A thiourea calix[6]arene-based synthon that generates a supramolecular porous crystal structure

Article abstract of DOI:10.1080/10610278.2013.814777

The role of intra- and intermolecular interactions which lead to the self-assembly in a porous crystalline structure of a thiourea-based calix[6]arene synthon containing three thiourea groups, has been investigated by X-ray diffraction and quantum chemical calculations. 2013

Full text of DOI:10.1080/10610278.2013.814777

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Supramolecular Chemistry
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A thiourea calix[6]arene-based synthon that generates
a supramolecular porous crystal structure
Arturo Arduini a , Rocco Bussolati a , Chiara Massera a , Andrea Pochini a , Federica
Rapaccioli a , Andrea Secchi a & Franco Ugozzoli a
a Dipartimento di Chimica , Università degli Studi di Parma , Parco Area delle Scienze 17/A,
I-43124 , Parma , Italy
Published online: 28 Aug 2013.
To cite this article: Supramolecular Chemistry (2013): A thiourea calix[6]arene-based synthon that generates a
supramolecular porous crystal structure, Supramolecular Chemistry, DOI: 10.1080/10610278.2013.814777
To link to this article: http://dx.doi.org/10.1080/10610278.2013.814777
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Supramolecular Chemistry, 2013
http://dx.doi.org/10.1080/10610278.2013.814777
A thiourea calix[6]arene-based synthon that generates a supramolecular
porous crystal structure
Arturo Arduini*, Rocco Bussolati, Chiara Massera, Andrea Pochini, Federica Rapaccioli, Andrea Secchi and
Franco Ugozzoli*
`
Dipartimento di Chimica, Universita degli Studi di Parma, Parco Area delle Scienze 17/A, I-43124 Parma, Italy
(Received 15 May 2013; final version received 6 June 2013)
The role of intra- and intermolecular interactions which lead to the self-assembly in a porous crystalline structure of a
thiourea-based calix[6]arene synthon containing three thiourea groups, has been investigated by X-ray diffraction and
quantum chemical calculations.
Keywords: calix[6]arenes; self-assembly; X-ray diffraction; quantum chemical calculations; thioureas
1. Introduction
2. Results and discussion
Because of their extreme versatility, calix[n]arenes have
been extensively employed as molecular platform to orient
in space functional groups and binding sites yielding a large
variety of receptors for ions and neutral molecules (1).
More recently, they demonstrated their potential also for the
construction of self-assembled supramolecular species (2).
In this latter context, non-covalent intermolecular inter-
actions have been exploited as driving force for the
formation and for the design of dimeric (3) or tubular (4)
supramolecular architectures. We have recently shown that
heteroditopic calix[4]arene and calix[6]arene derivatives,
when mixed with suitable ion pair-based guests, may give
rise to highly ordered aggregates of self-assembled
capsules (5) and oriented channels (6) in the solid state.
Among the several non-covalent interactions responsible of
the formation of these supramolecular architectures, the
bifurcated H-bonding between the phenylurea moieties
present on the wide rim of these macrocycles and the anion
of the ion pairs plays a fundamental role. On the other side,
the role that these urea-type additional binding units play on
the conformational preferences of the macrocycles and on
the tuning of their self-assembly properties has been far less
studied. Based also on our previous studies on model urea-
type compounds (7), herein we report on the structural and
quantum mechanical studies of a thiourea-based calix[6]
arene compound whose molecular conformation allows the
self-organisation in one-dimensional polymeric chains via
multiple intra- and intermolecular hydrogen bonds. The
self-assembly of the polymeric chains in the crystal lattice
generates a porous crystalline structure.
The thiourea calix[6]arene 5 was prepared using the
synthetic pathway illustrated in Scheme 1 and fully
characterised through NMR and mass measurements.
Crystals suitable for X-ray diffraction measurements
were obtained from slow evaporation of a solution of 5 in
toluene. The single crystal X-ray structure is illustrated in
Figure 1. The macrocycle is blocked in a ‘1,2,3-alternate’
conformation by the two intramolecular hydrogen bonds
involving the thiourea nitrogen atoms N2A and N2E (see
Table 1).
The stronger N2EZH· · ·O2C attraction [H· · ·O1C
˚
2.142(2) A] involves the ether oxygen O2C blocking the
phenolic rings E and C in the mutual transorientation. At
the same time, the weaker intramolecular hydrogen bond
˚
N2AZH· · ·O1B [H· · ·O1B 2.470(2) A] orients the pheno-
lic ring B in trans with respect to ring A. In such a way, the
role of the two intramolecular hydrogen bonds becomes
pivotal for the pre-organisation of the macrocycle towards
two different kinds of non-covalent intermolecular
interactions between individual calix[6]arenes. This
leads to very large spatial separations between the three
thiourea groups. In particular, those at rings A and E are
exposed at the molecular surface with their donor N1ZH
and acceptor S1 groups available for multiple cooperative
hydrogen bonding. The third thiourea group at the
phenolic ring C protrudes outside the macroring acting
as a long ‘tong’ towards the neighbouring calix[6]arene
via hydrogen bonds through their N2ZH and S1 groups as
illustrated in Figure 1.
*Corresponding authors. Email: arturo.arduini@unipr.it; franco.ugozzoli@unipr.it
q 2013 Taylor & Francis

2
A. Arduini et al.
Scheme 1.
The complete and unequivocal description of the
Table 1. Intra- and intermolecular hydrogen bonds in 5.
conformation of the macrocycle is accounted by both the
dihedral angles d between the weighted least-squares plane
through the four methylene bridging groups which link the
six aromatic rings and the weighted least-squares planes
through the six benzene rings (8) and by the confor-
mational parameters f and x (1b, 9) collected in Table 2.
The sequence of signs of f and x indicates that the
symbolic representation of the molecular conformation of
the macrocycle is C1þþ, 2þ , 2þ , 22 ,
þ2 , þ2 .
˚
D· · ·A (A)
˚
H· · ·A (A)
Bond
DZH· · ·A (8)
N2AZH· · ·O1Ba
N2E-H· · ·O2Ca
N2C-H· · ·S1Cb
N1A-H· · ·S1Ec
N1E-H· · ·S1Ac
3.185(3)
2.946(3)
3.271(3)
3.297(3)
3.357(3)
2.470(2)
2.142(2)
2.492(1)
2.476(1)
2.537(1)
138.8(2)
151.6(2)
147.8(2)
155.6(2)
155.5(2)
a Intramolecular hydrogen bond.
b Symmetry equivalent: 2x 2 1, 2y, 1 2 z.
c Symmetry equivalent: 2x, 1 2 y, 2z.
In the symmetry-expanded structure, infinite one-
dimensional polymeric chains are generated by two
different sets of four and two hydrogen bonds,
respectively, as illustrated in Figure 2. The four hydrogen
bonds allow the formation of a centrosymmetric dimer due
to one calix[6]arene which donates the two N1AZH and
N1EZH hydrogen bonds to the acceptor sulphur atoms
Table 2. Dihedral angles d (8) between the molecular reference
plane R (the weighted least-squares plane through the four CH2
groups which link the four aromatic rings) and the weighted least-
squares planes of the benzene rings; conformational parameters
f and x (8) in the molecular structures of 5.
d (8)
f (8)
x (8)
Figure 1. (Colour online) Stick view of the molecular
conformation of 5. Elements mapping: C, white circles; O,
dark grey circles; N, white circles with grids; S, shaded large
white circles. Only relevant hydrogen atoms are reported for
clarity (small white circles). Intramolecular hydrogen bonds
evidenced by dashed lines.
R^A
R^B
R^C
R^D
R^E
80.7(5)
291.5(8)
216.4(6)
282.1(6)
80.7(7)
A–B
B–C
C–D
D–E
E–F
93.6(3)
210.9(4)
294.3(4)
2105.1(5)
28.7(3)
97.5(4)
88.7(5)
31.7(3)
293.8(4)
281.9(4)

Supramolecular Chemistry
3
Figure 2. (Colour online) Perspective view of the one-dimensional polymeric chain of 5 with intermolecular hydrogen bonds evidenced
by dashed lines (crystallographic centres of symmetry evidenced by black spots).
S1E and S1A of the adjacent calix[6]arene at the
equivalent position 2x, 1 2 y, 2z. At the same time,
it accepts with its S1E and S1A the hydrogen bonds
donated by the N1AZH and N1EZH groups of the
symmetry-related calix[6]arene at the equivalent position
2x, 1 2 y, 2z.
In order to highlight this aspect, we performed
extensive quantum chemical calculations addressed
to a characterisation of the electron density displacement
Dr(x, y, z) during the formation of complexes A and
B. More in detail, Dr(x, y, z) (calculated as difference
betweenthe electron density of the complex and thoseof the
individual monomers) is a measure of the electronic charge
that is accumulated or depleted at each point within the
complex and provides directly the whole spatial extent of
the charge fluctuation. In this way, the chemical meaning of
Dr(x, y, z), is free from the arbitrariness inherent in any
charge decomposition model. The isosurfaces of the Dr(x,
y, z) maps for complexes A and B are plotted in Figure 3 and
clearly show that in complex A the charge shift occurs only
within the region of the two hydrogen bonds. On the
contrary, due to the close proximity between monomers in
complex B, the charge shift is not restricted to the four
As shown in Figure 2, the two thiourea groups which
protrude from both sides of the dimer at the phenolic rings C
become the structure-directing factor for the self-assembly
of the dimers in infinite one-dimensional polymeric chains
via two hydrogen bonds: the N2CZH group donates the
hydrogen bond to the acceptor sulphur atom S1C of the
nearest neighbouring dimer at the equivalent position
2x 2 1, 2y, 1 2 z; vice versa, the N2CZH group donates
the hydrogen bond to the sulphur S1C atom of the previous
dimer. It is noteworthy that the four and two sets of multiple
hydrogen bonds lie on two non-equivalent crystallographic
inversion centres as shown in Figure 2. However, the
mechanistic hypothesis that the self-assembly in dimers
occurs prior polymerisation, is based on the assumption that
a greater driving force is expected for four hydrogen bonds
rather than for two. To give a theoretical ground to our
hypothesis, the binding processes for dimerisation and
polymerisation were investigated separately by quantum
chemical calculations. To this purpose, due to the enormous
number of atoms which prevents the use of rich basis sets,
the quantum mechanical calculations were carried out with
a semiempirical method at PM6 level (10). After having
minimised the molecular geometry of the monomer, two
modelshavebeen selected: complexA for calculation of the
binding energy under polymerisation and complex B for
calculation of the binding energy involved in the
dimerisation process. The two structures were then
minimised and their final geometries are shown in Figure 3.
The calculated binding energies are 229.78 kJ/mol in
complex A and 290.24 kJ/mol in complex B, confirming
that the highest attraction (the energy is more negative)
occurs in the dimerisation of calix[6]arenes via four
hydrogen bonds. However, such difference between the two
energy values suggests that the greater attraction between
the two calix[6]arenes in complex B is due to the
contribution of other weak non-covalent interactions beside
hydrogen bonds.
Figure 3. (Colour online) Calculated isosurfaces at 0.0008 e/
bohr3 of the charge displacement Dr(x, y, z) in complex A (top)
and B (bottom). The total displaced charge is 0.61 and 1.57 e,
respectively. Colours: violet, positive Dr values (accumulation of
charge); brown, negative Dr values (depletion of charge).

4
A. Arduini et al.
Figure 4. (Colour online) Stick view of 27 unit cells (3a·3b·3c) showing the self-assembly of 5 in the crystal lattice. The voids left by the
tubular pores running along the crystallographic a-axis are evidenced by dashed circles.
hydrogen bonds but it spreads as far as the macrocycles,
suggesting that the mutual polarisation between monomers
also contributes to stabilise the complex. This is also
supported by the calculation of the total amount of
displaced electric charge: 0.61 and 1.57 e in the two
complexes. All these theoretical results support the
hypothesis that the final observed crystal structure is the
result of the polymerisation process after dimerisation. The
symmetry expansion extended to 27 unit cells (3a·3b·3c)
shows a tertiary structure generated by the self-assembly of
the one-dimensional polymeric chains in the crystal lattice
as depicted in Figure 4. The polymeric chains, elongated
parallel to the crystallographic bc plane, generate a porous
structure with the channels running along the crystal-
lographic a-axis. This justifies the calculated density value
(0.899 g £ cm23) lower than what could be expected for an
organic compound. The estimated percentage of volume of
the tubular pores does correspond to the10% of the cell.
self-assembly of the polymeric chains in the crystal lattice.
Quantum mechanical calculations have been carried out to
demonstrate that polymerisation process should follow the
formation of the dimers, the latter being more energeti-
cally favoured with respect to the polymerisation.
4. Experimental
4.1 General
All reactions were carried out under nitrogen; all solvents
were freshly distilled under nitrogen and stored over
molecular sieves for at least 3 h prior to use. Chemical shifts
reported are referred either to the tetramethylsilaneorresidual
solved resonances. ESI-MS spectra were recorded with a
Waters Acquity UPLC system (Waters Corporation, Milford,
MA, USA). Meltingpointsare uncorrected and were recorded
with an Electrothermal instrument (Bibby Scientific Limited,
Stone, Staffordshire, UK). Silica gel layers (SiO2, Merck
60 F254, Merck KGaA, Darmstadt, Germany) were used for
˚
thin layer chromatography. A 60 A silica gel (Merck, 0.04–
3. Conclusions
0.063mm, 230–240 mesh) were used for column chroma-
tography. Compounds 3 and 4 were synthesised according to
reported procedures (11). All other reagents were of reagent
grade quality as obtained from commercial suppliers and
were used without further purification.
The urea-type moieties attached to the wide rim of a calyx
[6]arene have been exploited to make the conformation of
the macrocycles pre-organised for their self-assembly in
infinite polymeric chains. X-ray diffraction analysis on
single crystal has shown that thiourea groups are not only
responsible of the 1,2,3-alternate conformation of the
macrocycle via intramolecular hydrogen bonds, but also of
the formation of one-dimensional polymeric chains of
dimers via intermolecular hydrogen bonds. A porous
crystalline structure is generated as tertiary structure by the
4.2 Synthesis
4.2.1 Tris-(N-phenylthioureido)calix[6]arene (5)
To a solution of calix[4]arene 5 (0.8 g, 0.7 mmol) in dry
CH2Cl2 (25 ml), phenyl isothiocyanate (0.5 g, 3.7 mmol)

Supramolecular Chemistry
5
was added. After stirring overnight at room temperature,
the reaction was quenched by the addition of 20 ml of
water. The organic phase was separated, dried over
anhydrous Na2SO4 and evaporated to dryness under
reduced pressure. Pure compound 5 was obtained in 20%
yield after chromatographic separation of the residue
(n-hexane:ethyl acetate ¼ 3:2) as pale yellow solid.
set. Final unit cell constants were calculated using SAINT
on the final merged data-sets. All the data were corrected
for Lorenz, polarisation and absorption using SADABS
(13). The structure was solved by direct methods using the
SIR2004 program (14) and refined on F2o by full-matrix
least-squares procedures using the SHELXL-97 program
(15) in the WinGX suite (16). All non-hydrogen atoms
were refined with anisotropic atomic displacements
excepting the carbon atoms of the benzene ring attached
to N2C and the five carbon atoms of the ether chains which
were refined with isotropic atomic displacements. The
hydrogen atoms were included in the refinement at
1
mp . 3008C; H NMR (300 MHz, CDCl3): d 8.5 (br. s,
3H), 8.2 (br. s, 3H), 7.8–7.7 (m, 6H), 6.4 (br. s, 6H), 4.7
(br. s, 6H), 4.0 (br. s, 6H), 3.6 (br. s, 6H), 3.6–3.5
(m, 12H), 2.6 (br. s, 9H); 1.36 (s, 27H), 1.25 (t, 9H,
J ¼ 7 Hz); 13C NMR (100 MHz, CDCl3): d 154.6, 153.5,
146.7, 138.0, 136.4, 132.8, 129.5, 128.9, 127.9, 125.9,
124.7, 118.2, 72.3, 69.8, 66.9, 60.8, 34.3, 31.6, 15.3; MS
(ESI): m/z (%): 1537 (100) [M þ Na]þ.
˚
idealised geometry (C–H 0.95 A) and refined ‘riding’ on
the corresponding parent atoms with isotropic atomic
displacement 1.2 times that of the parent atom. The
weighting scheme used in the last cycle of refinement was
w ¼ 1=½s2F2oꢀ. Crystallographic data (excluding structure
factors) for the structure reported have been deposited with
the Cambridge Crystallographic Data Centre with
supplementary publication no. CCDC-928852 and can be
obtained free of charge on application to the CCDC, 12
Union Road, Cambridge, CB2 IEZ, UK (fax: þ44 1223
336 033; e-mail: deposit@ccdc.cam.ac.uk or http://www.
ccdc.cam.ac.uk).
4.3 X-ray crystallographic analysis
Crystal data and experimental details for data collection
and structure refinement are reported in Table 3. The
crystal structure of 5 was determined by X-ray diffraction
methods. Intensity data and cell parameters were recorded
at 190(2) K on a Bruker APEX II (Mo Ka radiation
˚
l ¼ 0.71073 A) equipped with a charge-coupled device
(CCD) area detector and a graphite monochromator.
Orientation matrices and unit-cell parameters were
improved by least-square refinement of reflections,
integrated with SAINT (12) taken from the entire data-
4.4 Calculations
All calculations were carried out with the Gaussian 09
program (17) using the semiempirical PM6 method. The
calculation of the electron density difference Dr(x, y, z)
three-dimensional map was carried out with the pixel
method: the cubes of the electron densities of the dimer
and of those of the two individual monomers were
Table 3. Crystal data and structure refinement information
for 5.
Chemical formula
C90H108N6O9S3
Formula weight
Crystal system
Space group
1514.058
Triclinic
P–1
15.401(9)
15.986(9)
24.510(9)
82.96(1)
78.21(1)
71.64(1)
5595(5)
2
0.899
1.111 (Mo Ka)
49.35
190
˚
generated at the PM6 level using a grid of 0.2£0.2 £ 0.2 A
3
(the volume of each pixel was of 0.008 A ) and the Dr(x, y,
˚
˚
z) cube was calculated by subtracting pixel by pixel the
electron densities of the two monomers from the electron
density of the dimer, and this leads to regions where the
electron density increases (positive Dr values) and regions
depleted of electron density (negative Dr values). The total
displaced charge in a dimer was calculated as a sum over
all the positive Dr values in the cube of the Dr(x, y, z). This
value is of course equal to the sum over all the negative Dr
values in the cube.
a (A)
˚
b (A)
˚
c (A)
a (8)
b (8)
g (8)
3
˚
V (A )
Z
rcalc. (g/cm3)
m (cm21
)
2u max for data collection (8)
Temperature (K)
Data collected (h, k, l)
Total reflections
Unique reflections
(217, 218, 228) to (17, 18, 28)
56,093
56,093 (Rint ¼ 0)
13,795 [Fo . 4.0s(Fo)]
56,093/15/881
0.510
Acknowledgements
This work was supported by the Italian MIUR (PRIN
2008HZJW2L and PRIN 2010CX2TLM) and by the University
of Parma.
Observed reflections
Data/restraints/parameters
Goodness-of-fit on F 2a
Final R indices (obs. data)b
Largest diff. peak and
R1 ¼ 0.0652, wR2 ¼ 0.0066
0.40/–0.26
23
)
˚
hole (e/A
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a Goodness-of-fit S ¼ ½ wðFo2 2 F2cÞ =ðn 2 pÞꢀ
,
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.
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Supramolecular Chemistry
7
Arturo Arduini, Rocco Bussolati, Chiara Massera, Andrea Pochini,
Federica Rapaccioli, Andrea Secchi and Franco Ugozzoli
A thiourea calix[6]arene-based synthon that generates a supramolecular
porous crystal structure
1–7