Molecular recognition patterns of 2-aminopurine versus adenine: a view through ternary copper(II) complexes

In contrast to the comprehensive structural information about metal complexes with adenine, the corresponding to its isomer 2-aminopurine (H2AP) is extremely poor. With the aim to rationalize the metal binding pattern of H2AP, we report the molecular and/or crystal structure of four novel compounds with various iminodiacetate-like (IDA-like) copper(II) chelates: [Cu(IDA)(H2AP)(H2O)]·H2O (1), [Cu(MIDA)(H2AP)(H2O)]·3H2O (2), {[Cu(NBzIDA)(H2AP)]·1.5H2O}n (3) and [Cu(MEBIDA)(H2AP)(H2O)]·3.5 H2O (4), where IDA, MIDA, NBzIDA and MEBIDA are R=H, CH3, benzyl- and p-tolyl- in R-N-(CH2-COO-)2 ligands, respectively. Synthesis strategies include direct reactions of copper(II) chelates with H2AP (alone, for 1 and 3) and/or with the base pairs H2AP:thymine (1-4) or H2AP:cytosine (3). Moreover, these compounds have been also investigated by spectral and thermal methods. Regardless of the N-derivative of the IDA chelator, molecular recognition between H2AP and the referred Cu(II)-chelates only displays the formation of the Cu-N7(purine-like) bond what is clearly in contrast to what was previously reported for adenine. The metal binding pattern of 2-aminopurine is discussed on the basis of the electronic effects and steric hindrance of the 2-amino exocyclic group.

Comparison of the surprising metal-ion-binding properties of 5- and 6-uracilmethylphosphonate (5Umpa2- and 6Umpa2-) in aqueous solution and crystal structures of the dimethyl and di(isopropyl) esters of H2(6Umpa)

5- and 6-Uracilmethylphosphonate (5Umpa(2-) and 6Umpa(2-)) as acyclic nucleotide analogues are in the focus of anticancer and antiviral research. Connected metabolic reactions involve metal ions; therefore, we determined the stability constants of M(Umpa) complexes (M(2+)=Mg(2+), Ca(2+), Mn(2+), Co(2+), Cu(2+), Zn(2+), or Cd(2+)). However, the coordination chemistry of these Umpa species is also of interest in its own right, for example, the phosphonate-coordinated M(2+) interacts with (C4)O to form seven-membered chelates with 5Umpa(2-), thus leading to intramolecular equilibria between open (op) and closed (cl) isomers. No such interaction occurs with 6Umpa(2-). In both M(Umpa) series deprotonation of the uracil residue leads to the formation of M(Umpa-H)(-) complexes at higher pH values. Their stability was evaluated by taking into account the fact that the uracilate residue can bind metal ions to give M(2)(Umpa-H)(+) species. This has led to two further important insights: 1) In M(6Umpa-H)-cl the H(+) is released from (N1)H, giving rise to six-membered chelates (degrees of formation of ca. 90 to 99.9 % with Mn(2+), Co(2+), Cu(2+), Zn(2+), or Cd(2+)). 2) In M(5Umpa-H)$-cl the (N3)H is deprotonated, leading to a higher stability of the seven-membered chelates involving (C4)O (even Mg(2+) and Ca(2+) chelates are formed up to approximately 50 %). In both instances the M(Umpa-H)-op species led to the formation of M(2)(Umpa-H)(+) complexes that have one M(2+) at the phosphonate and one at the (N3)(-) (plus carbonyl) site; this proves that nucleotides can bind metal ions independently at the phosphate and the nucleobase residues. X-ray structural analyses of 6Umpa derivatives show that in diesters the phosphonate group is turned away from the uracil residue, whereas in H(2)(6Umpa) the orientation is such that upon deprotonation in aqueous solution a strong hydrogen bond is formed between (N1)H and PO(3) (2-); replacement of the hydro gen with M(2+) gives the M(6Umpa-H)-cl chelates mentioned.

A Windmill-Shaped Hexacopper(II) Molecule Built Up by Template Core-Controlled Expansion of Diaquatetrakis(μ2-adeninato-N3,N9)dicopper(II) with Aqua(oxydiacetato)copper(II)

The windmill-shaped hexanuclear copper(II) cluster {(H(2)O)(2)Cu(2)(mu(3)-(Ade)(4)[Cu(oda)(H(2)O)](4)}.6H(2)O (1-o) has been synthesized in aqueous medium by in situ core-controlled expansion of the neutral building block Cu(2)(mu(2)-N3,N9-Ade)(4)(H(2)O)(2) (2) with Cu(oda)(H(2)O) (3-o) (Ade = adeninato(1-) and oda = oxydiacetato(2-) ligands). Crystal data for 2-b (2.5H(2)O): triclinic, space group P(-)1; a = 9.374(1), b = 9.440(1), c = 10.326(1) A; alpha = 78.72(1), beta = 76.77(1), gamma = 63.51(1) degrees ; final R(1) = 0.059; T = 100(2) K. Crystal data for 1-o: monoclinic, space group P2(1)/n; a = 15.203(2), b = 10.245(1), c = 19.094(2) A; beta = 101.61(1) degrees ; final R(1) = 0.049; T = 293(2) K. The X-shaped hexanuclear molecule consists of a central core (2) and four terminal arms (3-o) linked together by bridging mu(3)-N3,N7,N9-Ade ligands. There are three crystallographic independent metal atoms (two terminals, one central). All Cu(II) atoms exhibit a 4 + 1 coordination, of which one is an aqua apical ligand. The basal coordination sets complete the CuN(4) + O or CuO(3)N + O chromophores for the central or terminal metal atoms, respectively. Thermal stability and spectral and magnetic properties were also studied. Analogous compounds to 1-o with tridentate or tripodal tetradentate ligands L(2-), instead of oda, have also been synthesized.

Characterization and biological activities of two copper(II) complexes with diethylenetriamine and 2,2'-bipyridine or 1,10-phenanthroline as ligands

Two new mixed ligand copper(II) complexes with diethylenetriamine, 2,2'-bipyridine and 1,10-phenanthroline have been synthesized. The crystal and molecular structures of [Cu(dien)(phen)](ClO(4))(2) and [Cu(dien)(bipy)](BF(4))(2) (dien=diethylenetriamine, phen=1,10-phenanthroline, bipy=2,2'-bipyridine) were determined by X-ray crystallography from single crystal data. These two complexes have similar structures. The EPR spectral data also suggest that these complexes have distorted square pyramidal geometry about copper(II). Anti-microbial and superoxide dismutase activities of these complexes have also been measured. They show the higher SOD activity than the corresponding simple Cu(II)-dien/Cu(II)-PMDT (PMDT=N,N,N',N',N''-pentamethyldiethylenetriamine) complexes because of a strong axial bond of one of the nitrogen atoms of the alpha-diimine. Both the complexes have been found to cleave plasmid DNA in the presence of co-reductants such as ascorbic acid and glutathione.

Ternary copper(II) complexes with N-carboxymethyl-l-prolinato(2−) ion and imidazole or creatinine: A comparative study of the interligand interactions influencing the molecular recognition and stability

The compounds {[Cu(CMP)(Him)].H(2)O}(n) (I) and [Cu(CMP)(crea)H(2)O].3H(2)O (II) were synthesized and characterized by X-ray diffraction, thermal, spectral and magnetic methods (CMP=N-carboxymethyl-;l-prolinato(2-) ion, Him=imidazole and crea=creatinine). Appropriate structural comparison with other compounds such as {[Cu(CMP)(H(2)O)].H(2)O}(n), [Cu(crea)(2)Cl(2)] and [Cu(dipeptide)(crea)(H(2)O)(x)].nH(2)O (x=0 or 1) have been made in order to prove that crea can act as an imidazole-like ligand (because it is able to promote the same fac- to mer-CMP tridentate conformational change in copper(II) complexes) as well as to discuss the interligand interactions which control the 'Cu(CMP) complex-crea, molecular recognition processes. In contrast to that found in related ternary complexes, we have concluded that direct CMP-crea interligand interactions are missing in the Cu-CMP-crea complex due to the inappropriate correspondence between the donor and/or acceptor H-bonding properties of these ligands. CMP can only act as H-acceptor by its two terminal carboxylate group, and crea can display H-donor and H-acceptor roles by its exocyclic -NH(2) and O moieties, respectively. That promotes the reinforcement of the Cu-N(crea) bond by a bridge -N-H(crea)...O(aqua) (2.867(3)A, 176.4 degrees).

X-ray, spectral and biological (antimicrobial and superoxide dismutase) studies of oxalato bridged CuII–NiII and CuII–ZnII complexes with pentamethyldiethylenetriamine as capping ligand

X-band electron spin resonance (ESR) and electronic spectra of oxalatobridged heterodinuclear Cu-Ni and Cu-Zn complexes, viz., [(PMDT)Cu-Ox-Ni(PMDT)](BPh(4))(2).2CH(3)CN and [(PMDT)Cu-Ox-Zn(PMDT)](BPh(4))(2).2CH(3)CN, where PMDT=pentamethyldiethylenetriamine, Ox=oxalate ion have been described. Complex [(PMDT)Cu-Ox-Ni(PMDT)](BPh(4))(2).2CH(3)CN has been structurally characterized. This complex crystallizes in the monoclinic space group, C(2) (No. 5) with the unit parameters a=20.445(4) A, b=14.884(3) A, c=23.174(5) A, alpha=90 degrees, beta=102.693(4) degrees, gamma=90 degrees, V=6880(2) A(3) and Z=4. The structure refined to R=0.0354 and R(w)=0.0853 for 21,109 reflections with I>2 sigma(I) using 765 parameters, shows the presence of a MN(3)O(2) chromophore in a distorted trigonal-bipyramidal (TBP) heterometallic complex with oxalate dianion. Taking with an equatorial Cu-O=2.137(8) A and an axial Cu-O=1.961(6) A coordination site at Cu(II) ion and equatorial Ni-O=2.178(7) A and axial Ni-O=1.994 (9) A coordination site at Ni(II) ion. The Cu-Ni distance is 5.3532(9) A and Cu-C(2)O(4)-Ni unit is planar. The [(PMDT)Cu-Ox-Ni(PMDT)](2+) shows the ESR spectrum of the antiferromagnetic spin exchange with each dinuclear delocalization of the unpaired electron over the unit and spin-doublet ground state which demonstrates the Cu-Ox-Ni core. Antimicrobial and superoxide dismutase (SOD) activities of these complexes have also been measured.

Metal Ion-Binding Properties of (1H-Benzimidazol-2-yl-methyl)phosphonate (Bimp2-) in Aqueous Solution.⊥Isomeric Equilibria, Extent of Chelation, and a New Quantification Method for the Chelate Effect

The acidity constants of the 2-fold protonated (1H-benzimidazol-2-yl-methyl)phosphonate, H2(Bimp)(+/-), are given, and the stability constants of the M(H;Bimp)+ and M(Bimp) complexes with the metal ions M2+ = Mg2+, Ca2+, Ba2+, Mn2+, Co2+, Cu2+, Zn2+, or Cd2+ have been determined by potentiometric pH titrations in aqueous solution at I = 0.1 M (NaNO3) and 25 degrees C. Application of previously determined straight-line plots of log KM(M(Bi-R)) versus pKH(H(Bi-R)) for benzimidazole-type ligands, Bi-R, where R represents a residue which does not affect metal ion binding, proves that the primary binding site in the M(H;Bimp)+ complexes is (mostly) N3 and that the proton is located at the phosphonate group; outersphere interactions seem to be important, and the degree of chelate formation is above 60% for all metal ion complexes studied, except for Zn(H;Bimp)+. A similar evaluation based on log KM(M(R-PO3)) versus pKH(H(R-PO3)) straight-line plots for simple phosph(on)ate ligands, R-, where R represents a residue which cannot participate in the coordination process, reveals that the primary binding site in the M(Bimp) complexes is (mostly) the phosphonate group with all metal ions studied. In this case, the formation degree of the chelates varies more widely in dependence on the kind of metal ion involved, i.e., from 17 +/- 11% to nearly 100% for Ba(Bimp) and Cu(Bimp), respectively. For all the M(H;Bimp)+ and M(Bimp) systems, the intramolecular equilibria between the isomeric complexes are evaluated in a quantitative manner. The fact that for Bimp2- the metal ion affinity of the two binding sites, N3 and PO3(2-), can be calculated independently, i.e., the corresponding micro stability constants become known, allows us to present for the first time a method for the quantification of the chelate effect solely based on comparisons of stability constants which carry the same dimensions. This effect is often ill defined in textbooks because equilibrium constants of different dimensions are compared, which is avoided in the present case. For the M(Bimp) complexes, it is shown that the chelate effect is close to zero for Ba(Bimp) whereas for Cu(Bimp) it amounts to about four log units. This method is also applicable to other chelating systems. Finally, considering that benzimidazole as well as phosphonate derivatives are employed as therapeutic agents, the potential biological properties of Bimp, especially regarding nucleic acid polymerases, are briefly discussed.