Ring vibrations pyrimidine

The IR spectra of pyrimidopyrimidines are extremely similar to those of the isomeric pteri-dines.106 IR spectral data for amino- and anilino-substituted pyrimido[4,5-rf]pyrimidines indicate NH absorptions in the range of 3130-3470 cm-1 (see Table 16).108,113 114 The ring vibrations for tetra-substituted derivatives are observed in the range 1550-1600 cm-1.108... 

According to the IR-spectra (Fig. 3), addition of the polymer to a freshly prepared Ag-Au colloid shifted the band in the 1560-1700 cm1 region, which is characteristic for the stretching vibrations of benzene rings of pyrimidine group. The band at 1664 cm1 is shifted to a... 

IR spectral data for most known 1,2,4-triazines have been published. The absorption of the 1,2,4-triazines in the IR region are those expected for this system. The IR spectrum of the parent compound (1) shows three absorption bands for the C—H stretching vibrations at 3090, 3060 and 3030 cm-1, five bands for C=N and C=C stretching vibrations at 1560, 1529,1435,1380 and 1295 cm-1, three for the C—H in-plane deformations at 1163,1135 and 1113 cm-1, two for the characteristic ring skeleton vibrations at 1050 and 995 cm-1 and three bands for the C—H out-of-plane deformation vibrations at 851,768 and 713 cm-1 (68CB3952). These values are in good agreement with similar bands for pyridine, pyridazine, pyrimidine and pyrazine. Alkyl and aryl derivatives of 1,2,4-triazine show similar bands in their IR spectra, with additional bands from the substituents. 

An analysis of character and frequencies of normal vibrations and scan of relaxed potential energy surface represents two complementary approaches to investigation of conformational flexibility of pyrimidine rings in nucleic acid bases. A combined application of these approaches allows estimating population of conformations with nonplanar rings for each molecule. 

In the case of discussed molecules, it means that for the nucleobase molecules populating zero vibrational level for every vibration, the planar or nearly planar geometry (Fig. 21.3) is the most probable. Molecules with considerably nonplanar conformation of pyrimidine ring will populate higher vibrational levels. Therefore, we can estimate a fraction of molecules with essentially nonplanar geometry based on population of vibrational levels characterized by number 1 and higher. Similar approach is used for analysis of structure and vibrational spectra of molecules with large amplitude motions [34]. 

Fig. 21.3 Probability density function for different vibrational levels of normal vibrations. Dependence of energy change on the value of torsion angle corresponding to the out-of-plane deformation of pyrimidine ring in uracil. MP2/6-31G(d,p) level calculations...

Estimation of population of the ground and excited vibrational levels for ring out-of-plane-vibrations demonstrate that even in the case of unsubstituted pyrimidine ring, 18% of molecules possess considerably nonplanar geometry of ring... 

The most complete picture of conformational flexibility of pyrimidine rings in nucleic acid bases has been provided by molecular dynamics study of isolated molecules using ab initio Carr-Parinello method [45]. According to these studies, the population of planar conformation of heterocycle does not exceed 20% for thymine, cytosine, and guanine and amounts to about 30% for adenine (Table 21.4). These values are considerably smaller as compared to estimations based on vibrational frequencies mentioned above. Such difference is quite natural because in the case of vibrational analysis, only the lowest ring out-of-plane normal mode is considered. However, there are also smaller contributions of the other ring out-of-plane vibrations not included in this analysis. Therefore, such estimation should be considered as an upper limit for assessment of population of planar conformation of ring. 

A nucleic acid gives more than 40 well-defined absorption bands in the IR spectrum (300-4000 cm region). For elucidating the nature of the normal vibrations of a nucleic acid, it is helpful to examine the effects of base composition on the vibrational frequencies, as well as the intensity and anisotropy of the IR absorption. Three of the four natural bases of a DNA (adenine, guanine, and cytosine) have an amino group w hich is considered to be nearly coplanar, because the purine or pyrimidine rings have aromatic character and the C—N bonds have some double-bond character. 

Important TP bands of some non-oxo derivatives can be found in Table 9. These bands were usually denoted as C = N bands. Later the two most characteristic bands, named Vtp (about 1610 1650 cm ) and Vpy (about 1505-1550 cm ), were assigned to an overall triazolopyrimidine and pyrimidine ring mode vibrations, respectively (00JCS(D)867, OOPOL965 cf. 06JOM693). 

In nucleic acids, most attention has been focused on the IR spectral region 1500-1800cm , which contains vibrations of the carbonyl and the double bonds of the purine and pyrimidine rings. The vibrations are highly sensitive to base pairing because the atoms involved participate directly in the formation of hydrogen bonds. Furthermore, each of the four common bases has a distinct IR spectrum in this spectral region (Thomas, 1969). Thus it is possible to examine A-T(U) and G-C pairs separately. 

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