Uracil cations, structure

J. Gu, J. Leszczynski, A theoretical study of thymine and uracil tetrads structures, properties, and interactions with the monovalent k+ cation. J. Phys. Chem. A 105, 10366-10371 (2001)... 

A comparison of these nucleobase-derived metallacalixarenes with natural nucleobase-derived tetrands may be advisable. In the non-natural quartets formed by interconnection of uracil, purine or its derived nucleobases with coordinative metals, the cationic character lies on the metals in the periphery and anions are bound in the cavity. In natural tetrands of these nucleobases, the hydrogen bonds interconnect the bases and the structures are stabilized by a cation located in the centre whereas phosphate groups located in the periphery carry negative charge (2005AGE668). As against the existence of only natural... 

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... 

Several blue tetra- and octanuclear Pt complexes, prepared upon reaction of cis-[Pt(NH3)2(H20)2]2+ with open and cyclic amides, as well as cyclic imides and a uracil nu-cleobase, and comprised of binuclear building blocks interacting through Pt-Pt bond formation, have been isolated and structurally characterized in recent years. Without exception, the average Pt oxidation state in these compounds is 2.25. Nevertheless, the structure and mode of action as antitumor agents of the Platinum Pyrimidine Blues , as prepared by Rosenberg in the early 70 s, remain elusive. This account represents a summary of our present knowledge on cationic Platinum Blues , with a focus on those blues obtained from cis-[Pt(NH3)2(H20)2]2+ and pyrimidine nucleobases, and presents speculations on reasonable alternative structures. 

The nitrate salt of the analogous [ (en)PtnAg(UrH, A (7),A (5),(9(2), 0(4)) 4]8+ cation exhibits a different structure, which can be formally derived from that of the pinched-cone conformer of Fig. 15,a, by coordination of silver ions to the uracilate oxygens. In all the octanuclear complexes, two metal units, Pt(en) and M, represent each corner of the boxes. These results demonstrate that, irrespective of the 120° angle between the Pt-N(l)... 

Figure 7.9 X-Ray structure of the [Pt(ethane-1,2-diamine) cis-Pt(NH )2)(uracil-2H)] cation ...

The tetranuclear metal complex, [(l,2-diaminoethane)Pt(uracilate-AM,A(3)] , can be considered a special heterocalixarene, a metal analogue of calix[4]arene which functions as hosts for small molecules or ions and possesses metal binding properties, either in the cavity or at the periphery. The bridging unit of the classical calix[4]arene, usually a CH2 group, is replaced by the (en)Pt(II) unit in the Pt-complex. This change, the replacement of the p-phenol by the 2,4-dioxopyrimidine and the positive charge introduced by the metal cations, leads to a number of differences as compared with the classical calix[4]arenes. Their preparation, x-ray crystal structure, and solution behavior have been described <94JA616>. 

Two works were devoted to the ab initio cluster calculations of the interactions between minerals of the kaolinite group with thymine (TH) and uracil (U). The key purpose of such studies was to determine (i) the equilibrium adsorption of selected nucleic acids, differing in chemical, molecular structure and functions (DNA, RNA) on specific clay mineral surfaces and (ii) the nature of the interaction between nucleic acids and clay using computational chemistry methods and modeling. An additional objective was to assess the effect of presence of water and sodium cation commonly occurring in soils on the process of adsorption. 

The calculations of solvated (hydrated) complexes simulated by explicit inclusion of water molecule shows the energy loss only for the tetrahedral systems, which is due to the structural changes of the substrate induced by water adsorption [151]. It amounts to about 3 kcal/mol. In the case of octahedral systems presence of water does not increase the Ecorr value for K(3o)NaW-U but it stabilizes thymine by 1.7 kcal/mol. Isolated uracil is more stable in the water-cation environment than in the microcosmic environment with only water [157]. In all K(3o)NaW systems orientation by 02 towards Na+ remains to be the most favorable. On the other hand, in study of hydrated Li+-thymine and Li+-uracil complexes binding of (H20)Li+ to the 04 site is stabilized by 1.7- 2.9 kcal/mol over the binding to the 02 site [156],... 

Physical-chemical studies have indicated that polynucleotide chains such as polyuiidylic acid (U) and polyadenylic acid (A) combine with one another in aqueous solution to form a two-stranded (A -b U) 212, 218) and a less stable three-stranded helical structure 214,216) [(A -f U) -b U]. In the A - - U structure adenine is hydrogen-bonded to uracil and the bindings are dependent upon the presence of cations. Magnesium and... 

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