Ribose conformation

Narayanan P, Berman H (1975) A crystallographic determination of a chemical structure 6-Ammo-10-(y9-D-ribofuranosylamino)pyrimido-[5,4-d]pyrimidinc, an example of an unusual D-ribose conformation. Carbohydr Res 44 169-180... 

Figure 6.12 Ribose conformations and locked nucleic acid.

Lemieux, R. U., L. Anderson, and A. H. Conner The Mutarotation of 2-Deoxy-p-D-erythro-Vtniost ( 2-Deoxy-p-D-Ribose). Conformations, Kinetics and Equilibria. Carbohydr. Res. 20, 59 (1971). 

Inspection of the data in Table I shove that 7-zaethylation has an important influence on ribose ring conformational distribution. The ribose conformation which prefers E sugar pucker in 5 GMP registers a decrease of 23% on 7-zaethylation, so much so, the ribose in 7-Me-5 GMP prefers E pucker. This is the first example of a purine--mononucleotide which shows preference for E pucker in aqueous solution. The data further reveal that 7-methylation has very little influence on the population of conformers about C -O bond, but has a significant effect on the conformational preference about CU -C bond. There is an increase of 2Qf% in the gg (4 =60 ) population in... 

Notice that the eclipsed conformation of d ribose derived directly from the Fischer pro jection does not have its C 4 hydroxyl group properly oriented for furanose ring forma tion We must redraw it m a conformation that permits the five membered cyclic hemi acetal to form This is accomplished by rotation about the C(3)—C(4) bond taking care that the configuration at C 4 is not changed... 

Conformation of D ribose suitable for furanose ring formation... 

The other important feature of the primary stmcture of RNA is the presence of the 2 -hydroxyl group in ribose. Although this hydroxyl group is never involved in phosphodiester linkages, it does impose restrictions on the heHcal conformations accessible to double-stranded RNA. 

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. 

A difference in the solid state and solution conformation of 5 -de-oxyadenosylcobinamide (cobinamide coenzyme) has been inferred from the NMR spectrum of cobinamide coenzyme 123) which indicates that the resonance due to the proton at carbon R-l of the ribose is shifted significantly upfield from its expected position. Such an upfield shift would probably have to arise from the ring current of the adenine ring. 

A stereospecific total synthesis of polyoxin C and related nucleosides is reported, in which the reaction of 1 -(pheny lthio)-1 -nitroalkenes with nucleophiles and subsequent ozonoly sis are key reactions. Addition of potassium trimethylsilanoate to l-(phenylthio)-nitroalkenes derived from D-ribose followed by ozonolysis gives the a-hydroxy thioester, which is formed with excellent diastereoselectivity (Scheme 4.5).46 This conformation meets the stereo-electronic requirements for antiperiplanar addition of the nucleophile with the result of high 5-(S) stereochemical bias in the reactions. 

The differing conformations of the ribose have been named with respect to that ring atom which puckers out of the plane given by the other ring atoms. The most prominent conformations are Cy-endo in B-helices and Cy-endo in A-helices. At room temperature both conformers are in a dynamic equilibrium. Intermediates between Cy-endo and Cy-endo are found in several (time-averaged) structures obtained from X-ray crystallography or NMR. When changing the pucker phase... 

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