An Insight into the Efficient Dimethoate Adsorption on Graphene-Based Materials—A Combined Experimental and DFT Study

Round 1

Reviewer 1 Report

This work deals with a thermodynamic and structural study of  the interaction of DMT with two G-based sorbents, pristine G and GO. The study has been done on the basis of adjusting the data from adsorption isotherms on both sorbents to suitable theoretical models, together to modelization of the adsorbent-adsorbate systems. Concerning this last the models elected for the graphene surfaces seems too simple (particularly that of GO). Probably the study could have been improved if previous characterization of the oxygen functional groups had been done through XPS data from used GO.

The work is well done, although it doen`t provide striking results; on the contrary, these were quite predictable, i.e. the adsorbent-adsorbate interactions are mainly directed by The Van der Waals forces. Nevertheless the work methodology is interesting for the researchers working in this research field.

Another issues the author should address:

1) In page 9 (294 row) The Eads value done is 2,5 (units) but in accordance with Table 4, the right value should be c.a. 2,6 (units).

2) In the text of page 6 of the manuscript, it is stated that "...obtained ne gative values of Gibbs`s free energy  of adsorption in all investigated cases confirm that  adsorption at 298 K is exothermic and spontaneous...." but spontaneity should derives from the enthalphy of the process.

3) The results when applying the Langmuir equation to the isotherm data from DMT adsorption on IG (Figure 4a) need an special comment in the text.

4) English should be revised.

On the basis of the above, a should recommend the piublication of this paper once the above point have been addressed  

Author Response

1. Comment: The study has been done on the basis of adjusting the data from adsorption isotherms on both sorbents to suitable theoretical models, together to modelization of the adsorbent-adsorbate systems. Concerning this last the models elected for the graphene surfaces seems too simple (particularly that of GO).

Answer: Thank you for the interesting observation. Beside the MV and oxydefect, two additional defect model surfaces (Stone-Wales defect and N-defect) are now included in the DFT investigation. The results are presented in Section 3.2.  We hope that it will be satisfactory for you.

2. Comment: Probably the study could have been improved if previous characterization of the oxygen functional groups had been done through XPS data from used GO.

Answer: The detailed analysis of used adsorbents was performed in our previous paper (Ref.20).  The following text is  inserted in the second paragraph of the Introduction (after the second sentence) to give some information concerning the characterization of GO and IG and oxygen functional groups:

The spectroscopic analysis of GO and IG includes Raman,  XRD, XPS (C 1s and O 1s spectra), and FTIR methods [20]. IG has a specific surface area (SSA)  600 m² g⁻¹  with a relatively small concentration of oxygen functional groups and effectively separated graphene layers. However, the aggregation of graphene sheets cannot be excluded. GO with SSA of 10 m² g⁻¹ has a highly disordered structure and low fraction of sp² hybridized carbons due to a large concentration of different oxygen functional groups attached to its surface. Due to a large concentration of oxygen functional groups, this material is highly hydrophilic and easily dispersed in water with effectively separated sheets and the dispersed material. XPS method confirmed a significant variation in the C/O ratio among the studied adsorbents, and GO contains almost 30 at% oxygen. The adsorbent, denoted as IG contains approximately 6 at% oxygen and a largely preserved π electron system.

3. Comment: In page 9 (294 row) The E_ads value done is 2,5 (units) but in accordance with Table 4, the right value should be c.a. 2,6 (units).

Answer:  Thank you for careful reading. However, following the remarks of other two reviewers, in the revised version the calculations were completely redone with denser k-point grid, and the number slightly changed. The new Eads value now is 2.43, and the accompanying text is also modified:

This process resulted in the overall stabilization of the system by 2.35 eV in case of O-binding, and 2.43 eV in case of S-binding geometry(Eq 1, Table 4). 

4. Comment: In the text of page 6 of the manuscript, it is stated that "...obtained ne gative values of Gibbs`s free energy  of adsorption in all investigated cases confirm that  adsorption at 298 K is exothermic and spontaneous...." but spontaneity should derives from the enthalphy of the process.

Answer: We accepted the suggestion and deleted the word  ”spontaneous”.

5. Comment: The results when applying the Langmuir equation to the isotherm data from DMT adsorption on IG (Figure 4a) need an special comment in the text.

Answer: To comment the results presented in Fig.4a, two corrections were introduced:

3. The following text was included at the end of the first paragraph in the Section 3.1.2.:

However, a significant deviation was observed when applying Langmuir isotherm for DMT adsorption on 2 g dm^-3 IG (Fig.4a). We believe that certain agglomeration occurred at its increased concentration. In that way, the monolayer formation of DMT on IG surface was disturbed, and the Langmuir model was not appropriate for that case.

1. b) The note below Table 2 is added:
2. ^a) Langmuir isotherm parameters are given for 0.25 g dm^-3 IG
3. Comment: English should be revised.

Answer: English was revised by using the Advanced version of Open Grammarly  Premium digital writing assistance tool.

Author Response File: Author Response.pdf

Reviewer 2 Report

In this experimental and theoretical collaboration, the authors studied the adsorption of dimethoate (DMT) on industrial graphene (IG) and graphene oxide (GO). In experiments, the authors measured the concentration of bounded DMT versus (1) the free concentration of DMT in one case and (2) the concentration of binding sites of IG and GO in another case. Analysis of the measured data indicates cooperative binding and yields thermodynamic parameters of the binding process. The authors also performed density-functional- theory-based calculations to reveal the adsorption energies with and without defects. The findings are interesting. I would recommend its publication in Applied Sciences after the following questions are addressed. 

1. Could the authors comment on temperature effects on the adsorption process? 

2. In Fig. 5, the PDOS of pristine graphene exhibits many peaks within 3 eV, which indicates that the number of k points is insufficient. More k points are needed to calculate the PDOS. The authors should also check whether more k points are needed to calculate the adsorption energy. The k-point sampling should be described in section 2.4. 

3. In lines 213-215, the authors compared fitted \Delta G with DFT Eads and claim a good agreement. I don’t see why there is good agreement since (1) the entropy contribution to free energy is not included in DFT, and (2) the lower DFT Eads (most preferable adsorption) is more than two times larger than the fitted \Delta G in magnitude. 

4. Why not considering Stone–Wales defects in graphene, which are more common than single carbon vacancies? 

5. In lines 298 and 299, the authors used a PDOS peak at ~ -12 eV as evidence for chemical bond changes. Intuitively, chemical bonds are formed by frontier orbitals which should be close to the Fermi level while -12 eV is far below the Fermi level. Could the authors elaborate on the relation between the PDOS peak at ~12 eV and chemical bond changes? 

6. The rest comments/questions are on writing and figures. 

6.1 In Fig. 1, what are the vertical lines? The symbols for chemical elements are too small. 

6.2 The abbreviation QE should be defined when it is used for the first time in line 117. 

6.3 In Figs. 2, 3, and 4, the x/y labels and legends are too small. It may also be better to use thicker lines and larger dots.

6.4 The abbreviation PDOS, which usually stands for the projected density of states, is misused. The authors can use DOS when presenting the total density of states. 

Author Response

1. Komentar: Da li autori mogu da komentarišu temperaturne efekte na proces adsorpcije?

Odgovor: Temperaturni efekat na proces adsorpcije procenjen je korišćenjem 0,250 mg/ml GO u prisustvu 5x10^-4 M DMT. Štaviše, u nastavku našeg rada na tom polju, neki pesticidi, uključujući I DMT, na seriji drugih GO materijala su pod istragom i novi papir je pod pripremom. U korigovanoj verziji sadašnjeg papira, sledeći tekst je umetnut na kraju odeljka 3.1.2, ispod tabele 2.

U nezavisnom eksperimentu, 0.250 mg/ml GO je korišćen za adsorpciju 5x10^-4 M DMT kao model sistema za procenu temperaturnog efekta na proces adsorpcije. Primećeno je blago povećanje sorbed DMT koncentracije (5.90x10^-6 M,^{6.53x10 -6}M i 7.98x10^-6 M na 298, 303 odnosno 308 K). Vredi primetiti da su temperaturni efekti DMT adsorpcije na neke slične komercijalne grafenske materijale (SM GO i GNA GO) ukazali na isti trend koji zavisi od temperature (koji treba objaviti). Ovakvo ponašanje je karakteristično za hemijsku adsorpciju zbog visoke energije aktivacije kada se obim stope adsorpcije poveća u početku i mogao bi da se smanji kako se temperatura dodatno povećava.

2. Komentar: U Sličju 5, PDOS prištinski grafen ispoljava mnoge vrhove u krugu od 3 eV, što ukazuje na to da je broj k poena nedovoljan. Za izračunavanje PDOS-a potrebno je više k tačaka. Autori bi takođe trebalo da provere da li je potrebno više k poena za izračunavanje energije adsorpcije. Uzorak k-tačke treba opisati u odeljku 2.4.

Odgovor: Hvala na veoma korisnoj primedbi. U prvoj verziji izračunavanja rukopisa urađeno je samo u gama tački. U izmenjenoj verziji korišćen je Monkhorst – Pack k-point uzorak, a energija adsorpcije i DOS-a se ponovo izračunavaju. Gustina K-point mreže je bila 4x4x1 za 32-atom ćeliju i 2x2x1 za 128-atom ćeliju. Bilo je nemoguće izvršiti izračunavanje sa mrežom veće gustine u realnom vremenu, zbog tehničkih ograničenja raspoloživih kompjuterskih resursa. Međutim, broj vrhova je smanjen i doS plotovi se menjaju nakon adsorpcije sada se lakše prate (Smokve 5 i 7).

U odeljku 2.4 dodata je rečenica:

Uzorkovanje k-poena izvršeno je korišćenjem šeme Monkhorst-Pack (4×4×1 k-poen za ćeliju od 32 atoma i 2×2×1 k-poen za ćeliju od 128 atoma) [33].

3. Komentar: U redovima 213-215, autori su uporedili fited \Delta G sa DFT Eads i tvrde da je to dobar dogovor. Ne vidim zašto postoji dobar dogovor s obzirom da (1) entropski doprinos slobodnoj energiji nije uključen u DFT, a (2) donji DFT Eads (najpožetnija adsorpcija) je više od dva puta veći od uklopljenog \Delta G u magnitudi.

Hvala na važnom zapažanju. Kazna je izbrisana. U izmenjenoj verziji, poređenje između DeltaG-a i Eads-a je potpuno isključeno iz rukopisa, jer je bilo nemoguće izvršiti proračune entropskog doprinosa u realnom vremenu.

U izmenjenoj verziji, Eads vrednosti na netaknutom grafenu su izračunate i u 128-atomu i u ćeliji od 32 atoma, a utvrđeno je da mogu biti zavisne od pokrivenosti – niže su u velikoj ćeliji (oko 0,6 eV) u poređenju sa manjim ćelijama (oko 1 eV). Shodno tome, umesto direktnog poređenja apsolutne eksperimentalne i teorijske energetike, diskusija o DFT istragama je sada prilično fokusirana na osnovne principe i prirodu procesa adsorpcije.

U tekst su uključene sledeće rečenice:

Dobijena adsorpciona energija potvrđuje eksperimentalne nalaze - da je vezivanje dimetoata na grafenu termodinamički povoljno, najverovatnije zbog fiziorpcije. Štaviše, veća snaga adsorpcije u manju (3×3) supercelu podrazumeva da energija adsorpcije zavisi od površinskog pokrivanja u istraženi opseg.

4.Komentar: Zašto ne uzimajući u obzir stoun–Vels nedostatke u grafenu, koji su češće od jednog upražnjenog mesta ugljenika?

Odgovor: Hvala na korisnom predlogu. SW defekt je sada uključen u model površine grafena. Rečenica je dodata:

Uporedo sa adsorpcijom na netaknutom grafenu, razmatrano je i nekoliko neispravnih površina modela – Stone-Wales defect, N-defect, oxydefect i monovakancy defect.

Međutim, MV defekt je zadržan u studiji s obzirom da je jedini među istraženim nedostacima koji su ispoljali određenu hemijsku reaktivnost prema dimetoatu. Za druge nedostatke tipa, uključujući SW, primećena reaktivnost je bila prilično slična kao u slučaju netaknutog grafena.

5. Comment: In lines 298 and 299, the authors used a PDOS peak at ~ -12 eV as evidence for chemical bond changes. Intuitively, chemical bonds are formed by frontier orbitals which should be close to the Fermi level while -12 eV is far below the Fermi level. Could the authors elaborate on the relation between the PDOS peak at ~12 eV and chemical bond changes? 

In the revised version with denser k-point grid, the observed peak dissapeared. According to your suggestion, discussion is now focused on the changes in the range from Fermi level to -3 eV. Moreover, with denser k-grid, in case of MV defect, the DOS minimum at the Fermi level that appeared upon the dimethoate adsorption, most obviously points to the stabilization of the system.

The sentence “Redistribution of chemical bonds observed in geometry optimization is followed by a significant transfer of electrons to the graphene surface. The formation of a novel PDOS peak at about -12 eV also points to chemical bond changes upon adsorption (Fig. 7a).”

was replaced with:

Widening of DOS peaks is obvious, particularly for the peaks from the Fermi level to about -2.5 eV. Particularly, the appearance of a DOS minimum at the Fermi level represents the evidence of system stabilization upon dimethoate adsorption on MV-defect surface.

6. Comment: The rest comments/questions are on writing and figures.

6.1 In Fig. 1, what are the vertical lines? The symbols for chemical elements are too small. 

-The explanation and color code were added in the legend of Figure 1:

Figure 1. 3D structure of DMT. Horizontal and vertical lines represent the dimensions of the rectangular box used for estimation of the size of adsorption site (Section 3.1.1). Color code: carbon=black, sulphur= light yellow, phosphorus= yellow,oxygen=dark red, hydrogen= turquoise, nitrogen=grey.

We hope that the clarity of the image is now improved.

6.2 The abbreviation QE should be defined when it is used for the first time in line 117. 

-In Section 2.4 it was added Quantum ESPRESSO (QE).

6.3 In Figs. 2, 3, and 4, the x/y labels and legends are too small. It may also be better to use thicker lines and larger dots.

-The size of symbols is now increased. The high-resolution images in .tiff format are also attached.

6.4 The abbreviation PDOS, which usually stands for the projected density of states, is misused. The authors can use DOS when presenting the total density of states. 

-The mistake is now corrected.

Reviewer 3 Report

The authors present an experimental and theoretical study of the adsorption of DMT on graphene. In the theoretical part of the work, there are serious shortcomings that should be eliminated before re-consideration of the manuscript.

1. DMT has only one double C=O bond. Hypothetically, this bond could play an important role in the DMT interaction with graphene. However, the interaction of this active oxygen atom with graphene has not been considered.
2. In Table 3, a weaker interaction corresponds to a higher charge transfer. This strange fact should be explained.
3. In Table 4, the concave position of the oxygen atom is considered for oxygen-doped graphene. This position corresponds to a low reactivity. If one places the DMT on the other side of the graphene (convex position of oxygen atom), the stronger interaction will probably be observed.
4. Dissociation of DMT on graphene with a vacancy most likely requires overcoming the activation barrier, which must be calculated.
5. The two defects selected (MV and O) do not seem to be the most frequent defects in graphene. If they are really more common than other defects, please provide a reference that clearly confirms this fact. Otherwise, more likely defects (such as the Stone-Wales defect and the embedded nitrogen atom) should be also considered.
6. In summary, I recommend to reconsider the Manuscript after major revision.

Author Response

The authors present an experimental and theoretical study of the adsorption of DMT on graphene. In the theoretical part of the work, there are serious shortcomings that should be eliminated before re-consideration of the manuscript.

1.Comment  DMT has only one double C=O bond. Hypothetically, this bond could play an important role in the DMT interaction with graphene. However, the interaction of this active oxygen atom with graphene has not been considered.

Answer: Thank you for your suggestion. In the revised version, the DFT caluclations were redone, and C=O (“O-binding”) input geometry has been added into consideration on all investigated surface models. Results are presented in Section 4.2.

2.Comment  In Table 3, a weaker interaction corresponds to a higher charge transfer. This strange fact should be explained.

Answer: Thank you for the interesting observation. Although the observed effect is not completely impossible (for example, in systems with strong covalent binding) it would be quite unusual in our system.  This was probably an artefact due to poor electronic sampling (in the first version calculations were done only in gamma point).

In the revised version of the manuscript, caluclations were completely redone with denser k-point grid (4x4x1 k-points instead of  only gamma point in previous version). We believe that now electronic structure properties are more reliable. The charge transfer analysis in the revised version has shown that, (except, eventually, in case of MV-defect) there was no significant charge transfer in any of the considered system – in all cases it was below 0.012 electrons per DMT molecule. This was expected, as the DOS analysis and optimized adsorbate-to-surface distances point to physisorptive rather than chemisorptive interaction. Hence, in the revised version, the charge analysis is, along with DOS analysis, employed rather to confirm the absence of the chemical bond than to analyze its nature. Results are presented in Section 3.2, Tables 3 and 4.

3.Comment: In Table 4, the concave position of the oxygen atom is considered for oxygen-doped graphene. This position corresponds to a low reactivity. If one places the DMT on the other side of the graphene (convex position of oxygen atom), the stronger interaction will probably be observed.

Answer: Thank you for the interesting observation. In the revised version of the manuscript, adsorbate was positioned on the convex site of defect surface. Unfortunately, it did not contribute to the increase of interaction strength or formation of the chemical bond between DMT and defect – optimized output gemetry and energetic and electronic properties remain similar to these of pristine graphene.

4.Comment: Dissociation of DMT on graphene with a vacancy most likely requires overcoming the activation barrier, which must be calculated.

Answer: Thank you for opening an important question. The observed dissociation process is more complex than only adsorption, and thus adsorption energy cannot be used as the reliable descriptor. Unfortunately, it was not possible to calculate the activation barrier of the process, due to the limited computational resources. The following text was added:

The dissociation represents a chemical change, where DMT oxygen or sulfur atoms (depending on the input geometry) are incorporated into the vacant site of the gra-phene structure. This process resulted in the overall stabilization of the system by 2.35 eV in case of O-binding, and 2.43 eV in case of S-binding geometry(Eq 1, Table 4). As observed dissociation process is more complex than simple non-dissociative chemi-sorption, electron transfer was not calculated for the case of MV defect, while “adsorp-tion energy” rather refers to “stabilization energy”, denoted by »-sign in Table 4.

5. Comment: The two defects selected (MV and O) do not seem to be the most frequent defects in graphene. If they are really more common than other defects, please provide a reference that clearly confirms this fact. Otherwise, more likely defects (such as the Stone-Wales defect and the embedded nitrogen atom) should be also considered.

In the revised version, Stone-Wales defect and embedded nitrogen (N-defect) were taken into consideration, along with MV and O defects. Results are presented in Section 4.2. We hope that it contributed to the more complete and reliable description of graphene surface features.

The sentence “most frequent surface features” is replaced with “surface features that could be of potential interest for their interaction with DMT molecule”.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

The authors completely rewrote the theoretical part of the work. In the revised form, it looks much more adequate. I think that the manuscript can be accepted.

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.