Cytosine complexes

What would be the geometry of the guanine-cytosine complex were there no hydrogen bonds or, more to the point, were chemists not to know about the benefits of hydrogen bonding More than likely, it would be a more closely-packed geometry, such as the following. 

The Mg+ complexes of cytosine, thymine and uracil are the most complex system studied via photodissociation spectroscopy to date . A complication for these systems is that these nucleobases can exist in various tautomeric forms and that complexation of a metal can change the stability order of the tautomers. DFT calculations located four tautomeric Mg(cytosine)+ complexes, and three of these (29, 30, and 31) were suggested to be responsible for the four reactive photofragment ions 32-35 observed at a wavelength of 360 nm (Scheme 4) . Related photofragmentation reactions were observed for the Mg(thymine)+" and Mg(uracil)+" complexes . ... 

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 first-order electrostatic interaction can also play an important role in base-base stacking. The 0) term can, depending on the system and the configuration, stabilize or destabilize stacked nucleic acid complexes. In most cases, the A HL term is positive which indicates that the 0) contribution is canceled out by the exchange component. Similar observations have also been reported recently [25,32]. In the case of guanine-guanine and cytosine-cytosine complexes, the electrostatic term has positive value. The average values of first-order electrostatic component... 

None of the two-bond base pairs has been found in a guanine-cytosine complex except for the configuration GC32 in transfer RNA (Part III, Chap. 20, Fig. 20.9). Presumably this is because configurations with only two hydrogen bonds are less stable than those with three hydrogen bonds. 

Hunter, K. C. Rutledge, L. R. Wetmore, S. D. The hydrogen bonding properties of cytosine A computational study of cytosine complexed with hydrogen fluoride, water, and ammonia, J. Phys. Ghent A 2005,109, 9554-9562. 

Fig. 22. The complexation induced shifts of the energies of the lowest excitations of nucleic acid bases in the dimers. Shifts are calculated with respect to the free molecule (guanine or cytosine in the guanine-cytosine complex and adenine or thymine in the adenine-thymine complex). For each monomer four excitations are given singlet-singlet A , singlet-singlet A , singlet-triplet A , and singlet-triplet A . Data taken from [Wesolowski, J. Am. Chem. Soc., 126, (2004) 11444].

Fig. 23. The KSCED embedding potential (Eq. 53 at the LDA level) generated by the frozen electron density of cytosine in the guanine-cytosine complex. The lines are drawn in the plane of the molecules at —0.1, 0.0, 0.2, 0.4 and 0.7 atomic units.

Following the empirical trends offered in the previous two sections, it might be expected that the role of intracomplex steric factors for such complexes would be intermediate between those for a cis-bis(N(7)-bound gtianine) complex and those for a cis-bis(N(3)-bound cytosine) complex. The conformational parameters displayed in Figure 5 seem to be in accord with this... 

Both, purine and pyrimidine bases incorporated into nucleic acids, or in synthetic nucleic acid analogs, are able to bind specifically different metal ions [138]. For example, thymine yields a thymine-Hg -thymine complex, while cytosine forms specifically a cytosine-Ag -cytosine complex. Such properties of the nucleic acids were utilized to develop QDs-based Hg -ion and Ag + -ion sensors, with differentsized QDs being implemented for the multiplexed analysis of Hg and Ag + [139]. Two different-sized CdSe/ZnS QDs were modified with nucleic acids of specific ionbinding properties blue-emitting QDs ()iem = 560 nm) were functionalized with the thymine-rich nucleic acid (16) that binds Hg + -ions, while the red-emitting QDs (Xem = 620nm) were functionalized with the cytosine-rich nucleic acid (17) that associated with Ag + -ions (Figure 6.9a). The formation of Hg -modified complexes... 

Yang B, Wu RR, Polfer NC, Berden G, Oomois J, Rodgers MT (2013) IRMPD action spectroscopy of alkali metal cation-cytosine complexes effects of alkali metal cation size on gas phase conformation. J Am Soc Mass Specttom 24 1523-1533... 

Model studies with nucleobases such as 5 -GMP showed that Pt(II) products are formed [27] but results from oxidation of Pt(II)-cytosine complexes are indicating novel modes of reaction and binding for the oxidized species [28] (see also Chapter 4). 

The exchange on uracil and cytosine complexes has also been noted [44], and the formation of substituted uracil from the CI2 oxidation of Pt(II)—uracil complexes to Pt(IV) also reflects the increased reactivity... 

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