Ribose in aqueous solution

FIGURE 25 5 Distribution of furanose pyranose and open chain forms of d ribose in aqueous solution as mea sured by H and NMR spectroscopy... 

N.m.r. studies of the binding of calcium and lanthanum ions to o-lyxose and D-ribose in aqueous solutions show the existence of 1 1 metal-sugar complexes. It has been suggested that the pyranose has a conformation which has ax-eq-ax arrangements of the three consecutive cis-hydroxy-groups. 

Because six membered rings are normally less strained than five membered ones pyranose forms are usually present m greater amounts than furanose forms at equilib rium and the concentration of the open chain form is quite small The distribution of carbohydrates among their various hemiacetal forms has been examined by using H and NMR spectroscopy In aqueous solution for example d ribose is found to contain the various a and p furanose and pyranose forms m the amounts shown m Figure 25 5 The concentration of the open chain form at equilibrium is too small to measure directly Nevertheless it occupies a central position m that mterconversions of a and p anomers and furanose and pyranose forms take place by way of the open chain form as an inter mediate As will be seen later certain chemical reactions also proceed by way of the open chain form... 

It has been shown already that C-2 of ribose is the precursor of the methyl group, and C-l is eliminated in the biosynthesis. The following observation can be pertinent to the point. Pyrimidine (58) is very unstable and quickly decar-boxylates in aqueous solution at room temperature to give pyramine (Scheme 32).67 Thus, if a C-l -C-2 fragment of the ribose part of AIRs became attached by C-2 to C-2 of a pyrimidine, oxidation of C-l to produce a carboxylic acid function could result in its smooth elimination. 

It has been noticed that branched sugars are more likely to assume the furanose than the pyranose form,354 and it was, in fact, proved424 by 1H-and 13C-n.m.r. spectroscopy that, in aqueous solution, hamamelose (2) affords much more of the furanose (71%) than does ribose (24%). More, systematic research is desirable on this subject. 

The formation of these products from the dialkyl dithioacetals falls into two categories. The first group comprises compounds readily formed (or isolated), and is confined to derivatives of D-glucose, D-glucuronic acid, 2-acetamido-2-deoxy-D-glucose, and D-ribose. The products are obtained in high yield the formation is generally accomplished in aqueous solution, with one mole of mercuric chloride per mole of dithioacetal, and the solution is kept neutral. 

The methyl ester was crystallized and its absolute stereochemistry was determined by x-ray diffraction to be as in equation 8.37. This product corresponds to an in-line attack. When incubated with ribonuclease in aqueous solution, the methyl ester re-forms the original cyclic phosphorothioate (structure 8.36). This result is expected from the principle of microscopic reversibility, since the forward and reverse reactions must go through the same transition state. But it does show directly that the cyclization step involves an in-line attack an adjacent attack of the ribose hydroxyl in the cyclization of the methyl ester as in the right-hand structure 8.38 would give the enantiomer of structure 8.36. 

Heberger K, Lopata A (1998) Assessment of nudeophilicity and electrophilicity of radicals, and of polar and enthalpy effects on radical addition reactions. J Org Chem 63 8646-8653 HerakJN, Behrens G (1986) Formation and structure of radicals from D-riboseand 2-deoxy-D-ribose by reactions with SO4 radicals in aqueous solution. An "in-situ" electron spin resonance study. Z Naturforsch 41c 1062-1068... 

Stelter L, von Sonntag C, Schulte-Frohlinde D (1975a) Radiation chemistry of DNA-model compounds VIII. Dephosphorylation products from reactions of OH radicals with ribose-5-phos-phate in aqueous solution. The effect of oxygen. Z Naturforsch 30b 609-615 Stelter L, von Sonntag C, Schulte-Frohlinde D (1975b) Radiation chemistry of DNA-model compounds, VII. On the formation of 5-deoxy-D-eryffrro-pentos-4-ulose and the identification of 12 further products from y-irradiated aqueous solutions of ribose-5-phosphate. Z Naturforsch 30b 656-657... 

The mutarotation of ribose was first observed by Phelps, Isbell and Pigman47 48 who studied both the d- and L-isomers in aqueous solution at 1°. The mutarotation of L-ribose in water at 0°, shown in Fig. 1, is a complex one, due probably to the existence of equilibria involving both furanose and pyranose forms. There is considerable evidence to support this view. Bredereck, Kothnig and Berger26 found that, while the mutarotation of D-ribose in pyridine at 20° is complex, the mutarotation of 5-trityl-D-ribose (which can exist only in the furanose form) in pyridine at 3° is of the normal, first order type. Isbell and Pigman48... 

C resonances were not assigned in detail, but the values of were used to infer that the motions of this molecule in aqueous solution are isotropic.169 The Tt values (0.19-0.23 sec) of the, 3C nuclei of the furanoid ring of 55 were found to be measurably longer than those (0.15-0.16 sec) of the protonated 13C nuclei of the base, thus indicating that the rotational motion of the base is more restricted than that of the D-ribose moiety, possibly as a result of intermolecular base-stacking.169... 

In other 13C studies of raffinose, stachyose,170 various vitamin B12 derivatives,171 and the anomeric equilibria of D-fructose and D-turanose in aqueous solution,172 partially relaxed, Fourier-transform spectra, and the values of obtained from them, have been elegantly used to confirm the spectral assignments. The T, values of the 13C nuclei of thermally denatured, yeast fRNA indicate that its D-ribose phosphate backbone undergoes rapid segmental motion at 81°. In contrast, the values of Tx for folded fRNA yielded no evidence of segmental motion.1720... 

Irradiation of cytosine, cytidine, and 2 -deoxycytidine has recently been reported to produce 4,5 -linked dimers (154 R = H, j3-D-ribose, 2-deoxy-/3-D-ribose, respectively) 210 this reaction is accompanied by deamination. Photodimerization (in aqueous solution) of uracil211 and thymine212 affords the 4,6 -linked dimer (155 R = R = H and Me, respectively) the oxetane (156) (probably formed by 1,2-cycloaddition of a triplet carbonyl to an olefinic bond) is proposed as the precursor.212... 

The application of LSR to amino-acids has received some attention. (451-456, 498) Such studies are an essential preliminary to the use of LSR for amino-acid sequence determination in simple peptides and proteins. The latter are discussed more comprehensively in Section G. A detailed study has been made (453) of the interaction of Eu(iii), Pr(iii), Gd(iii), and La(iii) with iV-acetyl-L-3-nitrotyrosine in order to characterize the nitrotyrosine residue as a potential specific lanthanide binding site in proteins. The parameters of the dipolar interaction indicate a significant contribution from non axially symmetric terms. The conformations of the nucleotides cyclic j8-adenosine 3, 5 -phosphate (3, 5 -AMP) (457, 458) and adenosine triphosphate (ATP) (459) have been deduced using LSR. In the former case the conformation of the ribose and phosphate groups is consistent with the solid state structure. A combination of lanthanide shift and relaxation reagents was used to deduce the most favoured family of conformations for ATP in aqueous solution. One of these conformations corresponds closely to one of the crystal structure forms. 

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