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EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy xxx (2015) xxx–xxx
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EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal _ Yıldırım a, B. Karabulut b,⇑, O. Büyükgüngör c I. a
Department of Radiotherapy, Vocational School of Health Services, Biruni University, Topkapı 34010, Istanbul, Turkey Department of Computer Engineering, Faculty of Engineering, Ondokuz Mayis University, Kurupelit 55139, Samsun, Turkey c Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayis University, Kurupelit 55139, Samsun, Turkey b
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
The magnetic properties of the
[Co(HOr)(na)(H2O)3]CH3OHH2O single crystals is characterized by EPR technique. 2+ The Cu ions enter the host lattice in substitutional position. The site symmetry is slightly tetragonally distorted.
a r t i c l e
i n f o
Article history: Received 23 June 2014 Received in revised form 15 January 2015 Accepted 30 January 2015 Available online xxxx Keywords: EPR Cu2+ ion X-ray Orotate FT-IR
a b s t r a c t We have studied the Cu2+ ion doped orotato(nicotinamid)cobalt(II) complex by using EPR spectroscopy and X-ray diffraction. The single crystal is triclinic with the space group P1. The unit cell dimensions of the crystal are a = 7.2785(4) Å, b = 10.2349(5) Å, c = 12.7372(6) Å, a = 69.297(4)°, b = 74.791(4)° and c = 76.995(4)°, with Z = 2. We analyzed the EPR spectra of both single crystal and powder of the complex at room temperature. EPR analysis indicates the presence of only one Cu2+ site. We obtained the spin Hamiltonian parameters from the single crystal data for the complex. The spin Hamiltonian parameters are gx = 2.032, gy = 2.116, gz = 2.319, Ax = 28 G, Ay = 66 G, Az = 126 G. These data indicate that the symmetry of paramagnetic center is rhombic. We constructed the ground state wave function of the Cu2+ ion. Ó 2015 Elsevier B.V. All rights reserved.
Introduction In biological systems, orotic acid (1,2,3,6-tetrahydro-2,6-dioxo4-pyrimidine carboxylic acid, 6-carboxyuracil, vitamin B13, H3Or) has a great importance. Many living organisms have it in their cells and body fluids [1–3]. Orotic acid has multidentate functionality in transition metal complexes and play an important role in bioinorganic chemistry [4]. Metal orotates find wide applications in medicine [5]. Some researchers have screened platinum, palladium and nickel orotates with various substituents as therapeutic agents for cancer [6]. Zinc(II) and cobalt(II) orotates have shown antimicrobial ⇑ Corresponding author. Tel.: +90 3623121919 1085; fax: +90 3624576081. E-mail address: [email protected] (B. Karabulut).
activity [7]. Orotic acid is also an organic building block in coordination chemistry [6,8]. It coordinates to metal ions as a bidentate ligand through both the N atom of the pyrimidine ring and the O atom of the carboxyl group. Examples can be found in the crystal structures of Co(II)–orotate complexes with water, ethylenediamine [9], nicotinamide [10] or di-2-pyridylamine [11]. The orotate ligand acts as a bridging bidentate ligand in the polymeric complex [Co(HOr)(H2O)3]n [4,11,12]. It acts as a monodentate ligand through the carboxylate O atom in the complex [Co(H2Or)2(H2O)4]H2O [13]. It also acts as a counter-ion in the complex [Co(H2O)2(phen)2] (H2Or)2 (phen = 1,10-phenanthroline) [14]. In this paper, we examined the structure of [Co(HOr)(na) (H2O)3]CH3OHH2O complex by using X-ray diffraction and IR spectroscopy. We also determined the magnetic properties of
http://dx.doi.org/10.1016/j.saa.2015.01.100 1386-1425/Ó 2015 Elsevier B.V. All rights reserved.
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
_ Yıldırım et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy xxx (2015) xxx–xxx I.
2
Cu2+ ion doped complex by electron paramagnetic resonance (EPR) spectroscopy. We can consider a transition metal ion as a probe and use it to determine the environmental symmetry of the complexes in host lattices by EPR technique [15–18].
perpendicular axes a⁄, b and c⁄ at 10° steps. The g-value was obtained by comparison with DPPH (diphenylpicrylhydrazyl) of g = 2.0036. We measured the FT-IR spectra in the 4000-400 cm1 region with a Bruker Vertex 80V FT-IR spectrometer using KBr pellets.
Experimental
Results and discussion
Preparation of complex
Crystal structure of complex
Synthesis of [Co(HOr)(na)(H2O)3]CH3OHH2O [(HOr):C5H2N2O4, [(na):C6H6N2O] is as given in Scheme 1. A solution of orotic acid monohydrate (0.348 g, 2 mmol) was dropped into a stirred solution of NH3 (0.034 g, 2 mmol) and nicotinamid (0.489 g, 4 mmol) and Co(NH3)26H2O (0.582 g, 2 mmol) in mixture of water/MeOH at ambient temperature. The dark red crystals of title complex suitable for X-ray analyses were collected. To dope [Co(HOr) (na)(H2O)3]CH3OHH2O complex with Cu2+ impurities, small amount of CuCl22H2O (0.05% by wt) was added to saturated aqueous solution of [Co(HOr)(na)(H2O)3]CH3OHH2O and left for slow evaporation at ambient temperature. After 3 weeks, we selected well-developed single crystals of suitable size for EPR study.
The complex is in the space group P1 with 2 molecules in the unit cell. Fig. 1 shows an ORTEP-3 [21] view of the complex. The Co(II) cation coordinates to three aqua, one orotic acid (HOr) and one nicotinamide (na) ligand. The complex has a distorted octahedral geometry. Solvent molecules of water and methanol crystallize in the asymmetric unit. The na ligand acts as a monodentate via the pyridine N atom while the HOr ligand acts as a bidentate N, O-chelator. The equatorial plane of the octahedron is formed by three water molecules (O6, O7, and O8) and O3 atom of HOr ligand. The axial positions in the octahedron are occupied by the pyridine N2 atom of the na ligand and heterocyclic N3 atom of HOr ligand. The orotic acid forms an essentially planar five-membered chelate ring (Co1/O3/C7/C8/N3), the maximum deviation from the plane being 0.0612(17) Å for atom C7. As can be seen from the trans angles, which vary from 171.75(8)° to 177.70(8)°, and the cis angles, which vary from 78.94(8)° to 96.72(8)°, the coordination octahedron around the Co(II) ion can be visualized as being distorted. In the complex, the Co–O and Co–N bond distances [Co1–O3 = 2.111(2), Co1–O6 = 2.146(2), Co1–O7 = 2.096(2), Co1–O8 = 2.129(2), Co1–N2 = 2.196(2) and Co1–N3 = 2.085(2) Å] are similar to the literature values [10,12,22]. Selected bond distances and angles are listed in Table 2. Examination of the structure with PLATON [23] shows that the crystal structure contains two intramolecular and thirteen intermolecular hydrogen bonds of types O–H O, C–H O, N–H O and C–H N, which stabilize the structure. The detailed geometry of the intra- and intermolecular interactions (including symmetry codes) are collected in Table 3.
X-ray, EPR, FT-IR analyses We performed X-ray data for single crystal on a STOE IPDS II image plate detector using Mo Ka radiation (k = 0.71073 Å) at 296 K. We solved the structure by direct methods using SHELXS13 [19]. All non-hydrogen atoms were refined anisotropically by the full matrix least squares procedure based on F2 using SHELXL13 [19]. Data collection: STOE X-AREA [20]. Cell refinement: STOE X-AREA [20]. Data reduction: STOE X-RED [20]. We give the details of crystal data, data collection and refinement parameters in Table 1. Molecular diagrams were obtained using ORTEP-3 [21]. We recorded EPR spectra on a Varian E-109C EPR spectrometer operating at X-band frequencies, having a 100 kHz field modulation at room temperature. We performed the measurement of EPR spectra by rotating the single crystal about the three mutually
O O HN
NH
NH2 O
O
H2O
Co(NO3)2 6H2O
NH 3 N
O H N
O
H2O
OH2
O
N
Co N
O
OH2
O
O
CH3OH H 2O
NH2
Scheme 1. The formation and structure of [Co(HOr)(na)(H2O)3]CH3OHH2O.
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
_ Yıldırım et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy xxx (2015) xxx–xxx I. Table 1 Details of crystal data, data collection and refinement parameters for title complex. Color/shape
Dark red/block
Chemical formula Formula weight Temperature (K) Wavelength (Å) Diffractometer/measurement method Crystal system Space group
[Co(HOr)(na)(H2O)3]CH3OHH2O 439.25 296 0.71073 Mo Ka STOE IPDS II/rotation (x scan)
Unit cell parameters a, b, c (Å) a, b, c (°) Volume (Å3) Z Dcal. (g/cm3) l (mm1) F000 Crystal size (mm3) h Range for data correction (°) Index ranges Measured reflections Independent reflections Observed reflections [I > 2r(I)] Absorption correction Tmax., Tmin. Rint Refinement method Data/restraints/parameters Goodness-of-fit on F2 R indices [I > 2r(I)] R indices (all data) Dqmax., Dqmin. (e/Å3)
Triclinic P1 7.2785(4), 10.2349(5), 12.7372(6) 69.297(4), 74.791(4), 76.995(4) 847.25(8) 2 1.722 1.077 454 0.51 0.40 0.28 2.150–26.893 9 6 h 6 9; 12 6 k 6 13; 16 6 l 6 16 13298 3609 3399 Integration (X-RED32) 0.7459, 0.6631 0.0933 Full-matrix least-squares on F2 3609/21/276 1.076 R1 = 0.0586, wR2 = 0.1442 R1 = 0.0611, wR2 = 0.1460 1.182, 0.976
3
EPR study We recorded the EPR spectra of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal between 0° and 180° at 10° steps by rotating the crystal in c⁄a⁄, bc⁄ and a⁄b planes at room temperature. The a⁄ axis is perpendicular to both b and c⁄ axes. Fig. 2 shows the EPR spectra of the complex when the magnetic field is in a⁄b plane making 10° and 120° angles with the b axis. In Fig. 2, the EPR spectra consist of four lines, which is a characteristic of Cu(II) ion with nuclear spin 3/2. We couldn’t resolve clearly the hyperfine lines of 63Cu2+ and 65Cu2+ nuclei at all orientations, because the line width is broad. Fig. 3 shows the angular variation of g2 in three planes. The plotting shows a single set of four hyperfine lines in all planes. This is consistent with the triclinic symmetry of the complex. We can say that the Cu2+ ions replace Co2+ ions in the lattice, since the ionic radius of Co2+ (82 pm) is large enough for the substitution of Cu2+ (72 pm). The spectra were resolved by fitting each line to the expression: 2
g 2k ðhÞ ¼ g 2ii cos2 h þ g 2jj sin h þ 2g 2ij sin h cos h
ð1Þ
where i, j, k = x,y,z are cyclic coordinates and h is the rotation angle in the related plane. g 2ii , g 2jj and g 2ij correspond to the g tensor elements, which can be found after fitting procedure [24]. We can fit the spectrum to the rhombic spin Hamiltonian having only electronic Zeeman and hyperfine interactions as follows:
H ¼ He þ HHF þ HSO
ð2Þ
We ignored the nuclear Zeeman and quadrupole interactions due to their small contributions. To find g and A values, we used an iterative numerical technique [25]. We found that both g (gz > gx > gy) and hyperfine (Az > Ay > Ax) splitting values of the complex suit the rhombic symmetry. The results are given in Table 4.
Fig. 1. The molecular structure of [Co(HOr)(na)(H2O)3]CH3OHH2O shown with 30% probability displacement ellipsoids and illustrating the atom-numbering scheme. H atoms are shown as small spheres of arbitrary radii.
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
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4
Table 2 Selected bond lengths (Å) and bond angles (°) for title complex. Bond lengths (Å) Co1–N3 Co1–O7 Co1–O3
2.085(2) 2.096(2) 2.111(2)
Co1–N2 Co1–O8 Co1–O6
2.126(2) 2.129(2) 2.146(2)
Bond angles (°) N3–Co1–O7 N3–Co1–O3 O7–Co1–O3 N3–Co1–N2 O7–Co1–N2 O3–Co1–N2 N3–Co1–O8 O7–Co1–O8
92.97(9) 78.94(8) 89.98(9) 174.81(8) 89.84(9) 96.72(8) 93.28(9) 87.66(9)
O3–Co1–O8 N2–Co1–O8 N3–Co1–O6 O7–Co1–O6 O3–Co1–O6 N2–Co1–O6 O8–Co1–O6
171.75(8) 91.18(9) 89.21(9) 177.70(8) 91.13(8) 88.03(9) 91.52(9)
Table 3 Hydrogen-bond parameters (Å, °). D–H A
D–H (Å)
H A (Å)
D A (Å)
D–H A (°)
O8–H1O8 O4 C5–H5 O8 O6–H1O6 O9 N4–H4 N O1i N1–H2N1 O6ii N1–H1N1 O5iii O7–H2O7 O9iv O7–H1O7 O2v O8–H2O8 O1vi O6–H2O6 O3ii O9–H2O9 O10vii C12–H12C N4viii O9–H1O9 O10 O10–H10 O9 O10–H10 O4
0.82(2) 0.93 0.81(2) 0.86 0.86 0.86 0.81(2) 0.84(2) 0.82(2) 0.81(2) 0.81(2) 0.96 0.88(2) 0.82 0.82
1.91(3) 2.52 1.90(2) 1.95 2.32 2.10 1.98(2) 1.84(2) 2.14(2) 2.00(2) 1.85(2) 2.52 2.36(3) 2.51 2.34
2.648(3) 3.074(4) 2.703(4) 2.812(4) 3.179(3) 2.955(4) 2.783(4) 2.659(3) 2.934(3) 2.784(3) 2.610(8) 3.284(10) 2.956(10) 2.956(10) 2.778(7)
150(5) 119 176(4) 176 172 171 171(6) 167(4) 165(6) 162(5) 156(5) 137 126(2) 116 114
Symmetry codes: ix, y 1, z + 1; iix, y, z; iiix, y + 1, z 1; y, z; vix, y + 1, z; viix1, y, z + 1; viiix1, y, z.
iv
x + 1, y, z; vx + 1,
Fig. 2b. (b) EPR spectrum of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal when the magnetic field is in the a⁄b-plane and 120° away from the b-axis.
In an octahedral crystal field, the energy levels of d orbitals of an ion split into a doublet (eg) and a triplet (t2g) symmetry states. A distorted octahedral field removes the degeneracy of the energy levels of eg (dx2 y2 and d3z2 r2 ) orbitals. When the site symmetry is tetragonal the ground state is either (dx2 y2 or d3z2 r2 ) [26]. When the site symmetry is rhombic or lower the ground state is an admixture of these two orbitals. The Hamiltonian (Eq. (2)) can be solved for rhombic environment giving equalities for principal hyperfine splitting constants [27]:
pffiffi 3 1 3aþpffiffi3b j þ 27 a0 ða2 b2 Þ þ ðg x g e Þ 14 g Þ ðg y e a 3b 5 Ax ¼ P 4 pffiffi pffiffi 0 þ 143ab ðg z g e Þ 4 37a ab 2
ð3aÞ pffiffi 3 1 3aþpffiffi3b j þ 27 a0 ða2 b2 Þ þ ðg y g e Þ 14 g Þ ðg x e a 3b 5 Ay ¼ P 4 pffiffi pffiffi 0 þ 143ab ðg z g e Þ 4 37a ab 2
ð3bÞ 2
3 pffiffi 1 3aþpffiffi3b j þ 27 a0 ða2 b2 Þ þ ðg z g e Þ 14 g Þ ðg x e a 3b 6 7 pffiffi Az ¼ P 4 5 1 3aþpffiffi3b þ 14 g Þ ðg y e a 3b ð3cÞ 0
These equations can be solved for a , j, a and b and the ground state wave function of metal ion can be constructed as follows: Fig. 2a. (a) EPR spectrum of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal when the magnetic field is in the a⁄b-plane and 10° away from the b-axis.
w ¼ a0 ½ajx2 y2 i þ bj3z2 r2 i
We also recorded the X-band EPR powder spectrum of the complex at room temperature as in Fig. 4. We obtained the principal values of g and A tensors for the powder spectrum as follows: gx = 2.109, gy = 2.030, gz = 2.310, Ax = 33 G, Ay = 59 G, Az = 121 G. So, we can easily say that the symmetry of paramagnetic center is rhombic.
where j is the core polarization constant, a0 is the covalency parameter and its square is the probability of finding the electron in the d orbitals of the metal, P is dipolar hyperfine parameter for metal ion [28,29]. The parameters, a and b are mixing coefficients for dx2 y2 and d3z2 r2 orbital. The normalization condition for the mixing coefficients a and b is:
ð4Þ
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
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Fig. 3. Angular variations of the EPR spectra of Cu2+ ion doped title complex.
Table 4 Principal g and hyperfine (A) values and their direction cosines of Cu2+ doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal (Dg = ±0.0005, DA = ±0.5 G). g
gx = 2.116 gy = 2.032 gz = 2.319
Direction cosines
A (G)
a⁄
b
c⁄
0.490 0.862 0.479
0.726 0.321 0.608
0.483 0.393 0.783
Direction cosines
Ax = 28 Ay = 66 Az = 126
a2 þ b2 ¼ 1
ð5Þ 2+
We constructed the ground state wave function of the Cu in the complex as:
ion
ð6Þ
a⁄
b
c⁄
w ¼ ð0:907Þ1=2 ½0:979jx2 y2 i þ 0:203j3z2 r 2 i
0.636 0.760 0.142
0.675 0.454 0.581
0.377 0.464 0.801
From the result, we can say that the unpaired electron spends most of its time on the dx2 y2 orbital of Cu2+ ion. We compared the ground state wave function parameters of Cu2+ in different lattices as given in Table 5.
Fig. 4. EPR spectrum of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O powder at room temperature.
Table 5 Comparison of ground state wave function parameters for Cu2+ in different lattices. Lattice
Site
[Co(HOr)(na)(H2O)3]CH3OHH2O Powder [Co(dmp)(dpc)]0.76H2O [Co(mein)2(H2O)4](sac)2
[Co(ein)2(H2O)4](sac)2
I II Powder I II Powder
a0 2
a
b
j
Refs.
0.907 0.860 0.789 0.813 0.807 0.781 0.899 0.904 0.890
0.979 0.978 0.864 0.935 0.949 0.954 0.987 0.982 0.985
0.203 0.207 0.502 0.355 0.316 0.299 0.185 0.189 0.167
0.273 0.287 0.190 0.280 0.268 0.281 0.302 0.300 0.301
This work [30] [31]
[32]
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
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Fig. 5. FT-IR spectrum of [Co(HOr)(na)(H2O)3]CH3OHH2O complex.
FT-IR study
Acknowledgements
Fig. 5 shows the FT-IR spectra of the complex. In the complex, the stretching modes of the free water and coordinated water appeared at 3493 and 3389 cm1, respectively. We observed the m(N–H) stretching vibration at 3153 cm1. The two bands at 1690 and 1642 cm1 correspond to the m(C@O) and m(C@C) stretching modes of the orotato and nicotinamide ligands. The medium intensity band at 1483 cm1 can be attributed to the m(C–N) vibration in the ring of the orotic acid. This frequency is higher than that of the stretching vibration of single C–N bond [9] and disappearance of the band at 1431 cm1 in free orotic acid [10] suggests the deprotonation of the N3 atom and coordination to Co(II) ion. In the title complex, the orotato ligand is coordinated to the Co(II) ion in bidentate form via the N3 atom from the pyrimidine ring and the carboxylic O3 atom. Pyridine ring vibrations of free nicotinamide at 1592 cm1 [10] shift to higher wavenumbers in the spectra of the complex due to coordination of the pyridine N2 atom.
We are grateful to Ondokuz Mayis University – Turkey for supporting our work by the following project number: PYO.FEN.1904.10.18. References [1] [2] [3] [4] [5] [6] [7] [8] [9]
[10]
Conclusions
[11] [12]
We synthesized the title complex and determined its crystal structure and EPR parameters at room temperature. The crystallographic results indicate that the Co(II) cation coordinates to three water molecules, one orotic acid and one nicotinamide ligand and has a slightly distorted octahedral geometry. EPR study of the Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O complex shows that the Cu2+ ions give a single set of four hyperfine lines in all three planes. EPR study also indicates that the paramagnetic centers have rhombic symmetry g and A values. The ground state of the unpaired electrons in the complex is predominantly dx2 y2 and the unpaired electrons spend most of their time in this orbital.
Supplementary material CCDC 958811 contains the supplementary crystallographic data for this paper. Copies of the data can be obtained, free of change, on application to CCDC, 12 Union Road, Cambridge, CB12 1EZ, UK, fax: +44 1223 366 033, email: [email protected] or on the web: http://www.ccdc.cam.ac.uk.
[13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32]
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_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
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Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy journal homepage: www.elsevier.com/locate/saa
EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal _ Yıldırım a, B. Karabulut b,⇑, O. Büyükgüngör c I. a
Department of Radiotherapy, Vocational School of Health Services, Biruni University, Topkapı 34010, Istanbul, Turkey Department of Computer Engineering, Faculty of Engineering, Ondokuz Mayis University, Kurupelit 55139, Samsun, Turkey c Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayis University, Kurupelit 55139, Samsun, Turkey b
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
The magnetic properties of the
[Co(HOr)(na)(H2O)3]CH3OHH2O single crystals is characterized by EPR technique. 2+ The Cu ions enter the host lattice in substitutional position. The site symmetry is slightly tetragonally distorted.
a r t i c l e
i n f o
Article history: Received 23 June 2014 Received in revised form 15 January 2015 Accepted 30 January 2015 Available online xxxx Keywords: EPR Cu2+ ion X-ray Orotate FT-IR
a b s t r a c t We have studied the Cu2+ ion doped orotato(nicotinamid)cobalt(II) complex by using EPR spectroscopy and X-ray diffraction. The single crystal is triclinic with the space group P1. The unit cell dimensions of the crystal are a = 7.2785(4) Å, b = 10.2349(5) Å, c = 12.7372(6) Å, a = 69.297(4)°, b = 74.791(4)° and c = 76.995(4)°, with Z = 2. We analyzed the EPR spectra of both single crystal and powder of the complex at room temperature. EPR analysis indicates the presence of only one Cu2+ site. We obtained the spin Hamiltonian parameters from the single crystal data for the complex. The spin Hamiltonian parameters are gx = 2.032, gy = 2.116, gz = 2.319, Ax = 28 G, Ay = 66 G, Az = 126 G. These data indicate that the symmetry of paramagnetic center is rhombic. We constructed the ground state wave function of the Cu2+ ion. Ó 2015 Elsevier B.V. All rights reserved.
Introduction In biological systems, orotic acid (1,2,3,6-tetrahydro-2,6-dioxo4-pyrimidine carboxylic acid, 6-carboxyuracil, vitamin B13, H3Or) has a great importance. Many living organisms have it in their cells and body fluids [1–3]. Orotic acid has multidentate functionality in transition metal complexes and play an important role in bioinorganic chemistry [4]. Metal orotates find wide applications in medicine [5]. Some researchers have screened platinum, palladium and nickel orotates with various substituents as therapeutic agents for cancer [6]. Zinc(II) and cobalt(II) orotates have shown antimicrobial ⇑ Corresponding author. Tel.: +90 3623121919 1085; fax: +90 3624576081. E-mail address: [email protected] (B. Karabulut).
activity [7]. Orotic acid is also an organic building block in coordination chemistry [6,8]. It coordinates to metal ions as a bidentate ligand through both the N atom of the pyrimidine ring and the O atom of the carboxyl group. Examples can be found in the crystal structures of Co(II)–orotate complexes with water, ethylenediamine [9], nicotinamide [10] or di-2-pyridylamine [11]. The orotate ligand acts as a bridging bidentate ligand in the polymeric complex [Co(HOr)(H2O)3]n [4,11,12]. It acts as a monodentate ligand through the carboxylate O atom in the complex [Co(H2Or)2(H2O)4]H2O [13]. It also acts as a counter-ion in the complex [Co(H2O)2(phen)2] (H2Or)2 (phen = 1,10-phenanthroline) [14]. In this paper, we examined the structure of [Co(HOr)(na) (H2O)3]CH3OHH2O complex by using X-ray diffraction and IR spectroscopy. We also determined the magnetic properties of
http://dx.doi.org/10.1016/j.saa.2015.01.100 1386-1425/Ó 2015 Elsevier B.V. All rights reserved.
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
_ Yıldırım et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy xxx (2015) xxx–xxx I.
2
Cu2+ ion doped complex by electron paramagnetic resonance (EPR) spectroscopy. We can consider a transition metal ion as a probe and use it to determine the environmental symmetry of the complexes in host lattices by EPR technique [15–18].
perpendicular axes a⁄, b and c⁄ at 10° steps. The g-value was obtained by comparison with DPPH (diphenylpicrylhydrazyl) of g = 2.0036. We measured the FT-IR spectra in the 4000-400 cm1 region with a Bruker Vertex 80V FT-IR spectrometer using KBr pellets.
Experimental
Results and discussion
Preparation of complex
Crystal structure of complex
Synthesis of [Co(HOr)(na)(H2O)3]CH3OHH2O [(HOr):C5H2N2O4, [(na):C6H6N2O] is as given in Scheme 1. A solution of orotic acid monohydrate (0.348 g, 2 mmol) was dropped into a stirred solution of NH3 (0.034 g, 2 mmol) and nicotinamid (0.489 g, 4 mmol) and Co(NH3)26H2O (0.582 g, 2 mmol) in mixture of water/MeOH at ambient temperature. The dark red crystals of title complex suitable for X-ray analyses were collected. To dope [Co(HOr) (na)(H2O)3]CH3OHH2O complex with Cu2+ impurities, small amount of CuCl22H2O (0.05% by wt) was added to saturated aqueous solution of [Co(HOr)(na)(H2O)3]CH3OHH2O and left for slow evaporation at ambient temperature. After 3 weeks, we selected well-developed single crystals of suitable size for EPR study.
The complex is in the space group P1 with 2 molecules in the unit cell. Fig. 1 shows an ORTEP-3 [21] view of the complex. The Co(II) cation coordinates to three aqua, one orotic acid (HOr) and one nicotinamide (na) ligand. The complex has a distorted octahedral geometry. Solvent molecules of water and methanol crystallize in the asymmetric unit. The na ligand acts as a monodentate via the pyridine N atom while the HOr ligand acts as a bidentate N, O-chelator. The equatorial plane of the octahedron is formed by three water molecules (O6, O7, and O8) and O3 atom of HOr ligand. The axial positions in the octahedron are occupied by the pyridine N2 atom of the na ligand and heterocyclic N3 atom of HOr ligand. The orotic acid forms an essentially planar five-membered chelate ring (Co1/O3/C7/C8/N3), the maximum deviation from the plane being 0.0612(17) Å for atom C7. As can be seen from the trans angles, which vary from 171.75(8)° to 177.70(8)°, and the cis angles, which vary from 78.94(8)° to 96.72(8)°, the coordination octahedron around the Co(II) ion can be visualized as being distorted. In the complex, the Co–O and Co–N bond distances [Co1–O3 = 2.111(2), Co1–O6 = 2.146(2), Co1–O7 = 2.096(2), Co1–O8 = 2.129(2), Co1–N2 = 2.196(2) and Co1–N3 = 2.085(2) Å] are similar to the literature values [10,12,22]. Selected bond distances and angles are listed in Table 2. Examination of the structure with PLATON [23] shows that the crystal structure contains two intramolecular and thirteen intermolecular hydrogen bonds of types O–H O, C–H O, N–H O and C–H N, which stabilize the structure. The detailed geometry of the intra- and intermolecular interactions (including symmetry codes) are collected in Table 3.
X-ray, EPR, FT-IR analyses We performed X-ray data for single crystal on a STOE IPDS II image plate detector using Mo Ka radiation (k = 0.71073 Å) at 296 K. We solved the structure by direct methods using SHELXS13 [19]. All non-hydrogen atoms were refined anisotropically by the full matrix least squares procedure based on F2 using SHELXL13 [19]. Data collection: STOE X-AREA [20]. Cell refinement: STOE X-AREA [20]. Data reduction: STOE X-RED [20]. We give the details of crystal data, data collection and refinement parameters in Table 1. Molecular diagrams were obtained using ORTEP-3 [21]. We recorded EPR spectra on a Varian E-109C EPR spectrometer operating at X-band frequencies, having a 100 kHz field modulation at room temperature. We performed the measurement of EPR spectra by rotating the single crystal about the three mutually
O O HN
NH
NH2 O
O
H2O
Co(NO3)2 6H2O
NH 3 N
O H N
O
H2O
OH2
O
N
Co N
O
OH2
O
O
CH3OH H 2O
NH2
Scheme 1. The formation and structure of [Co(HOr)(na)(H2O)3]CH3OHH2O.
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
_ Yıldırım et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy xxx (2015) xxx–xxx I. Table 1 Details of crystal data, data collection and refinement parameters for title complex. Color/shape
Dark red/block
Chemical formula Formula weight Temperature (K) Wavelength (Å) Diffractometer/measurement method Crystal system Space group
[Co(HOr)(na)(H2O)3]CH3OHH2O 439.25 296 0.71073 Mo Ka STOE IPDS II/rotation (x scan)
Unit cell parameters a, b, c (Å) a, b, c (°) Volume (Å3) Z Dcal. (g/cm3) l (mm1) F000 Crystal size (mm3) h Range for data correction (°) Index ranges Measured reflections Independent reflections Observed reflections [I > 2r(I)] Absorption correction Tmax., Tmin. Rint Refinement method Data/restraints/parameters Goodness-of-fit on F2 R indices [I > 2r(I)] R indices (all data) Dqmax., Dqmin. (e/Å3)
Triclinic P1 7.2785(4), 10.2349(5), 12.7372(6) 69.297(4), 74.791(4), 76.995(4) 847.25(8) 2 1.722 1.077 454 0.51 0.40 0.28 2.150–26.893 9 6 h 6 9; 12 6 k 6 13; 16 6 l 6 16 13298 3609 3399 Integration (X-RED32) 0.7459, 0.6631 0.0933 Full-matrix least-squares on F2 3609/21/276 1.076 R1 = 0.0586, wR2 = 0.1442 R1 = 0.0611, wR2 = 0.1460 1.182, 0.976
3
EPR study We recorded the EPR spectra of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal between 0° and 180° at 10° steps by rotating the crystal in c⁄a⁄, bc⁄ and a⁄b planes at room temperature. The a⁄ axis is perpendicular to both b and c⁄ axes. Fig. 2 shows the EPR spectra of the complex when the magnetic field is in a⁄b plane making 10° and 120° angles with the b axis. In Fig. 2, the EPR spectra consist of four lines, which is a characteristic of Cu(II) ion with nuclear spin 3/2. We couldn’t resolve clearly the hyperfine lines of 63Cu2+ and 65Cu2+ nuclei at all orientations, because the line width is broad. Fig. 3 shows the angular variation of g2 in three planes. The plotting shows a single set of four hyperfine lines in all planes. This is consistent with the triclinic symmetry of the complex. We can say that the Cu2+ ions replace Co2+ ions in the lattice, since the ionic radius of Co2+ (82 pm) is large enough for the substitution of Cu2+ (72 pm). The spectra were resolved by fitting each line to the expression: 2
g 2k ðhÞ ¼ g 2ii cos2 h þ g 2jj sin h þ 2g 2ij sin h cos h
ð1Þ
where i, j, k = x,y,z are cyclic coordinates and h is the rotation angle in the related plane. g 2ii , g 2jj and g 2ij correspond to the g tensor elements, which can be found after fitting procedure [24]. We can fit the spectrum to the rhombic spin Hamiltonian having only electronic Zeeman and hyperfine interactions as follows:
H ¼ He þ HHF þ HSO
ð2Þ
We ignored the nuclear Zeeman and quadrupole interactions due to their small contributions. To find g and A values, we used an iterative numerical technique [25]. We found that both g (gz > gx > gy) and hyperfine (Az > Ay > Ax) splitting values of the complex suit the rhombic symmetry. The results are given in Table 4.
Fig. 1. The molecular structure of [Co(HOr)(na)(H2O)3]CH3OHH2O shown with 30% probability displacement ellipsoids and illustrating the atom-numbering scheme. H atoms are shown as small spheres of arbitrary radii.
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Table 2 Selected bond lengths (Å) and bond angles (°) for title complex. Bond lengths (Å) Co1–N3 Co1–O7 Co1–O3
2.085(2) 2.096(2) 2.111(2)
Co1–N2 Co1–O8 Co1–O6
2.126(2) 2.129(2) 2.146(2)
Bond angles (°) N3–Co1–O7 N3–Co1–O3 O7–Co1–O3 N3–Co1–N2 O7–Co1–N2 O3–Co1–N2 N3–Co1–O8 O7–Co1–O8
92.97(9) 78.94(8) 89.98(9) 174.81(8) 89.84(9) 96.72(8) 93.28(9) 87.66(9)
O3–Co1–O8 N2–Co1–O8 N3–Co1–O6 O7–Co1–O6 O3–Co1–O6 N2–Co1–O6 O8–Co1–O6
171.75(8) 91.18(9) 89.21(9) 177.70(8) 91.13(8) 88.03(9) 91.52(9)
Table 3 Hydrogen-bond parameters (Å, °). D–H A
D–H (Å)
H A (Å)
D A (Å)
D–H A (°)
O8–H1O8 O4 C5–H5 O8 O6–H1O6 O9 N4–H4 N O1i N1–H2N1 O6ii N1–H1N1 O5iii O7–H2O7 O9iv O7–H1O7 O2v O8–H2O8 O1vi O6–H2O6 O3ii O9–H2O9 O10vii C12–H12C N4viii O9–H1O9 O10 O10–H10 O9 O10–H10 O4
0.82(2) 0.93 0.81(2) 0.86 0.86 0.86 0.81(2) 0.84(2) 0.82(2) 0.81(2) 0.81(2) 0.96 0.88(2) 0.82 0.82
1.91(3) 2.52 1.90(2) 1.95 2.32 2.10 1.98(2) 1.84(2) 2.14(2) 2.00(2) 1.85(2) 2.52 2.36(3) 2.51 2.34
2.648(3) 3.074(4) 2.703(4) 2.812(4) 3.179(3) 2.955(4) 2.783(4) 2.659(3) 2.934(3) 2.784(3) 2.610(8) 3.284(10) 2.956(10) 2.956(10) 2.778(7)
150(5) 119 176(4) 176 172 171 171(6) 167(4) 165(6) 162(5) 156(5) 137 126(2) 116 114
Symmetry codes: ix, y 1, z + 1; iix, y, z; iiix, y + 1, z 1; y, z; vix, y + 1, z; viix1, y, z + 1; viiix1, y, z.
iv
x + 1, y, z; vx + 1,
Fig. 2b. (b) EPR spectrum of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal when the magnetic field is in the a⁄b-plane and 120° away from the b-axis.
In an octahedral crystal field, the energy levels of d orbitals of an ion split into a doublet (eg) and a triplet (t2g) symmetry states. A distorted octahedral field removes the degeneracy of the energy levels of eg (dx2 y2 and d3z2 r2 ) orbitals. When the site symmetry is tetragonal the ground state is either (dx2 y2 or d3z2 r2 ) [26]. When the site symmetry is rhombic or lower the ground state is an admixture of these two orbitals. The Hamiltonian (Eq. (2)) can be solved for rhombic environment giving equalities for principal hyperfine splitting constants [27]:
pffiffi 3 1 3aþpffiffi3b j þ 27 a0 ða2 b2 Þ þ ðg x g e Þ 14 g Þ ðg y e a 3b 5 Ax ¼ P 4 pffiffi pffiffi 0 þ 143ab ðg z g e Þ 4 37a ab 2
ð3aÞ pffiffi 3 1 3aþpffiffi3b j þ 27 a0 ða2 b2 Þ þ ðg y g e Þ 14 g Þ ðg x e a 3b 5 Ay ¼ P 4 pffiffi pffiffi 0 þ 143ab ðg z g e Þ 4 37a ab 2
ð3bÞ 2
3 pffiffi 1 3aþpffiffi3b j þ 27 a0 ða2 b2 Þ þ ðg z g e Þ 14 g Þ ðg x e a 3b 6 7 pffiffi Az ¼ P 4 5 1 3aþpffiffi3b þ 14 g Þ ðg y e a 3b ð3cÞ 0
These equations can be solved for a , j, a and b and the ground state wave function of metal ion can be constructed as follows: Fig. 2a. (a) EPR spectrum of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal when the magnetic field is in the a⁄b-plane and 10° away from the b-axis.
w ¼ a0 ½ajx2 y2 i þ bj3z2 r2 i
We also recorded the X-band EPR powder spectrum of the complex at room temperature as in Fig. 4. We obtained the principal values of g and A tensors for the powder spectrum as follows: gx = 2.109, gy = 2.030, gz = 2.310, Ax = 33 G, Ay = 59 G, Az = 121 G. So, we can easily say that the symmetry of paramagnetic center is rhombic.
where j is the core polarization constant, a0 is the covalency parameter and its square is the probability of finding the electron in the d orbitals of the metal, P is dipolar hyperfine parameter for metal ion [28,29]. The parameters, a and b are mixing coefficients for dx2 y2 and d3z2 r2 orbital. The normalization condition for the mixing coefficients a and b is:
ð4Þ
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
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5
Fig. 3. Angular variations of the EPR spectra of Cu2+ ion doped title complex.
Table 4 Principal g and hyperfine (A) values and their direction cosines of Cu2+ doped [Co(HOr)(na)(H2O)3]CH3OHH2O single crystal (Dg = ±0.0005, DA = ±0.5 G). g
gx = 2.116 gy = 2.032 gz = 2.319
Direction cosines
A (G)
a⁄
b
c⁄
0.490 0.862 0.479
0.726 0.321 0.608
0.483 0.393 0.783
Direction cosines
Ax = 28 Ay = 66 Az = 126
a2 þ b2 ¼ 1
ð5Þ 2+
We constructed the ground state wave function of the Cu in the complex as:
ion
ð6Þ
a⁄
b
c⁄
w ¼ ð0:907Þ1=2 ½0:979jx2 y2 i þ 0:203j3z2 r 2 i
0.636 0.760 0.142
0.675 0.454 0.581
0.377 0.464 0.801
From the result, we can say that the unpaired electron spends most of its time on the dx2 y2 orbital of Cu2+ ion. We compared the ground state wave function parameters of Cu2+ in different lattices as given in Table 5.
Fig. 4. EPR spectrum of Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O powder at room temperature.
Table 5 Comparison of ground state wave function parameters for Cu2+ in different lattices. Lattice
Site
[Co(HOr)(na)(H2O)3]CH3OHH2O Powder [Co(dmp)(dpc)]0.76H2O [Co(mein)2(H2O)4](sac)2
[Co(ein)2(H2O)4](sac)2
I II Powder I II Powder
a0 2
a
b
j
Refs.
0.907 0.860 0.789 0.813 0.807 0.781 0.899 0.904 0.890
0.979 0.978 0.864 0.935 0.949 0.954 0.987 0.982 0.985
0.203 0.207 0.502 0.355 0.316 0.299 0.185 0.189 0.167
0.273 0.287 0.190 0.280 0.268 0.281 0.302 0.300 0.301
This work [30] [31]
[32]
_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100
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Fig. 5. FT-IR spectrum of [Co(HOr)(na)(H2O)3]CH3OHH2O complex.
FT-IR study
Acknowledgements
Fig. 5 shows the FT-IR spectra of the complex. In the complex, the stretching modes of the free water and coordinated water appeared at 3493 and 3389 cm1, respectively. We observed the m(N–H) stretching vibration at 3153 cm1. The two bands at 1690 and 1642 cm1 correspond to the m(C@O) and m(C@C) stretching modes of the orotato and nicotinamide ligands. The medium intensity band at 1483 cm1 can be attributed to the m(C–N) vibration in the ring of the orotic acid. This frequency is higher than that of the stretching vibration of single C–N bond [9] and disappearance of the band at 1431 cm1 in free orotic acid [10] suggests the deprotonation of the N3 atom and coordination to Co(II) ion. In the title complex, the orotato ligand is coordinated to the Co(II) ion in bidentate form via the N3 atom from the pyrimidine ring and the carboxylic O3 atom. Pyridine ring vibrations of free nicotinamide at 1592 cm1 [10] shift to higher wavenumbers in the spectra of the complex due to coordination of the pyridine N2 atom.
We are grateful to Ondokuz Mayis University – Turkey for supporting our work by the following project number: PYO.FEN.1904.10.18. References [1] [2] [3] [4] [5] [6] [7] [8] [9]
[10]
Conclusions
[11] [12]
We synthesized the title complex and determined its crystal structure and EPR parameters at room temperature. The crystallographic results indicate that the Co(II) cation coordinates to three water molecules, one orotic acid and one nicotinamide ligand and has a slightly distorted octahedral geometry. EPR study of the Cu2+ ion doped [Co(HOr)(na)(H2O)3]CH3OHH2O complex shows that the Cu2+ ions give a single set of four hyperfine lines in all three planes. EPR study also indicates that the paramagnetic centers have rhombic symmetry g and A values. The ground state of the unpaired electrons in the complex is predominantly dx2 y2 and the unpaired electrons spend most of their time in this orbital.
Supplementary material CCDC 958811 contains the supplementary crystallographic data for this paper. Copies of the data can be obtained, free of change, on application to CCDC, 12 Union Road, Cambridge, CB12 1EZ, UK, fax: +44 1223 366 033, email: [email protected] or on the web: http://www.ccdc.cam.ac.uk.
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_ Yıldırım et al., EPR study of Cu2+ ion doped orotato(nicotinamid)cobalt(II) single crystal, Spectrochimica Acta Part A: Please cite this article in press as: I. Molecular and Biomolecular Spectroscopy (2015), http://dx.doi.org/10.1016/j.saa.2015.01.100