Structures and interaction with DNA of ternary palladium(II) complexes: [Pd(Gly)(X)] (Gly=glycine; X=2,2'-bipyridine, 1,10-phenanthroline and 2,2'-bi-pyridylamine).

The structures of the ternary palladium(II) complexes of the formulations [Pd(Gly)(bpy)](+)Cl(-).4H(2)O (Gly=glycine; bpy=2,2'-bipyridine) (1), [Pd(Gly)(phen)](+)Cl(-).4H(2)O (2) (phen=1,10-phenanthroline) and {[Pd(Gly)(bpa)](+)Cl(-)}(2).6H(2)O (3) (bpa=2,2'-bipyridylamine) were determined. All complexes are positively charged and neutralized by the chloride anion located nearby the complexes. The central Pd(II) atoms of the complexes 1, 2 and 3 have a similar distorted square planar coordination geometry, in which each Pd(II) atom is coordinated to two N atoms of the bidentate heterocyclic ligand, and N and O atoms of the bidentate glycine ligand. The interaction of the complexes with calf thymus (CT) DNA was also studied using the fluorescence method. All complexes showed the inhibition of ethidium bromide binding to CT DNA, and the DNA-binding strengths were reflected as the relative order 2>1>3. The remarkable reduction of UV absorption intensity of 2 caused in the presence of DNA suggests the presence of pi-pi stacking interaction between the heterocyclic ring of the phen ligand and nucleobases. The intercalative DNA-binding of 2 is suggested by UV and CD measurements. DNA cleavage studies indicated that the cleavage of the plasmid supercoiled pBR322 DNA in the presence of H(2)O(2) and ascorbic acid could be enhanced by the complexes.

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.

Tetrakis(mu(2)-1,8-naphthyridine)-1:2kappa(4)N:N';3:4kappa(4)N:N'-bis(mu(2)-salicylato)-1:4kappa(2)O:O';2:3kappa(2)O:O'-tetrakis(salicylic acid)-1kappaO,2kappaO,3kappaO,4kappaO-tetrasilver(I)(4 Ag-Ag).

The title complex, [Ag4(C7H5O3)2(C8H6N2)4(C7H6O3)4], lies about an inversion centre and has a unique tetranuclear structure consisting of four Ag(I) atoms bridged by four N atoms from two 1,8-naphthyridine (napy) ligands to form an N:N'-bridge and four O atoms from two salicylate (SA) ligands to form an O:O'-bridge. The Ag atoms have distorted octahedral coordination geometry. The centrosymmetric Ag4 ring has Ag-Ag separations of 2.772 (2) and 3.127 (2) A, and Ag-Ag-Ag angles of 107.70 (4) and 72.30 (4) degrees . All SA hydroxy groups take part in intramolecular O-H...O hydrogen bonding. In the crystal packing, the napy rings are oriented parallel and overlap one another. These pi-pi interactions, together with weak intermolecular C-H...O contacts, stabilize the crystal structure.

(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.

Crystal structures and spectroscopic properties of zinc(II) ternary complexes of vitamin L, H' and their isomer m-aminobenzoic acid with bipyridine.

The crystal structures of the three Zn(II) complexes, [Zn(bpy)(o-AB)2] (1) (bpy=2,2'-bipyridine, o-AB=o-aminobenzoic acid=Vitamin L), [Zn(bpy)(m-AB)Cl]2 (2) (m-AB=m-aminobenzoic acid), [Zn(bpy)(p-AB)Cl]*p-AB*H2O (3) (p-AB=p-aminobenzoic acid=Vitamin H'), have been determined and the basic coordination geometries and architectures organized by hydrogen-bonds and pi-pi interactions also characterized. The substitute amine group at ortho-, meta-, and para-position of AB plays an important role to produce completely different coordination motif of these complexes, further, in all complexes, aromatic amines are not coordinated to Zn(II) atom. While two different types of coordination modes of the carboxylate O atoms are present in these complexes: one mode consists of the usual Zn-O bond lengths (2.009(2)-2.251(2) A) in complex 1, 2 and 3; another consists of a very long Zn-O bond lengths (2.422(2) A) in complex 1. Each of the complexes has the characteristic UV absorption bands around 250-310 nm region, and the intense fluorescence band at near 325 nm.

X-ray structure characterization of palladium(II) ternary complexes of pyridinedicarboxylic and phthalic acid with phenanthroline and bipyridine.

The crystal structures of the series of four ternary complexes, [Pd(phen)(2,6-PDCA)].4H(2)O (1) (phen=1,10-phenanthroline; 2,6-PDCA=2,6-pyridinedicarboxylic acid), [Pd(bpy)(2,3-PDCA)].3H(2)O (2) (bpy=2,2'-bipyridineand; 2,3-PDCA=2,3-pyridinedicarboxylic acid) and [Pd(phen)(PHT)].2.5H(2)O (3) (PHT=o-phthalic acid ) and [Pd(bpy)(PHT)].1.5H(2)O (4), are determined and the coordination modes of palladium(II) ternary complexes are characterized. All complexes take the mononuclear Pd(II) complexes, in which central Pd(II) atom of each complex has a similar distorted square-planar four coordination geometry. In all complexes, the aromatic heterocyclic compounds, phen and bpy, behave as a bidentate N, N' ligand. In the complex 1 and 2, 2,6-PDCA and 2,3-PDCA behave as a bidentate N, O ligand, and in complex 3 and 4, PHT behaves as a bidentate O, O' ligand.

(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.

catena-Poly[[(di-2-pyridylamine)silver(I)]-mu-nicotinato] and catena-poly[[(di-2-pyridylamine)silver(I)]-mu-2,6-dihydroxybenzoato].

In catena-poly[[(di-2-pyridylamine-kappa(2)N,N')silver(I)]-mu-nicotinato-kappa(2)N:O], [Ag(C(6)H(4)NO(2))(C(10)H(9)N(3))](n), the Ag(I) atom is tetracoordinated by two N atoms from the di-2-pyridylamine (BPA) ligand [Ag-N = 2.3785 (18) and 2.3298 (18) angstroms] and by one N atom and one carboxylate O atom from nicotinate ligands [Ag-N = 2.2827 (15) angstroms and Ag-O = 2.3636 (14) angstroms]. Bridging by nicotinate N and O atoms generates a polymeric chain structure, which extends along [100]. The carboxyl O atom not bonded to the Ag atom takes part in an intrachain C-H...O hydrogen bond, further stabilizing the chain. Pairs of chains are linked by N-H...O hydrogen bonds to generate ribbons. There are no pi-pi interactions in this complex. In catena-poly[[(di-2-pyridylamine-kappa(2)N,N')silver(I)]-mu-2,6-dihydroxybenzoato-kappa(2)O(1):O(2)], [Ag(C(7)H(5)O(4))(C(10)H(9)N(3))](n), the Ag(I) atom has a distorted tetrahedral coordination, with three strong bonds to two pyridine N atoms from the BPA ligand [Ag-N = 2.286 (5) and 2.320 (5) angstroms] and to one carboxylate O atom from the 2,6-dihydroxybenzoate ligand [Ag-O = 2.222 (4) angstroms]; the fourth, weaker, Ag-atom coordination is to one of the phenol O atoms [Ag...O = 2.703 (4) angstroms] of an adjacent moiety, and this interaction generates a polymeric chain along [100]. Pairs of chains are linked about inversion centers by N-H...O hydrogen bonds to form ribbons, within which there are pi-pi interactions. The ribbons are linked about inversion centers by pairs of C-H...O hydrogen bonds and additional pi-pi interactions between inversion-related pairs of 2,6-dihydroxybenzoate ligands to generate a three-dimensional network.

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.

(2,2'-Bipyridine-kappa2N,N')(1,1-cyclobutanedicarboxylato-kappa2O,O')palladium(II), (1,1-cyclobutanedicarboxylato-kappa2O,O')(1,10-phenanthroline-kappa2N,N')palladium(II) monohydrate and (1,1-cyclobutanedicarboxylato-kappa2O,O')(1,10-phenanthroline-kappa2N,N')palladium(II) dihydrate.

In the three title compounds, [Pd(C(6)H(6)O(4))(C(10)H(8)N(2))], (I), [Pd(C(6)H(6)O(4))(C(12)H(8)N(2))].H(2)O, (IIa), and [Pd(C(6)H(6)O(4))(C(12)H(8)N(2))].2H(2)O, (IIb), respectively, each Pd(II) atom has a similar distorted cis-planar four-coordination geometry, completed by two O atoms of a bidentate 1,1-cyclobutanedicarboxylate anion and two N atoms of either a 2,2'-bipyridine or a 1,10-phenanthroline 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.