Consequence of presence and absence of π-clouds at strategic locations of designed binuclear Pd(II) complexes on packing: Self-assembly of self-assembly by intermolecular locking and packing

Article abstract of DOI:10.1021/cg301085t

Self-assembled binuclear coordination cages of general formula [Pd ₂(N-N)₂(L)₂](X)₄, 1a/b-4a/b are prepared by the combination of N,N′-bis(m-pyridyl)urea, L, with a variety of cis-protected palladium(II) components, Pd(N-N)(X)₂. The cis-protecting units "N-N" employed for the synthesis of 1-4 are ethylenediamine (en), tetramethylethylenediamine (tmeda), 2,2′-bipyridine (bpy), and 1,10-phenanthroline (phen), respectively. The term "X" stands for nitrate and perchlorate for a and b, respectively. The assemblies are characterized by NMR and electrospray ionization mass spectrometry (ESI-MS) techniques, and in some cases (i.e., 1a, 2b, 3b, 4a, and 4b) the structures are confirmed by single crystal X-ray diffraction. The conformations of bound L in the crystal structures of all the Pd(II) complexes are found to be syn-syn. The influence of the presence and absence of π cloud at the cis-protecting units on the crystal packing has been studied in detail. In the packing of [Pd ₂(phen)₂L₂](NO₃)₄, 4a, one unit of [Pd₂(phen)₂L₂]⁴⁺ is associated with two other units by π-π stacking interactions thus giving a one-dimensional growth as envisioned on the basis of a design principle. In the case of [Pd₂(en)₂(L)₂](NO₃) ₄, 1a, and [Pd₂(tmeda)₂(L)₂] (ClO₄)₄, 2b, such packing is not observed due to the absence of π-cloud at the strategic locations, instead notable H-bonding interactions are seen. However, [Pd₂(bpy)₂(L) ₂](ClO₄)₄, 3b, displays a π-π interactions using only two units of [Pd₂(bpy)₂(L) ₂]⁴⁺(ClO₄)^-.

Full text of DOI:10.1021/cg301085t

Article
pubs.acs.org/crystal
Consequence of Presence and Absence of π‑Clouds at Strategic
Locations of Designed Binuclear Pd(II) Complexes on Packing: Self-
Assembly of Self-Assembly by Intermolecular Locking and Packing
Mili C. Naranthatta, Deepika Das, Debakanta Tripathy, Himansu S. Sahoo, Venkatachalam Ramkumar,
and Dillip K. Chand*
Department of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India
S
* Supporting Information
ABSTRACT: Self-assembled binuclear coordination cages of
general formula [Pd2(N−N)2(L)2](X)4, 1a/b−4a/b are pre-
pared by the combination of N,N′-bis(m-pyridyl)urea, L, with a
variety of cis-protected palladium(II) components, Pd(N−
N)(X)2. The cis-protecting units “N−N” employed for the
synthesis of 1−4 are ethylenediamine (en), tetramethylethyle-
nediamine (tmeda), 2,2′-bipyridine (bpy), and 1,10-phenanthro-
line (phen), respectively. The term “X” stands for nitrate and
perchlorate for a and b, respectively. The assemblies are characterized by NMR and electrospray ionization mass spectrometry
(ESI-MS) techniques, and in some cases (i.e., 1a, 2b, 3b, 4a, and 4b) the structures are confirmed by single crystal X-ray
diffraction. The conformations of bound L in the crystal structures of all the Pd(II) complexes are found to be syn-syn. The
influence of the presence and absence of π cloud at the cis-protecting units on the crystal packing has been studied in detail. In
the packing of [Pd2(phen)2L2](NO3)4, 4a, one unit of [Pd2(phen)2L2]4+ is associated with two other units by π−π stacking
interactions thus giving a one-dimensional growth as envisioned on the basis of a design principle. In the case of
[Pd2(en)2(L)2](NO3)4, 1a, and [Pd2(tmeda)2(L)2](ClO4)4, 2b, such packing is not observed due to the absence of π-cloud at
the strategic locations, instead notable H-bonding interactions are seen. However, [Pd2(bpy)2(L)2](ClO4)4, 3b, displays a π−π
interactions using only two units of [Pd2(bpy)2(L)2]4+(ClO4)−.
molecules where the value of “x” ranges from 1 to 4 and the
general molecular formula is represented as [Pdx(N−N)x(L)x]-
(monoanion)2x.1a,b,2 In this formula “N−N” stands for a
chelating bidentate ligand, e.g., ethylenediamine (en), tetrame-
thylethylenediamine (tmeda), 2,2′-bipyridine (bpy), and 1,10-
phenanthroline (phen), etc. The term L stands for a
nonchelating bidentate ligand (i.e., a bis-monodentate ligand),
frequently pyridine appended in nature. A single discrete
structure is obtained in most of the designs, whereas in a few
cases a dynamic equilibrium of more than one structures,3 for
instance, M2L2 and M3L3,4 is observed. Design and synthesis of
single discrete M2L2 complexes of the general formula [Pd2(N−
N)2(L)2](monoanion)4 is well studied and reviewed.1a The
relative positions of the two Pd(N)4 square planes confined in a
M2L2 architecture is determined mostly by the spatial positions
of the coordination vectors contributed by the nonchelating
bidentate ligand component. In a majority of the structures, the
two PdN4 square-planes are located almost in the same plane
and are well separated from each other by two units of the
bridging bidentate ligands as shown in Figure 1a.1a,5 However,
only a few structures6 are reported where one of the square-
INTRODUCTION
■
The construction of discrete and designed molecular
architectures, using a selected metal component and an
artistically chosen ligand system, through metal-driven self-
assembly routes, has attracted intense interest in recent years.1
These self-assembled coordination cages have remarkable
significance in crystal engineering because of their fascinating
structural diversity. The creation of a tailor-made crystalline
system where several numbers of the discrete structures are
packed in a precise and targeted manner should be possible by
cleverly coding the required information in the molecular
framework. During the growth of crystals from a solution
containing a discrete structure, the embedded information
could be spontaneously decoded for the intended packing.
Well-defined intermolecular interactions such as H-bonding
and π-π stacking are the factors that govern the definite
arrangement of the discrete molecules in the crystals. Such a
predesigned packing could be termed as the self-assembly of
self-assembly.
Palladium(II) is one of the significant metal centers that is
exploited for preparation of self-assembled coordination cage
molecules by complexing suitable Pd(II) components with a
variety of ligands.1a,b,2 Complexation of a cis-protected
palladium(II) component with a nonchelating bidentate ligand
is known to provide discrete MxLx type coordination cage
Received: July 30, 2012
Revised: October 16, 2012
Published: October 25, 2012
© 2012 American Chemical Society
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Figure 3. Chemical structure of the ligand N,N′-bis(m-pyridyl)urea, L.
shown in Figure 3 is seemingly a suitable choice for the targeted
packing indicated in our objective. This choice is made on the
basis of a few factors including the reported crystal structure of
the ligand. The ideal conformations of the free ligand L are syn-
syn, syn-anti, and anti-anti. Analysis of the reported crystal
structures point out the presence of the syn-syn conformer in
the absence of any solvent of crystallization and the anti-anti
form in the presence of water of crystallization.7,8 No crystal
structures are reported with the syn-anti form of the free ligand.
There are only a few reports on the complexation study of
the ligand L with transition metal ions.6d,7,8b,9 Analysis of all of
these reported crystal structures made us consider that
complexation of the ligand L with Pd(bpy)2+ should afford
binuclear assembly belonging to M2L2 family where the
complexed ligand moieties are anticipated to exist in syn-syn
form. The nonbonded distance between the two Py(N) in the
syn-syn conformer of the ligand L is 8.16 Å, and the
coordination vectors are positioned in a slightly opened
manner subtending an angle of approximately 23 degrees.
Thus the resulting M2L2 framework would display the two π-
surfaces due to the bpy moieties, one above the other. The
dispositions of these two π-surfaces could facilitate intermo-
lecular locking, in the solid state, as shown in Figures 2 and 5.
We prepared eight discrete M2L2 cages (Figure 4) from the
ligand L and a variety of cis-protected Pd(II) components
having nitrate and perchlorate as counteranions (X). Complex-
ation of the ligand L with Pd(bpy)(X)2 were carried out aiming
at the intended packing in the solid state. However, the packing
of the complexed cation present in [Pd2(bpy)2(L)2](ClO4)4
were not matched to the target; nevertheless the outcome was
remarkable. Subsequently, another cis-protecting system with a
somewhat larger π-surface than bpy was chosen. Thus, the
M2L2 coordination cages constructed from complexation of L
with Pd(phen)(X)2 were crystallized that resulted in success as
the packing was found to be close to what was planned for
(Figure 5). Four other analogous compounds were prepared by
complexing L separately with non-π-surface containing metal
components, i.e., Pd(en)(X)2 and Pd(tmeda)(X)2, for compar-
Figure 1. Diagram showing the relative positions of PdN4 square
planes in the M2L2 self-assembly constructed from cis-protected Pd(II)
and bidentate nonchelating ligands where the square planes are located
(a) in same plane, and (b) in different planes but one above the other.
planes is located almost above the square-plane of the other as
shown in Figure 1b, that resembles opened jaws.
We considered new complexes of the type shown in Figure
1b to construct a special kind of packing in the solid-state. It
was anticipated that the presence of a π-cloud in the cis-
protecting unit of the opened jaws design should result in
special intermolecular association through crystal packing as
shown in Figure 2 where a given molecule is interlocked with
two adjacent molecules by π-stacking. In this design the
distance between the two π-surfaces in a M2L2 molecule is
required to be around 10.2 Å, considering 3.4 Å as the ideal
distance for π-stacking. Thus, judicial choice of the separation
between the coordination sites and the relative direction of the
coordination vectors in a ligand are the vital requirements for
the packing of the M2L2 units in a manner envisioned in this
work.
Herein we report the complexation of N,N′-bis(m-pyridyl)-
urea (Figure 3) with a variety of cis-protected Pd(II)
components (Figure 4) and successful demonstration of the
targeted packing (Figures 2 and 5) through π-locking as
realized in the crystal structure of [Pd2(phen)2(N,N′-bis(m-
pyridyl)urea)2](NO3)4. The structure/packing are analyzed and
also compared with the structures obtained from few analogous
crystals where the presence and absence of π-surfaces at the
strategic locations were probed.
RESULTS AND DISCUSSION
■
Design of the Self-Assembly of Self-Assembly. The
orientation of the pyridyl units and the distance between them
in the urea spacered ligand7 N,N′-bis(m-pyridyl)urea, L, that is
Figure 2. A designed self-assembly of self-assembly where the M2L2 units are associated by intermolecular locking and packing by π-stacking in a
linear sequence.
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Figure 4. The self-assembled M2L2 complexes [Pd2(N−N)2(L)2](X)4, 1a/b−4a/b.
Figure 5. Intermolecular locking of [Pd2(phen)2(L)2]4+ units by π-stacking interactions. The hashed line between phen units represent π-stacking.
Figure 6. 500 MHz 1H NMR spectra in DMSO-d6 (TMS as external standard) for (i) ligand L; (ii) [Pd2(en)2(L)2](ClO4)4, 1b (iii)
[Pd2(tmeda)2(L)2](ClO4)4, 2b; (iv) [Pd2(bpy)2(L)2](ClO4)4, 3b; and (v) [Pd2(phen)2(L)2](ClO4)4, 4b.
ison purposes. Since these resulting cages are handicapped with
respect to the requisite π-surfaces at the strategic locations, the
crystal structures offered a dissimilar packing yet worth noting.
Thus the influence and importance of the π-surface in the
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Figure 7. Crystal structures of the complexed cations of 1a, 2b, 3b, and 4a. Views (a) across, and (b) along the Pd−Pd axis.
locking and packing was confirmed and the objective was
accomplished. A further detail of the synthesis of the complexes
and description of the crystal structures is described below.
Synthesis and Characterization of the M2L2 Self-
Assemblies. In a typical complexation reaction the ligand L
was combined with an equimolar amount of a cis-protected
palladium(II) component in acetonitrile−water(1:1) and
stirred at room temperature. The clear solution so obtained
afforded the corresponding binuclear complex upon evapo-
ration at room temperature. Eight binuclear complexes (1a/b−
4a/b) were isolated by using four variants of the cis-protecting
units (i.e., en, tmeda, bpy, and phen) and two different choices
of counteranions (i.e., nitrate and perchlorate) as shown in
Figure 4. Recently we have come across the synthesis of 1a but
the crystal structure of the same is not reported.6d However,
utilization of a phosphine based cis-protecting unit, i.e., 1,3-
bis(phenylphosphino) propane, in fact afforded a mixture of
binuclear and trinuclear complexes in dynamic equilibrium
where the binuclear compound was crystallized.6d
structures of the complexes 1a, 2b, 3b, 4a, and 4b also
confirmed the binuclear architectures. More importantly, the
packing in the solid state are found to be greatly influenced by
the cis-protecting moieties crafted around the metal center.
Crystal Structures. Single crystals were obtained for five
out of the eight complexes prepared. The crystal structures of
1a, 2b, 3b and 4a are discussed in detail and that of 4b is
provided in Supporting Information. The data obtained for 4b
were not of good quality and hence complete refinement on 4b
could not be done. However, the molecular structures of the
complexed cations as well as the intermolecular locking
comprehended in 4a and 4b are comparable. Thus, a
preliminary comparison of the packing seen in 4a and 4b
suggested that one can neglect the differences exhibited if any
by the counteranions, i.e., nitrate and perchlorate respectively.
Comparison of the crystal structures revealed a wide variety of
intermolecular interactions upon varying the cis-protecting
moiety crafted around the palladium(II) center. Two different
views of the binuclear complexed cations of the crystal
structures are shown in Figure 7. While the views across the
Pd−Pd axis is depicted in Figure 7a, the views along the Pd−Pd
axis is displayed in Figure 7b. The coordination geometry
around the metal centers and the related bond lengths and
bond angles in all the structures are well in the range of
expectation. However, the relative positions of the two square-
planes in the binuclear complexes seem to depend on the
nature of the cis-protecting group employed around palladium-
(II). The conformation of the ligand moieties in all the
complexes is found to be syn-syn. The two Py-N atoms in a free
ligand, in syn-syn form are separated by 8.136 Å. The Py(N) to
Py(N) nonbonded distances in the two ligand strands in the
complexes are 8.194/8.250 Å (for 1a), 8.063/8.078 Å (for 2b),
7.814/7.795 Å (for 3b), 8.157/8.222 Å (for 4a). Thus the order
of the average distances between Py(N) to Py(N) is (8.222 Å)
1a > (8.189 Å) 4a > (8.136 Å) L > (8.070 Å) 2b ≫ (7.804 Å)
3b, which is also reflected in the bond angles around the urea
moieties. The order of nonbonded distances between the metal
centers is (9.349 Å) 1a > (9.164 Å) 4a > (8.817 Å) 2b > (8.174
Å) 3b, that is in line with above-mentioned order of Py(N) to
Py(N) distances. Thus, upon complexation the overall
geometries of the ligand moieties are slightly tempered but
considerably so for 3b. In the case of 3b two units of the
complexed cations are reasonably intercalated with each other
by π−π interactions using the π-surfaces of the bpy moieties.
1
The complexes were characterized by H NMR, 13C NMR,
H−H COSY, HSQC, IR, electrospray ionization mass
spectrometry (ESI-MS) and single crystal X-ray diffraction
(XRD) methods. The 1H NMR spectra of the ligand and all the
complexes have been recorded in DMSO-d6. A simple pattern
in the 1H NMR spectra of each of the complexes indicated the
formation of single, discrete compounds. All the signals with
exception of Ha and He (Figure 6) could be assigned
unambiguously. It was possible to distinguish the signal of Ha
from He by using HSQC because one is connected to a carbon
and the other to a nitrogen atom. The signals due to the
protons Ha, Hb, Hc, and He of all the complexes (1a/b−4a/b)
are downfield shifted with respect to that of the free ligand
(Figure 6). A stacking diagram showing the 1H NMR spectra of
the ligand L and the complexes 1b−4b is presented in Figure 6
for comparison. This downfield shift of the signals is attributed
to the loss of electron density from the ligand L to the
palladium(II) centers. In all the complexes Hd showed an
upfield shift when compared with the signal of the ligand,
probably due to some spatial location of the proton.
The formation of the binuclear complexes of M2L2
formulations was confirmed from ESI-MS data of the
complexes. The mass spectra of 1a−4a show peaks at m/z =
442 for ([1a-2NO3]2+), 218 for ([2a-4NO3]4+), 1139 for ([3a-
+
NO3] ) and 250 for ([4a-4NO3]4+) respectively. The crystal
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Table 1. Crystallographic Data and Structure Refinement Parameters (CCDC Nos. 888465−888467 and 890214)
1a
2b
3b
4a
empirical formula
formula weight
crystal system
space group
a (Å)
C34H52N16O18Pd2
1185.72
C40H71Cl3N14O15Pd2
1307.26
C42H36Cl4N12O19Pd2
1367.43
C96H76N30O19Pd4
2379.47
triclinic
triclinic
triclinic
triclinic
P1
̅
P1
̅
P1
P1
̅
̅
11.9558(13)
13.9593(15)
4.9742(16)
75.258(4)
82.855(4)
88.532(4)
2398.0(4)
2
13.275(9)
15.216(16)
15.513(9)
110.66(3)
104.68(2)
101.53(3)
2688(4)
2
13.7721(11)
14.3283(11)
15.2061(11)
72.723(3)
78.255(3)
76.979(3)
2761.3(4)
2
12.1745(14)
15.9854(19)
16.9763(18)
66.886(3)
74.165(4)
69.919(3)
2817.2(6)
1
b (Å)
c (Å)
α (°)
β (°)
γ (°)
volume (Å)3
Z
wavelength (Å)
temperature (K)
calculated density (g/cm3)
absorption coefficient
0.71073
298(2)
0.71073
293(2)
0.71073
298(2)
0.71073
173(2)
1.642
1.393
1.645
1.349
0.838
0.927
0.926
0.699
(mm−1
)
F(000)
1208
1144
1368
1146
crystal dimensions (mm)3
0.25 × 0.20 × 0.18
1.51/28.36
0.25 × 0.20 × 0.15
1.50/29.07
0.35 × 0.20 × 0.15
1.51/29.91
0.25 × 0.20 × 0.15
1.32/27.24
θ min/max (deg)
reflections collected/unique
29909/10335 [R(int) =
0.0479]
15377/8339 [R(int) = 0.0681] 38587/13923 [R(int) =
0.0507]
19724/7255 [R(int) = 0.0807]
data/restraints/parameters
goodness-of-fit on F2
final R indices [I > 2σ(I)
R indices (all data)
10335/7/601
8339/8/670
13923/0/712
7255/0/639
1.025
0.860
1.044
1.013
R1 = 0.0493, wR2 = 0.1326
R1 = 0.0850, wR2 = 0.1557
0.992 and −0.859
R1 = 0.0781, wR2 = 0.2221
R1 = 0.1494, wR2 = 0.2869
1.377 and −1.270
R1 = 0.0730, wR2 = 0.2204
R1 = 0.1292, wR2 = 0.2547
2.186 and −1.231
R1 = 0.1212, wR2 = 0.3178
R1 = 0.2046, wR2 = 0.3932
3.018 and −0.944
̂
largest diff peak and hole·A
Figure 8. Crystal structure of 1a showing the views of (a) the H-bonding interactions around a complexed cation (b) the fit-in of two molecules
where one unit uses the cavity of the other and (c) further growth showing the packing of fit-in units.
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Presumably this stacking along with binding of one anion in
between the metal centers is responsible for the compression
observed in the molecular structure along the Pd−Pd axis. The
crystal structures of 2b and 3b, when viewed along the Pd−Pd
axis, clearly display the oxygen atoms of the ligand tilted away
from the plane of the concerned ligand. This tilting can be
related to the H-bonding interactions of one molecule of the
complex with a neighboring one, directly (as in 3b) or via water
molecules (as in 2b). More detail on the intermolecular
interactions observed in the crystal structures is discussed
below and the crystallographic data are collected in Table 1.
Crystal Structure of [Pd2(en)2(L)2](NO3)4, 1a. Single
crystals suitable for X-ray diffraction studies were obtained by
slow diffusion of dioxane into a solution of 1a in water. The
complex crystallized in triclinic space group P1. The structure is
̅
composed of the complexed cation [Pd2(en)2L2]4+, four nitrate
ions and two dioxane molecules. Several H-bonding inter-
actions are present in the structure. As many as eight nitrates
and one dioxane molecule are located and H-bonded around a
complexed cation in the extended structure. The urea protons
of the two ligand moieties are bonded to nitrate ions, one each.
The amine protons present in the en moieties are also bonded
to six nitrates and one dioxane molecule (Figure 8a). All the
nitrates are further H-bonded utilizing the urea protons and en
protons of neighboring units of the complex thus providing an
extended network. Since two en units present in the complex
are pointed away from each other, there is enough space in
between them. Interestingly, two molecules are found to fit-in
one another to fill the space in the cavity accessible between the
cis-protected metal centers of a given molecule (Figure 8b,c).
[Pd2(tmeda)2(L)2](ClO4)4, 2b. Single crystals suitable for X-
ray diffraction studies were obtained by slow evaporation of a
solution of 2b in acetonitrile−water. The complex was
Figure 9. Crystal structure of 2b showing a H-bonded dimer
composed of two units of the complexed cations, four water molecules
and four perchlorates.
between the metal centers probably by short contact with
several H-atoms delineated in the cavity, as well as by
electrostatic interactions with Pd−O distances of 3.315 and
3.397 Å. The steric hindrance caused due to the methyl groups
of tmeda apparently prevents the locking or fit-in between two
units of the complex; rather a perchlorate ion is accommodated
in the available space. Such encapsulation of perchlorate
depends on several factors such as shape, size and binding
modes of the anion inside the host molecule.10
crystallized in triclinic space group P1. The structure contains
̅
[Pd2(bpy)2(L)2](ClO4)4, 3b. Single crystals suitable for X-ray
diffraction studies were obtained by slow evaporation of a
solution of 3b in acetonitrile−water. The complex crystallized
one [Pd2(tmeda)2L2]4+ cation, three perchlorate ions, two
water molecules and one uncoordinated tmeda unit. One of the
perchlorate ions could not be located in the structure. The
origin of uncoordinated tmeda, located in the crystal lattice (see
Supporting Information Figures S46 and S47), is attributed to
the dissociation of the complex during the crystallization
in triclinic space group P1. The structure contains
̅
[Pd2(bpy)2L2]4+ cation and four perchlorate ions. One of the
perchlorates is present inside the cavity between the metal
centers and other three are outside the cavity. The urea protons
of one of the two strands of the ligand are H-bonded to a
perchlorate ion and the urea oxygen is remarkably tilted away
from the ligand toward the cavity pointing at the trenchlike
zone between the ligands. The bonded perchlorate is not
further H-bonded to any other groups. The tilted oxygen is
involved in H-bonding to facilitate the dimerization of two
identical units of the complex. The other strand of the ligand
behaved somewhat differently in that the urea protons
participate in H-bonding for dimerization, whereas the oxygen
atom present in this urea moiety is not much tilted away from
the ligand and not H-bonded with any groups. Two different
views of the H-bonded dimer are shown in Figure 12.
Interestingly, one H-bonded dimeric unit is found to be
associated with two more dimeric units via π-stacking of the
bpy moieties in an intercalating manner as shown in Figure 13.
One of the two pyridine rings of a bpy moiety is involved in the
stacking, though not completely, thus the π-surfaces are not
fully utilized. As seen in previous reports, two bipyridine units
usually interact in an offset or parallel displaced mode.6f,11
Nevertheless, one-dimensional growth is observed and
attributed to π−π stacking interactions. The plane of a bpy
rings is separated from the adjoining stacked bpy ring(s) by
approximately 4 Å with the consequence of a severe
1
process. H NMR of a batch of sample, obtained by slow
evaporation to grow crystals, shows some amount of free ligand
L and free tmeda along with the parent complex. The urea
protons of one of the two strands of the ligand are H-bonded to
a perchlorate ion, and the urea oxygen is found to be free and
not tilted away from the ligand. The perchlorate is not further
H-bonded to any other groups. In the other strand of the
ligands, the urea oxygen is remarkably tilted away from the
complex, and the urea moiety thus exhibits a different fashion
of binding. Here the urea protons are H-bonded to one water
molecule which is further H-bonded to the tilted oxygen of the
urea moiety of a neighboring unit of the complex. The
neighboring unit also behaved similarly and returns the same
favor, and hence a dimer of the complex is created. Each of
these water molecules is further H-bonded to a water molecule
followed by a perchlorate ion. Such a H-bonded dimer is shown
in Figure 9. Interestingly, the two terminal perchlorates,
bonded to water, are each encapsulated in the cavities of
adjacent neighboring dimers. The zone where a perchlorate is
encapsulated in the cavity is the one that exists between the two
cis-protecting tmeda units. The packing thus formed in one-
dimension is shown in Figure 10. The encapsulated
perchlorates, as shown in Figure 11, are held in the cavity
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Figure 10. Interaction of a H-bonded dimer of 2b with two other units of the dimers in the packing.
compression within the structure. Since this is not the ideal
distance for optimum interactions, the compression in the
molecule is also assisted by the encapsulation of a perchlorate
ion between the metal centers (Figures 13 and 14). A
perchlorate ion is held in the cavity by electrostatic interactions
with Pd−O distances of 3.092 and 3.007 Å. Thus, the overall
packing is attributed to H-bonding between urea moieties, π−π
interactions of bpy moieties and electrostatic interactions due
to metal−perchlorate−metal contacts.
[Pd2(phen)2(L)2](NO3)4] 4a. Single crystals suitable for X-
ray diffraction studies were obtained by slow diffusion of
dioxane into a solution of 4a in acetonitrile−water. The
complex crystallized in triclinic space group P1. The structure
̅
contains [Pd2(phen)2L2]4+cation and two nitrate ions. Two
other nitrates could not be located in the structure. Both the
strands of the ligands are found to be almost identical. The urea
protons of one ligand strand are H-bonded to one nitrate and
the other strand to another nitrate ion (Figure 15). The oxygen
of urea moieties possesses no H-bonding interactions. There is
no further H-bonded network in the structure. However, the
Figure 11. Crystal structure showing the closest approach of two units
of 2b and binding of one perchlorate ion per cavity.
Figure 12. Crystal structure of 3b showing different orientations of a H-bonded dimer composed from two units of the complexed cations and two
perchlorates.
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Figure 13. Interaction of H-bonded dimers of 3b in the packing by π−π stacking; also shown the encapsulated perchlorate ion one per cavity.
neighboring molecules by locking that continues to give a
one-dimensional growth (Figures 16 and 17). Complexes are
Figure 14. Crystal structure showing the closest approach of two units
Figure 16. Crystal structure showing the closest approach of the
of 3b and binding of a perchlorate ion per cavity.
molecules in 4a by incorporating segment of two neighboring units per
cavity.
packed in the crystal lattice in a perfectly stacking manner due
to π−π stacking interactions. The π−π stacking becomes more
favorable in the case of phenanthroline units because of its
extended aromatic ring systems.11a Thus there is a near face to
face π-stacked arrangement of phenanthroline units. The
shortest distance between the two stacked phen units is
found to be 3.79 Å. The Pd−Pd axes are not exactly collinear
and shifted slightly toward one side and repeatedly as the
molecules are associated (Figure 17b). Thus the allied units are
not exactly one above the other in the crystal array. No anions
are located in the cavity indicating strong preference of π−π
stacking.
[Pd2(phen)2(L)2](ClO4)4, 4b. Single crystals were obtained
by slow evaporation of a solution of 4b in acetonitrile−water.
The complex crystallized in monoclinic space group P2(1)/n.
Two units of complexes are stacked due to π−π interactions in
one unit cell itself. Six out of eight perchlorate anions and few
other atoms were located all outside the cavity. Some of the
urea protons of the ligand are hydrogen bonded to perchlorate
anions directly or via water molecules. Since the quality of the
crystals was not good we restrict detailed discussion on this
structure. More importantly the focused intermolecular π−π
Figure 15. Crystal structure of 4a showing the H-bonding interactions
around a molecule.
most important feature in this crystal structure is the
intermolecular interactions through π-stacking to provide our
intended packing. Each molecule is stacked with two
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Figure 17. (a, b) Crystal structure showing two different views of the intermolecular locking and packing.
stacking present in 4b is quite similar to that of 4a. Notably
perchlorate did not obstruct the stacking. Crystallographic data
of 4b has been given in Supporting Information.
broad pattern at 1371 cm−1 along with a shoulder peak at 1426
cm−1 attributable to the N−O stretching frequencies. Presence
of a shoulder peak indicates that all the three O of a given
−
coordinated NO3 are possibly not in same environments.
Influence of cis-Protecting Moiety on the Packing in
1a, 2b, 3b and 4a. Most interesting observation has been the
influence of the presence and absence of π-cloud on the
intermolecular interactions in the solid state. In the case of 4a
one unit of the complexed cation, i.e., [Pd2(phen)2 (L)2]4+, is
found to be associated with two other units by π−π stacking
interactions thus giving a one-dimensional growth like a rod. In
the case of [Pd2(en)2(L)2]4+ of 1a no such interaction was seen
in the packing due to the absence of π-cloud at the strategic
locations. The Pd−Pd distances of 4a and 1a are comparable.
However, to fill the available space in the cavity two units of the
complexed cation of 1a are associated with each other in a fit-in
manner, without tempering the overall framework. Such a fit-in
is not observed in [Pd2(tmeda)2(L)2]4+ of 2b due to steric
hindrance by the tmeda group. Rather a perchlorate anion is
encapsulated in the cavity where the Pd−Pd distance is
somewhat shortened indicating electrostatic interactions.
Examination of the packing seen in [Pd2(bpy)2(L)2]4+ of 3b
showed π−π stacking interactions between only two units of
the complexed cation where one unit is intercalated with
another unit causing a severe compression unlike the structure
of 2b. This compression is also associated with the binding of a
perchlorate per cavity, probably in a synergetic manner.
Further, the broad nature of the band does not allow precise
interpretation of the number and variety of bonding modes
around the four nitrate ions present in a molecule. In 2a, the
N−O stretching frequency appears at 1379 cm−1 with a
shoulder at 1420 cm−1. So the mode of binding of anions in the
complex 2a may be comparable to 1a, at least with respect to
bonding with urea protons. In 3a, N−O stretching band is very
broad with signals at 1428, 1375, and 1340 cm−1. This suggests
that the symmetry of nitrate anion is lost upon coordination
and the anions are bonded in a somewhat different fashion
compared to 1a and 2a. Possibility of nonbonded nitrates
cannot be ruled out due to the very broad nature of the band.
The nature of the band for 4a is comparable to 3a, and hence
overall situations of the anions of 3a and 4a may be considered
comparable. Occurrence of a very intense and a broad band
around 1110 cm−1 is a characteristic feature of a free
perchlorate ion. The Cl−O stretching frequency around this
region is analyzed for the complexes 1b−4b. Broad Cl−O
stretching appears around 1096, 1087, 1087, and 1078 cm−1 for
1b to 4b respectively. The broad bands indicate that the
perchlorate ions are bonded in a variety of modes.
CONCLUSION
IR Spectra. The N−O stretching frequency of a free nitrate
anion appears around 1405 cm−1. Broad bands are observed
around 1371, 1379, 1375, and 1375 cm−1 for the complexes 1a,
2a, 3a and 4a, respectively. The compound 1a displayed a
■
The nature of cis-protecting group around Pd(II) can have a
significant influence on the growth of the crystal from a
solution of self-assembled coordination cage molecules
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ESI-MS: m/z = 442 corresponding to [1a−2NO3]2+. Single crystals
were obtained by slow diffusion of dioxane into solution of 1a in water.
FT-IR (cm−1): 3201, 3077, 1715, 1586, 1556, 1482, 1426, 1371,
1278, 1212, 1135, 1057, 904, 812, 699.
constructed from suitable ligand and cis-protected Pd(II)
components. Particularly the packing can definitely influence
the overall structure of the complexes in the solid state. The
influence of solvent, counteranions, guest molecules, and
variation of substituent on the ligand component as well as
cis-protecting moieties may provide a rich chemistry and open a
new avenue.
1
1b: Yield: (80%). M.P.: 220 °C. H NMR (500 MHz, DMSO-d6
external TMS/CDCl3) δ: 10.33 (s, 4H, a), 10.02 (s, 4H, e), 9.13(t, J =
3.5 Hz, 4H, b), 8.13 (d, J = 1 Hz, 8H, c and d), 6.05 (s, 8H, f), 3.22 (s,
8H, g).13C NMR (125 MHz, DMSO-d6) δ: 151.56, 145.80, 140.60,
137.92, 129.30, 126.26, 46.68.
FT-IR (cm−1): 3242, 3073, 1715, 1593, 1549, 1483, 1433, 1382,
1281, 1213, 1096, 808, 697, 627.
EXPERIMENTAL SECTION
■
General. PdCl2 and AgClO4 were obtained from Aldrich, whereas
AgNO3, nicotinic acid, 3-aminopyridine and all the common solvents
were obtained from Spectrochem, India. The deuterated solvent
(DMSO-d6) was obtained from Aldrich and Cambridge Isotope
1
2a: Yield: (93%). M.P.: 200 °C. H NMR (500 MHz, DMSO-d6
external TMS/CDCl3) δ:10.91 (s, 4H,e), 10.56 (s, 4H, a), 9.42 (d, J =
5.5 Hz, 4H, b), 8.14−8.12 (m, 4H, c), 8.03 (d, J = 8.5 Hz, 4H, d),
3.67−3.54 (m, 8H, h and i), 3.17−3.04 (m, 24H, j and k). 13C NMR
(125 MHz, DMSO-d6) δ: 151.07, 144.86, 139.67, 138.70, 128.79,
126.89, 62.73, 62.02, 50.40, 50.11. ESI-MS: m/z = 218 corresponding
to [2a−4NO3]4+.
1
Laboratories. H and 13C NMR spectral data were obtained from a
Bruker 500 MHz FT NMR spectrometer using external TMS in
CDCl3 and residual solvent as reference, respectively. The mass
spectra were obtained from a Micromass Q-TOF Mass Spectrometer.
The crystal structures were determined using a Bruker X8 Kappa XRD
instrument. The FT-IR spectra of the samples were recorded as KBr
pellets using a JASCO FT/IR-4100 spectrometer. The samples were
finely powdered with oven-dried spectroscopic-grade KBr and pressed
into pellets. The ligand L was synthesized by slight modification of a
reported procedure.7 The cis-protected Pd(II) components were
obtained following well-known processes.12
Synthesis of the Ligand L. Nicotinic acid (0.732 g, 5.95 mmol)
was added to 10 mL of thionyl chloride and the mixture was refluxed
for 30 min. The resulting clear solution was reduced under a vacuum
to yield white, shiny crystals of nicotinoyl chloride hydrochloride. To
the suspension of nicotinoyl chloride hydrochloride in 10 mL of dry
DCM, sodium azide (0.387 g, 5.95 mmol) was added and stirred for 8
h. The suspension so obtained was then washed with saturated sodium
bicarbonate solution followed by water and extracted with DCM. The
organic layer was dried over anhydrous Na2SO4. Evaporation of the
DCM under a vacuum yielded the nicotinoyl azide intermediate as a
white solid (0.498 g, 3.36 mmol), which was dissolved in 15 mL of
toluene and refluxed for about 2.5 h to generate the isocyanate
intermediate. To the yellow color solution so obtained, 3-amino-
pyridine (0.316 g, 3.36 mmol) was added and the mixture was refluxed
for 2 h. The product was precipitated as a white solid which was
collected by filtration, washed with DCM, and dried. Yield: (75%).
M.P.: 225 °C. 1H NMR (500 MHz, DMSO-d6 external TMS/CDCl3)
δ: 9.53 (s, 2H, e), 9.15 (d, J = 2.5 Hz, 2H, a), 8.75 (dd, J1 = 4.5 Hz, J2
= 1.5 Hz, 2H, b), 8.49 (m, 2H, d), 7.86 (m, 2H, c). 13C NMR (125
MHz, DMSO-d6) δ: 152.54, 143.01, 140.14, 136.04, 125.28, 123.49.
Synthesis of the Complexes. A typical method for the synthesis
of 1a and 1b is described below. The other complexes, 2a/2b, 3a/3b
and 4a/4b, were prepared following the same procedure by taking
appropriate cis-protected Pd(II) components.
FT-IR (cm−1): 3234, 3060, 1709, 1546, 1480, 1379, 1275, 1207,
806, 702, 621,537.
1
2b: Yield: (72%). M.P.: 250 °C (decomposition). H NMR (500
MHz, DMSO-d6 external TMS/CDCl3) δ: 10.48 (d, J = 2.5 Hz, 4H,
a), 9.92 (s, 4H, e), 9.42 (d, J = 5.6 Hz, 4H, b), 8.15−8.12 (m, 4H, d),
8.06 (d, J = 8.5 Hz, 4H, c), 3.67−3.52 (m, 8H, h and i), 3.16−3.04 (m,
24H, j and k). 13C NMR (125 MHz, DMSO-d6) δ: 150.90, 145.09,
139.40, 138.37, 129.31, 126.95, 62.09, 50.41, 50.22. Single crystals
were obtained by slow evaporation of solution of 2b in acetonitrile−
water.
FT-IR (cm−1): 3349, 3084, 2926, 1715,1665, 1613, 1587, 1546,
1482, 1429, 1336, 1278, 1212, 1087, 1044, 1007, 954, 809, 705, 624.
1
3a: Yield: (85%). M.P.: 242 °C. H NMR (500 MHz, DMSO-d6,
external TMS/CDCl3) δ: 10.74 (s, 4H, a), 10.42 (s, 4H, e), 9.44 (s,
4H, b), 9.28 (d, J = 8 Hz, 4H, o), 9.01 (t, J = 7.6 Hz, 4H, n), 8.31−
8.22 (m, 12H, d, c and m), 8.05 (d, J = 4.76 Hz, 4H, l). 13C NMR (125
MHz, DMSO-d6) δ: 155.77, 151.48, 150.01, 145.02, 142.66, 139.9,
138.84, 129.92, 128.61, 127.99, 124.52. ESI-MS: m/z = 1139
correspondingto [3a−NO3]+.
FT-IR (cm−1): 3247, 3071, 1712, 1591, 1555, 1480, 1428, 1375,
1340, 1275, 1214, 1114, 1031, 777, 700.
1
3b: Yield: (90%). M.P: 223 °C. H NMR (500 MHz, DMSO-d6,
external TMS/CDCl3) δ:10.72 (s, 4H, a), 10.18 (s, 4H, e), 9.4 (s, 4H,
b), 9.22 (d, J = 7 Hz, 4H, o), 8.96 (bs, 4H, n), 8.25−8.19 (m, 12H, d, c
and m), 8.01 (d, J = 5.5 Hz, 4H, l). 13C NMR (125 MHz, DMSO-d6)
δ: 155.71, 151.43, 149.95, 144.96, 142.65, 139.90, 138.75, 130.04,
128.58, 127.94, 124.50. Single crystals were obtained by slow
evaporation of solution of 3b in acetonitrile−water.
FT-IR (cm−1): 3312, 3086, 1712, 1672, 1589, 1552, 1434, 1281,
1216, 1099, 807,772, 697, 625, 419.
1
4a: Yield: (88%). M.P.: 320 °C (decomposition). HNMR (500
MHz, DMSO-d6 external TMS/CDCl3) δ:10.8 (d, J = 1.5 Hz, 4H, a),
10.41(s, 4H, e), 9.58−9.56 (m, 4H, r), 9.51−9.50 (m, 4H, b), 8.88 (s,
4H, s), 8.53−8.50 (d, J = 5.1 Hz, 4H, q), 8.44−8.32 (m, 4H, p), 8.32−
8.30 (m, 8H, c and d). 13C NMR (125 MHz, DMSO-d6) δ: 151.57,
151.00, 145.96, 145.38, 141.44, 140.25, 138.91, 130.50, 130.10, 128.05,
126.82. ESI-MS: m/z = 250 corresponding to [4a−4NO3]4+. Single
crystals were obtained by slow diffusion of dioxane into solution of 4a
in acetonitrile−water.
[Pd2(en)2(L)2](NO3)4,1a. To a solution of Pd(en)(NO3)2 (8.7 mg,
0.03 mmol) in 1:1 acetonitrile−water (3.0 mL), ligand L (6.4 mg, 0.03
mmol) was added and the mixture was stirred at room temperature for
48 h. The resulting solution was evaporated by standing at room
temperature, washed with acetone, and dried under a vacuum to obtain
the complex 1a as a yellow solid.
[Pd2(en)2 (L)2](ClO4)4, 1b. To a solution of Pd(en)Cl2 (9.5 mg, 0.04
mmol) in 1:1 acetonitrile−water (4 mL), silver perchlorate was added
(16.6 mg, 0 0.08 mmol) which led to immediate precipitation of AgCl.
The resulting mixture was heated for 30 min and centrifuged. The
yellow color solution of Pd(en)(ClO4)2 so formed was separated by
filtration. To the clear yellow solution, ligand L (8.6 mg, 0.04 mmol)
was added and the mixture was stirred at room temperature for about
48 h. The resulting solution was evaporated, washed with acetone, and
dried under a vacuum to obtain the complex 1b as a white solid.
Analytical Data of the Complexes. 1a: Yield: (90%). M.P.: 210
FT-IR (cm−1): 3271, 3234, 3058, 1710, 1598, 1544, 1481, 1415,
1375, 1283, 1207, 838, 711.
1
4b: Yield: (88%). M.P.: 280 °C (decomposition). HNMR (500
MHz, DMSO-d6 external TMS/CDCl3) δ: 10.79 (s, 4H, e), 10.28 (s,
4H, a), 9.61−9.59 (m, 4H, r), 9.49−9.48 (m, 4H, b), 8.91 (s, 4H, s),
8.55−8.52 (m, 4H, q), 8.46−8.45 (m, 4H, p), 8.34−8.33 (m, 8H, c and
d). 13C NMR (125 MHz, DMSO-d6) δ: 151.30, 150.98, 145.81,
145.31, 141.47, 140.15, 138.83, 130.48, 130.16, 127.99, 126.85. Single
crystals were obtained by slow evaporation of solution of 4b in
acetonitrile−water.
1
°C. H NMR (500 MHz, DMSO-d6 external TMS/CDCl3) δ: 10.35
(s, 4H, a), 10.15 (s, 4H, e), 9.15 (d, J = 4.5 Hz, 4H, b), 8.11 (d, J = 5.5
Hz, 8H, c and d), 6.13 (s, 8H, f), 3.23 (s, 8H, g). 13C NMR (125 MHz,
DMSO-d6) δ: 151.48, 145.71, 140.53, 137.92, 129.09, 126.18, 46.63.
FT-IR (cm−1): 3274, 3062, 1710, 1663, 1600, 1585, 1542, 1519,
1480, 1426, 1328, 1278, 1205, 1139, 1108, 1078, 840, 806, 709, 623.
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Single Crystal X-ray Diffraction. X-ray data collection was
performed with a Bruker AXS Kappa Apex II CCD diffractometer
equipped with graphite monochromated Mo(Kα) (λ = 0.7107 Å)
1998, 27, 417−425. (e) Fujita, M.; Tominga, M.; Hori, A.; Therrien,
B. Acc. Chem. Res. 2005, 38, 371−380.
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(b) Albrecht, M.; Stortz, P.; Engeser, M.; Schalley, C. A. Synlett
2004, 15, 2821−2823.
́
radiation. Crystal fixed at the tip of the glass fiber was mounted on the
Goniometer head and was optically centered. The automatic cell
determination routine, with 32 frames at three different orientations of
the detector was employed to collect reflections and the program
APEX2-SAINT (Bruker, 2004) was used for finding the unit cell
parameters. Four-fold redundancy per reflection was utilized for
achieving good absorption correction using a multiscan procedure.
Besides absorption, Lorentz polarization and decay correction were
applied during data reduction. The program SADABS was used for
absorption correction using the multiscan procedure. The structures
were solved by direct methods using SHELXL-97 (Sheldrick, 1997)13
and refined by full-matrix least-squares techniques using SIR92
(WinGX) computer program. All hydrogen atoms were fixed at
chemically meaningful positions and riding model refinement was
applied. At the final stage of refinement, 4a and 4b were subjected to
SQUEEZE calculations. Molecular graphics were generated using
Mercury programs. The crystal data with refinement details are
summarized in Table 1.
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ASSOCIATED CONTENT
■
(6) (a) Oskui, B.; Sheldriz, W. S. Eur. J. Inorg. Chem. 1999, 1325−
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* Supporting Information
1H NMR,13C NMR, H−H COSY, HSQC and IR spectra of 1a/
1
b−4a/b, ESI-MS spectra of 1a−4a, stacked H NMR spectra
for1a/1b, 2a/2b, 3a/3b and 4a/4b, crystal packing diagrams of
4b, structural refinement table for 4b and X-ray crystallographic
files for complexes 1a, 2b, 3b, 4a, and 4b in CIF format.This
material is available free of charge via the Internet at http://
pubs.acs.org.
(d) Troff, R. W.; Hovorka, R.; Weilandt, T.; Lutzen, A.; Cetina, M.;
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AUTHOR INFORMATION
Corresponding Author
*Tel: +91-4422574224, Fax: +91-4422574202, E-mail: dillip@
iitm.ac.in.
■
(8) (a) Reddy, L. S.; Basavzju, S.; Vangala, V. R.; Nangia, A. Cryst.
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Notes
The authors declare no competing financial interest.
This article is dedicated to Prof. P. K. Bharadwaj on the
occasion of his 60th birthday.
ACKNOWLEDGMENTS
■
The authors thank the Department of Science and Technology,
Government of India (Project No. Sr/S1/IC-28/2009) for
financial support. The NMR and ESI-MS facility at the
Department of Chemistry, IIT Madras funded by DST, India
is gratefully acknowledged. We profoundly acknowledge the
single crystal X-ray Diffractometer facility funded by IIT
Madras. We thank Prof. M. N. S. Rao for helping us in
interpreting IR spectra.
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