The favored uns-cis geometry in octahedral nickel(II) complexes containing linear tetradentate edda-type ligands forming six-membered rings. Crystal structure of uns-cis-[Ni(1,3-pdda)(H2O)2]

Radanović, Dušan J.; Matović, Vesna Č.; Matović, Zoran D.; Battaglia, L. P.; Pelizzi, Giancarlo; Ponticelli, G.

doi:10.1016/0020-1693(95)04674-x

Cited by 20 publications

(5 citation statements)

References 42 publications

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“…1(b)) and unsymmetrical-cis (unsy-cis), or the optical isomers, Δ and Λ enantiomers, where two glycinato moieties of the edda ligand are distinctly different in their orientation. 9,22,23 The X-ray crystal analysis of [Zn(II)( phen)-(edda)] indicated that the synthesized complex is a racemic mixture of the sy-cis form. 9 The DFT calculations gave the difference in the energy between the sy-cis and unsy-cis forms as 8.61 kJ mol −1 , suggesting that the slow conformational equilibrium between the two forms might cause the broadening of the NMR signals as shown in Fig.…”

Section: Structure Of the Complexesmentioning

confidence: 99%

The DNA binding site specificity and antiproliferative property of ternary Pt(ii) and Zn(ii) complexes of phenanthroline and N,N′-ethylenediaminediacetic acid

et al. 2013

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The binding site specificity of the ternary complexes, [M(II)(phen)(edda)] (M(II) = Pt(2+) and Zn(2+); phen = 1,10-phenanthroline; edda = N,N'-ethylenediaminediacetic acid), for the self-complementary oligonucleotides (ODNs), ds(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12))(2) (ODN1) and ds(C(1)G(2)C(3)G(4)T(5)A(6)T(7)A(8)C(9)G(10)C(11)G(12))(2) (ODN2), was studied by NMR measurements. The results indicated that [Pt(ii)(phen)(edda)] was partially intercalated between C(3)/G(10) and G(4)/C(9) base pairs of ODN1 and ODN2 in the major grooves, whereas [Zn(II)(phen)(edda)] was bound specifically to the TATA region of ODN2 in the minor groove and to the terminal G(2)/C(11) base pair of ODN1 in the major groove. The preference for the TATA sequence over the AATT sequence in the binding of [Zn(phen)(edda)] was attributed to the wider minor groove width of the TATA sequence. The bindings of the complexes to ct-DNA were also studied by UV, CD, and fluorescence spectroscopy. Additionally, the antiproliferative property of [Pt(II)(phen)(edda)] towards MCF7 breast cancer cells and normal MCF10-A cells was compared with that of [Zn(II)(phen)(edda)].

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Section: Structure Of the Complexesmentioning

confidence: 99%

The DNA binding site specificity and antiproliferative property of ternary Pt(ii) and Zn(ii) complexes of phenanthroline and N,N′-ethylenediaminediacetic acid

et al. 2013

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“…The structure was solved by direct-methods [32] and refined by a full-matrix least-squares procedure on F 2 with anisotropic displacement parameters for non-hydrogen atoms, Cand N-bound hydrogen atoms in their calculated positions and a weighting scheme of the form w ¼ 1=½r 2 [32]. The complex molecule was found to crystallize with 3.5 water molecules of solvation; one of these was disordered about a center of inversion and was refined with a 50% occupancy factor.…”

Section: X-ray Crystallographymentioning

confidence: 99%

“…symmetrical-cis (sy-cis) and unsymmetrical-cis (unsycis), where the two glycinato moieties of the edda ligand are distinctly different in their orientation ( Fig. 1) [2]. Additionally, Jahn-Teller distortion can vary the proximity and direction of the hydrogen donor and acceptor groups on the edda ligand with respect to the nucleobases when the phen ligand is intercalated between the adjacent nucleobase pairs.…”

Section: Introductionmentioning

confidence: 98%

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda)

Seng

Ong

Rahman

et al. 2008

Journal of Inorganic Biochemistry

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The binding selectivity of the M(phen)(edda) (M=Cu, Co, Ni, Zn; phen=1,10-phenanthroline, edda=ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(II) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N(4)O(2) octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling.

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“…[14][15][16] While s-cis geometry of the pure [Cu(edda)(H 2 O) 2 ] complex is not yet crystallographically confirmed, the X-ray structure of the s-cis-[Ni(edda)(H 2 O) 2 ] complex was reported by several authors. 18,19 Furthermore, nickel(II) ion surrounded by bis N-hydroxymethyl-edda ligand (abbreviated as OHMeedda) also adopts s-cis geometry 19 while for the Ni-1,3-pdda complex (1,3-pdda stands for 1,3-propanediamine-N,N′-diacetate anion) the uns-cis geometry was found to be dominant one 20 by X-ray analysis. In the case of Ni-eddp (eddp stands for ethylenediamine-N,N′-di-3-propionate ion) the proposed uns-cis geometry accounts for the larger six-membered carboxylate arms being able to encircle nickel(II) in equatorial plane.…”

Section: Introductionmentioning

confidence: 98%

“…In the case of Ni-eddp (eddp stands for ethylenediamine-N,N′-di-3-propionate ion) the proposed uns-cis geometry accounts for the larger six-membered carboxylate arms being able to encircle nickel(II) in equatorial plane. 20 For the edda-type ligands having mixed (five-and six-membered) carboxylate arms, the geometrical isomers differ in the number (0, 1, or 2) of six-membered rings lying in the G (equatorial) plane. The tetradentate ligand dacoda (1,5-diazacyclooctane-N,N′-diacetate ion), due to the steric make-up of its backbone chelate, allows the coordination of only one additional ligand and the square-pyramidal [M(dacoda)(H 2 O)] complex with the ligand being coordinated in the equatorial plane (M = Co(II), Ni(II), Zn(II) or Cu(II)) has been prepared.…”

Section: Introductionmentioning

confidence: 99%

Nickel(ii) in chelate N2O2 environment. DFT approach and in-depth molecular orbital and configurational analysis

et al. 2013

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The O-N-N-O-type tetradentate ligands H2S,S-eddp (H2S,S-eddp stands for S,S-ethylenediamine-N,N'-di-2-propionic acid) and H2edap (H2edap stands for ethylenediamine-N-acetic-N'-3-propionic acid) and the corresponding novel octahedral nickel(II) complexes have been prepared and characterized. N2O2 ligands coordinate to the nickel(II) ion via four donor atoms (two deprotonated carboxylate atoms and two amine nitrogens) affording octahedral geometry in the case of all investigated Ni(II) complexes. A six coordinate, octahedral geometry has been verified crystallographically for the s-cis-[Ni(S,S-eddp)(H2O)2] complex. Structural data correlating similarly chelated Ni(II) complexes have been used to carry out an extensive configuration analysis. Molecular mechanics and Density Functional Theory (DFT) have been used to model the most stable geometric isomer, yielding, at the same time, significant structural and spectroscopic (TDDFT) data. The results from density functional studies have been compared to X-ray data. Natural Bond Orbital (NBO) and Natural Energetic Decomposition Analysis (NEDA) have been done for the [Ni(edda-type)(H2O)(2-n)] and nH2O fragments. Molecular orbital analysis (MPA) is given as well. The infra-red and electronic absorption spectra of the complexes are discussed in comparison to the related complexes of known geometries.

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The favored uns-cis geometry in octahedral nickel(II) complexes containing linear tetradentate edda-type ligands forming six-membered rings. Crystal structure of uns-cis-[Ni(1,3-pdda)(H2O)2]

Cited by 20 publications

References 42 publications

The DNA binding site specificity and antiproliferative property of ternary Pt(ii) and Zn(ii) complexes of phenanthroline and N,N′-ethylenediaminediacetic acid

The DNA binding site specificity and antiproliferative property of ternary Pt(ii) and Zn(ii) complexes of phenanthroline and N,N′-ethylenediaminediacetic acid

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda)

Nickel(ii) in chelate N2O2 environment. DFT approach and in-depth molecular orbital and configurational analysis

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