Conformation cis—trans

AM1, highest occupied (HOMO) and lowest unoccupied (LUMO) tr orbital values in eV. cis,trans conformation. cis,trans (dione) conformation (ref. 94). 

A conformational cis-trans isomerization has been observed in the cation Au(S2P(OH)Ph)2+. The structures of both cis and trans stereoisomers have been determined by X-ray diffraction analyses. In solution, a facile isomerization occurs (Scheme 12)19. 

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). 

High temperature searches of conformational space (see Quenched Dynamics on page 78), can produce unwanted conformational changes, such as cis-trans peptide flips, ring inversions, and other changes that you cannot reverse easily by geometry optimization. You can use restraints to prevent these changes. 

Disubstituted cyclohexanes can exist as cis-trans isomers as well as axiaEequatorial conformers. Two isomers are predicted for 1,4-dimethylcyclohexane (see Fig. 1.9). For the trans isomer the diequatorial conformer is the energetically favorable form. Only one cis isomer is observed, since the two conformers of the cis compound are identical. Interconversion takes place between the conformational (equatoriaEaxial) isomers but not configurational (cis-trans) isomers. 

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. 

Fig. 8. Rephcation. The amino adenosine X and the pentafluorophenyl ester Y form a hydrogen-bonded dimer XY, prior to reaction between the amine and the activated ester groups (shown in the circle). The reaction product is a <7 -amide conformer cis-Z that isomeri2es to the more stable trans- acnide Z. The rephcative process is cataly2ed by the reaction product Z (also referred to as the template). First, a termolecular complex XYZ is formed from X, Y, and Z.

Individual chains are planar with alternating cis—trans conformation along the chain, and the interaction with neighboring chains leads to a highly ordered matrix. 

Table 3 fists cycloaliphatic diamines. Specific registry numbers are assigned to the optical isomers of /n t-l,2-cyclohexanediamine the cis isomer is achiral at ambient temperatures because of rapid interconversion of ring conformers. Commercial products ate most often marketed as geometric isomer mixtures, though large differences in symmetry may lead to such wide variations in physical properties that separations by classical unit operations are practicable, as in Du Font s fractional crystallisation of /n t-l,4-cyclohexanediamine (mp 72°C) from the low melting (5°C) cis—trans mixture. 

Three different conformations are possible for monomeric chalcogen diimides (Eig. 10.1). Variable-temperature NMR spectra indicate that the cis,trans isomer of S(NR)2 is most stable in solution for small organic groups (R = Me, Bu). With bulkier organic substituents, small amounts of the trans,trans isomer exist in equilibrium with the cis,cis isomer. " The cis,cis isomer is observed in solutions of certain sulfur diimides with... 

The only selenium diimide to be structurally characterized in the solid state, Se(NAd)2 (Ad = adamantyl), ° adopts the cis, trans conformation consistent with conclusions based on H and C NMR studies for Se(N Bu)2. ... 

The geometries and relative energies of the different conformations of model chalcogen diimides E(NR)2 (E = S, Se R = H, Me, Bu and SiMe3) have been investigated by using ab initio and DET molecular orbital methods.The cis,trans conformation is predicted to be most stable with the exception of the parent molecules E(NH)2 and the unsymmetrical systems RNSNH, for which the cis,cis conformation is slightly more stable than the cis, trans isomer. 

Diazenes of the type REN=C(R )N=NC(R )=NER have a rich structural chemistry. The selenium derivatives 15.11a,b display a cis,trans,cis conformation with two short l,5-Se N contacts (2.65 A). Several sulfur analogues, e.g., 15.1c, have the same structure, but a different cis,trans,cis conformer 15.12 with two 1,4-S N contacts (2.83 A) has also been characterized. A third type of diazene is the trans,trans,trans isomer 15.13a,b with no intramolecular short contacts. ... 

A study195 based on the NMR lanthanide-induced shifts (LIS) for a series of cis- and trans-3-substituted, and 3,3-disubstituted thietane oxides concluded that all cis-substituted oxides (5c R = CH3, t-Bu and aryl) exist exclusively in the diequatorial conformation. The trans-3-substituted isomers (185) prefer the equatorial oxygen conformation (R = CH3,86% t-Bu, 65-75% aryl, 75%), which means an axial preference for the substituents (e.g. 185d), at least when they are bound to a shift reagent (equation 75). 

Hogeveen138 measured apparent acidity constants of substituted /i-phenylthio-, /J-phenylsulfinyl- and / -phenylsulfonyl-acrylic acids (cis and trans) in 50% v/v ethanol. The p values for transmission through SCH=CH, SOCH=CH and S02CH=CH were 0.531, 0.389 and 0.320 respectively for the cis acids and 0.652, 0.282 and 0.331 for the trans acids. These results were discussed in considerable detail and compared with those of pertinent related systems. Little importance was attached to the small differences between p values for cis/trans isomers, and the relative transmissions were taken as the mean p values 0.59,0.34 and 0.33. The superior transmission of SCH=CH was attributed to greater polarizability. The values for pKJtrans) — pKJcis) of isomeric acids were also discussed. For the sulfonyl acids this is almost constant at 0.1 unit for the sulfinyl adds there is some variation about a mean value of 0.26 unit, and for the thio adds there is also some variation about a mean value of — 0.15 unit. The differing behavior of the three systems in this respect was explained in terms of hypothetical conformations and electrostatic interactions therein. 

The structures, energies, torsional barriers and vibrational spectra of three rotamers of tetrasulfane, H2S4, have been examined by Drozdova, Miaskiewicz and Steudel at the MP2/6-311G level [34]. Surprisingly, the cis-trans conformation (motif -l-H— symmetry Ci) is found to be most stable, followed by the all-cfs form (h—t symmetry C2), while the helical all-... 

If peptide residues are converted to peptoid residues, the conformational heterogeneity of the polymer backbone is likely to increase due to cis/trans isomerization at amide bonds. This will lead to an enhanced loss of conformational entropy upon peptoid/protein association, which could adversely affect binding thermodynamics. A potential solution is the judicious placement of bulky peptoid side chains that constrain backbone dihedral angles. 

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

In an attempt to isolate the anomeric effects, analogous phosphonites have been studied. Equilibration of cis- (109) and /ra 5-2-methyl-5-t-butyl-l,3,2-dioxaphosphorinanes(l 10) demonstrated the thermodynamic preference for cis over trans (72% and 28% respectively at 40 °C). This surprising result must mean that axial P-methyl is more stable than equatorial even when no anomeric effects are present, and the authors interpret their n.m.r. results in terms of two equilibrating conformers for trans- 10)... 

In summary, all the experiments expressly selected to check the theoretical description provided fairly clear evidence in favour of both the basic electronic model proposed for the BMPC photoisomerization (involving a TICT-like state) and the essential characteristics of the intramolecular S and S, potential surfaces as derived from CS INDO Cl calculations. Now, combining the results of the present investigation with those of previous studies [24,25] we are in a position to fix the following points about the mechanism and dynamics of BMPC excited-state relaxation l)photoexcitation (So-Si)of the stable (trans) form results in the formation of the 3-4 cis planar isomer, as well as recovery of the trans one, through a perpendicular CT-like S] minimum of intramolecular origin, 2) a small intramolecular barrier (1.-1.2 kcal mol ) is interposed between the secondary trans and the absolute perp minima, 3) the thermal back 3-4 cis trans isomerization requires travelling over a substantial intramolecular barrier (=18 kcal moM) at the perp conformation, 4) solvent polarity effects come into play primarily around the perp conformation, due to localization of the... 

The preference for the axial position in unhindered thiane-1-oxides has been known for some time. The spectra of the cis and trans isomers of the 2-, 3- and 4-methyl thiane-1-oxides, 169-171, were also measured. It was concluded from the chemical shifts that the methyl groups preferred the equatorial positions. A comparison of the chemical shifts obtained for sulfoxides 169-174 with those obtained for the cis and trans sulfoxide isomers of trans-1-thiadecalin, 175 and 176, was consistent with this proposal. Sulfoxide 175 with the S=0 axial gave a shift about 17 ppm upheld from that of its equatorial isomer 176. For sulfoxides 169-174, the conformers proposed to have the S=0 axial gave shifts that were upheld from those of the supposed equatorial conformers. For trans-3, trans-5-dimethylthiane-l-oxide (177) with the oxygen axial, the 0 signal was 21 ppm upheld from the signal observed for the equatorial oxygen in cis-3, cis-5-dimethylthiane-l-oxide (178). 

Entry 21 involves addition to a glyoxylic hydrazone and the cis ring junction is dictated by strain effects. The primary phenylselenyl group is reductively removed under the reaction conditions. Entry 22 involves generation of a stannyloxy radical by addition of the stannyl radical at the carbonyl oxygen. Cyclization then ensues, with the cis-trans ratio being determined by the conformation of the cyclization TS. 

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