ARTICLE
https://doi.org/10.1038/s41467-019-10526-0
OPEN
In situ observations of an active MoS2 model
hydrodesulfurization catalyst
1234567890():,;
Rik V. Mom
1,
Jaap N. Louwen2, Joost W.M. Frenken1,3 & Irene M.N. Groot
1,4
The hydrodesulfurization process is one of the cornerstones of the chemical industry,
removing harmful sulfur from oil to produce clean hydrocarbons. The reaction is catalyzed
by the edges of MoS2 nanoislands and is operated in hydrogen-oil mixtures at 5–160 bar
and 260–380 °C. Until now, it has remained unclear how these harsh conditions affect the
structure of the catalyst. Using a special-purpose high-pressure scanning tunneling microscope, we provide direct observations of an active MoS2 model catalyst under reaction
conditions. We show that the active edge sites adapt their sulfur, hydrogen, and hydrocarbon
coverages depending on the gas environment. By comparing these observations to density
functional theory calculations, we propose that the dominant edge structure during the
desulfurization of CH3SH contains a mixture of adsorbed sulfur and CH3SH.
1 Huygens-Kamerlingh Onnes Laboratory, Leiden University, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands. 2 Analytical Research and Quality
Department, Albemarle Corporation, Nieuwendammerkade 1-3, 1022 AB Amsterdam, The Netherlands. 3 Advanced Research Center for Nanolithography,
Science Park 110, 1098 XG Amsterdam, The Netherlands. 4 Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The
Netherlands. Correspondence and requests for materials should be addressed to R.V.M. (email: mom@physics.leidenuniv.nl)
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
1
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
he hydrodesulfurization (HDS) process is used to remove
environmentally harmful sulfur from ~2500 million tons of
oil annually1. Thus, it is an essential step in the production
of clean fuels. To accomplish the removal of sulfur, the oil is
mixed with hydrogen at a pressure between 5 bar and 160 bar,
with the temperature between 260 °C and 380 °C, producing H2S
and clean hydrocarbons2.
MoS2-based catalysts are widely used to drive the HDS reaction
owing to their high activity, stability, and low cost2. While
research into these catalysts started as early as the 1920’s3, the
atomic-scale mechanism of the reaction is still under debate. Ex
situ microscopy data showed that MoS2 is present as nanoislands
that consist of one or more layers of an S–Mo–S sandwich4–10.
The edges of the islands serve as active sites during catalysis11–14.
Hence, mechanistic understanding of the HDS process requires
detailed knowledge of the properties of the edge sites.
In most cases, the MoS2 islands exhibit a high degree of
crystallinity, resulting in island shapes close to the thermodynamically favored truncated triangle4–8,15,16. Consequently,
two types of edge termination are mainly observed, usually
referred to as the Mo edge and the S edge, with the Mo edge being
dominant. Ab initio thermodynamics calculations predict that
the sulfur coverage on both edge structures depends on the gas
environment15,17–19. The essential element is the balance between
the chemical potentials of hydrogen and sulfur atoms in the gas
phase. In a sulfur-rich feed, two S edge atoms per Mo edge atom
(100% coverage) are predicted. Excess hydrogen can lower this
number, in the limit of pure H2 even to zero (0% coverage).
Experimental studies in several gas environments confirmed
that the edge sulfur coverage varies, depending on the balance
between hydrogen-containing and sulfur-containing species in
the feed15,20,21. However, it remains extremely challenging to
study a minority species such as edge atoms under operando
conditions. As a result, a conclusive determination of the active
site structure during HDS has so far not been achieved.
Here, we present direct observations of the active MoS2 edge
structure under reaction conditions. Using a special-purpose highpressure scanning tunneling microscope (STM), we have obtained
atomically resolved images evidencing a mixed hydrocarbon-sulfur
edge structure during the desulfurization of CH3SH on a model
T
a
catalyst. We explain the observations by comparing the STM images
with density functional theory (DFT) calculations, also taking into
account the role of the reaction kinetics in determining the active
site structure.
Results
Instrument development and model system. The combination
of high pressures of corrosive gases and high temperature provides a challenging environment for STM experiments. To meet
this challenge, we have used the ReactorSTM previously developed in our group22. At the heart of this system is a 0.5 ml flow
reactor containing the STM tip. The reactor walls are defined
by a cap placed inside the scan piezo, the catalyst sample, the
STM body, and polymer seals in between these elements. Gas
capillaries drilled in the STM body provide a connection to a gas
supply system that controls the composition, flow, and pressure
of the gases in the flow reactor.
To mimic realistic industrial conditions, the pressure can be raised
up to 1 bar, while the sample is heated up to 300 °C using a filament
located on the backside of the sample. A key element in the design
is that the scan piezo is not in contact with the gases in the reactor.
This geometry, in combination with a careful choice of chemically
resistant materials (see “Methods” section), allows for the use of
highly corrosive gases such as H2S at elevated temperatures. The use
of PtIr tips prevents tip degradation during the measurements,
albeit that frequent changes in imaging quality cannot be avoided.
To combine the high-pressure experiments with more traditional
ultrahigh vacuum (UHV) surface preparation and characterization
techniques, the flow reactor can be opened and closed inside a UHV
system, which contains among others an ion gun, an evaporation
source, and an X-ray photoelectron spectroscopy apparatus.
As a first step, we established a suitable model catalyst; one that
is conductive to allow for STM measurements and stable under
HDS conditions. Following the successful recipe of the Århus
group4,15, we synthesized MoS2 particles on a Au(111) substrate
(see “Methods” section), yielding crystalline islands with a
predominantly triangular shape (see Fig. 1a). These islands were
shown to nearly exclusively expose the Mo edge15, which we will
focus on hereafter.
b
c
Fig. 1 STM images of a MoS2/Au(111) model catalyst and its stability under desulfurization conditions. a Catalyst after preparation in UHV. 16 × 16 nm2, Ubias
pA. b Clean Au surface imaged in 1 bar CH3SH at 250 °C, showing the (1 × 1) Au lattice. 6 × 6 nm2, Ubias = −0.3 V, It = 550 pA. c MoS2/
Au(111) after 1 day in 1 bar of a 1:9 CH3SH/H2 mixture, showing a sulfur overlayer on the Au(111) substrate. 20 × 20 nm2, Ubias = −0.3 V, It = 645 pA
= −0.3 V, It = 320
2
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
To allow for unambiguous identification of edge structures in
STM during HDS, we chose the simple CH3SH molecule as our
organosulfur compound to be desulfurized. Naturally, a single
organosulfur compound can never fully represent the complex
mixture in oil. However, mercaptans such as CH3SH constitute a
major component in crude oil23. Our applied temperature and
pressure (250 °C, 1 bar) are close to the typical hydrodesulfurization conditions applied for the light naphtha fraction (260–380 °C,
5–10 bar)2 and are sufficient to achieve catalytic turnover24.
The stability of the model catalyst during HDS depends on the
chosen conditions. Like all thiols, CH3SH readily adsorbs on
gold surfaces25. However, at the temperature of our catalytic
experiments (250 °C), only the (1 × 1) Au lattice is imaged, even
in 1 bar CH3SH (see Fig. 1b). Nonetheless, the absence of the
herringbone reconstruction observed on clean Au(111)26 indicates that some (dissociated) CH3S is present on the surface.
Decomposition of CH3S or H2S leads to the formation of a sulfur
layer over time (see Fig. 1c), with a structure resembling that
observed by Lay et al.27. The formation of the sulfur overlayer
occurred independent on whether MoS2 particles were present on
the Au(111) substrate or not. As long as H2S is not added to the
reactor feed, the overlayer formation requires hours, making it
too slow to interfere with the HDS catalysis on the MoS2 particles
through sulfur spillover. However, the encapsulation of the MoS2
particles by the sulfur overlayer on the Au substrate, depicted in
Fig. 1c, could limit the accessibility of the active edge sites. To
prevent this, we restricted the duration of our HDS experiments
to a few hours, after which a fresh model catalyst was prepared.
Experimental observations on MoS2 edge structures. As a next
step, we characterized the appearance of the fully sulfided MoS2
a
b
As prepared
d
edge structure obtained after preparation of the MoS2 particles in
2 × 10–6 mbar pure H2S. Using DFT calculations, Lauritsen et al.15
identified the resulting edge structure as the 100%S edge, which
contains an S dimer on every Mo edge atom. Its appearance in STM
images is characterized by a periodicity of one lattice spacing along
the edge and by a registry shift of half a lattice spacing in the
apparent position of the edge atoms with respect to those on the
basal plane. Indeed, Fig. 2a shows that the apparent location of
the edge atoms does not follow the registry of the basal plane atoms,
as also confirmed by the non-differentiated image in Supplementary
Fig. 3. The observed registry shift is smaller than the expected half
lattice spacing, which was also observed in some cases in the
literature9,15,28. We attribute this to asymmetry in the tip apex,
which can lead to slight distortions in the observed edge structure.
Note from the 100% S ball model in Fig. 2a that the apparent
position of the edge atoms in STM deviates from their geometrical
position. This is a result of the fact that the electronic states around
the Fermi level, which are probed by STM, are mostly located in
between the edge atoms (see Supplementary Fig. 1a). To clearly
separate the nomenclature for apparent and actual edge atom
positions, we refer to the apparent positions of the edge atoms as
edge protrusions hereafter. We should also point out that the STM
images in Fig. 2 were differentiated to highlight the atomic contrast.
In this display method, the metallic “bright” edge states that are
usually observed at the edges of the MoS2 particles are less apparent.
Our first step towards reaction conditions is to image the model
catalyst in high H2 pressure and at high temperatures. Ab initio
thermodynamics calculations predict that these conditions should
trigger a shape change in the particles to a more hexagonal shape
(as opposed to the predominantly triangular shape of the as-prepared
particles). However, we did not observe a decrease in the fraction of
c
H2
e
100%S
HDS
f
50%S
Fig. 2 MoS2 edge structure in various gas environments. The bottom panels (d, e, f) show the original images, which were differentiated (in the fast
scanning direction) to highlight the atomic contrast. The top panels (a, b, c) depict the averaged edge unit cell obtained from the bottom panels (d, e, f).
The ball models represent the 100%S and 50%S structures that could directly be identified for (a) and (b), respectively, from comparison to simulated
STM images (see Supplementary Figs. 1 and 2). Blue: Mo, yellow: S. a, d Catalyst after preparation in 2 × 10−6 mbar H2S at 450 °C, imaged in UHV at room
temperature. 6.6 × 6.6 nm2, Ubias = −0.3 V, It = 560 pA. b, e Catalyst imaged in 1 bar H2 at 50 °C. 6.6 × 6.6 nm2, Ubias = −0.3 V, It = 630 pA. c, f Catalyst
during the desulfurization of CH3SH in 1 bar 1:9 CH3SH/H2 at 250 °C. 8 × 8 nm2, Ubias = −0.3 V, It = 400 pA
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
3
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
triangular particles, which we attribute to kinetic limitations. Indeed,
shape changes were experimentally only observed at higher
temperatures29. On the more detailed scale however, we see that
the appearance of the atomic structure of the edge sites does change
(see Fig. 2b), indicating that the particle edges have been reduced.
The registry shift of the edge protrusions with respect to the basal
plane atoms that was apparent for the 100%S edge has been removed,
while maintaining the periodicity along the edge of one lattice
spacing. Note again that some tip asymmetry could not be avoided,
resulting in somewhat asymmetrical image sharpness. To prevent
misinterpretation, the conclusions from Fig. 2b were corroborated
using additional data (see Supplementary Fig. 4). In all cases, we find
that the edge protrusions are located precisely in registry (average 2%
of a lattice spacing shift measured with respect to the basal plane
registry). The structure in Fig. 2b was not dependent on temperature
within the range from 50 °C to 250 °C probed here. It should be
noted however that at elevated temperatures STM may probe a timeaveraged structure, which could obscure diffusing S vacancies or
adsorbed S and H atoms.
The edge structure without registry shift in Fig. 2b was
also observed after deposition of Mo in H2S/H2 mixtures15 or
dimethylsulfide30. It was interpreted as the 50%S structure by
comparison with simulated STM images. Our STM simulations
corroborate this assignment, although hydrogen adsorption
cannot be excluded (see Supplementary Figs. 1 and 2). In
agreement with the observations on reduced MoS2 edge
structures in the literature, the bright metallic edge states are
maintained (see Supplementary Fig. 7). We note that Bruix et al.
did not find the registry shift between the 100%S and the 50%S
edge structures for MoS2/Au(111) in their STM simulations21.
However, none of the structures described in their work matches
the experimental observations of the reduced edge structure.
Having established our ability to observe changes in the MoS2
edge structure under high-pressure, high-temperature conditions,
we are ready to study our model catalyst in its active form during
the desulfurization of CH3SH. Fig. 2c shows the structure
observed in a 1 bar 1:9 CH3SH/H2 mixture at 250 °C. Before
imaging, the flow reactor was allowed to stabilize for more than
2 h to ensure a steady-state situation. Fig. 2c shows that the edge
structure under hydrodesulfurization conditions has changed
with respect to the structure in pure hydrogen (see also
Supplementary Fig. 5 and see Supplementary Fig. 6 for the
alignment procedure of the grid overlay). The observed registry
shift of the edge protrusions is similar to that observed for the
100%S-covered edge in Fig. 2a: on average 20% of a lattice
spacing out of registry in Fig. 2a and 18% in Fig. 2c and S5. Again,
we note that the registry shift is asymmetric with respect to the
lattice, which we attribute to asymmetry in the tip apex. Indeed,
one can observe that in both Fig. 2a, c the resolution on the basal
plane atoms is higher for the horizontal direction than for the
vertical direction, which explains why the two edge structures
show the same asymmetry. Based on the registry of the edge
protrusions, one could assign the structure under HDS conditions
to an (almost) 100%S-covered edge. An alternative explanation is
the formation of CH3SH adsorption structures. Mo carbide
formation can be excluded, since our low-temperature, sulfur-rich
HDS environment is far away from the conditions for which
Mo2C or MoSxCy formation were observed31–33.
Theoretical modeling. To enable an unambiguous assignment of
the edge structure observed during the hydrodesulfurization of
CH3SH, we consider the thermodynamic and kinetic aspects
of the catalytic process using DFT calculations. First, we assess
the thermodynamic stability of various edge structures in a gas
environment that only consists of H2 and H2S. Fig. 3 depicts the
most stable edge structure for Au-supported MoS2 as a function
of ΔμS and ΔμH. These quantities are directly related to the
temperature, the H2S pressure, and the H2 pressure through
Eqs. 5 and 6 in the “Methods” section. The phase diagram in
Fig. 3 corroborates the observation that the MoS2 edge structure
depends on the gas environment, showing large variations in both
S and H coverage. A quantitative comparison with earlier work
shows an agreement to within 0.15 eV for the relative stability of
the 50%S and 100%S structures15,18,19 (see Supplementary
Table 1). Remarkably however, we find a preference for lowsymmetry structures such as 38%S-x%H and 63%S-x%H over a
PH2S/PH2
10–6
10–4
10–2
100
102
104
@ 523 K
Mo
S
H
0.0
38%S–25%H
“HDS’’
∆H (eV)
–0.4
63%S–25%H
–0.6
38%S–25%H
10–2
50%S
63%S
10–8
38%S
50%S
63
–1.0
–0.8
–0.6
–0.4
∆S (eV)
–0.2
10–11
63%S–25%H
10–14
63%S–50%H
100%S
Prep.
–1.2
–1.2
101
10–5
–0.8
–1.0
38%S
104
63%S–50%H
H2
PH2 (bar)
–0.2
0.0
0.2
100%S
Fig. 3 Ab initio thermodynamics phase diagram of the MoS2 edge structures in H2/H2S mixtures for Au-supported MoS2. On the axes, ΔμS and ΔμH
designate the entropic parts of the chemical potentials of S and H atoms in the gas phase, respectively. These are directly related to the temperature, the
H2S pressure, and the H2 pressure (see Methods section). The experimental conditions during catalyst preparation, in 1 bar hydrogen (assuming 1 ppm H2S
contamination), and during HDS (naïve approximation) are indicated in blue. The ball models represent side views of the structures present in the phase
diagram. Note that the edges are periodic in the left-right direction
4
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
wide range of conditions. These structures were not taken into
account in earlier studies and therefore did not show up in the
predicted phase diagrams (see Supplementary Note 3 for details).
We have excluded that the stability of the low-symmetry structures is the result of the Au-MoS2 interaction (see Supplementary
Note 2), which generally favors a higher sulfur coverage, but does
not seem to favor the low-symmetry structures in particular.
However, we should point out that for a larger unit cell size, an
even larger variety of structures may appear in the phase diagram.
The trends of the sulfur and hydrogen coverages in various gas
environments can be understood based on the variation in
adsorption strength per H or S atom of the various structures.
Generally, one expects the adsorption strength per S or H atom to
decrease at higher S or H coverage. Hence, higher-coverage structures
require a higher chemical potential in order to form. This trend is
indeed observed in the phase diagram. However, the 75%S and 88%S
structures do not appear. In this coverage range, the registry of the S
edge atoms changes with respect to the S atoms on the basal plane,
leading to unstable structures with strained bonds. For the
hydrogenated phases, 63%S-x%H shows a remarkably large range
of stability. An explanation for this comes from the comparison of
the 50%S and 63%S structures. For the 50%S case, hydrogen
adsorption induces buckling of the edge S atoms (Supplementary
Fig. 1), implying the presence of compressive stress. The buckling
disappears upon the adsorption of a sulfur atom (yielding the 63%S50%H structure, see Fig. 3), implying a stabilizing stress relief. For the
small particles used in HDS, corner sites may provide similar stress
relief. It is therefore not a priori clear whether the 63%S-x%H
structures are similarly stable in such more realistic catalysts.
Using Eqs. 5 and 6 (see Methods section), we have placed the
experimental conditions in the phase diagram of Au-supported
MoS2. For the freshly prepared particles, we have used an H2S
pressure of 2 × 10−6 mbar H2S and a temperature of 300 °C for the
calculation, even though imaging was performed in vacuum at room
temperature. We chose these conditions because the edge structure is
not capable of changing in vacuum at temperatures below 300 °
C15,21. As expected, the phase diagram indicates the observed 100%S
structure to be the most stable under these conditions. For the
reduction in 1 bar H2, we assumed an H2S contamination level of 1
ppm. Depending on the temperature, the phase diagram indicates an
edge coverage of 38%S to 63%S, with hydrogen adsorption on most
structures. Again, this is in good agreement with the time-averaged
50%S-X%H structure observed with STM.
To represent the hydrodesulfurization experiment in the phase
diagram, we need to assume that the gas environment can be
described solely in terms of H2S and H2 chemical potentials. This
would be the case if the adsorption of hydrocarbons, e.g., CH3SH, is
ignored and the overall HDS reaction is either completely
equilibrated or slow with respect to the reactions of H2 and H2S
with the MoS2 edges. From mass spectroscopic product analysis, we
know that in our case the conversion of CH3SH is low due to the
a
b
extremely low number of active sites on our planar model catalyst.
Even at an extremely high turnover frequency of 1000 s−1 per site,
only ~1 mbar H2S would be generated. If we assume this upper limit
and ignore CH3SH adsorption, the chemical potential of sulfur in our
HDS experiment is determined by the temperature (250 °C), the H2S
pressure (~0.001 bar) and the H2 pressure (0.9 bar), as indicated in
Fig. 3. This would lead to a 63%S-50%H structure, which has a
slightly higher S coverage than the 50%S-50%H structure predicted in
earlier studies for these conditions15,18. It should be clear however
that the 100%S structure is not a likely candidate for the structure we
observe in STM under reaction conditions.
To investigate the possibility of CH3SH adsorption structures, we
calculated the CH3SH adsorption energy for several edge S and H
coverages on Au-supported MoS2 (see Supplementary Note 4). While
CH3SH can bind in all cases, only the 38%S-25%CH3SH structure in
Fig. 4 is thermodynamically more stable (ΔGform = −0.08 eV) than
the clean 63%S-50%H structure under our reaction conditions
(PCH3SH = 0.1 bar, PH2S = ~0.001 bar, PH2 = 0.9 bar, 250 °C). Hence,
if H2, H2S, and CH3SH would equilibrate with our model catalyst, i.e.,
if the HDS reaction would be slow enough not to affect this
thermodynamic equilibrium, the 38%S-25%CH3SH structure should
prevail. For H2S pressures lower than the upper limit of 1 mbar, the
preference for the 38%S-25%CH3SH structure is further increased.
Fig. 4b shows an STM simulation of the 38%S-25%CH3SH structure.
The irregular appearance of the edge structure will be time-averaged
in the STM images at 250 °C, because of the fast adsorption/
desorption kinetics of CH3SH (free energy barriers of 0.51 eV and
0.87 eV, respectively). In Fig. 4c, we have taken this effect into
account by averaging the local density of states over the four edge
positions. Clearly, the averaged edge protrusions are out of registry
with respect to the basal plane S atoms, in agreement with the
experimental observations.
Since we have come close to industrial conditions in our HDS
experiment, we expect conversion of CH3SH to CH42,24. Hence,
the reaction should be in a steady state rather than in the static
equilibrium discussed in the previous paragraph. To model how
this affects the prevalent edge structure, we computed a reaction
network linking a set of reaction intermediates on Au-supported
MoS2 (see Fig. 5). The catalytic cycles in the network consist of
three stages: the conversion of CH3SH to CH4, leaving behind a
sulfur atom on the MoS2 edge, the desorption of this sulfur atom
as H2S, and the adsorption of hydrogen. From Fig. 5, it is clear
that the conversion of CH3SH is essentially a one-way reaction
due to its high energy gain. In contrast, the adsorption/desorption
steps of H2, H2S, and CH3SH are all reversible.
Putting this in a simple steady state rate equation model we
obtain:
CH3 SHads ! CH4ðgÞ þ Sads
ð1Þ
Sads þ H2ðgÞ þ CH3 SHðgÞ "H2 SðgÞ þ CH3 SHads
ð2Þ
c
Fig. 4 Thermodynamically preferred structure under the experimental desulfurization conditions (PCH3SH = 0.1 bar, PH2S = ~0.001 bar, PH2 = 0.9 bar, 250 °C).
a Ball model. b Simulated STM image for Us = −0.3 V, using an electron density contour value of 1 × 10−6 AU. c Simulated STM image taking into account
thermal averaging due to diffusion, adsorption and desorption. The green grid highlights the registry shift of the edge atoms with respect to the basal plane
S atoms, which was also observed in the experiment
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
5
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
H2S
CH3SH
50%S–50%H
50%S–50%H-MT
38%S
∆Ga =
1.14 eV
∆Ga =
1.44 eV
∆Ga =
1.32 eV
ss: 0.09%
eq: 0.09%
ss: 4.34%
eq: 4.35%
CH3SH
∆Ga =
0.74 eV
H2
∆Ga =
0.87 eV
∆Ga =
1.03 eV
∆Ga =
1.24 eV
∆Ga =
0.92 eV
ss: 8.2 × 10–4%
eq: 8.5 × 10–4%
∆Ga =
3.22 eV
∆Ga =
1.37 eV
CH4
63%S–50%H
38%S-MT
50%S
∆Ga =
2.87 eV
ss: 80.6%
eq: 80.7%
∆Ga =
1.25 eV
∆Ga =
1.65 eV
∆Ga =
1.36 eV
ss: 1.18%
eq: 1.17%
ss: 13.8%
eq: 13.7%
H2S
CH4
Fig. 5 Reaction network for CH3SH desulfurization on MoS2/Au(111). The activation free energy barriers (ΔGa) indicated in the arrows were calculated
based on the experimental conditions (PCH3SH = 0.1 bar, PH2S = ~0.001 bar, PH2 = 0.9 bar, 250 °C). The abundances of intermediates in steady state
conditions and in an equilibrium where the C–S bond breaking step is disabled are designated by ss and eq, respectively. The steady state concentrations
were derived using transition state theory and rate equation modeling (see Methods section). MT corresponds to methane thiol
k 1 þ k 2 PH2 S
½Sads
¼
½CH3 SHads k2 PH2 PCH3 SH
ð3Þ
Although highly simplified, this model provides some insight
into the effect of CH3SH conversion on the MoS2 edge structure.
When the conversion faces a high barrier, rate constant k1 will be
low. In such a case, the edge structure should be close to the
equilibrium of Eq. 2. In contrast, when the barrier for CH3SH
conversion would be lower than the H2/H2S adsorption/
desorption barriers, one should expect that adsorbed CH3SH
would be largely replaced by sulfur atoms.
Figure 5 shows that the C–S bond breaking barriers are slightly
higher than the H2S desorption barriers. Because the rate
constants have an exponential dependence on the energy barrier,
this translates into orders of magnitude difference in rate. Indeed,
when we quantify the abundances of all reaction intermediates
(see “Methods” section), we still find an 80.6% abundance of the
38%S-CH3SH edge state, compared with 80.7% under equilibrium conditions. Hence, it appears that the structure observed in
our HDS experiment is the 38%S-CH3SH edge state.
In a more general view, our theoretical analysis identifies two
mechanisms that can steer the MoS2 edge structure away from its
equilibrium with H2 and H2S during the HDS reaction. First, the
adsorption of organic molecules may favor different edge S and H
coverages. In our experiments, this leads to the counterintuitive
observation that the edge S content is reduced due to CH3SH
adsorption: the 63%S-50%H structure is favored in the absence of
CH3SH adsorption, whereas the 38%S-25%CH3SH structure is the
most stable one when we do take CH3SH adsorption into account.
6
This effect is likely also present for other industrially important
reaction intermediates such as reduced thiophenes, which adsorb
even stronger than CH3SH34. Indeed, infrared spectroscopy has
shown that thiophene adsorption is much more pronounced in a
reducing atmosphere35. Other compounds were also found to
adsorb under HDS conditions36. However, weakly adsorbing and/
or sterically hindered (e.g., dimethyldibenzothiophene) organosulfur molecules may not have sufficient interaction with the MoS2
edge to significantly alter the catalyst’s resting state.
A second mechanism that steers the edge structure out of
equilibrium is the deposition of sulfur via C–S bond scission.
Although this appears to have only a minor effect in our experiment,
subtle changes in the barrier for C–S bond breaking can have major
consequences for the average edge structure. For instance, if the C–S
barrier in the network in Fig. 4 were lowered by 0.3 eV, the 63%S50%H structure would become dominant. Hence, support effects, the
presence of defects such as corner sites, and the nature of the
hydrocarbons that are desulfurized can all cause large variations in
the average structure of MoS2 under reaction conditions.
Discussion
In summary, we have studied the catalytically active edge structure of
MoS2 nanoparticles on Au(111) in mixtures of H2, H2S, and CH3SH
at temperatures up to 250 °C using a dedicated high-pressure scanning tunneling microscope. In hydrogen, trace amounts of sulfur in
the feed are sufficient to maintain a sulfur coverage of 1 edge S atom
per edge Mo atom. Surprisingly, the edge is reduced during the
hydrodesulfurization of CH3SH to accommodate CH3SH adsorption.
Due to the slow C–S bond scission on our model catalyst, the system
remains close to an equilibrium state. However, our theoretical
analysis indicates that small changes in the reaction rate or the
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
reaction mechanism, which could originate from support effects or
from the presence of different hydrocarbons, can have a major
influence on the average MoS2 edge structure. In particular, for highly
active MoS2 catalysts one may expect that sulfur deposition by the
conversion of organosulfur compounds increases the edge S coverage
under hydrodesulfurization conditions, rather than to decrease it, as
was found here. Hence, we conclude that the prevalent structure
of the active sites during hydrodesulfurization catalysis on MoS2
likely depends both on the precise type of catalyst and the nature
of the feedstock.
Methods
Model catalyst preparation. Clean, atomically smooth Au(111) was prepared by
cycles of 1 keV Ar+ bombardment and annealing at 627 °C. MoS2 particles were
deposited by evaporation of Mo in 1 × 10−6 mbar H2S, with the Au substrate at
150 °C, followed by annealing at 450 °C in 2 × 10−6 mbar H2S.
High-pressure experiments. The employed gases (Westfalen AG), Ar N5.0, H2 N5.0,
and CH3SH N2.8 (main impurities dimethylsulfide and dimethyldisulfide) were fed
through particle filters before use. Their purity was confirmed using mass spectroscopy.
To prevent corrosion, the gas lines were made of Hastelloy C alloy, whereas the reactor
consists of PEEK, Zerodur glass, and Kalrez. Measurements on the bare Au(111) surface
under HDS conditions confirmed the absence of impurity deposition other than the
slow formation of a sulfur overlayer. All gas lines were flushed with argon for at least 30
min prior to each experiment. To start the high-pressure exposure, the reactor was
slowly pressurized in H2 and subsequently heated to the desired temperature. For the
HDS experiments, CH3SH was mixed in the reactor feed only after reaching 250 °C. In
order to minimize the thermal drift in the microscope, the system was allowed an
equilibration period of ~90 min. To cope with the remaining drift, image acquisition
times of around 20 s per image were employed and a drift correction was applied
(making use of the well-defined 60/120 degree angles in the particles). As the noise level
increased under high-pressure, high-temperature conditions, a 3 × 3 pixel averaging was
applied for clarity.
Theoretical analysis. All DFT calculations were carried out with the BAND program
package37–41, using the PBE density functional42, Grimme van der Waals corrections43,
and scalar relativistic corrections. A triple-ζ plus polarization basis set was used for the
valence orbitals, while the core orbitals were kept frozen in the same state as in the free
atoms. In general, default settings of the BAND program were used. The Self-Consistent
Field convergence criterion was set at 10−6 Hartree atomic units, while the geometrical
optimization criterion was set at 10−2 Hartree per nanometer.
A (4 × 4) MoS2 unit cell was employed, in the form of a stripe with periodicity
in one direction. The stripe contains both an S-type edge and an Mo-type edge. The
S-type edge was kept fully covered in all calculations (2 S edge atoms per Mo edge
atom). The length of the unit cell was kept at the value optimized for 50%S
coverage: 1.248 nm. For the calculations where the gold support was included, the
Au(111) surface was modeled by a 2 layer slab with a lattice parameter
commensurate with the MoS2 stripe. The S-Mo-S-Au-Au stacking was chosen as
A-B-A-B-C, with a S-Au layer spacing of 0.442 nm. The number of k points chosen
for sampling the Brillouin zone was 3 throughout.
Transition states were located as follows: for a chosen reaction coordinate (usually
an interatomic distance) total energies were computed for a range of fixed values
(while optimizing all other degrees of freedom). For the structure of highest energy a
partial hessian was calculated, including atoms at or close to the reaction site. The
most negative eigenvalue of this partial hessian was used to locate the saddle point. In
most cases the search had to be restarted several times by recomputing the partial
hessian on the structure with the smallest gradient found so far. It was checked that
the partial hessian of the final structure had precisely one negative eigenvalue.
The reaction energies (ΔEr) used in the computation of phase diagrams were
calculated per unit cell as:
ΔEr ¼ EMoS2 ;Sx Hy
EMoS2
1
y
2
x EH2 S
x EH2
ð4Þ
In Eq. 4, Ex denotes the total electronic energy obtained from DFT for the
respective structure. In order to calculate the free energy of an edge structure,
entropic corrections need to be applied:
ΔμS ¼ RT ln
ΔμH ¼
PH2 S
PH2
!
T SoH2 S
1
RT ln PH2
2
T SoH2
SoH2
ð5Þ
ð6Þ
The standard entropies (Sox) in these equations were obtained from
thermodynamic tables44. Using the entropic corrections, one can compute the free
energy change involved in a reaction as:
ð7Þ
ΔGr ¼ ΔEr x ΔμS y ΔμH
The structure with the lowest free energy per unit cell at a particular
combination of ΔμS and ΔμH values will be the phase present under those
conditions. Note that with this definition of the free energy, we assume that all solid
phases have zero entropy and that there is no change in heat capacity during the
reaction.
To model the adsorption of CH3SH, we first calculated the adsorption energy:
ΔEads ¼ EMoS2 ;Sx Hy ;MTz
EMoS2 ;Sx Hy
z EMT
ð8Þ
In Eq. 8, MT corresponds to CH3SH. The thermodynamic stability of the
adsorbed CH3SH structure was calculated as its formation free energy with respect
to the most stable phase in the absence of CH3SH adsorption:
ΔGf ¼ ΔEads
z ΔμMT þ ΔGr
MoS2 ;Sx Hy
ΔGr
MoS2 ;Sn Hm
ð9Þ
ð10Þ
ΔμMT ¼ RT lnðPMT Þ TSoMT
In Eq. 9, MoS2,SnHm is the most stable structure in the absence of CH3SH
adsorption.
Finally, we performed a kinetic analysis using the standard free energy barriers
that link the reaction intermediates. Entropic corrections (for standard conditions)
were again applied using Eqs. 5, 6, and 10. Rate constants were calculated from the
standard free energy barriers (ΔG°a) using transition state theory:
kB T kΔGToa
ð11Þ
e B
h
Here, we assume that there is no communication between adjacent unit cells.
Furthermore, it is assumed that only the six unit cell structures in Fig. 5 can be
formed. When the reaction reaches steady state, the coverages of all six structures
will be fixed. Thus, we obtain a set of linear equations, shown here for the example
of an intermediate with two links to other intermediates.
dθn
ð12Þ
¼ kn 1 θn 1 þ k n θnþ1
k ðn 1Þ þ kn θn ¼ 0
dt
In Eq. 12, n designates a particular structure, whereas n−1 and n+1 are the
structures before and after structure n in the reaction chain, respectively. Reactions
in the backwards direction are indicated by a minus sign (e.g., k-n). By solving this
set of equations, one obtains the steady state coverage of the various intermediates.
For a more detailed description of the model, see Supplementary Note 5.
k¼
Data availability
The data that support the findings in this study are available from the corresponding
author upon reasonable request. The STM images shown in the paper, the total energies
of the DFT of all considered edge structures (with and without Au support), and gas
phase molecules and the local density of state (summed between 0 eV and −0.3 eV vs. the
Fermi level) are provided as a Source Data file. Only commercially available software was
used for the analysis and representation of data.
Received: 15 May 2017 Accepted: 13 May 2019
References
1.
Silvy, R. P. Refining catalyst market begins to recover in 2010. Oil Gas. J. 108,
40–43 (2010).
2. Fahim, M. A., Al-Sahhaf, T. A. & Elkilani, A. Fundamentals of Petroleum
Refining. (Elsevier, Oxford, UK, 2010).
3. Farbenindustrie A. G., I. G. British Patent 315,439 (1928).
4. Helveg, S. et al. Atomic-scale structure of single-layer MoS2 nanoclusters.
Phys. Rev. Lett. 84, 951–954 (2000).
5. Hansen, L. P. et al. Atomic-scale edge structures on industrial-style MoS 2
nanocatalysts. Angew. Chem. Int. Ed. 50, 10153–10156 (2011).
6. Zhu, Y. et al. Visualizing the stoichiometry of industrial-style Co-Mo-S
catalysts with single-atom sensitivity. Angew. Chem. Int. Ed. 53, 10723–10727
(2014).
7. Kibsgaard, J. et al. Cluster-support interactions and morphology of MoS2
nanoclusters in a graphite-supported hydrotreating model catalyst. J. Am.
Chem. Soc. 128, 13950–13958 (2006).
8. Kibsgaard, J. et al. Scanning tunneling microscopy studies of TiO2-supported
hydrotreating catalysts: anisotropic particle shapes by edge-specific MoS2support bonding. J. Catal. 263, 98–103 (2009).
9. Tuxen, A. et al. Size threshold in the dibenzothiophene adsorption on MoS2
nanoclusters. ACS Nano 4, 4677–4682 (2010).
10. Brorson, M., Carlsson, A. & Topsøe, H. The morphology of MoS2, WS2,
Co-Mo-S, Ni-Mo-S and Ni-W-S nanoclusters in hydrodesulfurization
catalysts revealed by HAADF-STEM. Catal. Today 123, 31–36 (2007).
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications
7
ARTICLE
NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-10526-0
11. Lauritsen, J. V. et al. Hydrodesulfurization reaction pathways on MoS2
nanoclusters revealed by scanning tunneling microscopy. J. Catal. 224, 94–106
(2004).
12. Tuxen, A. K. et al. Atomic-scale insight into adsorption of sterically hindered
dibenzothiophenes on MoS2 and Co-Mo-S hydrotreating catalysts. J. Catal.
295, 146–154 (2012).
13. Moses, P. G., Hinnemann, B., Topsøe, H. & Nørskov, J. K. The hydrogenation
and direct desulfurization reaction pathway in thiophene hydrodesulfurization
over MoS2 catalysts at realistic conditions: a density functional study. J. Catal.
248, 188–203 (2007).
14. Moses, P. G., Hinnemann, B., Topsøe, H. & Nørskov, J. K. The effect of Copromotion on MoS2 catalysts for hydrodesulfurization of thiophene: a density
functional study. J. Catal. 268, 201–208 (2009).
15. Lauritsen, J. V. et al. Atomic-scale insight into structure and morphology
changes of MoS2 nanoclusters in hydrotreating catalysts. J. Catal. 221,
510–522 (2004).
16. Baubet, B. et al. Quantitative Two-Dimensional (2D) Morphology-Selectivity
Relationship of CoMoS Nanolayers: a Combined High-Resolution High-Angle
Annular Dark Field Scanning Transmission Electron Microscopy (HR HAADFSTEM) and Density Functional Theory (DFT) Study. ACS Catal. 6, 1081–1092
(2016).
17. Bollinger, M. V., Jacobsen, K. W. & Nørskov, J. K. Atomic and electronic
structure of MoS2 nanoparticles. Phys. Rev. B 67, 085410 (2003).
18. Prodhomme, P. Y., Raybaud, P. & Toulhoat, H. Free-energy profiles along
reduction pathways of MoS2 M-edge and S-edge by dihydrogen: a firstprinciples study. J. Catal. 280, 178–195 (2011).
19. Cristol, S. et al. Theoretical study of the MoS2(100) surface: a chemical
potential analysis of sulfur and hydrogen coverage. J. Phys. Chem. B 106,
5659–5667 (2002).
20. Dinter, N., Rusanen, M., Raybaud, P., Kasztelan, S. & Toulhoat, H.
Temperature-programed reduction of unpromoted MoS 2 -based
hydrodesulfurization catalysts: Experiments and kinetic modeling from first
principles. J. Catal. 267, 67–77 (2009).
21. Bruix, A. et al. In situ detection of active edge sites in single-layer MoS 2
catalysts. ACS Nano 9, 9322–9330 (2015).
22. Herbschleb, C. T. et al. The ReactorSTM: atomically resolved scanning
tunneling microscopy under high-pressure, high-temperature catalytic
reaction conditions. Rev. Sci. Instrum. 85, 083703 (2014).
23. Anabtawi, J. A., Alam, K., Ali, M. A., Ali, S. A. & Siddiqui, M. A. B.
Performance evaluation of HDS catalysts by distribution of sulfur compounds
in naphtha. Fuel 74, 1254–1260 (1995).
24. Wilson, R. L. & Kemball, C. Catalytic reactions of methyl mercaptan on
disulfides of molybdenum and tungsten. J. Catal. 3, 426–437 (1964).
25. Häkkinen, H. The gold–sulfur interface at the nanoscale. Nat. Chem. 4,
443–455 (2012).
26. Barth, J. V. V., Brune, H., Ertl, G. & Behm, R. J. Scanning tunneling
microscopy observations on the reconstructed Au(111) surface: atomic
structure, lon-range superstructure, rotational domains, and surface defects.
Phys. Rev. B 42, 9307–9318 (1990).
27. Lay, M. D., Varazo, K. & Stickney, J. L. Formation of sulfur atomic layers on
gold from aqueous solutions of sulfide and thiosulfate: studies using EC-STM,
UHV-EC, and TLEC. Langmuir 19, 8416–8427 (2003).
28. Lauritsen, J. V. et al. Location and coordination of promoter atoms in Co- and
Ni-promoted MoS2-based hydrotreating catalysts. J. Catal. 249, 220–233 (2007).
29. Grønborg, S. S. et al. Visualizing hydrogen-induced reshaping and edge
activation in MoS2 and Co-promoted MoS2 catalyst clusters. Nat. Commun.
9, 2211 (2018).
30. Füchtbauer, H. G. et al. Morphology and atomic-scale structure of MoS2
nanoclusters synthesized with different sulfiding agents. Top. Catal. 57,
207–214 (2014).
31. Kelty, S. P., Berhault, G. & Chianelli, R. R. The role of carbon in catalytically
stabilized transition metal sulfides. Appl. Catal. A Gen. 322, 9–15 (2007).
32. Jeon, J. et al. Epitaxial synthesis of molybdenum carbide and formation of
Mo2C/MoS2 hybrid structure via chemical conversion of molybdenum
disulfide. ACS Nano 12, 338–346 (2018).
33. Zhang, G., Chang, H., Wang, L. & Chou, K. Study on reduction of MoS2
powders with activated carbon to produce Mo2C under vacuum conditions.
Int. J. Miner. Metall. Mater. 25, 405–412 (2018).
34. Joshi, Y. V., Ghosh, P., Venkataraman, P. S., Delgass, W. N. & Thomson, K. T.
Electronic descriptors for the adsorption energies of sulfur-containing
molecules on co/mos2, using dft calculations. J. Phys. Chem. C. 113,
9698–9709 (2009).
35. Diemann, E., Weber, T. & Müller, A. Modeling the thiophene HDS reaction
on a molecular level. J. Catal. 148, 288–303 (1994).
8
36. Zhang, J., Yin, W., Shang, H. & Liu, C. In situ FT-IR spectroscopy
investigations of carbon nanotubes supported Co-Mo catalysts for selective
hydrodesulfurization of FCC gasoline. J. Nat. Gas. Chem. 17, 165–170 (2008).
37. Philipsen, P.H.T. et al. BAND 2014., SCM, Theoretical Chemistry, Vrije
Universiteit, Amsterdam, The Netherlands, http://scm.com (2014).
38. Te Velde, G. & Baerends, E. J. Precise density-functional method for periodic
structures. Phys. Rev. B 44, 7888–7903 (1991).
39. Wiesenekker, G. & Baerends, E. J. Quadratic integration over the threedimensional Brillouin zone. J. Phys. Condens. Matter 3, 6721–6742 (1991).
40. Franchini, M., Philipsen, P. H. T. & Visscher, L. The becke fuzzy cells
integration scheme in the amsterdam density functional program suite.
J. Comput. Chem. 34, 1819–1827 (2013).
41. Franchini, M., Philipsen, P. H. T., Van Lenthe, E. & Visscher, L. Accurate
Coulomb potentials for periodic and molecular systems through density
fitting. J. Chem. Theory Comput. 10, 1994–2004 (2014).
42. Perdew, J. P., Burke, K. & Ernzerhof, M. Generalized gradient approximation
made simple. Phys. Rev. Lett. 77, 3865–3868 (1996).
43. Grimme, S., Ehrlich, S. & Goerigk, L. Effect of damping function in dispersion
corrected density functional theory. J. Comput. Chem. 32, 1456–1465 (2010).
44. NIST. Computational Chemistry Comparison and Benchmark Database.
http://cccbdb.nist.gov/ (2016).
Acknowledgements
This project was financially supported by a Dutch SmartMix grant and by NIMIC
partner organizations through NIMIC, a public–private partnership. I.M.N.G.
acknowledges the Dutch organization for scientific research for her Veni fellowship. The
Dutch organization for scientific research is also thanked for providing computing
time on the Cartesius facility (grant numbers 15283 and SH-325-15). The authors thank
Dr. Stig Helveg (Haldor Topsøe company), Dr. Bart Nelissen (Albermarle Corporation)
and Prof. Dr. Eelco Vogt (Albemarle Corporation/Utrecht University) for fruitful
discussions.
Author contributions
R.V.M., I.M.N.G. and J.W.M.F. designed the STM experiments. J.N.L. preformed the
DFT calculations. R.V.M. performed the STM experiments, the thermodynamic analysis
and wrote the paper. All authors contributed to discussions and interpretation of
the data.
Additional information
Supplementary Information accompanies this paper at https://doi.org/10.1038/s41467019-10526-0.
Competing interests: The authors declare no competing interests.
Reprints and permission information is available online at http://npg.nature.com/
reprintsandpermissions/
Journal peer review information: Nature Communications thanks Yucheng Huang and
other anonymous reviewer(s) for their contribution to the peer review of this work. Peer
reviewer reports are available.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations.
Open Access This article is licensed under a Creative Commons
Attribution 4.0 International License, which permits use, sharing,
adaptation, distribution and reproduction in any medium or format, as long as you give
appropriate credit to the original author(s) and the source, provide a link to the Creative
Commons license, and indicate if changes were made. The images or other third party
material in this article are included in the article’s Creative Commons license, unless
indicated otherwise in a credit line to the material. If material is not included in the
article’s Creative Commons license and your intended use is not permitted by statutory
regulation or exceeds the permitted use, you will need to obtain permission directly from
the copyright holder. To view a copy of this license, visit http://creativecommons.org/
licenses/by/4.0/.
© The Author(s) 2019
NATURE COMMUNICATIONS | (2019)10:2546 | https://doi.org/10.1038/s41467-019-10526-0 | www.nature.com/naturecommunications