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Sodium ion association via bridging water molecules for different charged
p-phosphonated calix[4]arene bilayers{
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Published on 03 October 2012 on http://pubs.rsc.org | doi:10.1039/C2CE26207J
Irene Ling,*a K. Swaminathan Iyer,b Charles S. Bond,b Alexandre N. Sobolev,bc Yatimah Aliasa and
Colin L. Raston*d
Received 27th July 2012, Accepted 26th September 2012
DOI: 10.1039/c2ce26207j
Cone conformation p-phosphonatocalix[4]arene forms bilayer and columnar arrays with sodium ions
clustering above the calixarene cavity involving bridging water molecules, and a molecular ‘glue’ of
either DMF or carbonate ion. The DMF has a methyl group directed into the cavity of the calixarene
which takes on a 5-charge, whereas in the carbonate-containing structure the calixarene takes on an
8-charge, with a hydroxyl group coordinated to sodium directed into the cavity. The nature of the
interactions in both structures has been probed using Hirshfeld surface analysis.
Introduction
Calix[n]arenes are phenolic [1]n-metacyclophanes, obtained
through the base-induced condensation of para-substituted
phenols and formaldehyde in the presence of alkali metal
hydroxide as the templating catalyst for cyclisation.1 Interest in
these compounds is multifaceted, from their conformational
characteristics, through to their applications, which includes
catalysis, and selective and high affinity metal ion binding
incorporated in chemical sensors.1,2 Even the directly synthesised
p-tert-butylcalix[4,6,8]arenes are efficient transporters of alkali
metal ions in liquid membranes.3 The conformations of
calixarenes can be pre-organised/perturbed by shape-specific
metal…p–arene interactions within their cavities (endo-cavity
interactions) and via metal ion complexation involving the socalled lower rim phenolic oxygen centres.4 For example, the
oxygen centres in calix[4]arene in a quasi-planar arrangement
can bind to a single metal centre whereas other conformations
are possible for binding two or more metal centres.5
The supramolecular chemistry of water soluble p-phosphonatocalix[n]arenes is beginning to emerge,6 following the extensive studies
on the isoelectronic p-sulfonatocalix[n]arenes, in building intricate
architectures, in association with other supramolecular synthons in
forming multi-component arrays. p-Phosphonatocalix[n]arenes
a
Chemistry Department, Faculty of Science, University of Malaya, 50603
Kuala Lumpur, Malaysia. E-mail: [email protected];
Fax: +603 7967 4193; Tel: +603 7967 6774
b
School of Chemistry and Biochemistry, University of Western Australia,
Perth, W. A. 6009, Australia
c
Centre for Microscopy, Characterisation and Analysis, M313;
The University of Western Australia, Perth, W. A. 6009, Australia
d
Centre for Strategic Nano-Fabrication, School of Chemistry and
Biochemistry, University of Western Australia, Perth, W. A. 6009,
Australia. E-mail: [email protected]; Fax: +61 86488 1005;
Tel: +61 86488 3045
{ CCDC 892216 and 892217. For crystallographic data in CIF or other
electronic format see DOI: 10.1039/c2ce26207j
This journal is ß The Royal Society of Chemistry 2012
have potential for self association involving a large number of
different degrees of deprotonation of the diprotic phosphonic acid
moieties relative to the monoprotic sulfonic acid moieties of
p-sulfonatocalix[n]arenes.7 Both of these systems are capable of
deprotonation of the lower rim phenolic protons, as well as being
involved in weak interactions akin to self assembly, notably
p-stacking and C–H…p interplay.8,9 p-Phosphonated calixarenes
can assemble into bilayers in the solid state with the cavitands
involved in extensive hydrogen bonding between the phosphonic
acid groups and aligned to form molecular capsules;10,11 or form
nanorafts7,9 in solution and the gas phase presumably through
similar interactions, unlike for the sulfonated calixarenes. In
addition, the extra ionisable proton per upper rim functional
group makes the phosphonated calixarenes distinctly different to
the sulfonated analogues. For example, the uptake of calcium ions
in the solid state involving a similar arrangement of bilayers with
variable amounts of calcium ions incorporated between them is
associated with different degrees of deprotonation of the
phosphonic acid moeities.10,12 p-Phosphonated calix[6]arene
bearing O-methyl groups at the lower rim also binds Ca2+ ions
in the solid state, with a classical ‘double partial cone’ conformation for the hexameric ring system.12
In further developing the metal ion chemistry of p-phosphonatocalix[n]arene we have explored the binding of sodium ions
with the smallest ring system, n = 4. A focus is on understanding
how the assembled solids deal with a greater build up of charge
on the calixarene associated with varying the level of deprotonation of the phosphonic acid moieties for a simple monovalent
metal ion. We also explore the ability of the calixarene to bind a
simple imidazolium cation in its cavity, or a large cyclic
oligopeptide antibiotic, thiostrepton, to ultimately compare this
with the diversity of binding of such species with p-sulfonated
calix[4]arene, as well as facilitate the crystallisation process.
Despite the simplicity of the system, forming discrete complexes
of a p-phosphonatocalix[4]arene with sodium ions proved rather
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challenging. Two complexes were ultimately isolated and
characterised, Scheme 1, one with the calixarene taking on
5-charge, with a dimethylformamide (DMF) molecule included
in the cavity and bound to five sodium ions. The other has a
carbonate ion acting as a linker between some of the sodium
ions, with the calixarene taking on 8-charge, with a hydroxyl
group (OH2), located in the calixarene cavity on a 4-fold axis
and attached to a sodium atom (H-atom occupancy is 0.25). In
both structures there is a bilayer arrangement of calixarenes,
with the sodium ions clustering above the phosphonate moieties
associated with bridging water molecules, and the DMF
molecule, complex 1, or the carbonate ion, complex 2.
Results and discussion
Both complexes 1 and 2 have p-phosphonatocalix[4]arene
assembled in a bilayer-linear arrangement with only subtle
difference between them. This is a new structural motif for the
interplay of p-phosphonatocalix[4]arenes, which is distinctly
different to the previously reported bilayer structures containing
p-phosphonated calix[4]arene where they form ‘molecular
capsules’ with calcium ions around the equatorial seam.10 In
complexes 1 and 2 the calixarenes are assembled into an antiparallel column-like arrangement yet retaining the common
bilayer arrangement in the extended structure, having the
calixarene upper rim from one bilayer positioned directly above
the base (lower rim) of another calixarene of the next bilayer
Fig. 1. In contrast, the bilayer for the calcium complexes are
more compact having the cavities from adjacent bilayers facing
each other.10 The bilayers contain alternating layers of inorganic
as chains of sodium ions and water molecules, Fig. 1. Such
arrangement has been noted for p-sulfonatocalix[4]arene.13
The cavity of p-phosphonatocalix[4]arene is occupied by either
a DMF molecule, complex 1, or a hydroxyl group attached to a
sodium ion for complex 2. For the latter, this is despite the
presence of positively charged imidazolium ions in solution,
which are positioned outside the calixarene cavity, unlike in
imidazolium complexes of p-sulfonatocalix[4]arene.14 The phosphonate groups in complex 1 are partially protonated with a
total charge of 52. For complex 2, the phosphonic groups in the
calixarene are entirely deprotonated with a total charge of 82
and with a charge of 32 from the carbonate and hydroxyl group,
the overall electrical neutrality is satisfied by 9 sodium ions and
two imidazolium cations.
Scheme 1 Synthesis of complexes 1 and 2.
8542 | CrystEngComm, 2012, 14, 8541–8546
Fig. 1 Bilayer arrangement with chains of sodium ions for complex 1
and 2.
Crystal structure
Complex 1. Complex 1 crystallizes in the orthorhombic space
group Pmn21, Z = 2, with the asymmetric unit comprised of one
p-phosphonatocalix[4]arene molecule in the cone conformation
positioned on a crystallographic mirror plane, hosting a DMF
molecule in the hydrophobic cavity along with five aquated and
O-bridging sodium ions, in close proximity to the calixarene
upper rim. The restricted space in the cavity perturbs the shape
of the calixarene in interacting with the DMF molecule, being in
a slightly pinched cone conformation, having dihedral angles at
121.4(1)u and 126.4(1)u (calculated between the planes of the
phenyl rings and the basal plane of the four methylene carbon
atoms). Hydrogen atoms of one methyl group of the included
DMF molecule are directed towards the nearest calixarene
aromatic ring centroids, as a bifurcated C–H…p(centroid)
interaction, at a distance of 2.80 Å. The other methyl group of
the DMF molecule has its hydrogen atoms close to the
phosphonic acid oxygen atoms with C–H…O at 3.00 Å, Fig. 2.
The P–O distances range from 1.493(6) to 1.548(5) Å (consistent
with the P–O distances of phosphoric acid15), reflecting partial
deprotonation of the phosphonic acid groups.
The interactions of the solvent molecule with its surroundings,
and the overall interactions in the complex, have been
investigated using Hirshfeld surface analysis (generated from
CrystalExplorer16). The breakdown of the fingerprint plot for
pattern identification associated with specific interactions such
Fig. 2 Stick representation for complex 1 showing close contacts of
solvent molecule with calixarene (black dotted lines = C–H…p(centroid)
interaction, yellow dotted lines = C–H…O interaction).
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as hydrogen bonding and C–H…p(centroid) interaction is
depicted in Fig. 3. The red regions illustrated by the dnorm
surface for complex 1 imply that the intermolecular contacts
between the calixarene and the solvent molecule are closer than
the van der Waals separation. Quantitative analysis shows that
complex 1 contains the highest fraction (42%) of H…H contacts,
26% of C–H…O contacts (acceptor), 16% of C–H…O contacts
(donor), while the lowest fraction (14%) corresponds to C–
H…p(centroid) contacts. Also, the interactions are evident on
the shape index and curvature mapped using the Hirshfeld
surface analysis where bright red spots (concave regions) on the
shape index surface and a visible large flat area in the centre of
the cavitand depict the characteristic close contacts between the
molecules, Fig. 4.
A stunning motif/arrangement in complex 1 is the interaction
between the embedded DMF molecule and sodium ions with
multiple coordination environments, Fig. 5a. Firstly, the DMF
oxygen atom is bound to three fully occupied sodium ions; with
Na1 atom positioned on a crystallographic mirror plane, and
coordinated by six oxygen atoms. The adjacent sodium ion Na2
has five oxygen atoms in the coordination sphere with two of
Fig. 3 Hirshfeld surface analysis for complex 1 showing C–
H…p(centroid) and C–H…O interactions with the corresponding
fingerprint plots (below).
This journal is ß The Royal Society of Chemistry 2012
Fig. 4 Shape index (a) and curvature (b) for the calix[4]arene in
complex 1.
them bridging to another sodium ion, Na3. In turn Na3 is
further connected (via bridging) to adjacent sodium ions, and
such interactions propagate along the c axis forming linear
arrays which engage the calixarenes in a ‘hand-in-hand’ manner,
Fig. 5b and c. The penta sodium complex of the corresponding
p-sulfonated calix[4]arene has been structurally authenticated,
with one of the phenolic groups deprotonated with a sodium
bound to the oxygen centre.8,17 In the present structure there is
no such deprotonation, which is not surprising given the
additional ionisable proton per upper functional group.
The p-phosphonated calix[4]arenes in complex 1 can be
considered as being arranged in bilayers, Fig. 6, but they are
rather open, unlike the compact bilayers in the calcium
complexes and the structure of the parent phosphonic acid.9,10
Fig. 5 Ball and stick representation for (a) the coordination environment of the sodium ions, Na–O contacts 2.296(11) to 3.015(9) Å, and (b)
the ‘hand-in-hand’ arrangement of calixarenes in complex 1. Sodium ion
network in the extended structure, viewed along b axis (c).
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Fig. 6 Projection down (a) a axis and (b) b axis showing the extended
structure for the complex 1.
In 1, a cavity of one calixarene is skewed relative to the cavity of
a calixarene in the next bilayer. The bilayers are ca. 11 Å thick
and involve linear arrays of the calixarenes units with the
included DMF solvent molecule in the cavity and are stabilized in part by the electrostatic interaction of the polymeric
coordinated sodium ions in the hydrophilic region, i.e. the
negative charge on the calixarene is balanced by the clustering of
sodium ions involving bridging water molecules. The distance
between neighbouring calixarenes is now significantly larger,
with no p…p interactions found in the compact bilayers of the
calixarene.8 The inorganic layer is ca. 5 Å thick and there is no
hydrogen bonding between phosphonic acid groups across
different bilayers.
Complex 2. Complex 2 with a composition of one calixarene,
two disordered 1-ethyl-3-methylimidazoliums, one disordered
carbonate ion, nine aquated sodium ions along with eight
crystalline water molecules, crystallizes in the tetragonal space
group P4/ncc, Z = 4. The overall three-dimensional arrangement
can be described as a bilayer system in which the tetragonal axis
is normal to the bilayers with the cone-shaped calix[4]arenes
residing on a 4-fold symmetry axis with dihedral angles of
117.9(1)u. The imidazolium molecules have a partial occupancy
of 0.25 and are positioned exo relative to the calixarene, close to
four calixarene phenyl rings with p(centroid)…p(centroid)
separation at 3.55 Å along with hydrogen bonding to the
calixarene methylene bridge with close C–H…H–C contacts at
2.33 to 2.45 Å. This is in contrast to our previous structures
involving sulfonated calixarenes where the imidazolium head
group is selectively drawn into the cavity of the calixarene.14
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Fig. 7 Space filling representation of disordered carbonate ion (light
blue) in complex 2 along with: (a) stick representation of close contacts of
aquated sodium network with calixarene (black dotted lines = hydroxyl
O–H…p(centroid) interaction, yellow dotted lines = water O–H…O
phosphonate interaction). (b) Ball and stick showing the aquated sodium
ion network. (c) Sodium ion network in the extended structure, viewed
along c axis.
The sodium ions in complex 2 have coordination numbers of
5 (Na1), 6 (Na3) and 7 (Na2). Na1 resides in the centre of the
calixarene upper rim, parallel to the plane of the four
phosphonate groups, Fig. 7a and b. In addition, the coordinated
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oxygen lying on a C4 crystallographic symmetry axis (O5) is
embedded in the calixarene cavity, as a hydroxyl group, which is
reflected in the much shorter Na–O distance (2.292(2) Å) relative
to the other Na–O contacts (2.3529(11) to 2.9090(11) Å). The
associated hydrogen atom is disordered, and interacts with the
phenyl ring with a short O…p(centroid) distance at 3.46 Å and
the H…p(centroid) separation at 2.64 Å. This interaction relates
to such interactions of water molecules embedded in the cavity of
sulfonated calix[4]arenes.13,18 Other sodium ions form a complicated network at the hydrophilic region of the calixarene,
Fig. 7c, which mimics an arrangement of a cage molecule, and
the hydrated sphere has hydrogen bonding to the phosphonate
groups with short separations from P–O…H–O 1.92 to 2.86 Å.
All the oxygen atoms of the phosphonate group are now
deprotonated with similar P–O distances of 1.5243(10) to
1.5291(10) Å. The intermolecular interactions are evident in
the Hirshfeld surface analysis where the O–H…O hydrogen
bonding is the main contributor with the highest fraction (46%)
while O–H…p(centroid) (15%) and H…H hydrogen bonding
(35%) complete the remaining fractions, Fig. 8.
In the extended structure of complex 2, the bilayer arrangement is ca. 11 Å thick with the inorganic layer ca. 5 Å thick
which is comparable to complex 1, as is the lack of alignment of
calixarenes into the ‘molecular capsules’ arrangement, Fig. 9.
The independent cavity of one calixarene resides directly above
the base of another calixarene with the bilayers separated by the
aquated sodium ions and water molecules. The upper rims are
not facing each other and the structure is also devoid of p…p
interactions between calixarenes.
Fig. 9 Projection down (a) a axis and (b) c axis showing the extended
structure for the complex 2.
Fig. 8 (a–c) Fingerprint plots for complex 2 showing O–H…p(centroid), O–H…O and H…H hydrogen bonding of the disordered included sodiumbound water molecule with the calixarene inner surface, (d–f) corresponding Hirshfeld surfaces.
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Conclusions
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We have gained insight into the complexation of p-phosphonated
calix[4]arene with sodium ions. The presence of other species to act
as a form of glue for bringing sodium ions together above the upper
rim of the macrocycle, either as a DMF molecule, or as a carbonate
ion is noteworthy. The role of these species to assist in clustering of
positively charged sodium ions represents an important factor in
balancing the significant negative charge on the calixarene. Indeed,
the use of other species to act in the same way is likely to be an
important design strategy in building complex arrays of this and the
other phosphonate-rich calix[n]arene.
Experimental
Synthesis of 1 and 2
p-Phosphonatocalix[4]arene,7 was synthesized according to
literature procedures. Slow evaporation of a 24 : 24 : 1
DMF : H2O : EtOH solution of p-phosphonatocalix[4]arene–
thiostrepton (1 : 1) resulted in the formation of large colourless
single crystals of complex 1 which were suitable for X-ray
diffraction studies. For complex 2, reaction of the p-phosphonic
acid calix[4]arene and 1-ethyl-3-methylimidazolium chloride
dissolved in water followed by concentration by slow evaporation, reproducibly afforded suitable crystals for X-ray diffractions studies after several days. The pH of water was adjusted to
11 by the addition of NaOH for both complexes. Several crystals
were checked for cell dimensions in establishing the homogeneity
of the materials.
X-ray crystallography
Data were measured from single crystals using an Oxford
Diffraction Gemini-R diffractometer at T = 100(2) K with
monochromatic Mo Ka radiation (l = 0.71073 Å). Following
analytical absorption corrections and solution by direct methods, the structure was refined against F2 with full-matrix leastsquares using the SHELXL-9719 and X-seed20 interface crystallographic package. Lp and absorption corrections applied.
Complex 1: C28H23O16P452, (C3H49NNa5O22)5+, 17(H2O),
C31H106NNa5O55P4, M = 1612.00, colourless plate, 0.66 6
0.40 6 0.10 mm3, orthorhombic, space group Pmn21 (No. 31),
a = 16.2938(4), b = 16.3581(3), c = 16.3290(4) Å, V = 4352.26(17)
Å3, Z = 2, Dc = 1.230 g cm23, m = 0.204 mm21. F000 = 1708,
2hmax = 58.4u, 62 012 reflections collected, 11 226 unique (Rint =
0.0611). Final GooF = 1.005, R1 = 0.0749, wR2 = 0.2006, R
indices based on 9008 reflections with I > 2s(I) (refinement on
F2), |Drmax| = 1.0(1) e Å23, 465 parameters, 1 restraint. Lp and
absorption corrections applied. Absolute structure parameter =
0.52(17) (H. D. Flack, Acta Crystallogr., 1983, A39, 876–881).
CCDC number = 892216.
Complex 1 is a pseudo-merohedral twin and the TWIN law
was employed during refinement.
Complex 2: C28H20O16P482, [Na9+, OH2, CO322, 28(H2O)],
2(C6H11N2+), 8(H2O), C41H115N4Na9O56P4, M = 1891.16,
colourless plate, 0.28 6 0.20 6 0.05 mm3, tetragonal, space
group P4/ncc (No. 130), a = b = 16.1842(4), c = 31.2772(7) Å,
V = 8192.4(3) Å3, Z = 4, Dc = 1.533 g cm23, m = 0.250 mm21.
F000 = 3984, 2hmax = 58.5u, 100 245 reflections collected, 5441
8546 | CrystEngComm, 2012, 14, 8541–8546
unique (Rint = 0.1260). Final GooF = 1.005, R1 = 0.0475, wR2 =
0.0966, R indices based on 2708 reflections with I > 2s(I)
(refinement on F2), |Drmax| = 1.12(7) e Å23, 286 parameters,
39 restraints. CCDC number = 892217.
Acknowledgements
We thank the University of Malaya (HIR UM-MOHE F0000421001), The University of Western Australia, and the Australian
Research Council for supporting this work. The authors
acknowledge the facilities, scientific and technical assistance of
the Australian Microscopy & Microanalysis Research Facility at
the Centre for Microscopy, Characterisation & Analysis, The
University of Western Australia, funded by the University, State
and Commonwealth Governments.
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