Ab-Initio Investigations on Hydrogen Dissociation and Cross-Linking of Hydrocarbon Chains of Self-Assembled Monolayers of Alkanes

Round 1

Reviewer 1 Report

Manuscript : applsci-1716684-peer-review-v1 report
Title

ab-initio investigations on hydrogen dissociation and cross-
linking of hydrocarbon chains of self-assembled monolayers of
alkanes

In this paper,  authors have performed first-principles calculations, to study the structural and electronic proper-
ties of hydrocarbon chains of self-assembled monolayers with a hydrogen bombardment. It is found
that the hydrogen impact could lead to form H2 molecules by striping the nearby hydrogen atoms
in the chains and leave the neighboring carbons to be free radical.

Authors, found that among H atoms, protons, and H2 molecules, H atoms may be the better candidate
to cleave the hydrogen atoms from the chains.
Authors claim that the present study should be helpful for the enhancement of mechanical and chemical strength of self-assembled monolayers and enlarge the scope of the application of low-dimensional organic materials.

Recommendation

I consider the reported results are relevant, and can be published in  the journal, "Applied Sciences", after revision.

Comments

1. In the title, first letter should be CAPITAL 
   "ab-initio investigations on hydrogen dissociation" should change to  "Ab-initio investigations on hydrogen dissociation"
   

2 In the abstract

 "hydrogen impact could lead to form H2 molecules" please rewrite to  "hydrogen impact could lead to the formation of H2 molecules"

3. In the Introduction part, few important citations are missing: 

3.1. Acc Chem Res. 2015 Apr 21;48(4):1053-64
3.2. J. Phys. Chem. A 2010, 114, 2655–2664
3.3. Molecules. 2020 Dec 13;25(24):5900
Authors should cite these journals.

4. Authors have given adsorption energy of three  typical adsorption, for example,  H, H+, or H2,  
   based on the adsoption energy, the authors should describe what kind of interaction involved there, say example, 
Van der Waals, or Hydrogen bonding or non-covalent interactions ?

5. Authors state that "alkane is a common polymer precursor and widely used as a functional organic material", provide citation there.

6. Page 5 authors conclude that "the unoccupied states are pushed downward and filled due to the
forming of the C-C direct bond", any quantum chemical proof for such a statement ?

7. In the experiments, the long molecules may prefer the ‘shoulder to shoulder’ 
cross-linking, while the short molecules prefer the cross-linking mode of ‘head to head’.

please provide enough citations from experimental side for this comment.

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

The paper “ab-initio investigations on hydrogen dissociation and cross-2 linking of hydrocarbon chains of self-assembled monolayers of 3 alkanes” is well written and meet the standards of the Journal “Applied Sciences” for publication. But, I have certain queries/ suggestions regarding this work:

1. Page-2, Line No. 70, “change-correlation interaction descried by the projector-augmented” should be “change-correlation interaction described by the projector-augmented”
2. Page 3, Line 110 “The bond lengths and bond angles of the carbon atoms with the dangling bonds in the chain vary much during the process”---This sentence needs a change for better clarity. The suggested change is “The bond lengths and bond angles of the carbon atoms with the dangling bonds in the chain vary substantially during the process”
3. There are number of places where H₂ is mistakenly written as H2 e.g., Page 2, Line 86, Page -4, Line -123 and Line -127 etc. The author is advised to check the manuscript thoroughly.

Comments for author File: Comments.pdf

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

The paper by Zhu et al discusses DFT calculations of hydrogen adsorption on simple hydrocarbon chains. There are some interesting aspects in the research carried out, and the paper may be worth publishing. However, there are some critical issues which have to be tackled before publication. In addition, the paper contains quite few new results. The presentation is also partly lacking.

1) Lines 99-117: The adsorption of single hydrogen atoms is explained quite
badly.

First, if the adsorption energy is described as in Eq. (1) this means that
positive adsorption energy corresponds to non-binding situation. This means that adsorption of H on the chain is not stable. The relaxation of ions in the
simulation can lead to configuration with a positive adsorption energy only if
the adsorption site is metastable. Is this the case here? The potential energy
curve of Figure 3 corresponds to repulsion - and is definitely not a curve
describing adsorption (not even metastable) since it totally lacks any minima.

The calculations carried out to produce the data in Figure 3 are not explained
either: Were some of the ions relaxed during the calculations? If not, then the
data is not worth much. Using, e.g., NEB to calculate the barrier would
drastically increase the informative value here. Another option would be to
start from the calculated H adsorption site and withdraw the H atom while
allowing ions close to H to relax during each step further from the chain.

The obtained -0.87 eV energy is actually very interesting since it show that
there is a process where a single H atom getting close enough to the chain could detach another H atom and form H2 molecule with it. This is of course the result the authors are looking for, but this is not emphasized in the text.

Second, if I understood it correctly there are not three adsorption but the
authors tried three different initial configurations which all lead to some
final configuration. As discussed above, I think that this configuration
corresponds to metastable situation.

2) Table 1: The simulations with H+ are very suspicious. In plane wave DFT the electrons are relaxed and do not belong to any of the ions. The normal way to carry out this kind of calculation is to remove one electron from the whole system. This again leads to two possibilities: Either the super cell is charged which leads to such problems that the calculated adsorption energies are not reliable at all, or one uses constant background charge. This is not discussed at all. I suggest that the authors remove H+ calculation data if they are not sure what they have calculated, or improve the discussion.

3) Lines 150-168: The cross-linking is also quite interesting but the authors
could provide more data on this, e.g., what is the energetic difference between structures of Fig 4a and 4b.

4) Lines 192-212:  The comparison of shoulder-to-shoulder vs head-to-head interaction needs also some more discussion. Are the ions relaxed in the calculation? I would suspect that there would H-bonds between the chains in shoulder-to-shoulder -structures which would have an impact on the total energy. Also the super cells are of different sizes so affects total energy. 

Small things:
Abstract: There are no calculations of hydrogen bombardment carried out
here. Please rephrase. 
Line 73_ 10^-5
Lines 93-117: Doesn't the angle confirm that actually a C-C double bond has been formed?

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

I recommend the manuscript for publication

Reviewer 3 Report

The paper has been significantly improved after last reviewing round. Even though the computations are not at state-of-the-art level, the connection to the experiments makes the paper certainly of interest to the readers of the special issue. Thus, I recommend publishing the paper.