Journal of Fluorine Chemistry 127 (2006) 270–276

www.elsevier.com/locate/fluor

A comparative study of crystal structures and inclusion

properties of fluorinated triazines
Katharina Reichenbaecher a, Helen Stoeckli-Evans b, Edwin Weber c, Juerg Hulliger a,*
a
Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
b
Institute of Chemistry, University of Neuchâtel, Av. Bellevaux 51, CH-2007 Neuchâtel, Switzerland
c
Institute of Organic Chemistry, TU Bergakademie Freiberg, Leipziger Str. 29, D-09596 Freiberg/Sachsen, Germany
Received 19 September 2005; received in revised form 5 December 2005; accepted 5 December 2005

Abstract
Three perfluorinated host compounds of the triazine type, namely 2,4,6-tris(pentafluorophenoxy)-1,3,5-triazine (1), 2,4,6-tris(pentafluor-
othiophenoxy)-1,3,5-triazine (2) and 2,4,6-tris(pentafluorophenamin)-1,3,5-triazine (3), were synthesized differing only in the linking heteroatom
(O, S and NH) between the triazine core and the pentafluorophenyl groups. The crystal structures involving compounds 1, 2 and their inclusion
compounds are dominated by a variety of fluorine interactions (phenyl-perfluorophenyl, C–H


F, F


F, C–F


pF). However, in the structure of 3,
possessing additional hydrogen atoms of the linkage NH-groups, the formation of hydrogen bonds is favoured, whereas fluorine contacts are less
apparent. Investigations by powder X-ray diffraction and thermogravimetric analysis revealed substantial differences in the host–guest interactions
of the inclusion compounds.
# 2005 Elsevier B.V. All rights reserved.

Keywords: Fluorine compounds; Triazines; Inclusions; Host–guest compounds; Fluorine interactions

1. Introduction interaction. One example stems from coordination chemistry,

where the fluorination of ligands prevents an interpenetration
Over the last few years fluorine has become more and more of molecules allowing the formation of flexible networks
important in crystal engineering [1]. Up to now a number of [10].
fluorinated compounds were synthesised to investigate phenyl- Recently, we reported on a series of phenoxy-substituted
perfluorophenyl [2], H


F [3], F


F [4] and C–F


pF 1,3,5-triazines providing evidence for a supramolecular control
[5] interactions to study their influence on crystal structures of fluorine. Here, the highly fluorinated compound 2,4,6-
[6,7]. tris(pentafluorophenoxy)-1,3,5-triazine 1 forms channel-type
However, unexpected behaviour of fluorine is seen in the inclusions with p-xylene and p-chlorotoluene [11]. Conse-
case of hydrogen bonds: as fluorine has the highest electro- quently, it is of interest to know, how inclusion properties
negativity, it is predestined to form strong hydrogen interac- change by replacing the linkage atom between the triazine core
tions. In fact, F is one of the best hydrogen acceptors, but the and the pentafluorophenyl groups (S or NH). Therefore, we
so called ‘‘organic fluorine . . . hardly ever accepts hydrogen synthesized the compounds 2,4,6-tris(pentafluorothiophe-
bonds’’ forming only weak interactions [3]. Except the phenyl- noxy)-1,3,5-triazine 2 and 2,4,6-tris(pentafluorophenamin)-
perfluorophenyl stacking, showing a stabilizing energy of about 1,3,5-triazine 3. The present article is highlighting a
30 kJ mol1 [8,9], fluorine interactions are mostly weak. comparison of five crystal structures involving the free host
There are only a few examples of fluorine containing and respective inclusion compounds with mesitylene and 1,4-
compounds that deal with fluorinated inclusion compounds dioxane.
involving the influence of fluoro substituents on host–guest
2. Results and discussion

* Corresponding author. Tel.: +49 31 6314241; fax: +49 31 631 3993. A comparison of compounds 1–3 (Fig. 1) revealed
E-mail address: [email protected] (J. Hulliger). substantial differences in the crystal structures and inclusion
0022-1139/$ – see front matter # 2005 Elsevier B.V. All rights reserved.
doi:10.1016/j.jfluchem.2005.12.003
 K. Reichenbaecher et al. / Journal of Fluorine Chemistry 127 (2006) 270–276 271

Table 2
Phenyl-pentafluorophenyl contacts in crystal structures of inclusion compounds
of 1–3
Atoms Centroid– Angle (8)
phenyl(A)


pentafluorophenyl(B) centroid
distance
(Å)
1 p-Xylene C31


C4 4.17 30.8
2 Mesitylene C56


C35 3.59 12.4
C47


C23 3.70 15.7
C47


C29 3.66 16.0
3 Mesitylene C56


C3 3.75 20.7
C93


C24 3.67 20.6
Phenyl and pentafluorophenyl groups are given by one carbon atom A and B of
Fig. 1. Molecular structures of perfluorinated triaznes. each group. The centroid is calculated based on six atoms and the angles are
determined between the centroid–centroid line and the normal of the phenyl
plane.
properties caused by the replacement of the linkage atom
oxygen by sulfur or NH-group. All three compounds yielded
inclusions with typical guest molecules summarized in Table 1. molecules are accommodated in channels showing a van der
Inclusions of 1 crystallized all in the same structure, whereas 2 Waals cross section of 7.6  3 Å2. The channel wall is mainly
showed channel inclusions exhibiting various crystal packings made up by stacked pentafluorophenyl groups. Short host–
depending on the guest molecule. In the case of 3, major guest interactions formed by CH3-groups involve weak C–
differences between crystal structures of inclusions were H


O (2.9 Å, 117.88) [12] as well as C–H


pF hydrogen bond
observed, which seems to be caused by the hydrogen atoms of type interactions investigated by solid-state NMR [11].
the NH-group. Consequently, the crystal structures and Measured phenyl-pentafluorophenyl contacts do not show
inclusions of 1 and 2, on one hand, and that of 3 will be typical values of phenyl-perfluorophenyl stacking (Table 2).
discussed separately. Therefore, this feature seems to be caused by the hydrogen
interactions of the CH3-groups.
2.1. Crystal structures of the solvent free compounds and Compound 2 formed channel-type inclusions with p-xylene,
inclusions of 1 and 2 p-chlorotoluene, p-methylbenzotrifluoride (host:guest ratio:
1:2) and mesitylene (host:guest ratio: 1:1) featuring a larger
A previous paper [11] dealt with the crystal structure of the size.
host compound 1, showing that triazine molecules are arranged The crystal structure of 2
mesitylene (space group P21/n) is
in layers, which are stacked congruently along the a-axis. built up by layers, which are formed by host and guest
Compound 2 features similar properties. Here, triazines build molecules, where one guest is surrounded by four triazines
up two different layers that are stacked alternating along the a- (Fig. 2). These layers are stacked congruently along the b-axis
axis. Neither compound 1 nor 2 show specific interactions. with a distance of about 7.9 Å, generating channels with van der
Molecules are closed packed featuring F


F distances in the Waals cross section of 3.1  5.5 Å2 which are smaller
range of 2.6–2.8 Å. compared with the inclusions of 1 (see above). Moreover,
Compound 1 is known to form channel-type inclusions with unlike 1
( p-xylene)0.5, where the guest molecules are located
guest molecules such as p-xylene, p-chlorotoluene and p- around a centre of symmetry, the channels of 2
mesitylene are
methylbenzotrifluoride showing a host:guest ratio of 2:1. All unsymmetrical, where one side of the channel wall is built up
these inclusions crystallize in the same structure with the by fluorine atoms. Thus, in contrast to 1, the channel wall of the
triclinic space group P1̄. Triazines are stacked congruently present structure shows a higher density of fluorine atoms
along the a-axis featuring a distance of about 6 Å. Guest giving rise to a higher number of short F


H contacts (2.4–
2.8 Å) between host and guest molecules (Table 3).
Table 1 2
Mesitylene shows phenyl-perfluorophenyl stacking with a
Host:guest ratios for inclusions of 1–3 with various guest molecules centroid–centroid distance of 3.6–3.7 Å and angles of 12–168
1 2 3
(Table 2), which is within the limit of reported values [2].

Xylene 2:1 1:2 1:1 2.2. Crystal structures and inclusion properties of 3
Toluene – 1:2 1:1
Mesitylene – 1:1 1:1
Benzene – – 1:1 Unsolvated single crystals of 3 (obtained by sublimation)
4-Methylbenzotrifluoride 2:1 1:2 crystallized in the space group P21/n. The structure features a
Dioxane – – 1:2.5 congruent stacking of triazines along the a-axis with a distance
In the case of 1 and 2, the ratios were determined by thermogravimetric analysis of 7.8 Å. Similar to the host compounds mentioned above,
while the inclusions of 3 were analysed by NMR. compound 3 does not show a three-fold symmetry. An essential
272 K. Reichenbaecher et al. / Journal of Fluorine Chemistry 127 (2006) 270–276

Fig. 3. Motif of hydrogen bond type interactions in the crystal structure of 3.

difference in the crystal structure of 3 compared to 1 and 2 is

caused by the hydrogen atoms of the NH-groups, forming
hydrogen bonds between neighbouring triazines (shortest
contacts of 2.1 Å) (Table 3), which seem to dominate the
structure (Fig. 3). In addition, F


H–N hydrogen bond type
contacts were found with a distance of 2.2 Å, being unusually
short compared to reported organic fluorine compounds [3].
Measurements of an attractive F


H–N interaction in thrombin
Fig. 2. Channel structure of 2
mesitylene. derivates yielded a value of 0.8–1.5 kJ mol1 [13], which is
weak compared to known N–H


N interactions (20–
40 kJ mol1) [14]. A similar kind of interaction pattern was
observed in crystal structures of polyfluorophenyl substituted-
Table 3
Hydrogen bond-type interactions in crystal structures of 1–3
4,5-dihydropyrazole derivates, where a slightly larger F


H
distance (2.32 Å) was measured [15].
Distance (Å) Angle (8) As expected, the particular property of the amino group is
D–B


A B


A D


A D–B


A also reflected in the inclusion behaviour of 3, which is broader
1
( p-Xylene)0.5 C30–H34A


O1 2.89 3.46 117.75 compared with 1 and 2, respectively (Table 1). A closer look
C30–H34C


F9 2.68 3.57 150.75 shows that the host:guest ratios are different in the
C30–H34A


F14 2.90 3.65 133.76 corresponding inclusions of 3 compared with those of 1 and
C33–H32


F8 3.09 3.99 159.88 2 (except the inclusion of 2 and 3 with mesitylene).
2
Mesitylene C64–H64A


F26 2.87 3.86 176.88 Furthermore, 1,4-dioxane was excepted to act as guest
C62–H62C


F25 2.63 3.61 177.66 molecule in the host lattice of 3. This stimulated the study
C62–H62A


F2 2.68 3.60 155.62 of inclusions of 3 with mesitylene and 1,4-dioxane.
C59–H59


F27 2.88 3.81 165.46
C63–H63C


F4 2.91 3.52 103.22
The inclusion compound of 3 with mesitylene (host–guest
C53–H53B


F11 2.95 3.87 158.23 1:1) was crystallized by isothermal evaporation. The structure
C53–H53A


F17 2.88 3.22 101.55 provides oval channels along the c-axis with dimensions of
3 N4–H4


N3 2.12 2.96 174.07 5.7  3.5 Å2, built up by four host molecules (Fig. 4a). Two
N6–H5


N2 2.28 3.10 170.00 molecules each are connected by N


H hydrogen bonds
N5–H6


F11 2.20 2.99 163.91 (N


H: 2.22–2.25 Å) and short F


H contacts (F


H: 2.37–
3
Mesitylene N13–H13A


N6 2.22 3.04 153.74 2.44 Å) to form a unit, where two such units are linked by
N18–H18A


N3 2.25 3.06 153.65 pentafluorophenyl groups showing a close packing of fluorine
N17–H17A


F1 2.37 2.98 126.12 atoms (F


F: 2.71–2.87 Å). The mesitylene molecules are
N15–H15A


F16 2.45 3.09 130.58 orientated in the oval channels planar to the pentafluorophenyl
C121–H121


F4 2.72 3.49 114.80
C97–H97A


F16 2.95 3.85 154.31
substituents of the host showing a centroid–centroid distance of
C96–H96C


F29 2.90 3.72 142.21 3.7 Å (Fig. 4b, Table 2).
The inclusion compound of 3 with 1,4-dioxane shows a
3
(1,4-Dioxane)2.5 N2–H2


O1 2.10 2.90 160.23
host:guest ratio of 1:2.5 and crystallizes in the space group R3̄.
 K. Reichenbaecher et al. / Journal of Fluorine Chemistry 127 (2006) 270–276 273

Fig. 4. Crystal structure of 3
mesitylene: (a) view along the channel of the inclusion; (b) motif showing the host–guest interaction.

Three different positions of guest molecules were found. One structure, which could be rebuild by sorption of guest
dioxane molecule (guest 1), involving atom O1, features a molecules from the gas phase.
centre of symmetry (Ci), while the two remaining dioxane Inclusion compounds 2
mesitylene and 3
mesitylene,
molecules (guest 2 and guest 3) both possess a three-fold obtained by isothermal evaporation, were exposed to the
inversion axis (C3i). Guest molecules 2 and 3 are stacked vacuum for 1 h. The resulting solids were analysed by powder
alternatively with triazines along the c-axis following an order X-ray diffraction. Afterwards, these solids were used for
of guest 2–host–guest 3–host (Fig. 5b). Guest 1 is located sorption experiments, carried out in a closed flask, in which the
between two host molecules in the (a,b)-layer and forms host (powder) and the guest component (liquid) were kept in
hydrogen bonds with the amino group of the hosts (O


H: open separated glasses. After 4 days of exposure solid phases
2.1 Å, N–H. . .O: 1608), which can be classified as strong were analysed by powder X-ray diffraction.
interaction [14] (Fig. 5a and Table 3). Thus, each host is In all three cases, desorption of guest molecules leads to
surrounded symmetrically by three dioxane molecules. the structure of the corresponding unsolvated host compound,
Noteworthy, this relation leads to a three-fold symmetry of having lost its specific channel architecture (Fig. 6). However,
the host molecule, which is only seen in this structure. Fluorine these channel structures were rebuilt by sorption of guest
interactions could not be observed here, which might be molecules from the gas phase. This occured at relative low
avoided in favour of strong hydrogen bonds. temperatures (performed at 25 and 50 8C) for all three cases
indicating a rather low energetic activation to convert the
guest free to the channel structure. A comparison of guest free
2.3. Sorption properties and channel structure showed, that only weak F


F contacts
are broken while more intensive host–guest interactions, such
In the previous paper we have described the reversible as phenyl-perfluorophenyl, C–H


pF or C–H


O contacts,
sorption property of 1
( p-xylene)0.5 [11]. Here, desorption of are generated.
the guest molecules leads to a complete collapse of the channel

Fig. 5. Crystal structure of 3
(dioxane)2.5: (a) stacking along the c-axis (order: guest 2–host–guest 3–host); (b) hydrogen bonds of the NH-group with 1,4-dioxane.
274 K. Reichenbaecher et al. / Journal of Fluorine Chemistry 127 (2006) 270–276

form an alternate stacking, which leads to weaker contacts

being manifested by the low onset temperature of guest release.
Nevertheless, the sum of all the weak interactions affords
formation of inclusion compounds.

3. Conclusion

Three perfluorinated triazine compounds differing only in

the linking heteroatom (O, S and NH) form inclusions with a
number of typical solvent molecules. The alteration of
heteroatoms shows an essential effect on crystal structures
and inclusion properties.
Fig. 6. Reversible sorption properties of the inclusion compounds: 1
( p- The crystal structures of the unsolvated hosts of 1 and 2 as
xylene)0.5, 2
mesitylene and 3
mesitylene. well as their inclusion compounds are dominated by a variety of
fluorine interactions (phenyl-perfluorophenyl, C–H


F, F


F,
2.4. Thermogravimetic analysis (TG) C–H


pF). On the other hand for compound 3, possessing
additional hydrogen atoms, the formation of hydrogen bonds is
Inclusions of compound 2 showed a onset of desorption of favoured while fluorine contacts are less apparent. This fact is
guest molecules already at room temperature. However, reflected in the inclusion properties of the host molecules. Here,
inclusions of 1 and 3 featured a higher thermal stability, compounds 1 and 2 include only aromatic solvent molecules,
whereas the onset temperature of desorption for the case of 3 is whereas 3 also accepts 1,4-dioxane as a guest may be due to the
ordered according to the boiling temperature of the guest. The formation of hydrogen bonds.
inclusion compound 3
(1,4-dioxane)2.5 represents an exception Furthermore, a change of the linkage heteroatom effects the
since here strong hydrogen bonds act as host–guest interactions. sorption properties of the host compounds. Thermogravimetric
Inclusions of 1 feature a quite interesting case of thermal analysis revealed clear differences between the thermal
stability. Here, the temperature of desorption of guests stability of corresponding inclusions. Particularly, inclusions
decreased in the order: p-xylene, p-chlorotoluene, p-methyl- of 1 featured a decrease of thermal stability with a decreasing
benzotrifluoride (Fig. 7a). Thus, exchange of a CH3 group by a number of CH3-groups of guest molecules, showing that these
chlorine atom, being roughly of the same size, leads to a groups have an essential impact on host–guest interactions. In
decrease of the desorption temperature of about 10 8C, which the case of 2 and 3, this behaviour could not be observed, as the
might be attributed to a loss of hydrogen bonds. This is a CH3-groups of the guest molecules do not directly contribute to
suggestive fact that CH3-groups participate in host–guest the host–guest contacts.
interactions (C–H


O and C–H


pF hydrogen bonds), being
confirmed by solid-state NMR [11]. 4. Experimental
A further type of important host–guest contact, found in
inclusions of 2 and 3, is the phenyl-perfluorophenyl interac- 4.1. General
tion. This kind of interaction is reported to be strong if the
phenyl and perfluorophenyl groups are stacked in an All starting materials were commercially available and were
alternating manner. However, inclusions of 2 and 3 do not used without further purification. Melting points (mp) were
measured with a Buechi 510. IR spectra of the compounds were
analysed with the spectrometer Perkin-Elmer Spectrum One.
1
H and 13C NMR spectra were recorded with a Bruker Avance
300 spectrometer operating at 300.18 and 75.48 MHz,
respectively. The chemical shifts are given in ppm (internal
standard Me4Si). 19F NMR were determined with a Bruker
DRX 400 operating at 376.46 MHz (external standard CCl3F).
Acetone-d6 was used as solvent in all NMR measurements. MS
spectra were obtained by Perkin-Elmer SCIEX (API QSTAR
Pulser) spectrometer.

4.2. 2,4,6-Tris(pentafluorothiophenoxy)-1,3,5-triazine (2)

A 5 g (25 mmol) pentafluorothiophenole and 0.92 g

(5 mmol) cyanuric chloride were heated at 140 8C for 15 h.
The mixture was washed with hot methanol and purified by
column chromatography (SiO2 60 [40–63 mm] eluent: chloro-
Fig. 7. TG analyses of inclusions of 1. form/n-hexane 1:1) to yield 16.4% of a white solid. mp: 115 8C;
 K. Reichenbaecher et al. / Journal of Fluorine Chemistry 127 (2006) 270–276 275

Table 4
Crystal data for 2, 3 and their inclusions
2 2
Mesitylene 3 3
(Dioxane)2.5 3
Mesitylene
Crystallisation method Isothermal evaporation Isothermal evaporation Sublimation Isothermal evaporation Isothermal evaporation
in n-hexane in mesitylene in dioxane in mesitylene
Empirical formula C21F15N3S3 C30H12F15N3S3 C21H3F15N6 C31H23F15N6O5 C30H15F15N6
Formular weight (g/mol) 675.42 795.61 624.29 844.55 744.48
T (K) 153 153 373 153 173
l (Å) 0.71073 0.71073 0.71073 0.71073 0.71073
Crystal system Orthorhombic Monoclinic Monoclinic Trigonal triclinic
Space group Pbca P21/n P21/n R3̄ P1̄
a (Å) 9.1975(3) 21.1449(15) 7.7622(5) 18.255(4) 9.6282(11)
b (Å) 19.8966(8) 7.8900(4) 27.823(3) 18.255(4) 11.9830(11)
c (Å) 24.8044(9) 37.882(3) 10.4393(8) 17.130(4) 26.613(3)
a (8) 90 90 90 90 96.523(8)
b (8) 90 97.024(9) 97.904(6) 90 90.152(8)
g (8) 90 90 90 120 90.930(8)
V (Å3) 4539.2(3) 6272.5(7) 2233.1(3) 4943.7(19) 3050.2(6)
Z 8 8 4 6 4
r (g cm3) 1977 1.685 1.857 1.702 1.621
2Qmax (8) 59 52 52 59 50
m(Mo Ka) (mm1) 0.470 0.355 0.203 0.173 0.163
Measured reflexes 53960 42724 19567 15903 10224
Independent reflexes 6308 12063 3981 2905 10224
Rint 0.0454 0.0404 0.0790 0.05 0.1
R1 [I > 2s(I)] 0.0316 0.0341 0.0371 0.042 0.1052
wR2½I > 2sðIÞ 0.0777 0.0798 0.0869 0.1144 0.3017
CCDC 290172 290171 290173 290174 290175

IR (KBr): nmax (cm1) 1644 (perfluorinated arom.), 1490 in Table 4. The intensity data were recorded on a Stoe IPDS
(triazine), 1259 (C–F), 1099(s), 984 (s), 870/835 (s). 13C NMR diffractometer. The structures were solved by direct methods
(acetone-d6): d = 103.0 (C1, t, 2JCF = 20.5 Hz), 137.0 (C2, d, using the programme SHELXS-97 [16]. The refinement and all
1
JCF = 254.5 Hz), 143.6 (C4, d, 1JCF = 257.0 Hz), 147.0 (C3, d, further calculations were carried out using SHELXL-97 [17]. In
1
JCF = 252.7 Hz). 19F NMR (acetone-d6): d = 132.2 (F1, d), cases where it was possible to locate the H-atoms from Fourier
150.65 (F3, t), 163.1 (F2, dd). MS m/z (rel. int.): 675 (28.8) difference maps, they were refined isotropically. The non-H
[M] +, 476 (41.4) [MSC6F5] +, 251 (37.4) [M434] +, 199 atoms were refined anisotropically, using weighted full-matrix
(100) [SC6F5], 155 (66.1) [M520]+. least-squares on F2. The corresponding crystallographic data
are summarized in Table 4. CCDC reference numbers 290,
4.3. 2,4,6-Tris(pentafluorophenamino)-1,3,5-triazine (3) 171–175.

5 g (27.3 mmol) pentafluoroaniline and 0.72 g (3.9 mmol) 4.5. Thermogravimetric analysis
cyanuric chloride in 30 ml n-decane were heated at 100 8C for
15 h. The mixture was washed with hot n-hexane and Thermogravimetric data were measured with a Mettler
recrystallized from benzene to yield 37.2% of a white solid. Toledo TGA 50.
mp: 172 8C; IR (KBr): nmax (cm1) 3224–2951 (N–H), 1595
(perfluorinated arom.), 1497 and 1445 (triazine), 1367 (C–F), Acknowledgement
1099 (s), 999 and 977 (s). 1H NMR (acetone-d6): d = 8.6 (H–N,
s). 13C NMR (acetone-d6): d = 114.9 (C1, t, 2JCF = 15.6 Hz), This work was supported by the Swiss NFP 47 program,
136.6 (C2, d, 1JCF = 274.0 Hz), 139.0 (C4, d, 1JCF = 249.1 Hz), project no. 4047-057476/2-3.
143.3 (C3, d, 1JCF = 241.5 Hz), 166.9 (N–C–N, s). 19F NMR
(acetone-d6): d = 146.7 (F1, d), 160.2 (F3, t), 166.5 (F2, s). References
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