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• Crystal structure of a dinuclear Rh2+ complex of theophylline was determined. • The Rh‒Rh core is occupied at either axial-side by theophylline ligands through N9. • Metal bonding not to expected N7 but to N9 is due to the crystal packing effect. • A discrete, cyclic hexameric water cluster intercalates between theophylline rings. • Metal binding sites of theophylline are reviewed in terms of interligand interaction. Reaction of theophylline with [Rh 2 (μ-OAc) 2 (μ-HNOCCF 3) 2 ] gave [Rh 2 (μ-OAc) 2 (μ-HNOCCF 3) 2 (theophylline) 2 ]·6H 2 O (1), whose crystal structure was determined by single-crystal X-ray diffraction. The dirhodium core, where the two different acetato and acetamidato ligands bridging the Rh‒Rh bond are in a trans configuration, is occupied at either axial-side by two theophylline ligands through N(9) with the formation of two kinds of intra-molecular interligand C−H (theophylline)···O hydrogen bonds, one being a bifurcated hydrogen bond between the C(3)-methyl hydrogen as a donor and the acetato and amidato oxygens as acceptors and the other between the C(8) hydrogen and the acetato oxygen. In the crystal lattice, a discrete, hydrogen-bonding, cyclic hexameric water cluster with the flattened chair conformation is sandwiched between theophylline bases, providing the first water hexagon that intercalates between aromatic rings. The participation of the acetamidato NH group in the formation of a hydrogen bond with a water molecule belonging to the water hexagon that governs the crystal packing makes it impossible for the acetamidato ligand to form an intra-molecular hydrogen bond with O(6), causing the failure of the metal bonding to theophylline through N(7). A critical review on metal bonding properties of theophylline observed in so far reported crystal structures is given, emphasizing the significance of intra-molecular interligand interactions (H-bonding, electrostatic repulsion, and steric constraint) as a factor that could affect metal binding sites/modes of theophylline. [ABSTRACT FROM AUTHOR]

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]

Abstract: Reaction between xanthine, tris(2-aminoethyl)amine (tren) and M(ClO4)2 (M=Zn2+, Cd2+, Ni2+ or Cu2+) under alkaline conditions gave five ternary tren–metal ion–xanthine complexes, among which crystal structures of [Zn(tren)(H2xan)]·ClO4 ·H2O (1), [Cd(tren)(H2xan)]·ClO4 ·H2O (2), [Ni(tren)(H2xan)(H2O)]·ClO4 ·H2O (3), and [Cu2{(μ-Hxan)Cu(tren)}2(μ-Hxan)2(H2O)2]·10H2O (4) (H3xan=neutral xanthine) were determined by X-ray diffraction. In the Zn2+ (1) and Cd2+ (2) complexes, which are isostructural to each other, the tren-capped metal ion binds to xanthine through N(7) with the formation of an intramolecular interligand hydrogen bond between the amino nitrogen of tren and O(6) of the base. The Ni2+ complex (3) involves the metal bonding to N(7) of the base with the formation of two intramolecular hydrogen bonds between O(6) of the base and the amino group of tren and the aqua ligand. The tetranuclear Cu2+ complex (4) forms a paddle-wheel type of centrosymmetrical dicopper tetraxanthinate structure, where the two copper ions are bridged by four xanthine ligands through N(3)/N(9) chelation and, in addition, two among the four xanthine ligands are metalated each by the tren-capped copper ion through N(7) with the formation of an intramolecular hydrogen bond between the amino group of tren and O(6) of the base. The significance of intramolecular interligand interaction as a factor that affects site-specific metal bonding is emphasized. A review of metal bonding properties of so far reported xanthine–metal complexes is given. [Copyright &y& Elsevier]

The structure of poly[3-[(4-amino-2-methylpyrimidin-1-ium-5-yl)meth­yl]-5-(2-hydroxy­ethyl)-4-methyl­thia­zolium octa-μ-bromo/chloro­(4.4/3.6)-tricadmate(II)], {(C12H18N4OS)[Cd3 Br4.41Cl3.59]} n consists of hydrogen-bonded thia­mine mol­ecules and polymeric cadmium bromide/chloride anions in an organic–inorganic hybrid fashion. The one-dimensional anion ribbons are formed by edge-sharing octa­hedra and vertex-sharing tetra­hedra. Thia­mine mol­ecules adopting the S conformation are linked to anions via three types of inter­actions, namely an N(amino)—H⋯anion⋯thia­zolium bridging inter­action, an N(pyrimidine)—H⋯anion hydrogen bond and an O(hydr­oxy)—H⋯anion hydrogen bond. [ABSTRACT FROM AUTHOR]

The title compound, 3-[(4-amino-2-methyl­pyrimidin-5-yl)­meth­yl]-5-(2-hydroxy­eth­yl)-4-methyl­thia­zolium tetra­phenyl­borate monohydrate, C12H17N4OS+·C24H20B−·H2O, is a salt in which the thiamine cations are linked by hydrogen bonds into a two-dimensional network having (4,4)-topology. The stacked sheets form channels, which are occupied by the anions; the cations and anions are linked by C—H⋯π(arene) hydrogen bonds. [ABSTRACT FROM AUTHOR]

Treatment of cytosine with tris(2-aminoethyl)amine (tren) and Cu(ClO 4 ) 2 ·6H 2 O under alkaline conditions gave a ternary tren–Cu 2+ –cytosine complex, [{Cu(tren)} 2 (cytosinato)]·(ClO 4 ) 3 ·0.5H 2 O, whose crystal structure was determined by X-ray diffraction. In the structure of the [{Cu(tren)} 2 (cytosinato)] 3+ cation, two tren-capped square-pyramidal Cu 2+ ions bind to a cytosinate anion, one through the deprotonated N(1) of cytosine with the formation of an intra-molecular interligand hydrogen bond between the keto substituent O(2) of the base and the amino group of tren and the other through both the ring nitrogen N(3) and the exocyclic O(2) of the base, forming a four-membered chelate-ring. An overview on metal bonding properties of N(1)-unsubstituted cytosine observed in so far reported crystal structures is given, emphasizing the significance of intra-molecular interligand interaction as a factor that affects metal-binding sites of cytosine. [ABSTRACT FROM AUTHOR]

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]

Summary: The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-d-Ala-d-Ala and acetyl-d-Ala-d-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-d-Ala-d-lactate) were determined at atomic resolutions of 1.80 Å, 1.07 Å, and 0.93 Å, respectively. These structures not only reconfirm the “back-to-back” dimerization of vancomycin monomers and the ligand-binding scheme proposed by previous experiments but also show important structural features of strategies for the generation of new glycopeptide antibiotics. These structural features involve a water-mediated antibiotic–ligand interaction and supramolecular structures such as “side-by-side” arranged dimer-to-dimer structures, in addition to ligand-mediated and “face-to-face” arranged dimer-to-dimer structures. In the diacetyl-Lys-d-Ala-d-lactate complex, the interatomic O⋯O distance between the carbonyl oxygen of the fourth residue of the antibiotic backbone and the ester oxygen of the d-lactate moiety of the ligand is clearly longer than the corresponding N–H⋯O hydrogen-bonding distance observed in the two other complexes due to electrostatic repulsion. In addition, two neighboring hydrogen bonds are concomitantly lengthened. These observations provide, at least in part, a molecular basis for the reduced antibacterial activity of vancomycin toward vancomycin-resistant bacteria with cell-wall precursors terminating in –d-Ala-d-lactate. [Copyright &y& Elsevier]

Abstract: Novel coordination polymers of the type, [(H2en)(ntpMCl2)] n [M=ZnII (1), CdII (2), HgII (3), ntp=3,3′,3″-nitrilotripropionic acid, en=ethylenediamine] have been prepared by the reaction of a tripodal ligand, ntp, and MCl2 in the presence of en. Ntp, which exists as a zwitterion [NH+(CH2CH2COOH)2(CH2CH2COO)−] in aqueous medium, results in a ditopic anion, ntp2−, on successive deprotonation by en. Thus en acts as a cation based template resulting in coordination polymers involving [ntpMCl2]−2 building units, maintained via hydrogen bonding interactions. The compounds have been characterized by elemental analyses, conductivity, IR and 1H NMR spectroscopic studies. Single crystal X-ray analyses of the compound 1 shows a single stranded helicate architecture where the coordination number four around the zinc ion is maintained by two oxygen donors from ntp2− ligands and two chloride anions. Diquaternary ammonium H2en2+ cations are incorporated into the groove of the helical chain, , by forming hydrogen bonds. A fluorescence measurement study on compound 1 reveals a good binding ability to the DNA helix. [Copyright &y& Elsevier]

The structure of poly[3-[(4-amino-2-methylpyrimidin-1-ium-5-yl)meth­yl]-5-(2-hydroxy­ethyl)-4-methyl­thia­zolium octa-μ-bromo/chloro­(4.4/3.6)-tricadmate(II)], {(C12H18N4OS)[Cd3 Br4.41Cl3.59]} n consists of hydrogen-bonded thia­mine mol­ecules and polymeric cadmium bromide/chloride anions in an organic–inorganic hybrid fashion. The one-dimensional anion ribbons are formed by edge-sharing octa­hedra and vertex-sharing tetra­hedra. Thia­mine mol­ecules adopting the S conformation are linked to anions via three types of inter­actions, namely an N(amino)—H⋯anion⋯thia­zolium bridging inter­action, an N(pyrimidine)—H⋯anion hydrogen bond and an O(hydr­oxy)—H⋯anion hydrogen bond. [ABSTRACT FROM AUTHOR]