Oxygen Interactions with Covalently Grafted 2D Nanometric Carboxyphenyl Thin Films—An Experimental and DFT Study

Round 1

Reviewer 1 Report

The manuscript describes a method for covalently attaching carboxyphenyl
(PhCOOH) groups to a gold electrode. The resulting grafted surface has been
characterized using CV ellipsometry and XPS. Finally, DFT approaches has been used to get insights into the  interaction with oxygen of the PhCOOH adsorbed on Au.

The paper can be considered for publication provided that the following issues are addressed.

1) At the end of page 6: "As seen in Figure 5 (P3 and P4), the interaction is influenced by the oxygen molecule's initial arrangement." Does this mean that P1 and P2 are not influenced? Why?

2) The P1-P4 geometries in figure 5 are not described. The procedure envisaged would be: first, the the CP molecule are probed on different binding sites, e.g., top, bridge, fcc-hollow and hcp bridge, to find the most stable one(s); second, different adsorption configurations around the molecule are probed with the O2 molecule. In the manuscript, instead, four Au-Ph-COOH || O2 geometries are suddenly shown in figure 5, without any description. It is not clear why the four configurations shown are the most relevant among all the other possible ones, and which are the adsorption sites considered. I understand that the configuration P2 is reported to be the most stable with Ph-COOH in bridge position, but it is not clear why that position of the O2 molecule, and how the different position of the O2 molecule have been probed. Figure 5 should be substituted with a high resolution one.

3) The table 3 has to be corrected to report that the configuation investigated are the ones before and after O2 adsorption, and for the one and two Ph-COOH cases. The correct system notations in the first column are Au-PhCOOH, Au-2PhCOOH, Au-PhCOOH/O2 and Au-2PhCOOH/O2.

5) At page 8: "The Au-C bond formed between PhCOOH and Au20 was 2.053 Å and 2.057 Å after the interaction with oxygen molecule." --> "The Au-C bond formed between PhCOOH and Au20 was 2.053 Å and 2.057 Å before and after the interaction with oxygen molecule, respectively."

6) Why moving from the PBC model to the cluster model?

7) The definition of BDE should be explicited in the paper.

8) In the section "2.3 Molecular Modeling" figures 1a and 1b are referred but not shown.

9) No mention to figure 7 is found in the text of the manuscript.  Caption of figure 7 should be changed to define the adsorption energy in the inset B.

Author Response

1. At the end of page 6: "As seen in Figure 5 (P3 and P4), the interaction is influenced by the oxygen molecule's initial arrangement." Does this mean that P1 and P2 are not influenced? Why?

            Author’s response
            The interaction of oxygen molecules with the grafted surface causes structural changes in all geometries, but especially when the molecule is closer to the phenyl ring's side. Check       the response to comment no 2 below.

2. The P1-P4 geometries in figure 5 are not described. The procedure envisaged would be: first, the the CP molecule are probed on different binding sites, e.g., top, bridge, fcc-hollow and hcp bridge, to find the most stable one(s); second, different adsorption configurations around the molecule are probed with the O2 molecule. In the manuscript, instead, four Au-Ph-COOH || O2 geometries are suddenly shown in figure 5, without any description. It is not clear why the four configurations shown are the most relevant among all the other possible ones, and which are the adsorption sites considered. I understand that the configuration P2 is reported to be the most stable with Ph-COOH in bridge position, but it is not clear why that position of the O2 molecule, and how the different position of the O2 molecule have been probed. Figure 5 should be substituted with a high resolution one.

Author’s response
Four distinct initial geometries: P1 on top of the Au-surface; P2 on top of the attached Ph-COOH moiety; P3 bridge on the Au-surface; P4 fcc-hollow, were explored to investigate the interaction between the grafted Au-PhCOOH surface and molecular oxygen (as presented in Figure 5). The interaction of oxygen molecules with the grafted surface causes structural changes in all geometries, but especially when the molecule is closer to the phenyl ring's side. This probably is related to electron-rich aromatic rings and oxygen lone pairs that exhibit attractive interactions (https://pubs.acs.org/doi/10.1021/jo702170j. The above text is added in section 3.7. Figure 5 is also substituted with another figure with high resolution.

3. The table 3 has to be corrected to report that the configuation investigated are the ones before and after O2 adsorption, and for the one and two Ph-COOH cases. The correct system notations in the first column are Au-PhCOOH, Au-2PhCOOH, Au-PhCOOH/O2 and Au-2PhCOOH/O2.

Author’s response

Correction is made in the table, as suggested by the reviewer.

4. At page 8: "The Au-C bond formed between PhCOOH and Au20 was 2.053 Å and 2.057 Å after the interaction with oxygen molecule." --> "The Au-C bond formed between PhCOOH and Au20 was 2.053 Å and 2.057 Å before and after the interaction with oxygen molecule, respectively."

Author’s response

Correction is made in the manuscript, as suggested by the reviewer

5. Why moving from the PBC model to the cluster model?

Author’s response

This is due to a software constraint (Dmol3) that does not permit NCI calculation and plotting of PBC model. Thus, to compute and visualize NCI, we had no choice but to use Gaussian software, Multiwfn, and VMD, were a gold cluster served as an Au model.

6. The definition of BDE should be explicited in the paper.

Author’s response
Corrected. Definition of BDE is included in the manuscript. The following text is added:

The bond dissociation enenrgy (BDE) is calculated as follows:

BDE(Au-PhCOOH) = −(EA−PhCOOH+EPhCOOH+EAu)

where EAu-PhCOOH is the total energy of the grafted Au  cluster by apHCOOH moiety,  EPhCOOH and Eau represent the energies of the isolated Au and PhCOOH entities respectivelly.

7. In the section "2.3 Molecular Modeling" figures 1a and 1b are referred but not shown.

            Author’s response
            Corrected. The part within parenthesis (figures 1a and 1b) is omitted.

8. No mention to figure 7 is found in the text of the manuscript.  Caption of figure 7 should be changed to define the adsorption energy in the inset B.

Author’s response
Corrected. Reference to the figure is included in the text, in the last sentence above the figure.

Moreover:

• Reviewer 1 jumped over 3 when numbering the comments. So, the number of comments from reviewer 1 is 8 and not 9.
• In the manuscript “with changes marked” the text added is marked yellow and the text omitted is marked with brown text (stricken-through).

Author Response File: Author Response.pdf

Reviewer 2 Report

This paper studies the oxygen interactions with covalently grafted 2D nanometric carboxyphenyl thin films using a combined experimental and theoretical method. The authors performed a few analyses especially the density functional theory (DFT). The topic is interesting. However, the DFT calculation and modeling methods have some major problems. 

1. The unit cell of Au considered for calculations is too small, which leads to an artificial "stand-up" configuration of the adsorbed molecule (Figure 7). This may lead to an incorrect conclusion. A more favorable configuration should be a lay-down structure.
2. The Van der Waals interactions should be included in a more precise way.
3. The comparison between the experimental and theoretical results should be illustrated in a more straight forward way. 
4. Entropic and zero-point energy corrections should be added to the results. These more precise information may change the conclusion.
5. As a common sense, Au is never perfect. That means there will always be defective sites on Au due to its soft electronic structure. It would be more important to analyze defective Au sites instead of just a perfect 111 surface. 

Author Response

Reviewer 2

This paper studies the oxygen interactions with covalently grafted 2D nanometric carboxyphenyl thin films using a combined experimental and theoretical method. The authors performed a few analyses especially the density functional theory (DFT). The topic is interesting. However, the DFT calculation and modeling methods have some major problems. 

1. The unit cell of Au considered for calculations is too small, which leads to an artificial "stand-up" configuration of the adsorbed molecule (Figure 7). This may lead to an incorrect conclusion. A more favorable configuration should be a lay-down structure.

            Author’s response

It is known that aryl groups prefer the stand-up position and there are numerous references describing this, for instance:

• the paper by: a. De-en Jiang in J. Am. Chem. Soc.  - - https://pubs.acs.org/doi/10.1021/ja061439f  For the grafted Phenyl moiety: Au(111) fcc 24.0 kcal/mol  stand-up configuration (more stable) vs.  flat only 17.6 kcal/mol Level of theory: GGA – PBE (GPAW)
• Ambroiso et al.  Scientific Reports volume 10, Article number: 4114 (2020) https://www.nature.com/articles/s41598-020-60831-8
• Li  et al. Langmuir 2019, 35, 17, 5693–5701 https://pubs.acs.org/doi/10.1021/acs.langmuir.8b04288

Regarding the unit cell size: although we understand the comment, the selection of the Au model size is based on previous calculations, in which the actual experimental surface concentration of the grafted aryl groups is taken into account:

https://pubs.acs.org/doi/10.1021/ja061439f   
https://pubs.acs.org/doi/abs/10.1021/acs.langmuir.8b01584
https://pubs.acs.org/doi/10.1021/acs.langmuir.7b01371

1. The Van der Waals interactions should be included in a more precise way.

            Author’s response
            Actually, the calculations are performed at GGA/DND level of theory with TS. So, we     have added the following text, including a reference, in the manuscript: The van der        Waals interactions were taken into account using the Tkatchenko-Scheffler (TS) method [22].        In other works performed by other authors, the Van der Waals interactions are omitted in      the calculations, so the work as reported here can be regarded as an improvement.

1. The comparison between the experimental and theoretical results should be illustrated in a more straight forward way. 

Author’s response
The experimental results were focused on providing evidence for the grafting of PhCOOH groups, afterwards we have demonstrated using DFT how the oxygen (a radical “inhibitor”, that hinders the grafting efficiency) interacts with bare and grafted Au surfaces.

1. Entropic and zero-point energy corrections should be added to the results. These more precise information may change the conclusion.

Author’s response

The numerical basis set provided in Dmol3, in contrast to Gaussian, has almost negligible basis set superposition error (BSSE) values as described elsewhere,  https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20782, thus we didn’t consider them in our work.

1. As a common sense, Au is never perfect. That means there will always be defective sites on Au due to its soft electronic structure. It would be more important to analyze defective Au sites instead of just a perfect 111 surface. 

Author’s response
we agree that Au(111) surface is viewed as best compromise closest to Au surface. In our case, the Au surface which we use in our experiments has the same crystallographic orientation. To have understanding on the surface sites an Au cluster was also considered in the calculations.  The cluster, as it is not under PBC conditions, the orientation of the gold atoms will adopt more to the influence of the grafted PhCOOH group. Moreover, in this case we also included a most suitable description of the van Der Waals Interactions [Grimme’s dispersion correction (GD3)] as suggested in the reviewers 2^nd comment.

Moreover:

• In the manuscript “with changes marked” the text added is marked yellow and the text omitted is marked with brown text (stricken-through).

Author Response File: Author Response.pdf

Reviewer 3 Report

The paper, presented to me for review, concerns an experimental and theoretical study (based on DFT) about oxygen interactions with covalently grafted 2D nanometric carboxyphenyl thin films.

The topic taken up by the Authors is recently very interesting and it becomes more and more important in electrochemistry and material sciences.

The article presents a high level. It can be accepted for publication, however only after a major revision.

I suggest adding “cyclic voltammetry” as a keyword.

Please supplement the introduction with information on the practical application of aryl radicals to modify / functionalize surfaces.

Materials and Methods - no information about the specifications of ATR and FTIR. Please complete in main manuscript or prepare them in a separate supplementary.

2.3. Molecular Modeling - please explain why such a calculation variant was chosen (it is best to support it with relevant publications).

What programs were used to visualize the spectra? Please complete this information.

Bond Dissociation Energy – Please describe the method in more detail

DFT calculation - please complete figures and tables with information on the level of theory used.

After reading "Results and discussion", I think that the Authors should include in the introduction more a diagram of the visualization of what will be described. This will allow readers to better understand the section "Results and discussion"

Please format the bibliography according to the template. Currently, it is performed incorrectly.

Author Response

Reviewer 3

The paper, presented to me for review, concerns an experimental and theoretical study (based on DFT) about oxygen interactions with covalently grafted 2D nanometric carboxyphenyl thin films.

The topic taken up by the Authors is recently very interesting and it becomes more and more important in electrochemistry and material sciences.

The article presents a high level. It can be accepted for publication, however only after a major revision.

1. I suggest adding “cyclic voltammetry” as a keyword.

Author’s response
Corrected. “cyclic voltammetry” is added to the keywords

2. Please supplement the introduction with information on the practical application of aryl radicals to modify / functionalize surfaces.

Author’s response
Corrected. The following text, including reference, is added in the introduction: The grafted surfaces have found a vast number of practical applications in biomedicine, microfluidics, sensors, biosensors, corrosion protection, energy conversion [11].

3. Materials and Methods - no information about the specifications of ATR and FTIR. Please complete in main manuscript or prepare them in a separate supplementary.

            Author’s response
            Corrected. The following text is added in section 3.1:  (registered using Bruker IFS 66 v/S FT-IR                 spectrometer with a 2 cm^-1 resolution, and plotted by Origin software). Concerning ATR: as         presented in section 2.1 the spectra were collected in the 600-4000 cm^-1 region in       Attenuated Total Reflectance (ATR) mode using a Vertex 60/v spectrometer (Bruker).

4. 3. Molecular Modeling - please explain why such a calculation variant was chosen (it is best to support it with relevant publications).

            Author’s response
            Corrected. The following text, with references, is added in section 2.3: Cell dimensions        were 9.99 Å ´ 9.99 Å ´ 7.951 Å (with the addition of a 20 Å vacuum layer along the c axis) grafted           with carboxyphenyl groups. The van der Waals interactions were taken into account using    the Tkatchenko-Scheffler (TS) method [22]. The interaction of the oxygen molecules (in vacuum                and water using the Conductor like Screening Model) [23-25] with the bare and grafted gold surfaces was evaluated at different reaction sites

5. What programs were used to visualize the spectra? Please complete this information.

            Author’s response
            Corrected: The following information is added in section 3.1: (registered using Bruker      FS 66 v/S FT-IR spectrometer, and plotted by Origin software)

6. Bond Dissociation Energy – Please describe the method in more detail

            Author’s response
            Corrected. The following text is added in section 2.3: The bond dissociation energy          (BDE) is calculated as follows:
           
            BDE (Au-PhCOOH ) = −(EAu−PhCOOH + EPhCOOH + EAu)  where:  EAu-PhCOOH            is the total energy of the grafted Au surface grafted by a PhCOOH moiety, EPhCOOH and EAu represent the energies of the isolated Au and PhCOOH entities)

7. DFT calculation - please complete figures and tables with information on the level of theory used.

            Author’s response
            Corrected. Information about the level of theory is included in Figures 5-7 and Table 2.

8. After reading "Results and discussion", I think that the Authors should include in the introduction more a diagram of the visualization of what will be described. This will allow readers to better understand the section "Results and discussion"

            Author’s response

             Corrected. The following schematic diagram is included in the introduction.

                Scheme 1. (check attached file)

9. Please format the bibliography according to the template. Currently, it is performed incorrectly.

            Author’s response
            corrected

Moreover:

• In the manuscript “with changes marked” the text added is marked yellow and the text omitted is marked with brown text (stricken-through).

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

The authors have improved the presentation of the results.

Minor revision is requested to reply to the following concern:

In the manuscript the bond dissociation energy (BDE) is defined as −(E_(Au−PhCOOH) + E_PhCOOH + E_Au) . In order to calculate the bonding energy, I expected  to see calculated the difference between the sum of total energy of the isolated Au and PhCOOH systems (E_PhCOOH + E_Au) and the total energy of the bound Au−PhCOOH system, i.e. BDE= (E_PhCOOH + E_Au) - E_(Au−PhCOOH) (rather than the opposite of the sum of all the total energies).

Author Response

The authors have improved the presentation of the results.

Minor revision is requested to reply to the following concern:

In the manuscript the bond dissociation energy (BDE) is defined as −(E_(Au−PhCOOH) + E_PhCOOH + E_Au) . In order to calculate the bonding energy, I expected  to see calculated the difference between the sum of total energy of the isolated Au and PhCOOH systems (E_PhCOOH + E_Au) and the total energy of the bound Au−PhCOOH system, i.e. BDE= (E_PhCOOH + E_Au) - E_(Au−PhCOOH) (rather than the opposite of the sum of all the total energies).

Author’s response

Changed to:

BDE_{(Au-PhCOOH )} = (E_PhCOOH + E_Au) - (E_Au−PhCOOH)

Reviewer 2 Report

It can be accepted now.

Author Response

Reviewer 2

wrote: It can be accepted now

No more comments from the authors

Reviewer 3 Report

Comments and suggestions were taken into account. The manuscript can be published in present form.