C/s-conformer

Dipole Moments of the c/s-Conformers of Betaines of the First and the Third Group... 

It should be emphasized that this analysis is based on the assumption of some appreciable 2—5 overlap in all-c/s and cis-gauche 1,3,5-hexatriene. Furthermore, it should be pointed out that our analysis of the conformational preference of 1,3,5-hexatriene is aiming at revealing electronic patterns. In reality, the all-c/s conformation of 1,3,5-hexatriene is unfavorable due to repulsive interactions between the two methylene groups, i.e. conformational preference varies in the order all-frans > cis-gauche. 

Pray, T. R. Reiling, K. K. Demirjian, B. G. Craik, C. S. Conformational Change Coupling the Dimerization and Activation of KSHV Protease. Biochemistry 2002, 41, 1474-1482. 

A (4 + 2) cycloaddition can take place between singlet oxygen and conjugated dienes that are free (or constrained) to adopt an s>c/s conformation (2.93). When such a reaction occurs with an aryl-conjugated alkene (2.94), the first-formed cycloadduct is itself a conjugated triene, and the overall reaction produces a bis-(4 + 2) adduct. 

It has been found that cyclopropyl ketone exhibits a conformer mixture The preferred component has been identified as the bisected s-c/s conformer At the present time, however, it is not clear whether the second conformer (less stable) corresponds to the bisected s-trans form or anti-gauche form. On the other hand, on the basis of a theoretical analysis (on the semiempirical INDO-level) and a proton NMR investigation for the cis-trans isomeric 2-methylcyclopropyl-l (methyl) ketones 15 and 16 it was suggested that the trans compound 15 exists as an equilibrium of the bisected s-cis and s-trans conformers. The s-c/s and s-trans conformers are separated by a rotational barrier of 5.7 kcal mol ... 

As mentioned earlier, conformational isomerization about the formal single bonds of polyene systems is facile in the ground state, where it occurs with activation barriers on the order of 2-4 kcalmol in acyclic systems . The process also occurs in acyclic dienes upon direct excitation, as was shown by SquiUacote and coworkers using low temperature matrix isolation techniques, at temperatures where thermal conformational reequilibration is suppressed (10-20 K) . Thus, direct irradiation of trans-1,3-butadiene in an argon matrix at 15 K results in the efficient formation of the c/s-conformer, distinguishable from the trans-conformer by its distinct UV absorption and infrared spectra . The process is quite general, at least for aliphatic dienes such as isoprene (2), 2-isopropyl-1,3-butadiene (24), 2,4-hexadiene (5) and 2,3-dimethylbutadiene... 

Fig. 31. Dominant stabilizing pi orbital interaction in the Cee and C s conformers of 2-propyl cation. The symmetry labels are assigned with respect to a mirror plane...

Cyclic dienes that are permanently in the s-c/s conformation are exceptionally good at Diels-Alder reactions—cyclopentadiene is a classic example—but cyclic dienes that are permanently in the s-trans conformation and cannot adopt the s-c/s conformation will not do the Diels-Alder reaction at all. The two ends of these dienes cannot get close enough to react with an alkene and, in any case, the product would have an impossible trans double bond in the new six-membered ring. (In the Diels-Alder reaction, the old a bond in the centre of the diene becomes a k bond in the product and the conformation of that a bond becomes the configuration of the new n bond in the product.)... 

The Diels-Alder reaction only occurs when the diene is in an s-c/s conformation. 

Draw the s-c/s conformation of the dipeptide Phe-Phe and identify the source of steric hindrance. 

Encapsulation of any of these c/s-conformers into libraries of columnar supra-molecular dendrimers eliminates the intramolecular electrocyclization and replaces the hehx-coil transition with an unprecedented helix-helix transition and a reversible transition from cw-transoidal to cis-cisoidal. When the repeat unit of the dendronized polymer also contains a stereocenter, this reversible process can be monitored by circular dichroism (CD) and visualized by different methods [104-111]. This concept was used to elaborate molecular machines that were interfaced for the first time with the real world to lift heavy objects [111]. 

Narasimhan, C. and Lai, C.-S., Conformational changes of plasma fibronectin detected upon adsorption to solid substrates. Biochemistry 28,5041,1989. 

In order to participate in a Diels-Alder reaction, the conjugated diene must be in an 5 -cis conformation because C-1 and C-4 in an. v-trans conformation are too far apart to react with the dienophile in a concerted reaction. Therefore, a conjugated diene that is locked in an s-trans conformation cannot undergo a Diels-Alder reaction because it cannot achieve the required c/s-conformation. 

Peptoids bearing Ca-chiral substituents have been shown to favor the cis-con-formation (Fig. 5b) [53, 54]. Another way to favor a c/s-conformation of the amide bond is to implement a favorable interaction between the backbone and the substituent orbital of an adjacent aromatic side chain, which was possible using A -a-chiral acetanilide or A-l-naphtylethyl substituents (n —> r c=o and hydrogen bonding or n r Ar and steric interactions, respectively) [55]. Interestingly, the cis-conformation was only favored in polar solvents, whereas in non-polar solvents... 

Brase, Muhle-Goll and coworkers reported on functional peptoid helices [77]. In order to create cell-penetrating peptoids, butylamine residues were incorporated into peptoids. NMR spectroscopy and molecular modeling revealed an extended pseudo-helical structure with predominant c/s-conformation in the backbone. The electrostatic repulsion between the side chains leads to maximization of the spacing of the ammonium residues and thus dominates the conformation of the peptoid. With a pitch of 7.7 A, the charge distribution is somewhat less dense compared to a-helical peptides. Nevertheless, the peptoids were effective transporters, similar to other cell-penetrating peptides. 

Reactivities in Diels-Alder Reactions Rates of Diels-Alder reactions are affected by steric as well as electronic factors. For Diels-Alder reaction to proceed dienes must have double bonds on the same side of central-single bond, i.e. there must be c/s-conformation because this is high energy conformation. 

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