Palladium(II) complexes of 2-pyridylmethylamine and 8-aminoquinoline: A crystallographic and DFT study

Article abstract of DOI:10.1016/j.molstruc.2015.02.077

Two nominally square planar palladium(II) chelates: dichloro-(2-aminomethylpyridine-N,N′)-palladium(II) ([Pd(L1)Cl₂]) and dichloro-(8-aminoquinoline)-palladium(II) ([Pd(L2)Cl₂]) have been synthesised and studied by X-ray crystallography and DFT methods. [Pd(L1)Cl₂] crystallised in the monoclinic space group C2/c. In the solid state this compound exists as a one-dimensional supramolecular structure supported by N-HCl hydrogen bonds and metallophilic PdPd interactions. The same hydrogen bonding motif leads to a two-dimensional supramolecular structure in the case of [Pd(L2)Cl₂]; this structure is devoid of metallophilic interactions. DFT simulations show that the planar geometry of [Pd(L1)Cl₂] in the solid state is not the lowest energy conformation. An out-of-plane distortion of the methylene group leads to a structure ca. 11 kJ mol^-1 lower in energy. The NBO partial charges provide insight into the stability of the hydrogen bonding motif. TD-DFT calculations were used to delineate the experimental UV-visible spectra.

Full text of DOI:10.1016/j.molstruc.2015.02.077

Journal of Molecular Structure 1091 (2015) 74–80
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Palladium(II) complexes of 2-pyridylmethylamine
and 8-aminoquinoline: A crystallographic and DFT study
⇑
Kate J. Akerman, Chané Venter, Leigh A. Hunter, Matthew P. Akerman
School of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
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
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
Two cis-dichloropalladium(II)
chelates were synthesised.
The chelates were studied by single
crystal X-ray crystallography.
Two different supramolecular
structures were formed.
DFT simulations were used to
understand the H-bonding.
Transition energies and oscillator
strengths were calculated using TD-
DFT.
a r t i c l e i n f o
a b s t r a c t
Two nominally square planar palladium(II) chelates: dichloro-(2-aminomethylpyridine-N,N0)-
palladium(II) ([Pd(L1)Cl2]) and dichloro-(8-aminoquinoline)-palladium(II) ([Pd(L2)Cl2]) have been syn-
thesised and studied by X-ray crystallography and DFT methods. [Pd(L1)Cl2] crystallised in the mono-
clinic space group C2/c. In the solid state this compound exists as a one-dimensional supramolecular
structure supported by NAHꢁ ꢁ ꢁCl hydrogen bonds and metallophilic Pdꢁ ꢁ ꢁPd interactions. The same
Article history:
Received 19 January 2015
Received in revised form 24 February 2015
Accepted 24 February 2015
Available online 3 March 2015
hydrogen bonding motif leads to
a two-dimensional supramolecular structure in the case of
Keywords:
[Pd(L2)Cl2]; this structure is devoid of metallophilic interactions. DFT simulations show that the planar
geometry of [Pd(L1)Cl2] in the solid state is not the lowest energy conformation. An out-of-plane distor-
tion of the methylene group leads to a structure ca. 11 kJ molꢂ1 lower in energy. The NBO partial charges
provide insight into the stability of the hydrogen bonding motif. TD-DFT calculations were used to delin-
eate the experimental UV–visible spectra.
2-Pyridylmethylamine
8-Aminoquinoline
DFT
TD-DFT
X-ray crystallography
Palladium(II)
Ó 2015 Elsevier B.V. All rights reserved.
Introduction
these compounds i.e. 1:1, 1:2 and 1:3. These variable ratios lead
to a range of coordination geometries. These ligands have been
The bidentate N,N0-donor ligands 2-pyridylmethylamine (amp)
and 8-aminoquinoline (amq) have been coordinated to a variety
of metal centres including, but not restricted to, Pt(II), Cu(II),
Zn(II), Fe(II), Ru(II), Sn(II), Cd(II), Hg(II), Cr(III) and Co(III) [1–14].
Various metal to ligand ratios have been used in the synthesis of
favoured as the nitrogen donors stabilise the metal centres and
the aromatic rings yield complexes with many desirable fluores-
cent and structural properties [5]. The coordination complexes of
these ligands have therefore found application in a variety of inter-
esting studies.
Much of the coordination chemistry research into these ligands
was fuelled by the discovery of the anti-tumour effects of cis-
Pt(NH3)2Cl2 [15]. Despite the initial success of cis-Pt(NH3)2Cl2,
⇑
Corresponding author. Tel.: +27 (0)33 260 5293; fax: +27 (0)33 260 5009.
E-mail address: akermanm@ukzn.ac.za (M.P. Akerman).
http://dx.doi.org/10.1016/j.molstruc.2015.02.077
0022-2860/Ó 2015 Elsevier B.V. All rights reserved.

K.J. Akerman et al. / Journal of Molecular Structure 1091 (2015) 74–80
75
various Pt(II) and Pd(II) complexes with N-donor and cis-chloro
ligands were synthesised in order improve drug efficacy and over-
come drug resistance [1,2]. Coordination complexes of amp and
amq formed part of these studies. The ligand amp has been coordi-
nated to Pt(II) to form [PtCl2(amp)] to compare the anti-tumour
activity of the complex with [cis-[PtCl2(NH3)(2-methylpyridine)]
which has been effective in clinical trials for the treatment of ovar-
ian cancers, which are resistant to other platinum-based drugs
[16,17]. The amq ligand has also been coordinated to Pt(II) and
Pd(II), forming complexes with the general formula [ML2X2]
(where X = Cl or Br) to investigate their interaction with calf thy-
mus DNA in an attempt to better understand their biological mode
of action [2].
relative to DMSO-d6: 1H, 2.50 ppm and 13C, 39.51 ppm. FTIR spec-
tra were recorded using Bruker Alpha FTIR spectrometer
a
equipped with an ATR platinum Diamond 1 reflectance accessory.
The machine acquired the information in 32 scans with a spectral
resolution of 1.0 cmꢂ1. The abbreviations used in the text are as fol-
lows; br, broad; s, strong; m, medium and w, weak signals.
Electronic spectra were recorded using a Shimadzu UVPC-1800
double beam UV–vis scanning spectrometer (1.0 cm path length
cuvette). Spectra were recorded from 700 to 280 nm in DMSO.
High resolution masses were determined with a Waters Acquity-
LCT Premier coupled high performance liquid chromatograph–
mass spectrometer (time-of-flight) using electrospray ionization
in positive mode.
Additionally, amp has been coordinated to Cu(II) in a variety of
metal to ligand ratios yielding a range of complexes with various
coordination geometries. These coordination compounds have
been characterised by X-ray crystallography and used in studies
to correlate structural and magnetic properties [18–24]. The
Ru(II) chelates of this ligand have been used as a pre-catalyst for
the reduction of acetophenone in transfer-hydrogenation condi-
tions [8].
The amq ligand has also been previously reported coordinated
to Co(II), Ni(II) and Cu(II) to investigate the compounds’ thermal
behaviour and to study decomposition pathways [11]. The amq
ligand was similarly coordinated to Ru(II) as part of an electro-
chemistry study as the aromatic rings were found to stabilize the
target oxidation intermediates [7].
Despite the extensive research into the coordination complexes
of 2-pyridylmethylamine and 8-aminoquinoline ligands, a detailed
crystallographic and computational study of the Pd(II) chelates has
not been reported. Herein, we report the solid-state structures of
the cis-dichloropalladium(II) chelates of 2-pyridylmethylamine
and 8-aminoquinoline (Scheme 1). The complexes have been fully
characterised by NMR, IR and UV–visible spectroscopy as well as
mass spectrometry and X-ray crystallography. DFT simulations
have been used to further understand the solid-state and electronic
structures of the metal chelates.
The X-ray data were recorded on a Bruker Apex Duo diffrac-
tometer equipped with an Oxford Instruments Cryojet operating
at 100(2) K and an Incoatec microsource operating at 30 W power.
Crystal and structure refinement data are given in Table 1. Selected
bond lengths and angles are reported in Table 2. For both struc-
tures, the data were collected with Mo Ka (k = 0.71073 Å) radiation
at a crystal-to-detector distance of 50 mm. The data collections
were performed using omega and phi scans with exposures taken
at 30 W X-ray power and 0.50° frame widths using APEX2 [26]. The
data were reduced with the program SAINT [26] using outlier
rejection, scan speed scaling, as well as standard Lorentz and polar-
ization correction factors. A SADABS semi-empirical multi-scan
absorption correction [26] was applied to the data. Direct methods,
SHELXS-97 [27] and WINGX [28] were used to solve both struc-
tures. All non-hydrogen atoms were located in the difference den-
sity map and refined anisotropically with SHELXL-97 [27]. The
amine hydrogen atoms were located in the difference density
map and allowed to refine isotropically. The remaining hydrogen
atoms were included as idealized contributors in the least squares
process. Their positions were calculated using a standard riding
model with CAHaromatic distances of 0.95 Å and Uiso = 1.2 Ueq and
CAHmethylene distances of 0.99 Å and Uiso = 1.2 Ueq
.
Table 1
Crystal data and structure refinement details for [Pd(L1)Cl2] and [Pd(L2)Cl2].
Experimental
Crystal data
[Pd(L1)Cl2]
C6H8Cl2N2Pd
285.44
[Pd(L2)Cl2]
C9H8Cl2N2Pd
321.47
Chemical formula
Materials and methods
Molar mass (g molꢂ1
)
Crystal system, space group
Temperature (K)
a, b, c (Å)
Monoclinic, C2/c
100
Monoclinic, P21/n
100
All starting materials used in the syntheses were purchased
from Sigma–Aldrich (Germany) and used as received. Organic sol-
vents were purchased from Merck (South Africa) and were of spec-
troscopic grade. All solvents were dried using a Puresolv™ MD 7
purification system from Innovative Technologies prior to use.
NMR spectra were recorded with a Bruker Avance III 400 spec-
trometer equipped with a Bruker magnet (9.395 T) using a 5 mm
TBIZ probe at frequencies of 400 MHz and 100 MHz for the 1H
and 13C spectra, respectively. The spectra were recorded at 30 °C.
All NMR experiments were conducted using Bruker Topspin 2.1,
patch level 6 [25]. All proton and carbon chemical shifts are quoted
9.7497(7),
17.2465(16),
10.2923(7)
98.868(3)
1709.9(2)
8
4.7287(3),
17.9637(12),
11.5934(7)
97.208(3)
977.02(11)
4
b, (°)
V (Å)
Z
Radiation type
Mo Ka
Mo K
2.40
a
l
(mmꢂ1
)
2.73
Crystal size (mm)
0.28 ꢃ 0.25 ꢃ 0.20 0.18 ꢃ 0.04 ꢃ 0.02
Data collection
Diffractometer
Absorption correction
Tmin, Tmax
Bruker APEXII CCD diffractometer
Multi-scan, SADABS, Bruker 2012
0.516, 0.612
0.672, 0.954
No. of measured, independent and 13517, 1641, 1631 8373, 1911, 1835
observed [I > 2 (I)] reflections
Rint
r
0.021
0.020
Refinement
R[F2 > 2 (F2)], wR(F2), S
r
0.029, 0.073, 1.29 0.018, 0.043, 1.12
No. of reflections
No. of parameters
No. of restraints
H-atom treatment
1641
108
1
1911
135
H atoms treated by a mixture of
independent and constrained
refinement
1.82, ꢂ0.77
qmin (e Åꢂ3
)
0.70, ꢂ0.45
Scheme 1. Structure and naming scheme of the Pd(II) chelates synthesised in this
work.
D
qmax
,
D

76
K.J. Akerman et al. / Journal of Molecular Structure 1091 (2015) 74–80
Table 2
Results and discussion
Selected bond lengths (Å) and bond angles (°) for [Pd(L1)Cl2] and [Pd(L2)Cl2], standard
uncertainties are given in parentheses.
Synthesis and spectroscopic characterisation
[Pd(L1)Cl2]
[Pd(L2)Cl2]
The Pd(II) chelates were both synthesised using a simple one-
pot, two stage reaction. The palladium(II) chloride starting material
was firstly converted to the bis(acetonitrile)dichloropalladium(II)
complex by refluxing in acetonitrile. We found that omitting this
step lead to the formation of a black precipitate (likely palladium
colloids) upon addition of the bidentate ligands. The addition of
one equivalent of the bidentate ligands to the refluxing acetonitrile
solution of bis(acetonitrile)dichloropalladium(II) resulted in the
immediate formation of a yellow/tan precipitate of the desired pro-
duct in high yields. The 1:1 metal to ligand ratio renders a neutral
metal chelate with two chloride ligands coordinated in the third
and fourth positions. Spectroscopic grade acetonitrile was used
for the reaction, but no further measures were required to shield
the reaction from moisture or oxygen.
Bond
PdACla
2.310(1)
2.017(4)
2.030(4)
2.301(9)
2.016(2)
2.045(2)
PdANpyridine
PdANamine
Angles
ClAPdACl
cis-ClAPdANamine
cis-ClAPdANpyridine
91.16(4)
90.9(1)
95.2(1)
82.9(2)
175.6(1)
173.0(1)
92.18(2)
90.20(6)
94.84(6)
83.12(8)
175.63(7)
171.44(6)
NpyridineAPdANamine
trans-ClAPdANamine
trans-ClAPdANpyridine
a
Mean bond length.
General procedure for the synthesis of [Pd(L1)Cl2] and [Pd(L2)Cl2]
The characterisation (NMR, IR and UV/visible spectroscopy and
mass spectrometry) of the chelates was routine, no unusual results
were noted. The fully assigned 1H and 13C NMR and IR spectra are
available in the electronic supplementary information.
[Pd(L1)Cl2] and [Pd(L2)Cl2] were synthesised using the same
general procedure. The metal precursor, palladium(II) chloride
(100 mg, 0.564 mmol), was refluxed in acetonitrile (20 mL) for
1 h to form the bis(acetonitrile)dichloropalladium(II) complex.
The respective ligands; 2-pyridylmethylamine (61.0 mg,
0.564 mmol) or 8-aminoquinoline (70.4 mg, 0.564 mmol), were
added to the reaction mixture. A yellow precipitate formed
immediately and the solution was refluxed for an additional
20 min. The yellow precipitate was collected by centrifugation,
washed with two portions of diethyl ether and dried under a
stream of nitrogen.
X-ray crystallography
[Pd(L1)Cl2] and [Pd(L2)Cl2] were studied by single crystal X-ray
diffraction. The compounds both crystallised in the monoclinic
crystal system. [Pd(L1)Cl2] crystallised in the C2/c spacegroup
while [Pd(L2)Cl2] crystallised in the P21/n spacegroup, each struc-
ture contains one molecule in the asymmetric unit (Z = 8 and 4,
respectively). The structures, [Pd(L1)Cl2] and [Pd(L2)Cl2], show that
the Pd(II) ion has adopted a square planar coordination geometry
with chelation of the bidentate 2-pyridylmethylamine and 8-
aminoquinoline ligands, respectively. The third and fourth
coordination sites are occupied by chloride ligands in a cis-config-
uration (Fig. 1). This square planar coordination geometry is
expected due to the d8 electronic configuration of Pd(II) and is con-
sistent with reported structures of this class of cis-chloro Pd(II)
compounds [29–31].
[Pd(L1)Cl2] is largely planar with the pyridyl ring lying at an
angle of 2.3° relative to the coordination sphere. The NACACAN
torsion angle of the chelation ring measures 7.1(7)° illustrating
that this complex deviates less from planarity than a previously
reported platinum(II) analogue for which the equivalent torsion
angle measures ꢂ22.2(9)° [1]. [Pd(L2)Cl2] exhibits a similar, nomi-
nally planar geometry with an NACACAN torsion angle of
ꢂ1.5(3)°. The most notable deviation from the ideal square planar
geometry of [Pd(L2)Cl2] is a slight rotation of the chloride ligands
out of the 8-aminoquinoline mean plane. The mean plane of the
8-aminoquinoline ligand (non-H atoms) subtends an angle of ca.
7° relative to the mean plane defined by the chloride ligands and
Pd(II) ion.
Dichloro-(2-aminomethylpyridine-N,N0)-palladium(II)
[Pd(L1)Cl2] was synthesised as described above, yield 135 mg
(84%). Brown crystals suitable for X-ray diffraction were obtained
by slow evaporation of the reaction mixture.
1H NMR (400 MHz, DMSO-d6, 303 K) [d, ppm]: 4.10 (t, 2H, CH2),
5.59 (br, 2H, NH2), 7.50 (t, 1H, NCHCH), 7.61 (d, 1H, NCCH), 8.05 (td,
1H, NCCHCH), 8.76 (d, 1H, NCH). 13C NMR (100 MHz, DMSO-d6,
303 K) [d, ppm]: 52.35 (CH2), 122.12 (NCHCH), 124.12 (NCCH),
140.22 (NCCHCH), 149.22 (NCH), 166.19 (NC). IR [cmꢂ1]: 423.83
(m, PdACl stretch), 783.71 (s, CAH out-of-plane bend), 1284.76
(m, CAN stretch), 1556.32 (m, C@C stretch), 1610.42 (m, NH2 scis-
soring), 3214.76 (m, NH2 stretch). M.p.t. > 260 °C (decomposition).
ES+: 326.9541 [M ꢂ Cl + DMSO]+. UV–vis: kmax (nm) [
e
(Mꢂ1 cmꢂ1)]
370 [3.60 ꢃ 102].
Dichloro-(8-aminoquinoline)-palladium(II)
[Pd(L2)Cl2] was synthesised using the general procedure
described above, yield 161 mg (89%). Brown crystals suitable for
X-ray diffraction were obtained by slow liquid diffusion of ethanol
into a DMSO solution of [Pd(L2)Cl2].
A Mogul [32] structural search shows that the PdACl and PdAN
bond lengths are within the ranges of previously reported
structures. The ClAPdACl bond angles for [Pd(L1)Cl2] and
[Pd(L2)Cl2] measure 91.16(4)° and 92.18(2)°, respectively. The
1H NMR (400 MHz, DMSO-d6, 303 K) [d, ppm]: 7.69–7.81 (m,
3H, NH2CCHCHCH), 7.85 (br, 2H, NH2), 8.03 (d, 1H, NCHCH),
8.76 (d, 1H, NCHCHCH), 9.12 (d, 1H, NCH). 13C NMR (100 MHz,
DMSO-d6, 303 K) [d, ppm]: 123.54 (NH2CCH), 127.09
(NH2CCHCHCH), 128.16 (NCHCH), 129.09 (NH2CCHCHCHC),
130.20 (NH2CCHCH), 140.11 (NC; NCHCHCH), 148.02 (NH2C),
151.26 (NCH). IR [cmꢂ1]: 436.61 (w, PdACl stretch), 773.18
(s, CAH out-of-plane bend), 1215.06 (m, CAN stretch), 1565.36
(s, C@C stretch), 1571.64 (m, NH2 scissoring), 3044.50 (m, NH2
stretch). M.p.t. > 287 °C (decomposition). ES+: 362.9539 [M ꢂ Cl +
NpyridineAPdANamine angles for both complexes are considerably
more acute, measuring 82.9(2)° and 83.12(8)°, respectively. This
smaller bond angle is attributed to the fixed bite angle of the
bidentate ligands. The chloride ligands have a larger degree of free-
dom and can adopt a more obtuse bond angle, which will minimise
non-bonded repulsion. Selected bond lengths and bond angles for
the structures are available in Table 2.
DMSO]+. UV–vis: kmax (nm) [
e
(Mꢂ1 cmꢂ1)] 307 [5.85 ꢃ 103],
Both complexes exhibit a number of intermolecular interactions
including hydrogen-bonding (the NH2 groups acting as hydrogen-
363 [1.06 ꢃ 103], 505 [5.80 ꢃ 102].

K.J. Akerman et al. / Journal of Molecular Structure 1091 (2015) 74–80
77
Fig. 2. (A) One-dimensional hydrogen-bonded network of [Pd(L1)Cl2] formed in the
solid state. (B) Repeating unit of the two-dimensional hydrogen-bonded network of
[Pd(L2)Cl2]. Both supramolecular structures are supported by NAHꢁ ꢁ ꢁCl hydrogen
bonds (illustrated as dashed purple tubes). (For interpretation of the references to
colour in this figure legend, the reader is referred to the web version of this article.)
two-dimensional structure. The consequence of this alternative
hydrogen bonding pattern is that the metallophilic interactions
have seemingly been eliminated with the separation between adja-
cent Pd(II) ions measuring 4.7287(4) Å, substantially longer than
the sum of the van der Waals radii. It would appear that the stabil-
ity gained through the alternative hydrogen bonding pattern out-
weighs any stability gained from potential metallophilic
interactions. The hydrogen bond parameters for [Pd(L1)Cl2] and
[Pd(L2)Cl2] are summarised in Table 3.
The hydrogen bond lengths summarised in Table 3 are signifi-
cantly shorter than the sum of the van der Waals radii of the inter-
acting atoms. Although hydrogen bond length may not necessarily
correlate linearly with bond strength due to packing constraints in
the lattice [34], it is likely that these short interactions are moder-
ately strong. This statement is further supported by the fact that
the bond angles do not deviate significantly from ideality (180°).
Fig. 1. Thermal ellipsoid plot (50% probability surfaces) showing the atom
numbering scheme of (A) [Pd(L1)Cl2] and (B) [Pd(L2)Cl2]. Hydrogen atoms have
been rendered as spheres of arbitrary radius.
bond donors and the chloride ligands of the adjacent molecules
acting as hydrogen-bond acceptors) and metallophilic interactions.
In [Pd(L1)Cl2] there is complementary hydrogen bonding between
the amine group and the chloride ligand of an adjacent molecule.
The amine group therefore bridges two molecules. This hydrogen
bonding pattern propagates a one-dimensional column, which
runs transversely across the ac plane (Fig. 2). This hydrogen-
bonded column is further stabilised by Pdꢁ ꢁ ꢁPd interactions. The
Pdꢁ ꢁ ꢁPd interactions within the supramolecular structure alternate
between longer 3.4388(4) Å and shorter 3.4105(4) Å contacts.
These metallophilic interactions are comparable in length to
related, neutral cis-chloro Pd(II) chelates and are shorter than the
sum of the van der Waals radii indicating an attractive interaction
[33]. Adjacent one-dimensional columns of molecules are not
linked by any significant intermolecular interactions.
[Pd(L2)Cl2] employs the same hydrogen bonding motif as
[Pd(L1)Cl2] i.e. NAHꢁ ꢁ ꢁCl, however, each molecule is hydrogen-
bonded to four adjacent molecules (Fig. 2). This hydrogen bonding
pattern leads to a two-dimensional hydrogen-bonded network co-
planar with the ac plane. The two-dimensional supramolecular
structure can be considered to comprise one-dimensional columns
which are cross-linked by hydrogen bonds, leading to the
Table 3
Hydrogen bond lengths (Å) and bond angles (°) for [Pd(L1)Cl2] and [Pd(L2)Cl2].
DAH (Å)
Hꢁ ꢁ ꢁA (Å)
Dꢁ ꢁ ꢁA (Å)
DAHꢁ ꢁ ꢁA (°)
[Pd(L1)Cl2]
N1AH102ꢁ ꢁ ꢁCl1i
0.87(5)
0.85(6)
2.44(5)
2.50(6)
3.273(4)
3.347(4)
162(4)
171(5)
N1AH101ꢁ ꢁ ꢁCl2ii
[Pd(L2)Cl2]
N1AH101ꢁ ꢁ ꢁCl2iii
0.86(4)
0.83(3)
2.52(3)
2.54(3)
3.368(2)
3.355(2)
171(3)
168(3)
N1AH102ꢁ ꢁ ꢁCl1iv
i
ii
iii
Symmetry codes: ꢂx, y, 1.5 ꢂ z; ½ ꢂ x, ½ ꢂ y, 2 ꢂ z; ꢂ1/2 + x, 1.5 ꢂ y, ꢂ1/2 + z;
iv
and ꢂ1 + x, y, z.

78
K.J. Akerman et al. / Journal of Molecular Structure 1091 (2015) 74–80
DFT simulations
Density functional theory (DFT) simulations were used to gain a
deeper understanding of the solid-state structures and electronic
configuration of the square planar Pd(II) complexes; [Pd(L1)Cl2]
and [Pd(L2)Cl2]. The simulations were performed using Gaussian
09 W [35] using the PBE hybrid functional [36,37]. A split basis
set was applied in the simulations, this split basis set specified
the 6–311G level of theory [38,39] for the C, H, Cl and N atoms
and the LanL2DZ (which makes use of effective core potentials)
basis set for the palladium(II) ion [40–43]. The LanL2DZ basis
set also takes into account relativistic effects, which can be signifi-
cant in heavy metal ions [44]. The X-ray coordinates of the metal
chelates were used for input structures. Normal geometry conver-
gence criteria were applied and no symmetry constraints imposed.
Transition energies and oscillator strengths were calculated for 18
excited singlet states using the TD-DFT method [45–51] using the
same split basis set applied to the geometry optimizations. The
molecular orbitals were assigned by studying the spatial dis-
tributions of their isosurfaces. To account for solvent effects, a
Polarizable Continuum Model (PCM) was included in the calcula-
tion of the transition energies and oscillator strengths [52–54].
The input files were prepared using GaussView 5.0 [55]; the same
program was used to analyse the output files. Structural overlays
were performed using Mercury 3.1 [56].
The geometry optimisation simulations were run at the above
mentioned level of theory. The resulting structures were concluded
to be the true lowest energy conformations on the global potential
energy surface by the lack of negative vibrational frequencies. The
geometrical parameters of the experimental (solid-state) and
simulated (in vacuo) structures are compared in Table 4. The data
in Table 4 show that the structures are in good agreement; this
would suggest that the level of theory applied to the simulations
is appropriate and the bulk of the results are therefore likely to
be reliable. The largest difference in the calculated bond angles is
the ClAPdACl bond angle. In the absence of lattice constraints, it
would seem that the chloride ligands have moved further apart
to relieve non-bonded repulsion.
Fig. 3. Least-squares fit of DFT-calculated (blue) and X-ray crystal structures
(yellow) of (A) [Pd(L1)Cl2] and (B) [Pd(L2)Cl2]. Root mean square deviations
(RMSDs, Å units) for all non-hydrogen atoms for each structure are indicated on the
diagram. (For interpretation of the references to colour in this figure legend, the
reader is referred to the web version of this article.)
to the experimental structure which can be considered to be
fundamentally planar (Cmethylene atom in the plane defined by the
coordination sphere). This out-of-plane distortion of the carbon
atom allows the methylene group to adopt an angle closer to ide-
ality for an sp3 hybridised carbon, this is illustrated by the
CACmethyleneANamine bond angle which measures 110.7° and
112.5(4)° in the calculated and experimental structures, respec-
tively. The geometry optimised structure (with the out of plane
methylene group) is ca. 11 kJ molꢂ1 lower in energy than the pla-
nar structure. This is a modest energy difference and seemingly
the stability gained through the more favourable packing of the
planar molecule in the solid state is sufficient to offset this energy
difference. The energy of the planar structure was calculated by
fixing the NpyridineACpyridineACmethyleneANamine torsion angle of the
input structure during the geometry optimisation. This planar con-
figuration exhibits a single negative vibrational frequency, indicat-
ing that it is a saddle point on the potential energy surface. The
more rigid ligand of [Pd(L2)Cl2] is less likely to be distorted in
the solid state by packing forces and therefore the solid-state and
gas phase structures are in better agreement. The hydrogen bond-
ing in the solid state does not seem to have resulted in a significant
distortion from the lowest energy conformation, as has been
reported for other hydrogen-bonded supramolecular structures
[57].
The similarity of the calculated and experimental structures is
further illustrated by the structural overlays (least squares fits).
The similarity of the structures is measured by the root-mean-
square deviations (RMSDs, measured in Å units). The RMSDs show
that the structures are in good agreement, refer to Fig. 3. The RMSD
for [Pd(L1)Cl2] is significantly larger than that of [Pd(L2)Cl2]. The
difference lies predominantly in the methylene group for which
the carbon atom, in the lowest energy conformation, sits below
the plane defined by the coordination sphere. This is in contrast
Natural Bond Orbital (NBO) analysis was used to better under-
stand the hydrogen bonding in the solid-state structure, the partial
charge distribution (NBO charges, measured in electrons) of the
molecules were calculated; refer to Fig. 4. These clearly show that
the amine hydrogen atoms carry the largest partial positive charge
and the chloride ligands the largest partial negative charge. If a
hydrogen bond can be generally considered an electrostatic inter-
action then the NBO charges clearly explain the stability of this
hydrogen bonding motif.
Table 4
Comparison of DFT-calculated and experimental bond lengths (Å) and bond angles (°)
of [Pd(L1)Cl2] and [Pd(L2)Cl2].
[Pd(L1)Cl2]
(DFT)
%
[Pd(L2)Cl2]
(DFT)
%
The experimental UV–visible spectrum of [Pd(L1)Cl2] shows
just a single broad peak in the spectral window of 280–700 nm
with a wavelength of maximum absorption at 370 nm. The poor
solubility of the chelates necessitated the use of DMSO for spectro-
scopic characterisation and hence the high energy UV transitions
(200–280 nm) are obscured by the solvent. The additional aro-
maticity afforded by the 8-aminoquinoline ligand of [Pd(L2)Cl2]
results in a more complex spectrum with peaks at 307, 363 and
505 nm. The absorption spectra were calculated using the TD-
DFT method with the same split basis set applied to the geometry
optimisations. A DMSO solvent continuum was included in the
simulations to account for solvent effects. Table 5 summarises
the main transitions, as determined by the magnitude of the oscil-
Diffa
Diffa
Bond
PdACl
PdANpyridine
PdANamine
2.316
2.056
2.091
0.26
1.93
3.00
2.315
2.045
2.099
0.61
1.44
2.64
Angles
ClAPdACl
cis-ClAPdANamine
cis-ClAPdANpyridine
94.20
89.36
95.19
81.26
176.42
170.57
3.33
ꢂ1.69
ꢂ0.01
ꢂ1.98
0.47
94.17
88.72
94.95
82.16
177.11
170.88
2.16
ꢂ1.64
0.11
ꢂ1.15
NpyridineAPdANamine
trans-ClAPdANamine
trans-ClAPdANpyridine
0.84
ꢂ1.40
ꢂ0.56
a
Difference between DFT-calculated and experimental bond parameters
À
Á
DFT-EXP
EXP
ꢃ 100% .
lator strength, for [Pd(L1)Cl2].
A superposition plot of the

K.J. Akerman et al. / Journal of Molecular Structure 1091 (2015) 74–80
79
Fig. 4. NBO partial charges (e) for [Pd(L1)Cl2] illustrating the partial negative and
positive charges on the chloride ligands and amine hydrogen atoms, respectively. A
similar plot for [Pd(L2)Cl2] is available in the ESI.
Table 5
Summary of the calculated electronic transitions for [Pd(L1)Cl2] and the correspond-
ing molecular orbitals.
Fig. 6. Schematic MO diagram of [Pd(L1)Cl2]. The energy gap between the HOMO
Assignmentc
and LUMO is 2.36 eV (227.7 kJ molꢂ1, 525.4 nm).
Wavelength
(nm)a
Molecular
orbitalsb
Oscillator
strength
p⁄(pyridine)
p ?
Pd[dz2]Cl p⁄(pyridine)
The simulated data show one dominant transition at 358.64 nm
with additional, less significant transitions at 375.48 and
391.47 nm; this is consistent with the single broad peak observed
in the experimental spectrum.
The data in Table 5 show that the majority of the transitions can
be considered to originate in occupied, metal-based orbitals. The
transitions are mostly to p⁄ orbitals located on the pyridine ring.
The transitions could therefore be loosely classified as metal-to-li-
gand charge transfer (MLCT) bands. Similar data for [Pd(L2)Cl2] is
available in the electronic supplementary information.
358.64
53 ? 57
54 ? 57
51 ? 56
54 ? 57
55 ? 57
0.0879
Pd[dxz]Lp ?
375.48
391.47
0.0070
0.0071
r
Cl ? Pd[d(x2 ꢂ y2)]Lr⁄
Pd[dz2]Cl p⁄(pyridine)
p ?
Pd[dz2] ? p⁄(pyridine)
a
Three of the 18 calculated excited states are listed.
The highest occupied molecular orbital (HOMO) is orbital 55, the lowest
unoccupied molecular orbital (LUMO) is 56.
b
c
Pd[d(xz)]L
p refers to an orbital which comprises predominantly mixed metal–
ligand bonding character.
p
A possible avenue for further development of this work is the
inclusion of spin orbit coupling (SOC) effects in the simulations.
These effects can be particularly significant for heavy metal ions
such as palladium(II). The work by Minaev et al. [58,59] has shown
that by including non-diagonal SOC, which allows for the mixing of
singlet and triplet states, UV–visible spectroscopic features and
other physico-chemical properties can be further explained.
Conclusions
Coordination of 2-methylaminopyridine and 8-aminoquinoline
to Pd(II) yielded two nominally square planar coordination com-
pounds. The bidentate ligands occupy two of the coordination sites;
two chloride ligands in a cis configuration complete the coordina-
tion sphere. [Pd(L1)Cl2] and [Pd(L2)Cl2] formed one and two-dimen-
sional hydrogen-bonded networks in the solid state, respectively.
The supramolecular structures were both supported by NAHꢁ ꢁ ꢁCl
hydrogen bonds; [Pd(L1)Cl2] was further stabilised by metallophilic
Pdꢁ ꢁ ꢁPd interactions. DFT simulations showed that in vacuo the low-
est energy conformation of [Pd(L1)Cl2] was not planar; the methy-
lene group showed an out-of-plane distortion. This non-planar
configuration is ca. 11 kJ molꢂ1 lower in energy than the planar X-
ray structure. The calculated NBO charges clearly explained the sta-
bility of the solid-state hydrogen bonding. TD-DFT was used to bet-
ter understand the experimental spectroscopic results.
Fig. 5. Superposition of the TD-DFT calculated (DMSO solvent continuum) and
experimental UV–visible spectra of [Pd(L1)Cl2]. A similar superposition plot for
[Pd(L2)Cl2] is available in the ESI. Extinction coefficients of calculated spectra have
been scaled.
experimental and calculated UV–visible spectra is shown in Fig. 5.
This plot shows that there is reasonable agreement between the
spectra and therefore an analysis of the orbitals involved in the cal-
culated transitions should provide insight into the experimental
transitions. A schematic diagram showing the spatial distributions
and calculated energies of the molecular orbitals (MOs) involved in
the highest intensity transitions between occupied and unoccupied
orbitals, alluded to in Table 5, is shown in Fig. 6.
Acknowledgements
The authors wish to thank the University of KwaZulu-Natal for
their financial support and for the use of their facilities as well as

80
K.J. Akerman et al. / Journal of Molecular Structure 1091 (2015) 74–80
[24] H. Kooijman, A.L. Spek, D. Rehorst, W.L. Driessen, J. Reedijk, Acta Cryst. C53
(1997) 1596–1598.
[25] Bruker Topspin 2.1 (pl6) from Bruker BioSpin, 2010.
[26] Bruker APEX2, SAINT and SADABS, Bruker AXS Inc., Madison, Wisconsin, USA,
2012.
the National Research Foundation (South Africa) for their financial
support.
Appendix A. Supplementary material
[27] G.M. Sheldrick, Acta Cryst. A64 (2008) 112–122.
[28] L.J. Farrugia, J. Appl. Crystallogr. 45 (2012) 849–854.
[29] E. Tomas-Mendivil, J. Diez, V. Caderno, Polyhedron 59 (2013) 69–75.
[30] C. Luque, J. Pons, T. Calvet, M. Font-Bardia, J. Garcia-Anton, J. Ros, Inorg. Chim.
Acta 367 (2011) 35–43.
The CCDC contains the supplementary crystallographic data of
[Pd(L1)Cl2] and [Pd(L2)Cl2] (CCDC 1043743 and 1043742, respec-
tively). The data can be obtained free of charge via http://www.
ccdc.cam.ac.uk/conts/retrieving.html or from the Cambridge
Crystallographic Data Centre, 12 Union Road, Cambridge CB2 IEZ;
fax:+44 1223 336 033; or email: deposit@ccdc.cam.ac.uk.
Supplementary data associated with this article can be found in
the online version. Supplementary data associated with this article
can be found, in the online version, at http://dx.doi.org/10.1016/
j.molstruc.2015.02.077.
[31] S. Hanesa, Organometallics 26 (2007) 6551–6555.
[32] C.F. Macrae, I.J. Bruno, J.A. Chisholm, P.R. Edgington, P. McCabe, E. Pidcock, L.
Rodriguez-Monge, R. Taylor, J. van de Streek, P.A. Wood, J. Appl. Cryst. 41
(2008) 466–470.
[33] I.M. Sluch, A.J. Miranda, O. Elbjeirami, M.A. Omary, L.M. Slaughter, Inorg.
Chem. 51 (2012) 10728–10746.
[34] T. Steiner, Chem. Commun. 8 (1997) 727–734.
[35] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman,
G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato,
X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M.
Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y.
Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, Jr., J.E. Peralta, F. Ogliaro,
M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J.
Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M.
Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo,
J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C.
Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth,
P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman,
J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 09, Revision D.01, Gaussian Inc.,
Wallingford CT, 2009.
References
[1] V.P. Munk, C.I. Diakos, L.T. Ellis, R.R. Fenton, B.A. Messerle, T.W. Hambley,
Inorg. Chem. 42 (2003) 3582–3590.
[2] P. Umapathy, R.A. Harnesswala, C.S. Dorai, Polyhedron 9 (1985) 1592–1602.
[3] H.A. Hudali, J.V. Kingston, H.A. Tayim, Inorg. Chem. 18 (1979) 1391–1394.
[4] M.E. Quiroz-Castro, G.A. van Albada, I. Mutikainen, U. Turpeinen, J. Reedijk,
Inorg. Chim. Acta 297 (2000) 129–133.
[5] L. Canovese, F. Visentin, G. Chessa, C. Levi, P. Nikolov, Inorg. Chim. Acta 362
(2009) 3925–3933.
[6] K.W. Törnroos, D. Chernyshov, M. Hostettler, Hans-Beat Bürgi, Acta Cryst. C61
(2005) m450–m452.
[7] M.K. O’Neill, A.F. Trappey, P. Battle, C.L. Boswell, D.N. Blauch, Dalton Trans.
(2009) 3391–3394.
[8] D.A. Cavarzan, F.D. Fagundes, O. Fuganti, C.W.P. da Silva, C.B. Pinheiro, D.F.
Back, A. Barison, A.L. Bogado, M.P. de Araujo, Polyhedron 62 (2013) 75–82.
[9] C. Niu, X. Wan, X. Zheng, H. Zhang, B. Wu, Y. Niu, H. Hou, J. Coord. Chem. 61
(2008) 1997–2007.
[10] M. Mirzaei, H. Eshtiagh-Hosseini, M. Mohammadi Abadeh, M. Chahkandi, A.
Fronterac, A. Hassanpoor, Cryst. Eng. Comm. 15 (2013) 1404–1413.
[11] A.M. Donia, H.A. El-Boraey, J. Therm. Anal. 48 (1997) 1325–1336.
[12] D.J. Ayres, D.A. House, W.T. Robinson, Inorg. Chim. Acta 277 (1998) 177–185.
[13] A. Hazell, K.F. Thong, J. Oyanc, L.E. Khoo, Acta Cryst. C53 (1997) 1226–1228.
[14] M.K. Paira, J. Dinda, T.-H. Lu, A.R. Paital, C. Sinha, Polyhedron 26 (2007) 4131–
4140.
[15] B. Rosenberg, L. Van Camp, J.E. Trosko, V.H. Mansour, Nature 222 (1969) 385–
386.
[16] F.I. Raynaud, F.E. Boxall, P.M. Goddard, M. Valenti, M. Jones, B.A. Murrer, M.
Abrams, L.R. Kelland, Clin. Cancer Res. 3 (1997) 22063–22074.
[17] L.R. Kelland, S.Y. Sharp, C.F. O’Neill, F.I. Raynaud, P.J. Beale, I.R. Judson, J. Inorg.
Biochem. 77 (1999) 111–115.
[18] C.J. O’Connor, E.E. Eduok, F.R. Fronczek, O. Kahn, Inorg. Chim. Acta 105 (1985)
107–113.
[19] H.M. Hu, D.-L. Long, H.-Y. Zeng, W.-D. Cheng, J.-S. Huang, Acta Cryst. C55
(1999) IUC9900049.
[20] H.M. Helis, W.H. Goodman, R.B. Wilson, J.A. Morgan, D.J. Hodgson, Inorg.
Chem. 16 (1977) 2412–2416.
[21] A.W. Maverick, M.L. Ivie, F.R. Fronczek, J. Coord. Chem. 21 (1990) 315–322.
[22] A.G. Hatzidimitriou, M. Uddin, Polyhedron 16 (1997) 1651–1654.
[23] C.J. O’Connor, E.E. Eduok, J.W. Owens, E.D. Stevens, C.L. Klein, Inorg. Chim. Acta
117 (1986) 175–181.
[36] J.P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 77 (1996) 3865–3868.
[37] J.P. Perdew, K. Burke, M. Ernzerhof, Phys. Rev. Lett. 78 (1997) 1396.
[38] A.D. McLean, G.S. Chandler, J. Chem. Phys. 72 (1980) 5639–5648.
[39] K. Raghavachari, J.S. Binkley, R. Seeger, J.A. Pople, J. Chem. Phys. 72 (1980) 650–
654.
[40] T.H. Dunning Jr., P.J. Hay, in: Modern Theoretical Chemistry, in: H.F. Schaefer
III (Ed.), vol. 3, Plenum, New York, 1976, pp. 1–28.
[41] P.J. Hay, W.R. Wadt, J. Chem. Phys. 82 (1985) 270–283.
[42] P.J. Hay, W.R. Wadt, J. Chem. Phys. 82 (1985) 299–310.
[43] W.R. Wadt, P.J. Hay, J. Chem. Phys. 82 (1985) 284–298.
[44] C.E. Check, T.O. Faust, J.M. Bailey, B.J. Wright, T.M. Gilbert, L.S. Sunderlin, J.
Phys. Chem. A 105 (2001) 8111–8116.
[45] R. Bauernschmitt, R. Ahlrichs, Chem. Phys. Lett. 256 (1996) 454–464.
[46] M.E. Casida, C. Jamorski, K.C. Casida, D.R. Salahub, J. Chem. Phys. 108 (1998)
4439–4449.
[47] R.E. Stratmann, G.E. Scuseria, M.J. Frisch, J. Chem. Phys. 109 (1998) 8218–8224.
[48] C. Van Caillie, R.D. Amos, Chem. Phys. Lett. 308 (1999) 249–255.
[49] C. Van Caillie, R.D. Amos, Chem. Phys. Lett. 317 (2000) 159–164.
[50] F. Furche, R. Ahlrichs, J. Chem. Phys. 117 (2002) 7433–7447.
[51] G. Scalmani, M.J. Frisch, B. Mennucci, J. Tomasi, R. Cammi, V. Barone, J. Chem.
Phys. 124 (094107) (2006) 1–15.
[52] S. Miertuš, E. Scrocco, J. Tomasi, Chem. Phys. 55 (1981) 117–129.
[53] S. Miertuš, J. Tomasi, Chem. Phys. 65 (1982) 239–245.
[54] J.L. Pascual-Ahuir, E. Silla, I. Tuñón, J. Comp. Chem. 15 (1994) 1127–1138.
[55] R. Dennington, T. Keith, J. Millam, GaussView, Version 5, Semichem Inc.,
Shawnee Mission KS, 2009.
[56] C.F. Macrae, I.J. Bruno, J.A. Chisholm, P.R. Edgington, P. McCabe, E. Pidcock, L.
Rodriguez-Monge, R. Taylor, J. van de Streek, P.A. Wood, J. Appl. Cryst. 41
(2008) 466–470.
[57] M.P. Akerman, V.A. Chiazzari, J. Mol. Struct. 1058 (2014) 22–30.
[58] B.F. Minaev, Phys. Chem. Chem. Phys. 2 (2000) 2851–2856.
[59] C. Daniel, D. Guillaumont, C. Ribbing, B.F. Minaev, J. Phys. Chem. A 103 (1999)
5766–5772.