Synthesis, Crystal Structure, Hirshfeld Surfaces Analysis, Interaction with DNA and Comparation of Different Bases in Hirshfeld Atom Refinement of New Polymorph of Chlorido(η⁶-p-cymene)(diclofenac)Ruthenium(II) Organometallic Compound

Round 1

Reviewer 1 Report

The authors have reported on the synthesis of a clorofenac-ruthenium(II) complex obtained by reaction of clorofenac with the ruthenium dimer [Ru(p-cymene)Cl2]2, using essentially the reported procedure for the synthesis of the same complex (clorofenac)Ru(p-cymene)Cl described in reference 35. The complex obtained from crystallization of the crude product exhibits the same bidentate coordination mode of clorofenac to ruthenium as described in the original article published in Dalton in 2018. Crystal structure, 1H NMR and IR spectral data for the complex have already been published. The complex prepared in this study was crystallized under a slightly modified procedure thus affording a different polymorph with respect to the complex described by Mandal and collaborators, which is quite a common phenomenon. Due to the different molecular packing and geometry, the supramolecular structure and contacts are different.

The authors also report on a UV-titration experiment which allows to determine an association constant of the complex with ct-DNA. This study appears inconclusive with regard to key features of associative phenomena, such as binding sites or comparison with literature data.

The experiments described in the manuscript and related discussion can be regarded as minor incremental information of a ruthenium complex already known and are not suitable for publication in this journal. The article may be of specific interest to journals involved in details of crystal structure analysis or simply published in a crystal structure database, pending the opinion of their reviewers.

Minor:

The authors have not indicated at the end of the introduction the objectives of their work.

Line 57: catena- ?

Line 60:  But ?

Line 87: the apparent association constant is… (NOT association of the constant)

Line 108: 0.318 g

Line 109: ..was stirred to stirr…?

Line 190:  smallest chemical shift is not appropriate definition in NMR spectroscopy.

Line 206:  can a Ru-Cl bond exhibit a Ru-O1 bond length?

Author Response

The experiments described in the manuscript and related discussion can be regarded as minor incremental information of a ruthenium complex already known and are not suitable for publication in this journal. The article may be of specific interest to journals involved in details of crystal structure analysis or simply published in a crystal structure database, pending the opinion of their reviewers.

The aim is not to repeat the experiments on another polymorph and description of known things, but to study the bases set selection for HAR on the crystal structure parameters of the complex that is interesting from the point of view of bioinorganic chemistry, since solid-phase chemistry (in this case, the study of methods of obtaining the most accurate refinements of the structures!) and the study of the phenomenon of polymorphism of substances are among the important pillars in the research of molecules with potential application in the pharmaceutical industry.

Minor:

The authors have not indicated at the end of the introduction the objectives of their work.

The objectives of the paper were added to the introduction. However, the primary aim of the paper has been completely overlooked from our point of view.

Line 57: catena- ?

Thank you very much for noticing that the word "poly" is missing in the formula and the prefix catena should be in italics. This prefix describes linear chains of unspecified length in the nomenclature of coordination compounds.

Line 60:  But ?

The abbreviation „But“ refers to butyl anion (1-). To make the formula easier to understand, we have included an explanation of this abbreviation.

Line 87: the apparent association constant is… (NOT association of the constant)

Thank you for noticing this serious error. We have identified where in the process of writing and correcting of the manuscript this misunderstanding of the term occurred. The error is, of course, corrected in the manuscript. 

Line 108: 0.318 g

Thank you for noticing. The missing "gram" symbol has been added.

Line 109: ..was stirred to stirr…?

Thank you for noticing. This error occurred while tracking changes in text.

Line 190:  smallest chemical shift is not appropriate definition in NMR spectroscopy.

Thank you for your advice. The smallest has been replaced by the lowest.

Line 206:  can a Ru-Cl bond exhibit a Ru-O1 bond length?

Of course, this is an unnoticed typo. Thank you!

Author Response File: Author Response.docx

Reviewer 2 Report

The paper describes Synthesis, crystal structure, Hirshfeld surfaces analysis, inter- 2 action with DNA and comparation of different bases in Hirshfeld Atom Refinement of new polymorph of chlo- chrido(η6 -p-cymene)(diclofenac)ruthenium(II) organometallic compound. The analysis are well describes, the paper presents data which can be interesting to the readers of Inorganic. But before publication, some changes have to be made:

"The yield of the 113 obtained product was 0.258 g"- 4 decimal places should be given.

1H NMR data -  coupling constant is missing.

Fragment"Initially, a rapid decrease in absorbance was 284 observed, and later an increase was observed. A blue shift (hypsochromic) of the band to 285 lower wavelengths was observed." Authors should find some synonyms for the word observed.

Author Response

The paper describes Synthesis, crystal structure, Hirshfeld surfaces analysis, inter- 2 action with DNA and comparation of different bases in Hirshfeld Atom Refinement of new polymorph of chlo- chrido(η6 -p-cymene)(diclofenac)ruthenium(II) organometallic compound. The analysis are well describes, the paper presents data which can be interesting to the readers of Inorganic. But before publication, some changes have to be made:

"The yield of the 113 obtained product was 0.258 g"- 4 decimal places should be given.

Thank you for your advice. Due to the weighing error, we used to give the weights to 3 decimal places. This has been corrected in the body of the text.

1H NMR data -  coupling constant is missing.

Information about multiplets was added. thank you for noticing.

Fragment"Initially, a rapid decrease in absorbance was 284 observed, and later an increase was observed. A blue shift (hypsochromic) of the band to 285 lower wavelengths was observed." Authors should find some synonyms for the word observed.

Thank you for your advice, which will improve the level of description.

Author Response File: Author Response.docx

Reviewer 3 Report

1.     The authors only list the IR data, but not describe it in detail. Please work such part.

2.     “On the other hand, the supramolecular structure of the orthorhombic polymorph is stabilized by two types π-π stacking interactions. Specifically, between two symmetrically equivalent chloride-substitued.” I find not any values from the Fig.2, I think the author could draw more figures to illustrate it.

3.     If it is possible, please draw clear structures for both clusters (using for example chem draw). Now, recognizing the structures is difficult.

4. As to the Hirshfeld surfaces analysis, I suggest the authors to condier the below refs, such as Theor. Chem. Acc. 2022, 141, 68; J Comput Chem, 2018, 39, 117–129; J. Phys. Chem. A, 2019, 123, 6751−6760 and Monatsh Chem, 2017, 48,1259–1267

5. The stability of the clusters in the solution also must be checked. It is not sufficient to check their stability in the solid state.

6. In the UV-Vis study increasing the absorption is due to the addition of DNA and it could not be used for calculating Kb. The authors must use other parts of the spectra for investigating the interaction otherwise, the calculations contain huge error.

7. There are many methods for studying the complex -DNA interaction such as: Circular Dichroisms, Gel electrophoresis, Viscosity measurements. I recommend that some other methods add to the methods of interaction studies.

Author Response

1. The authors only list the IR data, but not describe it in detail. Please work such part.

Since IR spectroscopy was used in order to confirm the structural motifs observed in the structures (from X-ray analysis), we have only discussed this spectrum at a minor level. Of course, we have added the IR description to the discussion. Thank you for your advice, which will lead to a higher quality paper.

2. “On the other hand, the supramolecular structure of the orthorhombic polymorph is stabilized by two types π-π stacking interactions. Specifically, between two symmetrically equivalent chloride-substitued.” I find not any values from the Fig.2, I think the author could draw more figures to illustrate it.

Thank you for your advice. The figure showing the individual π-π interactions was drawn and added to the ESI. Full details of this interaction are available in the cited article describing the structure of this polymorph.

3. If it is possible, please draw clear structures for both clusters (using for example chem draw). Now, recognizing the structures is difficult.

A picture from chemdraw would not provide a better explanation in the case of these two polymorphs. The difference in the two polymorphs is also in the intermolecular interactions, but the picture would not be able to capture the reality and would therefore be very simplistic.

4. As to the Hirshfeld surfaces analysis, I suggest the authors to condier th e below refs, such as Chem. Acc. 2022, 141, 68; J Comput Chem, 2018, 39, 117–129; J. Phys. Chem. A, 2019, 123, 6751−6760 and Monatsh Chem, 2017, 48,1259–1267

Thank you for the recommendation! After studying the articles, we thought it appropriate to include most of them in the article.

5. The stability of the clusters in the solution also must be checked. It is not sufficient to check their stability in the solid state.

The stability of the complexes in solution is confirmed by NMR spectra. The spectra were not measured immediately, but only after a long time after the solution was made. However, information about the type of polymorph is lost after dissolving. Therefore, the study of the properties of the complex in solution was limited to supplementing the already published information in order to best investigate the properites of the complex.

6. In the UV-Vis study increasing the absorption is due to the addition of DNA and it could not be used for calculating Kb. The authors must use other parts of the spectra for investigating the interaction otherwise, the calculations contain huge error.

Thank you for your advice. We have kept the value of the constant at 270 nm in the text (so that there is no doubt that calculations based on data from this maximum are loaded with a large error due to DNA absorption) and we have added a new one, calculated based on data at 233 nm. This constant is loaded with a smaller error (exactly as you wrote).

7. There are many methods for studying the complex -DNA interaction such as: Circular Dichroisms, Gel electrophoresis, Viscosity measurements. I recommend that some other methods add to the methods of interaction studies.

This complex has already been studied by fluorescence quenching of the EB-DNA complex. From our point of view, this method is well complemented by UV-VIS monitored titration, as it can provide several valuable information. Our group also uses viscosity measurements, but this complex is not soluble in water (we had to use a solution with a high DMSO content). When we measured this complex we observed that its interaction with DNA did not give much different changes in viscosity compared to DMSO and therefore the whole measurement is clouded by a huge error and gives significantly biased results. However, the other two methods are not routinely used in our group, and if they are used in some outputs, it is only thanks to national and international collaboration.

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

The authors have addressed main previous concerns and the article is publishable in the present form

Reviewer 3 Report

it could be accepted just now.