1 - cytosine intermolecular

Contrary to H-bonded nucleic acid base pairs discussed in the previous section, the nature of intermolecular interactions in complexes of stacked bases was analyzed more extensively. The values of minimal, maximal, and average total stabilization energies, corrected for BSSE, for a set comprising over 80 stacked bases, are plotted in Fig. 20.1. In the case of guanine-adenine and adenine-cytosine complexes, the results are presented for two sequence contexts, i.e., A/G-G/A and A/C-C/A. The symbol AA denotes the 2-oxo-adenine - complexes of oxidized bases, and this... 

The intramolecular photodimerization and [2 + 2]-photocycloaddition in DNA involves thymine or cytosine as the chromophore. This chemistry has been intensively investigated with regards to DNA damage and repair [131]. Despite the fact that the area is of continuous interest [132], the synthetic applications are limited and are not covered here in detail. However, some preparative aspects of 4-pyrimidinone photocycloaddition chemistry will be addressed. Aitken et al. have prepared a plethora of constrained cyclobutane P-amino acids by intra- or intermolecular [2 + 2]-photocycloaddition to uracil and its derivatives [133, 134]. In a chiral adaptation of this method, the uracil-derived enone 140 was employed to prepare the diastereomeric cyclobutanes 141 in very good yield (Scheme 6.49). The compounds are easily separated and were - despite the relatively low auxiliary-induced diastereoselectivity - well suited to prepare the as-2-aminocyclobutanecarboxylic acids 142 in enantiomerically pure form. Enantioselective access to the corresponding trans-products was feasible by epimerization in a-position to the carboxyl group [135],... 

Figure 16-13. CASPT2(12,12)/ANO-S C,N,0[3s2pld]/H[2slp] potential energy curves built with respect to the intermolecular distance R(C5-C5 ) of two face-to-face tr-stacked cytosine molecules involving the ground and the two lowest singlet excited states (a) and superimposing also the two lowest triplet excited states (b)...

Figure 16-14. Computed energy levels for the ground state (S0) and the lowest triplet excited state (T) of the cytosine dimer in its triplet locally excited state 3(LE), step-wise intermediate 3(SWI), and ground-state cyclobutane cytosine (CBC) dimer. The main intermolecular geometric parameters (in A) for 3(SWI) are included. At the 3(SWI) optimized structure a singlet-triplet crossing, (T1/S0)x, takes place...

In the cytosine-guanine Watson-Crick base-pair, radiationless decay occurs instead via an intermolecular charge transfer state, and is triggered by proton transfer. The locally excited states that were studied in the isolated cytosine are rapidly displaced to higher energy along the proton transfer coordinate. Here the protein environment causes a part of the conical intersection seam to become accessible which cannot be reached in the gas phase. 

Storoniak P, Kobylecka M, D bkowska I, Rak J, Gutowski M (2007). Comparison of intermolecular proton transfer in the Watson-Crick anionic guanine-cytosine and 8-oxoguanine-cytosine pairs. To be submitted. 

Figure 25.19 (a) Base-pair formation by adenine and thymine and by cytosine and guanine, p) The double-helical strand of a DNA molecule held together by hydrogen bonds (and other intermolecular forces) between base pairs A-T and C-G. 

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