Peer review of: Site-dependent reactivity of MoS2 nanoparticles in hydrodesulfurization of thiophene (2020)

REVIEWER COMMENTS

Reviewer #1 (Remarks to the Author): 

In this paper, the authors investigate a very important catalytic reaction, hydrodesulfurization. Although 
a lot has been found about this process, still many details remain unclear. This paper sheds new light on 
HDS of thiophene, and especially on the question how it adsorbs to the catalyst to have its S atom 
abstracted. The insight that S atoms of the catalyst move to create space for the bulky thiophene is very 
interesting for the community. Therefore, I advise this paper to be published, after the following minor 
issues have been solved. 

line 67: what are exact MoS2 structures? Please rephrase. 
Fig. 1a: It is clear from the STM image that the number of vacancies is different on the three Mo edges. 
Is this a general observation for all MoS2 nanoparticles? Has this been analyzed for many nanoparticles 
and can the difference be explained by statistical fluctuations? Or is there possibly another explanation? 
Please clarify this in the text. 
Fig. 1c: in the bottom structure, the vacancies are named with M, but they are also adjacent to a corner, 
so A. Why do you choose for M, and not A? Is it because they behave more as M? Please clarify. 
Fig. 2d: label x-axis. For readers less familiar with HDS and its conventions it would be more clear to call 
it the Mo edge instead of M-edge. 
Fig. 3a: add labels to the edges in the STM image. 
around line 221: if the adsorption of thiophene to certain sites is hindered by its structure, i.e. is a steric 
effect, how can it then be explained that the adsorption changes at higher temperature? Does the size 
of the vacancy change at higher T? The size of the thiophene will not change. Please clarify. 
line 231: how do you know that this is due to hydrogenolysis and not just desorption of thiophene 
because of the higher T? 
Fig. 4: please label the edges. 
line 275: how does the thiophene adsorb over both the A and M sites? Probably not via the S atom to 
the vacancy. Please explain. 
Fig. 5: this figure can be improved in the following way: 
a) remove more black so that MoS2 can be bigger 
b) label S2 is unreadable 
c) mention in the caption what the blue arrow in a corresponds to 
d) mention in the caption the tunneling parameters 
line 335: it is not clear to me how the authors conclude on the amount of V_s under reaction conditions 
since their work is performed under UHV conditions. If, however, this is my mistake, and their work has 
been performed under reaction conditions, this should be made clearer from the text. 



Reviewer #2 (Remarks to the Author): 
Salazar et al. report a model study of the industrially-relevant hydrodesulfurization on MoS2 catalysts. A 
model catalyst, single-layer MoS2 nano-islands grown on Au(111), and a model reaction, thiophene 
(hydro)desulfurization, were employed and studied by experimental (mainly STM) and theroretical (DFT) 
methods. 

Distinct differences in the thiophene-catalysts interactions at preformed S-vacancies at edge and corner 
sites (and even differently within edges) were observed. Thiophene adsorption alone leads to 
restructuring of the S atoms on neighboring sites around the initial vacancy sites. One could question 
whether the model compound thiophene really mimics the much more stable sulfur-containing 
compounds in gas oil feeds, but that´s true for all model studies. 

The work was performed on the highest technical level and all analysis and interpretations are thorough 
and sound. My main concern is rather that the very same model system was studied for about two 
decades and the major breakthroughs of this model system have already been published in general high 
impact journals, whereas the further progress – although important – seems rather incremental and 
only relevant for specialist in the field. 



Reviewer #3 (Remarks to the Author): 

The authors present a combined STM-DFT study of thiophene absorption on edge sites of MoS2 
nanoparticles and suggest a mechanism of S-deplacement to allow incorporation of larger functional 
groups onto neighbouring edge sites. 

In general I find that the subject of the paper is interesting, and the approach of combining STM with 
DFT studies is useful. However a problem with such an approach is that the images can be easily 
interpreted many different ways, and attention focussed just on specific aspects of the images. That 
appears to be the case with the current paper where the argument is heavily "driven" in favour of the 
model proposed by the authors, and alternative explanations and mechanisms are not covered and 
quantitatively dismissed sufficiently. 

As some specific examples, the authors state there is no change in basal plane properties after exposure 
to thiophene, but do not provide any quantitative support for this statement. Basal plane vacancies 
appear visible in their STM images, and to justify their claim it would necessary to show for example 
statistics of basal plane vacancy concentration before and after thiophene treatment to demonstrate 
this does not change (an extension of Figure 3b). 

Similarly the discussion focusses on the Mo-edges, but the shorter S-terminated edges appear to show 
extensive changes and variation in the different images. For example in Figure 5 there appears extensive 
variation in functionalisation, presence of vacancies, intensity variation (suggesting mono-S rather than 
S2?) etc. The authors would need to also exclude these more quantitatively from their study to show 
thiophene treatment is indeed functionalising purely the Mo-edges. 

Other candidates are S2 dimers and extrinsic impurities. There is often varying contrast along the image 
edges in the author's STM images, can the authors exclude S2 dimers and also extrinsic impurities? (for 
example alongside the top and right corners of Figure 1a, but not the left). Although formally charged, 
S2 structures could be stabilised by charge transfer from the gold substrate. 

Secondly, the authors discuss variation in vacancy concentrations but do not provide sufficient statistics. 
How many flakes and sites were examined? And what was the statistical breakdown of particle size 
(side-length)? What fraction of examples have multiple vacancies on the same side? There is a brief 
discussion of coupled vacancy formation energy right near the end but this would be useful also when 
vacancy formation is first discussed. Detailed quantitative information on the statistics (including ideally 
expansion of the various Figure 2 images) is important, not least because it may be certain side-lengths 
(/particle sizes) dominate the catalytic behaviour. This is information which needs to be in the paper. 

Figure 2d should be extended to also include the equivalent lines for A and M sites. 

Concerning the theoretical calculations, these seem strong and I particularly appreciated Table S1. A few 
points: 
- Could the authors quote the vacancy formation energy for periodic 1H-MoS2 calculated this way, as a 
reference value? (and/or for continuous stripe models, as the authors already have these). 
- H2S is used as the reference source for sulfur in the formation energy calculation. Can the authors 
explain why (and not, for example, S6 rings?) 
- The Gaussian smearing used is quite high and suggests there were some issues achieving convergence 
(which could be linked to the spin). The authors say the formation energies were not significantly altered 
by spin but I suspect the energy difference would be higher with a much lower Gaussian smearing. Since 
the energies are not really being used quantitatively here it doesn't seem critical to the arguments in the 
paper. 
- If possible, calculated STM images of the structures would improve the paper (there are freeware 
packages given the authors are using VASP). 

Minor points: 

There appears a difference between the modelling and experiment for the S-edge; it appears as if the 
central S-pair extend further out from the edge in the DFT image, whereas in Figure 1a the exprimental 
image appears to show the inverse. Can the authors explain this. 

Line 97 refers to Figure 1a but this does not really show the atomic structures as suggested in the text. 

In general I find that it is a strong and well-constructed paper, but at the moment it is too focussed and 
lacking the "broad interest" aspect for a Nature Communications (but would be an excellent article in a 
more specialised journal). If the authors were to convincingly address all of the wider points above, it 
might then be suitable for Nature Communications.