Pyrimidines hydrogen bonding

Rate constants for purine-pyrimidine hydrogen bond association... 

Note that two molecules of 31 form a pseudosymmetric dimer associated by pyrimidine -pyrimidine hydrogen bonds. Both molecules are rotamers with a different orientation of the hydroxymethyl groups. 

Section 28 8 The most common form of DNA is B DNA which exists as a right handed double helix The carbohydrate-phosphate backbone lies on the outside the punne and pyrimidine bases on the inside The double helix IS stabilized by complementary hydrogen bonding (base pairing) between adenine (A) and thymine (T) and guanine (G) and cytosine (C)... 

The structure of lumazine has been studied more precisely by X-ray analysis (72AX(B)659). The crystal structure is built up of almost coplanar, hydrogen-bonded dimers of lumazine with the oxygens of the pyrimidine moiety in the keto form and the observed bond distances indicating the pyrazine ring electrons to be delocalized. 

These factors are sufficient to produce similar amounts of aminated isomers from 2,4-dichloropyrimidine which gives predominantly 4-alkoxylation products. Thus, a mixture of 2-amino-4-chloro- (302) and 4-amino-2-chloro-pyrimidine (303) is obtained on treatment of 2,4-dichloropyrimidine with alcoholic ammonia (25°, <18 hr), the reagent here being better at hydrogen bonding than piperidine. 

Various nucleophilic reactions of polysubstituted 5-halopyri-midines are described in Section II,E,2,e with postulates to explain the degree of reactivity. For pyrimidine derivatives, the effect of the following on nucleophilic substitution is included in earlier sections hydrogen bonding and cationization in Section II, C, the leaving group in Section II, D, and the nucleophile in Sections II,E,2,e and II, F. 

Most studies concerning pyrimidines originate from biochemical questions. Since these systems are dominated by hydrogen-bonding and/or dispersion contributions, methods beyond the Hartree-Fock level are mandatory. The success of quantum chemical studies in this field is impressive and many effects could be explained on the basis of these theoretical investigations. 

X-Ray analyses and solid-state IR spectra were recorded for a number of 1,4-and 1,6-dihydropyrimidines, demonstrating the dependency of the tautomeric composition in the crystal on the substitution in the pyrimidine ring and on the ability of these compounds to form intermolecular hydrogen bonds. Thus,... 

Moreover, with a change of solvent, a new tautomeric form can arise owing to formation of intermolecular hydrogen bonds in place of the previously existent intramolecular hydrogen bonds. This situation is characteristic, for example, for pyrimidine derivatives 49, for which the use of polar (DMSO, DMF, MeOH, HMPT) solvents or specifically solvating cosolvents (S) (e.g., a small amount of water or A-methylpyrrolidinone) leads to the appearance of ylidene tautomer 49b with the p-quinonoid disposition of the double bonds (Scheme 18) [88KGS521 90UK457]. 

This is consistent with there not being enough space (20 °) for two purines to fit within the helix and too much space for two pyrimidines to get close enough to each other to form hydrogen bonds between them. These relationships are often called the rules of Watson-Crick base pairing. 

In the course of this study, the authors determined /Lvalues for dibenzyl, methyl phenyl, methyl p-nitrophenyl, di-p-tolyl, di-isopropyl and tetramethylene sulphoxides and for diethyl, dipropyl and dibutyl sulphites. The /Lscales are applied to the various reactions or the spectral measurements. The /Lscales have been divided into either family-dependent (FD) types, which means two or more compounds can share the same /Lscale, family-independent (FI) types. Consequently, a variety of /Lscales are now available for various families of the bases, including 29 aldehydes and ketones, 17 carboxylic amides and ureas, 14 carboxylic acids esters, 4 acyl halides, 5 nitriles, 10 ethers, 16 phosphine oxides, 12 sulphinyl compounds, 15 pyridines and pyrimidines, 16 sp3 hybridized amines and 10 alcohols. The enthalpies of formation of the hydrogen bond of 4-fluorophenol with both sulphoxides and phosphine oxides and related derivatives fit the empirical equation 18, where the standard deviation is y = 0.983. Several averaged scales are shown in Table 1588. 

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