The crystallographic study of left-handed Z-DNA d(CGCGCG)2 and thermine complexes crystallized at various temperatures and at various concentration of cations.

In crystals of complexes of thermine and d(CGCGCG)2 molecules grown at 4, 10, and 20 degrees C, the numbers of thermine molecules connected to the DNA molecule were dependent on the temperature of the crystallization. Two molecules of thermine and one Mg2+ ion were connected to DNA molecule when thermine and d(CGCGCG)2 were co-crystallized at 4 and at 20 degrees C. When an increased concentration of magnesium and thermine molecules were co-crystallized with d(CGCGCG)2 molecules at 10 degrees C, three Mg2+ ions and only one thermine molecule were bound with a d(CGCGCG)2 molecule. The number of polyamines and of Mg2+ ions connected to DNA was dependent on the atomic values of the polyamine and of the metal ion. The binding of more Mg2+ ions occurred when the atomic value of Mg2+ exceeded that of the corresponding mono- or polyamine, and when the Mg2+ ion concentration was elevated. Furthermore, this study is the first documentation of a naturally occurring polyamine bound to the minor groove of DNA in a crystal structure.

Polyamines stabilize left-handed Z-DNA: using X-ray crystallographic analysis, we have found a new type of polyamine (PA) that stabilizes left-handed Z-DNA.

There are many great reports of polyamine stabilization of the Z-DNA by bridge conformation between neighboring, symmetry-related Z-DNA in the packing of crystals. However, polyamine binding to the minor groove of Z-DNA and stabilizing the Z-DNA structure has been rarely reported. We proved that the synthesized polyamines bind to the minor groove of Z-DNA and stabilize the conformation under various conditions, by X-ray crystallographic study. These polyamines consist of a polyamine nano wire structure. The modes of the polyamine interaction were changed under different conditions. It is the first example that the crystals consisted of metal free structure. This finding provides a basis for clarifying B-Z transition mechanics.

Structures and DNA-binding and cleavage properties of ternary copper(II) complexes of glycine with phenanthroline, bipyridine, and bipyridylamine.

The crystal structures of the series of three complexes, [Cu(Gly)(bpy)Cl].2H2O (1) (Gly=glycine; bpy=2,2'-bipyridine), [Cu(Gly)(phen)Cl]2.7H2O (2) (phen=1,10-phenanthroline), and [Cu(Gly)(bpa)(H2O)Cl] (3) (bpa=2,2'-bipyridylamine) were determined, and the coordination modes of Cu(II) ternary complexes were compared. The central Cu(II) atoms of complexes 1 and 3 have a similar distorted octahedral coordination geometry, while the Cu(II) atom of complex 2 has a distorted square pyramidal coordination. In all complexes, the aromatic heterocyclic compounds bpy, phen, and bpa, behave as a bidentate N,N' ligand, and Gly behaves as a bidentate N,O ligand. DNA-binding properties of the complexes to calf thymus (CT) DNA were studied by using the fluorescence method. Each of the complexes showed binding propensity to CT DNA with the relative order 2>3> or =1. DNA cleavage studies indicate that each of the complexes, especially 2, can cleave plasmid supercoiled pBR322 DNA in the presence of H2O2 and ascorbic acid with cleavage efficiency in the order 2>3 approximately 1. The degradation of the conformation of CT DNA by the complexes was also reflected in the decrease in the intensities of the characteristic CD bands with the relative order 2>3 approximately 1.

catena-Poly[[bis(mu2-4-methylbenzoato-kappa2O:O')disilver(I)(Ag-Ag)]-mu2-di-2-pyridylamine-kappa2N2:N2'] and catena-poly[[(di-2-pyridylamine-kappaN2)(mu2-4-nitrobenzoato-kappa2O:O')disilver(I)(Ag-Ag)]-mu3-4-nitrobenzoato-kappa3O:O':O'].

Both title compounds are polynuclear polymeric complexes with binuclear units. In the former compound, [Ag2(C8H7O2)2(C10H9N3)]n, the two Ag(I) atoms display distorted square-planar coordinations. This compound contains a twofold axis and a crystallographic inversion centre, and di-2-pyridylamine (DPA) ligands crosslink adjacent binuclear units to form infinite polymeric chains. Crystal packing is stabilized by van der Waals interactions and partial pi-pi stacking interactions between the chains. The latter compound, [Ag2(C7H4NO4)2(C10H9N3)]n, contains crystallographic inversion centres and the two Ag(I) atoms exhibit two types of distorted square-pyramidal coordination. Ag-Ag argentophilic interactions and Ag-O crosslinking between adjacent binuclear units contribute to form infinite polymeric chains. Weak pi-pi stacking interactions are observed in the polymer chain. Crystal packing is stabilized by C-H...O hydrogen bonds and by weak pi-pi stacking interactions.

Crystal structures of palladium(II) ternary complexes of 5-x-2-aminobenzoic acid with 1,10-phenanthroline and their interaction with calf thymus DNA (where X=Cl, Br and I).

The crystal structures of a series of three palladium(II) ternary complexes of 5-halogeno-2-aminobenzoic acid (5-X-AB, where X=Cl, Br and I) with 1,10-phenanthroline [Pd(5-Cl-AB)(phen)] (1), [Pd(5-Br-AB)(phen)] (2) and [Pd(5-I-AB)(phen)] (3) have been determined, and their coordination geometries and the crystal architecture characterized. All of the complexes are an isostructure in which each Pd(II) atom has basically similar square planar coordination geometry. The substitute halogen group at 5-position of AB plays an important role in producing the coordination bonds of the carboxylate and amino groups in which the carboxylate O atom and the amino N atom act as the negative monodentate ligand atoms. The coordination bond distances of O-Pd increase in the order 1<2<3, while those of N-Pd decrease in the same order. The binding of the complexes to the calf thymus DNA has also been studied by the fluorescence method. Each of the complexes shows high binding propensity to DNA which can be reflected as the relative order 1<2<3.

(2,2'-Biquinoline-kappa(2)N,N')dichloropalladium(II), -copper(II) and -zinc(II).

In the three title complexes, namely (2,2'-biquinoline-kappa(2)N,N')dichloropalladium(II), [PdCl2(C18H12N2)], (I), and the corresponding copper(II), [CuCl2(C18H12N2)], (II), and zinc(II) complexes, [ZnCl2(C18H12N2)], (III), each metal atom is four-coordinate and bonded by two N atoms of a 2,2'-biquinoline molecule and two Cl atoms. The Pd(II) atom has a distorted cis-square-planar coordination geometry, whereas the Cu(II) and Zn(II) atoms both have a distorted tetrahedral geometry. The dihedral angles between the N-M-N and Cl-M-Cl planes are 14.53 (13), 65.42 (15) and 85.19 (9) degrees for (I), (II) and (III), respectively. The structure of (II) has twofold imposed symmetry.

(Di-2-pyridylamine-kappa2N,N')(naphthalene-2,3-diolato-kappa2O,O')palladium(II) monohydrate and (di-2-pyridylamine-kappa2N,N')(3-oxidonaphthalene-2-carboxylato-kappa2O,O')palladium(II).

In the title complexes, [Pd(C10H6O2)(C10H9N3)].H2O, (I), and [Pd(C11H6O3)(C10H9N3)], (II), the Pd(II) centers have a distorted cis-square-planar geometry. In (I), the Pd(II) atom is coordinated to two N atoms of the di-2-pyridylamine (DPA) ligand and two O atoms of the naphthalene-2,3-diolate (ND) dianion. In (II), the Pd(II) atom is coordinated to two N atoms of the DPA ligand, one carboxylate O atom and one oxide O atom from the 3-oxidonaphthalene-2-carboxylate (NC) ligand. The dihedral angle between the planes of the two pyridine rings of DPA in (I) is 16.20 (12) degrees and that in (II) is 29.45 (10) degrees . In (I), the molecules are linked by N-H...O and O-H...O hydrogen bonds to generate centrosymmetric dimers. In (II), molecules are linked by N-H...O and C-H...O hydrogen bonds to generate spirals.

The development of crystallization and X-ray crystallography method of long stem DNA.

We clarified stabilization mechanism of left-handed Z-DNA by X-ray crystal structure analysis. I was able to achieve it by burying big minor groove of Z-DNA because metal ion and polyamine connected it to minor groove of Z-DNA. On that occasion I understood that an electric charge and length of polyamine gave big influence to a combination brain very much. I succeeded in crystallization of Z-DNA of a long chain, X-ray crystal structure analysis by examining these combination ability.

Stabilization of the left-handed Z-DNA with monoamines and polyamines.

It is known that the crystal structure of d(CG)3 become left-handed Z-DNA under high salt concentration and various polyamines stabilize the Z-DNA structure. We have structurally investigated how polyamines stabilize the Z-DNA by the X-ray crystallographic analysis of d(CG)3-polyamine cocrystals. In this study, we determined the Z-DNA structures with di- to pentavalent polyamines at high resolution. Comparison with the structures revealed that the valence of polyamine determined number of the polyamine(s) and metal ion(s) chelating to the Z-DNA. Furthermore, we succeeded in crystallizing d(CG)3-monoamine (methylamine and ethylamine) complexes.

Cobalt(II), nickel(II) and copper(II) complexes of isoquinoline-3-carboxylate.

The crystal structures of the title complexes, namely trans-bis(isoquinoline-3-carboxylato-kappa2N,O)bis(methanol-kappaO)cobalt(II), [Co(C10H6NO2)2(CH3OH)2], and the corresponding nickel(II) and copper(II) complexes, [Ni(C10H6NO2)2(CH3OH)2] and [Cu(C10H6NO2)2(CH3OH)2], are isomorphous and contain metal ions at centres of inversion. The three compounds have the same distorted octahedral coordination geometry, and each metal ion is bonded by two quinoline N atoms, two carboxylate O atoms and two methanol O atoms. Two isoquinoline-3-carboxylate ligands lie in trans positions, forming the equatorial plane, and the two methanol ligands occupy the axial positions. The complex molecules are linked together by O-H...O hydrogen bonds between the methanol ligands and neighbouring carboxylate groups.

(2,2'-bipyridine-kappa(2)N,N')(2,3-naphthalenediolato-kappa(2)O,O')palladium(II) and (2,2'-biquinoline-kappa(2)N,N')(2,3-naphthalenediolato-kappa(2)O,O')palladium(II).

In the title compounds, [Pd(C(10)H(6)O(2))(C(10)H(8)N(2))], (I), and [Pd(C(10)H(6)O(2))(C(18)H(12)N(2))], (II), each Pd(II) atom has a similar distorted cis-planar four-coordination geometry involving two O atoms of the 2,3-naphthalenediolate dianion and two N atoms of the 2,2'-bipyridine or 2,2'-biquinoline ligand. The overall structure of (I) is essentially planar, but that of (II) is not, as a result of intramolecular overcrowding leading to bowing of the biquinoline ligand.

The X-ray crystallographic study of the conformation of Z-DNA which bound to polyamine for the minor groove at room temperature and low temperature.

We succeeded in x-ray crystal analysis of d(CG)3 with N1-{2-[(2-amino-ethylamino)-ethylamino]-ethyl}-ethane-1,2-diamine complex at three conditions (1: room temperature 2: low temperature 3: highly salt condition). At room temperature two polyamines took extended form and bound to minor groove of d(CG)3, at low temperature two polyamines took U-shape form and lied in minor groove of d(CG)3, at highly salt condition two polyamines took fishhook form and one polyamine lied in upper side of minor groove and the other polyamine lied in down side of minor groove of d(CG)3.

fac-Tris(2-ethyl-4-oxo-4H-pyran-3-olato-kappa2O3,O4)iron(III) and its aluminium(III) analog.

The crystal structures of the title iron(III) and aluminium(III) ethyl maltolate complexes, [Fe(C(7)H(7)O(3))(3)] and [Al(C(7)H(7)O(3))(3)], respectively, are isomorphous. In each case, the three bidentate ligand molecules are bound to the metal atom, forming a distorted octahedral coordination geometry in a fac configuration.

catena-Poly[[[aqua(2-methyl-4-oxo-4H-pyran-3-olato-kappaO3,O4)copper(II)]-mu-chloro] monohydrate].

In the title complex, [Cu(C(6)H(5)O(3))Cl(H(2)O)].H(2)O(n), the Cu(II) atom has a deformed square-pyramidal coordination geometry formed by two O atoms of the maltolate ligand, two bridging Cl atoms and the coordinated water O atom. The Cu atoms are bridged by Cl atoms to form a polymeric chain. The deprotonated hydroxyl and ketone O atoms of the maltolate ligand form a five-membered chelate ring with the Cu atom. Stacking interactions and hydrogen bonds exist in the crystal.

Bis(5-hydroxy-2-hydroxymethyl-4-pyrone-kappa 2O4,O5)bis(2-hydroxymethyl-5-oxido-4-pyrone-kappa 2O4,O5)calcium(II) tetrahydrate.

In the title compound, [Ca(C(6)H(5)O(4))(2)(C(6)H(6)O(4))(2)].4H(2)O, which is a kojic acid-Ca(2+) complex, the Ca atom is on a twofold axis and is octacoordinated by O atoms from four pyrone ligand molecules. The hydroxyl and ketone O atoms of each ligand form a five-membered chelate ring with the Ca atom. The crystal structure is stabilized by partial stacking and O-H.O hydrogen bonds.

A lithium complex of pyridine-2,6-dicarboxylic acid.

The crystal structure of catena-poly[[(6-carboxypyridine-2-carboxylato-kappa3O,N,O')lithium(I)]-mu-aqua-kappa2O:O], [Li(C(7)H(4)NO(4))(H(2)O)](n), contains the Li(+) ion coordinated to two O atoms and the N atom of the 6-carboxypyridine-2-carboxylate ligand, and to two water O atoms, forming a pentavalent coordination geometry. The molecule resides on a mirror plane which contains the Li and N atoms, the para-CH unit, and the O atom of the coordinated water molecule. The O atom of the water molecule is coordinated to two Li atoms, forming an infinite polymeric chain.