Uracil dimer structure

Uracil dimers were studied at the MP2 level using the 6-3IG basis with modified polarization functions. Eleven low-energy minima were located Seven of them are H-bonded, one is T-shaped, and three correspond to various stacked arrangements. The most stable structure was found to be the H-bonded dimer with two Ni-H O2-H bonds (Scheme 85) [98JPC(A)6921]. 

An ab initio study on the structure and splitting of the uracil dimer anion-radical (see Scheme 3.72, R = H) gives preference to the one-step mechanism (Voityuk and Roesch 1997). Anion-radical anions of the pyrimidine dimers cleave with rate constants in excess of 10 s ... 

The dimer has been shown by Blackburn and Davies40 to have a geometrical structure similar to that of thymine dimer (10). The proof consisted in observation of the 13C—H satellite NMR spectrum of 5,5 -dideutero-,3,3 -dimethyl uracil dimer (prepared by methylation of the dimer from photolysis of uracil-5-rf). The magnitude of the H6H6 coupling constant showed that these hydrogens were vicinal, and was... 

Quinolone undergoes photochemical addition of tetramethylethylene to give (434) (70AHC(ii)50), l,3-oxazin-4-ones photocycloadd ketene acetals to give (435), and irradiation of 2,6-dimethylpyran-4-one yields the cage dimer (436). 2-Pyranones form [2 + 2] photodimers whose structure is similar to that of uracil dimers (432 or 433). 

An ab initio study on the structure and splitting of the uracil dimer anion radical (see Scheme 3-66 and keep R = H) gives preference to the one-step mechanism (Voityuk Roesch 1997). Anion radical anions of the pyrimidine dimers cleave with rate constants in excess of 106 sec 1 (Yeh Falvey 1991). However, the cyclobutyl dimer of a quinone, dithymoquinone, also cleaves upon single-electron reduction but much more slowly than the pyrimidine dimers (Robbins Falvey 1993). It is truly an unresolved issue as to why the anion radical cleavage depicted in Scheme 3-66 is so facile. Water participation can probably decrease the barrier of the cycloreversion on physiological conditions (Saettel Wiest 2001). 

The lifetime of Pyr +oPyr seemed to depend on the structure of the parent dimer. It was observed that the presence of a trimethylene bridge linking both pyrimidine units at N(l) and N(l ), as in the mixed thymine-uracil dimer 4 and in the thymine dimer 5, leads to significant stabilization of the corresponding dimer radical cation, whereas in unbridged dimers a maximum lifetime of 10-1°-10-9 s was proposed for their dimer radical cations [6]. It was further shown that in bridged pyrimidines dimers of types 4 and 5 the interconversion of dimer and... 

Table 7. Interaction energies (AE in kcal/mol), changes of Gibbs energies (AG° in kcal/mol) calculated within RR-HO-IG approximation using AMBER 4.1 and ab initio constants, and relative populations from NVE analysis for various structures of uracil dimer...

Among 11 minima found on the PES of uracil dimer, the H-bonded structure 4 was clearly dominant energy difference between this and other H-bonded and stacked structures was rather large. Methylation at the Nj position will prevent formation of this structure and it is possible to expect that all structures of the Nj-methyluracil dimer will be closer in energy. 

If we consider studies of nucleic acids and their components, there is currently only one reliable gas phase experiment (mass-field spectroscopy) on the energetics of nucleic acid base pairs [7a]. This experiment provides interaction enthalpies of several base pairs at rather high temperatures of 350-400K. The experimental technique does not allow for the determination of the geometry of complexes, and it is even not possible to distinguish between H-bonded and stacked structures. Recent state-of-the art theoretical analysis of gas phase thermodynamics of uracil dimer indicates that this pair exists as a mixture of several H-bonded and stacked structures [8]. Furthermore, their relative populations could vary depending on experimental conditions. It is likely that... 

Fig. 5). The fraction of hydrate formed at each water concentration was measured by the fraction of thermal reversal and reaches 100% at about 30% water (Fig. 6). The rate of hydrate formation is proportional to the square of the water concentration (Fig. 7). These results are to be compared with those observed for uracil in acetonitrile-water mixtures (Sect. V) the rate of uracil hydrate formation was proportional to the water concentration. A dimethyluracil dimer is formed in pure acetonitrile (indicated by photoreversal), but the structure of the dimer is not known. 

Two dimeric products are formed in the photolysis of frozen aqueous solutions of dimethyl uracil,346 with melting points of 252-253 and 263-264°C the structures and relationship of these products are not known. 

The probable structures of the dimers and hydrates are illustrated below for a uracil derivative. The constraints imposed upon the orientation of the pyrimidine residues in the dinucleotide should restrict the number of geometrical isomers possible, relative to the number of possibilities for a derivative containing only a single pyrimidine residue. 

An interesting and significant outcome is the finding that the pyrimidine bases of nucleic acids (uracil, thymine, and cytosine) are photoreactive and undergo [2 + 2] cycloadditions on irradiation with ultraviolet light. Thymine, for example, gives a dimer of structure 7 ... 

The replacement of thymine by uracil has no significant effect on the hydrogen bonding, as RNA does not use base pairing to form complementary dimers it is of less importance than it would be for DNA, but the removal of the methyl group may have an influence on the tertiary structures that RNA can adopt. From this it is clear that DNA is a better method of storing information whereas RNA is more suited to turn that information into a protein sequence. This is done by the ribosome, composed of ribosomal RNA (rRNA), which translates the codons of the mRNA sequence into a protein by matching three base sequences to those of tRNA that have the appropriate amino acids attached. 

Figure 21-20. B3LYP/6-31+- -G optimized structures of dimers UG1-UG4. I, II, III, and IV denote regions of the uracil monomer capable of forming two adjacent hydrogen bonds (Figure 2a of ref. [61]. Reprinted with permission. Copyright 2002 American Chemical Society.)...

Photoaddition of alkenes to the azathymine (227) affords the adducts (228) the structures of which were determined by -ray crystallography. Acetone-sensitized irradiation of the azauracil derivative (229) yields the cyclobutane (230). Irradiation of the uracil (231) in isotropic solvents is known to yield all four (2-1 2)-dimers in low yield especially at low concentrations. A study has shown that dimerization in smectic media affords a high yield (94X) of the trans-anti dimer (232). In frozen solutions the specificity is reversed and the CIS-anti dimer (233) is formed. The influence of a variety of media on this process was studied in detail. A theoretical treatment of the photochemical addition of alkenes to psoralens such as (234) has been published. ... 

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