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HPMPA is an acyclic nucleoside phosphonate analogue of AMP which displays antiviral properties. Therefore, its acid–base behavior as well as that of related compounds like PMEA, 9-[2-(phosphonomethoxy)ethyl]adenine, are for many reasons (e.g., binding to enzymes, coordination of metal ions) of general interest. HPMPA can accept two protons at the phosphonate and two more at the adenine residue, but not all acidity constants are accessible by potentiometric pH titrations. Therefore, we measured the chemical shifts of the nine non-exchangeable HPMPA protons by 1H NMR in D2O in dependence on pD in the range from 1 to 12. The corresponding results allowed identifying the protonation sites and, transferred to aqueous solution, they gave also the acidity constants. The most basic site is the phosphonate group followed by N1 of adenine. The pKa values increase from ca. −0.27 [–N7(H)+] via 1.27 [–PO(OH)2] and 4.23 [–N1(H)+] to 6.86 [–PO(OH)−]. In the fully protonated species charge repulsion exists between N1(H)+ and N7(H)+; therefore, the affinity of N7 for H+ is not correctly reflected by the measured acidity constant (ca. −0.27). Needed is the intrinsic micro acidity constant which reflects the H+ affinity of N7 under conditions where N1 is unprotonated; we abbreviate this species as +H·N7(HPMPA)N1. The corresponding microconstant is estimated to be pkN7–N1H·N7–N1Image ID:d2nj00543c-t1.gif 3.5; the minor species +H·N7(HPMPA)N1 occurs with an estimated formation degree between about 5 to 20%. The basicity of the adenine nitrogens decreases in the order N1 > N7 > N3.

The bio-relevant metals (and derived compounds) of the Periodic Table of the Elements (PTE) are in the focus. The bulk elements sodium (Na), potassium (K), magnesium (Mg), and calcium (Ca) from the s-block, which are essential for all kingdoms of life, and some of their bio-activities are discussed. The trace elements of the d-block of the PTE as far as they are essential for humans (Mn, Fe, Co, Cu, Zn, Mo) are emphasized, but V, Ni, Cd, and W, which are essential only for some forms of life, are also considered. Chromium is no longer classified as being essential. From the p-block metals only the metalloid (half-metal) selenium (Se) is essential for all forms of life. Two other metalloids, silicon and arsenic, are briefly mentioned, but they have not been proven as being essential for humans. All metals of the PTE and a plethora of their compounds are used in industry and many of them are highly toxic, like lead (Pb), which is discussed as a prime example. Several metals of the PTE, that is, their ions and complexes, are employed in medicine and we discuss the role of lithium, gallium, strontium, technetium, silver, gadolinium (the only f-block element), platinum, and gold.

Acyclic nucleoside phosphonates (ANPs) are of medical relevance and deserve detailed chemical characterization. We focus here on 1-[2-(phosphonomethoxy)ethyl]cytosine (PMEC), (S)-1-[3-hydroxy-2-(ph...

The thionucleoside 2-thiocytidine (C2S) as well as the thiouridines (US) occur in Nature, especially in transfer RNAs, and they also receive attention in diverse fields like nanotechnology and drug research. If (C2)O in cytidine (Cyd) is replaced by (C2)S to give the thio analogue C2S, the release of H+ from (N3)H in H(C2S)+ (pKa = 3.44) is facilitated somewhat [H(Cyd)+; pKa = 4.24], yet, the deprotonation of the (C4)NH2 group is much more affected: the pKa decreases from ca. 16.7 in Cyd to 12.65 in C2S. This is because the amino-thione tautomer dominating in the neutral C2S, transfers into the imino-thioate form, which has the charge largely localized on (C2)S−. As a consequence, the M(C2S)2+ species (M2+ = Zn2+ or Cd2+) transfer very easily into their deprotonated M(C2S − H)+ forms. This reaction is extremely facilitated by M2+coordination at (C2)S− and occurs already at a pH slightly above 3. It is shown that the (C2)S M2+ coordination dominates to more than 99% in both the M(C2S)2+ and the M(C2S − H)+ complexes; their structures, including chelate formation with the participation of N3, are evaluated. In 2-thiouridine (U2S), 4-thiouridine (U4S), and 2,4-dithiouridine (U2S4S), the release of H+ from (N3)H, compared to Urd (pKa = 9.18), is facilitated by ca. 1 to 2 pK units, the charge being largely localized on the (C)S sites; this leads with (U4S − H)− and (U2S4S − H)− to the reduction of Cu(II) to Cu(I), transforming the thiolate into a disulfide. In Cu(U2S − H)+ Cu(II) is stable, most likely due to steric constraints inhibiting disulfide formation. The stability of the M(US − H)+ complexes with Ni2+, Cu2+ or Cd2+ is enhanced by about 1.3 to 2 log units compared to the corresponding uridinate complexes. The properties of the biologically relevant Zn(US − H)+ are expected to be between those with Ni2+ and Cd2+. The relatively high affinity of the (C)S sites for these M2+ is reflected in the 2-thiouridine 5′-monophosphate (U2SMP2−) and 4-thiouridine 5′-monophosphate (U4SMP2−) complexes, M2+ being located to more than 99% at the thiouracil residue and only traces are coordinated at the phosphate group. In the N3-deprotonated Cu[(U2S − H)MP]− species the anti conformer is partly turned into the syn one allowing thus a formation degree of about 60% of the macrochelate formed by (C2)S− and the phosphate group. The corresponding coordination pattern also seems to hold for Cd[(U2S − H)MP]−, though the formation degree of the macrochelate is lower. No macrochelate formation is detected for Ni[(U2S − H)MP]−, as well as for Ni[(U4S − H)MP]− and Cd[(U4S − H)MP]−. The reasons for the indicated coordination patterns are discussed, as well as the biological implications of the summarized results, especially with regard to tRNAs.

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 (ATP4−). 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 (M2+ is Co2+, Ni2+, or Cu2+) 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 (AMP2−), 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 Cu2+ coordinated to phen and the phosphonate group of 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2−) 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.

Acyclic nucleoside phosphonates are of medical relevance and deserve detailed chemical characterization. We focus here on ( S )‐9‐[3‐hydroxy‐2‐(phosphonomethoxy)propyl]adenine (HPMPA) and include for comparison 9‐[2‐(phosphonomethoxy)ethyl]adenine (PMEA), as well as the nucleobase‐free (phosphonomethoxy)ethane (PME) and ( R )‐hydroxy‐2‐(phosphonomethoxy)propane (HPMP). The acidity constants of H 3 (HPMPA) + were determined and compared with those of the related phosph(on)ate derivatives; they are also needed to understand the properties of the metal ion complexes. Given that in vivo nucleotides and their analogues participate in reactions typically as divalent metal ion (M 2+ ) complexes, the stability constants of the M(H;HPMPA) + and M(HPMPA) species with M 2+ = Mg 2+ , Ca 2+ , Sr 2+ , Ba 2+ , Mn 2+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ were measured. Comparisons between the results for HPMPA 2- and the previous data for PMEA 2- , HPMP 2- and PME 2- revealed that for most M(HPMPA) complexes the enhanced stability (the enhancement relative to the stability of a simple phosphonate‐M 2+ coordination), can solely be explained by the formation of 5‐membered chelates involving the ether oxygen. These chelates occur in equilibrium with simple ′open′ phosphonate‐M 2+ species, the phosphonate group being the primary binding site. The only exceptions are the M(HPMPA) complexes of Ni 2+ , Cu 2+ , and Zn 2+ , which show an additional stability enhancement; in these instances not only the indicated 5‐membered chelates are formed, but M 2+ coordinates in addition to N3 of the adenine residue forming a 7‐membered chelate ring. This observation regarding N3 is important because it emphasizes the metal ion affinity of this site (which is often ignored). Note that in the DNA double helix N3 is exposed to the solvent in the minor groove. The stability data for the monoprotonated M(H;HPMPA) + complexes suggest that these carry H + at the phosphonate group whereas M 2+ is partly at the nucleobase and partly also at the phosphonate group. The ratios of these isomers depend on the metal ion involved, e.g., for Cu(H;HPMPA) the ratio of the isomers is about 1:1.

Pt(II) coordination, like of cis -(NH 3 ) 2 Pt(II), affects the acid-base properties of guanosine derivatives. The acidity constants of such complexes are calculated by curve-fitting procedures using published 1 H NMR shift data measured in aqueous solution (D 2 O) in dependence on pH (pD). Comparison of the p K a values of the ligands with those of the Pt(II) complexes reveals the expected behavior for (N7)-platination, i.e., (N1)H sites are acidified due to charge repulsion. These effects of Pt(II) are compared with those of Ni 2+ and Cd 2+ , allowing predictions for the acidification of Zn 2+ . Studied are the cis -(NH 3 ) 2 Pt(II) complexes of inosylyl(3′ → 5′)inosine, guanylyl(3′ → 5′)guanine (GpG) − , its 2′-deoxy relative d(GpG) − , and its phosphorylated derivative d(pGpG) 3− . The Pt(II) effect is mostly rather symmetrical, like with d(CpGpG) 2− , but it can also be quite asymmetrical, like with d(CpCpGpG) 3− or in the cyclohexylamine-substituted Cisplatin complex of d(GpG) − . Potential consequences for base pairing between the platinated guanine and the complementary cytosine are discussed. It is proposed that partial deprotonation of dG under the influence of Pt(II) at physiological pH leads in water to a marked reduction in pairs with intact Watson–Crick hydrogen bonds, thereby adding to the well established thermal destabilization of double-stranded DNA by G,G intrastrand cross-links of Cisplatin.

At the beginning of the last century a newborn in Europe had a life expectancy of about 45 years. Now, approximately 100 years later, this number has increased in the West to more than 80 years [1]. The reasons for this extended life span are manyfold, the more important ones being improved hygiene, progress in medicine, a reduced mortality of mother and child, control of epidemics, and better food provisions [2]. As we all know, this has led to a tremendous growth of the world population: About 1 billion (=10) people inhabited the Earth in 1804; it took nearly 125 years to double this number, by 1974 it was 4 billion, and the estimate for 2025 is 8 billion [1]. However, this story of success has a seamy side: because of the increased life span, cancer and other age-related diseases, especially those connected with neurodegeneration, mainly manifested in the brain, are getting more and more prominent. To this category belong, among others, Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), transmissible spongiform encephalopathy (prion disease; Creutzfeldt–Jakob disease), neurodegeneration with brain iron accumulation (NBIA; formerly Hallervorden–Spatz disease), Friedreich’s ataxia, progressive supranuclear palsy (PSP), and multisystem atrophy (MSA) [3]. The best known of these debilitating illnesses are certainly Alzheimer’s [3] and Parkinson’s [3, 4] diseases. About 29 million people worldwide suffered from Alzheimer’s disease in 2009; this is about 60% of those being affected by dementia. Computer models predict that the number of patients with AD will increase to 106 million by 2050 [1], which means one per 85 persons—even if this number should be off by a factor of 2, one out of 170 persons is still truly frightening! It is an old wisdom that metals are indispensable for life; in fact, several of them, like sodium, potassium, and calcium, are easily discovered in living matter [5]. However, the role of metals and their impact on life remained largely hidden until inorganic chemistry and coordination chemistry experienced a pronounced revival in the middle of the last century. The experimental and theoretical tools created and their application to biochemical problems led to the development of the field or discipline Bioinorganic Chemistry, which was established by 1970. It also became known as Inorganic Biochemistry and more recently as Biological Inorganic Chemistry [3]. At present there is substantial evidence that metal ions play a significant role in the pathogenesis and pathophysiology of neurodegenerative diseases, which reveal themselves mainly in the brain. This is not surprising because the brain utilizes metal ions for a myriad of biochemical reactions. The metal-related disorders are caused (1) by defects in metal ion transport or homeostasis, (2) by toxicological exposure to metals, and (3) they are associated with metalloprotein aggregation and/or misfolding and oxidative reactions [3]. This organizational frame is certainly helpful, yet to assign a given illness to a distinct category is not easy because of our lack in understanding the mechanisms involved in a given disease, though misfolded proteins are often implicated. Of course, toxic metal ions like mercury or cadmium are easily categorized, but with essential metal ions like copper, iron, zinc, or manganese, which may be toxic as well, matters are considerably more difficult and we are only at the brink of understanding the fine line between essentiality and toxicity. There is an urgent need to unravel the A. Sigel H. Sigel (&) Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, 4056 Basel, Switzerland e-mail: Helmut.Sigel@unibas.ch

Lead is widely distributed in the environment; it is known to mankind for thousands of years and its toxicity is nowadays (again) well recognized, though on the molecular level only partly understood. One of the reasons for this shortcoming is that the coordination chemistry of the biologically important lead(II) is complicated due to the various coordination numbers it can adopt (CN = 4 to 10) as well as by the 6s2 electron lone pair which, with CN = 4, can shield one side of the Pb2+ coordination sphere. The chapter focuses on the properties of Pb2+ complexes formed with nucleotides and their constituents and derivatives. Covered are (among others) the complexes formed with hydroxy groups and sugar residues, the interactions with the various nucleobases occurring in nucleic acids, as well as complexes of phosphates. It is expeced that such interactions, next to those like with lipids and proteins, are responsible for the toxic properties of lead. To emphasize the special properties of Pb2+ complexes, these are compared as far as possible with the corresponding properties of the Ca2+, Fe2+, Cu2+, Zn2+, and Cd2+ species. It needs to be mentioned that the hard-soft rule fails with Pb2+. This metal ion forms complexes with ligands offering O donors of a stability comparable to that of Cu2+. In contrast, with aromatic N ligands, like imidazole or N7 sites of purines, complex stability is comparable to that of the corresponding Fe2+ complexes. The properties of Pb2+ towards S donor sites are difficult to generalize: On the one hand Pb2+ forms very stable complexes with nucleoside 5'-O-thiomonophosphates by coordinating to nearly 100% at S in the thiophosphate group; however, on the other hand, once a sulfur atom replaces one of the terminal oxygen atoms in the phosphodiester linkage, macrochelate formation of the phosphate-bound Pb2+ occurs with the O and not the S site. Quite generally, the phosphodiester linkage is a relatively weak binding site, but the affinity increases further to the mono- and then to the di- and triphosphate. The same holds for the corresponding nucleotides, though the Pb2+ affinity had to be estimated via that of the Cu2+ complexes for some of these ligands. Complex stability of the pyrimidine-nucleotides (due to their anti conformation) is solely determined by the coordinating tendency of the phosphate group(s); this also holds for the Pb2+ complex of adenosine 5'-monophosphate. For the other purinenucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Pb2+ with the N7/(C6)O site of, e.g., the guanine residue. The extents of the formation degrees of these chelates are summarized. Unfortunately, information about mixed ligand (ternary) or other higher order comlexes is missing, but still it is hoped that the present overview will help to understand the interaction of Pb2+ with nucleotides and nucleic acids, and especially that it will facilitate further research in this fascinating area.

Lead is widely distributed in the environment; it is known to mankind for thousands of years and its toxicity is nowadays (again) well recognized, though on the molecular level only partly understood. One of the reasons for this shortcoming is that the coordination chemistry of the biologically important lead(II) is complicated due to the various coordination numbers it can adopt (CN = 4 to 10) as well as by the 6s2 electron lone pair which, with CN = 4, can shield one side of the Pb2+ coordination sphere. The chapter focuses on the properties of Pb2+ complexes formed with nucleotides and their constituents and derivatives. Covered are (among others) the complexes formed with hydroxy groups and sugar residues, the interactions with the various nucleobases occurring in nucleic acids, as well as complexes of phosphates. It is expeced that such interactions, next to those like with lipids and proteins, are responsible for the toxic properties of lead. To emphasize the special properties of Pb2+ complexes, these are compared as far as possible with the corresponding properties of the Ca2+, Fe2+, Cu2+, Zn2+, and Cd2+ species. It needs to be mentioned that the hard-soft rule fails with Pb2+. This metal ion forms complexes with ligands offering O donors of a stability comparable to that of Cu2+. In contrast, with aromatic N ligands, like imidazole or N7 sites of purines, complex stability is comparable to that of the corresponding Fe2+ complexes. The properties of Pb2+ towards S donor sites are difficult to generalize: On the one hand Pb2+ forms very stable complexes with nucleoside 5'-O-thiomonophosphates by coordinating to nearly 100% at S in the thiophosphate group; however, on the other hand, once a sulfur atom replaces one of the terminal oxygen atoms in the phosphodiester linkage, macrochelate formation of the phosphate-bound Pb2+ occurs with the O and not the S site. Quite generally, the phosphodiester linkage is a relatively weak binding site, but the affinity increases further to the mono- and then to the di- and triphosphate. The same holds for the corresponding nucleotides, though the Pb2+ affinity had to be estimated via that of the Cu2+ complexes for some of these ligands. Complex stability of the pyrimidine-nucleotides (due to their anti conformation) is solely determined by the coordinating tendency of the phosphate group(s); this also holds for the Pb2+ complex of adenosine 5'-monophosphate. For the other purinenucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Pb2+ with the N7/(C6)O site of, e.g., the guanine residue. The extents of the formation degrees of these chelates are summarized. Unfortunately, information about mixed ligand (ternary) or other higher order comlexes is missing, but still it is hoped that the present overview will help to understand the interaction of Pb2+ with nucleotides and nucleic acids, and especially that it will facilitate further research in this fascinating area.

Volume 17, entitled Lead: Its Effects on Environment and Health of the series Metal Ions in Life Sciences centers on the interrelations between biosystems and lead. The book provides an up-to-date review of the bioinorganic chemistry of this metal and its ions; it covers the biogeochemistry of lead, its use (not only as gasoline additive) and anthropogenic release into the environment, its cycling and speciation in the atmosphere, in waters, soils, and sediments, and also in mammalian organs. The analytical tools to determine and to quantify this toxic element in blood, saliva, urine, hair, etc. are described. The properties of lead(II) complexes formed with amino acids, peptides, proteins (including metallothioneins), nucleobases, nucleotides, nucleic acids, and other ligands of biological relevance are summarized for the solid state and for aqueous solutions as well. All this is important for obtaining a coherent picture on the properties of lead, its effects on plants and toxic actions on mammalian organs. This and more is treated in an authoritative and timely manner in the 16 stimulating chapters of Volume 17, which are written by 36 internationally recognized experts from 13 nations. The impact of this recently again vibrant research area is manifested in nearly 2000 references, over 50 tables and more than 100 illustrations (half in color). Lead: Its Effects on Environment and Health is an essential resource for scientists working in the wide range from material sciences, inorganic biochemistry all the way through to medicine including the clinic ... not forgetting that it also provides excellent information for teaching.

Stability constants of the ternary Cu(Arm)(H;PMEC)(+) and Cu(Arm)(PMEC) complexes were measured by potentiometric pH titrations and compared with those of Cu(Arm)(H;PMEA)(+) and Cu(Arm)(PMEA) {PMEA(2-)} and related species. The basicity of the terminal phosphonate group is similar in PMEC2- and PMEA(2-). Stability-constant comparisons reveal, that in the monoprotonated ternary u(Arm)(H;PMEC)(+) complexes H+ is at the phosphonate group, that the ether oxygen atom of the -CH2-O-CH2-P(O)(2)(-) (OH) residue participates, next to the P(O)(2)(-)(OH) group, in Cu(Arm)(2+) coordination. The Cu(Arm)(PMEC) complexes are considerably more stable than the corresponding Cu(Arm)(R-PO3) species. The stability enhancements are mainly attributed to intramolecular stacks and to the formation of five-membered chelates involving the ether oxygen atom of the -CH2-O-CH2-P(O)(3)(2-) residue of PMEC2-. Analysis of the intramolecular equilibria reveals that ca. 10% of the isomeric ternary complexes exist with Cu(Arm)(2+) solely coordinated to the phosphonate group, ca. 25% as a five-membered chelate involving the ether oxygen, and ca. 65% with an intramolecular pi-pi stack between the pyrimidine moiety of PMEC2- and the rings of Bpy or Phen. It seems feasible that the reduced stacking intensity of PMEC2- and a different hydrogen bonding, leads to a different orientation of the cytosine (compared to adenine) in the active site of the nucleic acid polymerases, resulting in a reduced antiviral activity of PMEC compared to PMEA.

The intrinsic acid-base properties of the hexa-2'-deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1∙G2∙G3∙C4∙C5∙T6)=(HNPP)⁵⁻] have been determined by ¹H NMR shift experiments. The pKa values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single-strand conditions (i.e., 10% D₂O, 47 °C, I=0.1 M, NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G∙G), the two (N3)H⁺ (C∙C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G∙G) and the (N3)H (T) sites. Based on measurements with 2'-deoxynucleosides at 25 °C and 47 °C, they were transferred to pKa values valid in water at 25 °C and I=0.1 M. Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pKa clusters occur, that is those encompassing the pKa values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five-fold protonated H₅(HNPP)(±) , the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4%, respectively. Tautomer distributions reveal pathways for proton-donating as well as for proton-accepting reactions both being expected to be fast and to occur practically at no "cost". The eight pKa values for H₅(HNPP)(±) are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1∙G2∙G3∙C4∙C5∙U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pKa values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.

The acyclic nucleoside phosphonate (ANP2–\ud ) 9-[2-(phosphonomethoxy)ethyl]guanine (PMEG) is\ud anticancer and antivirally active. The acidity constants of the threefold protonated H3(PMEG)+\ud were determined by potentiometric pH titrations (aq. sol.; 25°C; I = 0.1 M, NaNO3). Under the\ud same conditions and by the same method, the stability constants of the binary Cu(H;PMEG)+ and\ud Cu(PMEG) complexes as well as those of the ternary ones containing a heteroaromatic N ligand\ud (Arm), that is, of Cu(Arm)(H;PMEG)+ and Cu(Arm)(PMEG), where Arm = 2,2'-bipyridine\ud (Bpy) or 1,10-phenanthroline (Phen), were measured. The corresponding equilibrium constants,\ud taken from our earlier work for the systems with 9-[2-(phosphonomethoxy)ethyl]adenine\ud (PMEA) and 9-[2-(phosphonomethoxy)ethyl]-2,6-diamino-purine (PMEDAP) as well as those\ud for Cu(PME) and Cu(Arm)(PME), where PME2– = (phosphonomethoxy)ethane =\ud (ethoxymethyl)phosphonate, were used for comparisons. These reveal that in the\ud monoprotonated ternary Cu(Arm)(H;PE)+ complexes, the proton and Cu(Arm)2+ are at the\ud phosphonate group; the ether oxygen of the -CH2-O-CH2-P(O) 2\ud ! (OH) residue also participates to\ud some extent in Cu(Arm)2+ coordination. Furthermore, the coordinated Cu(Arm)2+ forms a bridge\ud with the purine moiety undergoing π-π stacking which is more pronounced with H·PMEDAP–\ud than with H·PMEA–\ud . Most intense is π stack formation (st) with the guanine residue of\ud H·PMEG–\ud ; here the bridged form Cu(Arm)(H·PMEG) st\ud + occurs next to an open (op), unbridged\ud (binary) stack, formulated as Cu(Arm)2+/(H·PMEG) op\ud ! . – The unprotonated and neutral ternary\ud Cu(Arm)(PE) complexes are considerably more stable than the corresponding Cu(Arm)(R-PO3)\ud species, where R-PO3\ud 2! represents a phosph(on)ate ligand with a group R that is unable to\ud participate in any intramolecular interaction. The observed stability enhancements are mainly\ud due to intramolecular stack formation (st) between the aromatic rings of Arm and the purine\ud residue in the Cu(Arm)(PE) complexes and also, to a smaller extent, to the formation of fivemembered\ud chelates involving the ether oxygen of the -CH2-O-CH2-PO 3\ud 2! residue (cl/O) of the\ud PE2– species. The quantitative analysis of the intramolecular equilibria reveals three structurally\ud different Cu(Arm)(PE) isomers; e.g., of Cu(Phen)(PMEG) ca. 1.1% exist as Cu(Phen)(PMEG)op,\ud 3.5% as Cu(Phen)(PMEG)cl/O, and 95% as Cu(Phen)(PMEG)st. Comparison of the various \ud 3\ud formation degrees reveals that within a given Cu(Arm)(PE) series the stacking tendency\ud decreases in the order PMEG2– ≥ PMEDAP2– > PMEA2–\ud . Furthermore, stacking is more\ud pronounced in the acyclic Cu(Arm)(PE) complexes compared with that in the Cu(Arm)(NMP)\ud species, where NMP2– = corresponding parent (2'-deoxy)nucleoside 5'-monophosphate. Here is\ud possibly one of the reasons for the biological activity of the ANPs. One is tempted to speculate\ud that the pronounced stacking tendency of PMEG2–\ud , together with a different H-bonding pattern,\ud leads to enhanced binding in the active site of nucleic acid polymerases, thus being responsible\ud for the pronounced anticancer and antiviral activity of PMEG.

The acidity constants of twofold protonated, antivirally active, acyclic nucleoside phosphonates (ANPs), H2(PE)±, where PE2−=9-[2-(phosphonomethoxy)ethyl]adenine (PMEA2−), 2-amino-9-[2-(phosphonomethoxy)ethyl]purine (PME2AP2−), 2,6-diamino-9-[2-(phosphonomethoxy)ethyl]purine (PMEDAP2−), or 2-amino-6-(dimethylamino)-9-[2-(phosphonomethoxy)ethyl]purine (PME(2A6DMAP)2−), as well as the stability constants of the corresponding ternary Cu(Arm)(H;PE)+ and Cu(Arm)(PE) complexes, where Arm=2,2′-bipyridine (bpy) or 1,10-phenanthroline (phen), are compared. The constants for the systems containing PE2−=PMEDAP2− and PME(2A6DMAP)2− have been determined now by potentiometric pH titrations in aqueous solution at I=0.1m (NaNO3) and 25°; the corresponding results for the other ANPs were taken from our earlier work. The basicity of the terminal phosphonate group is very similar for all the ANP2− species, whereas the addition of a second amino substituent at the pyrimidine ring of the purine moiety significantly increases the basicity of the N(1) site. Detailed stability-constant comparisons reveal that, in the monoprotonated ternary Cu(Arm)(H;PE)+ complexes, the proton is at the phosphonate group, that the ether O-atom of the CH2OCH2P(O)(OH) residue participates, next to the P(O)(OH) group, to some extent in Cu(Arm)2+ coordination, and that ππ stacking between the aromatic rings of Cu(Arm)2+ and the purine moiety is rather important, especially for the H⋅PMEDAP− and H⋅PME(2A6DMAP)− ligands. There are indications that ternary Cu(Arm)2+-bridged stacks as well as unbridged (binary) stacks are formed. The ternary Cu(Arm)(PE) complexes are considerably more stable than the corresponding Cu(Arm)(RPO3) species, where RPO represents a phosph(on)ate ligand with a group R that is unable to participate in any kind of intramolecular interaction within the complexes. The observed stability enhancements are mainly attributed to intramolecular-stack formation in the Cu(Arm)(PE) complexes and also, to a smaller extent, to the formation of five-membered chelates involving the ether O-atom present in the CH2OCH2PO residue of the PE2− species. The quantitative analysis of the intramolecular equilibria involving three structurally different Cu(Arm)(PE) isomers shows that, e.g., ca. 1.5% of the Cu(phen)(PMEDAP) system exist with Cu(phen)2+ solely coordinated to the phosphonate group, 4.5% as a five-membered chelate involving the ether O-atom of the CH2OCH2PO residue, and 94% with an intramolecular ππ stack between the purine moiety of PMEDAP2− and the aromatic rings of phen. Comparison of the various formation degrees of the species formed reveals that, in the Cu(phen)(PE) complexes, intramolecular-stack formation is more pronounced than in the Cu(bpy)(PE) species. Within a given Cu(Arm)2+ series the stacking intensity increases in the order PME2AP2−

The role that the amino group plays in the metal ion (M2+) binding properties of the adenine residue is of great relevance because this residue occurs widely in nature. It is the aim of this review to evaluate this role. We consider first several 9-methylpurine derivatives with amino and methyl substituents at various positions: the data indicate that substituents at C6 inhibit M2+ binding at both, the N1 and N7 sites. To separate these effects we use (i) o-amino(methyl)pyridines as models for the pyrimidine part of the adenine residue, i.e., for N1, and (ii) benzimidazole derivatives regarding the properties of N7. The inhibiting effects of ortho-amino and ortho-methyl groups on N1 of pyridines are identical, which agrees with the fact that such an amino group has no basic properties at all. This is different with 1-methyl-4-aminobenzimidazole (MABI) ( 9-methyl-1,3-dideazaadenine) and 1,4-dimethylbenzimidazole (DMBI) ( 6,9-dimethyl-1,3-dideazapurine) because the amino group in MABI still has some basic properties and thus, its steric inhibition is somewhat smaller than that of the methyl group in DMBI. It is suggested that the methyl group in DMBI mimics the steric effects of (C6)NH2 upon (N7)-M2+ coordination in the adenine residue. The evaluation of the N1 versus N7 dichotomy for 2,9-dimethylpurine, 2-amino-9-methylpurine, and 6-amino-9-methylpurine ( 9-methyladenine) reveals that the (N7)-M2+ isomer dominates. It is further suggested that the (C6)NH2 adenine group may act as a proton donor and the O atom of a coordinated water molecule as acceptor. The metal ion-binding properties of the two acyclic nucleotide analogues 9-[(2-phosphonomethoxy)ethyl]adenine (PMEA) and 9-[(2-phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), which are structural isomers due to the shift of the (C6)NH2 group in PMEA to the C2 site in PME2AP, fit into the indicated coordination patterns. In the monoprotonated species M(H;PMEA)+ and M(H;PME2AP)+ the proton is located at the phosphonate group and M2+ at N7. However, the M(H;PME2AP)+ complexes are considerably more stable than the M(H;PMEA)+ ones: indeed, the steric effect on N1 is the same in both types of complexes, but the one on N7 has disappeared in M(H;PME2AP)+. Furthermore, there is evidence that the (N7)-coordinated M2+ interacts with the P(O)2(OH)− group in an outersphere manner leading to practically identical formation degrees of the macrochelates formed with Mn2+, Co2+, Ni2+, Cu2+ or Zn2+ [on average 65 ± 15% (3σ)]. The coordination chemistry of PMEA2− and PME2AP2− differs for the 3d ions as well, whereas for the alkaline earth ions, which are primarily coordinated (like all other M2+) to the phosphonate group, 5-membered chelates form involving the ether O of the – CH 2 CH 2 – O – CH 2 – P O 3 2 − residue. In contrast, Co2+, Ni2+, and Cu2+ form with PMEA2− a further isomer, which involves next to the ether O also N3; macrochelates involving N7 and the phosphonate-coordinated M2+ are minority species, but for Ni2+ and Cu2+ they occur and formation degrees of all four isomers could be determined. In the M(PME2AP) complexes a N3 interaction practically does not occur; macrochelate formation of the phosphonate-coordinated M2+ with N7, which is the dominating species for Co2+, Ni2+, Cu2+ or Zn2+ is important here. The possible interrelations between M2+ coordination and the antiviral activity of the two acyclic nucleotide analogues, PMEA being especially active, are discussed shortly.

Introduction How Is the Extent of a Weak Interaction Best Quantified? Metal-Ion Complexes with Phosph(on)ate Groups as Primary Binding Sites Extent of the Hydroxyl−M2+ Interaction in Complexes of Hydroxymethylphosphonate Metal-Ion−Glycerol 1-Phosphate Systems: A Decreasing Solvent Polarity Favors Hydroxyl−M2+ Interactions Some Generalizations Regarding Phosph(on)ate Ligands with a Weakly Coordinating Second Site Metal-Ion Complexes with Carboxylate Groups as Primary Binding Sites Extent of Chelate Formation in Complexes of Hydroxyacetate and Related Ligands at I = 0.1 M Construction of the Reference Lines for Several M2+−Carboxylate Systems. Extent of Chelate Formation in Metal-Ion Complexes Formed with Hydroxy Carboxylates and Related Ligands Extent of Chelate Formation in Complexes of Hydroxyacetate-Type Ligands at I = 2 M Effect of Chelate-Ring Enlargement on the Hydroxyl−Metal-Ion Interaction Decreasing Solvent Polarity Favors the Hydroxyl−Metal-Ion Interaction in Complexes of Hydroxyacetate and Related O Ligands But Inhibits Thioether Interactions Metal-Ion Complexes with Amino Groups as Primary Binding Sites Estimation of Straight-Line Parameters for Complexes Formed with RCH2−NH2 Ligands Extent of Hydroxyl Group−Metal-Ion Binding in Complexes of 2-Aminoethanol and Related Ligands Comparison of the Metal-Ion-Binding Properties of 2-Aminoethanol and Triethanolamine Imidazole Residue as a Primary Binding Site in Ligands Containing also a Hydroxyl Group Pyridyl Nitrogen Is an Ideal Primary Metal-Ion-Binding Site for a Hydroxyl−Metal-Ion Interaction Isomeric Quantification of Metal-Ion Binding with Ligands Offering Two Hydroxyl Groups Effect of the Primary Binding Site on the Extent of the Hydroxyl−Metal-Ion Interaction Extent of Hydroxyl−Metal-Ion Interactions in Complexes Having a Bidentate Primary Binding Site Metal-Ion Complexes of Ligands with Two or More Hydroxyl Groups and at Least Four Binding Sites Complexes of the Alkaline EarthIons with Bistris and Some Related Buffers: Reduced Solvent Polarity Favors Metal-Ion−Hydroxyl Group Interactions Complexes of Several 3d and Related Metal Ions with Bistris and Derivatives Quest for Selectivity in Metal-Ion Coordination Involving Hydroxyl Groups General Conclusions

1. The Bioinorganic Chemistry of Cadmium in the Context of Its Toxicity Wolfgang Maret and Jean-Marc Moulis 2. Biogeochemistry of Cadmium and Its Release to the Environment Jay T. Cullen and Maria T. Maldonado 3. Speciation of Cadmium in the Environment Francesco Crea, Claudia Foti, Demetrio Milea, and Silvio Sammartano 4. Determination of Cadmium in Biological Samples Katrin Klotz, Wobbeke Weistenhoefer, and Hans Drexler 5. Imaging and Sensing of Cadmium in Cells Masayasu Taki 6. Use of 113Cd NMR to Probe the Native Metal Binding Sites in Metalloproteins: An Overview Ian M. Armitage Torbjoern Drakenberg and Brian Reilly 7. Solid State Structures of Cadmium Complexes with Relevance for Biological Systems Rosa Carballo, Alfonso Castineiras, Alicia Dominguez-Martin, Isabel Garcia Santos and Juan Niclos-Gutierrez 8. Complex Formation of Cadmium(II) with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids Roland K. O. Sigel, Miriam Skilandat, Astrid Sigel, Bert P. Operschall and Helmut Sigel 9. Cadmium(II) Complexes of Amino Acids and Peptides Imre Sovago and Katalin Varnagy 10. Natural and Artificial Proteins Containing Cadmium Anna F. A. Peacock and Vincent L. Pecoraro 11. Cadmium in Metallothioneins Eva Freisinger and Milan Vasak 12. Cadmium-Accumulating Plants Hendrik Kupper and Barbara Leitenmaier 13. Cadmium Toxicity in Plants Elisa Andresen and Hendrik Kupper 14. Toxicology of Cadmium and Its Damage to Mammalian Organs Frank Thevenod and Wing-Kee Lee 15. Cadmium and Cancer Andrea Hartwig 16. Cadmium in Marine Phytoplankton Yan Xu and Francois M. M. Morel

Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromatic-nitrogen 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.

The acidity constants of twofold protonated, antivirally active, acyclic nucleoside phosphonates (ANPs), H(2)(PE)(±), where PE(2-)=9-[2-(phosphonomethoxy)ethyl]adenine (PMEA(2-)), 2-amino-9-[2-(phosphonomethoxy)ethyl]purine (PME2AP(2-)), 2,6-diamino-9-[2-(phosphonomethoxy)ethyl]purine (PMEDAP(2-)), or 2-amino-6-(dimethylamino)-9-[2-(phosphonomethoxy)ethyl]purine (PME(2A6DMAP)(2-)), as well as the stability constants of the corresponding ternary Cu(Arm)(H;PE)(+) and Cu(Arm)(PE) complexes, where Arm=2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen), are compared. The constants for the systems containing PE(2-)=PMEDAP(2-) and PME(2A6DMAP)(2-) have been determined now by potentiometric pH titrations in aqueous solution at I=0.1M (NaNO(3)) and 25°; the corresponding results for the other ANPs were taken from our earlier work. The basicity of the terminal phosphonate group is very similar for all the ANP(2-) species, whereas the addition of a second amino substituent at the pyrimidine ring of the purine moiety significantly increases the basicity of the N(1) site. Detailed stability-constant comparisons reveal that, in the monoprotonated ternary Cu(Arm)(H;PE)(+) complexes, the proton is at the phosphonate group, that the ether O-atom of the -CH(2)-O-CH(2)-P(O)(2)(-)(OH) residue participates, next to the P(O)(2)(-)(OH) group, to some extent in Cu(Arm)(2+) coordination, and that π-π stacking between the aromatic rings of Cu(Arm)(2+) and the purine moiety is rather important, especially for the H·PMEDAP(-) and H·PME(2A6DMAP)(-) ligands. There are indications that ternary Cu(Arm)(2+)-bridged stacks as well as unbridged (binary) stacks are formed. The ternary Cu(Arm)(PE) complexes are considerably more stable than the corresponding Cu(Arm)(R-PO(3)) species, where R-PO(3)(2-) represents a phosph(on)ate ligand with a group R that is unable to participate in any kind of intramolecular interaction within the complexes. The observed stability enhancements are mainly attributed to intramolecular-stack formation in the Cu(Arm)(PE) complexes and also, to a smaller extent, to the formation of five-membered chelates involving the ether O-atom present in the -CH(2)-O-CH(2)-PO(3)(2-) residue of the PE(2-) species. The quantitative analysis of the intramolecular equilibria involving three structurally different Cu(Arm)(PE) isomers shows that, e.g., ca. 1.5% of the Cu(phen)(PMEDAP) system exist with Cu(phen)(2+) solely coordinated to the phosphonate group, 4.5% as a five-membered chelate involving the ether O-atom of the -CH(2)-O-CH(2)-PO(3)(2-) residue, and 94% with an intramolecular π-π stack between the purine moiety of PMEDAP(2-) and the aromatic rings of phen. Comparison of the various formation degrees of the species formed reveals that, in the Cu(phen)(PE) complexes, intramolecular-stack formation is more pronounced than in the Cu(bpy)(PE) species. Within a given Cu(Arm)(2+) series the stacking intensity increases in the order PME2AP(2-)PMEA(2-)PMEDAP(2-)PME(2A6DMAP)(2-). One could speculate that the reduced stacking intensity of PME2AP(2-), together with a different H-bonding pattern, could well lead to a different orientation of the 2-aminopurine moiety (compared to the adenine residue) in the active site of nucleic acid polymerases and thus be responsible for the reduced antiviral activity of PME2AP compared with that of PMEA and the other ANPs containing a 6-amino substituent.

Interplay between Metal Ions and Nucleic AcidsThe preceding Volume 9, Structural and Catalytic Roles of Metal Ions in RNA , wasto a large part devoted to ribozymes, a vibrant but well defi ned research area. Thepresent volume, though related to the previous one, is of a much wider characterby describing phenomena that are generally due to the interrelations between metalions and nucleic acids, especially DNA. Yet it should be noted that the role of metalion-nucleic acid interactions in medication, tumor diagnosis, and anticancerresearch is not specifi cally considered because these topics were dealt with inVolumes 41 and 42 of our series Metal Ions in Biological Systems . Instead, Volume10 focuses in 12 chapters on modern developments encompassing the wide rangefrom G-quadruplexes via DNAzymes to peptide nucleic acids (PNAs), topics ofrelevance, e.g., for chemistry and nanotechnology, but also for molecular biologyand genetic diagnostics.The volume opens with two general chapters. The fi rst one provides an overviewon metal ion-nucleic acid interactions and their characterization in solution bydescribing the identifi cation of metal ion binding sites with chemical and biochemicalmethods, the application of NMR, etc. It deals with the determination of bindingconstants and the effects of anions and buffers on metal ion binding to nucleic acids.The corresponding interactions as seen in the solid state by crystal structure analysisare the topic of Chapter 2. Though the interactions of metal ions with nucleic acidsand their constituents have attracted much attention over more than fi ve decades, thereview focuses mainly on results obtained during the past 15 years leading to tableswith over 200 entries. This large body of information is classifi ed and discussed.

Department of Chemistry, Inorganic Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland E-mail: Helmut.Sigel@unibas.ch Fax: + +41-61-2671017 Manuscript received 24 May 2011, accepted 25 May 2011 Noncovalent interactions play important roles in modern chemical research encompassing also bio-systems. Among these interactions aromatic-ring stacking is especially pronounced as, next to hydrogen bonding, hydrophobic and ionic interactions, it is crucial for the three-dimensional structure of nucleic acids (RNA, DNA) and proteins (enzymes). We have now measured by 1H-NMR shift experiments the stability of binary stacks formed between purine nucleosides or nucleotides (N) and the "indicator" ligand 1,10-phenanthroline (Phen), and we also reviewed the related literature. Surprisingly, we observe that the stability of the (Phen)(N) ad ducts is largely independent of the type of purine residue involved, including deprotonation, e.g., at (N1)H of a guanine moiety, and also of the location of the phosphate group at the ribosyl ring. This contrasts with the self-stacking tendency which decreases within the series adenosine > guanosine > inosine > cytidine - uridine. Interestingly, the formation of an ionic (+/-) or metal ion (M2+) bridge stabilizes the formation of stacks as observed, e.g., in mixed ligand Cu2+ complexes formed between Phen and adenosine 5'-monophosphate (5'-AMP2-); yet, in these instances the position of the phosphate group at the ribosyl ring affects the stability of the stacks: It decreases in the order 2'-AMP2- > 5'-AMP2- > 3'-AMP2- in the Cu(Phen)(AMP) complexes demonstrating a significant steric discrimination. The stability of stacks also depend~ on the size of the aromatic- ring systems involved; as one would expect, purines stack better than pyrimidines and Phen generally better than 2,2'-bipyridine. Results obtained with various mixed ligand metal ion complexes containing adenosine 5'-triphosphate (ATP4-) and an amino acid anion (Aa-) lead to the conclusion: The recognition of the adenine residue by the amino acid side chain in M(ATP)(Aa)3- complexes decreases in the series tryptophan (indole residue) > histidine (imidazoleresidue) > leucine (isopropyl residue) > alanine (methyl group). This type of selectivity is certainly of relevance foramino acid/protein interactions with nucleotides/nucleic acids. The addition of an organic solvent like 1,4-dioxane reduces the solvent polarity and decreases the stability of binary stacks like (Phen)(ATP)4- dramatically; in contrast, intramolecular stacks, as present in Cu(Phen)(ATP)2-, are much less affected. Because the "effective" dielectric constant or permittivity in the active site cavity of an enzyme or a ribozyme is lower than in bulk water, Nature has here a further tool to achieve selectivity. Here it needs to be noted that the involved changes in free energy (ΔG°) are small; e.g., a formation degree of 20% of an intramolecular stack in a mixed ligand complex corresponds only to about -0.6kJ mol-1 allowing Nature to shift such equilibria easily.