S-Indacene

The s-indacene (III) synthesized by Hafner s group and its 7-membered analogue (IX) are predicted to assume a skewed structure with a moderate double-bond fixation. As for (III), this conclusion supports the previous theoretical works and is in accordance with the experimental information. 

BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) Dyes... 

Fluorophores containing 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene as a core skeleton are commonly designated as BODIPY fluorophores. Due to their useful photophysical properties including high fluorescence quantum yields, high molar absorption coefficient, narrow absorption and emission band width, and their high photostability [50], BODIPY dyes are proven to be extremely versatile and useful in many biological applications Fig. 11 [68]. 

BODIPY is a short for 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene, the basic structure of this type of fluorophore (see Fig. 6.5). Derivatives of this dye have been created by modification of positions 1, 3, 5, 7, and 8, generating an array of fluorophores with very distinct excitation and emission properties [38]. Molecular Probes has synthesized a wide number of BODIPY dyes whose excitation... 

BODIPY fluorophores are a class of probes based on the fused, multi-ring structure, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (Figure 9.27) (Invitrogen) (U.S. patent 4,774,339). This fundamental molecule can be modified, particularly at its 1, 3, 5, 7, and 8 carbon positions, to produce new fluorophores with different characteristics. The modifications cause spectral shifts in its excitation and emission wavelengths, and can provide sites for chemical coupling to label biomolecules. 

BODIPY FL C3-SE is 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, succinimidyl ester (Invitrogen). The derivatization to the base BODIPY molecule... 

The PE spectra of cyclobutadiene 281192, tetra-t-butylcyclobutadiene 282193, 1,3,5-tri-t-butylpentalene 283194 and aceheptylene 284195, all of which are subject to second-order bond localization, have been described in the literature. Further examples are 1,3,5,7-tetra-t-butyl-s-indacene 285 (which exhibits a first double band 1,2 at I 2 = 6.75 eV, followed by two bands at I = 8.50 eV and I = 9.30 eV) and the tetracyclic hydrocarbon 1,3,6,8-tetra-t-butylpentaleno[2,l-a]pentalene 286 (the first two bands of which are observed at 6.40 eV and 7.65 eV)196. 

Schardt, S. and Hafner, K., Synthesis of l,3,5,7-tetra-ferf-butyl-4,8-diphospha-s-indacene, Tetrahedron Lett., 37, 3829, 1996. 

Heteroindacenes have been prepared and studied by Hafner and co-workers.198 199 The syntheses of 1,3,5,7-tetra-te/t-butyl-4-azaindacene, its AA-oxide, and l,3,5,7-tetra-tot-butyl-4-phospha-s-indacenes have been recently reported (Scheme 66).200 The 12-jt-electron delocalized systems have been studied by dynamic NMR and X-ray and were subjected to molecular orbital calculations, and there is strong evidence of electron delocalization. However, X-ray crystallographic data for 4-phospha-s-indacene 164 and the 4-7V-oxide 164 show that there is a dual orientation in the crystal this disorder with two different orientations of the molecule does not allow for conclusions regarding bond lengths or delocalization, and the mediated structures show a D2h symmetry rather than C2h with localized double bonds. 

The optical properties of organic dyes (Fig. ld-f, Table 1) are controlled by the nature of the electronic transition(s) involved [4], The emission occurs either from an electronic state delocalized over the whole chromophore (the corresponding fluorophores are termed here as resonant or mesomeric dyes) or from a charge transfer (CT) state formed via intramolecular charge transfer (ICT) from the initially excited electronic state (the corresponding fluorophores are referred to as CT dyes) [4], Bioanalytically relevant fluorophores like fluoresceins, rhodamines, most 4,4 -difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPY dyes), and cyanines (symmetric... 

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