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Structural features of nickel (II) complexes of bi- and terpyridine
according x-ray analysis
© Dudkina Y.B., Islamov D.R., Mikhailov D.Y., Krivolapov D.B., Litvinov I.A.,
Budnikova Y.H.
A.E.Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center of Russian
Academy of Sciences, Arbuzov str., 8, 420088 Kazan, Russian Federation,
e-mail [email protected]
Abstract
The structure of four previously undescribed nickel (II) complexes of bi- and terpyridine in crystals is
determined by X-ray analysis. The d2sp2 hybridization of nickel atom with coordination number 5 in crystal of
compounds III Ni(t-bu-tpy)I2 was determined. The regularities in the packing of molecules in crystals was
found. In particularly, in packing of compounds I [Nibpy2(H2O)Br]Br, II [Nibpy2(H2O)2]Br2, III Ni(t-butpy)I2 and IV [Ni(t-bu-tpy)2] (H2O)I2 the formation of ion and solvate canals was discovered. The
simultaneous existence of different form of nickel (II) complexes of different structure in the presence of diimine ligands in solution was assumed to determined some features of their physica-chemical properties, in
particular the reduction potentials.
Keywords: nickel, bipyridine, terpyridine complex, X-ray analysis
Introduction
Organonickel complexes with -diimine ligands play important roles in a variety of catalytic
reactions, C-C, P-C and other bonds formation [1-2]. The reason is the nickel to have a very
favorable combination of properties satisfying the requirements of organic reactions, passing through
the coordinate stage. Each step of the catalytic cycle includes elementary acts that require certain
properties of the metal, for example, a low ionization potential for favorable oxidative addition, the
relatively weak metal-carbon bonds, the tendency to form a square-planar complexes and achieve
pentacoordination in order to allow the inclusion of the substrate, as well as substantially high
electron affinity to prevent reductive elimination and so on. Some properties contradict each other
and a compromise made just in case the nickel complexes. The nature of ligands, cations, anions or
solvent can affect at each stage of the process, taking place on the metal both for catalytic and
stoichiometric reactions. The effect of these factors on the reaction rate, selectivity and
stereoselectivity, etc. can not be predicted, since the impact takes place in different ways in each step.
However, the information about the structure of even the most frequently used nickel catalysts,
their crystal structure are underrepresented in the literature. Perhaps this is due to the complexity of
crystallization. The knowing of the Ni (II) complexes with bipyridine and terpyridine ligands
structure will be useful to explain their electrochemical behavior, the ability to accept 1 or 2 electrons
in one step and the other previously observed and unexplained facts in terms of the compound
structure.
The understanding the details of the mechanism of the catalyzed reactions provides the
foundation for the synthesis of new and improvement of existing catalysts. To understand the
reaction mechanism the knowledge about the molecular structure of catalyst and its spatial structure
is useful. In this paper a new structure of four nickel (II) complexes of bis-and terpyridine was
established, the regularity of their molecular and spatial structure was revealed.
As a result of the search for the structures in the Cambridge crystallographic data base CCDC
[3] 6 compounds similar to studied by us in relation to the type of coordinated atoms and the
coordination polyhedron were found. In [4] the X-rays analysis of [Ni(phen)2(H2O)Br]Br∙3H2O (1)
compound (phen = 1,10-phenanthroline) showed that the central ion has a distorted octahedral
coordination (Fig. 1).
The form of the coordination nickel polyhedron in compound 2 [Ni(TBTP)Cl2] (TBTP – - 4,4',4''- tris-tert-butyl-2,2': 6',2"- terpyridine-N,N',N'') is trigonal bipyramid corresponding dsp3
hybridization [6]. Valence angles of the equatorial plane between the chlorine atoms are 127.4º, ones
between chlorine and nitrogen are 117.0º and 115.6º. The angle between the nitrogen atoms located
in an axial position is 157.0º.
Jones et al [7] described the crystals of compound 3 (Fig. 2). It is shown that nickel has a
coordination number 5, like the above discussed compound 2 [6]. However, the nickel atom
hybridization which is different in these two compounds has not been considered by the authors [7].
Reference [8] discloses a structure in which the bis (imino) -terpyridine bridging ligand
coordinate two nickel atoms (compound 4, Fig. 3). In the 4 molecule the nickel atoms have the same
shape of the coordination polyhedron (square pyramid) and d2sp2 hybridization.
In the same paper [8] the structure of mononuclear nickel complex with the same ligand is
described (compound 5, Fig. 4). In this crystal the compound 5 molecule is in special position on the
axis 2 (space group P42212). Nickel atom in this compound has a trigonal-bipyramidal coordination
appropriate to dsp3 hybridization. Imine nitrogen atoms are not coordinated to the nickel atom.
Thus, the amount of pentacoordinated nickel (II) complexes with ligands of the pyridine type
and halide ions characterized by XRD is very limited, in two cases nickel (II) dsp3 hybridization is
observed, and d2sp2 is in the two other cases.
Results and discussion
The nickel (II) complexes with bpy and t-bu-tpy were selected as the objects of the study,
obtained after the catalytic reaction by reaction mixtures crystallization, in particular olefins
perfluoroalkylation [2], and after separating of the desired products . Efficient regeneration of the
Ni(II)Ln catalyst after synthesis confirms the possibility of their repeated use. It has been found that
the nickel (II) complex with bipy crystallizes in two distinct forms, designated as Compound I
[Nibpy2(H2O)Br]+Br-*СН2Сl2*Н2О and Compound II [Nibpy2(H2O)2]2+*2Br-. Transparent cubic
crystals of the compound II are readily able to separate from the prismatic light-green crystals of
compound I.
Ni atoms in the compound I have a distorted octahedral geometry of the coordination sphere
(Fig. 5), the angles N-Ni-N constitute 79.2(4)о and about 78.9(3)о for the nitrogen atoms of one
ligand, and for nitrogen atoms of different ligands are 93.9(3)o, 91.9(3)о, 93.0(3)о and 169.3(3)о (3 )
at cis -and trans - arrangement respectively. It is also found that the Ni-N bond in the trans position
with respect to the bromine atom is slightly longer than the other Ni-N bonds (2.119(9) Å vs.
2.082(10) Å, 2.065(8) Å, 2.078(8) Å). There are two possible explanations for this phenomenon. The
first include the trans- influence of bromine, and the second one is the inequality of axial and
equatorial bonds .
Nickel bond lengths with the adjacent atoms in the compound [Ni(phen)2(H2O)Br]Br∙3H2O
(1) and in the compound [Ni(dipy)2(H2O)Br]Br∙H2O (I) investigated by us coincide within
experimental errors. However, the differences in the distances between the nitrogen atoms of one
ligand (Table. 1) leads to a change in valent angles: Br-Ni-Ntrans 172.16 (6)0 of the compound 1 and
176.0(2)0 in the compound I.
The crystals of compound I consists from the associates formed by hydrogen bonds that
connect the solvation and coordinated water molecule with bromine atoms (Figure 6).
Table 1. Distances between the nitrogen atoms in 2,2-bipyridine and 1, 10-phenanthroline in the
compounds I and 1, respectively.
In compound I, Å
In compound 1, Å
Ligand 1
2.63(1)
2.685(3)
Ligand 2
2.68(1)
2.687(3)
As in the case of compound I, a coordination nickel polyhedron in compound II has a
distorted octahedral form (Fig. 7), but distortions are somewhat different. It can be seen from the
values of the angles N-Ni-N 78.73(19)0 and 78.88(19)о for the nitrogen atoms of one ligand, and for
nitrogens of various ligands 94.37(19)о, 101.3(2)о, 95.2(2)о and 174.11(19)о for cis- and trans
location, respectively, instead of the ideal 90 о for cis and 180 о for trans atoms. The angles N-Ni-N
2
for the nitrogen of one ligand were identified by the conformational bipyridine rigidity. When
comparing the bond lengths it was observed that Ni1-O1 bond is considerably shorter then Ni1-O2
bond, despite the formation of two stronger hydrogen bonds of hydrogen atoms of the first oxygen
atom compared to the two hydrogen bonds of the second oxygen atom (Table . 2) . The decisive
factor in this case is the inequality of axial and equatorial bonds .
Ion channels in the crystal of compound II are shown in Fig. 8 Compound II forms a chain of
molecules in the crystal along the a0c diagonal plane due to the formation of intermolecular
hydrogen bonds (Fig. 8).
Table 2: Parameters of hydrogen bonds in the crystal of compound II.
Bond
O1-H201...Br1
O1-H202...Br2
O2-H203...Br1
O2-H204…Br2
Symmetry
operation
1-x,1-y,2-z
1/2-x,
-1/2+y,3/2-z
1/2-x,
-1/2+y,3/2-z
1/2-x,
-1/2+y,3/2-z
d(O-H),
Ǻ
0.90(6)
0.92(9)
d(H…Br),
Ǻ
2.40(7)
2.78(9)
d(O…Br),
Ǻ
3.273(5)
3.572(5)
Angle
(ОH…Br),°
162(8)
145(8)
0.91(4)
2.33(4)
3.232(5)
171(7)
0.92(9)
2.33(9)
3.223(5)
164(9)
The possibility of the simultaneous existence of different forms of nickel (II) complex in the
presence of - diimine ligands with different structure can determine some of their physico-chemical
properties . Thus, the non-equivalence of the two bromide ions in the complex I and different Ni-Br
bond lengths leads to an energy difference (different potentials) of electron addition processes to this
complex. Thus, it was previously shown [5] that for the compounds Ni (II) with two bipy ligands the
complicated peak being a superposition of two peaks is observed in the electrochemical reduction
(Figure 9) . The voltammogram for Ni(II)bipy has a classic shape.
Two complexes are crystallized from the reaction mixture obtained after the electrocatalytic
synthesis involving complexes of Ni(II) with t-bu-tpy as ligand: Compound III [Ni(t-bu-tpy)I2] and
the compound IV [Ni(t-bu-tpy)]2(H2O)I2. The crystals of compound III are larger and darker than the
crystals of the compound IV, whereby they able to separate from each other. In the process of
refining the structure of compound III the thermal vibrations of atoms C7, C8 and C9 took the
characteristic form of the disorder for the tert-butyl group. Discovered disordering was considered
and refined with occupancy of 69% versus 31%.
As a result of XRD it was revealed that crystals of the compound IV are composed from
neutral di-iodide-terpyridinenickel complex and acetone in a 1: 1 ratio.
Analysis of the geometry of III compound leads to the conclusion that the shape of the
coordination nickel sphere is a distorted square pyramid (Fig. 10). Two types of hybridization - d2sp2
(square pyramid shape of a polyhedron) and dsp3 (trigonal bipyramid) are known for CN 5, but in the
case of trigonal bipyramid the N2-Ni1-I1 and N2-Ni1-I2 angles should be approximately equals, and
the sum of valent angles in the equatorial planes must be equal 360 о. The angle between axial
substituents must be equal to 180°.
However, the angles in the molecule of compound III are varied greatly I1-Ni1-N2 101.1(1)о, I2-Ni1-N2 - 144.1(1)о, and the angle I1-Ni1-I2 is 114.77(3) о. In the case of "square
pyramid" coordination, the sum of four angles in the equatorial plane must be 360о, and the angles
between the atom in the axial position and the atoms in the equatorial plane should be equal to 90°. If
we assume atom I1 as axial, the angles between the atom in the axial position and the atoms in the
equatorial plane are equal : 101.1(1); 94.0(1); 95.3(1) and 114.77(3) , and the sum of the equatorial
angles is 352,6o . Distortions are caused by steric factors, the repulsion of large size iodine atoms .
These data suggest that the coordination of nickel in the compound III is a distorted square pyramid.
Interestingly, the coordination of trigonal bipyramid corresponding to dsp3 hybridization is realised
in a similar structure 2 [6]. The hybridization changing apparently is caused by stronger cleavage of
nickel orbitals under the action of the chlorine atoms than the iodine atoms. The bond lengths in the
molecules of compounds III and 2 [6] are shown in Table 3. Despite the different hybridization of
3
the nickel atom (d2sp2 for compound III and dsp3 for compound 2) the bond lengths Ni-N in these
complexes are different slightly.Solvate channels and packing of the molecules in the crystal of
compound III is shown in Fig. 11.
Table 3. Some bond lengths of Ni (t-bu-tpy) I2 (III) and Ni (t-bu-tpy) Cl2 (2).
In compound III
In compound 2
Bond
d, Ǻ
d, Ǻ
Ni1-Hal1
2.633(1)
2.274(2)
Ni1-Hal2
2.596(1)
2.283(2)
Ni1-N1
2.077(4)
1.961(6)
Ni1-N2
1.960(4)
2.042(5)
Ni1-N3
2.068(4)
2.088(6)
According to X-ray analysis of the complex IV it is established that the bis- terpyridine nickel
cation, I- anions and solvate water molecules in 1: 2 (1.25) ratio, respectively are in the asymmetric
portion of the crystal.
The shape of the coordination polyhedron of the Ni atom in the compound IV is distorted
octahedron (Fig. 12), this is due to with the conformational rigidity of the ligand in our opinion.
Bond lengths Ni-N are in the range 1,98(2) - 2,10(2) Ǻ, which agrees well with the bond lengths in
similar structures found in the Cambridge crystallographic database [3] .
The refinement of structure IV revealed the disorder of the tert-butyl group, namely atoms
C7, C8 and C9. Discovered disordering was recorded and verified in the following with the
population of 64% and 36%, respectively. Hydrogen bonds and ion channels in the crystal of
compound IV are shown in Fig. 13 The system of hydrogen bonds forms a tetramer of iodide ions
and water molecules.
Table 4. Parameters of hydrogen bonds in the crystal of compound IV.
Bond
Symmetry
d(O-H),
d(H…Br),
d(O…Br),
operation
Ǻ
Ǻ
Ǻ
O2-H2A…I1
1-x,-y,1-z
1.06(9)
2.65(9)
3.686(7)
O2-H2B…I1
0.99(9)
2.69(10)
3.660(7)
Angle
(ОH…Br),°
168(7)
167(7)
Experimental
X-ray diffraction experiment was carried out on a diffractometer Bruker «Smart Apex II» λ (Mo-Kα)
= 0.71073 at room temperature (20 °C) in the Department of X-ray analysis of collective use center of RFBR
(CCU CAC) on the basis of diffraction methods laboratory of IOPC of KSC.
Crystal data and main parameters of structure refinement are given in Table 5. Semi empirical
absorption accounting with the SADABS program was carried out[ 9]. The structures were solved by direct
method on the SIR program [ 11]. Positions and temperature parameters of non-hydrogen atoms were refined
firstly in isotropic and then in anisotropic approximation on the SHELX-97 program [12]. The hydrogen
atoms were placed in geometrically calculated positions and were refined in the model "rider". All calculations
were performed using the program package WinGX [ 13] and APEX2 [ 14]. Drawings of molecules and
analysis of intermolecular interactions were performed using programs ORTEP [ 15] and PLATON [ 16].
4
Table 5. Crystallographic parameters and details of the refinement of structures I and II.
Parameter
I
II
III
Color, habit
Light green prismatic
Transparent cube
Dark brown prismatic
[C20H18BrN4NiO]+, Br-,
CH2Cl2, H2O
Shingon
triclinic
Space Group
P-1
The unit cell parameters.
a =10.31(2)  =89.05(2)
b =10.86(2)  =70.47(2)
c=12.04(2)Å =86.07(2)o
3
Volume, Å
1268(3)
Z
2
Molecular weight
651.86
Density (calc.)g/сm3
1.707
The absorption coefficient,
4.151
Мо, см-1
F(000)
648
Interval 
2.26    26
R(int)
0.0526
Interval of indices
-11  h  12,
measurement
-13  k  13,
-13  l  14
Reflections measured /
5939 / 4502
independent
The number of observed
2808
reflections with I  2(I)
The final values of the
R =0.0825
divergence factors
Rw =0.2409
R all = 0.1375
Rw all = 0.2893
Parameter fit
1.113
Gross formula
[C20H20N4NiO2]2+, 2Br-
[C27H35 I2 N3 Ni], C3 H6 O
IV
Transparent, with a brownish
tinge prismatic
[C54H70N6Ni]2+, 2I-, 1.25(H2O)
monoclinic
P21/n
a =8.43(1)  = 90.00
b =16.79(2)  = 100.629(2)
c =16.19(2)Å  = 90.00o
2255.8(5)
4
566.93
1.669
4.425
monoclinic
P21/c
a =11.907(3)  =90.00
b =12.804(3)  = 90.860(5)
c =21.369(5) Å  = 90.00o
3257.5(12)
4
772.17
1.574
2.516
triclinic
P-1
a =11.281(3)  =74.70(5)
b =11.762(3)  = 79.93(5)
c =21.900(6) Å  = 85.54(5)o
2758.3(18)
2
1138.19
1.370
1.512
1128
2.43    26
0.0269
-10  h  10,
-20  k  20,
-19  l  19
12123 / 4353
1536
2.34    26
0.0645
-14  h  14,
-15  k  15,
-25  l  26
23501 / 6392
1165
1.94    26
0.0632
-13  h  13,
-14  k  14,
-26  l  26
28035 / 10749
3215
4114
5745
R =0.0465
Rw =0.1439
R all = 0.0658
Rw all = 0.1574
1.036
R = 0.0489
Rw = 0.0935
R all = 0.0899
Rw all = 0.1070
1.008
R = 0.0647
Rw = 0.1351
R all = 0.1504
Rw all = 0.1865
1.015
/
The number of refined
parameters
0.000
305
0.001
278
0.000
356
0.000
619
Conclusion
Thus, the structure of four previously undescribed complex compounds of nickel (II) with bi-and terpyridine crystals was determined by X-ray
analysis. The hybridization of nickel atom (d2sp2) with coordination number 5 in the crystal of the compound III was detected. The patterns of
molecular packing in the crystal were found. In particular, the formation of ion and solvation channels in the crystals of compounds I, II, III and
IV was descovered. It is suggested that the simultaneous existence of different nickel (II) forms in the presence of -diimine ligands with
different structure determines some of their physico-chemical properties, in particular, the reduction potentials .
Acknowledgements
This work was supported by the Russian Science Foundation № 14-23-00016.
6
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Appendix
Fig. 1 Compound 1 diagram [4].
Fig. 2 Compound 3 diagram [[7]].
8
Fig. 3. The geometry of the molecules in the crystal of compound 4 [[8]].
Fig. 4. Scheme of compound 5 molecule [[8]].
9
Fig. 5. Geometry of compound I molecules in the crystal.
Fig. 6. Packing of molecules and the hydrogen bonds in the crystal of compound I (projection along the
0x axis).
10
Fig. 7. Geometry of compound II molecules in the crystal.
Fig.8. Ion channels and hydrogen bonds in multiples of compound II (shown in phantom).
11
Figure 9. Cyclic voltammogram of NiBr2bpy (1) and NiBr2bpy2 (2) complexes (DMF, 0.1 M Bu4NBF4,
ref.SCE )
Fig. 10. The geometry of the molecules in the crystal of compound III.
12
Fig. 11. Packing of the molecules in the crystal of compound III (projection along the 0x axis).
13
Fig. 12. Geometry of compound IV molecules in a crystal.
Fig. 13. Hydrogen bonds in package of compound IV (shown in phantom).
14