XAFS study of Ni (II)–aminovinylketone complexes

XAFS study of Ni (II)–aminovinylketone complexes

ARTICLE IN PRESS Radiation Physics and Chemistry 75 (2006) 1905–1908 www.elsevier.com/locate/radphyschem XAFS study of Ni (II)–aminovinylketone comp...

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ARTICLE IN PRESS

Radiation Physics and Chemistry 75 (2006) 1905–1908 www.elsevier.com/locate/radphyschem

XAFS study of Ni (II)–aminovinylketone complexes Galina E. Yalovegaa, Valerii G. Vlasenkob, Ali I. Uraevc, Alexander D. Garnovskiic, Alexander V. Soldatova, a Faculty of Physics, Rostov State University, Sorge str. 5, 344090 Rostov-on-Don, Russia Institute of Physics, Rostov State University, Stachki str. 194, 344090 Rostov-on-Don, Russia c Institute of Physical and Organic Chemistry, Rostov State University, Stachki Ave. 194/2, 344090 Rostov-on-Don, Russia b

Accepted 27 July 2005

Abstract The functional properties of the active sites in a metalloproteins depend on coordination geometry of metal, the number and the nature of coordination ligands. The Ni K-edge XAFS spectra of novel nickel complexes as models for the MeN2O2(S2) active site in metalloproteins were measured and analyzed. Theoretical analysis of the Ni K-edge XANES was performed using FDMNES code based on the finite difference method (FDM) to solve the Schro¨dinger equation beyond muffin-tin approximations and self-consistent full multiple-scattering approach (code FEFF8.2). It was found that the spectrum is almost totally formed by the octahedron of the nearest neighbor atoms around Ni ion in the II (Ni) complex. The III (Ni) complex active center exists in square-planar configuration with shorter distances. r 2006 Elsevier Ltd. All rights reserved. PACS: 61.10.Ht 61.66.Dk Keywords: XAFS; Ni complexes; Local structure

1. Introduction In metalloproteins, many important functional properties of the metallic cores depend on coordination geometry of metal, the number and the nature of coordination ligands. A numerous model compounds of mononuclear copper- and nickel-containing metalloenzymes, such as cytochrom oxidase, azurin, plastocyanin, etc., have been synthesized and reported (Uraev et al., 2000; Fernandez et al., 2000; Pereira et al., 1998). The structure of many metalloproteins has been elucidated from single-crystal X-ray diffraction. In recent years, the synthesis of small-molecule complexes, structural and Corresponding author. Tel.: +7 863 2975 126;

fax: +7 863 2975 120. E-mail address: [email protected] (A.V. Soldatov).

functional mimics of native metalloproteins have become an intensive area of research in chemistry. In this paper, we report the synthesis and XAFS study of novel nickel complexes as a models for the MeN2O2(S2) active site in metalloproteins. The purpose of the present investigation is to clarify the symmetry of nearest environment of Ni ion in II and III Ni complexes.

2. Experiment The ligands 1-phenyl-3-(2-phenylsulfanyl-phenylamino)pent-2-en-1-one C21H17NOS and 1-phenyl-3-(2-phenylsulfanyl-phenylamino)-but-2-en-1-one C22H19NOS were prepared according to the technique described in our

0969-806X/$ - see front matter r 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.radphyschem.2005.07.051

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G.E. Yalovega et al. / Radiation Physics and Chemistry 75 (2006) 1905–1908

previous papers (Uraev et al., 2002). The Ni II and III complexes were synthesized as follows. The corresponding ligand and metal acetate were dissolved in methanol. The reaction mixture was stirred and boiled for 40 min. The solids formed were filtered and purified in methanol. The resulting product was recrystallized from toluene and dried. The Ni K-edge XAFS spectra were measured in transmission using the EXAFS spectrometer with Si (1 1 1) double-crystal monochromator of Synchrotron Radiation Siberian center with the storage ring, operating at the energy beam 2 GeV and current of 80 mA. The intensities of both incident and transmitted X-ray beams were measured with ionization chambers filled with Ar gas. Samples were prepared as sandwich between two layers of Maylar film.

3. Methods of calculation For theoretical analysis of XANES, a self-consistent full multiple-scattering approach—FEFF8.2 code (Rehr, Ankudinov, 2005) was used. The MS approach used in the present investigation has been successfully applied to interpret a large number of XANES spectra for various materials (Durham, 1988; Della Longa et al., 1995) including amorphous alloys (Mansour et al., 2001) and such disordered systems as metalloproteins (Boffi et al., 2003). The algorithm of the scattering wave method was described earlier (Rehr, Ankudinov, 2005). Phase shifts of the photoelectron were calculated in the framework of the self-consistent crystal muffin-tin (MT) potential scheme with 15% overlapping MT spheres. The best agreement with experiment has been achieved for the spectra calculated with Hedin–Lundqvist potential in a presence of a core hole. In the calculation, phase shifts have been included with orbital momentum (l) up to 3 for Ni atoms and up to 2 for O atoms. For the experimental energy resolution, a value of 1.0 eV was used. These factors were treated as contributions to the imaginary part of the self-energy term. We utilized also the FDMNES package (Joly, 2001) which runs within the real space cluster approach and uses the finite difference method (FDM) to solve the Schrodinger equation. Its main advantage is the possibility to have a totally free potential shape, thus getting rid of the MT limitations. We make further a Lorentzian energy-dependent convolution of the spectrum to account for the multielectron and inelastic phenomena occurring in the absorption process. At the Fermi level, the Lorentzian width is due to both the interaction with the core hole and the monochromator resolution. For higher photoelectron energy, between 10 and 40 eV, the onset of plasmons collective interactions increase the Lorentzian width up to 6 eV.

4. Results and discussion Ni-complex II differs from Ni-complex III by replacement of R ¼ H by CH3, which is the reason for the considerable difference in the symmetry of the nearest environment of the active site of Ni (Fig. 1) and as sequent differences of physico-chemical properties of these compounds. Ni-complex II is brown and paramagnetic, while Ni-complex III is green and diamagnetic. It has been assumed that the surroundings of the Ni atoms in these complexes are essentially different. Fourier transforms of the Ni K-edge EXAFS function was calculated by FEFF7 using the atomic coordinates, which were taken from the single-crystal diffraction data for this compound (model RIBA) (Uraev et al., 2002). In order to make clear the information on local geometric surrounding of Ni ion in II, III Ni complexes, the theoretical analysis of the Ni K-edge XANES data was performed. To study possible structure environment of active site of Ni ion in II Ni complex, theoretical XANES have been simulated for model RIBA (Fig. 2).

O Ni/2 R

S

N

R=H (a)

O Ni/2 R

N

S

R=CH3 (b) Fig. 1. Structures of the II (a), III (b) Ni complexes.

ARTICLE IN PRESS G.E. Yalovega et al. / Radiation Physics and Chemistry 75 (2006) 1905–1908

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Table 1 Bonding distances of nearest environment of model molecules Molecule

Tipes of ligands

Bonding distances (A˚)

RIBA

Ni–O1 Ni–O2 Ni–S1 Ni–S2 Ni–N1 Ni–N2

2.02 2.00 2.463 2.472 1.998 2.00

ASALNI

Ni–O1 Ni–O2 Ni–N1 Ni–N2

1.844 1.844 1.905 1.905

ABIPIK

Ni–O1 Ni–O2 Ni–N1 Ni–N2

1.893 1.896 1.902 1.884

MODEL

Ni–O1 Ni–O2 Ni–N1 Ni–N2

1.804 1.823 1.813 1.817

Fig. 2. RIBA molecule from the single-crystal diffraction data (Uraev et al., 2002).

0.10

Absorption (rel.units)

Ni K-edge of Ni complex (II) (FDM) 19 atoms cluster

0.05

0.00 -20 -10 0

Experiment Theory+broad Theory

10 20 30 40 50 60 70 80 90 Energy(eV)

Fig. 3. Comparison of experimental Ni K-edge XANES spectrum with theoretical spectra calculated for Ni-complex II.

Fig. 4. ASALNI molecule from Cambridge Structural Database (CSD).

In Fig. 3, we show the comparison of the experimental Ni K-edge XANES spectrum II Ni complex with the theoretical spectra calculated for the cluster shown in Fig. 2 (selected atoms). Theoretical analysis of the II Ni complex K-edge XANES was performed using the FDMNES code within the cluster, including the 19 atoms. As seen from Fig. 3, the agreement between the experimental and the theoretical XANES spectra obtained for the RIBA structure is good. The distances of the neighboring atoms around the central Ni atom are given in Table 1. It was found that the spectrum is almost totally formed by the nearest neighbor atoms (an octahedron around Ni ion). According to the EXAFS data (Vlasenko et al., 2005), the average value of the Ni–O/N bond lengths for the III Ni complex is shorter than that for the complex II

(R ¼ 1.88 A˚ versus R ¼ 2.05 A˚). This is because of the absence of the sulfur atom coordination and such a short Ni–O/N bond length point on a square-planar configuration of the III (Ni) complex. To support the idea of the square-planar configuration of the III(Ni) complex active center, the theoretical XANES have been simulated for two model compounds: ASALNI (bis(N-allyl-salicylaldiminato)-nickel(II), C20H20N2NiO2) (full view Fig. 4) and ABIPIK (5,15-di-n-butyl-2,3,7,8,12,13,17,18-octaethyl-syn-5,15-dihydroporphyrinato)-nickel(II), C44H62N4Ni) (see Fig. 5) extracted from CSD. One can find exact values of bonding distances of Ni atom to the nearest neighbors in Table 1. For theoretical analysis of XANES, a self-consistent full multiplescattering approach (FEFF8.2) was used. In the case of the ABIPIK molecule, a pair of nitrogen atoms was

ARTICLE IN PRESS G.E. Yalovega et al. / Radiation Physics and Chemistry 75 (2006) 1905–1908

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the III (Ni) complex active center exists in square-planar configuration with shorter distances.

Acknowledgment This work was supported by RFBR (Grant 04-0332366).

References

Fig. 5. ABIPIK molecule from the Cambridge Structural Database (CSD).

40

Ni K-edge of Ni complex (III) (FEFF) A

Absorption(rel.units)

B

30

20

Experiment Model ABIPIK ASALNI

10

0 8250

8300

8350

8400

Energy(eV) Fig. 6. Comparison of experimental Ni K-edge XANES spectrum with theoretical spectra calculated for Ni-complex III.

substituted by oxygen atoms. In Fig. 6 one can see the results of the theoretical calculations of the Ni K-edge XANES for ASALNI and ABIPIK molecules. One can see the shape of XANES spectra for ABIPIK molecule is close, but small differences in the energy position and shape of peak B are present. It has been assumed that Ni–O/N distances are shorter than distances in ABIPIK molecule. Therefore, the model with shorter distances (Table 1) was included in the list of models. The best agreement between theoretical and experimental spectra was obtained for this model. The analysis of these data make it possible to conclude that

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