Conformational solvatomorphism in a [2]catenane

Article abstract of DOI:10.1021/acs.cgd.0c00421

The combination of a flexible pyridine-appended ligand (L1) with 4,4′-bipyridine (L2) and cis-protected Pd(II) units, Pd(L′)(NO3)2, in water yielded a concentration-dependent equilibrium mixture of the corresponding [2]catenanes [Pd2(L′)2(L1)(L2)]2(NO3)8 and their constituent macrocycles [Pd2(L′)2(L1)(L2)](NO3)4. The cis-protecting units (L′) used were ethylenediamine (en), tetramethylethylenediamine (tmeda), 2,2′-bipyridine (bpy), and 1,10-phenanthroline (phen). Crystallization of the [2]catenanes via slow evaporation of their CH3CN/H2O (1:1) solutions yielded a single crystalline form in the case of [Pd2(2,2′-bpy)2(L1)(L2)]2(NO3)8 and two concomitant crystalline forms (solvates) in the case of [Pd2(phen)2(L1)(L2)]2(NO3)8. The formation of the [2]catenane is facilitated by noncovalent interactions such as N-H···O, C-H···O, and C-H···πcontacts and π···πstacking. The solvates of [Pd2(phen)2(L1)(L2)]2(NO3)8 revealed differences in the orientation of the amide carbonyl group and conformational differences in the ligands and phen units in the macrocycles and may thus be termed conformational solvatomorphs. The molecular packing in all the structures was found to be driven by intermolecular π···πstacking interactions between the aromatic rings in their cis-protected Pd(II) units. However, because of the awkward shape of the molecules, the closest 2,2′-bpy and phen units in all the structures overlap differently rather than the commonly observed head-to-tail or head-to-head modes.

Full text of DOI:10.1021/acs.cgd.0c00421

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Article
Conformational Solvatomorphism in a [2]Catenane
Shobhana Krishnaswamy, Soumyakanta Prusty, Daniel Chartrand, Garry S Hanan, and Dillip K. Chand
Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.0c00421 • Publication Date (Web): 20 Jul 2020
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Conformational Solvatomorphism in a [2]Catenane
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Shobhana Krishnaswamy,†a Soumyakanta Prusty, †a Daniel Chartrand,b Garry S. Hananb and Dillip
K. Chand*a
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aDepartment of Chemistry, Indian Institute of Technology Madras, Chennai 600 036, India.
Email: dillip@iitm.ac.in
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bDepartment of Chemistry, University of Montreal, Montreal QC H3T-IJ4 (Canada)
† These authors contributed equally to this work.
ABSTRACT: The combination of a flexible pyridine-appended ligand (L1) with 4,4′-bipyridine
(L2) and cis-protected Pd(II) units, Pd(L′)(NO3)2 in water yielded a concentration-dependent
equilibrium mixture of the corresponding [2]catenanes [Pd2(L′)2(L1)(L2)]2(NO3)8 and their
constituent macrocycles [Pd2(L′)2(L1)(L2)](NO3)4. The cis-protecting units (L′) used were
ethylenediamine (en), tetramethylethylenediamine (tmeda), 2,2′-bipyridine (bpy) and 1,10-
phenanthroline (phen). Crystallization of the [2]catenanes via slow evaporation of their
CH3CN:H2O (1:1) solutions yielded a single crystalline form in the case of [Pd2(2,2′-
bpy)2(L1)(L2)]2(NO3)8 and two concomitant crystalline forms (solvates) in the case of
[Pd2(phen)2(L1)(L2)]2(NO3)8. The formation of the [2]catenane is facilitated by noncovalent
interactions such as N-H…O, C-H…O, C-H…π contacts and π…π stacking. The solvates of
[Pd2(phen)2(L1)(L2)]2(NO3)8 revealed differences in the orientation of the amide carbonyl group
and conformational differences in the ligands and phen units in the macrocycles and may thus be
termed conformational solvatomorphs. The molecular packing in all the structures was found to be
driven by intermolecular π…π stacking interactions between the aromatic rings in their cis-
protected Pd(II) units. However, due to the awkward shape of the molecules the closest 2,2′-bpy
and phen units in all the structures overlap differently rather than the commonly observed “head-
to-tail” or head-to-head” modes.
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INTRODUCTION
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Polymorphism is the ability of a compound to exist in two or more crystalline forms, which exhibit
differences in solid-state properties such as melting point, solubility, density and solid-state
reactivity.1-3 The occurrence of different conformers of the same molecule in the different crystal
forms is referred to as conformational polymorphism.4,5 Solvatomorphism is a related phenomenon
where a solvent cocrystallizes with the compound in its crystal lattice. Solvatomorphs may show
differences in molecular packing as compared to the solvent free forms and among each other.
Instances of polymorphism and solvatomorphism in active pharmaceutical ingredients (APIs) have
been extensively studied because of the possible effects on their stability and bioavailability.6,7
Although the incidence of polymorphism and solvatomorphism in small organic molecules is well
documented, these phenomena have also been observed in larger molecular systems, including
proteins. A statistical study of polymorphism using the Cambridge Structural Database (CSD)8
revealed no connection between the structural features of molecules such as size, hydrogen
bonding ability, conformational flexibility and their propensity to yield multiple crystalline forms.9
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Martins and coworkers recently described conformational polymorphs of a rotaxane and
investigated the differences between them at the intramolecular level.10 Baumes et al. obtained
two conformationally different crystal structures of a rotaxane in separate experiments,11 while
Mezei et al. studied the crystal structures of polymorphs and solvatomorphs of pseudorotaxanes.12
Stoddart and coworkers isolated four crystalline forms of a [3]catenane composed of two
cyclobis(paraquat-p-phenylene) rings threaded into a dinaphtho[50]crown-14 macrocycle.13 The
formation of these solvatomorphs was attributed to the innate flexibility of the framework of the
[3]catenane. These large systems belong to the class of mechanically interlocked molecules
(MIMs) and are challenging synthetic targets, exhibit intriguing structural features, dynamic
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behavior and find application as molecular machines and sensors.14-19 [2]Catenanes are a class of
MIMs composed of two rings interlocked via noncovalent interactions such as hydrogen
bonding,20,21 halogen bonding,22-24 aromatic donor acceptor interactions25-27 or synthesized using
templates.28-33 Transition metal ions can also be used in combination with chosen ligands to
prepare metallocycles in high yield, which can undergo catenation, promoted by various types of
donor-acceptor interactions.
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We recently described the crystal structures of solvatomorphs of tetranuclear Pd(II) based
molecular squares (Figure 1a) of the general formula [Pd(L′)(4,4′-bpy)]4(OTs)8 [where L′
represents 2,2′-bipyridine (bpy) or 1,10-phenanthroline (phen)] with emphasis on the modes of
molecular packing adopted by the different crystalline forms.34 The molecular packing in these
structures was driven by intermolecular π…π stacking interactions between aromatic rings of the
2,2′-bpy and phenanthroline units. The present work describes the reaction of a flexible, pyridine-
appended ligand, rigid 4,4′-bipyridine and cis-protected Pd(II) units (in 1:1:2 ratio) in water. A
concentration-dependent equilibrating mixture of heteroleptic metallomacrocycles and the
corresponding [2]catenanes (Figure 1b,c) was obtained. Crystals of the [2]catenanes containing
2,2′-bpy and 1,10-phenanthroline units were obtained upon slow evaporation of their acetonitrile-
water solutions. A pair of solvatomorphs was obtained for the [2]catenane where 1,10-
phenanthroline moieties were present in the cis-protected Pd(II) units, which showed differences
in the orientation of the amide carbonyl groups and aromatic rings of the ligand and cis-protecting
agent. These crystal structures provided us with an opportunity to examine the molecular packing
in a tetranuclear complex, where the Pd(II) square planes are not coplanar unlike those in the
Pd(II) molecular squares. The pairs of Pd(II) square planes present in the two interlocking
macrocycles of the [2]catenane lie in two different planes, oriented nearly orthogonal to each other.
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In the [2]catenanes, π…π stacking interactions were observed between the closest 2,2′-bpy and
phenanthroline units, which do not overlap in the commonly observed “head-to-head” or “head-
to-tail” manner.35 We briefly describe the synthesis of the [2]catenanes, their characterization in
the solution and solid states, analyses of their crystal structures and the differences in the crystal
structures and molecular packing of the conformational solvatomorphs in the following sections.
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Figure 1. Schematic representations of cis-protected Pd(II) directed self-assembled complexes:
(a) molecular square, (b) heteroleptic metallomacrocycle and (c) the corresponding [2]catenane.
(Key: green – cis-protecting agent; pink – Pd(II) and its square plane; orange – 4,4′-bpy; blue –
flexible pyridine-appended ligand.)
RESULTS AND DISCUSSION
Ligand L1 upon crystallization from acetone and acetonitrile-methanol solutions produced
two different solvated crystals belonging to the space groups R-3 and P21/n, respectively.36 The
molecules in both solvates adopt approximately anti-conformation in the solid state, with respect
to the two isonicotinamide moieties, where the pyridine rings are oriented in opposite directions
(Figure 2). The torsion angle C(Ar)-C(H2)-N(H)-C(=O) in the acetone solvate (88°) is smaller in
magnitude than that observed in the hydrate (110°).
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Figure 2. Conformation of the molecules (from single crystal structures) of the ligand L1 in its (a)
acetone solvate (SUNWEE)8 and (b) hydrate (SUNWII).8 (c) Chemical drawings of the anti and
gauche conformations of the ligand. Hydrogen atoms other than the amide N-H atoms are omitted
for clarity.
Synthesis and characterization of the macrocycle and [2]catenane. The reaction of L1, 4,4′-
bipyridine (L2) and cis-protected Pd(II) units resulted in the formation of the heteroleptic
macrocycles 1a-d, when DMSO was the medium of complexation (Scheme 1). A concentration-
dependent equilibrating mixture of the macrocycles (1a-d) and the corresponding [2]catenanes (2a-
d) was obtained when the reaction was performed in water. The formation of the macrocycle and
the [2]catenane requires the ligand to adopt the gauche conformation which is readily achieved by
rotation about the C(Ar)-C(H2) bond. In general, amides are structurally less flexible than the
corresponding esters due to restricted rotation about the amide bond. The amide hydrogen and
carbonyl oxygen atoms may engage in hydrogen bonding interactions with guest or solvent
molecules.
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a
b
O
Pd N
N
HN
e
f
c
d
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a
DMSO
b
HN
N
N
4NO3
O
Pd
N
O
HN
c
N
e
f
ONO2
ONO2
1a-d
d
Pd
+
+ 2
HN
L'
a'
b'
Pd( )(NO3)2
N
a
b
O
O
O
Pd
N
N
Pd N
N
O
L2
N
HN
N
Pd
N
e'
f '
HN
NH
c'
e
f
c
H2O
L1
High conc.
Low conc.
d'
N
d
NH
N
Pd
O
N
HN
N
HN
4NO3
Pd
N
Pd
N
O
O
8NO3
2a-d
1a-d
j
h
h
j
i1
h'
h'
j'
j'
i'1
g1
i2
g'1
H2N
g'2
NH2
i'2
g2
N
N
H2N
NH2
N
N
b
b
a
a
r'
r
r
r'
m'1
l'1
m1
l1
m'1
l'2
k'2
q'1
p'1
n
q1
n'
n'
N
n
q'2
p'2
o'2
m2
l2
q2
p2
o2
p1
N
N
N
N
N
N
N
o'1
o1
k1
k2
k'1
c
d
c
d
Scheme 1 Synthesis of the metallomacrocycles/[2]catenanes, 1a-d/2a-d.
1H NMR spectra (Figure 3) recorded for the complexes 1a-d in DMSO-d6 revealed a downfield
shift in the signals of the Ha and Hb protons of the ligand L1 and He and Hf protons of L2 upon
complexation. No significant change was observed in the chemical shifts of the protons
corresponding to the phenyl and methylene groups of the ligand. The protons of the cis-protecting
agent become non-equivalent after the formation of the heteroleptic macrocycles due to the loss of
their plane of symmetry. The complexes were characterized by 1D and 2D NMR spectroscopy.
(Figures S2-S23).
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1
Figure 3. H NMR spectra ([D6]DMSO, 25 °C, TMS as an external standard) of: (i) L1; and
metallomacrocycles (ii) 1a; (iii) 1b; (iv) 1c and (v) 1d. [Concentration with respect to Pd(II)
source: 10 mM for 1a-d].
1H NMR spectra for the complexes prepared at various concentrations in D2O each showed two
sets of peaks which belong to the macrocycle and [2]catenane, respectively (Figure 4). The signals
of the methylene protons (Hc′) and phenyl hydrogens (Hd′) of one set appear upfield as compared
to those of the second set (Hc and Hd). This is due to [2]catenane formation and occurs because of
the influence of the diatropic ring currents of five aromatic rings of one interlocked macrocycle
upon the other and vice versa as established earlier for a comparable catenane 3 (Scheme 2).37 The
composition and solution behavior of catenane 3 is comparable with that of the catenane 2c and
the notable structural difference is in terms of ester functionalities in the former and amide in the
latter. The chemical shifts of the macrocycles 1a-d and [2]catenanes 2a-d and their differences are
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summarized in Table S1. The complexes were characterized by 1D and 2D NMR spectroscopy
(Figures S24-S51). Evidence for the presence of the two species was also obtained from 2D DOSY
NMR spectra recorded for the four sets of equilibrium mixtures of macrocycle and [2]catenane
(Figures S52-S55).
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Figure 4. 1H NMR spectra (D2O, 25 °C, TMS as an external standard) of the
metallomacrocycle/[2]catenae mixtures: (i) 1a/2a (40 mM); (ii) 1b/2b (50 mM); (iii) 1c/2c (10
mM) and (iv) 1d/2d (12 mM). Values in parentheses denote concentrations of the solutions with
respect to Pd(II) source.
N
O
Pd
N
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N
O
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O
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N
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O
N
N
Pd
N
N
N
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Scheme 2 Chemical structure of the [2]catenane 3.
The macrocycle diffused faster than the [2]catenane due to its smaller size and hence, the DOSY
1
study assisted assignment of the two sets of signals observed in the H NMR spectra. The
concentration-dependent equilibrium between the macrocycle and [2]catenane in water was
1
studied by recording the H NMR spectra of the complexes in D2O at various concentrations
(Figures S56-S59). The plot of percentage of the rings present as [2]catenane/macrocycle as a
function of the concentration for all the equilibrium mixtures (Figure S60) shows that at high
concentration, the [2]catenane is present in larger amounts while the macrocycles are the dominant
1
species in dilute solutions. The equilibrium constants for the mixtures were calculated using H
NMR spectra recorded at different concentrations (Table S2). The measured diffusion coefficients
of the macrocycles and corresponding [2]catenanes and the estimated equilibrium constants for
their mixtures are summarized in Table 1. Additional evidence for the formation of the macrocycle
and [2]catenane was obtained from cold spray ionization mass spectrometry data (CSI-MS)
(Figures S61-S77). The isotopic patterns for the fragments showed good correspondence with the
theoretically predicted distributions.
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Table 1. Summary of equilibrium constants and diffusion coefficients estimated for the
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equilibrium mixtures of complexes.
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D (m2s-1)
Complexes Kc (mmol-1L)
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Macrocycle
(2.82 ± 0.03) × 10-10
(2.69 ± 0.04) × 10-10
[2]Catenane
(2.22 ± 0.01) × 10-10
(2.07 ± 0.01) × 10-10
1a/2a
1b/2b
1c/2c
1d/2d
0.89 ± 0.05
1.58 ± 0.08
0.18 ± 0.04
0.12 ± 0.03
(2.724 ± 0.002) × 10-10 (2.05 ± 0.02) × 10-10
(2.47 ± 0.03) × 10-10 (2.01 ± 0.01) × 10-10
Crystal structures of the [2]catenanes Attempts to crystallize the macrocycles 1a-d and the
[2]catenanes 2a and 2b via slow evaporation of their aqueous solutions or vapor diffusion
experiments were not fruitful. Crystals of the [2]catenanes 2c and 2d, however, were
spontaneously obtained by slow evaporation of CH3CN-H2O (1:1 v/v) solutions containing the
mixture of complexes 1c/2c and 1d/2d, respectively. This could be attributed to the fact that
concentrated aqueous media favor the formation of these catenanes.38 Crystals of solvatomorphs
2dI (C2/c) and 2dII (P21/n) were obtained concomitantly from a CH3CN-H2O solution of the
complex 2d. We recently reported37 the crystal structure (CSD8 refcode: RUSZAI) of the
tetranuclear [2]catenane (3) for which a chemical drawing is shown in scheme 2. An elaborate
discussion on the crystal structure of 3, not included in the earlier report, is warranted here.
Comparisons are drawn between the crystal structures and molecular packing in 2cI, 2dI, 2dII and
3. All the [2]catenanes crystallized in monoclinic space groups. The central phenyl ring of the
ligand of one macrocycle lies inside the cavity of the second macrocycle and the 4,4′-bpy units are
present outside in all the crystal structures. The asymmetric unit in 2cI (Figure S78) and 2dI
(Figure S79) contained a single macrocycle, whereas a pair of interlocked symmetry independent
macrocycles were present in the asymmetric unit in crystals of 2dII (Figure S80) and 3.37 The
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crystals of 2cI and 2dI were highly unstable and rapidly lost crystallinity when exposed to air. The
positions of disordered anions and solvent molecules in these crystals could not be determined
from the difference Fourier map, hence electron density corresponding to these moieties was
squeezed.39 The crystallographic data are briefly summarized in Table2 (see Table S3 for details).
The details of structure solution and ORTEPs are available in the Supporting Information.
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Table 2. Summary of crystallographic data for crystals of 2c and 2d.
2cI
2dI
2dII
Chemical Formula C50H42N10O2Pd2 C54H42N10O2Pd2
C108H146N28O59Pd4
3206.12
100
Monoclinic
P21/n
12.6708(11)
29.645(2)
36.539(3)
90
Mr
1027.73
296(2)
Monoclinic
C2/c
13.1208(5)
28.8866(10)
37.6371(11)
90
1075.77
296(2)
Monoclinic
C2/c
13.419(5)
28.900(5)
37.540(5)
90
Temperature (K)
Crystal system
Space group
a (Å)
b (Å)
c (Å)
α (°)
94.437(2)
90
14222.3(8)
8
0.960
10247
96.995(5)
90
14450(6)
8
0.989
5746
99.532(2)
90
13535.5(19)
4
1.573
30912
 (°)
γ (°)
V (Å3)
Z
Dcalc (g cm–3)
Unique reflns
Rint
0.0413
1.052
0.0368
1.108
0.050
1.026
GoF
0.0970
0.2972
0.1575
0.3509
1988795
0.0960
0.2653
0.1435
0.3480
1988797
0.0683
0.1858
0.0851
0.2048
1988796
R1[I > 2(I)]
WR2[I > 2 (I)]
R1_all data
Wr2_all data
CCDC No.
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Conformations of the macrocycles in the [2]catenanes. Scrutiny of the conformational
differences in the macrocycles that form the [2]catenane reveals the dissimilarities in the crystal
structures.
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Figure 5. Crystal structures of the [2]catenanes and overlaps of the catenating macrocycles in (a)
2cI; (b) 2dI; (c) 2dII and (d) 3 show the orientation of the ester and amide carbonyl groups in the
macrocycles.
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In each ring, the two ester/amide carbonyl groups may be aligned in syn (C=O groups facing
approximately the same direction) or anti (C=O facing approximately the opposite directions)
mode as substantiated with the measured torsion angles O=C- - - -C=O (Table 3) for ligand L1 in
its crystals and in the macrocycles in 2cI, 2dI, 2dII and 3. Since a single macrocycle is present in
the asymmetric unit of the crystal structures of 2cI and 2dI, respectively, the [2]catenanes are
composed of identical rings. The amide carbonyl groups are oriented anti to each other in 2cI
(Figure 5a) and 2dI (Figure 5b), whereas the ester carbonyl groups of the catenating rings in 3 are
oriented syn to each other (Figure 5d, Table 3). However, the overlay of the catenating rings in the
crystals of 2dII reveals that in macrocycle A (red, Figure 5c), the amide carbonyl groups are
aligned anti, while in macrocycle B (blue, Figure 5c), they are aligned syn to each other. These
differences in the orientation of the carbonyl groups in the crystal structures of 2cI, 2dI, 2dII and
3 revealed that their crystals contain equal proportions of enantiomorphic [2]catenanes.
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Figure 6. Overlaps of the macrocycle (yellow) in the crystals of 2dI with the symmetry
independent (a) macrocycle A and (b) macrocycle B in crystals of 2dII show the conformational
differences in the solvatomorphs.
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Further, the overlaps of the macrocycle in crystals of 2dI and macrocycles A (Figure 6a) and B
(Figure 6b) in 2dII revealed differences in the orientation of the central phenyl ring of the ligand
and the rings of the phenanthroline units of the two macrocycles in 2dII. Therefore, 2dI and 2dII
1
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are conformational solvatomorphs. A single sharp set of peaks is observed in the H NMR
spectrum for 2dII, suggesting that an averaged picture of the different conformations is seen in
the solution state. The orientations of these carbonyl groups influence the hydrogen bonding
interactions between the interlocked molecules.
The torsion angles C(Ar)-C(H2)-N(H)-C(=O) measured for the ligand L1 in its crystals and in the
macrocycles in 2cI, 2dI, 2dII and 3 are also summarized in Table 3. Two different values of the
angle were measured for the ligand in the crystals of the [2]catenanes, indicating the
unsymmetrical orientation of the two pyridyl arms of the coordinated ligand. These differences
may be due to the noncovalent interactions between the catenating rings during the process of
forming the interlocked structure and the interactions of the [2]catenane with anions and solvent
molecules.
Table 3. Comparison of the geometry of the ligand in the [2]catenanes.
Crystal
Ligand L1 (acetone solvate) -180
O=C- - - -C=O (°)
C(Ar)-C(H2)-N(H)/O-C(=O) (°)
88.0(2), -88.0(2)
110.8(1), -110.8(1)
92(1), 106(2)
Ligand L1 (hydrate)
2cI
180
-118(1)
-120(3)
125.7(6)
-14.5(5)
-2(2)
2dI
90(3), 110(3)
2dII (Macrocycle A)
2dII (Macrocycle B)
3 (Macrocycle C)
3 (Macrocycle D)
-86.4(7), -110.5(7)
-76.7(7), -88.4(6)
-90(2), 94(2)
-3(2)
93(1), -95(2)
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Interactions between the interlocked rings The catenating rings in 2cI (Figure 7a) and 2dI
(Figure 7b) interact via C-H···π interactions (C20-H20···Cg5 in 2cI and C21-H21···Cg7 in 2dI)
between the hydrogen atoms of the central phenyl ring and the pyridine rings of the ligand and
weak π···π interactions between the aromatic rings of the ligands. The interplanar distances
between the aromatic systems, (4,4′-bpy)-(phenylene)-(phenylene)-(4,4′-bpy), and the dihedral
angles between these planes span the range 4.27–4.69 Å and 8-14° (Table S4).
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Figure 7. Intermolecular interactions between pairs of interlocked molecules in crystals of (a) 2cI;
(b) 2dI; (c) 2dII and (d) 3. Solvent molecules, anions and hydrogen atoms not involved in
hydrogen bonding are omitted for clarity.
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The interlocked rings (macrocycles A and B) in 2dII interact via a short and linear N-H···O (N11-
H11···O2A) interaction between the amide hydrogen atom of ring A and carbonyl oxygen atom of
ring B. The interlinking of the rings is supported by C-H···O (C38A-H38A···O2), C-H···π (C51-
H51A···Cg26, C53A-H53A···Cg27, C53-H53···Cg11) and weak π···π interactions (Figure 7c).
The interplanar distances between the aromatic systems and the dihedral angles between the planes
of these aromatic rings lie in the range of 4.32-4.63 Å and 9-46°, respectively (Table S4).
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The interlocked rings (macrocycles C and D) in 337 interact through a pair of C-H···O interactions
(C4-H4···O8 and C54-H54···O2) between the pyridyl hydrogen atoms and the carbonyl oxygen
atoms of the ester groups. The interlocking is supported by weak π···π interactions between the
aromatic systems (Figure 7d). The interplanar distances between the aromatic systems and the
dihedral angles between the planes of these aromatic rings lie in the range 4.65–4.82 Å and 19-
45°, respectively (Table S4). The amide hydrogen atoms in 2cI and 2dI are not involved in
significant short contacts with the cationic portion of the molecule, unlike those in 2dII. The
interlocked macrocycles in 2dII are held together by stronger hydrogen bonding interactions than
those observed between the catenating rings in 3. The interplanar distances between the stacked
aromatic systems at the core of the catenane are marginally shorter in the structures of 2c and 2d
as compared to those observed in 3.
Packing of the [2]catenanes in their crystals. Despite the differences in the conformation of the
interlocked molecules, the apparent similarities in the patterns of molecular self-assembly in the
solid state are a consequence of the noncovalent interactions between the cis-protecting agents at
the metal centers of adjacent molecules. The structures of the [2]catenanes reveal that the p-
phenylene groups lie buried in the core of the molecule and the 2,2′-bpy/phen units lie at the
corners of an imaginary irregular tetrahedron with vertices corresponding to the Pd(II) metal
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centers. Views of the packing of the [2]catenanes in the crystals of 2cI (Figure 8a) and 3 (Figure
9a) along the a and b axes respectively, reveal association of the molecules through weak π…π
stacking interactions (~4.6 – 4.7 Å)40 between the closest 2,2′-bpy units, forming chains along the
c-axis. The chains in 2cI are linked by weak stacking interactions (~4.7 Å) between the pyridine
rings of the ligands along the a-axis (Figure 8b) and weak π…π stacking between 2,2′-bpy units
along the b-axis in 3 (Figure 9b).
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Zaric and coworkers studied the stacking interactions between square planar metal complexes
containing 2,2′-bpy ligands by analyzing crystal structures in the CSD8 and performing DFT
calculations.35 They defined the orientations of the interacting metal complexes as “head-to-head”
or “head-to-tail" using a measured torsion angle, T1.35 T1 is defined as the ΩC1−M1−M2−ΩC2 angle
where ΩC1 and ΩC2 represent the centers of the chelate rings in the two 2,2′-bpy units, respectively,
and M1 and M2 are the corresponding metal ions.35 The structures where T1 lies between 0°-10°
denote “head-to-head” orientation, while those where T1 lies between 170°-180° correspond to
“head-to-tail” orientation of the 2,2′-bpy units (Scheme 3). Inspection of the corresponding torsion
angles for the closest 2,2′-bpy units in 2cI (T1 = 43.75°) and 3 (T1 = 72.65°) indicates that these
rings do not overlap in “head-to-head” or “head-to-tail” fashion (Scheme 3), but rather in an in-
between manner.
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Pd
N
N
N
N
Pd
N
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N
N
N
Pd
Pd
Head-to-tail
Head-to-head
Scheme 3. Relative orientations of interacting 2,2′-bpy units in the crystals of various complexes.
(Adapted from reference 35, reprinted with permission from Petrovic, P. V.; Janjic, G. V.; Zaric,
S. D. Stacking Interactions between Square-Planar Metal Complexes with 2,2′-Bipyridine
Ligands. Analysis of Crystal Structures and Quantum Chemical Calculations. Cryst. Growth
Des. 2014, 14, 3880-3889. © 2014 American Chemical Society).
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Figure 8. Views of the packing in crystals of 2cI show (a) chain of [2]catenanes along the c axis
linked via π…π interactions between bpy units [(i) Cg4···Cg7, Table S4] and (b) weak π…π
interactions [(ii) Cg5···Cg5, Table S4] between the chains along the a-axis. Hydrogen atoms are
omitted for clarity.
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Figure 9. Views of the packing in crystals of 3 show (a) chain of [2]catenanes formed by π…π
interactions between bpy units [(i) Cg4···Cg7 along a-axis and (ii) Cg8···Cg19 along c-axis, Table
S4] and (b) weak π…π interactions [(iii) Cg7···Cg18, Table S4] between the chains along the b-
axis. Hydrogen atoms, anions and water molecules are omitted for clarity.
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This is perhaps due to the awkward shape of the molecule and the need to achieve efficiency in
molecular packing, utilizing the aromatic surfaces of the bpy rings. Interestingly, the tetranuclear
Pd(II) based molecular squares SERWEU and SERWIY reported by us earlier, also exhibit
molecular packing through π…π stacking interactions between 2,2′-bpy units.34 A striking
difference in the molecular packing in the solvatomorphs SERWEU and SERWIY is the “head-
to-tail” orientation of the interacting 2,2′-bpy units in SERWEU, unlike the weak overlap of these
units in SERWIY (Figure 10). This change is perhaps due to the presence of a guest (acetic acid)
and tosylate anions in SERWIY which influence the molecular organization of the squares.
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Figure 10. Schematic representation of the molecular association via side-on and end-on
overlap modes in
two
different
tetranuclear
Pd(II)
complexes. aStructure
SERWIY8; bStructures SERWEU, SERWOE, SERWUK.8 (Adapted from reference 34, reprinted
with permission from Krishnaswamy, S.; Prusty, S.; Chartrand, D.; Hanan, G. S.; Chand, D.
K. Self-Assembled Molecular Squares as Supramolecular Tectons. Cryst. Growth
Des. 2018, 18, 2016-2030. © 2018 American Chemical Society).
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Similar modes of molecular assembly are observed in the crystals of 2cI (Figure 8a) and 2dI
(Figure S81a). The replacement of bpy with phen as the cis-protecting agent for the Pd(II) center
often yields isostructural crystals.34,41-44 However, the π…π stacking interactions between the
closest phenanthroline units in 2dI that link the catenanes across the c-axis are marginally shorter
(~3.7-4.1 Å, Table S4) than those between the bpy units in 2cI, possibly due to the better overlap
between the aromatic rings of the phen moieties as compared to those of bpy. The second
significant difference is the presence of π stacking interactions (~3.7-4.1 Å) between phen units
which help in linking the chains along the b-axis. The chains are linked along the a-axis by C=O‧‧‧π
interactions between the amide carbonyl group and the one of the rings of a neighboring phen unit
(Figure S81b).
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In the crystals of 2dII (Figure 11a) the π…π stacking interactions (Table S4) that connect the
catenanes along the c-axis are shorter (~3.5-3.7 Å) than those in 2cI, 2dI and 3. The chains are
also linked along the b-axis by stacking interactions of phen units and along the a-axis by weak
stacking interactions (~4.3 Å) between the pyridine rings of the ligands. Therefore, the
solvatomorphs show slight differences in the modes of molecular packing in the crystal and the
strength of the π stacking interactions.
The torsion angles for the closely interacting phen units in 2dI (T1 = 42.62°) and 2dII (T1 = 46.40°,
29.05°) indicate that these rings do not overlap in “head-to-head” or “head-to-tail” fashion but in
an in-between manner similar to that observed in 2cI and 3. It is pertinent to note that the Pd(II)
molecular squares SERWOE34 and SERWUK34 exhibited “head-to-tail” overlap of the interacting
phen units in their crystals possibly due to the nearly coplanar nature of the Pd(II) square planes
(Figure 10). While the importance of an aqueous medium for the formation of these [2]catenanes
is now well understood, the crystal structures of these interlocked molecules (2dII and 3) also
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revealed the presence of a large number of water molecules which are involved in extensive
hydrogen bonding interactions with the nitrate counteranions (FigureS82).
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Figure 11. Views of the packing in crystals of 2dII show (a) chain of [2]catenanes along the c axis
linked via π…π interactions between phen units [see Table S4 for details of (i)-(vii)] and (b) weak
π…π interactions [(viii) Cg12···Cg26, Table S4] between the chains in the ac-plane. Hydrogen
atoms, anions and water molecules are omitted for clarity.
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EXPERIMENTAL SECTION
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4,4′-Bipyridine, PdCl2 and silver salts were acquired from Aldrich Chemicals. The cis-protected
Pd(II) units used were synthesized using reported procedures.45,46 The compounds represented by
Pd(L′)(BF4)2 were prepared by reacting Pd(L′)Cl2 with AgBF4. Ligand L1 was prepared using a
reported procedure.36 All common reagents and solvents were obtained from Spectrochem, India.
Deuterated solvents were obtained from Aldrich and Cambridge Isotope Laboratories. NMR
spectra were recorded on Bruker 400 and 500 MHz FT-NMR spectrometers using
tetramethylsilane as reference. Diffusion Ordered Spectroscopy (DOSY) NMR measurements
were performed on a Bruker Avance (AV III) 500 MHz NMR spectrometer, equipped with a 5-
mm broadband observe (BBO) z-axis gradient probe which delivers a maximum gradient strength
of 50 G/cm. The mass spectra were recorded using a Bruker ESI-TOF/ESI-TRAP/FTMS fitted
with a Bruker Cryospray system. Melting points were determined using a CINTEX apparatus and
were uncorrected. Single crystal X-ray diffraction data were recorded on a Bruker AXS Kappa
Apex II CCD diffractometer with graphite-monochromatized Mo-Kα (λ=0.71073 Å) radiation
and a Bruker Venture Metaljet diffractometer equipped with an Oxford Cryosystem liquid
nitrogen device, using Ga-Kα radiation (λ = 1.34180 Å).
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Synthesis of ligand L1. To a stirred suspension of isonicotinoyl chloride hydrochloride (0.57 g,
3.23 mmol) and 1,4-phenylenedimethanamine (0.20 g, 1.46 mmol) in dry dichloromethane (25
mL), triethylamine (0.5 mL) was added in a dropwise manner at 0-5 °C. The mixture was stirred
at room temperature for 24 h under nitrogen atmosphere. The solid obtained was filtered and
washed repeatedly with distilled water, followed by diethyl ether and dried under vacuum, yielding
a white solid. Isolated yield = 0.436 g, 86%, mp. 202 °C.
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1H NMR (500 MHz, DMSO-d6, 298 K): δ [ppm] = 9.85 (t, J = 5.8 Hz, 2H, -NH-), 9.25 (d, J = 6
Hz, 4H, Ha), 8.31 (d, J = 6 Hz, 4H, Hb), 7.8 (s, 4H, Hd), 5.01 (d, J = 5.9 Hz, 4H, Hc).
General procedure A: Synthesis of the complexes 1a-d. Ligand L1. (0.005 mmol), L2 (0.005
mmol), and the corresponding cis-protected Pd(II) unit (2 equiv.) were taken in DMSO or DMF
(3 mL) and stirred for 24 h at ambient temperature to obtain a clear yellow solution. In a typical
isolation process, addition of excess EtOAc gave an off-white precipitate which was separated by
filtration, washed several times with EtOAc and dried under vacuum to obtain an off-white solid.
All complexes were isolated by the same method.
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[Pd2(en)2(L1)(L2)](NO3)4, 1a: The complex was synthesized according to general procedure A (in
DMF) using L1 (1.7 mg, 0.005 mmol, 1 equiv), L2 (0.8 mg, 0.005 mmol, 1 equiv), and
Pd(en)(NO3)2 (3.0 mg, 0.010 mmol, 2 equiv). Isolated yield = 4.15 mg, mp. 230 °C (decomposed).
1H NMR (500 MHz, DMSO-d6) δ [ppm] = 9.89 (t, J = 5.7 Hz, 2H, -NH-), 9.47 (t, 8H, Ha+He),
8.60 and 8.39 (d and d, J = 6.5 and 6.5 Hz, 4H and 4H, Hb and Hf), 7.73 (s, 4H, Hd), 6.23 and
6.19 (s and s, 4H and 4H, Hg1, and Hg2), 4.90 (d, J = 5.6 Hz, 4H, Hc), 3.23 (s, 8H, Hh).
13C NMR (125 MHz, DMSO-d6): δ [ppm] = 162.72, 152.81, 152.75, 145.42, 144.32, 138.27,
128.86, 127.92, 124.21. 47.32, 46.37, 43.17.
MS (CSI): m/z calcd for [1a-2NO3]2+: 480.0663; found: 480.0674.
Pd2(tmeda)2(L1)(L2)](NO3)4, 1b: The complex was synthesized according to general procedure A
(in DMF) using L1 (1.8 mg, 0.005 mmol, 1 equiv), L2 (0.8 mg, 0.005 mmol, 1 equiv), and
Pd(tmeda)(NO3)2 (3.5 mg, 0.010 mmol, 2 equiv). Isolated yield = 4.80 mg, mp. 242 °C
(decomposed).
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1H NMR (500 MHz, DMSO-d6) δ [ppm] = 9.93 (t, J = 5.95 Hz, 2H, -NH-), 9.77 (t, 8H, Ha+He),
8.70 and 8.50 (d and d, J = 5.45 and 6.05 Hz , 4H and 4H, Hb+Hf), 7.73 (s, 4H, Hd), 4.89 (d, J =
5.6 Hz, 4H, Hc), 3.53 (s, 8H, Hj), 3.13 and 3.11 (s and s, 12H and 12H, Hi1+Hi2).
13C NMR (125 MHz, DMSO-d6) δ [ppm] = 162.48, 152.36, 145.09, 144.12, 138.59, 129.14,
125.09, 124.90, 62.89, 51.02, 50.97, 43.39.
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MS (CSI): m/z calcd for [1b-2NO3]2+: 536.1291, found: 536.1309.
[Pd2(bpy)2(L1)(L2)](NO3)4, 1c: The complex was synthesized according to general procedure A
(in DMSO or DMF) using L1 (1.8 mg, 0.005 mmol, 1 equiv), L2 (0.8 mg, 0.005 mmol, 1 equiv),
and Pd(bpy)(NO3)2 (4.0 mg, 0.010 mmol, 2 equiv). Isolated yield = 5.45 mg, mp. 222 °C
(decomposed).
1H NMR (500 MHz, DMSO-d6) δ [ppm] = 10.05 (t, J = 5.8 Hz, 2H, -NH-), 9.89 and 9.86 (d and
d, J = 5.8 and 5.5 Hz, 4H and 4H Ha+He), 9.33 (d, J = 8.2 Hz, 4H, Hn), 9.03-9.08 (m, 4H,
Hm1+Hm2), 8.82 and 8.61(d and d, J = 5.9 and 6.6 Hz, 4H and 4H, Hb+Hf), 8.21-8.35 (m, 4H and
4H, Hk1+Hk2 and Hl1+Hl2), 7.78 (s, 4H, Hd), 4.94 (d, J = 5.8 Hz, 4H, Hc).
13C NMR (125 MHz, DMSO-d6): δ [ppm] = 162.26, 156.23, 152.49, 152.41, 151.16, 145.86,
144.63, 143.29, 138.41, 129.14, 129.03, 125.61, 125.56, 125.10, 43.25.
MS (CSI): m/z calcd for [1c-3NO3]3+: 363.3816; found: 363.3857.
[Pd2(phen)2(L1)(L2)](NO3)4, 1d: The complex was synthesized according to general procedure A
(in DMSO or DMF) using L1 (1.8 mg, 0.005 mmol, 1 equiv), L2 (0.8 mg, 0.005 mmol, 1 equiv),
and Pd(phen)(NO3)2 (4.2 mg, 0.010 mmol, 2 equiv). Isolated yield = 5.90 mg, mp. 236 °C
(decomposed).
1H NMR (500 MHz, DMSO-d6) δ [ppm] = 10.07 (t, J = 5.9 Hz, 2H, -NH-), 9.97 and 9.94 (d and
d, J = 5.3 and 5.1 Hz, 4H and 4H, Ha and He), 9.68-9.72 (m, 4H, Hq1 and Hq2), 9.00 (s, 4H, Hr),
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8.88 and 8.66 (d and d, J = 5.4 and 6.6 Hz, 4H and 4H, Hb and Hf), 8.83 and 8.70 (d and d, J = 5.2
and 5.1 Hz, 2H and 2H, Ho1 and Ho2), 8.62 and 8.58 (dd and dd, J = 8.2, 5.3 and 8.3, 5.3 Hz, 2H
and 2H, Hp1 and Hp2), 7.81 (s, 4H, Hd), 4.97 (d, J = 5.8 Hz, 4H, Hc).
13C NMR (125 MHz, DMSO-d6): δ [ppm] = 162.36, 152.85, 152.73, 152.24, 146.38, 146.03,
144.78, 142.10, 138.48, 131.10, 129.08, 128.71, 127.44, 125.67, 43.31.
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MS (CSI): m/z calcd for [1d-3NO3]3+: 379.3817, found: 379.3842.
General procedure B Synthesis of equilibrium mixture of complexes 1a-d and 2a-d). Ligand
L1 (0.025 mmol), L2 (0.025 mmol), and the corresponding cis-protected Pd(II) unit (0.050 mmol)
were mixed in 5 mL water and stirred for 24 h at ambient temperature to obtain a clear solution,
which, upon slow evaporation yielded a pale yellow solid/crystals. The solid upon dissolution in
D2O, revealed two sets of signals corresponding to the macrocycle (1a-d) and [2]catenane (2a-d),
respectively.
[Pd2(en)2(L1)(L2)](NO3)4, 1a and [Pd4(en)4(L1)2(L2)2](NO3)8, 2a: The equilibrium mixture was
synthesized according to general procedure B using L1 (8.6 mg, 0.025 mmol, 1 equiv) L2 (3.9 mg,
0.025 mmol, 1 equiv), and Pd(en)(NO3)2 (14.5 mg, 0.050 mmol, 2 equiv). Isolated yield = 25.6
mg.
1a: 1H NMR (500 MHz, D2O): δ [ppm] = 8.83 and 8.81(d and d, J = 6.75 and 6.8 Hz, 4H and 4H,
Ha and He), 7.81 and 7.79 (d and d, J = 6.85 and 6.75 Hz, 4H and 4H, Hb and Hf), 7.19 (s, 4H,
Hd), 4.53 (s, 4H, Hc), 2.93 (s, 24H, Hh and Hhʹ).
2a: 1H NMR (500 MHz, D2O): δ [ppm] = 9.11 and 8.92 (d and d, J = 6.8 and 6.75 Hz, 8H and 8H,
Ha′ and He′), 7.96 and 7.66 (d and d, J = 6.85 and 6.8 Hz, 8H and 8H, Hb′ and Hf′), 4.82 (s, 8H,
Hd′), 3.73 (s, 8H, Hc′), 2.93 (s, 24H, Hh and Hh′).
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1a/2a: 13C NMR (125 MHz, D2O): δ [ppm] = 164.44, 152.45, 152.11, 145.42, 144.21, 135.38,
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[Pd2(tmeda)2(L1)(L2)](NO3)4, 1b and [Pd4(tmeda)4(L1)2(L2)2](NO3)8, 2b: The equilibrium
mixture was synthesized according to general procedure B using L1 (8.6 mg, 0.025 mmol, 1 equiv)
L2 (3.9 mg, 0.025 mmol, 1 equiv), and Pd(tmeda)(NO3)2 (17.3 mg, 0.050 mmol, 2 equiv). Isolated
yield = 26.20 mg.
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1b: 1H NMR (500 MHz, D2O): δ [ppm] = 9.14 and 9.07 (d and d, J = 5.45 and 5.60 Hz, 4H and
4H, Ha and He), 7.92 and 7.89 (d and d, J = 5.55 and 5.35 Hz, 4H and 4H, Hb and Hf), 7.16 (s,
4H, Hd), 4.52 (s, 4H, Hc), 3.14 (s, 8H, Hj), 2.72 and 2.69 (s and s, 12H and 12H, Hi1+Hi2).
2b: 1H NMR (500 MHz, D2O): δ [ppm] = 9.33 and 9.10 (d and d, J = 5.55 and 5.60 Hz, 8H and
8H, Ha′ and He′), 8.15 and 7.83 (d and d, J = 5.50 and 5.65 Hz, 8H and 8H, Hb′ and Hf′), 4.76 (s,
8H, Hd′), 3.76 (s, 8H, Hc′), 3.14 (s, 16H, Hjʹ), 2.75 and 2.66 (s and s, 24H and 24H, Hi1'+Hi2').
1b/2b: 13C NMR (125 MHz, D2O): δ = 163.79, 152.21, 151.81, 144.67, 144.56, 135.38, 127.21,
125.72, 124.36, 63.01, 50.60, 50.52, 42.71.
The mixture of 1b′ and 2b′ was prepared in a similar manner by using Pd(tmeda)(BF4)2 instead of
Pd(tmeda)(NO3)2. MS (CSI): m/z calcd for [1bʹ-3(BF4)]3+: 776.5281; found 776.5318 and m/z
calcd for [2bʹ-2(BF4)]2+: 560.6452; found: 560.6462.
[Pd2(bpy)2(L1)(L2)](NO3)4, 1c and [Pd4(bpy)4(L1)2(L2)2](NO3)8, 2c: The equilibrium mixture
was synthesized according to general procedure B using L1 (8.6 mg, 0.025 mmol, 1 equiv), L2
(3.9 mg, 0.025 mmol, 1 equiv), and Pd(bpy)(NO3)2 (19.3 mg, 0.050 mmol, 2 equiv). Isolated yield
= 27.20 mg.
1c: 1H NMR (400 MHz, D2O): δ [ppm] = 9.28 and 9.25 (d and d, J = 6.6 and 6.6 Hz, 4H and 4H,
Ha and He), 8.51-8.57 (m, 12H, Hn+Hnʹ), 8.39-8.50 (m, 12H, Hm1+ Hm2+Hm1ʹ+Hm2ʹ), 8.13 and
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8.06 (d and d, J = 6.6 and 6.8 Hz, 4H and 4H, Hb and Hf), 7.58-7.82 (m, 24H, Hk1+Hk2+ Hk1ʹ
+Hk2ʹ+Hl1+Hl2+Hl1ʹ+Hl2ʹ), 7.28 (s, 4H, Hd) and 4.63 (s, 4H, Hc).
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and He′), 8.51-8.57 (m, 12H, Hn+Hn′), 8.39-8.50 (m, 12H, Hm1+ Hm2+Hm1ʹ+Hm2ʹ), 8.32 and
8.03 (d and d, J = 6.7 and 6.8 Hz, 8H and 8H, Hb′ and Hf′), 7.58-7.82 (m, 24H, Hk1+Hk2+ Hk1ʹ
+Hk2ʹ+Hl1+Hl2+Hl1ʹ+Hl2ʹ), 5.03 (s, 8H, Hd′), and 3.92 (s, 8H, Hc′).
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1c/2c: C NMR (125 MHz, D2O): δ [ppm] = 165.48, 164.04, 156.86, 152.65, 152.33, 152.20,
150.45, 150.31, 150.16, 147.12, 145.73, 142.99, 136.89, 135.55, 128.26, 127.80, 127.39, 126.14,
125.83, 125.69, 125.24, 124.62, 124.55, 43.39, and 42.84.
The mixture 1c′/2c′ was prepared in a similar manner by using Pd(bpy)(BF4)2 instead of
Pd(bpy)(NO3)2. MS (CSI): m/z calcd for [1cʹ-3(BF4)]3+: 829.7782; found: 829.7838 and m/z calcd
for [2cʹ-2(BF4)]2+: 600.5827; found: 600.5831.
[Pd2(phen)2(L1)(L2)](NO3)4, 1d and [Pd4(phen)4(L1)2(L2)2](NO3)8, 2d: The equilibrium mixture
was synthesized according to general procedure B using L1 (8.6 mg, 0.025 mmol, 1 equiv), L2
(3.9 mg, 0.025 mmol, 1 equiv), and Pd(phen)(NO3)2 (20.5 mg, 0.050 mmol, 2 equiv). Isolated
yield = 28.5 mg.
1d: 1H NMR (400 MHz, D2O): δ [ppm] = 9.38 and 9.36 (d and d, J = 6.6 and 6.4 Hz, 4H and 4H,
Ha and He), 8.98-9.05 (m, 12H, Hq1+Hq2+Hq1ʹ+Hq2ʹ), 8.33 (s, 12H, Hr+Hrʹ), 8.21 (d, J = 6.7 Hz,
4H, Hb/Hf), 8.19-8.08 (m, 16H, Hb/Hf+Ho1+Ho2+Ho1ʹ+Ho2ʹ), 8.06-7.93 (m, 12H,
Hp1+Hp2+Hp1ʹ+Hp2ʹ), 7.31 (s, 4H, Hd), 4.66 (s, 4H, Hc).
2d: 1H NMR (400 MHz, D2O): δ [ppm] = 9.63 and 9.46 (d and d, J = 6.4 and 6.5 Hz, 8H and 8H,
Ha′ and He′), 8.98-9.05 (m, 12H, Hq1+Hq2+Hq1ʹ+Hq2ʹ), 8.37 (d, 4H, J = 6.5 Hz, Hbʹ/Hfʹ) and 8.12
(d, 4H, Hbʹ/Hfʹ merged with Hb/Hf), 8.33 (s, 12H, Hr1+Hr2+Hr1ʹ+Hr2ʹ), 8.19-8.08 (m, 16H,
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