From chains to ladders in co-crystals with 2,3-thiophene-15-crown-5, 2,3-naphtho-15-crown-5, and bis-(18-crown-6)-stilbene constructed by weak hydrogen bonding

Article abstract of DOI:10.1039/c005284c

For the first time a series of co-crystals of 2,3-thiophene-15-crown-5 1, 2,3-naphtho-15-crown-5 2, bis-(18-crown-6)-stilbene 3 with dithiooxamide a, 1,2,5-oxadiazole-3,4-diamine b, and 3-nitro-1H-1,2,4-triazole c with compositions 1a, 2a, 2b·H₂O, 2c, and 3a₂ were prepared and their structures were studied by X-ray crystallography. The components in the co-crystals demonstrate the different modes of mutual arrangement and contribution of diverse weak interactions to the final architecture. Infinite chains of the alternating component molecules linked by N-H...O hydrogen bonds characterise the structures of 1a and 2a, whereas in the case of 3a₂ formation of the loosely packed ladder-type structure was observed. In 2b·H₂O the planar naphtho- and oxadiazole moieties demonstrate their edge-to-face arrangement, while in 2c the partially overlapping naphtho- and triazole moieties provide effective face-to-face π-π stacking interactions. The improved synthetic strategy for 1 and 2 is given.

Full text of DOI:10.1039/c005284c

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From chains to ladders in co-crystals with 2,3-thiophene-15-crown-5,
,3-naphtho-15-crown-5, and bis-(18-crown-6)-stilbene constructed by
weak hydrogen bonding†
2
a
b
b
c
d
Eduard V. Ganin, Stepan S. Basok, Arkadii A. Yavolovskii, Mark M. Botoshansky and Marina S. Fonari*
Received 30th April 2010, Accepted 6th August 2010
DOI: 10.1039/c005284c
For the first time a series of co-crystals of 2,3-thiophene-15-crown-5 1, 2,3-naphtho-15-crown-5 2, bis-
(
18-crown-6)-stilbene 3 with dithiooxamide a, 1,2,5-oxadiazole-3,4-diamine b, and 3-nitro-1H-1,2,4-
triazole c with compositions 1a, 2a, 2b$H O, 2c, and 3a were prepared and their structures were
2
2
studied by X-ray crystallography. The components in the co-crystals demonstrate the different modes
of mutual arrangement and contribution of diverse weak interactions to the final architecture. Infinite
chains of the alternating component molecules linked by N–H/O hydrogen bonds characterise the
2
structures of 1a and 2a, whereas in the case of 3a formation of the loosely packed ladder-type structure
was observed. In 2b$H O the planar naphtho- and oxadiazole moieties demonstrate their edge-to-face
2
arrangement, while in 2c the partially overlapping naphtho- and triazole moieties provide effective face-
to-face p–p stacking interactions. The improved synthetic strategy for 1 and 2 is given.
Introduction
increased selectivity towards the complexing species. This is the
case for photochromic crown ethers, which allow the photo-
chemical control of cation binding, as well as for some optical
sensors, designed for cation recognition. The intermolecular
sandwich complexes based on bis-crown ethers range from
discrete face-to-face arrangements to extended supramolecular
architectures, which can generate nanosized aggregates and
materials. The variety of possible combinations with cations
bestows a particular interest in bis-crown dyes.
Crown ethers are widely utilised as efficient polydentate ligands
1
for metal and ammonium ions as well as for neutral species.
Supramolecular systems combining crown ethers and light-
absorbing groups attract considerable attention as they have
2
a potential for use in optical sensors for metal ions and in
3
photoswitchable molecular devices. The common approach in
this area is the organic functionalisation of the classic crown
4a,c
ethers with chromophoric substituents (e.g., anthracene, azo-
b,d
benzene,
The crown ethers and co-crystal partners used in the present
study are summarised in Scheme 1.
4
4e
4f
stilbene, or trityl ). The photoswitchable crown
compounds are created using functional groups that can undergo
5
substantial structural changes under the action of light.
The present article is aimed at the co-crystals of 2,3-thiophene-
9
5C5 1, intensively exploited nowadays 2,3-naphtho-15C5 2,
1
So far typical 2,3-naphtho crown ethers, involving one or two
large naphthylene groups, such as N15C5, N18C6 and DN18C6,
have been widely used in the field of electrochemistry and some
of their coordinating behaviors in solutions have been studied by
and promising bis-18C6-stilbene 3 (Scheme 1). Owing to their
bulky substituents, these crown ethers present non-covalent
6
CV and ESI-MS methods. Alongside, classic crown ethers
functionalised by the attachment of chromophoric or photo-
switchable units to the crown ether skeleton or incorporation of
7
a signal fragment into the crown framework, bis-crown ethers
with chromophoric or electron switchable bridges are the subject
8
of great interest nowadays. The crucial advantage of these
crowns is their possibility to act in a concerted way, thus forming
sandwich complexes around the guest. This often leads to
a
Odessa State Environmental University, Ministry of Education and
Science of Ukraine, Lvovskaya str., 15, 65016 Odessa, Ukraine. E-mail:
edganin@gmail.com
b
A.V. Bogatsky Physico-Chemical Institute, National Academy of Sciences
of Ukraine, Lustdorfskaya doroga 86, 650080 Odessa, Ukraine
c
Schulich Faculty of Chemistry, Technion-Israel Institute of Technology,
Technion City, 32000, Haifa, Israel. E-mail: botoshan@tx.technion.ac.il
d
Institute of Applied Physics, Academy of Sciences of Moldova, Academy
str., 5, MD2028 Chisinau, Moldova. E-mail: fonari.xray@phys.asm.md;
Fax: (+373 22) 72 58 87; Tel: (+373 22) 73 81 54
† CCDC reference numbers 771037–771042. For crystallographic data in
CIF or other electronic format see DOI: 10.1039/c005284c
Scheme 1 Structural formulae with crystallographic numbering.
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Scheme 2
forces in the crystal such as p–p stacking and cation–p inter-
actions, occurring between themselves or with the guest mole-
cules. Moreover, one can expect the contribution of sulfur of the
thiophene moiety for intermolecular interactions. No structural
data are available so far either for 1 or for its larger analogues
both in pure or complexed form. For 3 such information is
restricted by the macrocycle itself along with its two smaller
homologues and photosensitive co-crystallisation compound of
Scheme 3
and 3a
2
(where a ¼ dithiooxamide, b ¼ 1,2,5-oxadiazole-3,4-
3
with 1,2-bis[1-(3-ammoniopropyl)-4-pyridiniumyl]ethylene
diamine b, and c ¼ 3-nitro-1H-1,2,4-triazole) we present herein
the improved synthetic strategy for 1 and 2.
8
tetraperchlorate. This complex has a very high thermodynamic
stability that is provided by two-center host–guest bonding. Up
until now, structurally studied 15- or 18-membered 2,3-naphtho
10,11
crown ether complexes include preferably Na and K salts.
Experimental
Dou and co-authors on a series of these complexes have
demonstrated the contribution of p–p interactions between the
naphtho-units to the supramolecular organisation of the
complexes built on strong metal–Ocrown interactions. Two types
of the stacking models, between the inner and external aromatic
rings were found and discussed. On the other hand, Kiviniemi
and co-workers have studied the complexation of biologically
important aromatic, nitrogen-containing cations with various
Synthesis
Commercially available a–c from Aldrich Chemical Co trade
were used as purchased. 1 and all co-crystals were analysed for C,
H, N and S in a Perkin Elmer 240C instrument. Crystals suitable
for the X-ray diffraction experiments were isolated from the mass
of crystals obtained. Suitable microanalyses were obtained for all
compounds.
1
crown ethers using H NMR, mass spectrometric and crystallo-
2,3-Thiophene-15-crown-5 1 was obtained in three steps from
graphic methods. Hydrogen bonding appears to be the most
2,5-bis-(ethoxycarbonyl)-3,4-thiophendiol d using a modified
16
important interaction in complexation, but minor effects such as
procedure (Scheme 3).
12
p-stacking or cation-p interactions have also been observed.
It should be noted that the use of 1,11-diiodine-3,6,9-triox-
aundecane instead of tetraethyleneglycol ditosylate, and DMF as
a solvent at the cyclisation stage, and a copper catalyst at the
decarboxylation stage, allows us to simplify the synthetic proce-
dure for 1 and increase its overall yield from 18.6% up to 49.3%.
Diethyl-2,3,5,6,8,9,11,12-octahydrothieno[3,4-b]-1,4,7,10,13-
pentaoxacyclopentadecyn-14,16-dicarboxylate e. To a solution
In spite of interest in 1–3, no molecular co-crystals based on
them have been obtained so far. Along with other authors, we
have previously shown that molecules a–c are good candidates
13,14
for co-crystallization with crown ethers (CE).
They possess
the different sets of H-donor groups for hydrogen bonding. On
the other hand, they have the planar skeletons with the alterna-
tion of single and double bonds, so it is possible to expect
different modes of stacking interactions and mutual arrange-
ments with 1–3, which in turn are possessed by extended
aromatic systems. Dithiooxamide molecule a via its two trans-
oriented amino-groups, preferably forms a 1 : 1 alternative chain
with 15C5, B15C5, sterically hindered [1.5]dibenzo-18C6, and
1
7
of 2,5-bis(ethoxycarbonyl)-3,4-thiophendiol d,
(13.0 g,
0.05 mol) in 900 ml of anhydrous DMF in an argon atmosphere
at room temperature CsF (30.3 g, 0.199 mol) was added, and the
mixture was stirred for 1 h followed by addition of 1,11-diio-
dine-3,6,9-trioxaundecane (21.3 g, 0.0515 mol) in 100 ml of
anhydrous DMF. The temperature of the reaction mixture was
0
0
ꢀ
with lariat ethers, N,N -bis(benzyl)-N,N -diaza-18-crown-6 and
0
gradually increased up to 80 C, and the stirring at the same
0
N,N -bis(4-methoxybenzyl)-N,N -diaza-18-crown-6 as well as
temperature continued for 10 h. DMF was distilled off under
vacuum to a volume of 100 ml, the resulting solution was
diluted twice with water and extracted with benzene (3 ꢁ 150
ml). The combined extracts were washed with water (100 ml),
13,15
with azacycles.
The conformationally flexible 18C6 and its
dicyclohexyl-substituted analogues due to excess of their acces-
sible O-atoms as H-bond acceptors provide the coordination of
four dithiooxamide molecules to one CE makes it possible to
expand the supramolecular architecture up to 2D layer with the
second dithiooxamide molecule serving as a bridge between the
dried over MgSO and evaporated to dryness. The resulting dry
4
residue was purified on silica gel (Kiesilgel 60, 0.063–0.100 mm,
‘‘Merck’’), eluent, hexane–ethyl acetate (3 : 1). The target product
(
n
CE-dithiooxamide) alternative chains. Based on the previously
was additionally recrystallised from aqueous ethanol. Yield 16.3 g
16
(78%). Mp 66–67 C.
ꢀ
reported structures we could most probably expect the alterna-
tive chain motifs for 1–2, while two scenarios, ladder-type chain
motif or extended layer seem to be possible for 3 (Scheme 2).
Alongside the crystal structures for pure 1 and co-crystals
2,3,5,6,8,9,11,12-Octahydro-thieno[3,4-b]-1,4,7,10,13-pen-
taoxacyclopentadecyn-14,16-dicarboxylic acid f. To a solu-
tion of diester e (25.1 g, 0.06 mol) in 300 ml of ethanol at room
temperature and under stirring 300 ml of 5% aqueous NaOH
based on crown ethers 1–3 with compositions 1a, 2a, 2b$H O, 2c
2
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3
was synthesised following a procedure previously descri-
8c
bed.
Preparation of co-crystals
Equimolar amounts of the corresponding crown ethers 1–3 and
dithiooxamide a guest molecule were dissolved in boiling meth-
anol–ethyl acetate mixture and allowed to crystallise slowly at
room temperature. Similar synthetic procedure yielded the
Scheme 4
crystalline 2b$H O from methanol–benzene–n-butanol mixture
2
and 2c from acetone–hexane mixture. The resulting co-crystals
were separated by decanting. The crystallisation was repeated
and the desired co-crystals were obtained in nearly quantitative
yields. All the compositions were confirmed by elemental anal-
ysis. Melting points for co-crystals were determined and are
presented in Table 1 along with the melting points for the starting
compounds.
ꢀ
was added. The reaction mixture was stirred for 2 h at 60 C.
After the reaction ethanol was distilled off in vacuum. The
water solution was washed with benzene (2 ꢁ 100 ml), acid-
ified with concentrated HCl, cooled, and the precipitate
filtered off. The target product was purified by recrystallisa-
tion from minimal amount of hot water with 3–4 drops of
ꢀ
16
concentrated HCl. Yield 17.2 g (79%). Mp 244–245 C.
,3-Thiophene-15-crown-5 (2,3,5,6,8,9,11,12-octahydro-thieno-
3,4-b]-1,4,7,10,13-pentaoxacyclopentadecyne) 1. Diacid f (13.8 g,
.038 mol) and freshly prepared metal copper (1.5 g) were placed in
1
colorless crystals. Found, %: C, 52.59; H, 6.56; S, 11.64 for
2
C H O S. Calcd, % C, 52.54; H, 6.61; S, 11.69.
1
2
18
5
[
1
a (1/1) Yield 97%, transparent red crystals. Found, %: C,
0
4
4
2.66; H, 5.67; N,7.13; S, 24.35 for C H N O S . Calcd, %:C,
2
1
4
22
5 3
ꢀ
the refluxing unit for distillation and heated in an oil bath to 225 C
2.62; H, 5.62; N, 7.10; S, 24.38.
a (1/1) Yield 94%, transparent red crystals. Found, %: C,
2
at 20 mm Hg. Thus there is a vigorous selection of CO , which
2
ꢀ
ended after 1.5 h at 235 C. Then the pressure was reduced to 1 mm
ꢀ
5
4.73; H, 5.96; N, 6.37; S, 14.68 for C20
4.77; H, 5.98; N, 6.39; S, 14.62.
26 2 5 2
H N O S . Calcd, %: C,
Hg, bath temperature was increased to 250 C and the resulting 1
5
was distilled off, followed by additional purification by crystal-
16
lisation from heptane. Yield 8.3 g (80%). Mp 71–72 C.
,3-Naphtho-15-crown-5 2 was obtained by alkylation of 2,3-
2
b$H
Found, %:C, 55.01; H, 6.49; N, 12.89 for C20
:C, 55.04; H, 6.4; N, 12.84.
c (1/1) transparent colorless crystals. Found, %:C, 55.54; H,
.63; N, 12.92 for C H N O Calcd, %: C, 55.55; H, 5.59; N,
2
O (1/1/1) Yield 88%, transparent colorless crystals.
ꢀ
28 4 7
H N O
. Cacld,
2
%
dihydroxynaphthalene by tetraethyleneglycol di-p-tosylate in
2
conditions of phase catalysis (50% aqueous solution of NaOH,
5
1
2
0
24
4
7.
18
C
6
H
6
, 25 mol.% of tetrabutylammonium bromide), allowing
2.96.
a2 (1/2) Yield 15%, transparent rosy crystals. Found, %: C,
the 2.5 time output increase in comparison with the well-known
3
19
Pedersen’s method (Scheme 4).
5
1.37; H, 6.39; N, 6.35; S, 14.45 for C38
1.33; H, 6.35; N, 6.30; S, 14.43.
56 4 12 4
H N O S . Calcd, %: C,
To a solution of 2,3-dihydroxynaphthalene g (8.0 g, 0.05 mol)
and tetrabutylammonium bromide (4.0 g, 0,0125 mol) in 300 ml
of benzene was added with stirring 100 ml of 50% solution of
5
Crystallography†
ꢀ
NaOH, the temperature was raised to 60 C. The resulting
mixture was stirred for 30 min at this temperature, then the
solution of tetraethyleneglycol di-p-tosylate (25.85 g, 0.0515 mol)
in 300 ml of benzene was added. The reaction mixture was boiled
with stirring for 15 h. After cooling to room temperature, the
organic layer was separated, washed successively with 5% solu-
tion of HCl (100 ml), water (3 ꢁ 200 ml), saturated solution of
The crystallographic data collection for all six compounds was
carried out on a Nonius Kappa CCD diffractometer at 293 K,
using graphite-monochromated Mo-Ka radiation (l
¼
ꢀ
20
0.71073 A). The structure solution and refinement proceeded
21
similarly using SHELX-97 program package for all structures.
Direct methods yielded all non-hydrogen atoms of the asym-
metric unit. The non-hydrogen atoms were refined anisotropi-
4
NaCl (100 ml), and dried over MgSO . The solvent was evapo-
2
rated in vacuum; the resulting residue was extracted with boiling
cally by full-matrix least-squares calculations on F . Some
heptane (3 ꢁ 200 ml). The precipitate was filtered off and
2
disorder was found in 1a and 3a . In 1a dithiooxamide molecule
ꢀ
recrystallised from heptane. Yield 8.1 g (51%). Mp 118–119 C
ꢀ
is disordered over two positions with occupancies of 0.75 and
0.25, correspondingly. The minor component was refined in
18
(
lit. mp 117–119 C).
Table 1 Melting points for the studied co-crystals and starting materials
ꢀ
Starting materials/Mp ( C)
ꢀ
Co-crystal
Mp ( C)
1
2
3
a
b
c
1
2
2
2
3
a
a
b$H
162–163
197–199
84–85
111–113
205–207
71–72
245
245
118–119
118–119
118–119
2
O
160
c
212–214
a
2
153
245
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ꢀ
isotropic approximation. Only for the major component the
7.93 A (calculated as the distance between the centroids of
pentagons of five crown oxygen atoms) provides space for partial
interpenetration of the adjacent chains, the structure demon-
strates the low packing efficacy (Fig. 2(c)) with the packing index
(PI) of 66.6% practically equal to PI of 66.4% for pure 1.
Co-crystallisation of 2,3-naphtho-15-crown-5 2 with co-crystal
partners a–c results in the compounds of the compositions 2a,
hydrogen atoms of the amino-groups were localised. 3a was
2
obtained in a very low yield in the form of poor-quality crystals,
and the X-ray experiment was carried out from the only selected
very thin crystal. The whole structure is disordered over two
positions with partial occupancies of 0.79 and 0.21, corre-
spondingly. The minor component of the crown ether was refined
using the SAME restraints to make equivalent bond distances
and bond angles in two crown molecules equal. The crown and
dithiooxamide molecules that correspond to the minor occu-
pancies were refined in isotropic approximation. Only H-atoms
of the amino groups in the major position of dithiooxamide
molecule were localised and refined. In all structures C-bound
hydrogen atoms were added in calculated positions, and were
treated using a riding-model approximation, with Uiso(H) ¼
2
2b$H O, and 2c, respectively which are sustained by the different
sets of hydrogen bonds and auxiliary weak interactions. The co-
crystals demonstrate the different modes of component
arrangement. The extended naphthylene moiety imposes the
rigidity to the attached O-atoms, which are perfectly coplanar
with the aromatic unit, and prevents the 15C5 moiety from
attaining the ‘ideal crown’ conformation. Similar to 1a, 2a
represents a molecular complex of the 1 : 1 stoichiometry. The
formula unit for 2a is shown in Fig. 3(a). The compound crys-
1
.2Ueq(C). The N- and O-bound H-atoms were determined from
a difference Fourier map and were then allowed to refine iso-
1
tallises in the monoclinic space group P2 /m, with molecule
tropically with Uiso(H) ¼ 1.5Ueq(N/O). SADI restraints were
a being displayed in a mirror plane which intersects the naph-
thalene moiety and the macrocyclic cavity through the O(3)
atom; thus the planar units demonstrate the perfect T-shape
arrangement. At the concave side of 2, molecule a forms only one
2
applied to the N–H distances in amino-groups in 2b$H O and
3
2
a . Details of the crystal data, data collection and processing are
summarised in Table 2, hydrogen bonding geometry is given in
2
2
3
ꢀ
Table 3. All packing diagrams were produced using Mercury.
Packing Index (PI) was calculated with the program PLATON.
hydrogen bond, N(2)/O(3) ¼ 3.287(3) A, as the catechol oxygen
2
atoms are removed from the possible interaction area. Similar to
1
a via the second H N(1)-amino group that participates in two
2
NH/O hydrogen bonds, N(1)/O(1) ¼ 3.051(2), and N(1)/
Results and discussion
ꢀ
O(3) ¼ 2.943(3) A the complexes translated along the a direction
ꢀ
are ordered in the linear chain with a separation of 7.97 A
Macrocycle 1 crystallises in the orthorhombic space group Pbca
with one molecule per asymmetric unit. The overall view of the
molecule is shown in Fig. 1(a). The thiophene ring is almost
exactly planar; the overall conformation of the molecule is chair-
like with the dihedral angle between the thiophene ring and the
between the neighboring crown molecules. The packing of the
chains occurs in such mode to maximise the edge-to-face inter-
actions between the planar skeletons of a, and naphthylene-units
due to participation of the S(1) atom in the bifurcated C(6)/S(1)
ꢀ
ꢀ
ꢀ
mean plane of five oxygen atoms of 28.62(9) . The molecule is
contacts with H/S ¼ 2.97, C(6)/S(1) ¼ 3.894 A, :CHS ¼ 170
deviating from ideal crown conformation as two of the O–C
(Fig. 3(b)). Although visually no pronounced voids are evident in
2a (Fig. 3(c)) contrary to 1a, the PI indicates practically the same
value of 66.7%, thus demonstrating the insignificantly improved
packing efficacy in comparison with pure CE 2, for which PI is
65.7% (calculated using YENMOT entry with geometrically
generated H-atoms).
bonds adopt gauche-conformation being 83.3(3) for C(3)–O(2)–
ꢀ
C(4)–C(5), and ꢂ82.4(4) for C(8)–O(4)–C(7)–C(6), respectively.
The molecules have voids that could, in principle, accommodate
small guest molecules, although in the crystal structure access to
these voids is blocked by neighboring molecules connected via
CH/O weak interactions. The molecules pack in a herring-bone
motif affording the dihedral angle between the planes through
Co-crystal 2b$H
group, and represents a monohydrate of 1 : 1 : 1 stoichiometry.
The formula unit for 2b$H O is shown in Fig. 4(a).
2 1
O crystallises in the monoclinic P2 /c space
ꢀ
the thiophene rings in the neighboring molecules of 58.0
2
(
Fig. 1(b)). Apropos, the same herring-bone packing motif is seen
The syn-oriented amino-groups of molecule b are capable to
co-ordinate either to two different molecules of CE (as in the co-
crystals with 15C5, B15C5, dicyclohexano-18C6), thus gener-
ating the 1D chains built of alternative components, or to the
same water molecule inserted between the crown ether, (for
24
in the macrocycles 2–3 and their homologues in the solid state.
Of a–c only molecule a forms co-crystals with all macrocycles
1
–3. Compound 1a crystallises in the monoclinic P2 /n space
1
group. The content of the asymmetric unit is shown in Fig. 2(a).
The planar molecule a is inclined to the thiophene ring at an
example, [1.5]B18C6), and molecules b. In 2b$H O the water
2
ꢀ
molecule is perching at 2.07 A above the mean plane of five
ꢀ
ꢀ
angle of 28.74(9) and forms the dihedral angle of 72.95(5) with
the mean plane of the crown oxygen atoms. The molecules in the
co-crystal are held together via two NH/O crown hydrogen
crown oxygen atoms. It acts as a double donor towards crown
ꢀ
oxygen atoms at N/O distances of 2.842(3) and 3.134(3) A, and
as a double acceptor towards two amino groups of molecule b,
bonds provided by the H
2
N(2)-amino group. Through the
1
2
second H N(1)-amino group that affords one single and one
2
thus generating the R
(7) graph set. It is noteworthy that each
bifurcated NH/O crown hydrogen bonds the formula units are
combined in the helical chains where the components alternate
amino group uses only one of two hydrogen atoms in this
hydrogen bonding pattern. The second H-atom of N(2)-amino
group is pointed to the A cycle of the naphthalene moiety with
(
Fig. 2(b)). Two NH -groups of molecule a use all their H-donor
2
ꢀ
functions for hydrogen bonding with all crown oxygen atoms
the CgA/H ¼ 2.69 and CgA/N(2) ¼ 3.331 A (where CgA is the
which are involved in these interactions, the corresponding N/
ꢀ
O separations ranging within 2.993(12)–3.174(6) A (Table 3).
center of gravity for ring A). The edge-to-face arrangement of
molecule b and the naphthalene unit is described by the dihedral
ꢀ
Although the separation of the macrocycles in the chain of ca.
angle of 77.1(1) . Between the formula units related by the screw
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ꢀ
Table 3 Hydrogen bond distances (A) and angles ( ) for 1a, 2a, 2b$H
ꢀ
2
O, 2c, 3a
2
Symmetry transformation for
acceptor
D–H/A
d(D–H)
d(H/A)
d(D/A)
:(DHA)
1a
N(1)–H(1N1)/O(1)
N(1)–H(1N1)/O(5)
N(1)–H(2N1)/O(3)
N(2)–H(1N2)/O(2)
N(2)–H(2N2)/O(4)
0.72(3)
0.72(3)
0.75(4)
0.82(3)
0.82(3)
2.47(3)
2.56(3)
2.28(3)
2.29(3)
2.46(3)
3.048(8)
3.140(12)
2.993(12)
3.097(5)
3.175(6)
138(4)
139(4)
159(4)
173(3)
147(4)
x + 1/2, 1/2 ꢂ y, z + 1/2
x + 1/2, 1/2 ꢂ y, z + 1/2
x + 1/2, 1/2 ꢂ y, z + 1/2
x, y, z
x, y, z
2a
N(1)–H(1A)/O(3)
N(1)–H(1B)/O(1)
N(2)–H(2B)/O(3)
0.86(2)
0.79(3)
0.81(3)
2.27(3)
2.35(3)
2.48(3)
2.943(3)
3.051(2)
3.287(3)
135(2)
147(4)
176(3)
x + 1, y, z
x + 1, 1/2 ꢂ y, z
x, y, z
2
2b$H O
O(1w)–H(1w)/O(2)
O(1w)–H(2w)/O(4)
N(1)–H(2N1)/O(1w)
N(2)–H(2N2)/O(1w)
0.84(2)
0.86(2)
0.85(1)
0.94(2)
2.07(2)
2.03(2)
2.31(2)
1.91(2)
2.890(2)
2.886(2)
3.131(3)
2.839(3)
168(2)
179(3)
163(3)
173(3)
x, y, z
x, y, z
x, y, z
x, y, z
2c
N(4)–H(4)/O(4)
N(4)–H(4)/O(3)
C(8)–H(8A)/O(6)
C(5)–H(5A)/O(7)
0.86
0.86
0.97
0.97
2.06
2.47
2.54
2.53
2.887(3)
3.015(3)
3.245(4)
3.431(4)
161
122
130
154
x, y, z
x, y, z
1 ꢂ x, ꢂy, 1 ꢂ z
x, 1 + y, z
3a
2
N(1)–H(1N1)/O(6)
N(2)–H(2N1)/O(4)
N(2)–H(1N2)/O(3)
N(2)–H(2N2)/O(1)
0.85(4)
0.85(4)
0.98(4)
0.99(4)
2.49(5)
2.33(4)
2.35(5)
2.38(5)
3.275(11)
3.166(12)
3.253(14)
3.346(11)
153(6)
170(6)
152(6)
166(6)
x, y, z
x, y, z
x + 1, y, z
x + 1, y, z
ꢀ
ꢀ
axis there are weak CH(CH
2
)/N interactions of 3.398–3.478 A
Fig. 4(b)) that combine them into helical chains. The insertion of
3.015(3) A, respectively (Table 3). The CH/O crown distances
for the CH-group neighboring to the NH-group pointed inside
the heterocyclic cavity exceeding the reasonable value of CH/O
(
water molecules in the structure increases the number of small
voids and results in the lower PI of 65.9%.
ꢁ
The formula unit for 2c that crystallises in the triclinic P1 space
ꢀ
hydrogen bonding (H/O ¼ 2.6 A).
The molecule of 3-nitro-1H-1,2,4-triazole c has a planar skel-
ꢀ
eton with all non-hydrogen atoms being coplanar within 0.034 A.
group is shown in Fig. 5(a). It is constructed by one bifurcated
NH/O hydrogen bond, with N/O distances of 2.887(3) and
In the triazole cycle C–N distances range within 1.310(3)–
ꢀ ꢀ
.332(3) A, N–N distance being 1.342(3) A. Of all co-crystals
1
discussed herein only 2c demonstrates the face-to-face hetero-
meric p–p interactions between the cyclic units, being inclined at
ꢀ
an angle of 16.40(4) . Further packing of the complexes is
characterised by their pronounced segregation in stacks parallel
to the a axis with the interplane separation between the naph-
ꢀ
thylene unit and the molecule c ranging within of 3.14–4.06 A in
ꢀ
the complex and 2.68–3.60 A between the translated complexes
(
Fig. 5(b)). The inversion-related stacks are held in the crystal via
weak CH/O interactions with participation of nitro-group of c
as H-acceptor. The efficacy of the crystal packing of 2c is the
highest among the compounds described herein, as Kitaigor-
odskii’s PI of 69.6% indicates.
Concluding this section we can unambiguously state that the bulky
naphthalene moiety imposes an essential increase on the rigidity of
the crown ether framework in 2. It reduces the number of O-crown
atoms accessible for participation in the hydrogen bonding with
neutral molecules a–c that results in an elaboration of part of
potential H-donors from the overall interaction system. On the other
hand, the formation of 1a and 2a with the predicted 1D topology
confirms the previously demonstrated advantage of dithiooxamide
molecule as a suitable bidentate linker even in the case of the asym-
metric crown ethers with the reduced number of O-acceptors.
2
Complex 3a further demonstrates the facilities of dithiox-
Fig. 1 Structure of 1. View of molecule 1 with the numbering scheme (a);
fragment of the layer sustained by CH/O hydrogen bonds (the marked
amide molecule a as a suitable bidentate linker giving rise to the
ꢀ
CH/O contacts do not exceed 2.6 A) (b).
first ladder-type co-crystal based on bis-(18C6)-stilbene. The
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Fig. 3 View of 2a. Formula unit with the partial numbering scheme (a);
view of the linear chains with the shortest C/S intermolecular distances
shown in pink color (b); packing of the neighboring chains (c).
Fig. 2 View of 1a with the partial numbering scheme, only major
position for dithiooxamide molecule is shown (a); view of the helical
chains with the intermolecular distances including the shortest CH/S
ꢀ
form a hexagon with the side varying within 2.60–2.92 A. The
least-squares mean plane through the oxygen atoms is inclined
ꢀ
ꢀ
with respect to the benzene ring plane by 16.0 (39.7 in free
macrocycle). The dithiooxamide molecule is inclined at an angle
ꢀ
contacts shown in pink color (H/S ¼ 2.92, C(11)/S(2) ¼ 3.844 A,
ꢀ
:
CHS ¼ 171 ) (b); packing of the neighboring chains (c).
ꢀ
of 83.1 to the mean plane of six crown oxygen atoms. In the
formula unit for the 1:2 co-crystal 3a is shown in Fig. 6(a). The
2
formula unit molecule 3 and two molecules a are held via a couple
molecule 3 is situated at a symmetry centre, its E-stilbene frag-
ment being strictly planar. The dithiooxamide molecule occupies
general position. In 3, the oxygen atoms of the 18C6 subunit
of NH/O hydrogen bonds, N(1)/O(6) ¼ 3.275(11) and N(1)/
ꢀ
O(4) ¼ 3.166(12) A, the second H
2
N(2)-amino group is respon-
sible for the interaction with the translated crown molecule via
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Fig. 5 View of 2c. Formula unit with the partial numbering scheme (a);
space-filling presentation of the crystal packing along the crystallo-
graphic a axis (b).
ꢀ
moieties and voids with linear dimensions 7.71 ꢁ 15.97 A
determined as the distances between the centroids of the crown
ether rings separated by dithiooxamide molecule or stilbene
fragment, respectively. The neighboring ladders stack in
a partially interpenetrating mode with the part of the oxyethylene
chain buried within the voids via CH/S interactions, C(8)/
ꢀ
S(1) ¼ 3.939 A. The PI for 3c
2
adopts the smallest value of 65.3%
being essentially lower than 69.8% for pure 3 calculated using
QASVUC cif file. Nevertheless the multiple hydrogen bonding
provided by the bis-nature of the crown ether affords the rather
stable and predictable supramolecular architecture.
Fig. 4 View of 2b$H
2
O with the partial numbering scheme (a); space-
The reported data show that dithiooxamide can be used to
control the supramolecular architecture. Besides the discussed
crystal structures some physical properties change upon the
formation of the co-crystals. First of all we should mention that
the red-colored dithiooxamide assigns its color to the co-crystals
formed with the colorless CEs when the molecular mass of the
macrocyclic molecule does not essentially exceed the molecular
filling presentation of crystal packing along the crystallographic a axis (b–c).
ꢀ
two N(2)/O(3) ¼ 3.253(14) and N(2)/O(1) ¼ 3.346(11) A
hydrogen bonds. These rather weak NH/O hydrogen bonds
multiply by the bis-nature of 3. It allows to build the rigid ladder-
type framework with the parallel arrangement of the stilbene
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in this study possess the asymmetry imposed by the cyclic unit
attached to the crown ether framework, which explains the
generated asymmetric hydrogen-bonding patterns. Dithioox-
amide as a suitable bidentate linker permits the control of the
supramolecular architecture thus giving rise to the helical, linear,
or ladder-type alternating component chains for 1–3. The
extended naphtho-moiety of 2 is responsible for the edge-to-face
and face-to-face heteromeric stacking interactions with planar
1
,2,5-oxadiazole-3,4-diamine and 3-nitro-1H-1,2,4-triazole
molecules. Along with the crystal structure for 1 the improved
synthetic strategy for 1 and 2 is reported.
Acknowledgements
The diffraction data were collected at the Schulich Faculty of
Chemistry, Technion, Haifa, through the cooperation of Prof.
Menahem Kaftory, whom we would like to acknowledge.
References
1
(a) Cation Binding by Macrocycles, ed. Y. Inoue and G. W. Gokel,
Marcel Dekker, New York, 1990; (b) R. M. Izatt, K. Pawlak,
J. S. Bradshaw and R. L. Bruening, Chem. Rev., 1991, 91, 1721; (c)
J.-M. Lehn, Supramolecular Chemistry. Concepts and Perspectives,
VCH, Weinheim, 1995; (d) G. W. Gokel, W. M. Leevy and
M. E. Weber, Chem. Rev., 2004, 104, 2723.
2
(a) H.-G. L o€ hr and F. V o€ gtle, Acc. Chem. Res., 1985, 18, 65; (b) P. de
Silva, H. Q. N. Gunaratne, T. Gunnlaugsson, A. J. M. Huxley,
C. P. McCoy, J. T. Rademacher and T. E. Rice, Chem. Rev., 1997,
9
7, 1515; (c) M. V. Alfimov and S. P. Gromov, in Applied
fluorescence in chemistry, biology, and medicine, ed. W. Rettig, B.
Strehmel, S. Schrader and H. Seifert, Springer-Verlag, Berlin, 1999,
pp. 161–178; (d) B. Valeur and I. Leray, Coord. Chem. Rev., 2000,
2
05, 3.
3
(a) V. Balzani, A. Credi and M. Venturi, Molecular devices and
machines – A Journey in the Nano World, Wiley-VCH, Weinheim,
2
003; (b) Molecular Switches, ed. B. L. Feringa, Wiley-VCH,
Weinheim, 2001; (c) J. D. Badjic, V. Balzani, A. Credi, S. Silvi and
J. F. Stoddart, Science, 2004, 303, 1845; (d) D. S. Perekalin,
M. V. Babak, V. V. Novikov, P. V. Petrovskii, K. A. Lyssenko,
M. Corsini, P. Zanello and A. R. Kudinov, Organometallics, 2008,
Fig. 6 View of 3a
2
with the partial numbering scheme (a); ladder-type
assembly (b); space-filling presentation of the ladders packing (c).
2
7, 3654.
4
(a) J.-P. Desvergne and H. Bouas-Laurent, J. Chem. Soc., Chem.
Commun., 1978, 403; (b) S. Shinkai, T. Minami, Y. Kusano and
O. Manabe, J. Am. Chem. Soc., 1983, 105, 1851; (c)
J. H. R. Tucker, H. Bouas-Laurent, P. Marsau, S. W. Rileya and
J.-P. Desvergne, Chem. Commun., 1997, 1165; (d) M. S. Fonari,
E. Luboch, A. Collas, A. Bukrej, F. Blockhuys and J. F. Biernat, J.
Mol. Struct., 2008, 892, 195; (e) M. V. Alfimov, S. P. Gromov,
Y. V. Fedorov, O. A. Fedorova, A. I. Vedernikov, A. V. Churakov,
L. G. Kuz’mina, J. A. K. Howard, S. Bossmann, A. Braun,
M. Woerner, D. F. Jr. Sears and J. Saltiel, J. Am. Chem. Soc., 1999,
13,14
mass of dithiooxamide.
Only in the case of bis-(18C6)-stil-
bene the co-crystal coloring becomes less intense being light rosy
due to the increased mass portion of the colorless CE in the final
co-crystal. Co-crystals 1a, 2a, and 3a
intermediate between the parent compounds, while monohydrate
b$H O, and weakly bound 2c have melting points lower than
the initial components (Table 1). Along with the decrease of the
melting point the water insertion in 2b$H O also decreases the
2
possess the melting points
2
2
121, 4992; (f) K. Kimura, R. Mizutani, M. Yokoyama, R. Arakawa
and Y. Sakurai, J. Am. Chem. Soc., 2000, 122, 5448.
2
5
(a) S. Shinkai, in Comprehensive Supramolecular Chemistry, ed. J.-M.
Lehn, Pergamon Press, New York, 1996, 1; (b) S. P. Gromov and
M. V. Alfimov, Russ. Chem. Bull., 1997, 46, 611; (c) V. Lokshin,
A. Samat and A. V. Metelitsa, Russ. Chem. Rev., 2002, 71, 893; (d)
D. G. Amirsakis, A. M. Elizarov, M. A. Garcia-Garibay,
P. T. Glink, J. F. Stoddart, A. J. P. White and D. J. Williams,
Angew. Chem., Int. Ed., 2003, 42, 1126; (e) M. V. Alfimov,
O. A. Fedorova and S. P. Gromov, J. Photochem. Photobiol., A,
co-crystal PI by increasing the number of narrow void spaces in
the crystal. The essentially improved PI registered for 2c can be
explained by the most effective packing of the extended planar
moieties.
Conclusions
2
003, 158, 183.
For the first time the co-crystals of 2,3-thiophene-15C5 1, 2,3-
naphtho-15C5 2, and bis-(18C6)-stilbene 3, with dithiooxamide
alongside the co-crystals of naphtho-15C5 with 1,2,5-oxadiazole-
6 (a) M. Yamauchi, A. Jyo and N. Ishibashi, Anal. Chim. Acta, 1982,
136, 399; (b) M. Yamauchi, T. Imato, M. Katahira, Y. Inudo and
N. Ishibashi, Anal. Chim. Acta, 1985, 169, 59; (c) E. Luboch,
A. Cygan and J. F. Biernat, Tetrahedron, 1990, 46, 2461; (d)
Md. A. Rahman, H. Doe, N. Sakurada and R. Arakawa,
Electrochim. Acta, 2001, 47, 623.
3
,4-diamine, and 3-nitro-1H-1,2,4-triazole were synthesised and
their crystal structures were discussed. All the crown ethers used
6
82 | CrystEngComm, 2011, 13, 674–683
This journal is ª The Royal Society of Chemistry 2011

View Article Online
7
(a) G. Koshkakaryan, L. M. Klivansky, D. Cao, M. Snauko,
S. J. Teat, J. O. Struppe and Yi Liu, J. Am. Chem. Soc., 2009, 131,
2918; (c) C. B. Knobler, E. F. Maverick, K. N. Trueblood and
R. M. Weiss, Acta Crystallogr., Sect. C: Cryst. Struct. Commun.,
1999, 55, 2091.
2078; (b) E. Wagner-Wysiecka, M. Jamrogiewicz, M. S. Fonari and
J. F. Biernat, Tetrahedron, 2007, 63, 4414; (c) J. Szczygelska-Tao,
M. S. Fonari and J. F. Biernat, Supramol. Chem., 2008, 20, 651; (d)
N. G. Lukyanenko, T. I. Kirichenko, A. Yu. Lyapunov,
C. Yu. Kulygina, Yu. A. Simonov, M. S. Fonari and
M. M. Botoshansky, Tetrahedron Lett., 2004, 45, 2927; (e)
N. G. Lukyanenko, T. I. Kirichenko, A. Yu. Lyapunov,
A. V. Mazepa, Y. A. Simonov, M. S. Fonari and
M. M. Botoshansky, Chem.–Eur. J., 2005, 11, 262; (f)
N. G. Lukyanenko, A. Yu. Lyapunov, T. I. Kirichenko,
M. M. Botoshansky, Y. A. Simonov and M. S. Fonari, Tetrahedron
Lett., 2005, 46, 2109.
(a) W.-S. Xia, R. H. Schmehl and C.-J. Li, J. Am. Chem. Soc., 1999,
121, 5599; (b) S. P. Gromov, Russ. Chem. Bull., 2008, 57, 1325; (c)
A. I. Vedernikov, S. S. Basok, S. P. Gromov, L. G. Kuz’mina,
V. G. Avakyan, N. A. Lobova, E. Yu. Kulygina, T. B. Titkov,
Yu. A. Strelenko, E. I. Ivanov, J. A. K. Howard and
M. V. Alfimov, Russ. J. Org. Chem., 2005, 41, 843(Engl. Transl.);
12 (a) S. Kiviniemi, A. Sillanp €a €a , M. Nissinen, K. Rissanen,
M. T. L €a ms €a and J. Pursiainen, Chem. Commun., 1999, 897; (b)
M. Nissinen, S. Kiviniemi, K. Rissanen and J. Pursiainen,
CrystEngComm, 2000, 2, 102; (c) S. Kiviniemi, M. Nissinen,
M. T. L €a ms €a , J. Jalonen, K. Rissanen and J. Pursiainen, New J.
Chem., 2000, 24, 47.
13 (a) Y. A. Simonov, M. S. Fonari, M. J. Zaworotko, H. Abourahma,
J. Lipkowski, E. V. Ganin and A. A. Yavolovskii, Org. Biomol.
Chem., 2003, 1, 2922; (b) W. H. Watson, J. Galloy, D. A. Grossie,
F. Vogtle and W. M. Muller, J. Org. Chem., 1984, 49, 347; (c)
W. H. Watson and P. C. Jain, J. Inclusion Phenom., 1986, 4, 397;
(d) M. S. Fonari, Yu. A. Simonov, L. Croitoru, S. S. Basok,
E. V. Ganin and J. Lipkowski, J. Mol. Struct., 2006, 794, 110; (e)
M. S. Fonari, E. V. Ganin, Yu. M. Chumakov,
M. M. Botoshansky, K. Suwinska, S. S. Basok and
Yu. A. Simonov, New J. Chem., 2009, 33, 1646.
14 (a) R. Luboradzki, J. Lipkowski, Y. A. Simonov, M. S. Fonari,
E. V. Ganin and A. A. Yavolovskii, J. Inclusion Phenom.
Macrocyclic Chem., 2001, 40, 59; (b) R. Luboradzki, J. Lipkowski,
Y. A. Simonov, M. S. Fonari, E. V. Ganin and A. A. Yavolovskii,
J. Inclusion Phenom. Mol. Recognit. Chem., 1995, 23, 181; (c)
E. V. Ganin, M. S. Fonari, Yu. A. Simonov, G. Bocelli,
S. S. Basok, V. V. Tkachuk, S. A. Kotlyar and G. L. Kamalov, J.
Inclusion Phenom. Macrocyclic Chem., 2005, 52, 63.
8
(
d) S. P. Gromov, A. I. Vedernikov, E. N. Ushakov, N. A. Lobova,
A. A. Botsmanova, L. G. Kuz’mina, A. V. Churakov,
Y. A. Strelenko, M. V. Alfimov, J. A. K. Howard, D. Johnels and
U. G. Edlund, New J. Chem., 2005, 29, 881; (e) S. Fery-Forgues
and F. Al-Ali, J. Photochem. Photobiol., C, 2004, 5, 139.
(a) A. Berlin, G. Zotti, S. Zecchin and G. Schiavon, Synth. Met., 2002,
131, 149; (b) B. Jousselme, Ph. Blanchard, E. Levillain, J. Delaunay,
9
M. Allain, P. Richomme, D. Rondeau, N. Gallego-Planas and
J. Roncali, J. Am. Chem. Soc., 2003, 125, 1363; (c) D. T. McQuade,
A. E. Pullen and T. M. Swager, Chem. Rev., 2000, 100, 2537.
0 (a) X.-K. Gao, J.-M. Dou, D.-C. Li, F.-Y. Dong and D.-Q. Wang, J.
Chem. Crystallogr., 2005, 35, 107; (b) X. Gao, J. Dou, D. Li, F. Dong
and D. Wang, J. Coord. Chem., 2005, 58, 1127; (c) J. F. Biernat,
A. Cygan, E. Luboch, Yu. A. Simonov, T. I. Malinovski,
V. K. Bel’skii and N. F. Bolotina, J. Inclusion Phenom. Mol.
Recognit. Chem., 1993, 15, 369; (d) X.-K. Gao, J.-M. Dou, D.-
C. Li, F.-Y. Dong and D.-Q. Wang, J. Mol. Struct., 2005, 733, 181;
15 B. Piotrkowska, A. Wasilewska, M. Gdaniec and T. Polonski,
CrystEngComm, 2008, 10, 1421.
16 T. Sone, K. Sato and Y. Ohba, Bull. Chem. Soc. Jpn., 1989, 62, 838.
17 E. W. Fager, J. Am. Chem. Soc., 1945, 67, 2217.
18 T. Bogaschenko, S. Basok, C. Kulygina, A. Lyapunov and
N. Lukyanenko, Synthesis, 2002, 2266.
19 C. J. Pedersen, J. Am. Chem. Soc., 1967, 89, 7017.
20 Z. Otwinowski and W. Minor, in C. W. Carter & R. M. Sweet (ed.),
Methods in Enzymology, Macromolecular Crystallography, Part A,
Academic Press. London. 1996, 276, 307.
1
(
e) X. Gao, J. Dou, D. Li, F. Dong and D.-Q. Wang, J. Coord.
21 G. M. Sheldrick, Acta Crystallogr., Sect. A: Found. Crystallogr., 2008,
64, 112.
22 C. F. Macrae, P. R. Edgington, P. McCabe, E. Pidcock, G. P. Shields,
R. Taylor, M. Towler and J. van de Streek, J. Appl. Crystallogr., 2006,
39, 453.
Chem., 2005, 58, 1597; (f) Yu. A. Simonov, A. A. Dvorkin,
T. J. Malinovski, A. Cygan, E. Luboch and J. F. Biernat, Pol. J.
Chem., 1994, 68, 1783.
1 (a) X.-K. Gao, J.-M. Dou, D.-C. Li, F.-Y. Dong and D.-Q. Wang, J.
Inclusion Phenom. Macrocyclic Chem., 2005, 53, 111; (b) J. Dou, X.-
K. Gao, F. Dong, D.-C. Li and D.-Q. Wang, Dalton Trans., 2004,
1
23 A. L. Spek, J. Appl. Crystallogr., 2003, 36, 7.
24 F. N. Allen, Acta Crystallogr., Sect. B: Struct. Sci., 2002, 58, 380.
This journal is ª The Royal Society of Chemistry 2011
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