Ligand Isomerism in Coordination Cages

Article abstract of DOI:10.1021/acs.inorgchem.8b01884

Complexation reactions of palladium(II) nitrate with a set of 3-pyridyl appended nonchelating bidentate ligands possessing regioisomeric phenylene-diurea functionalities as spacers were carried out. The ligands utilized in this study are 1,1′-(1,2-phenylene)bis(3-(pyridin-3-yl)urea), L1; 1,1′-(1,3-phenylene)bis(3-(pyridin-3-yl)urea), L2; and 1,1′-(1,4-phenylene)bis(3-(pyridin-3-yl)urea), L3. The complexation reactions of the ligands (L1, L2, and L3) with palladium(II) produced single discrete isomeric cages (1, 2, and 3) of Pd₂L₄ formulation in each case and thereby illustrated ligand-isomerism in coordination cages. All 16 hydrogen atoms of eight urea moieties present in four ligand strands are delineated completely endohedrally in cage 1 and completely exohedrally in cage 3, whereas cage 2 exhibited half of the urea hydrogens in exohedral locations and the remaining half in endohedral locations. In addition to the variable number of solvent molecules, the cavities of cages 1 and 2 lodged four and two nitrate ions, respectively, using the endohedral (H)_urea atoms (i.e., NH groups) as binding sites, whereas the cavity of 3 remained anion free. The abilities of the complexes 1-3 for adsorption of CO₂ gas are demonstrated, and their behaviors are compared.

Full text of DOI:10.1021/acs.inorgchem.8b01884

Article
pubs.acs.org/IC
Cite This: Inorg. Chem. XXXX, XXX, XXX−XXX
Ligand Isomerism in Coordination Cages
Hareesha Dasary, Rajamony Jagan, and Dillip Kumar Chand*
Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
S
* Supporting Information
ABSTRACT: Complexation reactions of palladium(II) nitrate with
a set of 3-pyridyl appended nonchelating bidentate ligands possessing
regioisomeric phenylene-diurea functionalities as spacers were
carried out. The ligands utilized in this study are 1,1′-(1,2-
phenylene)bis(3-(pyridin-3-yl)urea), L1; 1,1′-(1,3-phenylene)bis(3-
(pyridin-3-yl)urea), L2; and 1,1′-(1,4-phenylene)bis(3-(pyridin-3-
yl)urea), L3. The complexation reactions of the ligands (L1, L2, and
L3) with palladium(II) produced single discrete isomeric cages (1, 2,
and 3) of Pd2L4 formulation in each case and thereby illustrated ligand-isomerism in coordination cages. All 16 hydrogen atoms
of eight urea moieties present in four ligand strands are delineated completely endohedrally in cage 1 and completely
exohedrally in cage 3, whereas cage 2 exhibited half of the urea hydrogens in exohedral locations and the remaining half in
endohedral locations. In addition to the variable number of solvent molecules, the cavities of cages 1 and 2 lodged four and two
nitrate ions, respectively, using the endohedral (H)urea atoms (i.e., NH groups) as binding sites, whereas the cavity of 3
remained anion free. The abilities of the complexes 1−3 for adsorption of CO2 gas are demonstrated, and their behaviors are
compared.
isomeric complexes from the combination of a metal ion with
the type-I isomeric ligands15 than that of the type-II ligands.16
Utilization of urea functionalized ligands for the con-
struction of PdmLn type cages is limited to a recent example
of the Pd2L4 type complex.9 Complexation of cis-protected
palladium(II) (i.e., PdL′) with selected urea functionalized
ligands are reported to construct certain PdxL′xLy type
complexes; there are only a handful of examples34−38 and
they include PdL′L2,36 Pd2L′2L2,37,38 Pd3L′3L2,35 and
INTRODUCTION
■
Combination of palladium(II) with selected nonchelating
bidentate or polydentate ligands under suitable reaction
conditions is a reliable strategy for the preparation of a variety
of self-assembled coordination cages of PdmLn formulations.1−6
However, the general formula of the cages obtained from
palladium(II) and a nonchelating bidentate ligand is PdmL2m in
which the value of “m” is usually dictated by the relative
directions of the two coordination vectors of the ligand
moiety.1−33 It can be stated that the more diverged the
coordination vectors of the ligand the higher is the nuclearity
of the ensuing PdmL2m cage. The formula of known PdmL2m
type cages are as varied as Pd2L4,1,3,4,6−18 Pd3L6,6,19−24
Pd4L8,1,6,19,23,24 Pd5L10,19 Pd6L12,5,6,19,25−27 Pd7L14 (opti-
mized),19 Pd8L16 (not isolated),28 Pd9L18,28 Pd12L24,5,6,29−31
Pd24L48,5,6,20,29 Pd30L60,32,33 and Pd48L96.32
The Pd2L4 type cages are simplest among the PdmL2m series,
yet the most explored. Structural diversity of these binuclear
cages is broadly covered under helical or nonhelical
architectures. A variety of functional aspects of such binuclear
cages are studied by tuning the steric and electronic nature of
the exo-/endohedral space of the architectures. The three-
dimensional cavity of Pd2L4 type cages has been exploited for
binding diverse guests such as dye molecules,7 fullerenes,14
radical initiators,12 metal complexes,13 and anions.10,17 The
formation of isomeric pairs of Pd2L4 cages from a pair of
isomeric ligands (i.e., ligand isomerism in coordination cages)
is a rare phenomenon.15,16 The backbones of two isomeric
ligands could be same, and the variable positions of innocent
substituents qualifies them as isomers (say Type-I). Alter-
natively, the backbones of the two isomeric ligands could be
very different (say Type-II). It is more obvious to afford
34
Pd3L′3L3 type designs. A Pd6La Lb type complex is
6
6
known,34 where La and Lb stand for ligands with and without
a urea spacer, respectively.
The endohedral spaces of Pd2L4 type complexes are usually
conducive to anionic guests due to the cationic nature of the
space; hence, counteranions are often lodged in the cavity. We
considered crafting regioisomeric phenylene-diurea function-
alities at the ligand backbones of 3-pyridyl appended bidentate
nonchelating ligands and anticipated constructing Pd2L4 type
cages (Figure 1). It is safe to predict that endohedral
delineation of the urea hydrogen atoms (Figure 1a) in a
Pd2L4 type cage might strongly facilitate encapsulation and
endohedral retention of the counteranions. In the same line,
we envisioned that exohedral delineation of the urea hydrogens
(Figure 1c) might facilitate exohedral dispositions of the
counteranions making the endohedral space of the cavity
accessible for other suitable guests.
The present work describes complexation behaviors of
palladium(II) separately with three nonchelating bidentate
ligands that are regioisomers (Scheme 1). The ligands utilized
Received: July 6, 2018
© XXXX American Chemical Society
A
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Figure 1. (a−c) Ligand isomerism in Pd2L4-type coordination cages (1−3) perceived from appropriate conformers of regioisomeric ligands (L1−
L3). (Magenta ball: palladium(II); blue rod: nonchelating bidentate ligand; red ball: oxygen of urea; orange strip: anionophilic zone of urea).
whereupon a white solid was precipitated out. The solid was separated
by filtration and washed with CH3CN and acetone followed by drying
are 1,1′-(1,2-phenylene)bis(3-(pyridin-3-yl)urea), L1; 1,1′-
(1,3-phenylene)bis(3-(pyridin-3-yl)urea), L2; and 1,1′-(1,4-
under a vacuum to afford the pure ligand L1. The ligands L2 and L3
phenylene)bis(3-(pyridin-3-yl)urea), L3. Crystal structures of
were prepared in a similar manner using 1,3-diaminobenzene and 1,4-
the corresponding complexes (1, 2, and 3) confirmed Pd2L4
diaminobenzene, respectively.
formulations for each architectures and thereby illustrating
1,1′-(1,2-Phenylene)bis(3-(pyridin-3-yl)urea) L1. Yield: (400 mg,
ligand-isomerism39 in the coordination cages using as many as
68%). Melting point: 164 °C. 1H NMR (500 MHz, DMSO-d6
three isomeric ligands. The positions of the urea moieties in
the isomeric cages are of particular interest from structural
viewpoints. The abilities of the complexes 1−3 for adsorption
of CO2 gas are demonstrated and their behaviors are
compared.
external TMS/CDCl3): δ = 9.82 (s, 2H, He), 9.16 (d, J = 2.3 Hz,
2H, Ha), 8.74 (s, 2H, Hf), 8.72 (dd, J1 = 4.6 Hz, J2 = 1.1 Hz, 2H, Hb),
8.48 (ddd, J1 = 8.3 Hz, J2 = 2.3 Hz, J3 = 1.4 Hz, 2H, Hd), 8.13 (dd, J1
= 6 Hz, J2 = 3.6 Hz, 2H, Hg), 7.85 (dd, J1 = 8.2 Hz, J2 = 4.7 Hz, 2H,
Hc), 7.66 (dd, J1 = 6 Hz, J2 = 3.5 Hz, 2H, Hh) ppm; 13C NMR (125
MHz, DMSO-d6 external TMS/CDCl3): δ = 154.3, 143.8, 140.8,
137.4, 132.0, 126.5, 125.5, 125.3, 124.7 ppm. ESI-MS: m/z = 349,
371, 387, 697, and 719 corresponding to (M + H)+, (M + Na)+, (M +
K)+, (2M + H)+ and (2M + Na)+, respectively. Anal. Calcd for
C18H16N6O2(H2O)2: C, 56.24; H, 5.24; N, 21.86. Found: C, 56.32;
H, 5.02; N, 21.72.
EXPERIMENTAL SECTION
■
Materials and Methods. PdCl2, nicotinoyl chloride hydro-
chloride, 1,2-diaminobenzene, 1,3-diaminobenzene, and 1,4-diamino-
benzene were acquired from Aldrich; AgNO3, NaN3, and all common
reagents solvents were obtained from Spectrochem, India, and were
used as received without further purification. The known ligands L240
and L341 were prepared by a slight modification of literature
procedures. Nicotinoyl azide required for the synthesis was prepared
freshly from nicotinoyl chloride hydrochloride and NaN3, by
following a reported procedure.38 The deuterated solvents were
1,1′-(1,3-Phenylene)bis(3-(pyridin-3-yl)urea) L2. Yield: (435 mg,
1
74%). H NMR (500 MHz, DMSO-d6 external TMS/CDCl3): δ =
9.40 (s, 2H, He), 9.31 (s, 2H, Hf), 9.16 (bs, 2H, Ha), 8.74 (bs, 2H,
Hb), 8.48 (d, J = 8.3 Hz, 2H, Hd), 8.24 (s, 1H, Hg), 7.86 (dd, J1 = 7.7
Hz, J2 = 4.4 Hz, 2H, Hc), 7.73 (t, J = 8 Hz, 1H, Hi), 7.64 (dd, J1 = 8
Hz, J2 = 1.6 Hz, 2H, Hh) ppm; 13C NMR (125 MHz, DMSO-d6
external TMS/CDCl3): δ = 153.0, 143.3, 140.5, 140.4, 136.9, 129.7,
125.6, 124.1, 112.6, 108.7 ppm.
1
obtained from Aldrich and Cambridge Isotope Laboratories Inc. H
and 13C NMR spectral data were obtained using a Bruker 400 or 500
MHz FT NMR spectrometer in DMSO-d6 by using TMS in CDCl3 as
an external reference. The ESI-MS spectra were obtained from Agilent
6545A Q-TOF and Micromass Q-TOF mass spectrometers. The
crystal structures were obtained using a Bruker X8 Kappa X-ray
diffraction (XRD) instrument. The powder XRD patterns were
obtained using a Bruker D8 Advanced instrument. Thermogravimetric
analysis (TGA) data were collected using a Q500 Hi-Res TGA
instrument under nitrogen atmosphere, starting from 30 to 910 °C at
a heating rate of 20 °C min−1.
1,1′-(1,4-Phenylene)bis(3-(pyridin-3-yl)urea) L3. Yield: (425 mg,
1
72%). H NMR (500 MHz, DMSO-d6 external TMS/CDCl3): δ =
9.33 (s, 2H, He), 9.22 (s, 2H, Hf), 9.14 (d, J = 2.4 Hz, 2H, Ha), 8.71
(dd, J1 = 4.6 Hz, J2 = 1.3 Hz, 2H, Hb), 8.47 (ddd, J1 = 8.3 Hz, J2 = 2.5
Hz, J3 = 1.5 Hz 2H, Hd), 7.92 (s, 4H, Hg), 7.84 (dd, J1 = 8.3 Hz, J2 =
4.6 Hz, 2H, Hc) ppm; 13C NMR (125 MHz, DMSO-d6 external TMS/
CDCl3): δ = 153.2, 143.2, 140.5, 137.1, 134.6, 125.6, 124.1, 119.8
ppm.
Synthesis of Binuclear Cages, 1−3. General Method. A
solution of Pd(NO3)2 was prepared by a salt-metathesis reaction
using PdCl2 (15 mg, 0.08 mmol) and AgNO3 (29 mg, 0.16 mmol) in
4 mL of DMSO. The reaction mixture was stirred at 60 °C for 1 h
followed by separation of the precipitated AgCl from the desired
Synthesis of the Ligands (L1−L3). General Method. Nicotinoyl
azide (500 mg, 3.37 mmol) and 1,2-diaminobenzene (182 mg, 1.68
mmol) were dissolved in 30 mL of dry CH3CN under nitrogen
atmosphere. The reaction mixture was stirred for 7 h at 70 °C
B
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Scheme 1. Synthesis of the Regioisomeric Ligands (L1, L2, and L3) and Pd2L4-type Isomeric Cages (1, 2, and 3)
orange-red colored solution by a centrifugation method. A solution of
the ligand L1 (59 mg, 0.16 mmol) in 4.5 mL of DMSO was combined
with the above-mentioned solution of Pd(NO3)2 to allow the
complexation reaction. The reaction mixture was stirred at room
temperature; however, during the complexation reaction a minor
amount of a second crop of AgCl was also formed. The AgCl was
separated from the reaction mixture by the centrifugation method to
obtain a clear solution. The desired complex was precipitated from the
clear solution using an excess amount of EtOAC, which was separated
by filtration. The isolated solid was washed with EtOAc and dried
under a vacuum to afford the cage 1 as a white solid. The cages 2 and
3 were prepared in a similar manner using L2 and L3, respectively.
[Pd2(L1)4](NO3)4, 1. Yield: (52 mg, 70%). Melting point = 185 °C.
1H NMR (400 MHz, DMSO-d6 external TMS/CDCl3): δ = 10.15 (s,
8H, He), 9.47 (s, 8H, Ha), 8.85 (d, J = 5.4 Hz, 8H, Hb), 8.78 (s, 8H,
Hf), 8.63 (d, J = 8.3 Hz, 8H, Hd), 8.01 (dd, J1 = 8.3 Hz, J2 = 5.8 Hz,
8H, Hc), 7.94 (s, 8H, Hg), 7.66 (dd, J1 = 5.6 Hz, J2 = 3.7 Hz, 8H, Hh)
ppm; 1H NMR (500 MHz, DMSO-d6 external TMS/CDCl3)
recorded at 70 °C: δ = 10.05 (s, 8H, He), 9.43 (d, J = 2.1 Hz, 8H,
Ha), 8.85 (d, J = 5.4 Hz, 8H, Hb), 8.73 (s, 8H, Hf), 8.70 (d, J = 8.5
Hz, 8H, Hd), 8.08 (dd, J1 = 8.5 Hz, J2 = 5.6 Hz, 8H, Hc), 8.03 (dd, J1
= 5.8 Hz, J2 = 3.6 Hz, 8H, Hg), 7.68 (dd, J1 = 6.0 Hz, J2 = 3.5 Hz, 8H,
Hh) ppm. 13C NMR (125 MHz, DMSO-d6): δ = 153.9, 145.4, 143.2,
139.6, 132.1, 131.0, 127.8, 126.3, 125.9 ppm; ESI-MS: m/z calculated
for [1-2NO3]2+, 865.1604; observed, 865.1570; and calculated for [1-
3NO3]3+, 556.1111; observed, 556.1095. Anal. Calcd for
C72H64N28O20Pd2(DMSO)3(H2O)5: C, 43.00; H, 4.26; N, 18.00.
Found: C, 42.61; H, 3.95; N, 18.43.
[Pd2(L2)4](NO3)4, 2. Yield: (50 mg, 70%). Melting point = 240 °C.
1H NMR (400 MHz, DMSO-d6 external TMS/CDCl3): δ = 10.25
(bs, 8H, Ha), 9.71 (s, 8H, He), 9.60 (s, 8H, Hf), 9.51 (bs, 8H, Hb),
8.48 (bs, 8H, Hd), 8.23 (s, 4H, Hg), 8.15−8.11 (m, 8H, Hc), 7.74−
1
7.70 (m, 12H, Hh and Hi) ppm; H NMR (500 MHz, DMSO-d6
external TMS/CDCl3) recorded at 70 °C: δ = 10.26 (s, 8H, Ha), 9.70
(s, 8H, He), 9.51 (s, 8H, Hf), 9.48 (d, J = 5.4 Hz, 8H, Hb), 8.49 (d, J =
7.1 Hz, 8H, Hd), 8.24 (d, J = 1.0 Hz, Hg), 8.11 (dd, J1 = 8.4 Hz, J2 =
5.6 Hz, 8H, Hc), 7.73−7.70 (m, 12H, Hh and Hi) ppm. 13C NMR
(125 MHz, DMSO-d6): δ = 152.5, 145.2, 141.3, 140.1, 139.2, 130.4,
130.2, 127.4, 113.6, 108.9 ppm; ESI-MS: m/z calculated for [2-
2NO3]2+, 865.1604; observed, 865.1589; calculated for [2-3NO3]3+,
556.1111; observed, 556.1105; and calculated for [2-4NO3]4+,
4 0 1 . 5 8 6 5 ; o b s e r v e d , 4 0 1 . 5 8 5 5 . A n a l . C a l c d f o r
C72H64N28O20Pd2(DMSO)3(H2O)2: C, 44.09; H, 4.08; N, 18.46.
Found: C, 44.29; H, 3.76; N, 18.34.
C
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[Pd2(L3)4](NO3)4, 3. Yield: (61 mg, 83%). Melting point = 220 °C.
1H NMR (500 MHz, DMSO-d6 external TMS/CDCl3): δ = 10.74 (s,
8H, Ha), 9.75 (s, 8H, He), 9.68 (d, J = 5.4 Hz, 8H, Hb), 9.52 (s, 8H,
Hf), 8.11 (dd, J1 = 8.2 Hz, J2 = 5.7 Hz, 8H, Hc), 8.06 (s, 16H, Hg),
8.00 (d, J = 8.3 Hz, 8H, Hd) ppm; 13C NMR (125 MHz, DMSO-d6):
δ = 152.4, 144.6, 141.5, 139.3, 134.4, 129.4, 127.1, 119.8 ppm; ESI-
MS: m/z calculated for [3-2NO3]2+, 865.1604; observed, 865.1572;
calculated for [3-3NO3]3+, 556.1111; observed, 556.1094; and
calculated for [3-4NO3]4+, 401.5865; observed, 401.5853. Anal.
Calcd for C72H64N28O20Pd2(DMSO)5(H2O)4: C, 42.51; H, 4.44; N,
16.93. Found: C, 42.99; H, 4.20; N, 16.40.
Crystallographic Data Collection and Refinement. X-ray data
were collected with a Bruker AXS Kappa Apex II CCD diffractometer
equipped with graphite monochromated MoKα (λ = 0.7107 Å)
radiation. A 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 36 frames at three different orientations
of the detector was employed to collect reflections, and the program
APEXII-SAINT (Bruker, 2008) was used for finding the unit cell
parameters.42 A 4-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 (Bruker, 2008)
was used for absorption correction using the multiscan procedure.
The structures were solved by direct methods using SHELXS-97,
(Sheldrick, 2008)43 and refined by full-matrix least-squares techniques
using the SHELXL-97 (Sheldrick, 2013)44 computer program. All
hydrogen atoms were fixed at chemically meaningful positions, and
riding model refinement was applied. Molecular graphics were
generated using Mercury programs. For compounds 1−3, PLA-
TON/SQUEEZE (Spek, 2009)45 was employed to remove the excess
electron density resulting from the disordered sea of solvent
molecules, subsequently resulting in improved refinement.
RESULTS AND DISCUSSION
■
Ligands (L1−L3). The ligands were prepared by
condensation of freshly prepared nicotinoyl azide with
appropriate diaminobenzene (Scheme 1). The peaks observed
in H and 13C NMR spectra of the ligands were assigned by
1
analyzing their COSY and HSQC spectra (see Supporting
Information, Figures S4−S7, S9−S12, and S14−S17). The
assignment of urea NH protons could be completed only after
analyzing the NOESY data of the compounds (see Supporting
Information, Figures S8, S13, and S18). Formation of the new
ligand L1 was further supported by electrospray ionization
mass spectrometry (ESI-MS) (see Supporting Information,
Figure S34), and its structure was also obtained using a single-
crystal X-ray diffraction technique.
The nonchelating bidentate ligands L1, L2, and L3 are 3-
pyridyl appended and regioisomeric in nature. The spacer units
of the ligands can be best described structurally as ortho, meta,
and para-phenylene-diurea for L1−L3, respectively. The
central phenylene and either of the terminal 3-pyridyl are
flanked by urea moiety. The strong preference of trans/trans
conformations around (C)urea−(N)urea bonds in acyclic 1,3-
disubstituted urea moieties is well-known, wherein the
carbonyl bond and N−H bonds are oriented in opposite
directions.46 However, a large number of conformational
isomers are reasoned for each of the regioisomers considering
rotation around (C)phenylene−(N)urea as well as (C)pyridyl
(N)urea bonds.
−
The positions of pyridine nitrogen atoms and urea oxygen
atoms present in a sequence (say, from top to bottom in the
drawing), i.e., (N)pyridyl----(O)urea-----(O)urea-----(N)-
pyridyl are considered as reference points to define the
conformers.41,47,48 The terms syn and anti are used to name the
conformers of a given ligand as identified in three regions of its
backbone, namely, (i) (N)pyridyl----(O)urea; (ii) (O)urea-----
(O)urea; and (iii) (O)urea-----(N)pyridyl. The plausible
conformers of the ligands are provided in Supporting
Information, Figures S1, S2, and S3 that are shown using
planar structures for convenience. However, global non-
planarity due to torsion around the urea substructure, in the
solid state, is an usual phenomenon.49 The conformations of
the bound ligands observed in the crystal structure of
corresponding Pd2L4 complexes are approximately comparable
to drawings shown in Figure 1 and Scheme 1(e.g., anti-syn-anti
form of L1 is observed in the structure of 1). The possibilities
of slow/fast conformational changes in the solution state for
the bound ligand moieties should not be discarded.
X-ray diffraction quality single crystals of ligand L1 were obtained
by slow evaporation of a solution of L1 in methanol−water (1:1). The
compound was crystallized in the triclinic crystal system with P1 space
̅
group. The asymmetric unit of the structure is composed of one unit
of ligand and two molecules of water. X-ray diffraction quality single
crystals of 1·1.5(DMSO)·2(H2O)·(DCE) were obtained by slow
vapor diffusion of 1,2-dichloroethane into a solution of cage, 1 in
DMSO. The cage molecule was crystallized in the monoclinic crystal
system with P21/n space group. The asymmetric unit contains half of
the molecule of 1 (i.e., two L1, one palladium(II) ion, and two nitrate
anions), two DMSO (one molecule with full and other with half
occupancies), two H2O molecules, and one dichloroethane disordered
over two sites (with half occupancies each). X-ray diffraction quality
single crystals of 2·4(DMSO)·3(dioxane) were obtained by slow
vapor diffusion of 1,4-dioxane into a solution of cage, 2 in DMSO.
The cage molecule was crystallized in the triclinic crystal system with
̅
P1 space group. The asymmetric unit contains two separate units of
half of the molecule of 2, (i.e., four L2, two palladium(II) ion, and
four disordered nitrate anions), four DMSO, and three dioxane
molecules (one dioxane with full occupancy, two dioxane with half
occupancy, and two dioxane as half molecule). X-ray diffraction
quality single crystals of 3·4(DMSO)·(dioxane) were obtained by
slow vapor diffusion of 1,4-dioxane into a solution of cage, 3 in
DMSO. The cage molecule was crystallized in the orthorhombic
crystal system with P21212 space group. The asymmetric unit contains
half of the molecule of 3 (i.e., two L3, one palladium(II) ion, and two
nitrate anions), two DMSO (one is disordered), and one dioxane
molecule (half occupancy).
Binuclear Pd2L4-type Cages (1−3). Combination of
palladium(II) with the bidentate ligands L1, L2, and L3 (at 2:4
ratios) in separate experiments afforded Pd2L4 type binuclear
cages 1, 2, and 3, respectively. The complexation reactions
were performed in DMSO at room temperature (Scheme 1),
and the targeted compounds were precipitated by addition of
excess ethyl acetate. All the isolated cages were characterized
by various spectroscopic techniques (see Supporting Informa-
tion, Figures S19−S33 and S35−S37), including 1H NMR, 13
C
Gas Adsorption. Gas adsorption measurements were performed
using a BelSorpmax instrument (Bel Japan). 99.999% purity CO2 and
N2 (employed as an inert gas) were used for sorption studies. Prior to
sorption measurements, powdered samples of the cages, 1−3 were
immersed in CH3CN in separate containers for 1 day followed by
centrifugation and decantation of solvent. The same procedure was
repeated three times, and the resulting solid samples were dried under
a vacuum to remove residual solvent molecules. The activated samples
of 1−3 were heated at 105 °C overnight.
NMR, COSY, HSQC, NOESY, ESI-MS, and single crystal X-
ray diffraction techniques. The assignment of urea NH protons
could be completed only after analyzing the NOESY data of
the compounds.
1
A stacking diagram of the H NMR spectra of the ligands
(L1−L3) and the corresponding cages (1−3) recorded in
DMSO-d6 is presented in Figure 2. While the signals of free
D
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Figure 2. 500 MHz 1H NMR spectra in DMSO-d6 at room temperature (TMS as external standard) for (i) L1; (ii) [Pd2(L1)4](NO3)4, 1 recorded
at 70 °C; (iii) L2; (iv) [Pd2(L2)4](NO3)4, 2 recorded at 70 °C; (v) L3; and (vi) [Pd2(L3)4](NO3)4, 3. (For the designation of the protons, i.e., a,
b, c, etc., see Scheme 1.)
ligand disappeared due to the complexation, a new set of
signals assignable to a coordination complex was observed in
each case. The signals of the complex 3 are sharp, indicating a
single discrete species. However, the signals of 1 and 2 were
found to be somewhat broad when the spectra were recorded
at room temperature, more so for 2 (see Supporing
Information, Figures S19, S19a, S24, and S24a), whereas
sharp signals were observed when recorded at 70 °C (see
Figure 2(ii), (iv)). Slow conformational changes at the ligand
backbone could be the reason behind the signal broadening.
The change in the chemical shift (Δδ) values for the pyridyl
and urea signals of the cages (Ha to Hf) as compared to the
free ligands is summarized in Table S1 (see Supporting
Information). The 1H NMR spectra of all cages showed
complexation induced downfield shift for the signals of pyridyl
protons that are close to the metal binding sites (Ha and Hb).
It is interesting to note that the magnitude of the downfield
shift for Ha and Hb in 1 is relatively small; also the signal of Hd
in 3 is found to be upfield shifted.
The Pd2L4 compositions of the cages (1−3) were further
supported by electrospray ionization mass spectrometry (ESI-
MS). The peaks at m/z = 865.1570 and 556.1095 for [1-
2NO3]2+ and [1-3NO3]3+; m/z = 865.1589, 556.1105, and
401.5855 for [2-2NO3]2+, [2-3NO3]3+, and [2-4NO3]4+; m/z =
865.1604, 556.1094, and 401.5853 for [3-2NO3]2+, [3-
3NO3]3+, and [3-4NO3]4+ (see Supporting Information,
Figures S35−S37) confirmed the molecular compositions.
The experimental isotopic pattern and the peak positions
corresponding to the cationic fragments (generated due to the
loss of counteranions) are in good agreement with the
corresponding calculated patterns (see Supporting Informa-
tion, Figures S35a-S35b; S36a-S36c; S37a-S37c).
conformation and remained almost coplanar with the central
phenylene moiety where the dihedral angle of urea-phenylene
planes is −2° and that of urea-pyridyl planes is −9°. However,
the other arm has an anti-conformation and disposed almost
perpendicular with respect to the phenylene plane where the
dihedral angle of urea-phenylene planes is 84° and that of urea-
pyridyl planes is −11°. Thus, the conformation of the ligand-
substructure by considering both of the (O)urea atoms is
somewhat gauche type, and overall a syn-gauche-anti con-
formation is observed for L1 in the solid state (Figure 3a).
Existence of this conformation in the solid state is probably
influenced by the packing of the molecules.
The two water molecules are part of a “water-tetramer core”,
which is further stabilized by H-bond donors like (H)urea, and
acceptors like (O)urea and (N)pyridine originated from six
different strands of ligands as shown in Figure 3b.
Intermolecular H-bonding, π−π stacking, and CH-π stacking
interactions generated a chainlike arrangement in one
dimension as shown in Figure 3c. A given one-dimensional
chain possesses further interactions with neighboring chains.
Crystallographic data and structure refinement parameters for
the ligand L1 are summarized in Table S2 (see Supporting
Information).
Crystal Structures of the Cages. Single crystal of the
complexes 1, 2, and 3 were obtained from their DMSO
solutions by vapor diffusion methods. Structures of the cationic
cages are shown side by side in Figure 4 for comparison. Two
square planar palladium(II) centers are bridged by four ligand
strands in each cage. Further description is provided in later
paragraphs. Crystallographic data and structure refinement
parameters for the cages (1−3) are summarized in Table S2
(see Supporting Information).
Crystal Structure of L1·2H2O. The crystal structure of
ligand L1 shows that one of the pyridyl-urea arms has a syn-
[Pd2(L1)4](NO3)4·1.5(C2H6SO)·2(H2O)·(C2H4Cl2). The
crystal structure of cage 1 shows that one of the PdN4 planes
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opposite positions (belonging to different ligand strands). It
can be seen that NH protons of the diagonally located urea
moieties are either all endohedral or all exohedral. The above
description defined the positions of all eight urea units of the
cage. The endohedral NH groups belonging to four urea
moieties of [Pd2(L2)4]2+ are involved in H-bonding inter-
actions with only two counteranions (i.e., nitrate) where a pair
of urea moieties are bridged by a nitrate ion (Figure 5b). The
endohedral NH groups are however pointed toward the
window of the cage, and the corresponding bound nitrates are
located at the window. Thus, the central cavity is available for
solvent inclusion. However, the exohedral NH groups
belonging to four urea moieties bind with two nitrate ions
and two DMSO molecules. The inner cavity of the cage is
found to accommodate two more DMSO molecules probably
by electrostatic interaction of (O)DMSO with metal ions and
several CH---O interactions using (O)urea and (H)DMSO to fill
the space.
[Pd2(L3)4](NO3)4·4(C2H6SO)·(C4H8O2). The crystal struc-
ture of cage 3 shows that one of the PdN4 planes is vertically
above the other one, and the nonbonded distance between the
metal centers was found to be 14.2 Å (longer than that of 1
and 2). The conformation of the bound ligand moieties is close
to syn−syn−syn. All the 16 NH groups of eight urea moieties
are oriented exohedrally, thus making the outside edge of the
cage suitable for interaction with anions. The interaction of the
cage with compatible chemical entities is shown in Figure 5c.
The inner cavity of the cage is found to accommodate two
DMSO molecules probably by electrostatic interaction of
(O)DMSO with metal ions and several CH---O interactions
using (O)urea and (H)DMSO to fill the space. In fact, the NH
groups of eight urea moieties of [Pd2(L3)4]2+ are involved in
H-bonding interactions separately with eight nitrate ions.
There are only four anions in the molecular formula of a cage
molecule. The presence of eight anions around a cage can be
explained very easily by analyzing the packing diagram as
discussed in the next section.
Intermolecular Interactions of the Cages in the Solid
State. Packing diagrams from the crystal structures of the
cages were generated and provided in the Supporting
Information (see Figures S47, S48, and S49) that showed
the existence of anions/solvents filled pores. It should be
possible to activate the compounds (removal of solvents) and
use the pores for gas adsorption study. However, the nature of
intermolecular interactions and the nature of intramolecular/
intermolecular pores could possibly change upon activation.
The packing diagram of cage 3 possesses unique structural
features and is discussed below.
Figure 3. Crystal structure of L1 showing (a) the asymmetric unit L1·
2H2O, (b) tetrameric water cluster found in lattice, and (c) one-
dimensional view of intermolecular interactions.
is vertically above the other one, and the nonbonded distance
between the two metal centers was found to be 10.5 Å. The
conformation of the bound ligand moieties, more appropri-
ately, is anti−gauch−anti owing to some torsion between the
urea versus pyridyl and urea versus phenylene. All 16 NH
groups of eight urea moieties are oriented endohedrally, thus
making the cage suitable for anion encapsulation. The NH
groups of eight urea moieties of [Pd2(L1)4]2+ are involved in
H-bonding interactions separately with eight chemical entities
(Figure 5a). These are four counteranions (i.e., nitrate), two
water molecules and two DMSO molecules (half occupancy
each). Two more water molecules are buried deep in the cavity
though not directly connected with urea H.
[Pd2(L2)4](NO3)4·4(C2H6SO)·3(C4H8O2). The crystal struc-
ture of cage 2 shows that one of the PdN4 planes is above the
other one but parallel displaced by approximately 10°, and the
nonbonded distance between the metal centers was found to
be 13.1 Å (longer than that of 1). The conformation of the
bound ligand moieties is close to syn−anti−anti. For any of the
ligand strands, the NH groups of one of the urea moieties are
endohedrally located, whereas that of the other are exohedrally
located. In the cage architecture, each of the four ligand strands
has two neighboring ligand strands disposed in a cis manner
and one ligand strand is disposed in a trans manner. Let us
consider two ligand strands that are located trans to each other
and compare the two urea moieties located in diagonally
Figure 4. Crystal structure of the cages (a) 1·1.5(DMSO)·2(H2O)·(DCE), (b) 2·4(DMSO)·3(dioxane), and (c) 3·2(DMSO)·(dioxane). The
counteranions, hydrogen, and solvent molecules are not shown for clarity.
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Figure 5. Crystal structures showing (a) endohedral binding of 4(NO3), 4(H2O), 2(DMSO) by [Pd2(L1)4]2+ (b) endohedral binding of 2(NO3),
2(DMSO); exohedral binding of 2(NO3), 2(DMSO), by[Pd2(L2)4]2+, and (c) endohedral binding of 2(DMSO); exohedral binding of 4(NO3) by
[Pd2(L3)4]2+. Blue enclosure and colored dots shown in the right-hand side figures represent cage and (H)urea, respectively.
Anion Supported Intermolecular Interactions in 3. As
explained above, the counteranions of the cationic cage of
[Pd2(L3)4]2+ are located at fixed sites at the periphery of the
cage, and the inner cavity is free of anions, though solvent
molecules are trapped. Investigation of the packing diagram in
the crystal structure of 3 revealed interesting anion bridged
arrangements as shown in Figure 6. A pair of ligand strands of
a cage unit that are located cis to each other and another such
cis-pair of a neighboring cage are bridged by four nitrate
moieties to create a tubular cavity. The other pairs of ligand
strands are further connected in a similar manner linearly to
afford a poly-cage chain. Thus, in addition to the anion free
Figure 6. Two views of the packing diagram to illustrate the nitrate
inherent cavity of cage 3 one could see anion free tubular
bridging of one unit of [Pd2(L3)4]2+ with two such units. Hydrogen
atoms and solvent molecules are omitted for clarity.
cavities created due to the nitrate bridged arrangements. While
the nonbonded distance between the metal centers of a cage
unit is 14.2 Å, such a distance between the metal centers of two
neighboring cages is also similar (14.3 Å). A given poly-cage
chain possesses further interactions with four neighboring
chains through weak interactions.
Gas Adsorption Studies. It may be noted that metal−
organic frameworks (MOFs)50−58 and covalent organic
frameworks (COFs)59−65 have been extensively investigated
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for gas adsorption studies, whereas self-assembled discrete
coordination cages for gas adsorption is employed only
recently.8 Prior to the adsorption study, the thermal stability
of the activated powdered samples of cages 1−3 was probed by
the TGA technique, which showed comparable thermal
stabilities for all the cages. The TGA curves of 1, 2, and 3
below 100 °C showed weight losses of 2.7% (calcd. 2.6%),
6.5% (calcd. 6.4%), and 7.4% (calcd. 7.3%), respectively, that
are consistent with losses of 1 CH3CN and 0.5 H2O for cage 1;
2 CH3CN and 2.5 H2O for cage 2; and 2 CH3CN and 3.5 H2O
for cage 3. All the cage materials were found to be stable up to
200 °C, and further heating resulted in gradual decomposition
(see Supporting Information, Figures S42, S43, and S44).
Preliminary gas adsorption studies were carried out using
activated samples of 1, 2, and 3. The powdered samples were
immersed in CH3CN for 3 days to exchange the solvents with
a higher boiling point (particularly DMSO) with the solvent of
lower boiling point, i.e., CH3CN. The sample was then
separated by filtration and dried under a vacuum for 1 day to
remove residual solvents.
type cage adsorbed 1.4 mol of CO2 per mol of cage.8 The
computed heat of adsorption at zero loading values for the
cages 1, 2, and 3 are 44.05, 45.74, and 31.38 kJ/mol,
respectively (see Supporting Information, Figure S46). The
high values indicated supportive roles of the functional sites
toward the adsorption of polar CO2. It is noteworthy to
mention that the heat of adsorption is much higher than those
reported previously (range: 25−35 kJ/mol).8 The comparison
re-emphasizes the superior roles of the functional groups in our
Pd(II)-cages.
CONCLUSIONS
■
Complexation of palladium(II) nitrate with a set of
regioisomeric nonchelating bidentate ligands (L1, L2, and
L3) afforded isomeric cages (1, 2, and 3) of Pd2L4 formulation.
The ligands employed are 3-pyridyl appended that are crafted
with 1,2 or 1,3 or 1,4phenylene-diurea functionalities as
spacers for L1, L2, and L3, respectively. Although the
conformation of the ligands in their coordinated forms are
found to be different in different cages, the cages are isomeric.
Thus, ligand-isomerism in coordination cages was illustrated.
The number of nitrates accommodated in the cavity of the
cages is controlled by the conformation of the bound ligand
(four for 1, two for 2, and none for 3). Essentially the
enohedral/exohedral dispositions of the (H)urea atoms are
responsible for the location of the bound nitrates. The isomeric
cages in the solid state displayed adsorption of CO2, and the
nature of adsorption is influenced by the isomers where cage 2
displayed superior binding abilities compared to the other
cages.
The CH3CN exchanged sample of the cage materials, 1−3
was activated at 105 °C for overnight under a vacuum for the
gas adsorption study. The CO2 adsorption isotherms were
recorded for all the three cages, 1−3 at 273 K (see Supporting
Information, Figure S45) and 298 K (Figure 7). The uptake
ASSOCIATED CONTENT
* Supporting Information
■
S
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acs.inorg-
chem.8b01884.
1D and 2D NMR and ESI-MS spectra, TGA curves,
CO2 adsorption isotherm plots (PDF)
Accession Codes
CCDC 1854022−1854025 contain the supplementary crys-
tallographic data for this paper. These data can be obtained
free of charge via www.ccdc.cam.ac.uk/data_request/cif, or by
emailing data_request@ccdc.cam.ac.uk, or by contacting The
Cambridge Crystallographic Data Centre, 12 Union Road,
Cambridge CB2 1EZ, UK; fax: +44 1223 336033.
Figure 7. CO2 adsorption isotherms recorded at 298 K for compound
1 (blue), compound 2 (green), and compound 3 (red).
amount for cage 2 was found to be substantially higher than
the other two cages (1 and 3) at both 273 and 298 K. This
difference in uptake amounts is probably related to the
orientation of the linkers in the cavity, both in terms of
accessibility to the functional sites and the extent of pore
windows. The complexation of pyridine groups with metal ion
and electron withdrawing nature of the urea moieties are the
possible forces that would make the (pyridine)α and phenylene
protons electron deficient. The urea protons when available are
also potential binding sites. These electron deficient protons
will possibly bind with CO2. Further investigations are required
to understand the mechanism of gas adsorption by these cages.
Nevertheless, preliminary data on the adsorption behavior
demonstrate the effect of ligand isomerization toward
influencing the adsorption properties in such coordination
cages.
AUTHOR INFORMATION
Corresponding Author
*E-mail: dillip@iitm.ac.in.
■
ORCID
Dillip Kumar Chand: 0000-0003-1115-0138
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
The authors thank the SERB, Government of India (Project
No. EMR/2017/002262), for financial support. D.H. thanks
CSIR, New Delhi, India, for a fellowship. We gratefully
acknowledge the NMR, ESI-MS (DST-FIST funded), TGA,
and single crystal X-ray diffractometer facility at the Depart-
ment of Chemistry, IIT Madras. We sincerely thank Dr. Sujit
Our best performing cage, i.e., [Pd2(L2)4](NO3)4, 2, was
found to adsorb ∼2.1 mol of CO2 per mol of cage at 298 K and
100 kPa. Under similar conditions, a previously reported Pd2L4
H
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DEDICATION
■
This article is dedicated to Prof. Vadapalli Chandrasekhar on
the occasion of his 60th birthday.
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DOI: 10.1021/acs.inorgchem.8b01884
Inorg. Chem. XXXX, XXX, XXX−XXX