Ternary complexes in solution. 45. Intramolecular aromatic-ring stacking interactions in dependence on the ligand structure, geometry of the coordination sphere of the metal ion, and solvent composition

Skilandat

Metal Ions in Life Sciences

et al. 2012

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Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromaticnitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono-to the di-and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono-or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.

Section: Some Definitions and General Commentsmentioning

confidence: 99%

Section: Some Definitions and General Commentsmentioning

confidence: 99%

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Skilandat

Metal Ions in Life Sciences

et al. 2012

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Bulletin of the Korean Chemical Society

“…This can be understood in terms of the covalent bonding character of Zn(II) bound ternary complexes as opposed to proton bound dimers with a noncovalent bonding character. [4][5][6][7][8][9] In the covalently bound ternary system, given collision energy resulted dominantly in loss of labile H 2 O or NH 3 rather than in that of the noncovalent monomer unit. The observation that internal covalent fragmentations were prevalent over noncovalent monomeric dissociations is consistent with those of previously reported CAD studies on the other transition metal bound complexes.…”

Section: Methodsmentioning

confidence: 99%

“…[3][4][5][6] Intensive investigations have been made on metal-mediated ligand-ligand interactions and have revealed that these interactions can be categorized as hydrophilic, hydrophobic, or electrostatic, depending on their chemical, physical characteristics. [3][4][5][6][7][8][9] Furthermore, some intrinsic properties of ligands are often found to lead to modifications in their metal coordination structures. Although a significant progress has already been made in our understanding of the ES complexes, further advances in our knowledge are now retarded by difficulties arising from the complexity of ES complexes.…”

Section: Introductionmentioning

confidence: 99%

Tandem Mass Spectrometric Evidence for the Involvement of a Lysine Basic Side Chain in the Coordination of Zn(II) Ion within a Zinc-bound Lysine Ternary Complex

2004

We present the tandem mass spectrometry applications carried out to elucidate the coordination structure of Zn(II) bound lysine ternary complexes, (Zn+Lys+Lys−H) + , which is a good model system to represent a simple (metallo)enzyme-substrate complex (ES). In particular, experimental efforts were focused on revealing the involvement of a lysine side chain ε-amino group in the coordination of Zn 2+ divalent ions. MS/MS fragmentation pattern showed that all the oxygen species within a complex fell off in the form of H 2 O in contrast to those of other ternary complexes containing amino acids with simple side chains (4-coordinate geometries, Figure 1a), suggesting that the lysine complexes have different coordination structures from the others. The participation of a lysine basic side chain in the coordination of Zn(II) was experimentally evidenced in MS/MS for Nε-Acetyl-L-Lys Zn(II) complexes with acetyl protection groups as well as in MS/MS for the ternary complexes with one NH 3 loss, (Zn+Lys+Lys−NH 3 −H) + . Detailed structures were predicted using ab initio calculations on (Zn+Lys+Lys−H) + isomers with 4-, 5-, and 6-coordinate structures. A zwitterionic 4-coordinate complex ( Figure 7d) and a 5-coordinate structure with distorted bipyramidal geometry (Figure 7b) are found to be most plausible in terms of energy stability and compatibility with the experimental observations, respectively.

“…Indeed, statistical considerations predict for Δ log K Cu a value of about -0.5 for the coordination of a monodentate ligand to Cu(Arm) 2+ [75]. However, for simple phosph(on)ates Δ log K Cu equals about 0.03 [70,76] Comparing the above with the results listed in column 6 of Table 2 shows that Δ log K Cu has a positive sign and is also larger than expected for all the ternary complexes, indicating that Equilibrium (9a) is shifted towards its right side.…”

Section: Indication For An Increased Stability Of the Mixed Ligand Cumentioning

confidence: 99%

Extent of intramolecular π stacks in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and the anticancer and antivirally active 9-[2-(phosphonomethoxy)ethyl]guanine (PMEG). A comparison with related acyclic nucleotide analogues

et al. 2016

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