Synthesis, characterization and structure of a new dinickel(II) complex as model for urease

Article abstract of DOI:10.1016/j.molstruc.2003.10.008

A new dinuclear nickel(II) complex [Ni₂(L)(OAc) ₂(H₂O)]·ClO₄·H₂O 1 with the unsymmetrical N₅O donor ligand 2-{[bis(2-pyridylmethyl) amino]methyl}-4-methyl-6-{[2-pyridylmethyl)amino]methyl}p

Full text of DOI:10.1016/j.molstruc.2003.10.008

Journal of Molecular Structure 688 (2004) 185–190
www.elsevier.com/locate/molstruc
Synthesis, characterization and structure of a new dinickel(II) complex
as model for urease
*
Alessandra Greatti , Marcos Aires de Brito, Adailton Joao Bortoluzzi, Augusto Susin Ceccato
˜
´ ˆ ´
LABINC Laboratorio de Bioinorganica e Cristalografia, Departamento de Quımica, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900
´
Florianopolis-SC, Brazil
Received 2 September 2003; revised 9 October 2003; accepted 9 October 2003
Abstract
A new dinuclear nickel(II) complex [Ni2(L)(OAc)2(H2O)]·ClO4·H2O 1 with the unsymmetrical N5O donor ligand 2-{[bis(2-
pyridylmethyl)amino]methyl}-4-methyl-6-{[2-pyridylmethyl)amino]methyl}phenol (HL) has been synthesized and characterized by
conductivity, UV–Vis–NIR and IR spectroscopy, electrochemical methods and X-ray crystallography. Complex 1 crystallizes as blue
˚
˚
˚
crystals in monoclinic crystal system, space group I2=a with a ¼ 21.171(4) A, b ¼ 12.147(2) A, c ¼ 29.771(6) A, b ¼ 99.67(3)8,
3
˚
V ¼ 7547(2) A and Z ¼ 8: In this complex both nickel ions have a distorted octahedral geometry. The nickel centers are endogenously
bridged by the phenolic oxygen atom of the deprotonated ligand and also bridged by the two acetate groups as exogenous bridge. A water
molecule as terminal ligand is coordinated to a NiII ion.
q 2003 Elsevier B.V. All rights reserved.
Keywords: Dinickel(II) complex; Urease; Crystal structure; Phenoxo bridge; X-ray diffraction
1. Introduction
[6–9]. We have interest in the synthesis of models for
metalloenzymes and, in this article, we describe the
synthesis, X-ray structural characterization and spectro-
scopic properties of a new dinickel(II) complex of the
hexadentade phenoxo bridging ligand 2-{[bis(2-pyridyl-
methyl)amino]methyl}-4-methyl-6-{[2-pyridylmethyl)ami-
no]methyl}phenol-HL (Chart 1). This ligand is of major
interest for us due to the possibility of providing a free
coordination site on one of the nickel centers allowing to
coordinate with a labile group that can be easily substituted
by the substrate. While this work was nearing completion
Koval et al. reported the synthesis and some properties of a
dicopper complex of ligand HL as model for catechol
oxidase [10].
Urease is a metallohydrolase that contains two proximate
nickel ions in its active site and catalyzes the hydrolysis of
urea to ammonia and carbon dioxide [1,2]. Recent X-ray
crystallographic studies of urease isolated from two
different microorganisms has provided details of the
dinickel active site [1–4]. The two nickel(II) centers are
bridged by a carbamylated lysine residue and a water
molecule or hydroxide ion. Each nickel ion is further
bonded by two histidine residues and a water molecule, and
one of the NiII ion is also coordinated by an monodentate
aspartate residue. This coordination system leads one nickel
center to be pentacoordinate with a square pyramidal N2O3
geometry and the other having a pseudo-octahedral N2O4
environment [1,4,5]. Phenol-based compartmental ‘end-off’
ligands containing N,O-donor groups can accommodate a
metal and so produce binuclear complexes with coordi-
nation environments resembling the urease active site
2. Experimental
Abbreviations: HL ¼ 2-{[bis(2-pyridylmethyl)amino]-
methyl}-4-methyl-6-{[2-pyridylmethyl)amino]methyl}phe-
nol, [TBA][PF6] ¼ tetrabutylammonium hexafluorphosphate,
BPMP ¼ 2,6-bis[(bis(2-pyridylmethyl)amino)methyl]-4-
methylphenolate, bimp ¼ 2,6-bis[(bis((1-methylimidazol-
2-yl)methyl)amino)methyl]-4-methylphenolate.
*
Corresponding author. Tel.: þ55-21-48-331-6826; fax: þ55-21-48-
331-6888.
E-mail addresses: adajb@qmc.ufsc.br (A.J. Bortoluzzi), greatti@qmc.
ufsc.br (A. Greatti), marcos@qmc.ufsc.br (M.A. de Brito).
0022-2860/$ - see front matter q 2003 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2003.10.008

186
A. Greatti et al. / Journal of Molecular Structure 688 (2004) 185–190
1
98%), H NMR (ppm) in CDCl3) 8.55, 7.60, 7.36, 7.13
(12H, pyridine H); 6.94, 6.86 (2H, aromatic H); 3.96 (s, 2H,
NH–CH2–py); 3.93 (s, 2H, Ar–CH2–NH); 3.86 (s, 4H,
(py–CH2–N)2); 3.73 (s, 2H, N–CH2–Ar); 2.22 (s,3H,
CH3).
Complex [Ni2(L)(OAc)2(H2O)]·ClO4·H2O 1. To a sol-
ution of Ni(ClO4)2·6H2O (0.73 g, 2 mmol) in methanol
(30 ml) were added a methanolic solution of HL (0.44 g,
1 mmol) and sodium acetate trihydrate (0.41 g, 3 mmol).
The blue solution resulting was heated to 40 8C and stirred
for 15 min at ambient atmosphere. After three days at room
temperature, a blue microcrystalline precipitate was formed,
which was filtered off and washed with water and ether.
Yield: 0.52 g (64% based on HL). Single crystals suitable
for X-ray crystallography were obtained by recrystallization
from a methanol–acetonitrile (1:1) solution of 1. (Caution!
Perchorate salts with organic ligands are potentially
explosive and should be handled with care.)
Chart 1.
2.1. Materials and general methods
All reagents and solvents for syntheses and analyses were
of analytical and/or spectroscopic grade and used without
further purification.
For the electrochemical and spectroscopic studies, high-
purity solvents were used as received from Merck. High-
purity argon was used to deoxygenate the solution.
Conductivity of the complex was taken at room temperature
using a Digimed CD-21 conductometer. The 1H NMR
spectrum was obtained on a Bruker-FT 200 MHz. Infrared
spectrum (KBr pellets) was taken in a FT-IR Perkin Elmer
Model 2000 spectrometer, and UV–Vis–NIR spectrum was
recorded in CH3CN with a Perkin Elmer Model L 19
spectrophotometer. Electrochemical measurements were
carried out using a Princeton Applied Research (PAR)
model 273 potentiostat/galvanostat. Cyclic and square wave
voltammograms were obtained at room temperature in
acetronitrile solution containing 1023 mol l21 complex and
0.1 mol l21 [TBA] [PF6] as the supporting electrolyte under
an argon atmosphere. The electrochemical cell employed
was of a standard three-electrode configuration: a glass
carbon working electrode, a platinum wire counter electrode
and a Ag/AgCl reference electrode constructed in our
laboratory. The Fcþ/Fc couple of ferrocene ðE1=2 ¼ 0:415
VÞ was used as an internal standard [11].
2.3. X-ray crystallography
The crystal data were measured on an Enraf–Nonius
CAD4 diffractometer, using graphite monochromated
ꢀ
Mo Ka radiation ðl ¼ 0:71069 AÞ; at room temperature. A
blue crystal was isolated in inert oil and quickly placed in a
glass capillary for the crystallographic analysis. These
crystals are very sensitive to solvent loss and they become
opaque in a few minutes when removed from the mother
solution. Unit cell parameters were determined from
centering of 25 reflections in the u range 8.60–15.318 and
refined by the least-squares method. Intensities were
collected using the v 2 2u scan technique in monoclinic
system with C centered cell diffraction pattern. Three
standard reflections were monitored every 200 reflections
throughout data collection and no significant intensity decay
was observed. All diffracted intensities were corrected for
Lorentz and polarization effects. Absorption correction was
employed c-scan method. The structure was solved by
direct methods and was refined by the full-matrix least-
squares method using SHELXS97 [13] and SHELXL97
[14] computer programs, respectively, in the space group
I2=a (no. 15). The non-standard space group was chosen to
give a more orthogonal unit cell and thereby reduce
correlation. The I2=a space group was defined applying
the transformation matrix (0 0 2 1/0 1 0/1 0 1) from the
standard space group C2=c with cell constants a ¼ 33:5065
2.2. Syntheses
Ligand HL.
A solution of 3-[(bis(2-pyridylmethyl)amino)methyl]-2-
hydroxy-5-methylbenzaldehyde [12] (3.16 g, 9.1 mmol) in
30:30 ml of methanol/tetrahydrofuran was added 2-pyr-
idylmethylamine (0.98 g, 9.1 mmol). The yellow resulting
solution was stirred at room temperature for ca. 30 min.
After addition of sodium borohydride (0.38 g, 10 mmol)
stirring was maintained for 1 h. It was then acidified to pH
5–6 with hydrogen chloride (2 mol l21). The solvent was
evaporated, and the product was redissolved in dichlor-
omethane and extracted with an aqueous NaHCO3 solution.
The organic layer was dried over Na2SO4, filtered and the
solvent was evaporated under reduced pressure at 40 8C,
resulting in a pale yellow oil. Yield: (3.92 g, 8.9 mmol;
ꢀ
ꢀ
ꢀ
A; b ¼ 12:1467 A; c ¼ 21:1706 A and b ¼ 118:8508: All
non-hydrogen atoms were refined with anisotropic displace-
ment parameters, except for the oxygen atoms of the
perchlorate counterion. Hydrogen atoms of the coordinated
water molecule were found from Fourier map, whereas all
other H atoms were placed at idealized positions using
standard geometric criteria. For the water molecule as
solvent of crystallization the H atoms were not found. A
highly disordered solvent was found in the crystal structure.
All attempts to model the disorder in that group were

A. Greatti et al. / Journal of Molecular Structure 688 (2004) 185–190
187
Table 1
n
asym=nsym stretching of the acetate ligand and the ClO42
Crystal data and structure refinement for complex 1
counterion. The asymmetrical stretching mode ðnasymÞ is
found at 1576 cm21 and the symmetrical ðnsymÞ at
Empirical formula
Formula weight
Temperature
Wavelength
Crystal system,
space group
Unit cell dimensions
a
C31H38ClN5Ni2O11
1444 cm21. The splitting of these two bands (132 cm21
)
809.53
293(2) K
˚
0.71073 A
suggests that the carboxylate ligands adopt the bridging
mode [18]. Stretching vibrations of the uncoordinated ClO42
are located at 1096 cm21 confirming the cationic character
of this complex according to the molar conductivity
experiment 140 cm2 V21 mol21 in acetonitrile typical of
1:1 electrolytes in this solvent [19].
Monoclinic, I2=a
˚
21.171(4) A
˚
12.147(2) A
b
˚
29.771(6) A
c
b
Volume
99.67(3)8
3.2. Electronic and electrochemistry properties
3
˚
7547(2) A
Z, Calculated density
Absorption coefficient
F(000)
8, 1.425 g cm23
1.129 mm21
The electronic spectrum of 1 (Fig. 1) displays two broad
absorption bands at 616 nm (e ¼ 16 M21 cm21) and
978 nm (e ¼ 25 M21 cm21) which can be assigned to the
3360
0.50 £ 0.36 £ 0.26 mm3
Crystal size
Theta range for
data collection
Index ranges
3
3
2.20–25.058
spin-allowed d–d transitions A2g ! T1g (F) and
3
3A2g ! T2g (F), respectively. A weak absorption also is
225 # h # 0; 0 # k # 14;
234 # l # 35
observed at 778 nm (e ¼ 8 M21 cm21) due to the spin-
3
1
Reflections collected/
unique
6866/6665 ðRint ¼ 0:0285Þ
forbidden A2g ! E1g transition. These results suggest an
octahedral environment for the two nickel(II) ions [20]. In
addition, the spectrum shows a strong absorption at 306 nm
(e ¼ 3636 M21 cm21) which may arise from a transition
involving nickel(II) and pyridine orbitals [21]. The redox
behavior of 1 was investigated by cyclic and square wave
voltammetry in acetonitrile solution. The complex shows
one irreversible redox process at 20.97 V vs Fcþ/Fc
assigned to the NiIINiII/NiIINiI couple. In anodic potential
one quasi-reversible wave appears at þ0.62 V vs Fcþ/Fc
attributed to the formation of NiIINiII/NiIINiIII species. This
value is in close agreement with the [Ni2BPMP
(O2CCH3)2]þ ion [21].
Absorption correction
Max. and min.
Psi-scan
0.939 and 0.824
transmission
Refinement method
Data/restraints/parameters
Goodness-of-fit on F 2
Final R indices ½I . 2sðIÞꢀ
R indices (all data)
Largest diff. peak and hole
Full-matrix least-squares on F 2
6665/0/432
1.068
R ¼ 0:0574; Rw ¼ 0:1630
R ¼ 0:1053; Rw ¼ 0:1799
23
˚
0.640 and 20.895 e A
unsuccessful. The investigation for solvent-accessible voids
with PLATON [15] showed a potential solvent volume of
3
900.9 A . The application of SQUEEZE [16] correction
˚
3.3. Description and discussion of the crystal structure of
complex 1
showed the same solvent-accessible voids and the number
of electrons in this volume is 88 with the estimated volume
3
per atom of 150 A . This is compatible with a presence of
˚
The structure of 1 consists of a discrete binuclear
[Ni2(L)(m-OAc)2(OH2)]þ cation, one uncoordinated
perchorate anion and one water of crystallization. A
ZORTEP view of the cation complex 1 is shown in Fig. 2
and the selected geometric parameters (bond lengths and
angles) are listed in Table 2. Both nickel centers are six-
coordinated in a distorted octahedral environment bridged
by the phenolate oxygen atom of the binucleating ligand L2
and by two carboxylate groups of the acetate ligands. The
three nitrogen atoms N1, N22 and N32 from the tertiary
amine and from the two pyridine groups, respectively,
complete the N3O3 coordination sphere of Ni1, while the
distorted octahedral N2O4 coordination sphere of Ni2
consists of two nitrogen atoms, N4 from the secondary
amine and N42 from the pyridine ring and by one oxygen
atom of a water molecule as exogenous terminal ligand. The
nitrogen atoms of amine and pyridine groups are coordi-
nated trans to the di-m-acetate bridge in both nickel(II)
centers. The water molecule in Ni2 center is coordinated in
trans position to phenoxo bridge, while in Ni1 center this
one disordered acetonitrile molecule in the asymmetric unit.
The subsequent refinement of the structure with corrected
reflection data from SQUEEZE procedure converged to the
final indices R ¼ 0:0574 and Rw ¼ 0:1630 for 4355
reflections with ½I . 2sðIÞꢀ: The ZORTEP [17] program
was used to generate the picture of the molecular structure.
Further relevant crystallographic data are summarized in
Table 1.
3. Results and discussion
3.1. Synthesis and general characterization
The synthesis of 1 was achieved by the reaction of
Ni(ClO4)2·6H2O, the ligand HL and sodium acetate in 2:1:3
ratio, according to the experimental conditions described in
section 2.2. The infrared spectrum of 1 is mainly
characterized by the skeletal ligand vibrations, the

188
A. Greatti et al. / Journal of Molecular Structure 688 (2004) 185–190
Fig. 1. Electronic spectrum of complex 1 in acetonitrile solution (1.1022 mol l21) and inset (5.1025 mol l21).
Fig. 2. A perspective view of molecular structure of complex 1 with atomic labeling. The ellipsoids are shown with 40% probability level.

A. Greatti et al. / Journal of Molecular Structure 688 (2004) 185–190
189
Table 2
˚
Selected bond lengths (A) and angles (8) for complex 1
Table 3
˚
Hydrogen-bonds parameters for complex 1 (A and 8)
Ni1–O1
2.001(3)
2.056(3)
D–H· · ·A
d(D–H)
D(H· · ·A)
d(D· · ·A)
/(DHA)
Ni1–O61
Ni1–O51
Ni1–N22
Ni1–N32
Ni1–N1
N(4)–H(4)· · ·O(2W)
O(1W)–H(1WB)
· · ·O(52)i
1.01
0.77
2.33
2.06
3.163(7)
2.805(5)
139.8
162.4
2.076(3)
2.085(4)
2.101(4)
2.132(4)
2.001(3)
2.044(3)
2.072(4)
2.093(4)
2.094(4)
2.127(3)
Symmetry code: (i) 2x þ 1=2; y; 2z þ 1:
Ni2–O1
Ni2–O52
Ni2–O62
Ni2–N42
Ni2–N4
average bond lengths also agree with the urease enzyme that
˚
has the values Ni–N (2.2 A) and Ni–O (2.05 A) [1,4]. The
˚
distances between the Ni atoms and the bridging phenolate
Ni2–O1W
˚
oxygen (2.001(3) A) and the corresponding Ni–O–Ni angle
(118.0(2)8) in 1 are close as those found in the m-phenolate
II
and di-m-acetate Ni complex (2.010 A and 1168, respect-
ively) [20], but it is significantly different from that
observed in only m-phenolate NiII complex (2.068(2) A
and 131.8(1)8) [7]. It is interesting to note that despite of
angles M–O–M in the diiron (113.9(2)8) [22] and
dimanganese (110.6(3)8) [23] complexes are smaller than
that in 1, the metal-metal distances in these complexes (av.
O1–Ni1–O61
O1–Ni1–O51
O61–Ni1–O51
O1–Ni1–N22
O61–Ni1–N22
O51–Ni1–N22
O1–Ni1–N32
O61–Ni1–N32
O51–Ni1–N32
N22–Ni1–N32
O1–Ni1–N1
97.19(14)
90.98(14)
91.36(14)
168.57(16)
93.69(16)
85.25(15)
87.58(15)
93.81(15)
174.77(15)
95.21(16)
91.14(14)
170.23(14)
93.62(14)
78.36(16)
81.39(15)
95.56(13)
91.89(14)
92.66(14)
87.67(14)
92.23(15)
175.11(15)
90.33(15)
170.90(15)
94.08(16)
81.05(16)
172.94(14)
89.66(13)
83.09(14)
96.90(15)
85.09(15)
118.01(16)
133.2(3)
˚
˚
˚
˚
3.42 A) are very similar. The Ni1· · ·Ni2 distance 3.431(1) A
in 1 is similar to that observed in [Ni2(bimp)(m-OAc)2]þ
O61–Ni1–N1
O51–Ni1–N1
N22–Ni1–N1
N32–Ni1–N1
O1–Ni2–O52
O1–Ni2–O62
O52–Ni2–O62
O1–Ni2–N42
O52–Ni2–N42
O62–Ni2–N42
O1–Ni2–N4
˚
(3.422(4) A) [20] and slightly shorter than that observed in
˚
Klebsiella aerogenes urease (3.5 A) [1] and Bacillus
˚
pasteuri urease (3.7 A) [4].
The amine and the water groups in complex 1 are
involved in intermolecular hydrogen bonds (Table 3). The
coordinated water molecules (O1W and O1Wi) are donors
in the hydrogen bonds with the oxygen atoms (O52 and
O52i) of the bridging acetate group, resulting in a tetrameric
structure (Fig. 3). The amine group is involved only in
hydrogen bond with uncoordinated water molecule.
O52–Ni2–N4
O62–Ni2–N4
N42–Ni2–N4
O1–Ni2–O1W
O52–Ni2–O1W
O62–Ni2–O1W
N42–Ni2–O1W
N4–Ni2–O1W
Ni1–O1–Ni2
C53–O51–Ni1
C53–O52–Ni2
C63–O61–Ni1
C63–O62–Ni2
In conclusion, a new dinickel (II) complex of interest in
the context of urease biomimetic model is reported. In both
complex 1 and native enzyme one NiII center show a similar
N2O4 distorted octahedral environment with one water
molecule coordinated as terminal ligand to this metal center,
that allow us to consider the complex 1 as a model complex
of urease enzyme. In order to evaluate the reactivity of 1 and
to compare with the enzyme activity, we are performing the
kinetic studies that will be reported later.
132.6(3)
131.9(3)
132.5(3)
position is occupied by a pyridine group of the final pendant
arm of the ligand. This kind of ligand induces a typical
coordination mode as showed for diiron [22] and dimanga-
nese [23] complexes, although it is not observed in the
dicopper (II) complex [10]. This can be explained by the
absence of the exogenous bridging groups in the copper
4. Supplementary material
The crystallographic data (atomic coordinates and
equivalent isotropic displacement parameters, calculated
hydrogen atom parameters, anisotropic thermal parameters
and bond lengths and angles) have been deposited at the
Cambridge Crystallographic Data Center (deposition num-
ber CCDC 218667). Copies of this information may be
obtained free of charge from: The Director, CCDC, 12
Union Road, Cambridge, CB2 1EZ, UK (Fax: þ44-1223-
˚
complex. The Ni1–N1 [2.132(4) A] and Ni2–O1W
˚
[2.127(3) A] are the largest distances in the coordination
sphere of the metal ions. The average bond lengths Ni–N
˚
˚
(2.093 A) and Ni–O (2.042 A) agree with the values
expected for octahedral NiII complex [7,20,24]. These

190
A. Greatti et al. / Journal of Molecular Structure 688 (2004) 185–190
Fig. 3. Hydrogen bonds in the crystal structure of complex 1 with partial atomic labeling. Symmetry code: (i) 2x þ 1=2; y; 2z þ 1:
[9] H. Adams, S. Clunas, D.E. Fenton, S.E. Spey, Dalton Trans. 4 (2003)
336-033; e-mail: deposit@ccdc.cam.ac.uk or http://www.
ccdc.cam.ac.uk).
625.
[10] I.A. Koval, D. Pursche, A.F. Stassen, P. Gamez, B. Krebs, J. Reedijk,
Eur. J. Chem. 9 (2003) 1669.
´
[11] A.E. Gagne, C.A. Koval, G.C. Lisensky, Inorg. Chem. 19 (1980)
2854.
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