM. CHEM. SOC. 9 VOL. 131, NO. 36, 2009
A R T I C L E S Voznyy et al.

as detailed in Figure 1f,g. The (CH3S)2Au complex comprises
the S-atoms of either the same type, R or S, yielding a trans-
(CH3S)2Au isomer (Figure 1f), or of opposite type, R and S,
yielding a cis-(CH3S)2Au (Figure 1g). The difference in the
adsorption energy between cis- and trans-complexes, calculated
here by DFT, is less than 0.1 eV; that is, they are thermody-
namically equivalent. However, the barrier to switch between
the two configurations, calculated using the nudged elastic band
method, amounts to 0.50 eV (at half of saturation coverage).
Thermally activated cis-trans isomerization should therefore
become facile already at T ) 200 K, which is the temperature
where the self-assembly of the thiolate species takes place in
our experiments. The existence of both cis- and trans-(CH3S)2Au
complexes is confirmed by STM images obtained at low and
intermediate coverages of methylthiolate (Figure 1a-c).
The adatom complexes of methylthiolate readily cluster at
low coverages, forming 1D-stripes up to 15 (CH3S)2Au in a
row along the 〈112j〉 direction (Figure 1a and Figure 2a). The
clustering is driven by the attractive interaction between trans-
(CH3S)2Au complexes (calculated to be ∼ 0.09 eV per com-
plex9) when they are located at a distance of �3a along the
〈112j〉 direction (a ) 2.885 Å is the gold surface lattice constant).
Minimization of steric repulsion within the stripes requires all
the complexes to have exactly the same trans-configuration, that
is, to be either of R,R- or S,S-type. No evident 2D-ordering of
the methylthiolate stripes is observed at intermediate coverages
(Figure 2a), indicating weak or even repulsive interstripe
interactions. However, the stripes of longer-chain alkylthiolates,
such as propylthiolate (C3H7S), exhibit a pronounced 2D-order
even at a low coverage as seen in Figure 2b. The 1D stripes
assemble along the 〈110j〉 direction, normal to the stripe-axis.
This is likely due to an increase of the van der Waals interactions
between the hydrocarbon tails compared to methylthiolate. The
2D-ordered striped phase possesses a rectangular (n × �3) unit
cell, where n is integer.1,25 Although 2D-stripe phases have been
routinely observed for longer alkanethiolates, an intriguing
property discovered here is a chiral recognition between the
1D stripes. It is manifested in the alternating type of the stripes
between R,R- and S,S- symmetries (Figure 2b) arising in order
to reduce the steric repulsion between stripes.
We naturally expect that the self-assembled structures beyond
striped phases will evolve from the building blocks available
within the striped phase and would at some point coexist with
the stripes. The self-assembly at high coverage may involve
cis-trans isomerization of the (CH3S)2Au complexes, their
rearrangement on the surface, or occurrence of new sulfur-to-
gold bonding motifs. We have found that increasing methylthi-
olate coverage past the striped phase brings out a new structural
motif, formed when two stripes, whose axes are displaced by
1.5a distance along the 〈11j0〉 direction, meet end-to-end as
illustrated in Figure 2a,c,d. Such a ‘tetramer’ comprises two
slightly overlapping trans-(CH3S)2Au complexes. Steric repul-
sion between the CH3-group in one complex and the Au-adatom
in the other makes two of the four CH3 groups slightly buckled,
increasing their apparent height in STM (Figure 2a). The STM
image of the tetramer is very similar to the building block of
the (3 × 4) phase previously reported by Kondoh et al.26
At near-saturation coverage, tetramers become a prevalent
species while the length of the 1D-stripes decreases (Figure 3a).
The tetramers form local arrangements with the periodicity of
either (3 × 4�3) (Figure 3b) or (3 × 4) (Figure 3c). Both unit-
cells correspond to saturation coverage of CH3S and differ only
by the relative positions and chirality of the constituent
tetramers. The (3 × 4) phase comprises tetramers of identical
spatial configuration (all R,R or all S,S complexes), arranged to
yield the (3 × 4) sublattice of the sulfur atoms (Figure 3e). In
contrast, the (3 × 4�3) phase comprises rows of the R,R and
S,S tetramers alternating along the 〈112j〉 direction, yielding the
(�3 × �3)R30° sublattice of the sulfur atoms (Figure 3d). Our
DFT calculations show that the (3 × 4) periodicity is more stable
than (3 × 4�3) by ∼0.12 eV per adatom complex, which is
consistent with their coexistence on the surface. The (3 × 4)
phase of methylthiolate has previously been reported in several
works.26,27 However, to the best of our knowledge, this is the
first observation of the (3 × 4�3) unit cell.
The STM observations may seem inconsistent with the results
of diffraction techniques where the signal is averaged over
a large surface area, such as low energy electron diffrac-
tion (LEED)5,26,27 and grazing-incidence X-ray diffraction
(GIXRD).10 These studies have reported the formation of the
(�3 × �3)R30° phase at the saturation coverage of methylthi-
olate on Au(111). The use of adatom complexes to build up
the SAM requires a unit cell that is bigger than that of (�3 ×
�3)R30°. To resolve this discrepancy, Mazzarello et al.10
proposed a different structural model, where the adatom-bonded
(25) Poirier, G. E. Chem. ReV. 1997, 97, 1117–1127.
(26) Kondoh, H.; Nozoye, H. J. Phys. Chem. B 1999, 103, 2585–2588.
(27) De Renzi, V.; Di Felice, R.; Marchetto, D.; Biagi, R.; del Pennino,
U.; Selloni, A. J. Phys. Chem. B 2004, 108, 16–20.
Figure 2. STM images of (a) intermediate coverage of methylthiolate on Au(111) revealing the coexistence of stripes, single cis- and trans-complexes, and
tetramers (T > 200 K during self-assembly). (b) Striped phase of propylthiolate with (11 × �3) unit cell, formed by thermal dissociation and subsequent
self-assembly of C3H7SH molecules at T > 250 K. The tetramer unit (c) and its schematic structure (d) correspond to the outlined area in panel (a).
J. AM. CHEM. SOC. 9 VOL. 131, NO. 36, 2009 12991
Self-Assembly of Methylthiolate on Au(111) A R T I C L E S

methylthiolate complexes coexist in a dynamic equilibrium with
the bridge-bonded thiolate species adjacent to vacancy, creating
a disordered monolayer. Upon averaging, the disordered struc-
ture satisfies the (�3 × �3)R30° symmetry observed by
GIXRD. Our STM images obtained at low and intermediate
coverages of methylthiolate (Figures 1a and 2a) show that the
dominant species on the surface are trans- and cis-(CH3S)2Au
complexes. This fact alone does not rule out the possible
existence of the vacancies or other kinds of CH3S species at
the saturation coverage. However, we have found that the
concept of disorder can be used to generate a macroscopically
observed (�3 × �3)R30° symmetry using only methylthiolate-
adatom complexes. In particular, we assumed the existence of
the (3 × 4�3) phase with a reduced long-range order at the
expense of smaller coverage (∼75% of saturation coverage),
as shown in Figure 4a. Simulated in-plane GIXRD pattern of
this structure (Figure 4b, for details see Supporting Information)
exhibits only (�3 × �3)R30° peaks despite the apparent lack
of this unit-cell on the local scale within the structure. Since
GIXRD is dominated by diffraction from Au adatoms;3,23 the
latter must occupy the �3 sublattice within the self-assembled
layer. This requires all the (CH3)2Au complexes to be aligned
along the same direction, since otherwise the adatoms end up
on the sites belonging to a (�3/2 × �3/2)R30° lattice (see
Supporting Iinformation), generating a corresponding pattern
in GIXRD. For comparison, the ordered (3 × 4�3) phase
produces the (3 × 2�3) GIXRD pattern (Figure 4c) corre-
sponding to the symmetry of adatoms, while being largely
insensitive to the positions of S and C atoms. This pattern is
practically identical to that of the c(4 × 2) phase of longer
thiols.8,19 The notion of the disordered structure that produces
a well-ordered pattern in reciprocal space is also consistent with
our STM images at near-saturation coverage; for example, in
Figure 3a, the Fourier transform of which also shows sharp (�3
× �3)R30° spots (Figure 4d).
Figure 3. High-coverage self-assembled structures of methylthiolate on Au(111) obtained by heating the gold crystal predosed with CH3SSCH3 to T > 250
K for ∼10 min. (a) The largely 1D-stripes of (CH3S)2Au coexisting with several patches of the (3 × 4�3) phase. (b) Close-up of the left (3 × 4�3) patch
in panel (a). (c) Close-up of the (3 × 4) patch found in the surface area adjacent to the area shown in panel (a). (d and e) DFT-optimized structural models
of the proposed saturated (3 × 4�3) and (3 × 4) phases, respectively, with unit cells indicated in black and (�3 × �3)R30° unit cell as dotted black. White
outlines correspond to tetramer patterns observed experimentally in panels (b) and (c).
Figure 4. (a) Structural model of the disordered phase derived from (3 × 4�3). Dashed and dotted lines show the (3 × 4�3) and (�3 × �3)R30° unit
cells, respectively. Calculated GIXRD patterns of this phase exhibiting the (�3 × �3)R30° symmetry (b) and of the ordered (3 × 4�3) phase (c). (d)
Fourier transform of the STM image in Figure 3a featuring sharp (�3 × �3)R30° peaks and a diffuse background due to disorder.
12992 J. AM. CHEM. SOC. 9 VOL. 131, NO. 36, 2009
A R T I C L E S Voznyy et al.