Cis, trans isomerization

In Chapter 3, we have seen that aromatic t-systems are planar, stabilized by tt-bonding. Out-of-plane motion of the carbon atoms is therefore an energy consuming process and the ground state is thus stable. In a tt tt excited state, part of the t-bonding disappears, however, and a number of processes become possible. We will be interested particularly in the cis-trans isomerization process. 

An ordinary CC single bond varies between 1.53 A (ethane) and 1.54 A (diamond) and has the bond energy 347 kJ/mol. The double bond in ethylene (ethene, C2H4) is considerably shorter (1.33 A) and stronger (611 kJ/mol). Hydrocarbons with a single CC double bond are called olefins. 

Excitation of an electron from the HOMO to the LUMO (both are Jt-orbitals) means that the i-bond is completely canceled. The Hiickel % MOs in ethylene have the coefficients and yj j2,--sjy2) in the HOMO and LUMO, 

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The definitions of the empirical rate laws given above do not exclude empirical rate laws of another fomi. Examples are reactions, where a reverse reaction is important, such as in the cis-trans isomerization of 1,2-dichloroethene ... 

Zhu S-B, Lee J, Robinson G W and Lin S H 1988 A microscopic form of the extended Kramers equation. A simple friction model for cis-trans isomerization reactions Chem. Phys. Lett. 148 164-8... 

Schoenlein R W, Peteanu L A, Wang Q, Mathles R A and Shank C V 1993 Femtosecond dynamics of cis-trans Isomerization In a visual pigment analog Isorhodopsin J. Phys. Chem. 97 12 087-92... 

Figure B2.4.2. Eyring plot of log(rate/7) versus (1/7), where Jis absolute temperature, for the cis-trans isomerism of the aldehyde group in fiirfiiral. Rates were obtained from tln-ee different experiments measurements (squares), bandshapes (triangles) and selective inversions (circles). The line is a linear regression to the data. The slope of the line is A H IR, and the intercept at 1/J = 0 is A S IR, where R is the gas constant. A and A are the enthalpy and entropy of activation, according to equation (B2.4.1)...

The Cyclooctene Isomerization. A reaction that attracted some attention in recent years is the cis-trans isomerization of cyclooctene [84]. The cis isomer is much less strained than the trans, but the latter is readily fonned upon direct photolysis and also upon photosensitization. In this case, two enantiomeric trans isomers are formed. The appropriate loop is a variation of that shown in Figure 14, as shown in Figure 34. This is a phase inverting i -type loop, that... 

INORGANIC COMPLEXES. The cis-trans isomerization of a planar square form of a rt transition metal complex (e.g., of Pt " ) is known to be photochemically allowed and themrally forbidden [94]. It was found experimentally [95] to be an inhamolecular process, namely, to proceed without any bond-breaking step. Calculations show that the ground and the excited state touch along the reaction coordinate (see Fig. 12 in [96]). Although conical intersections were not mentioned in these papers, the present model appears to apply to these systems. 

Both acids 3deld succinic acid, m.p. 185°, upon catalytic reduction (see Section 111,150), thus establishing their structures. Maleic and fumaric acids are examples of compounds exhibiting cis-trans isomerism (or geometric isomerism). Maleic acid has the cm structure since inter alia it readily 3delds the anhydride (compare Section 111,93). Fumaric acid possesses the trans structure it does not form an anhydride, but when heated to a high temperature gives maleic anhydride. 

Large annulenes tend to undergo conformational distortion, cis-trans isomerizations, and sig-matropic rearrangements (p. 40 and p. 100). Methylene-bridged conjugated (4n + 2)-ic cyclopolyenes were synthesized with the expectation that these almost planar annulenes should represent stable HOckel arenes (E, Vogel, 1970, 1975). 

The first identified complexes of unsubstituted thiazole were described by Erlenmeyer and Schmid (461) they were obtained by dissolution in absolute alcohol of both thiazole and an anhydrous cobalt(II) salt (Table 1-62). Heating the a-CoCri 2Th complex in chloroform gives the 0 isomer, which on standirtg at room temperature reverses back to the a form. According to Hant2sch (462), these isomers correspond to a cis-trans isomerism. Several complexes of 2,2 -(183) and 4,4 -dithiazolyl (184) were also prepared and found similar to pyridyl analogs (185) (Table 1-63). Zn(II), Fe(II), Co(II), Ni(II) and Cu(II) chelates of 2.4-/>is(2-pyridyl)thiazole (186) and (2-pyridylamino)-4-(2-pyridy])thiazole (187) have been investigated. The formation constants for species MLr, and ML -" (L = 186 or 187) have been calculated from data obtained by potentiometric, spectrophotometric, and partition techniques. 

Number of carbon atoms number of double bonds (geometric (cis, trans) isomerism). 

The three isomerizations, ct5-2-butene trans-2-huiene, 1-butene 2-butene, and butenes isobutylene, require increasingly severe reaction conditions. When the position of the double bond is shifted, cis—trans isomerization also occurs, and mixtures of butenes result when the carbon skeleton... 

Photochromism Based on Geometric Isomerism. The simplest examples of a photochromic reaction involving reversible cis-trans isomerization is the photoisomerization of azobenzene [103-33-3] C22H2QN2 (16). 

The cis-trans isomerization of stilbenes is technically another photochromic reaction (18). Although the absorption bands of the stilbene isomers, occur at nearly identical wavelengths, the extinction coefficient of the lowest energy band of cis-stilbene [645-49-8] is generally less than that of stilbene [103-30-0],... 

The stereochemistry of pyrazolines and pyrazolidines has already been discussed (Section 4.04.1.4.3). Optically active A - and A -pyrazolines have seldom been described (77JA2740, 79CJC360), but cis-trans isomeric pairs are common. The C-4 acid-catalyzed epimerization involves the mechanism shown in Scheme 38 (70TL3099), but in spite of some inconclusive arguments the C-5 epimerization has never been established with certainty. 

There are at least two mechanisms available for aziridine cis-trans isomerism. The first is base-catalyzed and proceeds via an intermediate carbanion (235). The second mechanism can be either thermally or photochemically initiated and proceeds by way of an intermediate azomethine ylide. The absence of a catalytic effect and interception of the 1,3-dipole intermediate provide support for this route. A variety of aziridinyl ketones have been found to undergo equilibration when subjected to base-catalyzed conditions (65JA1050). In most of these cases the cis isomer is more stable than the trans. Base-catalyzed isotope exchange has also been observed in at least one molecule which lacks a stabilizing carbonyl group (72TL3591). 

Figure 6 Thermodynamic cycle for multi-substate free energy calculation. System A has n substates system B has m. The free energy difference between A and B is related to the substate free energy differences through Eq. (41). A numerical example is shown in the graph (from Ref. 39), where A and B are two isomers of a surface loop of staphylococcal nuclease, related by cis-trans isomerization of proline 117. The cis trans free energy calculation took into account 20 substates for each isomer only the six or seven most stable are included in the plot.

In the native protein these less stable ds-proline peptides are stabilized by the tertiary structure but in the unfolded state these constraints are relaxed and there is an equilibrium between ds- and trans-isomers at each peptide bond. When the protein is refolded a substantial fraction of the molecules have one or more proline-peptide bonds in the incorrect form and the greater the number of proline residues the greater the fraction of such molecules. Cis-trans isomerization of proline peptides is intrinsically a slow process and in vitro it is frequently the rate-limiting step in folding for those molecules that have been trapped in a folding intermediate with the wrong isomer. 

Related to stereoregularity is the possibility of cis, trans isomerism. The molecule of natural rubber is a c/s-1,4-polyisoprene whilst that of gutta percha is the trans isomer. 

When two or more substituents are present on a cyclohexane ring, the interactions between the substituents must be included in the analysis. The dimethylcyclohexanes provide an example in which a straightforward interpretation is in complete agreement with the experimental data. For 1,2-, 1,3-, and 1,4-dimethylcyclohexane, the free-energy change of the equilibrium for the cis trans isomerization is given below. ... 

Although lupinine is thus a comparatively simple alkaloid its detailed chemistry has been difficult to unravel owing (a) to the presence in its molecule of two asymmetric carbon atoms as asterisked in (XI), and (6) the possibility of cis-trans isomerism in certain of its proximate (ieriva-tives. Winterfeld and Holschneider have pointed out that a further complexity arises from the presence in natural Z-lupinine of a structural isomeride, aZZolupinine for which formula (XII) is suggested. They also quote Kreig s observation that by the action of sodium on a benzene solution of Z-lupinine (m.p. 68-9° [ajo — 23-52°), the latter is converted... 

Consider a nucleus that can partition between two magnetically nonequivalent sites. Examples would be protons or carbon atoms involved in cis-trans isomerization, rotation about the carbon—nitrogen atom in amides, proton exchange between solute and solvent or between two conjugate acid-base pairs, or molecular complex formation. In the NMR context the nucleus is said to undergo chemical exchange between the sites. Chemical exchange is a relaxation mechanism, because it is a means by which the nucleus in one site (state) is enabled to leave that state. 

Consequently rotation about the carbon-nitrogen bond constitutes exchange of the methyl protons between nonequivalent sites, analogous to cis-trans isomerization ... 

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