Conjugated carbon chain

A quite different-looking rearrangement is the hydride shift 1.16 —> 1.17, also long known from the chemistry of vitamin D. In this case, the end of the H-C bond attached to the hydrogen atom (H-l1) remains attached to the hydrogen, but the other end moves seven atoms (C-l to C-7) along the conjugated carbon chain. This reactions is therefore called a [1,7] shift. 

Considered in this section are two groups of oxepine reactions (1) addition and cycloaddition reactions peculiar to their conjugated carbon chain, and (2) those characteristic of vinyl ethers, particularly, beginning from an attack on ring oxygen. Both reaction types are discussed in detail in CHEC(1984) and CHEC-II(1996) therefore, only several important new examples are given here. 

Carotene-A hydrocarbon consisting of a conjugated carbon chain attached to an ionone ring. Most frequently, a conjugated carbon chain terminated at each end with an ionone ring. 

The unique spectrum when in the liquid crystalline state is due to the resonance phenomenon exhibited by the two terminal groups and the conjugated carbon chain between them, and the ability of electrons to be shared between the individual molecules of the liquid crystal. 

The most important characteristics of the Rhodonines are not their hormonal properties, as in the case of the retinenes, but their electronic properties, especially when in the liquid crystalline state. These properties are not directly relatable to their relatives, the retinenes. They are more closely associated with another group of relatives, the oxonols. The oxonols consist of two oxygen atoms connected by a conjugated carbon chain. The oxonols and the phthaleins are members of the carboxylic acid family, a large well-known family of dyes. ... 

Figure 5.5.6-1 Conversion of the retinenes into chromophores. (a) Retinaldehyde as conventionally displayed, (b) presentation rotated to stress length of conjugated carbon chain, (c) presentation modified to stress total conjugation, (d) presentation modified to illustrate combined conjugation and electronic resonance over the maximum length of the molecule, (e) presentation modified to show the potential separation of the conjugated structure from the electronically resonant structure. See text for details...

There was no published discussion at that time of the rules of dye chemistry and how the purported material rhodopsin would exhibit compliance with these rales. As indicated above, the most widely used class of dyes incorporates two polar atoms connected to each other by a conjugated carbon chain, and generally named a chromophoric system. The presence of a conjugated carbon chain is required as a minimum in nearly all organic material exhibiting a color in the visual band. Lack of such a conjugated chain leads to a colorless material. The proteins are such an unconjugated and inherently colorless family of materials. It was proposed that rhodopsin was formed by a... 

Where visible absorption peaks have been found in natural photoreceptor material, no NMR or X-ray crystallographic data has been put forward to demonstrate the presence of a retinene in the material (See Chapter 7). It is proposed here that any such tests will demonstrate the presence of a Rhodonine instead. Rhodonine contains two polar groups separated by a conjugated carbon chain. It is further proposed that opsin is only present as a completely passive substrate. Its association with the liquid crystalline Rhodonine is via a weak hydrogen bond that does not change the electronic configuration of the Rhodonines. 

To test for the Rhodonine family by chemical means, it is necessary to test for the simultaneous presence of both auxochromes and the conjugated carbon chain. To test for the individual Rhodonines, even more sophisticated procedures will be required than that to identify the family characteristic. The difference between the Rhodonine with a polar atom at position C7 and the Rhodonine with a polar atom at Cl 1 is quite small. Fortunately, as it will be shown later, the Cl 1 form is only found in the insect world. The differentiation between the C5 and C9 form can probably be achieved by testing for the unique cyclohexene ring structure associated with the carbonyl group at C5. It is most useful to utilize an NMR test to explicitly determine the specific retinoid present. This test is highly deterministic and virtually foolproof. The details related to NMR testing appear in Chapter 6. 

Fig. 7.10 QM/MM simulations of rhodopsin. Dihedral angles (upper and middle panel) and bond lengths (lower panel) along the conjugated carbon chain of the RPSB in the dark state (black), in S, (dotted), and in the all-trans ground state (light grey). The dihedral angles ofthe all-trans ground state obtained from classical MD are shown in black stars. Reproduced with permission from J. Am. Chem. Soc. 2004, 726,15328-15329. Copyright 2004 American Chemical Society.

The dependence of the electronic structures of [-SiH2-(CH=CH) (-] (35), with a = 1-5 on the length of 7t-conjugated carbon chains in their unit cells has... 

Vitamin A is inactivated biologically in mammals either by oxidation at the C-4 position to yield hydroxy and oxoderivatives or by oxidative shortening of the conjugated carbon chain. 4-Oxoretinol and 4-oxoretinoic acid, however, show activity in some biological systems. The methyl groups may also be hydrox-ylated. 

Basic dyes have a positive charge on the dye molecule and as such are ammonium, sul-fonium, or oxonium salts. The positive charge can be pendant or delocalized where the charge resonates between two hetero-atoms connected by a conjugate carbon chain. 

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