Isomerization cis/trans isomerism

In comparison, photoremovable protecting groups such as 69 also release their protected molecule via intramolecular lactonization, but the photorelease is initiated by cis-trans isomerization. Cis-trans isomerization has been extensively used to turn molecular switches off and on, but there are a few examples where cis-trans isomerization has been used to activate photorelease. Initially, Stoermer showed that photoinduced cis-trans isomerization of trans-69 yields 71, presumably via intramolecular lactonization of cis-lQ (Scheme 37). In a similar way. 

Chemical compounds that have the same molecular formula but different structural formulas are said to be isomers of each other. These constitutional isomers (or structural isomers) differ in their bonding sequence, i.e. their atoms are connected to each other in different ways. Stereoisomers have the same bonding sequence, but they differ in the orientation of their atoms in space. Stereoisomerism can be further divided into optical isomerism (enantiomerism) and geometrical isomerism (cis—trans isomerism). The relationships between the different types of isomerism are shown in Figure 4.1. 

Pico second spectroscopic investigations of cis -trans -isomerization of stilbene and the derivative (25) have demonstrated the presence of an intermediate which is involved in the isomerization. cis -trans -Isomerization of several pyridinium analogues of stilbene have been studied. The salts (26) also undergo singlet state trans -cis -isomerization on irradiation. A detailed mechanistic examination of these systems has been carried out and a physical study of the influence of solvent and quencher on the decay of the excited singlet state of the stilbene derivatives (27) has been reported. The cis -trans isomerization of bis -heteroaryl ethenes has been reported in detail. ... 

A database search yields more than 20 000 references that contain Z-E isomerization, cis-trans isomerization, or geometric isomerization as keywords, and the general tendency is an increase in the number of papers devoted to the kinetic aspects of cis-trans isomerization (CTI) in all fields. The main isomerization pathways have probably been discovered, though many remain the object of intense theoretical (see Chapter 7) and experimental research (see Chapters 4—6, 8-10, 13, and 14). In the present chapter, general CTI mechanisms will be divided into homolytic and heterolytic cleavage of the 7r-bond which allows isomerization, though some molecular motifs such as amides are able to switch from cis to trans via both processes. An overview of CTI in metal complex (mainly thermal, photochemical, and oxidative isomerizations) will be the purpose of Chapter 14 and will not be detailed here. 

Van t Hoff said the tetrahedron need be regular only when the four groups are the same and equidistant, which is scarcely probable when the groups are different, because such a difference implies also a difference in the forces which bind the groups to the carbon atom. Van t Hoff in 1874 also explained the isomerism of fumaric and maleic acids (which are not optically active) as due to geometrical isomerism cis-trans isomerism, see p. 786). The tetrahedra sur-... 

Migratory insertion reactions involving olefins, that is, reactions of H/D exchange, isomerization, cis-trans isomerization, hydroformylation and other 0x0 syntheses. 

Here we introduce a further category of isomerism known as stereoisomerism, in which the molecules concerned have the same molecular formula and structural formula, but their atoms are arranged differently in space. There are three types of stereoisomerism — conformational isomerism, cis— trans isomerism and optical isomerism (Figure 20.46). Configurational isomers have permanent Figure 20.46 The different types of isomerism differences in their structural geometry and cannot... 

Cis-trans isomerizations Cis-trans isomerizations occur in stilbenes, azobenzene, azines, thioindigoids, as well as some biological receptors. 

In metal complexes the ligands may occupy different positions around the central atom. Since the ligands in question are usually either next to one another (cis) or opposite each other (trans), this type of isomerism is often referred to as cis-trans isomerism. Cis-trans isomerism is very common for square planar and octahedral complexes. Consider the square planar complexes shown in structures [5-1H5-4]. Cis-trans isomerism arises from the relative position of the ethylene ligands. Therefore, [5-1] and [5-3] are cis forms and [5-2] and [5-4] are trans forms, respectively. Norbornadiene-palladium dichloride [5-5] and rhodium (Ti-cycloocta-1,5-diene) chloride [5-6] can exist only in the cis structure because of the chelate nature of the diene. 

Coordination of Free Ions having Pyramidal Structure Coordinate Bond Vibration Modes Structural Isomerism Cis-trans isomerism Lattice Water and Aquo Complexes Metal-Alkyl compounds Metal Halides... 

The term cis describes geometric isomers in which two groups are attached on the same side of a double bond in an organic molecule, or along the same edge of a square in a square-planar complex, or at two adjacent vertices of an octahedral complex. (See also geometric isomerism.) cis-trans isomerism is a type of stereoisomerism. 

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)...

Figure 33. A loop containing a conical intersection for the cis-trans ethylene isomerization.

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. 

Take the Final Function Value of TINKER as the steric energy for this calculation. Compare the results with each other and with a standard value from a good elementar-y organic chemistry text (e.g., Ege, 1994). Calculate for the reaction cis trans and compare it with a standard text and with Kistiakowsky s original value. Kistiakowsky s original work was carried out at 355 K, but the temperature difference between 298 K and 355 K cancels for this isomerization. 

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. 

When two different substituents are attached to each carbon atom of the double bond, cis-trans isomers can exist. In the case of c T-2-butene (Fig. 1.11a), both methyl groups are on the same side of the double bond. The other isomer has the methyl groups on opposite sides and is designated as rran5--2-butene (Fig. l.llb). Their physical properties are quite different. Geometric isomerism can also exist in ring systems examples were cited in the previous discussion on conformational isomers. 

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

Qiana, introduced by Du Pont in 1968 but later withdrawn from the market, was made from bis(4-aminocyclohexyl)methane and dodecanedioic acid. This diamine exists in several cis—trans and trans—trans isomeric forms that influence fiber properties such as shrinkage. The product offered silk-like hand and luster, dimensional stabiUty, and wrinkle resistance similar to polyester. The yam melted at 280°C, had a high wet glass-transition temperature of - 85° C and a density of 1.03 g/cm, the last was lower than that of nylon-6 and nylon-6,6. Qiana requited a carrier for effective dyeing (see Dye carriers). 

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... 

The isomeric mixture is a colodess, mobile Hquid with a sweet, slightly irritating odor resembling that of chloroform. It decomposes slowly on exposure to light, air, and moisture. The mixture is soluble ia most hydrocarbons and only slightly soluble ia water. The cis—trans proportions ia a cmde mixture depend on the production conditions. The isomers have distinct physical and chemical properties and can be separated by fractional distillation. 

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. ... 

An interpretation of activation parameters has led to the conclusion that the bromination transition state resembles a three-membered ring, even in the case of alkenes that eventually react via open carbocation intermediates. It was foimd that for cis trans pairs of alkenes tiie difference in enthalpy at the transition state for bromination was greater than the enthalpy difference for the isomeric alkenes, as shown in Fig. 6.2. This... 

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