Pyrimidine bases, properties

Characteristic Organic Structures, 9-116 PSD, definition, 12-1 to 4 psia and psig, definition, 1-40 Purine bases, properties of, 7-5 Pyrimidine bases, properties of, 7-5 Pyrophoric chemicals, safe handling, 16-1 to 12... 

The first chemical synthesis of these substances, using a procedure which yields 1-ribofuranosyl derivatives by pyrimidine bases, was described by Hall. By using the mercuric salt of 6-azathymine and tribenzoate of D-ribofuranosyl chloride, he obtained a mixture of two monoribosyl derivatives and a diribosyl derivative. He determined the structure of the 3-substituted derivative by the similarity of spectra and other properties to those of 3-methyl-6-razauracil. The structure of the 1-ribosyl derivative was then determined from the similarity of the spectra with 6-azathymine deoxyriboside obtained enzymatically. 

The coordination properties of pyrimidine bases seem to be less versatile than those of purine derivatives. Various Pt(II) and Pt(IV) compounds, including cis- and rrans-DDP, preferentially bind to the N3 site in N1-substituted cytosine derivatives (Figure 7), as verified by a variety of methods [7]. Simultaneous binding to N3 and to the exocyclic amino group C(4)-NH2 upon loss of a proton has been observed in a bridged Pt(II) system and in a chelated Pt(IV) system [7]. With 1,3-di-methyluracil, Pt(II) coordination to the C5 atom has been ascertained by X-ray crystallography [22]. 

Because of the specific base pairing, the amount of A equals the amount of T, and the amount of G equals the amount of C. Thus, total purines equals total pyrimidines. These properties are known as Chargafif s rules. 

The understanding of the tautomeric properties of the purine and pyrimidine bases of the nucleic acids and the determination of the electronic properties of the principal tautomers are of fundamental importance in molecular biology, in particular in connection with the theory of mutations (for general references see, e.g. refs. 1-6.) B. Pullman and A. Pullman have presented recently in these Advances3 a detailed review of the problem as it concerns the purine bases. The present paper... 

As with polypeptides, the light absorption properties of polynucleotides reflect those of the individual components. The spectra of the purine and pyrimidine bases as ribonucleosides are shown in Fig. 5-5. The number of individual electronic transitions and their origins are not immediately obvious, but many measurements in solutions and in crystals, as well as theoretical computations,7 83 84 have been made. Cytosine has n-n transitions at -275, 230, 200, and... 

TABLE I. Electron Donor Properties of Purine and Pyrimidine Bases... 

Understand the properties of purine and pyrimidine bases and nucleosides, and nucleotides with varying amounts of phosphate. Recognize the structures of the various xanthines, cyclic nucleotides, uric acid, and bases found in nucleic acids. 

The chemical properties of the purine and pyrimidine bases include highly conjugated double bond systems within the ring structures. For this reason, nucleic acids have a very strong absorption maximum at about 260 nm, which is used for nucleic acid quantitation. Moreover, the bases can exist in two tautomeric forms, the keto and enol forms (Figure 10.2). In DNA and RNA, the keto forms are by far the more predominant, and this property makes it possible for the bases to form intermolecular hydrogen bonds (see Figure 10.18). 

Applying the same analysis to pyrimidines (3 and 6) leads to pyrimidones, examples of which are the pyrimidine bases in DNA and RNA. Thus deoxycytidine 46 and deoxythymidine 47 are two of the four 2 -deoxyribonucleosides that are the building blocks of DNA and uridine 48 is one of the four nucleoside building blocks of RNA. As for pyridones, the contribution of dipolar resonance hybrids to pyrimidones and other systems with exocyclic conjugation often helps to understand their properties, including their aromatic character. 

Theoretically, the purine- and pyrimidine-based nucleic acid constituents and the barbiturates have the potential to occur in several tautomeric forms of the keto/ enol and amino/imino type where the aromatic character of the six-membered pyrimidine ring is fully or, as in the barbiturates, partially retained, as illustrated in Fig. 15.4. In these molecular species, which are all feasible on the basis of organic chemical considerations, the hydrogen-bonding donor/acceptor properties of the functional amino, imino, enol and keto groups vary considerably, being donor in one form and acceptor in the other. 

The cyclooctadiene ligand is easily replaced by two molecules of CO. The vCO stretching frequencies of the carbonyl ligands can be used to estimate the electronic properties of the l,3,7,9-tetramethylxanthine-8-ylidene ligand. The electron donor ability is found to be less than for pyrimidine based carbenes [99] or imidazol-2-ylidenes [100]. It is also one of the strongest NHC rr-acceptor ligands known [98]. 

The reaction of hydrated electrons formed by radiolysis with peroxydisulfate yields the sulfate radical anion SO4 which is a strong chemical oxidant (Eqx = 2.4 V/NHE) [50, 58]. The oxidation of both purine and pyrimidine nucleotides by S04 occurs with rate constants near the diffusion-controlled limit (2.1-4.1 x 10 M s ). Candeias and Steenken [58a] employed absorption spectroscopy to investigate acid-base properties of the guanosine cation radical formed by this technique. The cation radical has a pKa of 3.9, and is rapidly deprotonated at neutral pH to yield the neutral G(-H) . Both G+ and G(-H) have broad featureless absorption spectra with extinction coefffcients <2000 at wavelengths longer than 350 nm. This has hampered the use of transient absorption spectra to study their formation and decay. Candeias and Steenken [58b] have also studied the oxidation of di(deoxy)nucleoside phosphates which contain guanine and one of the other three nucleobases by SO4 , and observe only the formation of G+ under acidic conditions and G(-H) under neutral conditions. 

Thus the two nucleic acids differ in composition as regards the constituent sugar and one pyrimidine base. The striking difference in the chemical and physical properties of the two acids is occasioned by the properties of the sugar component, so that they are known as ribose-nucleic acid and desoarj/nhose-nucleic acid, respectively. 

---