Complex formation of divalent metal ions with uridine 5'-O-thiomonophosphate or methyl thiophosphate: comparison of complex stabilities with those of the parent phosphate ligands

The stability constants of the 1:1 complexes formed in aqueous solution between Mg2+, Ca2+, Sr2+, Ba2+, Mn2+, Co2+, Ni2+, Zn2+, or Cd2+ (M2+) and methyl thiophosphate (MeOPS(2-)) or uridine 5'-O-thiomonophosphate (UMPS(2-)) (PS(2-)=MeOPS(2-) or UMPS(2-)) have been determined (potentiometric pH titrations; 25 degrees C; I = 0.1 M, NaNO(3)). Comparison of these results for M(PS) complexes with those known for the parent M(PO) phosphate species, where PO(2-)=CH(3)OPO(2-)(3) or UMP(2-) (uridine 5'-monophosphate), shows that the alkaline earth metal ions, as well as Mn2+, Co2+, and Ni2+ have a higher affinity for phosphate groups than for their thio analogues. However, based on the linear log K(M)(M(R-PO3)) versus pK(H)(H(R-PO3)) relationships (R-PO(2-)(3) simple phosphate monoester or phosphonate ligands with a non-interacting residue R) it becomes clear that the indicated observation is only the result of the lower basicity of the thiophosphate residue. In contrast, the thio complexes of Zn2+ and Cd2+ are more stable than their parent phosphate ones, and this despite the lower basicity of the PS(2-) ligands. This stability increase is identical for M(MeOPS) and M(UMPS) species and amounts to about 0.6 and 2.4 log units for Zn(PS) and Cd(PS), respectively. Since no other binding site is available in MeOPS(2-), this enhanced stability has to be attributed to the S atom. Indeed, from the mentioned stability differences it follows that Cd2+ in Cd(PS) is coordinated by more than 99% to the thiophosphate S atom; the same value holds for Pb(PS), which was studied earlier. The formation degree of the Sbonded isomer amounts to 76+/-6 % for Zn(PS) and is close to zero for the corresponding Mg2+, Ca2+, and Mn2+ species. It is further shown that Zn(MeOPS)(aq)(2+) releases a proton from a coordinated water molecule with pK(a) approximately 6.9; i.e., this deprotonation occurs at a lower pH value than that for the same reaction in Zn(aq)(2+). Since Mg2+, Ca2+, Mn2+, and Cd2+ have a relatively low tendency for hydroxo complex formation, it was possible, for these M2+, to also quantify the stability of the binuclear complexes, M(2)(UMPS-H)+, where one M2+ is thiophosphate-coordinated and the other is coordinated at (N3)(-) of the uracil residue. The impact of the results presented herein regarding M2+/nucleic acid interactions, including those of ribozymes (rescue experiments), is briefly discussed.

Intramolecular stacking interactions in ternary copper(II) complexes formed with 2,2'-bipyridine or 1,10-phenanthroline and 9-(4-phosphonobutyl)adenine (dPMEA), the carba relative of the antiviral nucleotide analogue 9

The stability constants of the mixed ligand complexes formed between Cu(Arm)2+, where Arm=2,2'-bipyridine (Bpy) or 1,10-phenanthroline (Phen), and the monoanion or the dianion of 9-(4-phosphonobutyl)adenine (dPMEA=3'-deoxa-PMEA), which is the carba analogue of the antivirally active 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA), were determined by potentiometric pH titrations in aqueous solution at 25 degrees C and I=0.1 M (NaNO3). Detailed stability constant comparisons reveal that in the monoprotonated ternary Cu(Arm)(H;dPMEA)+ complexes the proton is at the phosphonate group and that stacking between Cu(Arm)2+ and H(dPMEA)- plays a significant role. For the Cu(Arm)(dPMEA) complexes a large increase in complex stability (compared to the stability expected on the basis of the basicity of the phosphonate group) is observed, which is due to intramolecular stack formation between the aromatic ring systems of Phen or Bpy and the purine moiety of dPMEA2-. The formation degree of the stacked isomer in the Cu(Arm)(dPMEA) systems is on the order of 90%, though it is somewhat more pronounced with Phen than with Bpy. Comparisons of the Cu(Arm)(N) systems, where N=dPMEA2- and PMEA2- or adenosine 5'-monophosphate (AMP2-), reveal that the stacking properties of dPMEA2- and PMEA2-resemble closely those of their parent nucleotide AMP2-.

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.

Design, Synthesis, and Crystal Structure of a cis-Configuration N(2)S(2)-Coordinated Palladium(II) Complex: Role of the Intra- and Intermolecular Aromatic-Ring Stacking Interaction

A cis-configuration bis(4,5-diazafluorene-9-one thiosemicarbazone) palladium trihydrate, which exhibits approximately five times SHG (second harmonic generation) efficiency of urea, has been designed, synthesized, and structurally characterized. The complex, C(24)H(16)N(10)PdS(2).3H(2)O, crystallizes in trigonal space group P3(1) with cell parameters a = 10.749(2) Å, c = 19.872(4) Å, V = 1988.3(6) Å(3), and Z = 3. The coordination geometry about the Pd(II) is surprisingly a cis-configuration square-planar formed by two imino nitrogen atoms N(3) and N(8) and two sulfur atoms S(1) and S(2) from two thiosemicarbazone ligands. Intramolecular contact analyses in the crystals and 1D and 2D (1)H NMR spectra in solution show that the cis-positioning of the two ligands was stabilized by the pi-pi interaction between the two delocalized diazafluorene moieties. Detailed crystal structure analyses demonstrate that both the intermolecular pi-pi stacking between the diazafluorene planes in different molecules and intermolecular hydrogen bonds between the water molecules and the deprotonated ligands might be the factors that influence the molecules to be packed in the acentric space group P3(1). The crystal structure of the free ligand was also reported here for comparison. The ligand, C(12)H(9)N(5)S, crystallizes in orthorhombic space group Pbca with cell parameters a = 8.432(2) Å, b = 15.427(3) Å, c = 17.387(3) Å, V = 2272.7(8) Å(3), and Z= 8. The thiosemaicarbazone moiety adopts an E configuration with N(1) cis to N(3).

Synthesis, Characterization, Absorption Spectra, and Luminescence Properties of Organometallic Platinum(II) Terpyridine Complexes

A series of new organometallic platinum(II) complexes containing terdentate polypyridine ligands has been prepared and characterized. Their absorption spectra in 4:1 (v/v) MeOH/EtOH fluid solution at room temperature and luminescence in the same matrix at 77 K have been investigated. The new species are [Pt(terpy)Ph]Cl (3, terpy = 2,2':6',2"-terpyridine, Ph = phenyl), [Pt(Ph-terpy)Cl]Cl (4, Ph-terpy = 4'-phenyl-2,2':6',2"-terpyridine), [Pt(Ph-terpy)Me]Cl (5), and [Pt(Ph-terpy)Ph]Cl (6). The results have been compared with those for [Pt(terpy)Cl]Cl (1) and [Pt(terpy)Me]Cl (2). NMR data evidence that all the complexes but 3 and 6 oligomerize in solution leading to stacked species. The absorption spectra are dominated by moderately intense metal-to-ligand charge-transfer (MLCT) bands in the visible region and by intense ligand-centered (LC) bands in the UV region. All the compounds are luminescent in a 4:1 (v/v) MeOH/EtOH rigid matrix at 77 K, exhibiting a structured emission within the range 460-600 nm. This feature is assigned to formally (3)LC excited states which receive substantial contribution from closely lying (3)MLCT levels. Complexes 1, 2, 4, and 5 also exhibit a relatively narrow and unstructured luminescence band within the range 680-800 nm, which dominates the luminescence spectrum on increasing concentration and exciting at longer wavelengths. The band is assigned to a dsigma(metal) --> pi(polypyridine) ((3)MMLCT) state, originating from metal-metal interactions occurring in head-to-tail dimers (or polymers). A third broad band is shown by 1 and 4 under all concentration conditions and by 2 and 5 only in concentrated solutions and is attributed to excimeric species originating from pi-pi interactions due to stacking between polypyridine ligands.

The self-association of flavin mononucleotide (FMN2−) as determined by 1H NMR shift measurements

The concentration dependence of the (1)H NMR chemical upfield shifts of the protons H6, H9, H7alpha, and H8alpha of the 7,8-dimethylisoalloxazine residue of flavin mononucleotide (FMN(2-)) has been measured and the self-stacking tendency of FMN(2-) was quantified with the isodesmic model of indefinite non-cooperative self-association. The stacking tendency of FMN(2-) is considerable and described in the concentration range of 0.0025-0.1 M with the indicated model by K = 27 +/- 15 M(-1) (25 degrees C; I = 0.1-0.3 M). This result is compared with related ones from the literature. The caveats regarding the self-stacking properties of FMN(2-) and their dependence on the concentration are discussed.

Molecular Recognition Effects in Metal Complex Mediated Double-Strand Cleavage of DNA: Reactivity and Binding Studies with Model Substrates

Double-strand breaks in duplex DNA are thought to be significant sources of cell lethality because they appear to be less readily repaired by DNA repair mechanisms. We recently described the design and cleavage chemistry of ((2S,8R)-5-amino-2,8-dibenzyl-5-methyl-3,7-diazanonanedioato)copper(II) (1), which effects nonrandom double-strand cleavage of duplex DNA. After DNA nicking by generation of hydroxyl radicals, the key step in this process appears to occur through recognition by the metal complex of the nicked-abasic site on duplex DNA, followed by delivery of OH(*) to cleave at the opposing strand, forming a double-strand lesion. Through the use of model nucleic acid substrates and comparison to DNA scission chemistry, we have investigated the electrostatic and hydrophobic contributions to DNA binding by complex 1. We have complemented these reactivity studies with studies on the binding of 1 to a model nucleic acid substrate, using (2)H NMR spectroscopy with deuterated 1 and HDO T(1)()()relaxation enhancement methods to study the binding of 1 to nucleotide substrates. With these methods, we have estimated that the association constant for the 1(+).5'-AMP(2)(-) complex is approximately 16 M(-)(1) and that the binding interaction involves both electrostatic and aromatic stacking interactions between the nucleic acid base and the pendant aromatic side chains of 1.

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.

Structures and Stabilities of Ternary Copper(II) Complexes with 3,5-Diiodo-L-tyrosinate. Weak Interactions Involving Iodo Groups

Structures and stabilities of the ternary copper(II) complexes Cu(DA)(AA), where AA refers to 3,5-diiodo-L-tyrosinate (I(2)tyr) or L-tyrosinate (Tyr) and DA refers to 1,10-phenanthroline (phen), 2,2'-bipyridine (bpy), 2-(aminomethyl)pyridine (ampy), histamine (hista), or ethylenediamine (en), have been investigated by potentiometric, spectroscopic, and X-ray diffraction methods. The stability constants have been determined by potentiometric titrations at 25 degrees C and ionic strength I = 0.1 M (KNO(3)). The equilibrium constants K for a hypothetical equilibrium, Cu(DA)(Ala) + Cu(en)(AA) Cu(DA)(AA) + Cu(en)(Ala) where Ala refers to L-alanine, have been calculated from the determined overall stability constants of the ternary complexes for estimating the stability enhancement due to the stacking interaction between the aromatic rings in Cu(DA)(AA). Large positive log K values have been obtained for the Cu(DA)(I(2)tyrOH) and Cu(DA)(I(2)tyrO(-)) systems (DA = phen or bpy, OH and O(-) refer to the protonated and deprotonated forms of the phenol moiety, respectively), indicating that the complexes are stabilized by effective stacking. Differences between the log K values for Cu(DA)(I(2)tyr) and Cu(DA)(Tyr) systems indicate that the iodine substituents greatly contribute to the stability enhancement. A distinct circular dichroism (CD) magnitude anomaly was also observed for the systems with large log K value, supporting the existence of the stacking interaction in Cu(DA)(AA). Two complexes, [Cu(bpy)(I(2)tyrO(-))(H(2)O)].2H(2)O (1) and [Cu(bpy)(I(2)tyrOH)(NO(3))].CH(3)OH (2), have been isolated as crystals and analyzed by the X-ray diffraction method. Both 1 and 2 crystallized in the orthorhombic space group P2(1)2(1)2(1) with four molecules in a unit cell of dimensions a = 9.2339(4), b = 16.9230(8), and c = 14.8584(5) Å for complex 1, and a = 11.2240(8), b = 11.715(1), and c = 17.966(2) Å for complex 2. The central Cu(II) ion for both complexes has a similar distorted five-coordinate square-pyramidal geometry with the equatorial positions occupied by the two nitrogen atoms of bpy and the nitrogen and oxygen atoms of I(2)tyr, and the apical position is occupied by a water molecule (for 1) or a nitrate ion (for 2). The opposite site to the axial water or nitrate oxygen atom is intramolecularly occupied by the side chain aromatic ring, which is approximately parallel to the copper coordination plane with the average spacing of 3.31 or 3.30 Å for complex 1 or 2, respectively, directly exhibiting the effective stacking interaction between the aromatic rings in the solid state. Distances between the iodine and one of the pyridine rings of bpy (3.79 Å for 1 and 3.56 Å for 2) are shorter than the van der Waals distance (3.85 Å), implying that the iodine substituent may be involved in a weak bonding interaction with the pyridine ring. Effects of the iodine substituents on the stacking interactions between the diiodophenol side ring and the coordinated aromatic diamine and their possible biological relevance have been discussed.

Acid-base properties of nucleosides and nucleotides as a function of concentration. Comparison of the proton affinity of the nucleic base residues in the monomeric and self-associated, oligomeric 5'-triphosphates of inosine (ITP), guanosine (GTP), and adenosine (ATP)

The acid-base properties of the nucleic base residues of ITP, GTP, and ATP, and for comparison also as far as possible of the corresponding nucleosides, were studied in dependence on their concentration, i.e. on the effect of self-association. From the dependence between the 1H-NMR chemical shifts of H-2 (where applicable), H-8, and H-1', and the pD of the solutions, the acidity constants for the deprotonation of the D+(N-7) site in D2(ITP)2-, D2(GTP)2-, D(Ino)+, and D(Guo)+, and of the D+(N-1) site in D2(ATP)2- and D(Ado)+ were calculated. Chemical shift/pD profiles for a whole series of varying concentrations of the nucleic base derivatives (= N) were constructed, including those for infinite dilution (delta o), which give the acidity constant for the monomeric N, and for infinitely concentrated solutions (delta infinity), which give the acidity constant of an N in an infinitely long stack. The acidity constants determined from the delta o/pD plots are in excellent agreement with the pKa values measured by potentiometric pH titrations of highly diluted solutions of N. The effects of self-association are striking; e.g. the pKa value of the D+(N-7) site in D2(GTP)2- is lowered by about 1 (as calculated from the delta o/pD and delta infinity/pD profiles), while the pKa value of the D+(N-1) site in D2(ATP)2- is increased by approximately 0.3; i.e. in the first case deprotonation is facilitated and in the second it is inhibited. The increasing inhibition of the H+(N-1) deprotonation with an increasing ATP concentration is due to the high stability of the dimeric [H2(ATP)]2(4-) stack for which the intermolecular H+(N-1)/gamma-P(OH)(O)2- ion pairs between the two ATP molecules are crucial. In those cases where no other significant interaction but aromatic-ring stacking in the self-association process occurs, the release of protons from protonated nitrogen-ring sites is facilitated with increasing stacking; this holds not only for D2(GTP)2- as indicated above, but also for D2(ITP)2-, D(Ino)+, and D(Ado)+. The latter example especially suggests that the situation for the D2(ATP)2- system is exceptional. Some consequences of the considered acid-base properties for biological systems are indicated.

Comparison of the self-association properties of the 5'-triphosphates of inosine (ITP), guanosine (GTP), and adenosine (ATP). Further evidence for ionic interactions in the highly stable dimeric [H2(ATP)]2(4-) stack

The concentration dependence of the chemical shifts for the hydrogens H-2, H-8 and H-1' of ITP and for H-8 and H-1' of GTP has been measured in D2O at 25 degrees C under several degrees of protonation in the pD range 1.2-8.4. For reasons of comparison, inosine and guanosine have been included in the study The results are consistent with the isodesmic model of indefinite noncooperative stacking. The association constants for the nucleosides (Ns) inosine and guanosine decrease with increasing protonation: Ns greater than D(Ns)+/Ns in a 1:1 ratio greater than D(Ns)+. In contrast, a maximum is observed with ITP and GTP; the stacking tendency of GTP following the series: GTP4- less than or equal to D(GTP)3- (K approximately 0.7 M-1) less than D(GTP)3-/D2(GTP)2- in a 1:1 ratio (K approximately 2.9 M-1) greater than D2(GTP)2- greater than D3(GTP)- (K approximately 1.5 M-1). The order of the series with ITP corresponds to that with GTP, but the association constants are slightly smaller. At the maximum of the self-association tendency the triphosphate residue has only a minor influence; this follows from the fact that the association constants for the 1:1 ratios of Ino/D(Ino)+ and D(ITP)3-/D2(ITP)2- are identical within experimental error; this holds also for Guo/D(Guo)+ and D(GTP)3-/D2(GTP)2-; in all these pairs the K-7 site is 50% protonated. Comparison of the association constant for the deprotonated species shows that here charge effects, i.e. repulsion between the negatively charged triphosphate chains, are important: Ino (K approximately 3.3 M-1) greater than ITP4- (K approximately 0.4 M-1) and Guo (K approximately 8 M-1) greater than GTP4- (K approximately 0.8 M-1). In addition the series holds: Ado (K approximately 15 M-1) greater than Guo greater than Ino. However, most important is the comparison of the ITP and GTP series with previous data for ATP: ATP4- (K approximately 1.3 M-1) less than D(ATP)3- (2.1 M-1) less than 1:1 ratio of D(ATP)3-/D2(ATP)2- (6 M-1) much less than D2(ATP)2- (approximately 200 M-1) much greater than D3(ATP)- (K less than or equal to 17 M-1).(ABSTRACT TRUNCATED AT 400 WORDS)

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.