title: A quantitative appraisal of the ambivalent metal ion binding properties of cytidine in aqueous solution and an estimation of the anti-syn energy barrier of cytidine derivatives.
abstract: The recently defined log K (M)(M)(L) versus pK(H)(H)(L) straight-line plots for L = pyridine-type (PyN) and ortho-aminopyridine-type (oPyN) ligands now allow the evaluation in a quantitative manner of the stability of the 1:1 complexes formed between cytidine (Cyd) and Ca(2+), Mg(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) (M(2+)); the corresponding stability constants, K(M)(M)(Cyd) including the acidity constant, K(H)(H)(Cyd) for the deprotonation of the (N3)H(+) site had been determined previously under exactly the same conditions as the mentioned plots. Since the stabilities of the M(PyN)(2+) and M(oPyN)(2+) complexes of Ca(2+) and Mg(2+) are practically identical, it is concluded that complex formation occurs in an outer-sphere manner, and this is in accord with the fact that in the p K(a) range 3-7 metal ion binding is independent of K(H)(H)(Pyn) or K(H)(H)(oPyN). Ca(Cyd)(2+) and Mg(Cyd)(2+) are more stable than the corresponding (outer-sphere) M(PyN)(2+) complexes and this means that the C2 carbonyl group of Cyd must participate, next to N3 which is most likely outer-sphere, in metal ion binding, leading thus to chelates; these have formation degrees of about 50% and 35%, respectively. Co(Cyd)(2+) and Ni(Cyd)(2+) show no increased stability based on the log K(M)(M)(oPyN) versus pK(H)(H)(oPyN) hence, the (C2)O group does not participate in metal ion binding, but the inner-sphere coordination to N3 is strongly inhibited by the (C4)NH(2) group. In the M(Cyd)(2+) complexes of Mn(2+), Cu(2+), Zn(2+) and Cd(2+), this inhibiting effect on M(2+) binding at N3 is partially compensated by participation of the (C2)O group in complex formation and the corresponding chelates have formation degrees between about 30% (Zn(2+)) and 83% (Cu(2+)). The different structures of the mentioned chelates are discussed in relation to available crystal structure analyses. (1). There is evidence (crystal structure studies: Cu(2+), Zn(2+), Cd(2+)) that four-membered rings form, i.e. there is a strong M(2+) bond to N3 and a weak one to (C2)O. (2). By hydrogen bond formation to (C2)O of a metal ion-bound water molecule, six-membered rings, so-called semichelates, may form. (3). For Ca(2+) and Mg(2+), and possibly Mn(2+), and their Cyd complexes, six-membered chelates are also likely with (C2)O being inner-sphere (crystal structure) and N3 outer-sphere. (4). Finally, for these metal ions also complexes with a sole outer-sphere interaction may occur. All these types of chelates are expected to be in equilibrium with each other in solution, but, depending on the metal ion, either the one or the other form will dominate. Clearly, the cytidine residue is an ambivalent binding site which adjusts well to the requirements of the metal ion to be bound and this observation is of relevance for single-stranded nucleic acids and their interactions with metal ions. In addition, the anti- syn energy barrier has been estimated as being in the order of 6-7.5 kJ/mol for cytidine derivatives in aqueous solution at 25 degrees C.
authors.affiliation: Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056, Basel, Switzerland.
authors.forename: Bernd
authors.initials: B
authors.lastname: Knobloch
authors.forename: Helmut
authors.initials: H
authors.lastname: Sigel
mesh_terms: D001665:Binding Sites; D002118:Calcium / Q000737:chemistry / Q000378:metabolism; D003562:Cytidine / Q000737:chemistry* / Q000378:metabolism*; D007536:Isomerism; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D008345:Manganese / Q000737:chemistry / Q000378:metabolism; D008670:Metals / Q000737:chemistry* / Q000378:metabolism*; D012995:Solubility; D014867:Water / Q000737:chemistry
chemical_list: D008670:Metals; D014867:Water; D008345:Manganese; D003562:Cytidine; D008274:Magnesium; D002118:Calcium