Substitution of pyrimidines

After the nucleophilic aromatic substitution of pyrimidine 123, the isolated monosubstituted ether product 124 was cyclized with paraformaldehyde in dichloromethane under acidic Pictet-Spengler conditions to form pyri-mido[4.5-/+1.4- benzoxazcpinc 125 in good yield (62%) (Scheme 15) <2005JOC9629>. The same procedure has... 

In a separate report, the regioselectivity and reactivity problems in the substitution of pyrimidines were avoided using 4,6-dichloro-5-nitropyrimi-dine as starting material,17 a very electron-poor heterocycle, which is highly reactive in nucleophilic aromatic substitutions. It reacts readily with the free amino group of the (trialkoxybenzhydrylamine) Rink linker on solid phase. This heterocycle could serve as a scaffold by itself and could also be used as a building block (precursor) to make other heterocycles such as purines. 

One problem for targeting RNA is that the A U and G U base pairs have similar stability, and G U wobble pairs account for almost half of known non-Watson-Crick pairs. 2-Thiouridine will increase the specificity for pairing with adenosine by a factor of 10. It has been reported that the complete substitution of pyrimidines by C5-propynyl pyrimidines enhances this specificity 100-fold without altering base pairing specificity. " ... 

Despite considerable localization of tt-electrons at the nitrogen atoms of pyrimidine, the ring system is still sufficiently aromatic to possess substantial stability. This is a great advantage in the primary synthesis of pyrimidines, in the synthesis of pyrimidines from the breakdown or modification of other heterocyclic systems and in the myriad of metatheses required to synthesize specifically substituted pyrimidines. 

Substitution of two carbon atoms of a benzene ring by tervalent nitrogen atoms may occur in three ways, giving rise to pyridazines (see Chapter 2.12), the pyrimidines (see Chapter 2.13) and the pyrazines, with the nitrogen atoms occupying a 1,2-, 1,3- or 1,4-disposition respectively. 

The pyridine family of heteroaromatie nitrogen compounds is reactive toward nueleophilie substitution at the C-2 and C-4 positions. The nitrogen atom serves to aetivate the ring toward nueleophilie attack by stabilizing the addition intermediate. This kind of substitution reaction is especially important in the ehemistiy of pyrimidines. 

The CNDO method has been modified by substitution of semiempirical Coulomb integrals similar to those used in the Pariser-Parr-Pople method, and by the introduction of a new empirical parameter to differentiate resonance integrals between a orbitals and tt orbitals. The CNDO method with this change in parameterization is extended to the calculation of electronic spectra and applied to the isoelectronic compounds benzene, pyridine, pyri-dazine, pyrimidine and pyrazine. The results obtained were refined by a limited Cl calculation, and compared with the best available experimental data. It was found that the agreement was quite satisfactory for both the n TT and n tt singlet transitions. The relative energies of the tt and the lone pair orbitals in pyridine and the diazines are compared and an explanation proposed for the observed orders. Also, the nature of the lone pairs in these compounds is discussed. 

In addition, Namazi and coworkers expanded the DHPM core by constructing pyrrolo[3,4-rf pyrimidines via the classical approach. First, DHPM 59 was delivered in 60% yield using the standard Biginelli conditions. 59 was then brominated in high yield to afford 60. Substitution of bromide 60 with methylamine followed by cyclization of the intermediate amino ester furnished pyrrolo[3,4-rf pyrimidine 61 in 53% yield. 

Dondoni has elaborated this methodology to include C-glycosylated dihydro-pyrimidines/ The sugar residue can be a subunit in the aldehyde, 1,3-dicarbonyl, or urea consequently, substitution of the DHPM ring may occur in one of three places depending on which component originally contains the glycosidic residue. In the example... 

The versatility of pyrimidine substituted chloroquinazolines as intermediates is due to the ready replacement of the halogen atoms by hydrogen, alkyl, alkoxyl, amino, and mercapto groups (see Section VI, A). 

Reduction of pyrimidine substituted quinazoline 3-oxides, cata-lytically or with phosphorus trichloride, also leads to quinazolines. ... 

The replacement of a heterocyclic hydroxyl group (generally in the 0X0 form, Section II,E, 2,e) with thioxo or chloro groups by phosphorus pentasulfide or phosphorus oxychloride presumably proceeds through nucleophilic substitution (frequently acid-catalyzed, 21 and 86) of thiophosphoryloxy and dichlorophosphoryloxy intermediates. The 4-position in pyrimidine is more reactive than the 2-position and, at low temperature, this type of thionation of pyrimidine-2,4-diones is specific for the 4-position. In as-triazine... 

Alkylthio, arylthio, and thioxo. The thioxo group in pyrimidine-2,4-dithione can be displaced by amines, ammonia, and amine acetates, and this amination is specific for the 4-position in pyrimidines and quinazolines. 2-Substitution fails even when a 5-substituent (cf. 134) sterically prevents reaction of a secondary amine at the 4-position. Acid hydrolysis of pyrimidine-2,4-dithione is selective at the 4-position. 2-Amination of 2-thiobarbituric acid and its /S-methyl derivative has been reported. Under more basic conditions, anionization of thioxo compounds decreases the reactivity 2-thiouracil is less reactive toward hot alkali than is the iS-methyl analog. Hydrazine has been reported to replace (95°, 6 hr, 65% 3deld) the 2-thioxo group in 5-hexyl-6-methyl-2-thiouracil. Ortho and para mercapto- or thio- azines are actually in the thione form. ... 

The first generalization is illustrated by the behavior of the 2- and 4-vs. the 3-derivatives of pyridine, the second by the reactivity of 4- vs. 2-substituted pyridines, the third by the relation of 4- vs. 2-derivatives of pyrimidine, and the fourth by the appreciable reactivity of 3-substituted pyridines or 5-substituted pyrimidines compared to that of their benzene analogs. Various combinations of azine-nitrogens in other poly-azines supply further examples. Theoretical aspects of (1), (2) and (3) are discussed in Section II, B, 2. The effect involved in (4) is believed to be more the result of the inductive stabilization of an adjacent negative chaise in the transition state (cf. 251) than of the electron deficiency created in the ground state (cf. 252). The quantitative relation between inductive stabihzation and resonance stabilization is not precisely defined by available data. However, a... 

A process for the preparation of pyrimidine A-oxides from carboxamide oximes has been developed (98T4387). Direct oxidation of pyrimidines is inconvenient for the preparation of nonsymmetric substituted pyrimidines because it gives a mixture of oxidation products ( -N- and 3-A-oxides). Methoxybutenone with carboxamide oximes regioselectively forms A-oxides of pyrimidines 281, which indicates... 

Brown has also predicted, from localization energy calculations, that pyrrole and glyoxaline should react with radicals mainly at the 2-position, whereas pyrazole should be most reactive at the 3-position. Browm and Heffernan s calculation that the orientation in pyrimidine substitution should be 4 > 2 > 5 is in agreement with the results from the p-nitrophenylation of pyrimidine. ... 

These results show that inverse Diels-Alder reactions of pyrimidines open an easy access to a number of differently substituted pyridines and especially to compounds, in which the carbocyclic ring and the heterocyclic rings are annelated on the b position of pyridine. An interesting illustrating example... 

Bromo-4-chloro-lH-pyrazolo[3,4-d]pyrimidine could be easily fimc-tionalized at C-3 and C-4 in a one-pot two-step microwave-assisted process (Scheme 34) [55]. Ding and Schultz reported that nucleophilic substitution of the addition-elimination type at the C-4 position with amines and anilines smoothly occurred under acidic conditions in dioxane upon irradiation... 

Substituted pyrimidine N-oxides such as 891 are converted analogously into their corresponding 4-substituted 2-cyano pyrimidines 892 and 4-substituted 6-cya-no pyrimidines 893 [18]. Likewise 2,4-substituted pyrimidine N-oxides 894 afford the 2,4-substituted 6-cyano pyrimidines 895 whereas the 2,6-dimethylpyrimidine-N-oxide 896 gives the 2,6-dimethyl-4-cyanopyrimidine 897 [18, 19] (Scheme 7.6). The 4,5-disubstituted pyridine N-oxides 898 are converted into 2-cyano-4,5-disubsti-tuted pyrimidines 899 and 4,5-disubstituted-6-cyano pyrimidines 900 [19] (Scheme 7.6). Whereas with most of the 4,5-substituents in 898 the 6-cyano pyrimidines 900 are formed nearly exclusively, combination of a 4-methoxy substituent with a 5-methoxy, 5-phenyl, 5-methyl, or 5-halo substituent gives rise to the exclusive formation of the 2-cyanopyrimidines 899 [19] (Scheme 7.6). The chemistry of pyrimidine N-oxides has been reviewed [20]. In the pyrazine series, 3-aminopyrazine N-ox-ide 901 affords, with TCS 14, NaCN, and triethylamine in DMF, 3-amino-2-cyano-pyrazine 902 in 80% yield and 5% amidine 903 [21, 22] which is apparently formed by reaction of the amino group in 902 with DMF in the presence of TCS 14 [23] (Scheme 7.7) (cf. also Section 4.2.2). Other 3-substituted pyrazine N-oxides react with 18 under a variety of conditions, e.g. in the presence of ZnBr2 [22]. 

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