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Abstract: Metal ions play a key role in nucleic acid structure and activity. The elucidation of factors/rules that govern the binding of metal ions is therefore an essential step for the better understanding of nucleic acid functions. In this review, we deal with stereospecific intra-molecular interligand interactions as such a factor, involving hydrogen-bonding, electrostatic interaction, and steric constraints, especially focusing on their significance as a factor that could affect base-specific metal bonding to adenine and guanine bases in the solid state. [Copyright &y& Elsevier]

The reaction of [Rh2(OAc)4] with adenine, 9-methyladenine, 9-ethylguanine, adenosine, guanosine, deoxyguanosine, or inosine in methanolic aqueous solution at room temperature gave specifically and quantitatively pink complexes of adenine or its derivatives (=L), [Rh2(OAc)4(L)] (the dirhodium-core:L ratio of 1:1). The reaction of [Rh2(HNOCCF3)4] or [Rh2(OAc)2(HNOCCF3)2] with these nucleobases or nucleosides (=L) gave non-specifically pink or red complexes with dirhodium-core:L=1:1 for adenine derivatives while 1:2 for guanine derivatives. Recrystallization of a 9-methyladenine adduct from a nitric acid solution yielded [Rh2(OAc)2(HNOCCF3)2(9-methyladeninium)2]·(NO3)2 (1), whose crystal structure was determined by X-ray diffraction, showing that two N(1)-protonated 9-methyladeninium molecules coordinate to both the axial-positions of a [Rh2(OAc)2(HNOCCF3)2] nucleus through N(7) with the formation of an intramolecular interligand N(6)&z.sbnd;H⋯O(acetato) hydrogen bond. Crystal structures of guanine derivatives, [Rh2(OAc)2(HNOCCF3)2(9-ethylguanine)2]·2MeOH·2H2O (2), [Rh2(HNOCCF3)4(L)2]·3H2O (L=guanosine (3), deoxyguanosine (4), or inosine (5)), and [Rh2(OAc)2(HNOCCF3)2(guanosine)2]·3H2O (6) were determined, showing that the dirhodium core is occupied at either axial-side by two guanine or hypoxanthine moieties through N(7) with the formation of an intramolecular interligand N(amidato)&z.sbnd;H⋯O(6) hydrogen bond. Each of guanosine molecules in 3, 4, and 6 or inosine molecules in 5 adopts the syn, gauche–gauche (or gauche–trans for one molecule in 3), and C(2′)-endo (or C(2′)-endo-C(3′)-exo for one molecule in 4) conformations to form an intramolecular O(5′)&z.sbnd;H⋯N(3) hydrogen bond. The formation of interligand N(6)&z.sbnd;H⋯O hydrogen-bonding associated with the sterically constrained octahedral coordination geometry about the rhodium atom bonded to N(7), as observed in 1, and/or to N(1) of adenine may give a structural basis for the adenine-specific reactivity of [Rh2(OOCR)4], where the carboxylato ligand could function as hydrogen-bonding acceptor only. Similarly, the formation of interligand N&z.sbnd;H⋯O(6) hydrogen-bonding observed in 2–6 suggests that [Rh2(HNHNCR)4] could function as guanine-specific reagents, where the amidinato ligand could function as hydrogen-bonding donor only. The interligand steric constraint due to the octahedral coordination geometry may also explain no reactivity of [Rh2(OOCR)4] toward native B-DNA (right-handed double-stranded structure) but specific bonding to single-stranded and possibly to left-handed double-stranded structures. [Copyright &y& Elsevier]

Abstract: Reaction of 1,4,7,10-tetraazacyclododecane (cyclen) and Cu(ClO4)2·6H2O with nucleobases (adenine, hypoxanthine, xanthine, theophylline, cytosine, or uracil) under alkaline conditions gave four ternary cyclen–metal–nucleobase complexes, [Cu(cyclen)(adeninato)]·ClO4·2H2O (1), [{Cu(cyclen)}2(hypoxanthinato)]·(ClO4)3 (2), [Cu(cyclen)(theophyllinato)]3·(ClO4)3·2H2O (3), and [Cu(cyclen)(xanthinato)]·(0.7ClO4)·(0.3ClO4)·3H2O·(0.5H2O)3 (4), whose crystal structures were determined by X-ray diffraction. In the adenine complex 1, a cyclen-capped square–pyramidal Cu2+ ion binds to an adeninato ligand through N(9) with the formation of an intramolecular interligand hydrogen bond between the secondary amino nitrogen of cyclen and N(3) of the base. In the hypoxanthine complex 2, two cyclen-capped Cu2+ ions bind to a hypoxanthinato ligand, one through N(7) with the formation of an intramolecular N(cyclen)–H···O(6) hydrogen bond and the other through N(9) to form an intramolecular N(cyclen)–H···N(3) hydrogen bond. Similarly, in both the theophylline complex 3 and the xanthine complex 4, each cyclen-capped Cu2+ ion binds to a theophyllinato or xanthinato ligand through N(7) with the formation of an intramolecular N(cyclen)–H···O(6) hydrogen bond. However, unlike in 2, steric constraints between amino group(s) of cyclen and the methyl group at N(3) of theophylline in 3 or the proton attached to N(9) of xanthine in 4 preclude the metal bonding to N(9) in 3 or N(3) in 4. The significance of intramolecular interligand interaction as a factor that affects metal-binding site(s) on nucleobases is emphasized. [Copyright &y& Elsevier]

Abstract: Reaction between nucleobases (adenine, hypoxanthine, cytosine, and uracil), tris(2-aminoethyl)amine (tren) and M(ClO4)2 (M2+ =Zn2+, Cd2+, Ni2+ or Cu2+) under pH 8–9 gave eight ternary tren-metal ion-nucleobase complexes, among which seven crystal structures, [Zn(tren)(adeninato)]·ClO4 (1), [Cd(tren)(adeninato)]·ClO4 (2), [Ni(tren)(adeninato)(ClO4)] (3), [Zn(tren)(hypoxanthinato)]·ClO4 ·H2O (4), [{Cd(tren)}2(hypoxanthinato)]·(ClO4)3 ·0.5 H2O (5), [Ni(tren)(uracilato)(H2O)]·ClO4 ·(0.5H2O)2 (7), and [Cu(tren)(uracilato)]·ClO4 ·0.5H2O (8) were determined by X-ray diffraction. In each of the adenine complexes with Zn2+ (1), Cd2+ (2), and Ni2+ (3), among which 1 and 2 are isostructural to each other, a tren-capped metal ion binds to an adeninato ligand through N(9) with the formation of an intramolecular interligand hydrogen bond between the amino nitrogen of tren and N(3) of the base. In the hypoxanthine complexes 4 and 5, a tren-capped Zn2+ ion in 4 binds to a hypoxanthinato ligand through N(9) with the formation of an intramolecular N(tren)–H⋯N(3) hydrogen bond, while in 5 two tren-capped Cd2+ ions bind to a hypoxanthinato ligand, one through N(7) with the formation of an intramolecular N(tren)–H⋯O(6) hydrogen bond and the other through N(9) to form an intramolecular N(tren)–H⋯N(3) hydrogen bond. In each of the uracil complexes with Ni2+ (7) and Cu2+ (8), a tren-capped metal ion binds to an uracilato ligand through N(1) with the formation of an intracomplex O(aqua)–H⋯O(2) hydrogen bond in 7 or an intramolecular N(tren)–H⋯O(2) hydrogen bond in 8. Tren-capped metal ion-bonded nucleobases act as building blocks for the assembly of supramolecular structures, by versatile hydrogen bonding and/or stacking abilities of nucleobases. The significance of intramolecular interligand interaction as a factor that affects metal-binding site(s) on nucleobases is emphasized. [Copyright &y& Elsevier]