Protonation of Platinated Adenine Nucleobases. Gas Phase vs Condensed Phase Picture

Šponer, Judit E.; Leszczyński, Jerzy; Glahé, Frank; Lippert, Bernhard; Šponer, Jiřı́

doi:10.1021/ic001276a

Cited by 51 publications

(65 citation statements)

References 68 publications

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“…This feature is readily rationalized on the basis of simple electrostatics, reflecting the mutually antagonistic effects of H þ and M n þ when bonded to a ligand. It is supported by theoretical calculations under gasphase conditions [54], although diminished in condensed phase [55]. For the acidifying effects of [Ru(NH 3 ) 5 ] 3 þ , a qualitative relationship between the interatomic distance between the metal ion and the acidified H-atom in question has been proposed for mononuclear complexes [56].…”

Section: (Oh)]mentioning

confidence: 67%

Ligand‐pK_a Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Lippert

2008

Chemistry & Biodiversity

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Functional and crystallographic analyses of catalytically active RNA molecules ('ribozymes') have revealed a multitude of different routes by which nature accomplishes cleavage reactions of the RNA sugar-phosphate backbone. While there is agreement that these reactions involve general acid-base chemistry, the choice of 'acid' and of 'base' appears to be quite versatile. Among the numerous surprises that have emerged from these studies in recent years is the phenomenon of 'shifted pK(a) values' of nucleobases, hence, the fact that pK(a) values of isolated nucleobases in H(2)O can be shifted in either direction--upward or downward--into the physiological pH range, and that consequently allows these nucleobases to function as 'acids' or 'bases'. Another change in paradigm in recent years relates to the role of divalent metal ions in these catalytic reactions, which points to the possibility of an indirect involvement in the catalytic cycle rather than necessarily to a direct participation, as in the case with the hepatitis delta virus ribozyme. In this review, basic features of nucleobases and/or aqua ligand pK(a) shifts caused by metal coordination and H-bonding are discussed.

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Section: (Oh)]mentioning

confidence: 67%

Ligand‐pK_a Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Lippert

2008

Chemistry & Biodiversity

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“…[12,28] [d] This value refers to deprotonation of the (C6)NH 2 group [29] (see also point viii in Section 2.…”

Section: Acidity Constants Of H 3 a C H T U N G T R E N N U N G (Ado)mentioning

confidence: 99%

“…[13] The reason for this observation is probably connected with the N7,N9 dichotomy for H + binding. [12,28] iii) Replacement of the methyl group by a ribose moiety at the 9-position of adenine (Table 1, entries 2, 5) changes the solvation properties and thus affects the acidity constants and leads to acidification. This observation agrees with those made for guanine, [24] hypoxanthine, [24] and xanthine, [35] and it indicates that nucleosides are better "mimics" of nucleic acids than the nucleobases themselves.…”

Section: ) [E] H 3 a C H T U N G T R E N N U N G (Ado)mentioning

confidence: 99%

Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

Kapinos

Operschall

Larsen

et al. 2011

Chemistry A European J

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Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.

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“…The values [20] for threefold protonated N6′,N6′,N9-trimethyladenine, H 3 (TriMeA) 3+ [26], which have much in common with those of H 3 (9MeA) 3+ , and for protonated adenosine are listed in entries 2 and 5, respectively, of Table 1. Entry 7 contains the values [16,19] for threefold protonated purine [27].…”

Section: Macro Acidity Constants Of Some Protonated Adeninesmentioning

confidence: 99%

Acid—Base Properties of Purine Residues and the Effect of Metal Ions: Quantification of Rare Nucleobase Tautomers

Sigel¹

2005

ChemInform

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Abstract:The macro acidity constants valid for aqueous solutions of several adenine, guanine, and hypoxanthine derivatives are summarized. It is shown how the application of the corresponding constants, e.g., for 7,9-dimethyladenine, allows a quantification of the intrinsic acidic properties of the (N1)H 0/+ and (N7)H + sites via micro acidity constants, and how to use this information for the calculation of the tautomeric ratios regarding the monoprotonated species, that is, N7-N1ؒH versus HؒN7-N1, meaning that in one isomer H + is at the N1 site and in the other at N7. It is further shown that different metal ions coordinated to a given site, e.g., N7, lead to a different extent of acidification, e.g., at (N1)H; the effect decreases in the series Cu 2+ > Ni 2+ > Pt 2+~ Pd 2+ . Moreover, the application of micro acidity constants proves that the acidifications are reciprocal and identical. This means, Pt 2+ coordinated to (N1) -/0 sites in guanine, hypoxanthine, or adenine residues acidifies the (N7)H + unit to the same extent as (N7)-coordinated Pt 2+ acidifies the (N1)H 0/+ site. In other words, an apparently increased basicity of N7 upon Pt 2+ coordination at (N1) -/0 sites disappears if the micro acidity constants of the appropriate isocharged tautomers of the ligand are properly taken into account. There is also evidence that proton-proton interactions are more pronounced than divalent metal ion-proton interactions, and that these in turn are possibly larger than divalent metal ion-metal ion interactions. The indicated quantifications of the acid-base properties are meaningful for nucleic acids including the formation of certain nucleobase tautomers in low concentrations, which could give rise to mutations.

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Protonation of Platinated Adenine Nucleobases. Gas Phase vs Condensed Phase Picture

Cited by 51 publications

References 68 publications

Ligand‐pK_a Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Ligand‐pK_a Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

Acid—Base Properties of Purine Residues and the Effect of Metal Ions: Quantification of Rare Nucleobase Tautomers

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Protonation of Platinated Adenine Nucleobases. Gas Phase vs Condensed Phase Picture

Cited by 51 publications

References 68 publications

Ligand‐pKa Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Ligand‐pKa Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Understanding the Acid–Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

Acid—Base Properties of Purine Residues and the Effect of Metal Ions: Quantification of Rare Nucleobase Tautomers

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Ligand‐pK_a Shifts through Metals: Potential Relevance to Ribozyme Chemistry

Ligand‐pK_a Shifts through Metals: Potential Relevance to Ribozyme Chemistry