Protonated bis(quinuclidine) included in channel thiourea-bromide and ribbons thiourea-iodide lattice: New thiourea inclusion compounds

Abstract

Host-guest supramolecular complexes are of special interest for understanding the chemistry in low dimensional spaces. The molecular recognition involved in the formation of such structures sometimes may be a relevant model for the kind of organized system usually found in living organisms. Matrix effects and anisotropic features which are habitual of the chemistry in restricted spaces also appear as useful for the development of new material of scientific and technological importance (Takemoto and Sonoda, 1984). Urea and thiourea clathrates constitute interesting systems in which the matrix being structured by hydrogen bond interactions has a relatively high liability to structural changes caused by the interaction with the host (Lehn, 1996). The syntheses and crystal structure of two novel ternary inclusion compounds having protonated bis (quinuclidine) as a guest into anionic thiourea-bromide and thiourea-iodide hosts are reported: (thiourea(2)[quinuclidine(2)H]Br-+(-)), 1 and (thiourea(2)[(quinuclidine(2)H)(+)](2)(I-)(2)), 2. In the two structures thiourea molecules interact with each other via N-H....S hydrogen bonds to produce ribbon-like arrangements. In structure I these ribbons do not contain the halogen and define two non intersecting sets running along the a and b axis, linked through N-H....Br hydrogen bonds having the external halide ions as acceptors. This ribbon-crossover defines a channel structure along c with a cavity cross section of ca. 5.85 x 15.50 (A) over circle. In structure 2, ribbons contain iodide anions as well, bridging thiourea dimers into parallel 1D structures which align their flat side parallel to the (110) set of planes leaving a free spacing of ca. 8.25 (A) over circle.

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Protonated Bis(quinuclidine) Included in Channel Thiourea-Bromide and Ribbons
Thiourea-Iodide Lattice: New Thiourea Inclusion Compounds
JUAN MERCHA´N1, NICOLA´S YUTRONIC1,*, PAUL JARA1, MARI´A TERESA
GARLAND2and RICARDO BAGGIO3
1Department of Chemistry, Faculty of Sciences, Universidad de Chile, Casilla 653, Santiago, Chile;2Department
of Physics, Faculty of Physical and Mathematical Sciences, Universidad de Chile, Casilla 487-3, Santiago, Chile;
3Department of Physics, Comisio´n Nacional de Energı´a Ato´mica, Av. Gral. Paz 1499, 1650, San Martı´n, Buenos Aires,
Argentina
Key words: Ternary inclusion compounds, thiourea-bromide, thiourea-iodide
Abstract
Host-guest supramolecular complexes are of special interest for understanding the chemistry in low dimensional
spaces. The molecular recognition involved in the formation of such structures sometimes may be a relevant model
for the kind of organized system usually found in living organisms. Matrix effects and anisotropic features which are
habitual of the chemistry in restricted spaces also appear as useful for the development of new material of scientific
and technological importance (Takemoto and Sonoda, 1984). Urea and thiourea clathrates constitute interesting
systems in which the matrix being structured by hydrogen bond interactions has a relatively high liability to
structural changes caused by the interaction with the host (Lehn, 1996). The syntheses and crystal structure of two
novel ternary inclusion compounds having protonated bis (quinuclidine) as a guest into anionic thiourea-bromide
andthiourea-iodidehostsarereported:(thiourea2[quinuclidine2H]+Br)),
dine2H)+]2(I))2), 2. In the two structures thiourea molecules interact with each other via N–H....S hydrogen bonds
to produce ribbon-like arrangements. In structure 1 these ribbons do not contain the halogen and define two non
intersecting sets running along the a and b axis, linked through N–H....Br hydrogen bonds having the external
halide ions as acceptors. This ribbon-crossover defines a channel structure along c with a cavity cross section of ca.
5.85 · 15.50 A˚. In structure 2, ribbons contain iodide anions as well, bridging thiourea dimers into parallel 1D
structures which align their flat side parallel to the (110) set of planes leaving a free spacing of ca. 8.25 A˚.
1and(thiourea2[(quinucli-
Introduction
The nature of molecular guest-host interactions has re-
ceived increasing attention due to its relevance in the
behaviour of new materials with novel properties, viz.,
with applications in electronic and optoelectronics [1–3],
etc. Host materials such as urea, thiourea, cyclodextrins,
calixarenes, zeolites and perhydrotriphenylene allow for
specific host-guest architectures, where guest molecules
are incorporated along channels, within layers, or in
isolated cages [1, 4–12]. Among such materials thiourea
inclusion compounds (i.e. clathrates), have been exten-
sively investigated. X-ray diffraction studies have shown
that the typical binary compounds of thiourea are built
up with an hexagonal channel structure [13–18]. Guest
speciescontainingamineorazacycleasfunctionalgroups
are also included in urea and thiourea hosts. Using 1,2
diazabicycle[2¢2¢2]octane or hexamethylenetetramine as
a guest and thiourea as a host it has been possible to
obtain binary layered inclusion compounds [15, 19–21].
The thiourea host is formed by hydrogen bonding and a
variety of guest molecules of appropriate size and shape
can be included. The thiourea channel is appropriate, for
example, to store branched hydrocarbon chains, as its
characteristic diameter comprises values between 7 and
9 A˚. In this way, it is interesting to obtain derivatives of a
thiourea matrix containing channels or layers large en-
ough as to accommodate more bulky molecules. The
synthesisofternarycompoundsoffersthispossibilityand
if in addition host and guest possess an anionic and a
cationic character, respectively, it might be interesting to
study their conductivity properties.
Examples of halogenated ternary ammonium inclu-
sion complexes of thiourea are limited [17, 22–23]. We
have recently reported the structure and some related
properties (like conductivity, etc) of thiourea2[quinucli-
dine2H]+Cl). [22–23]. Pedersen [24] and Hilgenfeld et al.
[25] report a thiourea-iodide matrix structure formed by
* Author for correspondence: E-mail: nyutroni@uchile.cl

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ribbons in a compound, containing dibenzo [18] crown-
6, potassium iodide and thiourea. In the matrix the
thiourea molecules are not involved in the complexation
of the cation nor do they have any contact to the
polyether, but form polymeric, hydrogen-bonded chains
instead.
We chosed quinuclidine as a guest considering its
small cyclic structure and its basic properties. The pro-
ton affinity of quinuclidine is 236 Kcal/mol and the
three-dimensional model with space occupation indi-
cates that no tension energy exists as in other nitrogen
pyramidal such triethylamine [26].
In this work we describe the syntheses, structure
characterization and properties of thiourea2[quinucli-
dine2H]+Br)(1) and (thiourea2[(quinuclidine2H)+]2(I))2),
(2).
Experimental
Commercially available reagents were used as received.
The products were obtained at room temperature by
slow evaporation of the solvent from methanolic solu-
tions of thiourea, quinuclidine and lithium halide in
2:2:1 molar ratio. After about 48 h, well formed hex-
agonal crystals for 1 and thin plates for 2 could be
separated. Products were washed with cold methanol
and dried under vacuum. Crystals of 1 and 2 showed
underthepolarizingmicroscope
behaviour which allowed to distinguish them from
lithium halide, quinuclidine and pure thiourea, as veri-
fied by X-ray powder diffraction analysis of the prod-
ucts samples. Crystals decompose in water producing a
characteristic visually observable dynamic effect [27].
Single crystals were selected for X-ray diffraction anal-
ysis. Data were collected at room temperature on a
Siemens R3m/V diffractometer with graphite mono-
chromatedMoKa
radiation
structuresweresolvedby
SHELXS-97 [28]. Hydrogen atoms were located geo-
metrically and allowed to ride both in coordinates as in
their isotropic temperature factors. H1?s in the cations
were located in the difference Fourier map and con-
ventionally refined with isotropic temperature factors.
A fully completed CIF was deposited in the Cam-
bridge Crystallographic Data Centre: for 1 CCDC
229895 and for 2 CCDC 229896.
acharacteristic
(k = 0.71073 A˚). The
directmethodsusing
Results and discussion
The synthesis of the compounds was carried up in
methanol as solvent, where the partial hydrolysis of
lithium bromide and lithium iodide produced the pro-
tons and halides necessary to obtain the ionic guest and
host. Moreover, this synthesis method allowed to re-
move the water contained in the solvent and as a result
the crystals structures obtained do not contain water as
often occurs in ternary thiourea compounds [17].
The structural determination of 1 and 2 shows the
presence of supramolecular structures which allow
describing them as host-guest inclusion compounds.
Crystal data and relevant refinement parameters are
presented in Table 1. Selected H-bonding interactions
are shown in Tables 2 and 3.
In spite of being quite different, the structures share
some common aspects, like the fact of being constituted
by polyanionic matrices composed of neutral thiourea
and Br/I anions, in which voids the cationic [Q2H]+
entities lodge.
In the case of 1, the polyanionic array is a 3D mesh
conformed by two sets of non intersecting planar
ribbons normal to the c axis, each one made up of
H-bonded thiourea molecules linked along the chain to
neighbouring sulphur atoms through their syn N–H
protons [17]. Figure 1 shows a view of such an elemental
chain and Table 2 gives details of the H-bonding inter-
actions. One of these sets runs along [110] at a height
z = 0.50 and the other one, along [)110] at z = 0 and
1. The interaction between the quasi-orthogonal chains
is provided by H-bonds having the bromine anions,
which lie in between, as common acceptors. This chain-
crossover defines a set of cavities approximately 5.85 by
15.50 A˚, in which the [Q2H]+complex species are
stacked with a periodicity of ca. 11.4 A˚, Figure 2. Be-
sides the omnipresent coulombian forces due to the ionic
character of the structure, the only other interaction
holding the cationic groups seem to be van der Waals
interactions, as suggested by the distances between the
outermost hydrogens in the complex and the matrix,
which are always longer than 3 A˚. Nevertheless, these
interactions are strong enough as to prevent free rota-
tion of the cation, which appears very well resolved,
with no trace of disorder.
In the case of 2 the elemental unit of the anionic
network consists of hydrogen-bonded thiourea dimers
bridged by iodide anions through N–H....I)bonding
(Figure 3, Table 3) and which define ribbons running in
the c direction at x = 0, 1, y = 0.50. These ribbons,
which do not have any kind of direct interaction with
each other, align their flat side parallel to the (110) set of
planes (Figure 4), leaving a free spacing of ca. 8.25 A˚,
where the diquinuclidinium cations [Q2H]+reside. Here
again there is not direct linkage between the anionic
network and the embedded cations, the interactions
taking part being the coulombian as well as van der
Waal?s.
In both structures the guest species corresponds to an
adduct of a heterocyclic base with its conjugated cation.
In the case of 1 there are no differentiated roles for the
base/cation as the proton lays on a symmetry centre and
the group displays a [Q–H–Q]+linear arrangement
similar to one reported for diquinuclidinone [29]. The
considerably short 1.341(3) A˚
compound here described is similar to that determined
by neutron diffraction studies for the perchlorate
salt of the diquinuclidinium homoconjugated cation
(d(N–H) = 1.317 A˚, N–H–N angle = 175.7?) [29].
N–H distance in the

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The [Q2H]+group in 2, instead, is clearly differen-
tiated into a well defined QH+cation and a neutral Q
base to which it is strongly H-bonded, (N1A–H1:
0.99(9), H1...N1B: 1.71(9) A˚, N1A–H1...N1B: 175(7)?)
as shown in Figure 3.
Vibrational analysis of a [Q–H–Q]+linear arrange-
ment as the one in 1 predicts absorption at 668 cm)1for
the symmetric NÆÆÆN stretching mode, and 1260 cm)1for
the antisymmetric ion transfer vibrations. Correspond-
ing features are indeed apparent in the IR spectrum of
[Q2H]+,inwhichacharacteristic
2937 cm)1has been observed [30]. Thus, for 1 beside the
frequencyat
quinuclidine absorption (at 2930 cm)1) and the charac-
teristic stretching modes of the thiourea network (ob-
served normally at 1470 and between 3169 and
3367 cm)1) [31], a relatively intense absorption band at
1433 cm)1and a weak absorption at 659 cm)1are
clearly seen. Relative absorption values for thiourea,
quinuclidine, 1 and 2, are shown in Table 4.
If crystals of the products are left in contact with a
highly polar solvent as DMSO or water [27], the
quinuclidine appears to be rashly extracted from the
solid propelling the crystal through the liquid surface.
The evolution of the quinuclidine may be visually
Table 1. Crystal data and structure refinement for 1 and 2
Identification code12
Formula
Formula weight
Temperature
Wavelength
Crystal system
Space group
a/A˚
b/A˚
c/A˚
a/?
b/?
c/?
Volume/A˚3
Z
Dc/g cm)3
Absorption coefficient/mm)1
F(000)
Crystal size/mm3
Theta range for data collection
Index ranges
2(C H4N2S) Br)1(C14H27N2)+1
455.53
293(2) K
0.71073 A˚
Monoclinic
C2/c
13.418(10)
11.546(6)
14.916(10)
90
99.09(6)
90
2282(3)
4
1.326
1.996
960
0.14 · 0.05 · 0.02
2.34 to 25.06?.
0< = h< = 15, 0< = k< = 13,
)17< = l< = 17
2099
1993 [R(int) = 0.0913]
Psi-scan
0.9612 and 0.7675
1993 / 117
1.055
R1 = 0.0494, wR2 = 0.1181
R1 = 0.0749, wR2 = 0.1323
0.0087(11)
0.882 and )0.677
(C H4N2S) I)1(C7H14N)+1(C7H13N)
426.40
293(2) K
0.71073 A˚
Triclinic
P-1
10.1003(15)
10.1148(15)
10.9033(16)
63.889(2)
83.889(2)
77.779(2)
977.4(3)
2
1.449
1.746
436
0.10 · 0.04 · 0.01
2.06 to 23.24
)11< = h< = 11, )11< = k< = 9,
)12< = l< = 12
12774
2760 [R(int) = 0.0458]
Multi-scan
0.9828 and 0.8448
2760 / 195
1.044
R1 = 0.0443, wR2 = 0.1252
R1 = 0.0447, wR2 = 0.1258
0.020(3)
0.887 and )1.175
Reflections collected
Independent reflections
Absorption correction
Max. and min. transmission
Data/parameters
Goodness-of-fit on F2
Final R indices [I>2r(I)]
R indices (all data)
Extinction coefficient
Largest diff. peak and hole / e.A˚)3
Table 2. Hydrogen bonds for 1 [A˚and ?]
D–H...A d(D–H)d(H...A) d(D...A)<(DHA)
N(2)–H(2A)...Br(1)
N(2)–H(2B)...S(1)#1
N(3)–H(3A)...Br(1)
N(3)–H(3B)...S(1)#2
0.86
0.86
0.86
0.86
2.63
2.63
2.59
2.64
3.426(4)
3.476(4)
3.396(4)
3.470(4)
155.1
167.6
156.9
161.5
Symmetry transformations used to generate equivalent atoms: #1
)x + 1/2,)y + 1/2,)z + 1 #2 )x + 1,)y + 1,)z + 1 #3 )x + 1,
y, )z + 3/2.
Table 3. Hydrogen bonds for 2 [A˚and ?]
D–H...Ad(D–H) d(H...A) d(D...A)<(DHA)
N(2)–H(2A)...I(1)#1
N(2)–H(2B)...S(1)#2
N(3)–H(3A)...I(1)#1
N(3)–H(3B)...I(1)
N(1A)–H(1)...N(1B)
0.86
0.86
0.86
0.86
0.99(9)
2.92
2.60
2.89
2.89
1.71(9)
3.723(4)
3.433(4)
3.695(5)
3.723(4)
2.704(5)
155.9
164.6
157.2
163.5
175(7)
Symmetry transformations used to generate equivalent atoms: #1
)x,)y + 1,)z + 1 #2 )x,)y + 1,)z.

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observed by adding phenolphtalein to the solution. The
motion effect is thus accompanied by the formation of a
beautiful red ‘‘wake’’ in the liquid. This experiment
suggests that the hosts structures experiment a rupture
and it produces thiourea, Br)or I), proton and quinu-
clidine in dissolution.
Acknowledgement
Research financed by FONDECYT (1050287)
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Figure 1. Molecular ellipsoid diagram of 1, drawn at a 40% proba-
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ThioureaQÆÆÆÆQ12
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2937
1260
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