Claudia Giorgi

Affinity and nuclease activity of macrocyclic polyamines and their CuII complexes.

The stability constants of Cu(II) complexes that consist of either an oxaaza macrocycle with two triamine moieties linked by dioxa chains, or two macrocyclic ligands with a polyamine chain which are connecting the 2 and 9 positions of phenanthroline, have been determined by means of potentiometric measurements. The results are compared to those reported for other ligands with a similar molecular architecture. Of the complexes that contain phenanthroline in their macrocycle, the Cu(II) ion of the complex with the smallest and most rigid macrocycle (L3) has an unsaturated coordination sphere, while in the complex with the largest macrocycle (L5) the Cu(II) ion is coordinatively almost saturated. These results are corroborated by the crystal structure of the [CuL5](ClO4)2 complex. The affinity of the ligands and the complexes towards nucleic acids was studied by measuring the changes in the melting temperature, which showed that the affinity of the macrocyclic ligands towards double-stranded DNA or RNA is generally smaller than that of their linear analogues that bear a similar charge, with a strong preference for polyA-polyU, a model for RNA. However, the complexes of two of the changed macrocyclic ligands which contain a phenanthroline unit (L4, L5) showed a distinctly larger increase in their melting temperature deltaTm with DNA (polydA-polydT), which is reversed again in favor of RNA upon metallation to the dinuclear copper complex with L5. Experiments with supercoiled plasmid DNA showed a particularly effective cleavage with a mononuclear Cu(II) complex that contains a phenanthroline unit (L6). Related ligands showed less activity towards DNA, but not so towards the biocidic bis(p-nitrophenyl)phosphate (BNPP). In both cases (with DNA and BNPP) the activity seemed to increase with decrease of coordinative saturation of the Cu(II) ion, with the exception of one particular ligand (L6). Experiments with radical scavengers in the DNA experiments showed some decrease in cleavage, which indicates the participation of redox processes.

Tuning the Activity of Zn(II) Complexes in DNA Cleavage : Clues for Design of New Efficient Metallo-Hydrolases

The hydrolytic ability toward plasmid DNA of a mononuclear and a binuclear Zn(II) complex with two macrocyclic ligands, containing respectively a phenanthroline (L1) and a dipyridine moiety (L2), was analyzed at different pH values and compared with their activity in bis( p-nitrophenyl)phosphate (BNPP) cleavage. Only the most nucleophilic species [ZnL1(OH)]+ and [Zn2L2(OH)2]2+, present in solution at alkaline pH values, are active in BNPP cleavage, and the dinuclear L2 complex is remarkably more active than the mononuclear L1 one. Circular dichroism and unwinding experiments show that both complexes interact with DNA in a nonintercalative mode. Experiments with supercoiled plasmid DNA show that both complexes can cleave DNA at neutral pH, where the L1 and L2 complexes display a similar reactivity. Conversely, the pH-dependence of their cleavage ability is remarkably different. The reactivity of the mononuclear complex, in fact, decreases with pH while that of the dinuclear one is enhanced at alkaline pH values. The efficiency of the two complexes in DNA cleavage at different pH values was elucidated by means of a quantum mechanics/molecular mechanics (QM/MM) study on the adducts between DNA and the different complexed species present in solution.

Thermodynamics of Anion−π Interactions in Aqueous Solution

Thermodynamic parameters (ΔG°, ΔH°, TΔS°), obtained by means of potentiometric and isothermal titration calorimetry (ITC) methods, for the binding equilibria involving anions of high negative charge, like SO(4)(2-), SeO(4)(2-), S(2)O(3)(2-) and Co(CN)(6)(3-), and nitroso-amino-pyrimidine receptors in water suggested that anion-π interactions furnish a stabilization of about -10 kJ/mol to the free energy of association. These anion-π interactions are almost athermic and favored by large entropic contributions which are likely due to the reduced hydrophobic pyrimidine surface exposed to water after anion aggregation, and the consequent reduced disruptive effect on the dynamic water structure. The crystal structure of the {H(4)L[Co(CN)(6)]}·2H(2)O complex showed strong anion-π interactions between Co(CN)(6)(3-) and the protonated H(4)L(3+) receptor. The CN···centroid distance (2.786(3) Å), occurring with a cyanide N atom located almost above the centroid of the pyrimidine ring, is the shortest distance till now reported for the interaction between CN(-) ions and heteroaromatic rings.

Exploring the Binding Ability of Phenanthroline-Based Polyammonium Receptors for Anions: Hints for Design of Selective Chemosensors for Nucleotides

The synthesis of receptor 2,6,10,14,18-pentaaza[20]-21,34-phenanthrolinophane (L1), containing a pentaamine chain linking the 2,9 positions of a phenanthroline unit, is reported. The protonation features of L1 and of receptor 2,6,10,14,18,22-hexaaza[23]-24,37-phenanthrolinophane (L2) have been studied by means of potentiometric, (1)H NMR, and spectrofluorimetric measurements; this study points out that the fluorescent emission of both receptors depends on the protonation state of the polyamine chain. In fact, the receptors are emissive only at neutral or acidic pH values, where all the aliphatic amine groups are protonated. Potentiometric titrations show that L2 is able to bind selectively ATP over TTP, CTP, and GTP. This selectivity is lost in the case of L1. (1)H and (31)P NMR measurements and molecular mechanics calculations show that the phosphate chains of nucleotides give strong electrostatic and hydrogen-bonding interactions with the ammonium groups of the protonated receptors, while the nucleobases interact either via pi-stacking with phenanthroline or via hydrogen bonding with the ammonium groups. Of note, MM calculations suggest that all nucleotides interact in an inclusive fashion. In fact, in all adducts the phosphate chain is enclosed within the receptor cavities. This structural feature is confirmed by the crystal structure of the [(H(6)L2)(2)(TTP)(2)(H(2)O)(2)](4+) adduct. Fluorescence emission measurements at different pH values show that L2 is also able to ratiometrically sense ATP in a narrow pH range, thanks to emission quenching due to a photoinduced electron transfer (PET) process from an amine group of the receptor to the excited phenanthroline.

Anion Binding by Protonated Forms of the Tripodal Ligand Tren

The interaction of the protonated forms of tris(2-aminoethyl)amine (tren) with NO(3)(-), SO(4)(2-), TsO(-), PO(4)(3-), P(2)O(7)(4-), and P(3)O(10)(5-) was studied by means of potentiometric and microcalorimetric measurements in a 0.10 M NMe(4)Cl aqueous solution at 298.1 +/- 0.1 K, affording stability constants and the relevant energetic terms DeltaH degrees and TDeltaS degrees of complexation. Thermodynamic data show that these anion complexation processes are mainly controlled by electrostatic forces, although hydrogen-bond interactions and solvation effects also contribute to complex stability, leading, in some cases, to special DeltaH degrees and TDeltaS degrees contributions. The crystal structures of [H(3)L][NO(3)](3) and [H(3)L][TsO](3) evidence a preferred tridentate coordination mode of the triprotonated ligands in the solid state. Accordingly, the H(3)L(3+) receptor binds a single oxygen atom of both NO(3)(-) and TsO(-) by means of its three protonated fingers, although in the crystal structure of [H(3)L][TsO](3), one conformer displaying bidentate coordination was also found. Modeling studies performed on the [H(3)L(NO(3))](2+) complex suggested that the tridentate binding mode is the preferred one in aqueous solution, while in the gas phase, a different complex conformation in which the receptor interacts with all three oxygen atoms of NO(3)(-) is more stable.

Exploring the binding ability of polyammonium hosts for anionic substrates: selective size-dependent recognition of different phosphate anions by bis-macrocyclic receptors.

Binding of mono-, di-, and triphosphate, adenosine diphosphate (ADP), and adenosine triphosphatase (ATP) with receptors L1-L3, composed of two [9]aneN(3) units separated by a 2,9-dimethylene-1,10-phenanthroline (L1), a 2,6-dimethylenepyridine (L2), or a 2,3-dimethylenequinoxaline (L3) spacer, has been studied by means of potentiometric titrations, (1)H and (31)P NMR measurements in aqueous solutions, and molecular modeling calculations. In the case of inorganic phosphates, the binding properties of the receptors appear to be determined by their geometrical features, in particular the distance between the two [9]aneN(3) units imposed by the spacer separating the two macrocyclic units. While L1 is able to selectively bind triphosphate over di- and monophosphate, L3 selectively coordinates the smaller monophosphate anion. Finally, L2 shows preferential binding of diphosphate. (1)H and (31)P NMR measurements show that the complexes are essentially stabilized by charge-charge and hydrogen-bonding interactions between the anion and the protonated amine groups of the macrocyclic subunits of the receptors. Molecular dynamics simulations suggest that the larger distance between the two macrocyclic units of L1 allows this receptor to form a larger number of hydrogen-bonding contacts with triphosphate, justifying its selectivity toward this anion. Conversely, in the case of L3, the two facing [9]aneN3 units give rise to a cleft of appropriate dimensions where the small monophosphate anion can be conveniently hosted. Considering nucleotide coordination, L1 is a better receptor for ATP and ADP than L2, thanks to the higher ability of phenanthroline to establish stabilizing π stacking and hydrophobic interactions with the adenine units of the guests.

Binding and Removal of Sulfate, Phosphate, Arsenate, Tetrachloromercurate, and Chromate in Aqueous Solution by Means of an Activated Carbon Functionalized with a Pyrimidine-Based Anion Receptor (HL). Crystal Structures of [H3L(HgCl4)]·H2O and [H3L(HgBr4)]·H2O Showing Anion−π Interactions

Binding of anions of great environmental concern such as SO(4)(2-), PO(4)(3-), AsO(4)(3-), HgCl(4)(2-), and CrO(4)(2-) by the protonated forms of a tren-like (tren = tris(2-aminoethyl)amine) ligand (HL) functionalized with a pyrimidine residue was studied by means of potentiometric measurements and isothermal titration calorimetry (ITC) affording log K, ΔH°, and TΔS° values for the formation of the relevant complexes. The complexes show high to very high stability due to the particular topology and electronic properties of the ligand which is able to use two separated coordination environments to host the anions, the protonated tren site where electrostatic and hydrogen bond interactions are operating, and the pyrimidine ring which may act via anion-π interaction. A contribution of -8.9 ± 0.4 kJ/mol for pyrimidine-anion interaction in water was derived for SO(4)(2-) binding. The crystal structures of [H(3)L(HgCl(4))]·H(2)O (1), [H(3)L(HgBr(4))]·H(2)O (2), and that previously reported for [H(3)L(CdI(4))], clearly show these binding features in the solid state. A hybrid AC-HL material obtained by adsorption of HL on commercial activated carbon (AC) was used to study the removal of these anions from water. AC-HL shows enhanced adsorption capacity toward all the anions studied with respect to AC. This behavior is ascribed to the stronger interaction of anions with the HL function of AC-HL than with the Cπ-H(3)O(+) sites of the unfunctionalized AC.

Polyfunctional Binding of Thymidine 5'-Triphosphate with a Synthetic Polyammonium Receptor Containing Aromatic Groups. Crystal Structure of the Nucleotide-Receptor Adduct

The protonated forms of the new polyfunctional polyamine receptors L, containing two terpyridine units linked together by two diamine spacers, interact with the nucleotide thymidine 5‘-triphosphate (TTP) to form stable adducts in aqueous solution. Both solution studies and the crystal structure of the [(H4L)HTTP]·12H2O adduct show that tight association of the two partners is achieved by the formation of hydrogen bonds and salt bridges involving the ammonium groups of L and TTP phosphate oxygen atoms and multiple interactions of the nucleobase with aliphatic and aromatic groups of the ligand, mimicking the modes of interaction of TTP binding proteins.

Macrocyclic Polyamines Containing Phenanthroline Moieties – Fluorescent Chemosensors for H+ and Zn2+ Ions

The macrocyclic ligands L2 and L3, containing a triethylenetetraamine and a tetraethylenepentaamine moiety linked to the methyl groups of 2,9-dimethyl-1,10-phenanthroline, bind H+ and Zn2+ ions giving rise to modulation of the fluorescence emission intensity. The equilibrium constants and the enthalpy changes for ligand protonation were determined by means of pH-metric and microcalorimetric methods in 0.1 M Me4NCl solutions at 298.1±0.1 K. Also the stability constants of the Zn2+ complexes were determined under the same experimental conditions. L2 forms only mononuclear complexes, while L3 also forms dizinc(II) species. The phenanthroline group has fluorescence emission properties, but interaction with the lone pairs of benzylic nitrogen atoms produces an efficient quenching of the emission. Such a quenching effect can be avoided by deactivation of the benzylic nitrogen atoms by means of protonation or Zn2+ complexation. Hence, L2 and L3 behave as chemosensor for H+ and Zn2+, the photochemical properties of the ligands being modulated by the formation of different protonated and complexed species. In the case of L3, the fluorescence emission is also controlled by the metal to ligand molar ratio, because of the formation of an emissive binuclear complex.

A synthetic hexapeptide designed to resemble a proteinaceous p-loop nest is shown to bind inorganic phosphate

The hexapeptide Ser‐Gly‐Ala‐Gly‐Lys‐Thr has been synthesized and characterized. It was designed as a minimal soluble peptide that would be likely to have the phosphate‐binding properties observed in the P‐loops of proteins that bind the β‐phosphate of GTP or ATP. The β‐phosphate in such proteins is bound by a combination of the side chain ε‐amino group of the lysine residue plus the concavity formed by successive main chain peptide NH groups called a nest, which is favored by the glycines. The hexapeptide is shown to bind HPO42− strongly at neutral pH. The affinities of the various ionized species of phosphate and hexapeptide are analyzed, showing that they increase with pH. It is likely the main chain NH groups of the hexapeptide bind phosphate in much the same way as the corresponding P‐loop atoms bind the phosphate ligand in proteins. Most proteinaceous P‐loops are situated at the N‐termini of α‐helices, and this observation has frequently been considered a key aspect of these binding sites. Such a hexapeptide in isolation seems unlikely to form an α‐helix, an expectation in accord with the CD spectra examined; this suggests that being at the N‐terminus of an α‐helix is not essential for phosphate binding. An unexpected finding about the hexapeptide‐HPO42− complex is that the side chain ε‐amino group of the lysine occurs in its deprotonated form, which appears to bind HPO42− via an N···H‐O‐P hydrogen bond. Proteins 2012.