Crystal structure, configurational and density functional theory analysis of nickel(II) complexes with pentadentate 1,3-pd3a-type ligands

Article abstract of DOI:10.1016/j.ica.2013.01.014

The O-O-N-N-O-type pentadentate ligands H₃1,3-pd3a and H ₃1,3-pd2ap (H₃1,3-pd3a stands for 1,3-propanediamine-N,N, N′-triacetic acid; H₃1,3-pd2ap stands for 1,3-propanediamine-N, N′-diacetic-N-3-propionic acid) and the corresponding novel octahedral nickel(II) complexes have been prepared and characterized. H₃1,3-pd3a and H₃1,3-pd2ap ligands coordinate to nickel(II) ion via five donor atoms (three deprotonated carboxylate atoms and two amine nitrogens) affording octahedral geometry in case of all investigated Ni(II) complexes. A sixth place within octahedra has been occupied by the molecule of water. A six coordinate, octahedral geometry has been established crystallographically for the K[Ni(1,3-pd3a)(H₂O)]·3H₂O complex. Structural data correlating similar chelate Ni(II) complexes have been used for an extensive strain analysis. This is discussed in relation to information obtained for similar complexes. The infra-red and electronic absorption spectra of the complexes are interpreted and compared with related complexes of known geometries. Density functional theory (DFT) has been used to model the most stable geometry isomer and Natural Energy Decomposition Analysis (NEDA) to reveal the energetic relationship of these compounds. The results from density functional studies have been compared with X-ray data. NEDA has been done for the [LNi]^- and [H₂O] units.

Full text of DOI:10.1016/j.ica.2013.01.014

Inorganica Chimica Acta 399 (2013) 146–153
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Inorganica Chimica Acta
journal homepage: www.elsevier.com/locate/ica
Crystal structure, configurational and density functional theory analysis of nickel(II)
complexes with pentadentate 1,3-pd3a-type ligands
a
a
a
a
b
´
´
´
´
´
Svetlana Beloševic , Marina Cendic , Maja Djukic , Miorad Vasojevic , Auke Meetsma ,
a,
⇑
´
Zoran D. Matovic
a Department of Chemistry, Faculty of Science, University of Kragujevac, Kragujevac SRB-34000, Serbia
b Stratingh Institute for Chemistry and Chemical Engineering, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands
a r t i c l e i n f o
a b s t r a c t
Article history:
The O–O–N–N–O-type pentadentate ligands H31,3-pd3a and H31,3-pd2ap (H31,3-pd3a stands for 1,3-
propanediamine-N,N,N0-triacetic acid; H31,3-pd2ap stands for 1,3-propanediamine-N,N0-diacetic-N-3-
propionic acid) and the corresponding novel octahedral nickel(II) complexes have been prepared and
characterized. H31,3-pd3a and H31,3-pd2ap ligands coordinate to nickel(II) ion via five donor atoms
(three deprotonated carboxylate atoms and two amine nitrogens) affording octahedral geometry in case
of all investigated Ni(II) complexes. A sixth place within octahedra has been occupied by the molecule of
water. A six coordinate, octahedral geometry has been established crystallographically for the K[Ni(1,3-
pd3a)(H2O)]ꢀ3H2O complex. Structural data correlating similar chelate Ni(II) complexes have been used
for an extensive strain analysis. This is discussed in relation to information obtained for similar com-
plexes. The infra-red and electronic absorption spectra of the complexes are interpreted and compared
with related complexes of known geometries. Density functional theory (DFT) has been used to model
the most stable geometry isomer and Natural Energy Decomposition Analysis (NEDA) to reveal the ener-
getic relationship of these compounds. The results from density functional studies have been compared
with X-ray data. NEDA has been done for the [LNi]ꢁ and [H2O] units.
Received 18 October 2012
Received in revised form 4 January 2013
Accepted 20 January 2013
Available online 31 January 2013
Keywords:
Nickel(II) complexes
pd3a-Type ligands
Crystal structure
DFT modeling
NEDA analysis
Ó 2013 Elsevier B.V. All rights reserved.
1. Introduction
the d-electron configuration and size of the central metal ion are
important issues [8–10].
Nickel and its compounds are released into the atmosphere
from natural and anthropogenic sources [1]. Nickel is present in
the environment and also it is an important element in modern
industry. For many years there has been much more concern about
the toxicity of Ni, because Ni is an essential element to plants and
many other biota. Human health can be threatened by toxicity of
many metals and among other by nickel. Because of the signifi-
cance of nickel in human health and the environment our research
group studied the nature of Ni(II) compounds for many years [2–5].
We also took a survey of polyaminopolycarboxylate which are eas-
ily coordinated to ions of metal. A number of edta-type ligands
were synthesized in our research group [3,6,7]. Two new edta-type
acids, H31,3-pd3a and H31,3-pd2ap were prepared and reported
here. The 1,3-pd3a-type chelates can surround metal forming 5-
and 6-membered rings. Depending on the size of the ring, different
isomers can be formed: cis-equatorial, trans-equatorial and cis-
polar (Fig. 1.). The previous paper described the [Cu(pd3a-type)X]ꢁ
complex found in cis-equatorial configuration which has been
crystallographically verified [7]. From a structural point of view,
H31,3-pd3a and H31,3-pd2ap acids are unsymmetrical ligands
of 1,3-pd3a-type which contains one 6-membered 1,3-propanedi-
amine ring, 5-membered acetate rings and one b-propionic ring
in case of the H31,3-pd2ap ligand. Here we reported two new syn-
thesized complexes of Ni(II): K[Ni(1,3-pd3a)(H2O)]ꢀ3H2O and
Ba[Ni(1,3-pd2ap)(H2O)]2ꢀ12H2O. The IR and electronic spectra are
discussed in relation to their geometry.
To confirm the geometry of the isomers we undertook DFT com-
putational experiments [11]. Also, for better understanding of new
structures we used DFT (DFT stands for density functional theory)
theory in order to determine the actual energetic relationship.
Computational calculations are compared with X-ray results in
case where they were present. Natural Energetic Decomposition
Analysis (NEDA) [12] has been done for the LNiꢀ ꢀ ꢀOH2 unit.
2. Experimental
2.1. Materials
⇑
Reagent grade, commercially available, chemicals were used
Corresponding author. Tel.: +381 34336223; fax: +381 34335040.
E-mail address: zmatovic@kg.ac.rs (Z.D. Matovic´).
without further purification. 1,3-Propanediamine-N,N0-diacetic
0020-1693/$ - see front matter Ó 2013 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.ica.2013.01.014

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S. Beloševic et al. / Inorganica Chimica Acta 399 (2013) 146–153
Fig. 1. Geometrical isomerism of six-coordinate [M(pd3a-type)Xn] complexes: n = 1.
acid dihydrochloride, H21,3-pddaꢀ2HCl, was prepared by the meth-
od of Igi and Douglas [13]. 3-chloropropionic and chloroacetic
acids were purchased from Fluka and used as supplied.
ume (i.e., 20 ml). The reaction mixture (volume 20 ml) was of a
light yellow color.
2.3.3. Preparation of the potassium(1,3-propanediamine-N,N,N0-
triacetato(aquo)) nickelate(II) trihydrate, K[Ni(1,3-pd3a)(H2O)]ꢀ3H2O
(1)
2.2. Physical measurements
Elemental microanalyses for C, H, N were performed at the
Microanalytical laboratory, Faculty of Chemistry, University of Bel-
grade, Serbia. IR spectra in the 400–4000 cmꢁ1 region were re-
corded on a Perkin–Elmer FT-IR spectrophotometer Spectrum
One, using the KBr pellets technique. Electronic absorption spectra
were recorded on a Perkin–Elmer Lambda 35 spectrophotometer.
Melting points were measured by Stuart melting device with accu-
racy 1 °C.
The solution of NaOH (2.52 g, 63 mmol) in 5 ml H2O was added
to the prepared solution containing H31,3-pd3a (25 ml). That solu-
tion was then filtered to remove the excess of calcium hydroxide.
The filtrate was then added to the solution of NiCl2ꢀ6H2O (4.99 g,
21 mmol) in 8 ml H2O. The resulting mixture was stirred at 65 °C
for an hour and was then desalted with the gel-filtration technique
by a passage through a G-10 Sephadex column, with distilled water
as the eluent. The desalted solution was poured into a 5 ꢂ 60 cm
column containing Dowex 1-X8 (200–400 mesh) anion exchange
resin in the Clꢁ form. The column was then washed with water
(eluting zero charged cis-polar-[Ni(1,3pdda)(H2O)2] complex) and
eluted with 0.1 M KCl. Two bands appeared on the column. The ob-
tained eluate of each band was reduced to a small volume and then
desalted. The second pale-blue eluate presents K2[Ni(1,3-pdta)] of
known structure. The eluate of the first band (cis-polar isomer) was
reduced to a volume of 3 ml and stored in a desiccator over ethanol
for several days. The blue crystals of cis-polar-K[Ni(1,3-pd3a)
(H2O)]ꢀ3H2O were collected, washed with ethanol and then
ether, and air-dried (1 g). Melting point: 227 °C. Anal. Calc. for
C9H21KN2NiO10; Mw = 415.06: C, 26.04; H, 5.10; N, 6.75. Found:
C, 27.00; H, 5.03; N, 6.85%.
2.3. Preparation of compounds
2.3.1. Preparation of condensation mixture containing 1,3-
propanediamine-N,N,N0-triacetic acid, H31,3-pd3a
The 1,3-propanediamine-N,N,N0-triacetic acid, H31,3-pd3a was
prepared by the method described elsewhere [7]. Monochloroace-
tic acid (11.5 g, 120 mmol) was dissolved in 42 ml of demineralized
water and 4.7 g (84 mmol) calcium oxide was added to the solu-
tion. The pH rose from 1.0 to 11.2. Subsequently, 3.11 g (42 mmol)
of 1,3-propanediamine was added in 10 min. The temperature was
kept at about 50 °C without additional heating. After 1 h the tem-
perature was increased to 70 °C and the resulting mixture was left
for additional 5.5 h. During the entire reaction, the pH was kept
constant at 7.5–8.0 by the addition of calcium oxide. At the end
of the reaction, a total of 1.9 g (34 mmol) of calcium oxide was
added. The reaction mixture was filtered warm over a glass filter
to remove the excess of calcium hydroxide. The reaction mixture
(volume 50 ml) contains 1,3-pd3a (50%), 1,3-pdta (18%) i 1,3-pdda
(23%) ligands. This was checked by means of chromatography of
copper(II) complexes with above mixture.
2.3.4. Preparation of the barium-bis{(1,3-propanediamine-N,N0-
diacetato-N0-propionato)(aquo) nickelate(II)} dodecahydrate,
Ba[Ni(1,3-pd2ap)(H2O)]2ꢀ12H2O (2)
The solution of NiCl2ꢀ6H2O (9.50 g, 40 mmol) in 26.66 ml H2O
(pH 2.84) was added to the prepared solution containing H31,3-
pd2ap (40 mmol) acid. The solution was then heated and stirred
at 65 °C for an hour with maintained pH at 7.58 (by adding the
solution of NaOH). The color of the solution during the reaction
and after filtration was blue. The resulting filtrate was then
desalted with the gel-filtration technique by passage through a
G-10 Sephadex column, with distilled water as the eluent. The
desalted solution was poured into a 4 ꢂ 40 cm column containing
Dowex 1-X8 (200–400 mesh) anion exchange resin in the Clꢁ form.
The column was then washed with water (eluting again zero
charged cis-polar-[Ni(1,3pdda)(H2O)2] complex) and eluted with
0.05 M BaCl2. Two bands appeared on the column. The obtained
eluate of each band was reduced to a small volume and then de-
salted. The second blue eluate presents trans(O5)-Ba[Ni(1,3-
pddadp)] isomer of known structure. The eluate of the first band
(cis-polar Ni-1,3-pda2p isomer) was reduced to a volume of 2 ml
and stored in a desiccator over ethanol for a week. The light blue
crystals of cis-polar-Ba[Ni(1,3-pd2ap)(H2O)]2ꢀ12H2O were col-
lected, washed with ethanol and then ether, and air-dried
2.3.2. Preparation of condensation mixture containing 1,3-
propanediamine-N,N0-diacetic-N0-3-propionic acid, H31,3-pd2ap
Solution 1. H21,3-pddaꢀ2HCl (10.52 g, 40 mmol) was dissolved in
15 ml of water and solution of 6.40 g (160 mmol) NaOH in 16 ml of
water was added (pH 5).
Solution 2. 3-Chloropropionic acid (4.34 g, 40 mmol) was dis-
solved in 8.8 ml of water and solution of 1.6 g (40 mmol) NaOH
in 4 ml of water was added (pH 11).
Solutions 1 and 2 were mixed (pH 9–10) and the mixture was
stirred and heated at 50 °C for 2 h. After that, the mixture was
heated at 70 °C for 32 h. During the entire reaction, the pH was
kept constant at 7.0–8.0 by the addition of sodium hydroxide.
The reaction mixture was filtered warm over a glass filter to re-
move the excess of sodium hydroxide and the solution slowly
evaporated in the water-bath at 40 °C until it reached small vol-

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S. Beloševic et al. / Inorganica Chimica Acta 399 (2013) 146–153
Table 2
(1.25 g). Melting point: 275 °C. Anal. Calc. for C20H58BaN4Ni2O26
;
Structural data for K[Ni(pd3a)(H2O)]ꢀ3H2O (1).
Mw = 1025.39: C, 23.43; H, 5.70; N, 5.46. Found: C, 23.20; H,
5.95; N, 5.16%.
M–L bond lengths (Å)
M–O–C angles (°)
Ni–O1
Ni–O3
Ni–O5
Ni–O7
Ni–N1
Ni–N2
2.0235(1)
2.0730(1)
2.0401(1)
2.0899(1)
2.0576(1)
2.1002(1)
Ni–O1–C1
Ni–O3–C7
Ni–O5–C9
114.95(1)
113.87(9)
114.97(1)
2.4. Crystal structure analysis
Suitable blue-colored, block-shaped crystals were obtained by
recrystallisation from a mixture of H2O and ethanol. A crystal with
the dimensions of 0.47 ꢂ 0.43 ꢂ 0.39 mm was mounted on top of a
glass fiber and aligned on a Bruker [14] SMART APEX CCD diffrac-
tometer (Platform with full three-circle goniometer). The crystal
was cooled to 100(1) K using the Bruker KRYOFLEX low-tempera-
ture device. Intensity measurements were performed using graph-
cis angles (°)
O1–Ni–O3
O1–Ni–O5
O1–Ni–O7
O1–Ni–N1
O3–Ni–O5
O3–Ni–O7
99.14(4)
90.91(5)
87.12(5)
82.76(5)
88.52(5)
86.12(5)
O3–Ni–N2
O5–Ni–N1
O5–Ni–N2
O7–Ni–N1
O7–Ni–N2
N1–Ni–N2
82.26(5)
91.81(6)
83.78(6)
93.65(6)
98.32(6)
95.89(5)
ite monochromated Mo K
a radiation from a sealed ceramic
diffraction tube (SIEMENS). The final unit cell was obtained from
the xyz centroids of 5929 reflections after integration. Intensity
data were corrected for Lorentz and polarization effects, scale var-
iation, for decay and absorption: a multi-scan absorption correc-
tion was applied, based on the intensities of symmetry-related
reflections measured at different angular settings (SADABS) [15],
and reduced to Fo2. The program suite SAINTPLUS was used for space
group determination (XPREP) [14]. The unit cell [16] was identified
as triclinic. Reduced cell calculations did not indicate any higher
trans angles (°)
O1–Ni–N2
O3–Ni–N1
174.48(6)
178.07(5)
O5–Ni–O7
173.92(5)
2.5. Computational details
After testing various combinations of functional and basis sets,
geometries for Ni(II) complexes were optimized using GAUSSIAN 09
A01 program [12]. Starting geometries were taken either from
experimental X-ray structures or were pre-optimized using the
MM+ implemented in HYPERCHEM 7.01 [23]. For these calculations,
we used the unrestricted (triplet) B3LYP hybrid functional and
the Ahlrichs TZVP basis set [24]. The Polarizable Continuum Model
(PCM) using the integral equation formalism variant (IEFPCM) with
water as a solvent has been employed for all complexes [12]. Sub-
sequent frequency calculations at the same level of theory verified
that the optimized structures were true local minima on the poten-
tial energy surface i.e. there were no imaginary frequencies. For
calculating molecular interactions we used NEDA (NEDA stands
for Natural Energy Decomposition Analysis) analyses [12,25].
ꢀ
metric lattice symmetry [17]. Space group, P1, was determined
from considerations of the unit cell parameters, statistical analyses
of intensity distributions: the E-statistics [18] were indicative of a
centrosymmetric space group. Examination of the final atomic
coordinates of the structure did not yield extra crystallographic
or metric symmetry elements [19,20]. The structure was solved
by direct methods using the program SIR2004 [21]. Final refinement
on F2 was carried out by full-matrix least-squares techniques. Crys-
tal data and numerical details on data collection and refinement
are given in Table 1. Molecular geometry data are collected in
Table 2.
Table 1
Crystal data and details of the structure determination for K[Ni(pd3a)(H2O)]ꢀ3H2O.
3. Results and discussion
Formula
K+ꢀ[C9H15N2NiO7]ꢁꢀ3(H2O)
415.06
Formula weight (g molꢁ1
)
3.1. Preparation of unsymmetrical diaminotricarboxylate ligands and
corresponding Ni(II) complexes and their characterization
Crystal system
Space group, No.[22]
triclinic
P1, 2
ꢀ
a (Å)
b (Å)
c (Å)
7.2681(5)
7.9578(6)
15.377(1)
86.982(1)
78.640(1)
63.532(1)
779.93(9)
This paper deals with the two nickel(II) complexes with penta-
dentate edta-type ligands containing 5- and/or 6-membered car-
boxylate arms: 1,3-propanediamine-N,N,N0-triacetate (1,3-pd3a)
and 1,3-propanediamine-N0-diacetate-N-3-propionate (1,3-pd2ap).
Chelates of edta-type ligands can be prepared in several
ways: with the condensation method starting from neutralized
a
(°)
b (°)
(°)
V (Å3)
c
H
range unit cell: minimum–maximum (°); 2.70–29.70; 5929
a- or b-monohalogencarboxylic acid and corresponding diamine;
reflections
Formula Z
2
by condensation of acrylic acid and diamine (in case you wish to
obtain chelates with propionic arms); by condensation of dihalo-
gen derivatives of diamine with diverse amino-acids. In this paper
we deal with chelate pentadentate O–O–N–N–O ligands: H31,3-
pd3a and H31,3-pd2ap. We prepared them using 1,3-propanedi-
amine, neutralized monochloracetic acid or 3-chloropropionic acid
(in case of H3pd2ap). The calcium salt of H3ed3a acid was success-
fully isolated with the yield over 80% [7]. On the other hand, in case
of H31,3-pd3a and H31,3-pd2ap acids we were able to provide only
condensation mixtures, and used them for complexation with the
Ni(II) ion. Reaction has been done by using the nickel(II) chloride
hexahydrate (NiCl2ꢀ6H2O) salt and neutralized chelate acids as gi-
ven in the experimental part of work. The chromatography column
separation (dowex resin in an anionic Clꢁ form) was used. Apart
from the isomerism given in Fig. 1., the H31,3-pd2ap acid upon
complexation with the metal ion may actually yield two different
cis-polar isomers (Fig. 2), that is cis-polar(A) with a five-membered
SpaceGroup Z
2
1
Z0 (=Formula_Z/SpaceGroup_Z)
qcalc (g cmꢁ3
)
1.767
432
15.64
blue, block
F(000), electrons
ꢁ1
ꢀ
a
l
(Mo K
) (cm
)
Color, habit
Approx. crystal dimension (mm)
Radiation type; k (Å)
h range; minimum–maximum (°)
Index ranges
0.47 ꢂ 0.43 ꢂ 0.39
ꢀ
a
Mo K
, 0.71073
3.12, 28.28
h: ꢁ9 ? 9; k: ꢁ10 ? 10; l:
ꢁ20 ? 20
Minimum–maximum absorption
transmission factor
X-ray exposure time (h)
Total data
0.4894–0.5406
8.0
7144
3710
3596
0.0122
0.0195
Unique data
Data with criterion: (Fo P 4.0
r
(Fo))
]
2
2
Rint
Rsig
=
=
R
R
[|Fo ꢁ Fo2(mean)|]/
R
[Fo
2
r
(Fo2)/
R
[Fo
]

´
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S. Beloševic et al. / Inorganica Chimica Acta 399 (2013) 146–153
lecular and intramolecular contacts shorter than the sum of the
van der Waals radii [27] for the atoms.
In the crystal structure the Ni(II) ion is coordinated by six donor
atoms originating from: three deprotonated oxygen atoms of car-
boxylate groups, one oxygen atom from water and two nitrogen
atoms of diamine. The complex has distorted octahedral geometry.
Positions of carboxylate groups define the cis-polar geometry of
this complex, as one acetate ring occupy nickel in an axial position,
while the other two are in the equatorial plane. There are two long-
er bonds: Ni–O7 (2.0899(15) Å) and Ni–O3 (2.0730(12) Å). The
other distances in anionic complex are within the range: from
2.0235(11) Å to 2.0401(14) Å: Ni–N1 2.0576(14) Å; Ni–N2
2.1002(12) Å; Ni–O1 2.0235(11) Å; Ni–O3 2.0730(12) Å; Ni–O5
2.0401(14) Å; Ni–O7 2.0899(15) Å. The cis angles are in range from
82.26(5) Å to 99.14(4) Å and trans angles in range from 173.92(5) Å
to 178.07(5) Å. As can be seen (Fig. 3), the anion unit of [Ni(1,3-
pd3a)(H2O)]ꢁ contains different types of conformation rings. The
equatorial 1,3-propanediamine ring is found in a chair conforma-
tion. The two five-membered acetate rings in the equatorial plane
has a twisted-envelope conformation while the axial acetate ring is
planar.
Fig. 2. cis-polar isomers of six-coordinate [M(1,3-pd2ap)(H2O)] complex.
acetate ring in an axial position and cis-polar(B) with switched ace-
tate and b-propionate rings.
Finally, we isolated: blue crystals of cis-polar K[Ni(pd3a)
(H2O)]ꢀ3H2O and a light blue powder of cis-polar(B)-Ba[Ni(1,3-
pd2ap)(H2O)]2ꢀ12H2O. The complexes were characterized by
microanalysis and spectroscopic techniques (IR, UV–Vis). The
structural and spectral data of similar complexes are compared
and discussed in relation to their geometry. In case of
K[Ni(pd3a)(H2O)]ꢀ3H2O the cis-polar geometry was found and con-
firmed by an X-ray analysis. To explore the geometry of the
Ba[Ni(1,3-pd2ap)(H2O)]2ꢀ12H2O complex we analyzed and com-
pared spectral results (IR and UV–Vis) and computational methods.
Results from computational calculations that we used (Gaussian,
Firefly and NBO [26]/NEDA) serve for better understanding of ener-
getic and structural properties.
3.3. Structural parameters and strain analysis of nickel(II)-1,3-pd3a-
type complexes in relation to their geometry
The strain in complexes of the M(II)edta-type can be considered
from [28–30]:
(a) cis and trans angles located around the central metal ion;
(b) bond angles sum from different rings;
(c) Ni–O–C or Ni–N–C bond angles;
(d) bond angles which coordinated nitrogen build with others.
3.2. Description of the crystal structure of K[Ni(1,3-pd3a)(H2O)]ꢀ3H2O
(1)
Structural data related to stereochemistry of Ni(II) complexes
are given in Table 3.
A structural diagram of the cis-polar [Ni(1,3-pd3a)(H2O)]ꢁ an-
ion, with the adopted atom-numbering scheme and the packing
of the molecules in the unit cell are shown in Fig. 3. Each asymmet-
ric unit contains one formula unit, consisting of five moieties: a K
cation, an anionic Ni-complex and three H2O molecules. The tri-
clinic unit cell contains ten discrete units: two cations, two anions
and six water molecules. A search of the distances yielded intermo-
The strain analysis has been carried out for cis-polar-
[Ni(pd3a)(H2O)]ꢁ for which we obtained crystal structure. Com-
plexes [Ni(pdta)]2ꢁ and cis-eq-[Ni(ed3a)(H2O)]ꢁ were taken for
the comparison of obtained values (See Table 3). We compared
R
D
(Oh) (the sum of the absolute values of the deviations from
90° of the L–M–L0 bite angles),
(the deviation from the ideal
of the corresponding chelate rings’ bond angle sum), (M–O–C)
D
R
D
Fig. 3. X-ray crystal structure of the K[Ni(1,3-pd3a)(H2O)]ꢀ3H2O: Ortep diagram of the [Ni(1,3-pd3a)(H2O)]ꢁ anion; Crystal packing view along c axis.

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S. Beloševic et al. / Inorganica Chimica Acta 399 (2013) 146–153
150
Table 3
Strain analysis of nickel complexes with pd3a and comparable pdta ligands.
Complex
R
D
(Oh)a
D
R
(ring)b
D
(M–O–C)c
R
D
(N)d
Ref.
E(T)
R
G
R
G
cis-polar-[Ni(1,3-pd3a)(H2O)]ꢁ
59
+34
+1
ꢁ5
+5
+5
+11
+14
16
This work
cis-eq-[Ni(ed3a)(H2O)]ꢁ
70
60
ꢁ13
ꢁ1
ꢁ11
ꢁ11
+7
+6
+3
+6
[31]
[32]
[Ni(1,3-pdta)]2ꢁ
+33
+1
11
a
b
c
R
D
D
R
D
R
(Oh) is the sum of the absolute values of the deviations from 90° of the L–M–L0 bite angles. All values rounded off to the nearest degree.
(ring) is the deviation from the ideal of the corresponding chelate rings’ bond angle sum.
(M–O–C) (ring) is the mean value of the deviation of the corresponding rings’ M–O–C bond angle from the 109.5°.
(N) is the sum of the absolute values of the deviations from 109.5° of the six bond angles made by nitrogen atoms. A mean value for the two nitrogens is reported.
d
D
(the mean value of the deviation of the corresponding rings’ M–O–
C bond angle from the 109.5°) and (N) (the sum of the absolute
values of the deviations from 109.5° of the six bond angles made by
nitrogen atoms). The total deviation of octahedral angles ( (Oh))
depends on the size of the central ion [33] and the complex geom-
etry. Comparing
(Oh) values for cis-polar [Ni(pd3a)(H2O)]ꢁ, cis-
R
D
R
D
R
D
equatorial-[Ni(ed3a)(H2O)]ꢁ and trans(O5)-[Ni(pdta)]2ꢁ, one can
see that complexes with the six-membered T backbone ring show
lower deviation (59° and 60°) with respect to the E ring of
[Ni(ed3a)(H2O)] (70°). The 1,3-propanediamine (T ring) in cis-po-
lar-[Ni(1,3-pd3a)(H2O)]ꢁ shows a positive value of total deviation
by +34° again being quite close to trans(O5)-[Ni(pdta)]2ꢁ (+33°).
According to Table 3 all the examined structural strain parameters,
DR(ring), D(M–O–C) and RD(N) indicate a slightly lower strain
(deviation) of (1) than was found for the other two complexes
due to a less rigid pentadentate system with the 1,3-propanedi-
amine ring.
3.4. Computational chemistry
Having prepared nickel(II) complexes with pentadentate 1,3-
pd3a-type ligands with 5- and 6-membered carboxylate chelates,
one can compare their experimental spectroscopic and geometry
properties against the results of computational calculations. At
the first glance, we optimized the geometries of each of the poten-
tial geometric isomers (Figs. 1 and 2.) using DFT method imple-
mented in Gaussian09 [12]. We have modeled all three possible
geometrical isomers (cis-equatorial, cis-polar (A and B in case of
(2)) and trans-equatorial). The results obtained for (1) verified
the cis-polar isomer as the most energetically stable one: by
4.7 kcal/mol related to the cis-equatorial and just 0.1 kcal/mol re-
lated to the trans-equatorial isomer (Table 4).
Fig. 4. DFT optimized structure of the cis-polar(B)-[Ni(1,3-pd2ap)(H2O)]ꢁ anion.
cis-polar(B) isomer (Fig. 4) has been found as the most favorable.
Unfortunately, in the last compound, we failed to isolate a crystal
suitable for the X-ray to verify the proposed geometry.
In addition, we did NEDA calculations [12] using Firefly [25]
EES. We were interested to find out the energetics of LNiꢀ ꢀ ꢀOH2
interaction ([Ni(ed3a)(H2O)]ꢁ has been taken for comparison) as
these usually reflect how easy the pentacoordinated complex turns
on the hexacoordinated one. In other words, we were able to see
how electron-rich or electron-poor the pentacoordinated complex
behave toward the incoming molecule of water (Table 5). Intermo-
lecular forces and energy interactions inside the molecule are the
main characteristics of NEDA results.
As can be seen (see Table 4), observed bond lengths of the
experimental structure (1) and DFT calculations are in very good
agreement. The bond and angle differences were derived as a result
of solid state environment influence. In complex (2) the calculated
Table 4
Comparison of experimental (X-ray) and Gaussian (B3LYP/TZVP/PCM) obtained data for [Ni(1,3-pd3a-type)(H2O)] complex.
Ni–N (Å) in-plane Exp:
Gauss
Ni-O (Å) in-plane Exp:
Gauss
Ni–O (Å) axial Exp:
Gauss
Ni–O–C (°) (av.) Exp:
Gauss
cis-angles (°) (av.) Exp:
Gauss
trans-angles (°) (av.) Exp:
Gauss
Comparison of experimental (X-ray) and optimized [Ni(1,3-pd3a)(H2O)]ꢁ structure
2.058:2.105
2.100:2.135
2.024:2.066
2.073:2.061
2.040:2.054
114.6:115.8
90.02:89.98
175.5:177.4
2.090:2.265a
Geometrical isomer
cis-polar-[Ni(1,3-pd3a)(H2O)]ꢁ
Cis-polar-[Ni(1,3-pd2ap)(H2O)]ꢁ
Energy differences calculated in kcal/molb
cis-equatorial
cis-polar
4.7
0
1.6
0
trans-equatorial
0.1
0.16
a
Water molecule.
b
The isomer with the lowest energy has been indicated with 0 kcal/mol.

´
151
S. Beloševic et al. / Inorganica Chimica Acta 399 (2013) 146–153
Table 5
Contribution of NEDA (kcal/mol) calculated components.
CT
ES
POL
XC
DEF(SE) H2O
DEF(SE) Nipd3a-type
DE
[Ni(ed3a)(H2O)]ꢁ
ꢁ70.30
ꢁ49.10
ꢁ48.95
ꢁ36.90
ꢁ43.45
ꢁ39.67
ꢁ42.96
ꢁ22.28
739.82
645.70
115.68
97.35
88.10
49.40
55.65
41.70
ꢁ20.06
ꢁ16.62
ꢁ15.14
[Ni(1,3-pd3a)(H2O)]ꢁ
[Ni(1,3-pd2ap)(H2O)]ꢁ
ꢁ820.82
ꢁ710.78
ꢁ20.6 kcal/mol, showing the highest
DE value. The lowest DE for
In Table 5 the parameters of our interest are listed as follows:
CT stands for Charge Transfer; ES stands for Electrostatic compo-
nent; POL stands for Polarization component; XC stands for Ex-
change–correlation component; DEF stands for deformation
(2) (ꢁ15.14 kcal/mol) makes [Ni(1,3-pd2ap)(H2O)]ꢁ the most
affordable to release the water molecule in a potential substitution
reaction.
component and
DE stands for Total energy interaction:
3.5. Spectral analysis
D
E ¼ CT þ ES þ DEF þ BSSE;
where BSSE stands for basis set superposition error [12]. Charge
Transfer (CT) and Electrostatic component (ES) terms provide high-
er contribution to total energy interaction than the other terms.
From this point of view [Ni(ed3a)]ꢀ ꢀ ꢀwater complex is bound by
3.5.1. IR spectra of Ni(II) complexes with 1,3-pd3a-type ligands
Asymmetric carboxylate stretching frequencies between pro-
tonated carboxylate groups (1700–1750 cmꢁ1) and coordinated
carboxylate groups (1600–1650 cmꢁ1) [34–36] have long been
Fig. 5. Electronic absorption spectra of Ni(II) complexes: Nied3a
; Nipd3a
; Nipd2ap
.
Table 6
Electronic absorption data of Ni(II) complexes with pentadentate H31,3-pd3a and H31,3-pd2ap and comparable H3ed3a ligands.
Complex
Absorption
Assignments (Oh)
Ref.
k (cmꢁ1
)
e
cis-equatorial-[Ni(ed3a)(H2O)]ꢁ
I
II
III
IV
10.00
13.03
16.77
26.24
26
5
11
20
3A2g
?
3T2g(F)
[33]
?1Eg (D)
?3T1g(F)
?3T1g(P)
cis-polar-[Ni(pd3a)(H2O)]ꢁ
I
II
III
IV
9.36 (sh)
11.04
13.12
9.5
11.8
4.8
6
This work
16.67
27.85
9.80 (sh) 10.63
7.9
17.9
I
cis-polar-[Ni(1,3-pnd3a)]
II
III
IV
13.14
16.84
27.32
18.7
6.6
11.5
16
[39]
cis-polar-[Ni(1,3-pd2ap)(H2O)]ꢁ
I
II
III
IV
10.23
13.00
16.65
27.06
30.9
6.5
9.5
This work
13.2

´
S. Beloševic et al. / Inorganica Chimica Acta 399 (2013) 146–153
152
established as a criterion for distinguishing them. There is a gener-
ally accepted rule that the frequency assigned to five-membered
rings [37] lies at a higher energy level than the corresponding fre-
quency of six-membered chelate rings [38]. The IR data reported
here for diaminotricarboxylate nickel(II) complexes support the
above trend regarding the asymmetric frequencies of carboxylate
groups. The frequencies at 1602 cmꢁ1 and 1598 cmꢁ1 were as-
signed to the moieties of the five-membered acetato arms of Ni-
pd3a and Ni-pd2ap. The shoulder at 1571 cmꢁ1 from asymmetric
stretching vibrations of the b-propionate six-membered ring
proves that we isolated the Ni-pd2ap complex (see Supplemen-
tary). The absence of other absorptions at 1700–1750 cmꢁ1 show
that all carboxylate groups are coordinated.
1,3-propanediamine T ring makes LNiꢀ ꢀ ꢀOH2 energy interaction of
nickel(II) complexes lower than complexes imposed by E ring.
Acknowledgments
The authors are grateful to the Serbian Ministry of Science and
Education for the financial support (Project No. III41010). We also
´
appreciate Miss Tijana Matovic for her help in English.
Appendix A. Supplementary data
CCDC 900434 contains the supplementary crystallographic data
for this paper. These data can be obtained free of charge from The
Cambridge Crystallographic Data Centre via http://www.ccdc.ca-
m.ac.uk/data_request/cif. Supplementary data associated with this
article, such as hydrogen-bonding tables, IR spectra can be found,
in the online version, at http://dx.doi.org/10.1016/j.ica.2013.01.
014.
3.5.2. Electronic absorption spectra of Ni(II) complexes with 1,3-pd3a-
type ligands
Electronic absorption spectra were given in Fig. 5. We observed
Ni-1,3-pd3a, Ni-1,3-pd2ap and Ni-ed3a or cis-polar-[Ni(1,3-
pnd3a)]ꢁ [39] (1,3-pnd3a stands for 1,3-pentanediamine-N,N,N0-
triacetate anion) for the purpose of comparison. In cases of Ni-
1,3-pd3a, Ni-1,3-pd2ap and Ni-1,3-pnd3a complexes containing
the six-membered 1,3-propanediamine ring, the expansion of the
first absorption band on the lower energy side is expected. This oc-
curs as a result of a less pronounced presence of the tetragonal li-
gand field (D4h model). The best spectral interpretation of Ni(II)
complexes can be achieved over (Oh) model: 3A2g ? 3T2g(F) (band
I), 3A2g ? 3T1g(F) (band III) and 3A2g ? 3T1g(P) (band IV) (Fig. 5).
Each compound contains shoulder at about 13000 cmꢁ1 (band
II) on a higher energy side of the spin-allowed transition (see Ta-
ble 6). This appearance occurs as a result of spin–orbital coupling.
The bands I, III and IV (usually reflecting an average ligand field
strength – LFS) of Ni-1,3-pd3a and Ni-1,3-pd2ap were compared to
the Ni-ed3a or Ni-1,3-pnd3a [39] complex. Generally, the bands
belonging to complexes with 1,3-propanediamine backbone are
moved to higher energy which means that they have a stronger li-
gand field. Comparing Ni-1,3-pd3a and Ni-ed3a complexes, LFS
shift occurs as a consequence of the presence of two carboxylate
rings in the equatorial plane that exert greater influence on d-orbi-
tal along the x and y axes. Less molar absorptivity of (1) and (2)
(see Table 6) with regards to the Ni-ed3a complex is a consequence
of the presence of a less rigid six-membered 1,3-propanediamine
ring.
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