6- isocytosine, tautomerism

In tautomeric equilibria of some functionalized pyrimidine derivatives, such as isocytosine 52 (R = H) [77ZN(C)894] or pseudocytidine 52 (R = furanosyl) (99MI1), the potentially tautomeric oxo and amino groups are practically not involved, and only annular tautomeric interconversions N(1)H N(3)H are ob-... 

In isocytosine and anthranilic acid it seems that any given molecule is always of the same tautomeric form in the crystal that is, the proton is not moving from site to site in the hydrogen bond. In general, however, the question of whether the proton is localized or not was difficult to answer until the advent of solid-state NMR Thus, for example, there has been much controversy as regards imidazole, 48. On the one hand there were the proponents of delocalization on this basis Zimmerman introduced his controversial theory of proto-merism (106). Others argued for localization. Recently evidence from high-resolution l3C NMR of the solid has provided evidence in support of the latter (107). A similar situation exists for pyrazole, 49 (107). 

The X-ray crystallographic studies show that thiouracils and 2-thiocytosine exists in the crystalline state in forms 51 and 52, respectively, and that isocytosine exists as a mixture of two amine-lactam forms, 42 and 43. Several experimental studies on these pyrimidines in solution confirm the conclusions from the crystal. However, studies on the tautomerism of the minor pyrimidine bases are few. In a number of cases the conclusions about the dominant structures are intuitive rather than proved. We present the essential experimental data on the structure of the minor pyrimidine bases. 

Aza and 6-aza substitution cause a shift in the tautomeric equilibrium of isocytosine. In 5-azaisocytosine, form 42 predominates over form 43 by a factor of 102, whereas in 6-azaisocytosine, form 43 is more stable than form 42.508... 

Information on the tautomerism in thio analogs of cytosine and isocytosine is scanty. After comparing the UV spectra and ionization constants of these molecules with those of their methylated derivatives, Brown and Teitci511 suggested that thiocytosine exists as a mixture of 52 and 55 in aqueous solution, and isothiocytosine exists rather in form 56. As the 1-methyl derivative of isocytosine was not available, the latter conclusion is uncertain. In fact, the 77-SCF MO Cl calculations... 

The crystal structure of isocytosine [ICYTIN] is interesting since it is a 1 1 complex of the 1,4- and 3,4-dihydro tautomers and has both triple and double hydrogen-bond self-association (Fig. 16.7). As outlined in Chapter 15, this tautomerism is not observed in the naturally occurring nucleic acid bases. 

Fig. 16.7. In the crystal structure of isocytosine [ICYTIN], the base adopts two different tautomeric forms A, R This cannot occur with the natural bases found in the nucleic acids...

Jaworski, A., Kwiatkowski, J. S., and Lesyng, B. (1986). Inti. J. Quantum Chem. QBS12, 209—discussion of the relationship between tautomerism of isocytosine, isoguanine, and genetic code. 

According to MCD, absorption, and 13C NMR spectra, isocytosine exists in solution in equilibrium of two amino-oxo forms 202b and 202d (80BCJ3073, OOZOR1373). The similar tautomeric interconversion with predominating form 202d was observed in solution of its 6-substituted derivative, 6-(9-heptadecyl)isocytosine. 

There are five dihydropyrimidines. The 1,4- and the 1,6-dihydropyrimidines can readily interconvert by tautomerism because of the mobile NH proton. The common metals to effect hydrogenation can be used . Platinum has been the catalyst of choice for the reduction of the 5,6-double bond of uracils, for example, in the addition of deuterium to uracil to produce [5,6- H2]5,6-dihydrouracil. But in the reduction of 2(l/f)-pyrimidinone and its iV-methyl derivative it is the 1,6-dihydro derivatives which are formed. The addition of hydrogen to the 5,6-bond of thymidine and other 5-substituted uridines is stereospecific with rhodium-on-alumina as catalyst. Rhodium-on-charcoal has been useful for hydrogenation of the 5,6-double bond in uracils, uridine, and isocytosine. Raney nickel readily promotes saturation of the 5,6-double bond. Thio derivatives may either be dethiated or taken further to reduced forms by Raney nickel catalysts . 

Like in many heterocyclic molecules, tautomerism gives rise to different isomers of the UPy molecule, as shown in Scheme 1. In the parent heterocycle, isocytosine, the 3H tautomeric form is the most stable form [9]. In DMSO, a solvent that strongly competes for hydrogen bonding, UPy 2a is also present in this tautomeric form. However, in chloroform solution, 2a occurs almost exclusively (>99%) in its IH tautomeric form, while a very small amount of aromatic pyrimidinol tautomer is observed. 

We have first developed this apparatus to study very fast prototropic transformations in purine and pyrimidine aqueous solutions. For example Uracil with a pH above 9.5 exists in solution as a mixture of tautomeric anions. The interconversion of these two species is always very fast (100 ns < t < 3 ys) and must be studied with the laser T-jump technique. The study of the variation of the relaxation time with the pH and the concentration has allowed us to show that the N(1)H/N(3)H tautomeric interconversion of uracil monoanions proceeds via a dissociative mechanism as it does for cytosine and isocytosine >. ... 

Figure 11. Predicted tautomeric equilibria in cytosine - isocytosine complexes. The area where the different number of water molecules have been placed is colored in grey.

Finally we would like to mention the investigation of the so called reverse Watson-Crick isocytosine - cytosine base pair which mimic the parallel strand of the DNA [145]. Among the structures investigated at the MP2/6-31 G(d)//HF/6-3 lG(d) level, the complex presented in Figure 13, which includes the interaction of two rare tautomers, is only 9 Kcal mof less stable than canonical cytosine-isocytosine base pair. Inclusion of the hydration decreases this difference to 6 Kcal-mof. Thus the calculations indicate that possible involvement of minor tautomeric pairs should be considered when considering the structure of a parallel strand of DNA. 

The tautomerism of N-labeled isocytosine was reinvestigated in solution and in the solid state (Scheme 5.28) [75]. In the CP-MAS NMR spectra, a ratio... 

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