Nucleobases pyrimidine ring

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]. 

Applications to cis-bis(pyrimidine)Ft(II) Complexes. Considerably less stereochemical data are presently available for cis-bis(pyrimidine)Pt(II) complexes from X-ray diffraction studies (20, 33, 40-42). Of these, we have chosen to present conformational drawings in Figure 4 for the cis-[Pt(NH )9(l-methylcyto-sine)2] cation (33), the mixed base cation cis-[Pt(NH3)o(l-methylcytosine)(N(l)-deprotonated thymine monoanion)(41) and the [Pt(en)(7,9-dimethylhypoxanthine)2] cation (20). In the latter complex, the nucleobases are actually modified purines however, since the pyrimidine ring site N(l) of the purine base is bound to the Pt(II) center, this complex is included in the present series. 

In addition, the CMP and AMP conformers with an almost orthogonal orientation of the nucleobase with respect to the Cl -H bonds are found instead of the north/ syn conformers (Fig. 5.7). Such an orientation of the cytosine and adenine moiety is stabilized by the intramolecular N-H...0 hydrogen bond between the amino and the phosphate groups following significant out-of-plane deformation of the pyrimidine ring (Tables 5.2 and 5.3). The formation of this type of hydrogen bond is impossible... 

In the next sections we will focus on recent investigations of internal conversion in nucleobases and nucleobase models using dynamics simulations. First, we will explore aminopyrimi-dine (O Pig. 33-4), a model system that can help to understand how pyrimidine rings deactivate... 

Pyrimidine rings are structural subunits of aU five nucleobases. In fact, the strong UV absorption in the 260 nm band is due to the tttt transition in the pyrimidine ring of both pyrimidine and purine nucleobases. For this reason, it is especially relevant to understand how internal conversion takes place in these systems. 

The photochemical reactions of psoralens with DNA have been described in detail [1, 4, 5], and is proposed to proceed via a stepwise mechanism. First, the molecule intercalates between the base pairs in double stranded DNA interacting with the 7i-stack of the nucleobases. After irradiation with UVA light, the photo-excited furocoumarins react with DNA and form covalent adducts through a [2 + 2] pericyclic reaction. The photoaddition takes place mostly between the psoralen 4, 5 double bond (furan ring) and the C5, C6 double bond of a pyrimidine (usually thymine). The furan-side adduct can absorb an additional UVA photon, forming an interstrand cross-linked derivative through photoaddition at the 3, 4 double bond in the pyrone ring [6-8]. 

Nucleobase Modifications In the search for new therapeutic derivatives, substituted triazole rings have been introduced on both pyrimidines [2] and purine nucleosides [3-5] (Figure 10.1). Among all the synthesized compounds, some... 

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