Isomerization and Properties of Isomers of Carbocyanine Dyes

Round 1

Reviewer 1 Report

This review presents us a thorough analysis of the literature data on (photo)isomerization processes in a theoretically and practically important subclass of polymethine dyes — cationic carbocyanines. All the factors influencing their isomerization is logically classified and discussed: bulky substituents in the polymethine chain, solvent viscosity, solvent polarity, formation of ion pairs and dye aggregates, interaction with highly organized structures, e.g. DNA, etc.

I believe that, regardless of the fact that a good deal of the cited literature was published some 20 and more years ago, this is relevant and useful publication, which can help one to systematize the knowledge on isomerization of polymethine dyes. And presently new researches in this field is imminent, utilizing the improved time-resolved physical-chemical technics and modern quantum chemical methods, e.g. QM/MM explicit solvation models.

 There are still some minor remarks to the paper.

• The authors use non-IUPAC, somewhat obsolete, nomenclature of the carbocyanine dyes, which could be confusing for a general reader. Moreover, they do not give the structural formulas of the discussed dyes in the paper, only their names, which hampers the perception of the material. Therefore, I suggest modifying Figure 1, to show in it the actual structures of dyes to be discussed below instead of the examples of terminal groups.

• Subsection 2 of the paper (Structure and Spectral-Fluorescent Properties of Cyanine Dyes) should be slightly modified. Namely, its last paragraph should be moved to its very beginning, so that a reader had not been confused why only cationic polymethines are discussed. It should be noted also, that even the subclass of cationic polymethine dyes is not limited to the structures with "terminal nitrogen atoms". There are, for example, pyrilocyanines (also (thia,selena)pyrilocyanines) and even carbocyclic azulenecyanines.

• The authors should think about improving the nomenclature of isomers (see Figure 3, for example). The point is that the EZ-names differ for the same isomers of carbocyanines with different terminal groups. Thus, all-trans isomers of inda- dyes are EEEE, but those of thia- and oxa- dyes are ZEEZ. Not mentioning the fact that with meso-methoxy or meso-chloro substituent in the polymethine chain, the all-trans isomer of thiacarbocyanine will be ZZZZ.

• There is an interesting fact worth of discussing, namely the vast difference of the reverse thermal isomerization constants for rather similar dyes 2 and 3.

• Page 6: there is a misprint in the eq.3. Thus, one can read at page 7 that according to this equation "the reaction rate constant should be inversely proportional to the viscosity of the solvent". However, viscosity is not present in this equation (while it is in the corresponding equation in Ref.36).

• Russian-language book in Ref.17 is inaccessible to most of the readers. Therefore, I would suggest replacing it with the reference to the relative review: Ishchenko, A.A. Structure and spectral-luminescent properties of polymethine dyes. Russ. Chem. Rev. 1991, 60, 865–884, doi:10.1070/RC1991v060n08ABEH001116.

Author Response

1. The authors use non-IUPAC, somewhat obsolete, nomenclature of the carbocyanine dyes, which could be confusing for a general reader. Moreover, they do not give the structural formulas of the discussed dyes in the paper, only their names, which hampers the perception of the material. Therefore, I suggest modifying Figure 1, to show in it the actual structures of dyes to be discussed below instead of the examples of terminal groups. In accordance with the suggestions of the reviewer, changes were made to the manuscript figures. Figures 3 and 6 (page 3 and 8) are modified; the actual structural formulas of the described dyes were added. Corresponding changes were made to the captions to figures 3 and 6. On page 3 (in section 3. Isomerization of Carbocyanine Dyes) in the caption for Figure 3 “Generalized molecular structures of trans and cis isomers of unsubstituted carbocyanine dyes” has been changed to “Generalized molecular structures of trans and cis isomers of unsubstituted carbocyanine dyes and structural formulas of cyanines 1 - 6.” On page 8 (in section 6. Isomerization of Meso-Substituted Carbocyanine Dyes) the caption for Figure 8 “Structures of trans and cis isomers of meso-substituted carbocyanine dyes.” has been changed to “Generalized molecular structures of trans and cis isomers of of meso-substituted carbocyanine dyes and structural formulas of cyanines 7 - 21.” Figure 6 was placed at the beginning of section 6. 2. Subsection 2 of the paper (Structure and Spectral-Fluorescent Properties of Cyanine Dyes) should be slightly modified. Namely, its last paragraph should be moved to its very beginning, so that a reader had not been confused why only cationic polymethines are discussed. It should be noted also, that even the subclass of cationic polymethine dyes is not limited to the structures with "terminal nitrogen atoms". There are, for example, pyrilocyanines (also (thia,selena)pyrilocyanines) and even carbocyclic azulenecyanines. The text of section 2 has been modified in accordance with the comments of the reviewer. The last paragraph of the section has been moved to the beginning of the section. The introductory text has been reworked. On page 2 (in section 2. Structure and Spectral-Fluorescent Properties of Cyanine Dyes) The text “Polymethine (cyanine) dyes contain conjugated polymethine chains (with an odd number of CH groups) with terminal nitrogen atoms. The nitrogen atoms can be a part of amino groups or terminal heterocycles B1 and B2 (quinolinyl, indolenyl, benzimidazolyl, benzothiazolyl, benzoxazolyl, and other heterocyclic residues, see Figure 1) [17,18].” has been replaced by “Polymethine dyes contain conjugated polymethine chains (with an odd number of CH groups) with the general formula X(CH=CH)nCH=Y, where X and Y are terminal groups with heteroatoms (N, O, S, Se) or even C atoms (in case of carbocyclic azulene cyanines). The cationic type polymethine dyes are primarily cyanines, streptocyanines, rhodacyanines, hemicyanines, azacyanines, and styryl dyes, anionic polymethine dyes — oxonols. Neutral cyanines (merocyanines and ketocyanines) are subtypes of uncharged polymethine dyes. In this article, we confine ourselves to the most common subclass of polymethine dyes—carbocyanines with a positively charged chromophore with terminal nitrogen atoms. The nitrogen atoms can be a part of amino groups or terminal heterocycles B1 and B2 (quinolinyl, indolenyl, benzimidazolyl, benzothiazolyl, benzoxazolyl, and other heterocyclic residues, see Figure 1) [17,18]. Note that the total charge of such dyes can be not only positive, but also negative (or neutral) due to the presence of anionic substituents in heterocyclic residues.” On page 3 (in the first paragraph) after the first sentence, “At present, there is a wide variety of cationic carbocyanines: monomethine cyanines, carbocyanines (or trimethine cyanines), dicarbocyanines (pentamethine cyanines), tricarbocyanines (heptamethine cyanines), etc.” was added. The authors should think about improving the nomenclature of isomers (see Figure 3, for example). The point is that the EZ-names differ for the same isomers of carbocyanines with different terminal groups. Thus, all-trans isomers of inda- dyes are EEEE, but those of thia- and oxa- dyes are ZEEZ. Not mentioning the fact that with meso-methoxy or meso-chloro substituent in the polymethine chain, the all-trans isomer of thiacarbocyanine will be ZZZZ. EZ-nomenclature of isomers was removed from the text of the work 4. Page 6: there is a misprint in the eq.3. Thus, one can read at page 7 that according to this equation "the reaction rate constant should be inversely proportional to the viscosity of the solvent". However, viscosity is not present in this equation (while it is in the corresponding equation in Ref.36). A misprint in the equation on page 3 has been fixed. On page 7 (in section 4. Effect of Solvent Viscosity on the Kinetics of Photoisomerization and Back (Thermal) Isomerization) Equation 3 and the text have been corrected. Russian-language book in Ref.17 is inaccessible to most of the readers. Therefore, I would suggest replacing it with the reference to the relative review: Ishchenko, A.A. Structure and spectral-luminescent properties of polymethine dyes. Russ. Chem. Rev. 1991, 60, 865–884, doi:10.1070/RC1991v060n08ABEH001116. On page 14 (References ) the Ref. 17 “Ishchenko, A.A. Stroenie i spektral’no-luminestsentnye svoistva polimetinovykh krasitelei [Structure and Spectral-Luminescent Properties of Polymethine Dyes]; Naukova Dumka: Kiev, Ukraine, 1994; 231p, ISBN 978-966-439-897-5.” has been corrected: “17. Ishchenko, A.A. Structure and spectral-luminescent properties of polymethine dyes. Russ. Chem. Rev. 1991, 60, 865–884, doi:10.1070/RC1991v060n08ABEH001116.”

Reviewer 2 Report

In my opinion authors have presented very well the topics which are focused on photoisomerization of cyanine dyes.

Author Response

In my opinion authors have presented very well the topics which are focused on photoisomerization of cyanine dyes The authors sincerely thank the reviewer 2

Round 2

Reviewer 1 Report

Judging from Authors' response to my previous comments, the paper has been thoroughly revised, so that the minor flaws present in its older version has been eliminated.

To my regret, nothing more can be said on the point, since the link "Download Manuscript" leads to "Error 404" page and on the site only the previous, uncorrected version of the paper can be downloaded. And I was waiting more than ten days hoping that the technical error will be corrected by the publisher.

Author Response

Judging from Authors' response to my previous comments, the paper has been thoroughly revised, so that the minor flaws present in its older version has been eliminated. The authors thank the reviewer for their valuable comments. The manuscript was carefully checked and revised according to the comments of the reviewer. A number of minor errors were corrected in the text.