Syn-conformer

Although the same theoretical studies indicate very small energy differences between the syn and anti conformers of the 3-carbaldehydes of furan, thiophene and pyrrole with a slight preference for the syn conformer, in chloroform solution the furan- and thiophene-3-carbaldehydes adopt the anti conformers to the extent of 100 and 80% respectively (82X3245). However, A-substituted 3-(trifluoroacetyl)pyrroles exist in solution as mixtures of rotational isomers (80JCR(S)42). 

Stabilization of the syn conformer in the gas phase is explained rather intuitively in terms of the extra stabilization due to increased interactions between the H atom in the OH group and the O atom in C=0 group. As one can see in Figure 5, the extra stabilization in the anti confonner in aqueous solution arises from the solvation energy, especially at the carbonyl oxygen site. 

Figures 17A and 17B (p. 183) show energy as a function of rotation for a series of 1-substituted acetaldehydes, with 6 = 0° in the syn conformation and 6 = 180° in the anti conformation. The calculations were done using the PM3 method. Figure 17A for a vacuum, whereas Fig. 17B is for a solvent cavity with a dielectric constant of 4." The table gives the calculated barriers. Discuss the following aspects (a) rationalize the order Br > Cl > F for syn conformers (b) rationalize the shift to favor the am. conformation in the more polar environment. 

FIGURE 12.14 Comparison of the deoxy-guanosine conformation in B- and Z-DNA. In B-DNA, the Cl -N-9 glycosyl bond is always in the anti position (lefi). In contrast, in the left-handed Z-DNA structure, this bond rotates (as shown) to adopt the syn conformation. 

The main utility of Peterson olefination lies in the contrasting stereochemical requirements (6) for elimination, use of base requiring a syn conformation whereas acid conditions demand an anti conformation, with complementary geometrical results ... 

Finally, the pyrimidine nucleotide 4-thiouridine 5 -triphosphate, also presumably essentially in the syn conformation, cannot serve as a substrate for homopolymerization with E. coli RNA polymerase (54). Small amounts of 4-thiouridine were reported to have been found in naturally occurring transfer RNA from coli (55). Scheit has reported that as a monomer in CDCI3, the base can still pair with adenosine (56). 

Most nucleosides contain D-ribose or 2-deoxy-D-ribose linked to N-1 of a pyrimidine or to N-9 of a purine by a P-glycosidic bond whose syn conformers predominate. 

The conformational analysis of methyl pyruvate shows that it can have two conformers. In the second conformer the two carbonyls are in syn position. The anti-syn conformational change requires 3 kcal. The [CDqIq qJ - methyl pyruvate ] complex ((R) form) was also calculated and shown in Figure 8. In the above complex the "directionality" of the lone pair of electrons of the quinuclidine nitrogen is advantageous for interactions with both the keto and the ester carbonyl groups. 

The lack of excited state involvement for 24 is in contrast to behavior in systems that have substantial equilibrium concentrations of the syn conformer as discussed... 

Cyclic a-methylene ketones and lactones, in which the syn conformation is enforced, give predominantly exo adducts.14... 

Another common hydrogen transfer reaction of carbonyl triplet is the photoenolization of the c-methylbenzoyl chromophore, illustrated in reaction 3 for the syn conformer of c-methylaceto-phenone (j+). Reaction 3 can act as a very efficient energy sink, and a number of properties of this group led us to believe that this process could be used to reduce photodegradation i.e. the excellent absorption characteristics of the chromophore, the short triplet lifetime and the fact that the disappearance of the carbonyl triplet does not take place at the expense of the formation of another excited state. 

Finally, it should be mentioned that all our arguments and examples have centered on the syn conformer of the o-methylbenzoy1 group. In small molecules the syn-anti conformational equilibrium is known to play an important role in the photochemistry of the... 

Fluorescence probes possessing the PyU base 46 selectively emit fluorescence only when the complementary base is adenine. In this case, the chromophore of is extruded to the outside of the duplex because of Watson-Crick base pair formation, and exposed to a highly polar aqueous phase. On the contrary, the duplex containing a PyU/N (N = G, C and T) mismatched base pair shows a structure in which the glycosyl bond of uridine is rotated to the syn conformation. In this conformation, the fluorophore is located at a hydrophobic site of the duplex. The control of base-specific fluorescence emission is based on the polarity change in the microenvironment where the fluorophore locates are dependent on the l>yU/A base-pair formation. 

Gawronski et al.21 have used NMR spectroscopy, especially NOE experiments in order to assign conformation of the chiral calixsalen-type macrocycles, products from the [3 + 3] cyclocondensation of the trans-1,2-diaminocyclohexane with hydroxydialdehydes. It was shown that the macrocycles had C3-symmetrical structure and s-syn conformation of imine C—H/cyclohexane axial C—H bond systems and s-trans conformation of the bis-imine unit. 

C5 , then the atom is said to be endo, and if it is on the opposite side it is defined as exo. The conformation about the sugar-base linkage is defined as anti when the torsion angle (chi, 04 -Cl -Nl -C2 for pyrimidines and 041-Cl -N9-C4 for purines) lies near 180° and syn when it lies near 0°. These situations are illustrated in Figure 22. The glycosidic linkage are all anti in B-DNA and A-DNA, but in Z-DNA the guanine bases are in the syn conformation. 

Figure 24. Comparison of the structures of (a) deoxyadenosine and (b) an alkylated derivative. Note the syn conformation of the product of alkylation.

The two O -alkylated guanosine derivatives (117) shown in Figure 28, do not demonstrate a perpendicularity of hydrocarbon and base, presumably because the hydrocarbon is much smaller. However, again the nucleoside has the syn-conformation. This perpendicularity, however, is found for the acetylamino fluorine derivative. 

---