Ternary complexes in solution. Part 51. Intramolecular hydrophobic and stacking interactions in mixed ligand complexes containing Cu(II), 2,2′-bipyridyl or 1,10-phenanthroline, and a simple phosphate monoester, D-ribose 5′-monophosphate or a nucleoside 5′-monophosphate (CMP, UMP, TMP, TuMP) with a non-coordinating base residue

Comparison of the π-stacking properties of purine versus pyrimidine residues. Some generalizations regarding selectivity

Aromatic-ring stacking is pronounced among the noncovalent interactions occurring in biosystems and therefore some pertinent features regarding nucleobase residues are summarized. Self-stacking decreases in the series adenine > guanine > hypoxanthine > cytosine ~ uracil. This contrasts with the stability of binary (phen)(N) adducts formed by 1,10-phenanthroline (phen) and a nucleobase residue (N), which is largely independent of the type of purine residue involved, including (N1)H-deprotonated guanine. Furthermore, the association constant for (phen)(A)(0/4-) is rather independent of the type and charge of the adenine derivative (A) considered, be it adenosine or one of its nucleotides, including adenosine 5'-triphosphate (ATP(4-)). The same holds for the corresponding adducts of 2,2'-bipyridine (bpy), although owing to the smaller size of the aromatic-ring system of bpy, the (bpy)(A)(0/4-) adducts are less stable; the same applies correspondingly to the adducts formed with pyrimidines. In accord herewith, [M(bpy)](adenosine)(2+) adducts (M(2+) is Co(2+), Ni(2+), or Cu(2+)) show the same stability as the (bpy)(A)(0/4-) ones. The formation of an ionic bridge between -NH3 (+) and -PO3 (2-), as provided by tryptophan [H(Trp)(±)] and adenosine 5'-monophosphate (AMP(2-)), facilitates recognition and stabilizes the indole-purine stack in [H(Trp)](AMP)(2-). Such indole-purine stacks also occur in nature. Similarly, the formation of a metal ion bridge as occurs, e.g., between Cu(2+) coordinated to phen and the phosphonate group of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)) dramatically favors the intramolecular stack in Cu(phen)(PMEA). The consequences of such interactions for biosystems are discussed, especially emphasizing that the energies involved in such isomeric equilibria are small, allowing Nature to shift such equilibria easily.

Xanthosine 5'-monophosphate (XMP). Acid-base and metal ion-binding properties of a chameleon-like nucleotide

The four acidity constants of threefold protonated xanthosine 5'-monophosphate, H(3)(XMP)(+), reveal that in the physiological pH range around 7.5 (X - H x MP)(3-) strongly dominates and not XMP(2-) as commonly given in textbooks and often applied in research papers. Therefore, this nucleotide, which participates in many metabolic processes, should be addressed as xanthosinate 5'-monophosphate as is stated in this critical review. Micro acidity constant schemes allow quantification of intrinsic site basicities. In 9-methylxanthine nucleobase deprotonation occurs to more than 99% at (N3)H, whereas for xanthosine it is estimated that about 30% are (N1)H deprotonated and for (X - H x MP)(3-) it is suggested that (N1)H deprotonation is further favored, especially in macrochelates where the phosphate-coordinated M(2+) interacts with N7. The formation degree of these macrochelates in the (X - H x MP x M)(-) species of Co(2+), Ni(2+), Cu(2+), Zn(2+) or Cd(2+) amounts to 90% or more. In the monoprotonated (M x X - H x MP x H)(+/-) complexes, M(2+) is located at the N7/[(C6)O] unit as the primary binding site and it forms macrochelates with the P(O)(2)(OH)(-) group to about 65% for nearly all metal ions considered (i.e., including Ba(2+), Sr(2+), Ca(2+), Mg(2+)); this indicates outer-sphere binding to P(O)(2)(OH)(-). Finally, a new method quantifying the chelate effect is applied to the M(X - H x MP)(-) species, stabilities and structures of mixed-ligand complexes are considered, and the stability constants for several M(X - H x DP)(2-) and M(X - H x TP)(3-) complexes are estimated (112 references).

Interactions of 1,12-diamino-4,9-dioxadodecane (OSpm) and Cu(II) ions with pyrimidine and purine nucleotides: adenosine-5'-monophosphate (AMP) and cytidine-5'-monophosphate (CMP)

The interactions of Cu(II) ions with adenosine-5'-monophosphate (AMP), cytidine-5'-monophosphate (CMP) and 1,12-diamino-4,9-dioxadodecane (OSpm) were studied. A potentiometric method was applied to determine the composition and stability constants of complexes formed, while the mode of interactions was analysed by spectral methods (ultraviolet and visible spectroscopy (UV-Vis), electron paramagnetic resonance (EPR), (13)C NMR, (31)P NMR). In metal-free systems, molecular complexes nucleotide-polyamine (NMP)H(x)(OSpm) were formed. The endocyclic nitrogen atoms of the purine ring N(1), N(7), the nitrogen atom of the pyrimidine ring N(3), the oxygen atoms of the phosphate group of the nucleotide and the protonated nitrogen atoms of the polyamine were the reaction centres. The mode of interaction of the metal ion with OSpm and the nucleotides (AMP or CMP) in the coordination compounds was established. In the system Cu(II)/OSpm the dinuclear complex Cu(2)(OSpm) forms, while in the ternary systems Cu(II)/nucleotide/OSpm the species type MH(x)LL' and MLL' appear. In the MH(x)LL' type species, the main centres of copper (II) ion binding in the nucleotide are the phosphate groups. The protonated amino groups of OSpm are involved in non-covalent interaction with the nitrogen atoms N(1), N(7) or N(3) of the purine or pyrimidine ring, whereas at higher pH, deprotonated nitrogen atoms of polyamine are engaged in metallation in MLL' species.

Evidence for intramolecular aromatic-ring stacking in the physiological pH range of the monodeprotonated xanthine residue in mixed-ligand complexes containing xanthosinate 5′-monophosphate (XMP)

The stability constants of the mixed-ligand complexes formed between Cu(Arm)2+ [Arm = 2,2'-bipyridine (Bpy) or 1,10-phenanthroline (Phen)], and the di- or trianion of xanthosine 5'-monophosphoric acid [= XMP(2-) or (XMP - H)(3-)] were determined by potentiometric pH titration in aqueous solution (25 degrees C; I = 0.1 M, NaNO3). Those for the monoanion, i.e., the Cu(Arm)(H;XMP)+ complexes, could only be estimated; for these species it is concluded that the metal ion is overwhelmingly bound at N7 and the proton resides at the phosphate group. Similarly, in the Cu(Arm)(XMP)+/- [= Cu(Arm)(X - H.MP.H)+/-] complexes Cu(Arm)2+ is also at N7 but the xanthine residue has lost a proton whereas the phosphate group still carries one, i.e., stacking plays, if at all, only a very minor role, yet, the N7-bound Cu(Arm)2+ appears to form an outer-sphere macrochelate with P(O)2(OH)-, its formation degree being about 60%. All this is different in the Cu(Arm)(XMP - H)- complexes, which are formed by the (XMP - H)(3-) species, that occur at the physiological pH of 7.5 and for which previously evidence has been provided that in a tautomeric equilibrium the xanthine moiety loses a proton either from (N1)H or (N3)H. In Cu(Arm)(XMP - H)- the phosphate group is the primary binding site for Cu(Arm)2+ and the observed increased complex stability is mainly due to intramolecular stack (st) formation between the aromatic-ring systems of Phen or Bpy and the monodeprotonated xanthine residue of (XMP - H)(3-); e.g., the stacked Cu(Phen)(XMP - H) isomer occurs with approximately 76%. Regarding biological systems the most important result is that at physiological pH the xanthine moiety has lost a proton from the (N1)H/(N3)H sites forming (XMP - H)(3-) and that its anionic xanthinate residue is able to undergo aromatic-ring stacking.

Non-covalent and coordination interactions in Cu(II) systems with uridine, uridine 5'-monophosphate and triamine or tetramine as biogenic amine analogues in aqueous solutions

Reactions of metallation and non-covalent interactions have been studied in ternary systems of Cu(II) ions with uridine, uridine 5'-monophosphate and diamines or triamines. It has been found that in metal-free systems the reaction centres of the nucleoside with the polyamine are the donor nitrogen atoms N(3) and protonated -NH(x) groups of the amines. In comparison to systems with adenosine or cytidine, the pH range of complex formation is shifted towards higher values. It is a consequence of significantly higher basicity of uridine and in agreement with the ion-ion, ion-dipole interaction model assumed. Formation of molecular complexes of uridine 5'-monophosphate with polyamines at a low pH is the result of activity of the phosphate group which plays the role of a negatively charged reaction site. Non-covalent interactions interfere in processes of bioligand metallation. Centres of weak interactions are simultaneously binding sites of metal ions. In protonated Cu(Urd)(PA)H(x) complexes, coordination has been found to involve the N(3) atom from the nucleoside and two donor nitrogen atoms from the polyamine (PA). In the heteroligand species Cu(Urd)(PA), despite deprotonation of all amine groups, one of these groups is located outside the inner coordination sphere. In complexes with uridine-5'-monophosphate, the phosphate group is active in metallation. Moreover, in certain coordination compounds this group is engaged in non-covalent interactions with PA molecules, despite binding Cu ions, as has been shown on the basis of equilibrium and spectral studies.

Copper(II) complexes with uridine, uridine 5'-monophosphate, spermidine, or spermine in aqueous solution

Molecular complexes of the types (Urd)H(x)(PA) and (UMP)H(x)(PA) are formed in the uridine (Urd) or uridine 5'-monophosphate (UMP) plus spermidine or spermine systems, as shown by the results of equilibrium and spectral studies. Overall stability constants of the adducts and equilibrium constants of their formation have been determined. An increase in the efficiency of the reaction between the bioligands is observed with increasing length of the polyamine. The pH range of adduct formation is found to coincide with that in which the polyamine is protonated while uridine or its monophosphate is deprotonated. The -NH(x)(+) groups from PA and the N(3) atom of the purine base as well as phosphate groups from the nucleotides have been identified as the significant centres of non-covalent interactions. Compared to cytidine, the pH range of Urd adduct formation is shifted significantly higher due to differences in the protonation constants of the endocyclic N(3) donor atoms of particular nucleosides. Overall stability constants of the Cu(II) complexes with uridine and uridine 5'-monophosphate in ternary systems with spermidine or spermine have been determined. It has been found from spectral data that in the Cu(II) ternary complexes with nucleosides and polyamines the reaction of metallation involves mainly N(3) atoms from the pyrimidine bases, as well as the amine groups of PA. This unexpected type of interaction has been evidenced in the coordination mode of the complexes forming in the Cu-UMP systems including spermidine or spermine. Results of spectral and equilibrium studies indicate that the phosphate groups taking part in metallation are at the same time involved in non-covalent interaction with the protonated polyamine.

Isomeric equilibria in aqueous solution involving aromatic ring stacking in the sexternary complexes formed by the quaternary cis-(NH3)2Pt(2'-deoxyguanosine-N7)(dGMP-N7) complex and the binary Cu(2,2'-bipyridine)2+ or Cu(1,10-phenanthroline)2+ complexes (dGMP2- = 2'-deoxyguanosine 5'-monophosphate)

To the best of our knowledge, for the first time the stabilities of sexternary complexes are determined by potentiometric pH titrations in aqueous solution at 25 degrees C and I = 0.1 M (NaNO3). The sexternary complexes form by binding of the binary Cu(Arm)2+ complexes, where Arm = 2,2'-bipyridine (Bpy) or 1,10-phenanthroline (Phen), to the -PO3(2-) group present in the quaternary cis-(NH3)2Pt(dGuo)(dGMP) complex. It is shown by stability constant comparisons and spectrophotometric measurements (observation of charge-transfer bands for the Phen system) that the [cis-(NH3)2Pt(dGuo)(dGMP).Cu(Arm)]2+ complexes can fold in such a way that aromatic ring stacking between the aromatic rings of Bpy or Phen and a guanine residue (most probably the one of dGMP2-) becomes possible. The formation degree of the stacks reaches approximately 25 and 50% for the [cis-(NH3)2Pt-(dGuo)(dGMP).Cu(Bpy)]2+ and [cis-(NH3)2Pt(dGuo)(dGMP).Cu(Phen)]2+ species, respectively. By comparisons with Cu(Arm)(dGMP) complexes, it is shown that the cis-(NH3)2Pt2+ unit coordinated to N7 of the guanine residues in the sexternary complexes inhibits stacking but does not prevent it. This result is of general importance because it demonstrates that in aqueous solution purine residues of nucleotides or nucleic acids that carry a metal ion at N7 can still undergo stacking interactions with other suitable aromatic ring systems.

Extent of Intramolecular Aromatic-Ring Stacking in Ternary Cu(2+) Complexes Formed by 2,2'-Bipyridyl or 1,10-Phenanthroline and Flavin Mononucleotide (FMN(2)(-))(1)(,)(2)

The stability constants of the 1:1 complexes formed between Cu(Arm)(2+), where Arm = 2,2'-bipyridyl or 1,10-phenanthroline, and flavin mononucleotide (= FMN(2)(-) = riboflavin 5'-phosphate) were determined by potentiometric pH titrations in aqueous solution at 25 degrees C and I = 0.1 M (NaNO(3)). The experimental conditions were carefully selected such that only the monomeric complex species formed. On the basis of previously established log K versus pK(a) straight-line plots (Chen, D.; et al. J. Chem. Soc., Dalton Trans. 1993, 1537-1546) for the corresponding ternary complexes of simple phosphate monoesters and phosphonate derivatives, R-PO(3)(2)(-), where R is a noncoordinating residue, it is shown that the stability of the ternary Cu(Bpy)(FMN) and Cu(Phen)(FMN) complexes is considerably higher than is expected on the basis of the basicity of the phosphate group of FMN(2)(-). By comparison with the stability of the ternary Cu(Arm)(G1P) complexes, where G1P = glycerol 1-phosphate, which had previously been studied (Liang, G.; et al. J. Am. Chem. Soc.1992, 114, 7780-7785) and in which the coordination sphere of Cu(2+) is identical with the one in Cu(Arm)(FMN), it can unequivocally be shown that the mentioned enhanced stability of the Cu(Arm)(FMN) complexes is solely due to the formation of intramolecular stacks; their formation degree reaches for Cu(Bpy)(FMN) and Cu(Phen)(FMN) about 80 and 90%, respectively. These, as well as recent results regarding the self-stacking of FMN(2)(-) (Bastian, M.; Sigel, H. Biophys. Chem. in press) show that the flavin moiety is ideally suited for stacking and charge-transfer interactions, which are so important for the flavin coenzymes in nature.

Metal-ion-governed molecular recognition: extent of intramolecular stack formation in mixed-ligand--copper(II) complexes containing a heteroaromatic N base and an adenosine monophosphate (2'AMP, 3'AMP, or 5'AMP). A structuring effect of the metal-ion bridge

Stability constants of mixed-ligand Cu(Arm)(AMP) complexes [where Arm = 2,2'-bipyridyl (Bpy) or 1,10-phenanthroline (Phen) and AMP2- = 2'AMP2-, 3'AMP2- or 5'AMP2-] were determined by potentiometric pH titrations in aqueous solution at I = 0.1 M (NaNO3) and 25 degrees C. The ternary Cu(Arm)(AMP) complexes are more stable than corresponding Cu(Arm)(R-MP) complexes, where R-MP2- represents a phosphate monoester with a group R that is unable to participate in any kind of interaction within the complexes as, for example, D-ribose 5'-monophosphate. This increased stability is attributed, in agreement with previous results, to intramolecular stack formation in the Cu(Arm)(AMP) complexes between the purine residue of the AMPs and the aromatic rings of Bpy or Phen. Based on correlation lines (previously obtained from log K versus pKa plots) for Cu(Arm)(R-MP) complexes without a ligand-ligand interaction, a quantitative evaluation was carried out. The degree of formation of the species with the intramolecular stacks increases for the Cu(Arm)(AMP) complexes in the series: 3'AMP2- less than 5'AMP2- less than 2'AMP2-; e.g. in Cu(Bpy)(3'AMP) the stack reaches a formation degree of 45 +/- 11% and in Cu(Bpy)(2'AMP) one of 96.1 +/- 0.7% is obtained. It must be emphasized that these differences are due to the different steric orientations of the bridging metal ion, which result from the varying position of the phosphate group on the ribose ring. As shown by 1H-NMR shift measurements, there is no significant effect of the position of the phosphate group on the stability of the binary (Phen)(AMP)2- adducts (K approximately 36 M-1 in D2O); such an effect is seen only if a metal-ion bridge is formed between the moieties forming the stack, i.e. metal-ion coordination imposes individual properties on the AMPs. By also taking into account some recent results on other nucleoside 5'-monophosphate complexes, the following trend for an increasing stacking tendency of the nucleic base moieties can be established: uracil approximately less than cytosine approximately less than thymine much less than adenine less than 7-deazaadenine. Some additional conclusions of general importance are given and the relevance of the results with regard to bio-systems is indicated.