A Discrete Self-Assembled Pd12 Triangular Orthobicupola Cage and its Use for Intramolecular Cycloaddition

Article abstract of DOI:10.1002/chem.201803039

Water-soluble Pd₁₂L₆ coordination cage TC-1 was synthesized by coordination-driven self-assembly of symmetrical tetrapyridyl donor L with 90° ditopic acceptor cis-[Pd(NO₃)₂(tmeda)] [tmeda=N,N,N′,N′-tetramethylet

Full text of DOI:10.1002/chem.201803039

A Journal of
Accepted Article
Title: A Discrete Self-Assembled Pd12 Triangular Orthobicupola Cage
and its Use for Intramolecular Cycloaddition
Authors: Partha Sarathi Mukherjee, Imtiyaz Ahmad Bhat, Anthonisamy
Devaraj, and Ennio Zangrando
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To be cited as: Chem. Eur. J. 10.1002/chem.201803039
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A Discrete Self-Assembled Pd12 Triangular Orthobicupola Cage
and its Use for Intramolecular Cycloaddition
Imtiyaz Ahmad Bhat [a], Anthonisamy Devaraj [a], Ennio Zangrando [b] and Partha Sarathi Mukherjee*[a]
Dedication ((optional))
Abstract: A water soluble M12L6 coordination cage (TC-1) was
synthesized by coordination driven self-assembly of a symmetrical
tetrapyridyl donor (L) with the 90° ditopic acceptor cis-
In the last two-decades metal−ligand coordination driven self-
assembly has emerged as a promising strategy to design and
engineer numerous discrete two-dimensional (2D) and three-
(tmeda)Pd(NO3)2 [tmeda = N,N,N’,N’-tetramethylethane-1,2-diamine]. dimensional (3D) architectures.6 The inherent strong directional
The newly synthesized M12L6 coordination assembly represents an
uncommon example of coordination cage having triangular
nature of metal-ligand coordination bond and the versatility of
available organic donors have led to several molecular
architectures with predesigned shapes, sizes and functionality.
The reversibility of the metal-ligand coordination bonds gives the
thermodynamic control over the self-assembly process, which
allows to have self-correction to form thermodynamically most
stable architecture in quantitative yield. The barrel shaped
discrete open-shell architectures with windows of suitable size
are of desired interest for an easy access to both the ingress
and egress of big guest molecules.7 For this reason, purely
organic barrels have been extensively used in the area of
molecular transport, catalysis and sensing.8 However very few
examples of metallasupramolecular structures with barrel like
structures are known in literature and their applications are
largely unexplored.9 The M2nLn assembly type barrels have been
synthesized by the combination of cis-blocked PdII or PtII
complexes having two available coordination sites with tetratopic
N-donor ligands in 2:1 stoichiometric ratio. Most of the
coordination barrels reported so far are M8L4 and M6L3
assemblies with square prismatic and trigonal prismatic
geometries, respectively.10 To the best of our knowledge, only a
few examples of an M2nLn-type barrels with more than eight
metal centers have been reported so far, and these include a
hexagonal Pt12L6 complex reported by our group,11 and Pt10L5
and Pt16L8 reported by others.12 Herein, we report the formation
of a water soluble Pd12 cage, which represents the first example
of a triangular orthobicupola coordination architecture (Scheme-
1) of Pd(II) obtained by coordination self-assembly. Such a cage
with unique structural topology was obtained by self-assembly of
a long tetrapyridyl donor (L) with cis-blocked Pd(II) 90° acceptor.
a
orthobicupola-like geometry. It was characterized by multinuclear
NMR, ESI-MS and single crystal X-ray diffraction analysis (SCXRD).
Self-assembly of a tetratopic donor with a cis-blocked 90° ditopic
acceptor generally yields either tri-/tetra-/hexagonal barrels or closed
cubic cages. However, in the present case the donor and acceptor
are arranged in an unusual fashion to generate an orthobicupola
geometry in which two triangular cupola share a common irregular
hexagonal face. The cage was used to perform intramolecular
cycloaddition reactions of O-propargylated benzylidinebarbituric acid
derivatives in nitromethane. Several penta-/tetra-cyclouracil
derivatives were synthesized through cage catalyzed [4+2]
cycloaddition reactions in a concerted manner with good to high
conversion under mild reaction conditions, whereas in the absence
of cage TC-1 similar reaction led to less conversion of the cyclized
products in organic solvent. This approach is of particular
importance compared to the literature reports for the synthesis of
similar derivatives performed under high temperature reflux
conditions with high catalyst loading.
Introduction
Utilization of weak non-covalent interactions to modulate
complex biochemical processes is well established in nature. In
enzymes such interactions act through a substrate-binding
pocket called the active site.1 This strategy has inspired many
synthetic chemists to design new supramolecular structures with
inner cavity that can mimic their functions.2 The inner cavity of
the supramolecular architecture typically accelerates the
reaction of bound reactants through proximity effects, greatly
increasing the local concentration of the substrates (the effective
molarity), by decreasing the entropy of the reactants and/ or
through preorganization of the reactants in the correct
orientation to react,which is reminiscent of enzyme pocket.3 In
this endeavor, several molecular containers with well-defined
cavity have been reported so far.4-5
[a]
I. A. Bhat, Dr. A. Devaraj and Prof. Dr. P. S. Mukherjee
Inorganic and Physical Chemistry Department
Indian Institute of Science
Scheme 1. Schematic representation of the synthesis of triangular
orthobicupolar Pd12 cage (TC-1).
Bangalore, Karnataka, 560012 (India)
E-mail: psm@iisc.ac.in
FAX: 91-80-23601552
[b]
Prof. E. Zangrando
The cage was finally used to perform intramolecular
cycloaddition reaction of O-propargylated benzylidinebarbituric
acid derivatives in concerted manner with high conversion. In
Department of Chemical and Pharmaceutical Sciences
via, Giorgieri 1, 34127 Trieste, Italy.
Supporting information for this article is given via a link at the end of
the document
¯
aqueous medium, water soluble TC-1 with nitrate (NO3 ) counter
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anions gave hydrolyzed product of benzylidenebarbituric acid
derivatives more in addition to minor [4+2] cycloaddition
products.
reactions are mostly stoichiometric.13 The barrel like structure of
TC-1 with large open windows encouraged us to explore its use
in catalytic intramolecular [4+2] cycloaddition reactions.
The ligand L was synthesized by copper catalyzed Ullman
condensation reaction of 4,4-dipyridylamine with 1,4-
dibromobiphenyl at 160 °C in biphenyl ether.14 The compound
was fully characterized by 1H NMR, 13C NMR and ESI-MS
spectrometry (Figures S1-S3). The self-assembly of L with cis-
(tmeda)Pd(NO3)2 in 1:2 molar ratio at 60 °C for 12 h in aqueous
medium resulted a clear solution. The solution upon treatment
with excess of acetone afforded an off-white precipitate of TC-1
as a pure product. The TC-1 was isolated as an exclusive
product in quantitative yield despite the possibility of formation of
several discrete cages/barrels. The presence of nitrate counter
anions in ionic TC-1 makes it completely soluble in water. TC-1
was characterized by 1H NMR (Figure S4), 1H DOSY NMR
(Figure S6), 1H-1H COSY NMR (Figure S8) and ESI-MS (Figures
3 and S9).
Results and Discussion
We herein report the synthesis and the structural
characterization of Pd12L6 coordination cage with unusual
distorted triangular orthobicupola-like geometry (Figure 1B). This
newly reported Pd12L6 coordination cage adopts a triangular
orthobicupola-like geometry unlike the reported hexagonal
prismatic geometry (Figure 1A). In principle
– triangular
orthobicupola-like geometry can be constructed by a paneling
approach using face-capping tetratopic donor ligands in
combination with ditopic metal receptors in 1:2 stoichiometric
ratio (Figure 1B). However, the M12L6 assemblies reported to
date exhibit barrel-like structures with hexagonal prismatic
geometry (Figure 1A) or simple cubic structure.12 In geometry,
the triangular orthobicupola is one of the Johnson polyhedral
solids labelled with number 27 (J27). There are 92 Johnson
solids known in total, which contain all non-uniform, strictly
convex polyhedra based on regular faces. A polyhedron with
triangular orthobicupola geometry features twelve vertices,
twenty-four edges, and eight triangles plus six square faces. It
has an equal number of squares and triangles at each vertex.
Triangular orthobicupola can be constructed by connecting
two triangular cupolas (J3) along their hexagonal bases. The
triangular orthobicupola-like geometry is very rare and to the
best of our knowledge, herein we report the first example of
M12L6 assembly with this geometry (Fig. 1B). The M12L6
assembly was synthesized by combination of symmetric long
tetrapyridyl donor
L with a 90° acceptor M [M = cis-
(tmeda)Pd(NO3)2] in 1:2 stoichiometric ratio (Scheme 1).
Figure 2. Partial 1H NMR of ligand (L) in CDCl3 and TC-1 in D2O.
Noticeable downfield shift in the 1H NMR spectrum of TC-1 in
DMSO-d6 as compared with ligand L clearly indicated the
coordination of L to Pd(II) (Figure S5). The 1H NMR spectrum of
TC-1 in D2O showed the presence of ten distinct peaks in
aromatic region 9.5 ˗ 6.5 ppm (Figure 2b). The peaks of TC-1
were assigned based on the 1H-1H COSY NMR study (Figure
S8). The free ligand L showed only four peaks in the NMR
spectrum due to pyridyl and phenyl protons (Figure 2a).
However, upon complex formation three separate peaks with
integration ratio of 2:1:1 due to each pyridyl protons and two
separate peaks of equal intensity due to each phenyl protons
were observed in the 1H NMR spectrum (Figure 2b). The
splitting of phenyl protons into two different sets and pyridyl
protons into three different sets indicates that both the phenyl
ring and the pyridyl ring protons of the ligand have different
chemical environments in TC-1. Appearance of a clear single
Figure 1. (A) M12L6 assemblies with hexagonal prismatic geometry previously
reported. (B) Schematic representations of M12L6 polyhedron with triangular
orthobicupolar geometry. Thick green lines paneling the rectangular faces
represent tetratopic ligands and the metal ions by red spheres located at the
vertices. Only two out of six tetratopic ligands paneling one in the front face
and the other in the rear face have been shown for clarity.
Molecular cages with closed shell architectures are known to
perform intermolecular [4+2] cycloaddition reactions, but
because the products are trapped inside the cages such
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band at D= 14.3 × 10-11 m2/s (log D = -9.902 m2/s) in the
diffusion-ordered NMR spectroscopy (DOSY) of TC-1 confirmed
the single product formation (Figure S6). The water-soluble cage
and ligand are schematically depicted in Figures 4 and S11. The
ligands panel the six rectangular faces and the Pd atoms occupy
the twelve vertices of a triangular orthobicupola. The geometry
of TC-1 consists of a central irregular hexagon with two
equilateral triangles one at the top and one at the bottom (Figure
S11). The vertices of the central hexagon are occupied by six
palladium metal atoms (Pd1) with alternate short and long
distances of 8.699 and 17.031 Å, respectively. The irregular
distances between atoms Pd2 of the assembly arise because of
the rectangular shape of the bridging ligands which accounts for
the deviation from a perfect triangular orthobicupolar geometry.
However, it is noteworthy that the overall D3h symmetry is
approximately conserved.
¯
TC-1 was converted into corresponding PF6 analog, which is
soluble in organic solvents such as acetonitrile and
nitromethane. 1H NMR and high-resolution ESI-MS study
confirmed the exact composition of the self-assembled product
¯
(Figures S7 and S9). ESI-MS spectrum of TC-1 with PF6 as
counter anion in acetonitrile showed several prominent peaks at
m/z
= 1676.2740, 1373.0014, 1156.0012 and 993.3100
+5
+6
+7
−
−
−
corresponding to [TC-1-5PF6 ] , [TC-1–6PF6 ] , [TC-1–7PF6 ]
+8
−
and [TC-1–8PF6 ] charged fragments, respectively (Figure 3).
The experimentally obtained isotopic distribution patterns for
these charged fragments matches well with the theoretical
patterns (Figure S10), which further supported a [6 + 12]
composition of L and M in the resulting complex TC-1. From the
DOSY-NMR and ESI-MS analyses, formation of a single
structure was quite evident, however the actual reason of four
sets of peaks appeared due to the phenyl protons and six sets of
peaks for pyridyl protons in the 1H NMR spectrum of TC-1
remained unexplained.
Figure 4. (a) Capped sticks representation of the crystal structure of TC-1. (b)
Space fill representation of the crystal structure of TC -1 showing the inner
cavity. Color codes: cyan green = C, blue= N, red = Pd, Hydrogen atoms,
counter anions, and solvent molecules have been omitted for clarity.
The overall structure of complex TC-1 features two magnetically
different environments. The pyridyl protons coordinated to
central palladium atoms (Pd1) of hexagon give rise to two sets
of peaks. The pyridyl protons coordinated to top and bottom
palladium atoms (Pd2) of triangles are tilted towards the cavity
with an angle of 90° and thus give rise to four sets of peaks, two
for inner protons and two for outer protons (Figure S11a).
Moreover, the central phenyl rings of each ligand L are also
tilted towards the cavity with an angle of 60°, indicating the
different chemical environments and hindered rotation of the
central phenyl rings (Figure S11a). The structure is thus in
agreement with the 1H NMR spectrum of TC-1, which shows ten
distinct peaks: six peaks for pyridyl protons and four peaks for
phenyl protons (Figures S4 and S11a).The complex TC-1 has
an interior hydrophobic pocket enveloped by the six aromatic
walls (L). The dimensions of the inner cavity is ~ 23.74 × 22.66 ×
22.66 Å3, well enough to accommodate large organic guest
molecules. Moreover, the open nature of the complex TC-1
allows easy exit of product molecules. Both these features
inspired us to check the suitability of TC-1 as catalyst for hetero
Diels-Alder reaction. Before proceeding to perform catalysis, we
wanted to see possible encapsulation of three substrates i.e. O-
propargylated benzylidene derivatives (1a-1c) in aqueous
medium (Figure-5). 1H NMR spectra of the [cage + substrate]
mixtures were recorded after twelve hours of stirring in D2O at
room temperature. The 1H NMR of all the mixtures showed
substantial shift and peak broadening for host peaks along with
Figure 3. Experimental isotopic distribution patterns of TC-1 in acetonitrile
corresponding to the (a) [TC-1∙PF6- - 5PF6-]+5 (b) [TC-1∙PF6- - 6PF6-]+6 (c) [TC-
-
1∙PF6- - 7PF6-]+7 and [TC-1∙PF6- - 8PF6 ]+8 charged species.
Suitable single crystals of TC-1 for X-ray diffraction were grown
by slow vapour diffusion of dioxane into an aqueous solution of
TC-1 over a period of 10 days. Colorless rectangular block-
shaped crystals obtained were used for collecting X-ray data
using synchrotron radiation source. A crystallographic analysis
of complex TC-1 (CCDC-1825573) unambiguously established
the formation of an open distorted triangular orthobicupolar tube
as shown in Figure 4. The compound crystallized in hexagonal
P63/mmc space group. The assembly is located about a
crystallographic improper six-fold axis and displays an unusual
triangular orthobicupolar tube like geometry (Figure 4a), instead
of
a
hexagonal barrel structure, and thus providing an
1
explanation for the unusual H NMR data (Figures 2b, S5). The
connectivity of complex TC-1 and the relative positions of metal
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the appearance of new peaks for substrates (Figures S14, S16,
S18). H DOSY NMR of the complexes TC-1⊃1a, TC-1⊃1b and
hydrolysis and afforded hydroxy naphthaldehyde (78%) (Figure
S24).
1
TC-1⊃1c showed a single band at D = 10.5× 10-11 m2/s (log D =
-10.02 m2/s), D = 10.0 × 10-11 m2/s (log D = -10.10 m2/s) and D=
10.8 × 10-11 m2/s (log D = -10.01 m2/s), respectively (Figures
S15, S17, S19). Due to the peak broadening, we could not get
the exact stoichiometry.
Scheme 2. Catalysis promoted by TC-1 in nitromethane.
The same reaction when performed in absence of the cage TC-1
under similar reaction conditions gave 17% cyclized product and
only 11% hydrolyzed product (Figure S25). In aqueous condition,
the highly charged ionic cage TC-1 promotes the hydrolysis
reaction more as compared to the [4+2] cycloadddition reaction
Figure 5. Substrates investigated for encapsulation studies.
Hetero Diels-Alder reaction is particularly useful and represents
one of the most effective methods for the synthesis of fused
poly-heterocyclic compounds.15 These compounds are of prime
importance due to their promising bioactivity and are used as
intermediates in total synthesis of natural product.16 These
reactions feature an advantage of avoiding sequential chemical
transformations and lead to formation of two or more rings in a
concerted manner. However, very few examples of hetero
Diels– Alder reactions with unactivated acetylenes have been
reported.17 The limited use of alkynes as dienophiles is
becausesa of their low reactivity compared to alkenes. In
organic synthesis, the activation of alkynes toward a variety of
¯
(Scheme 2). Keeping this observation in mind, the PF6
analogue of TC-1 soluble in nitromethane and acetonitrile, was
tested to promote hetero Diels-Alder reaction in organic medium..
We expected that the TC-1 may bind the substrate and restricts
the flexibility of the dienophile part, forcing the dienophile closer
to the diene and eventually may facilitate the formation of a [4+2]
adduct in a concerted manner. The naphthylidenebarbituric acid
derivative (1a) was used as substrate to optimize the TC-1
catalyzed IMHDA (Table-1, entry-1). In order to check the
¯
catalytic efficiency of water insoluble TC-1 (PF6 analogue), we
have treated 1a in nitromethane with 5 mol% loading of TC-1 at
70-80°C over a period of 24 h and the reaction was monitored
using TLC. After the completion of reaction, the pentacyclic
scaffold (2a) was isolated by complete removal of nitromethane
and the product was extracted in chloroform. The crude product
was subsequently purified by column chromatography and fully
characterized by 1H, 13C NMR spectroscopy and ESI-MS
spectrometry (Figures S54-56). Single crystals of (2a) were
obtained after slow evaporation of chloroform, which showed
poor diffraction (not suitable for publication) but the XRD data
could reveal the formation of pentacyclic nature of the product
(2a) (Figure. S13). As expected, the newly synthesized cage
was found efficient to enhance the [4+2] cycloaddition of
naphthylidenebarbituric acid derivative (1a) to afford pentacyclic
framework (2a) with high yield (98 %).
organic transformations has attended
a lot of interest.
Nevertheless, many of the reported [4+2] cycloaddition reactions
with unactivated alkynes involve heating at high temperatures
with high catalyst loading.16 Such reaction often leads to poor or
moderate yields of products and require longer reaction time at
elevated temperature. Recently, our group has reported cage
catalyzed intramolecular cycloaddition reactions of O-allylated
benzylidinebarbituric acid derivatives containing alkene as
dienophile.7b In this direction, we made attempt to check the
suitability of our newly synthesized coordination cage (TC-1) as
catalyst to perform the hetero Diels-Alder reaction using less
reactive
alkyne
as
dienophile.To
start
with,
few
benzylidenebarbituric acid derivatives (1a-1f) containing
propargyl functionality were chosen as substrates which
comprise of an 1-oxa-1,3-butadiene as a heterodiene and a
terminal alkyne moiety as dienophile ( Table 1). The necessary
precursor i.e., naphthylidenebarbituric acid derivative (1a) was
obtained from 2-hydroxy-1-naphthaldehyde, propargyl bromide
and N,N-dimethylbarbituric acid through Williamson’s ether
synthesis followed by Knoevenagel condensation following the
reported procedure.17a we have chosen 1a as a substrate and
the reaction was performed in water under the catalytic influence
of TC-1. Only ~22 % pentacyclic chromenopyranpyrimidine
dione framework (2a) was formed when the investigation was
carried out with 1a in presence of 10 mol % of TC-1 in water
between 70-80 °C, while remaining of the substrate undergoes
Scheme 3. Catalysis promoted by TC-1 in nitromethane.
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The same reaction carried out under identical condition in the
absence of cage (TC-1) led to 25 % product, which clearly
demonstrates the supremacy of TC-1 in intramolecular hetero
Diels-Alder reaction of naphthylidenebarbituric acid derivative
(Figures S28 and S29).
guests 1b and 1e in the solvent of catalysis (nitromethane)
couldn’t be determined because of complex host-guest nature.
Nitromethane, which is the solvent of catalysis, was not chosen
for UV-Visible titration because it shows strong absorbance in
the range of 220-340 nm. Furthermore, the variable temperature
To further investigate the role of cage (TC-1) towards catalysis,
two inhibition studies of substrate 1b were carried out. First, by
adding the product 2b (20 mol %) at the beginning of reaction;
and second by adding the substrate-like competitor (Figure S32)
having non-active propyl group in place of alkyne group (20
mol %) of 1b. These reactions were also carried out for 24 h in
nitromethane separately under identical reaction condition. Both
the reactions showed significant decrease in the product
Table 1. Substrates and corresponding [4+2] cycloadducts obtained by using
TC-1 as catalyst (5 mol%) in nitromethane under 70-80 °C for 24 h.
Entry
Substrate
Product**
Conver
sion %
With
Conver
sion %
Without
catalyst
catalyst
1
formation as confirmed by H NMR spectroscopy. Due to similar
98
25
size and backbone of the competitor with that of 1b, it may
compete with the substrate 1b to get encapsulated inside the
cavity of the cage TC-1 during the course of the reaction and
thus inhibits the reaction which led to less product formation
(Figure S32). The presence of product 2b in the beginning of the
reaction also reduces the catalytic turnover probably for the
same reason. The competitive inhibition study provides an
indirect evidence that encapsulation of the substrates in the
cage TC-1 is a probable reason for higher catalytic turnover. To
further explore, we employed the same donor L with divalent
Ru(II) acceptor to design a cage (M1), which doesn’t have
enough confined space to accommodate the substrate (Figure-
S33). Reaction of 1b in presence of 15 mol % of the cage (M1)
in place of TC-1 yielded only 25% product (2b), which is much
less compared to 86% conversion (Figure S34) as obtained in
presence of TC-1. As the cage M1 is cationic and same ligand L
was used to design it, the above result rules out the possibility of
surface binding from the outside of the cage and polarity change
as key factors for enhanced catalytic turnover.
1
1a
2a
2
86
18
2b
1b
3
80
12
The cycloaddition reaction performed in acetonitrile as solvent
did not provide better conversion while compared with
nitromethane. Hence, nitromethane was used as the solvent of
choice for TC-1 promoted intramolecular hetero Diels-Alder
reaction. The conformational restriction of the substrate by TC-1
inside its confined cavity promotes the cycloaddition through
concerted manner, which signifies the role of supramolecular
catalysis in organic transformations towards the construction of
polyheterocyclic frameworks. Encouraged by the above results,
a series of five substrates (1b-1f) was subjected to undergo
[4+2] cycloaddition reaction in presence of the PF6 analogue of
the cage TC-1 (Scheme-3). This approach resulted in the
formation of tetracyclic products in very good conversion, and
the results are summarized in Table 1. Good diffraction quality
single crystals were obtained by slow evaporation of the
chloroform solution of 2f (CCDC-1825574).The crystal structure
of this product (2f) is shown in Figure 6.
2c
1c
4
95
27
1d
2d
84
10
To check the possible host-guest interaction in organic medium,
UV-Vis titration experiments of the host TC-1 with guests 1b and
1e were done separately in DMSO (Figure S26). With gradual
addition of solutions of 1b and 1e to the solution of TC-1, the
UV-Vis absorption at 326 nm started decreasing and a new peak
at 312 nm started to appear, which could be due to the host-
guest complex formation. The exact association constants for
5
1e
2e
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6
82
9
2f
1f
** Products were isolated by column chromatography. All the reactions were
carried out using 0.04 mmol of substrates in 4 ml of nitromethane with 5 mol%
loading of cage under 70-80 °C for 24h. Conversion percentage is based on
1H NMR of crude samples.
Scheme 4: Pictorial representation showing the proposed pathways of
intramolecular hetero diels-alder reaction relying on the product inhibition
study. “A” represents the empty cage TC-1.
Conclusions
In conclusion, to investigate the versatility of tetratopic donors on
cis-blocked 90° acceptor, we employed a long tetrapyridyl linker
(L) with cis-(tmeda)Pd(NO3)2. Surprisingly, such a simple self-
assembly led to the formation of a discrete water soluble Pd12L6
molecular architecture (TC-1), representing the first example of
a self-assembled Pd(II) triangular orthobicupolar cage. The
geometry obtained for the assembly TC-1 is in contrast to the
barrel-like structures, which are typically observed for M8L4 and
M12L6 coordination supramolecular assemblies with tetratopic
donors. The TC-1 cage features large cavities with wide-open
windows. The cage has been used for the catalytic
intramolecular cycloaddition reaction of substrates containing
less reactive alkyne dienophile. A series of tetra/pentacyclouracil
products in presence of 5 mol % of TC-1 was obtained from their
corresponding O-propargylated benzylidenebarbituric acid
derivatives under mild reaction condition. Less product formation
was observed in absence of TC-1, which successfully
establishes the catalytic role of the cage TC-1 for enhanced
conversion. Product inhibition study and the control reaction with
a closed cationic cage (M1) indicate encapsulation of the
substrate as a possible reason of higher conversion of the
cycloaddition reactions in presence of the cage. Overall, our
results represent further evidence towards the versatility of
tetratopic building blocks for the generation of unique self-
assembled architecture.
Figure 6. ORTEP view of the crystal structure of 2f drawn at the 50%
probability level. Color codes: cyan= C, blue= N, red= O and white= H.
1H NMR spectroscopy also revealed that TC-1 showed no sign
of deformation upon heating up to 80 ºC both in presence and
absence of the substrate 1c, which confirms thermal stability of
TC-1 during the course of reaction (Figures S22-S23).
Based on the results of product inhibition studies, we presume
that the reaction commenced with the encapsulation of substrate.
Inside the cage TC-1, the substrate molecule may lose the
conformational flexibility and orient its functional moieties i.e. the
diene and the dienophile in close proximity to facilitate [4+2]
intramolecular cyloaddition (S2 in Scheme 4). With the increase
in temperature, substrate attains the required activation energy
and undergoes [4+2] cycloaddition to form the corresponding
product (S3 in Scheme 4). Due to the non-planar
tetra/pentacyclic structure of the product (Figures 6 and S13), it
comes out to the bulk medium and makes the cage free for
further encapsulation of the substrate.
Experimental Section
Materials and Methods:
All the reagents and solvents were purchased from various commercial
suppliers and used without further purification. di(4-pyridyl)amine was
synthesized by reported procedure.18 NMR spectra were recorded in a
Bruker 400 MHz spectrometer. UV-Visible spectra was recorded in
Perkin Elmer Lambda-750 spectrophotometer. ESI-MS experiments were
done in Agilent 6538 Ultra-High Definition (UHD) Accurate Mass Q-TOF
spectrometer. Single crystal X-ray diffraction data for complex TC-1 were
collected at the X-ray diffraction beamline (XRD1) of the Elettra
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Synchrotron of Trieste (Italy), with a Pilatus 2M image plate detector and
a monochromatic wavelength of 0.700 Å (CCDC-1825573). Complete
dataset was collected at 100 K with nitrogen stream. On the other hand
SCXRD data for 2a and 2f (CCDC-1825574) were collected in a Bruker
D8 QUEST CMOS diffractometer. Diffraction data quality for 2a was not
suitable for publication, but the formation of product was evident from the
present data. The structures were solved by direct methods using SIR
program.19 The non-hydrogen atoms of the main fragments were refined
with anisotropic displacement coefficients by the full-matrix least-squares
methods based on F2 implemented in SHELXL-201420 incorporated in
WinGX21. Hydrogen atoms were assigned with isotropic displacement
coefficients, U(H) = 1.2U(C) or 1.5U (C-methyl), and their coordinates
were allowed to ride on their respective carbons. Proper restrains were
used to the minimum extent while solving the structure of TC-1. To
further improve the structure solutions, was performed by using
SQUEEZE tool of PLATON to take into account the void in the unit cell
filled by disordered solvent molecules and counter anions.
filtered and the precipitate thus obtained was washed with hot water and
ethanol and dried under vacuum to afford yellow solid compound (1a) in
92% yield. 1H NMR (400 MHz, CDCl3):  = 8.92 (s, 1H), 7.96-7.64 (m,
6H), 4.81 (d, 1H, J = 12 Hz), 3.47 (s, 3H), 3.28 (s, 3H), 2.52 (s, 1H). 13C
NMR (100 MHz, CDCl3):  = 162.26, 160.12, 153.87, 153.10, 151.93,
132.98, 132.04, 129.39, 129.12, 128.06, 125.11, 124.42, 122.33, 109.01,
114.32, 78.64, 76.44, 57.70, 29.32, 28.78. ESI-MS m/z: Calculated
[M+Na]+ = 371.1008; Found: 371.1538.
Synthesis of 1b: 1b was prepared by following same procedure as
described above using salicylaldehyde (2 mmol) as the starting material.
The pure product was obtained as yellow solid in 87% overall yield. 1H
NMR (400 MHz, CDCl3):  = 8.84 (s, 1H), 7.99-7.06 (m, 4H), 4.78 (s, 2H),
3.42 (s, 3H), 3.34 (s, 3H), 2.53 (s, 1H). 13C NMR (100 MHz, CDCl3):  =
162.85, 160.78, 157.71, 155.30, 151.10, 134.47, 133.10, 123.26, 121.10,
118.43, 112.37, 78.25, 76.73, 56.76, 29.40, 28.82. ESI-MS m/z:
Calculated [M+Na]+ = 321.0851 Found: 321.1538;
Synthesis of L: 4,4'-dibromo-1,1'-biphenyl (2 g, 0.0064 mol) and di(4-
pyridyl)amine (2.19 g, 0.0128 mol) were taken in a two-neck round
bottom flask containing 25 mL diphenylether. K2CO3 (2.29 g, 16.0 mmol),
CuSO4 anhydrous (0.792 g, 5.0 mmol) and 18-crown 6 (0.132 g, 5.0
mmol) were added to it. The reaction mixture was degassed and kept for
constant stirring at 160 °C for 5 days under N2 atmosphere. The solvent
was evaporated under vacuum and the solid mass was dissolved in a 1:1
mixture of dichloromethane and water. The organic part was extracted
and the compound was purified by column chromatography in silica gel
with a combination of ethyl acetate and methanol (90:10) as eluent.
Isolated yield: 0.95 g, 47 %. IR:  (cm-1) = 1576, 1486, 1343, 1283, 1218,
Synthesis of 1c: The similar protocol was used for the synthesis of 1c
by using 5-fluoro-2-hydroxybenzaldehyde (2 mmol) as the starting
material. The pure product was obtained as yellow solid in 85% overall
yield. 1H NMR (400 MHz, CDCl3):  = 8.73 (s, 1H), 7.78-7.00 (m, 3H),
4.75 (s, 2H, ), 3.41 (s, 3H), 3.34(s, 3H), 2.54 (s, 1H).13C NMR (100 MHz,
CDCl3):  = 162.54, 160.60, 157.91, 155.52, 153.92, 153.45, 151.72,
124.31, 124.22, 120.78, 120.54, 119.43, 119.27, 119.18, 113.65, 113.57,
78.07, 76.96, 57.39, 29.47; 28.89. ESI-MS m/z: Calculated [M+Na]+
339.2782; Found 339.5432.
=
Synthesis of 1d: 1d was synthesised by following similar protocol
described above by using 5-chloro-2-hydroxybenzaldehyde (2 mmol).
The compound was isolated as yellow solid in 92% yield.1H NMR (400
MHz, CDCl3):  = 8.69 (s, 1H), 7.95. (d, 1H, J = 4Hz), 7.42 (d, 1H J = 4Hz
), 7.01 (d, 1H, J = 8Hz), 4.76 (s, 2H), 3.42 (s, 3H), 3.35 (s, 3H), 2.54 (s,
1H). 13C NMR (100 MHz, CDCl3):  = 162.47, 160.51, 155.97, 153.22,
151.71, 133.54, 132.29, 126.34, 124.55, 119.47, 113.69, 77.87, 77.13,
57.08, 29.46, 28.92. ESI-MS m/z: Calculated [M+Na]+ = 355.7298;
Found: 355.8894.
1
1177, 990, 818, 711, 618, 525.85. H NMR (400 MHz, (CDCl3): δ = 8.44
(d, 8H J = 8Hz), 7.65 (d, 4H J = 8Hz) 7.27 (d, 4H J = 8Hz), 7.00 (d, 8H J
= 8Hz). 13C NMR (100 MHz, CDCl3): δ = 152.75, 151.51, 144.13, 138.94,
129.33, 128.40 and 117.17.
Synthesis of TC-1: L (0.021 g, 0.0426 mmol) and cis-[(tmeda)Pd(NO3)2]
(0.030 g, 0.0865 mmol) were taken in 4 mL vial; and 1.5 mL of Millipore
water was added to it. The suspension was kept at constant stirring at 60
°C for 12 h. The resulting faint yellowish solution was centrifuged and the
clear supernatant solution was diffused with acetone to afford off white
precipitate in pure form. Isolated yield: 0.043 g, 84%. IR:  (cm-1) = 1597,
1493, 1314, 1213, 1068, 1035, 810, 529. 1H NMR (400 MHz, D2O): δ =
8.90 (s, 12H ), 8.71 (d, 24H, J = 6.91 Hz ), 8.62 (d, 12H, J = 6.98 Hz),
8.01 (d, 24H, J = 8.89 Hz ), 7.81 (s, 12H), 7.68 (d, 12H, J = 6.57 Hz),
7.39 (d, 12H, J = 8.55 Hz), 7.24 (d, 12H, J = 8.28 Hz), 7.01 (s, 12H) and
6.80 (d, 12H, J = 6.57 Hz). ESI-MS experiment was done using the PF6¯
analogue of the complex, which was prepared by treating nitrate
analogue of the cage with excess KPF6. ESI-MS (m/z) = 2131.5850 [TC-
Synthesis of 1e: Same synthetic procedure was adopted to synthesize
1e by starting with 3,5-dichloro-2-hydroxybenzaldehyde (2 mmol) and the
product was obtained as yellow solid in 87% overall yield. 1H NMR (400
MHz, CDCl3):  = 8.69 (s, 1H), 7.95 (s, 1H), 7.01(d, 1H, J = 8Hz), 4.76 (s
,2H), 3.42(s, 3H), 3.35 (s, 3H), 2.54 (t, 1H, J = 4Hz);13C NMR (100 MHz,
CDCl3):  = 162.43, 160.50, 155.98, 153.04, 151.68, 133.50, 132.27,
126.31, 124.55, 119.49, 113.71, 78.03, 77.14, 57.10, 29.42, 28.82. ESI-
MS m/z: Calculated [M+Na]+ = 391.0042; Found: 391.2869.
− 4+
− 5+
1 – 4PF6
]
, 1676.2740 [TC-1 – 5PF6
]
and 993.3100 [TC-1 – 8PF6
Synthesis of 1f: Similar preparation protocol starting with 5-bromo-2-
hydroxybenzaldehyde (2 mmol) provided 1f as yellow solid in 80 % yield.
1H NMR (400 MHz, CDCl3):  = 8.69 (s, 1H), 7.95 (d, 1H, J = 4Hz), 7.44 -
7.41 (m, 1H), 7.01 (d, 1H J = 8Hz), 4.76 (d, 2H, J = 4Hz), .3.42 (s, 3H),
3.35 (s, 3H,), 2.54 (s, 1H). 13C NMR (100 MHz, CDCl3):  162.42, 160.49,
156.43, 152.97, 151.69, 136.38, 135.10, 125.02, 119.50, 114.12, 113.47,
− 8+
]
.
Synthesis of 1a: 1a was prepared in two steps. 2-hydroxy-1-
naphthaldehyde (4 mmol) in N,N′-dimethylformamide (10 mL) was taken
in a 50 mL RB flask and added with potassium carbonate (8 mmol). To
this mixture, propargylbromide (10 mmol) was added slowly and stirring
was continued for 4 h and added with 50 mL of water. The solution was
then extracted with chloroform. The organic layer was dried over sodium
sulphate and the solvent was evaporated to get crude product which was
purified by silica gel column chromatography (eluted with 10% ethyl
acetate in n-hexane) to get the intermediate 2-(prop-2-ynyloxy)-1-
naphthaldehyde (1aꞌ) as white solid. Yield: (90%).
77.87, 77.19, 57.02, 29.44, 28.91. ESI-MS m/z: Calculated [M+Na]+
399.9954; Found: 399.7596.
=
UV-Visible experiment procedure:
1 mg of guest 1b as solid was taken in 8 mL vial. To it 50 μL of stock
solution of TC-1 (1× 10-4 M) was added and diluted to 3 mL final volume
with distilled water. The suspension was kept for constant stirring at room
temperature for 24 h. The clear solution obtained after centrifugation was
In the later stage, 1aꞌ (2 mmol) was added to a solution of N,N-
dimethylbarbituric acid (2 mmol) and aqueous HCl (25 mL, 13%) with
constant stirring. After 4 h stirring at room temperature, the solution was
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10.1002/chem.201803039
Chemistry - A European Journal
FULL PAPER
taken for UV measurement. Same procedure was adopted for guests 1c
and 1d.
Synthesis of 2f: Diels-Alder reaction of 1f (0.04 mmol) led to 2f as
brown solid in 82% conversion. H NMR (400 MHz, CDCl3):  = 7.10-6.59
(m, 4H), 4.70-4.54 (m, 3H), 3.35 (s, 3H), 3.30 (s, 3H); 13C NMR (100
MHz, CDCl3):  =163.90, 154.40, 153.06, 150.94, 134.57, 131.35,
129.53, 129.32, 119.17, 113.36, 113.11, 86.40, 67.17, 29.55, 28.87. ESI-
MS m/z: Calculated [M+Na]+ = 400.1838; Found: 400.1923.
1
Detailed procedure for host : guest UV titration.
-
A 1 mM stock solution of TC-1 (PF6 analogue) was prepared by
dissolving 4.5 mg of TC-1 in 5 mL of DMSO. From the stock solution of
TC-1, 1 μM solution of host TC-1 was prepared in 3 mL DMSO and UV
was recorded. The UV spectrum of this solution showed a single
characteristic band at 326 nm. To the above solution, stepwise 30 μL of
5× 10-5 M of guest 1b was added and UV spectra were recorded after
every addition. Exactly the same procedure was adopted for guest 1e
with host TC-1.
Acknowledgements
P.S.M. thanks the Science and Engineering Research Board
(New Delhi) for a research grant [Grant No. EMR/2015/002353].
I.A.B and A.D are thankful to UGC-New Delhi for SRF fellowship
and the Dr. D. S. Kothari postdoctoral fellowship, respectively.
We are highly thankful to Dr. B. Roy and P. Howlader for their
help in crystallography.
General procedure for the catalytic [4+2] cycloaddition reaction:
Substrate 1a-1f (0.04 mmol) was added to a solution of TC-1 (0.002
mmol) in nitromethane (4 mL) and the reaction mixture was then heated
between 70-80 °C for 24h. After the completion of reaction as evidenced
by TLC, the solvent was evaporated completely and the residue was
extracted with chloroform. Percentage of conversion was calculated
Keywords: Supramolecular chemistry • self-assembly • cage
compounds • catalysis • coordination chemistry
1
based on H NMR of crude samples. The crude products obtained after
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(ethyl acetate: n-hexane 4:6) to afford analytical pure samples.
Synthesis of 2a: Starting with 1a (0.04 mmol), 2a was obtained as
brown solid in 98% conversion. 1H NMR (400 MHz, CDCl3):  = 7.78-7.15
(m, 6H), 6.63 (s, 1H), 4.99-4.72 (m, 3H), 3.49 (s, 3H), 3.47 (s, 3H). 13
C
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132.44, 130.60, 129.57, 129.42, 126.55, 123.94, 122.43, 119.88, 118.84,
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=
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1
= 7.12-6.78 (m, 4H), 6.63 (s, 1H), 4.81 (d, 1H, J = 12 Hz ), 4.73 (s, 1H),
4.62 (d, 1H, J = 12 Hz ), 3.46 (s, 3H), 3.39 (s, 3H); 13C NMR (100 MHz,
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126.90, 121.47, 117.41, 114.39, 87.05, 67.19, 30.72, 29.63. ESI-MS m/z:
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Synthesis of 2c: 2c was obtained from 1c (0.04 mmol) as brown solid in
80% conversion. 1H NMR (400 MHz, CDCl3):  = 7.26 (s, 1H), 6.83-6.64
(m, 2H), 4.78-4.58 (m, 3H), 3.45 (s, 3H), 3.40 (s, 3H); 13C NMR (100
MHz, CD3OD, CDCl3):  = 154.28, 150.94, 149.90, 134.30, 118.30,
118.22, 115.32, 115.09, 113.96, 113.76, 113.51, 86.61, 67.14, 30.84,
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Synthesis of 2d: 2d was formed as brown solid in 95% conversion by
1
the Diels-Alder reaction of 1d (0.04 mmol). H NMR (400 MHz, CDCl3): 
= 6.98-6.60 (m, 4H), 4.72 (d, 1H, J = 12Hz), 4.60-4.53 (m, 2H, ), 3.37 (s,
3H), 3.32 (s, 3H). 13C NMR (100 MHz, CDCl3):  = 163.89, 154.37,
152.55, 150.96, 134.53, 128.89, 128.46, 126.73, 125.98, 118.72, 113.51,
86.46, 67.21, 30.64, 29.59. ESI-MS m/z: Calculated [M+Na]+ = 355.7298;
Found: 355.2791.
Synthesis of 2e: Similarly 2e was obtained from 1e (0.04 mmol) as
brown solid in 84% conversion. 1H NMR (400 MHz, CDCl3):  = 7.21 (s,
1H), 6.93 (s, 1H), 6.68 (s, 1H.), 4.89 (d, 1H J = 12Hz), 4.77 (d, 1H J =
12Hz), 4.69 (s, 1H), 3.45 (s, 3H), 3.40 (s, 3H); 13C NMR (100 MHz,
CDCl3):  = 163.65, 154.35, 150.85, 148.44, 135.02, 130.04, 128.92,
125.96, 125.58, 122.83, 112.77, 86.15, 68.02, 30.90, 29.10. ESI-MS m/z:
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10.1002/chem.201803039
Chemistry - A European Journal
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A water-soluble Pd12L6 cage (TC-
Imtiyaz Ahmad Bhat†,
Anthonisamy Devaraj , Ennio
Zangrando ‡ and Partha Sarathi
Mukherjee†*
1)
was
synthesised
by
coordination driven self-assembly.
The cage TC-1 adopts the unusual
orto-bicupola geometry unlike the
usual barrel like structure. The
cage (TC-1) encapsulates the
various benzylidenebarbituric acid
derivatives and cataysis their
Page No. – Page No.
A Discrete Self-Assembled Pd12
Triangular Orthobicupola Cage
and its Use for Intramolecular
Cycloaddition
intramolecular
cycloaddition
reaction to form various cylised
product in good yield.
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This article is protected by copyright. All rights reserved.