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Isomerization and Properties of Isomers of Carbocyanine Dyes

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Isomerization and Properties of Isomers of Carbocyanine Dyes Review Isomerization and Properties of Isomers of Carbocyanine Dyes Pavel Pronkin * and Alexander Tatikolov N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin Str. 4, 119334 Moscow, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-495-939-7171 Received: 20 November 2018; Accepted: 26 November 2018; First Version Published: 29 November 2018 (doi:10.3390/sci1010005.v1) Second Version Published: 20 March 2019 (doi:10.3390/sci1010019) Abstract: One of the important features of polymethine (cyanine) dyes is isomerization about one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomerization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocyanine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,30-dimethyl-9-phenylthiacarbocyanine and 3,30-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be explained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric effect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes complexed with DNA and chondroitin-4-sulfate; for 3,30-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cyanine dyes can be used in various systems of information storage and deserves further investigation using modern research methods. Keywords: carbocyanine dyes; isomerization; trans and cis isomers; meso-substituted cyanines 1. Introduction Isomerization reactions, which involve rotation of a bulky molecular group around a body-fixed axis, often play a fundamental role in chemical and biological processes both in solution and in organized assemblies. In nature, the most important and known isomerization process is photoisomerization of 11-cis retinal, the chromophore of rhodopsin, which is a photoreceptive pigment for twilight vision [1,2]. Rotational isomerization is inherent in polyenic compounds, in particular, carotenoids and diphenylpolyenes [3]. Azo and azomethine dyes can also undergo cis-trans (or syn-anti) isomerization, while with more complex mechanisms [4,5]. The most abundant class of dyes that exhibit rotational isomerization is polymethine (cyanine) dyes. At present, cyanine dyes attract great attention of researches in different fields of science, technology engineering, pharmacology and medicine [6]. In particular, these dyes are widely used in laser technology (for creating tunable laser media in the near IR spectral range, passive Q-switches of lasers and other devices of quantum electronics and optoelectronics) [7,8]. Cyanine dyes also attract interest due to the prospects of their use as spectral-fluorescent probes and labels in the study of various biological systems [9–12], and in biomedicine for the purposes of visualization of tissues and photodynamic therapy [6,13–16]. This is due to the unique properties of cyanine dyes, which are Sci 2019, 1, 19; doi:10.3390/sci1010019 www.mdpi.com/journal/sci Sci 2019, 1, 19 2 of 17 SciSci2019 2019, 1, ,1 19, 19 22 ofof 17 17 determined by the key features of their molecular structure. Various fields of applications of cyanine determined by the key features of their molecular structure. Various fields of applications of cyanine dyes determine the need for studying their photophysical and photochemical properties in solutions determineddyes determine by the the key need features for studying of their their molecular photop structure.hysical and Various photochemical fields of applications properties in of solutions cyanine and molecularly organized media. dyesand determinemolecularly the organized need for studyingmedia. their photophysical and photochemical properties in solutions and molecularly organized media. 2. Structure and Spectral-Fluorescent Properties of Cyanine Dyes 2. Structure and Spectral-Fluorescent Properties of Cyanine Dyes 2. Structure and Spectral-Fluorescent Properties of Cyanine Dyes Polymethine dyes contain conjugated polymethine chains (with an odd number of CH groups) Polymethine dyes contain conjugated polymethine chains (with an odd number of CH groups) withPolymethine the general dyesformula contain X(CH=CH) conjugatednCH=Y, polymethine where X and chains Y are (with terminal an odd groups number with of CHheteroatoms groups) with the general formula X(CH=CH)nCH=Y, where X and Y are terminal groups with heteroatoms with(N, theO, S, general Se) or even formula C atoms X(CH (in=CH) case ofCH carbocyclic=Y, where azulene X and Y cyanines). are terminal The groups cationic with type heteroatoms polymethine (N, O, S, Se) or even C atoms (in case nof carbocyclic azulene cyanines). The cationic type polymethine (N,dyes O, S,are Se) primarily or even Ccyanines, atoms (in streptocyanines, case of carbocyclic rhodacyanines, azulene cyanines). hemicyanines, The cationic azacyanines, type polymethine and styryl dyes are primarily cyanines, streptocyanines, rhodacyanines, hemicyanines, azacyanines, and styryl dyesdyes, are anionic primarily polymethine cyanines, dyes streptocyanines, — oxonols. rhodacyanines,Neutral cyanines hemicyanines, (merocyanines azacyanines, and ketocyanines) and styryl are dyes, anionic polymethine dyes — oxonols. Neutral cyanines (merocyanines and ketocyanines) are dyes,subtypes anionic of uncharged polymethine polymethine dyes — oxonols. dyes. Neutral cyanines (merocyanines and ketocyanines) are subtypes of uncharged polymethine dyes. subtypesIn this of uncharged article, we polymethine confine ourselves dyes. to the most common subclass of polymethine dyes—carbo- In this article, we confine ourselves to the most common subclass of polymethine dyes—carbo- cyaninesIn this with article, a positively we confine charged ourselveschromophore to wi theth mostterminal common nitrogen subclass atoms. The of nitrogen polymethine atoms cyanines with a positively charged chromophore with terminal nitrogen atoms. The nitrogen atoms dyes—carbocyaninescan be a part of amino with groups a positively or terminal charged heterocycles chromophore B1 and B2 with(quinolinyl, terminal indolenyl, nitrogen benzimid- atoms. can be a part of amino groups or terminal heterocycles B1 and B2 (quinolinyl, indolenyl, benzimid- Theazolyl, nitrogen benzothiazolyl, atoms can benzoxazolyl, be a part and of other amino heterocyclic groups or residues, terminal see heterocycles Figure 1) [17,18]. B1 andNote B2that azolyl, benzothiazolyl, benzoxazolyl, and other heterocyclic residues, see Figure 1) [17,18]. Note that (quinolinyl,the total charge indolenyl, of such benzimidazolyl, dyes can be not benzothiazolyl, only positive, benzoxazolyl, but also negative and other(or neutral) heterocyclic due to residues, the pres- the total charge of such dyes can be not only positive, but also negative (or neutral) due to the pres- seeence Figure of anionic1)[ 17, 18substituents]. Note that in the heterocyclic total charge residues. of such dyes can be not only positive, but also negative ence of anionic substituents in heterocyclic residues. (or neutral) due to the presence of anionic substituents in heterocyclic residues. R R6 R 5 R6 5 R N n N R R 3 N N R 4 3 n 4 R R R 1 n= 1, 2, 3 R 2 1 n= 1, 2, 3 2 R R X S X S N NNN N N N NNN N N R R R R R R R R R R X= S, O, Se X= S, O, Se FigureFigure 1. 1.Generalized Generalized molecular molecular structure structure of of cyanine cyanine dyes dyes and and examples examples of of terminal terminal heterocycles heterocycles B1 B1 Figure 1. Generalized molecular structure of cyanine dyes and examples of terminal heterocycles B1 andand B2. B2. and B2. TheThe dye dye molecule molecule usually usually carries carries a positive a positive charge char distributedge distributed over over the the polymethine polymethine chain. chain. Due Due to The dye molecule usually carries a positive charge distributed over the polymethine chain. Due completeto completeπ-electronic π-electronic conjugation conjugation in the in polymethine the polymethine chain, chain, these dyes these have dyes narrow have narrow absorption absorption bands to complete π-electronic conjugation in the polymethine5 chain,1 these1 dyes have narrow absorption withbands high with extinction high extinction coefficients coefficients (of the order(of the of order 10 L of mol 10−5 Lcm mol− −)1 incm the−1) in spectral the spectral range range from 340from bands with high extinction coefficients (of the order of 105 L mol−1 cm−1) in the spectral range from to340 1400 to nm1400 [6 nm,9,17 [6,9,17,18].,18]. Note Note that symmetricthat symmetric polymethine polymethine dyes dyes are characterized are characterized by equalization by equalization of 340 to 1400 nm [6,9,17,18]. Note that symmetric polymethine dyes are characterized by equalization C–Cof C–C bonds bonds in the in chromophore the chromophore and approaching and approaching of their of orders their orders to one-and-a-half to one-and-a-half (polymethine (polymethine state).
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