Trans conformational states

FIGURE 10 6 Confor mations and electron delo calization in 1 3 butadiene The s CIS and the s trans con formations permit the 2p or bitalsto be aligned parallel to one another for maxi mum TT electron delocaliza tion The s trans conformation is more stable than the s CIS Stabilization resulting from tt electron de localization is least in the perpendicular conformation which IS a transition state for rotation about the C 2—C 3 single bond The green and yellow colors are meant to differentiate the orbitals and do not indicate their phases... 

Fi re 12.6 Schematic diagram Illustrating the proton movements in the photocycle of bacteriorhodopsin. The protein adopts two main conformational states, tense (T) and relaxed (R). The T state binds trans-tetinal tightly and the R state binds c/s-retinal. (a) Stmcture of bacteriorhodopsin in the T state with hflus-retinal bound to Lys 216 via a Schiff base, (b) A proton is transferred from the Schiff base to Asp 85 following isomerization of retinal and a conformational change of the protein. 

The barrier for conversion of the skew conformation to the s-trans conformation is 3.9kcal/mol. This energy maximum presiunably refers to the conformation (transition state) in which the two n bonds are mutually perpendicular. Various MO calculations find the s-trans conformation to be 2-5 kcal/mol lower in energy than either the planar or skew cisoid conformations. Most high-level calculations favor the skew conformation over the planar s-cis, but the energy differences found are quite small. ... 

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. ... 

One interesting phenomenon was the effect of the boron substituent on enantioselectivity. The stereochemistry of the reaction of a-substituted a,/ -unsatu-rated aldehydes was completely independent of the steric features of the boron substituents, probably because of a preference for the s-trans conformation in the transition state in all cases. On the other hand, the stereochemistry of the reaction of cyclopentadiene with a-unsubstituted a,/ -unsaturated aldehydes was dramatically reversed on altering the structure of the boron substituents, because the stable conformation changed from s-cis to s-trans, resulting in production of the opposite enantiomer. It should be noted that selective cycloadditions of a-unsubsti-tuted a,/ -unsaturated aldehydes are rarer than those of a-substituted a,/ -unsatu-... 

The diene must adopt what is called an s-cis conformation, meaning "cis-like" about the single bond, to undergo a Diels-Alder reaction. Only in the s-cis conformation are carbons 1 and 4 of the diene close enough to react through a cyclic transition state. In the alternative s-trans conformation, the ends of the diene partner are too far apart to overlap with the dienophile p orbitals. 

For reactions of A-acyliminium ions with alkenes and alkynes one has to distinguish between A-acyliminium ions locked in an s-trans conformation and those which (can) adopt an s-cis conformation. The former type reacts as a (nitrogen stabilized) carbocation with a C —C multiple bond. Although there are some exceptions, the intramolecular reaction of this type is regarded as an anti addition to the 7t-nucleophile, with (nearly) synchronous bond formation, the conformation of the transition state determining the product configuration. 

In the uniaxially oriented sheets of PET, it has been concluded that the Young s modulus in the draw direction does not correlate with the amorphous orientation fa or with xa "VP2(0)> 1r as might have been expected on the Prevorsek model37). There is, however, an excellent correlation between the modulus and x,rans,rans as shown in Fig. 15. It has therefore been concluded 29) that the modulus in drawn PET depends primarily on the molecular chains which are in the extended trans conformation, irrespective of whether these chains are in a crystalline or amorphous environment. It appears that in the glassy state such trans sequences could act to reinforce the structure much as fibres in a fibre composite. 

In view of the absolute configuration and their optical yields (88-96 %), it follows that the precursor of the (S)-4 should be 2a, which are formed highly diastereoselectively. It is likely that the predominant formation of 2a conforms to the mechanism of the bromolactonization, the S-trans transition state (ref. 3). 

With regard to the molecular structure of CCHn, both cyclohexyl rings having a chair conformation are substituted in the equatorial positions and the alkyl chain is completely extended in the all-trans conformation. The cyclohexyl rings are nearly coplanar. The crystal structures of the investigated CCHn show that various types of molecular overlapping are present in the crystal. The molecular packing in the crystalline state is quite different in all three compounds. 

The enantioselectivity was explained by the preference for a transition state 28, in which the diene approaches the face of the coordinated dienophile, which adopts an s-trans conformation (Fig. 14). 

That the high degree of torsional and other types of strain inherent in the triplet states or trans conformers of cyclohexene and cycloheptene may be responsible for their photochemical behavior is suggested by the reactions of compound (50), a moderately twisted olefin according to molecular models. Compound (50) quantitatively yields bicyclo[3.3.1]non-l-yl acetate (51) within 15 sec after being dissolved in glacial acetic acid(83> ... 

Comparing the potentials across each row, we can test the idea of additivity of ortAo-substituent effects for 2-fluoro, 6-chloro, and then 2-fluoro-6-chloro substitution. The definition of a = 0 changes across each row to permit easy visual addition of the potentials in the physically appropriate manner to assess the degree of additivity of ort/io-chlorine and ort/io-fluorine substituent effects. For o-fluorotoluene and 2-fluoro-6-chlorotoluene, a = 0 denotes the (minimum-energy) pseudo-trans conformation for o-chlorotoluene, a=0 denotes the pseudo-cis conformation. The notion of additivity has considerable merit in all three electronic states. 

Fig. 3 Protonation states, isomerism and mesomerism of the HBI chromophore (p-hydroxybenzi-lidene-imidazolinone). The chromophore is shown in its most stable Z ( cw ) conformation, conventionally associated to a 0° value of the dihedral angle t, while the E ( trans ) conformation corresponds to t = 180°. For model compound HBDI (4 -hydroxy-benzylidene-2,3-dimethyl-imidazolinone), Ri = R2 = CH3, for chromophore in GFP, Ri, and R2 stand for the peptidic main chains toward N-terminus and C-terminus, respectively, (a) Possible protonation states of HBI (a) neutral, (b) anionic, (c) enolic, (d) cationic, and (e) zwitterionic. (b) Two resonance structures of the anionic form of HBI...

Another possible source of modification of the HBI optical properties arises from cis-trans (or, more properly, Z-E) isomerization around its exocyclic ethylene bridge (dihedral angle x as depicted in Fig. 3a) [74, 75]. The absorption spectrum of trans HBI in different solvents is red-shifted by 5-10 nm compared to that of the cis conformation [76]. While the trans conformation is thermodynamically unfavorable and contributes only a minor population at room temperature, cis-trans isomerization seems to take place regardless of the chromophore ionization state, and involves a relatively low energy barrier of about 50 kJ/mol [75], a value that appears significantly lower than initially predicted from quantum mechanics [77, 78]. 

Because of the difference in energy of these two groups, temperature changes alter the population of the two states. Ab initio calculations indicated [57,58] that the high-frequency peak is due to the trans conformation and the lower frequency peak to the cis conformation. Analysis of the relative band area gives the population of the two states as a function of temperature and hence allows... 

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