Journal of Inclusion Phenomena and Macrocyclic Chemistry (2006) 54:153–157  Springer 2006

DOI 10.1007/s10847-005-6286-z

The Structure of New Host Molecules that form Channel Inclusion Compounds

NATALIA FRIDMAN MOSHE KAPON YANA SHEYNIN and MENAHEM

KAFTORY*
Department of Chemistry, Technion-Israel Institute of Technology, 32000, Haifa, Israel

(Received: 8 September 2004; in final form: 25 April 2005)

Key words: channel inclusion compounds, host-guest interactions, X-ray crystal structure

Abstract
1,3-Benzenediamine,N,N¢-bis(4,6-dichloro-1,3,5-triazine-2-yl) and 1,3,5-Triazine,2,2¢-[2-methyl-1,3-phenylenebis(oxy)]
bis(4,6-dichloro) were synthesized as host molecules. The inclusion compound of 1,3-Benzenediamine,N,N¢-bis(4,6-
dichloro-1,3,5-triazine-2-yl) crystallizes in the monoclinic crystal system in space group C2/c. The host molecule
occupies the space group 2-fold special position and packed in the crystal lattice in such a manner as to leave channels
running along the c axis of a rectangular cross-section. It crystallizes with two molecules of acetone that are hydrogen
bonded to the amino nitrogen atoms. Molecules of 1,3,5-Triazine,2,2¢-[2-methyl-1,3-phenylene bis(oxy)]bis(4,6-di-
chloro) are packed in the crystal in such a manner as to leave channels of a trapezoid cross-section that are running along
the a axis. Guest molecules such as metanol, ethanol, and ethyl acetate can be used to fill the channels. The crystal
structures of two inclusion compounds are described.

Introduction ‘‘cavitates’’ and the inclusion compounds obtained from

the second type of host molecules are also called ‘‘clath-
During the second half of the 19th century the field of rates’’ [5]. Among the solid-state clathrates of organic
non-covalent chemistry received momentum especially hosts the channel clathrates are very interesting and they
since the introduction of the notion ‘‘Supramolecular have been thoroughly studied because of their potential
Chemistry.’’ Supramolecular chemistry was defined as applications in separation between guest molecules. For
chemistry based on non-covalent interactions, such as example the inclusion compounds of urea [6], or trimesic
hydrogen bond, dipole–dipole, dipole-induced dipole, acid [7], both providing channels with hexagonal cross-
electrostatic, charge-transfer, hydrophobic, dispersive section, alicyclic diols [8], and tri-o-timotide [9], that
Van der Waals, coordination interactions, or in short as provide channels with triangle cross-section.
‘‘soft bonds’’[1]. Preceding to the use of the notion ‘‘Su- The interactions between the guest and the host
pramolecules,’’ other words have been used such as molecules may be weak (Van der Waals interactions) or
‘‘inclusion compounds,’’ ‘‘host-guest compounds’’ etc. strong (hydrogen bonds). In the present work we
Several books were written and the record was in 1996 describe the synthesis and the crystal structure of inclu-
when eleven volumes of Comprehensive Supramolecular sion compounds made up from two new host molecules
Chemistry were published [2]. In the narrower subject of based on cyanuric chloride: 1,3-Benzenediamine,N,N¢-
host-guest chemistry most of the effort was devoted to bis(4,6-dichloro-1,3,5-triazine-2-yl) (1) with acetone, and
the understanding of the interaction between the host and 1,3,5-Triazine,2,2¢-[2-methyl-1,3-phenylene bis(oxy)]bis
guest molecules, the physicochemical aspects [3], and to (4,6-dichloro) (2) with ethyl acetate (Scheme 2).
the design of new host compounds for possible applica-
tions [4]. The host compounds may be classified into two
main groups: (i) host molecule that has a shape that en-
ables the accommodation of a guest molecule. Examples Experimental section
for such host molecules are cyclodextrins, cyclophanes,
calixarenes, polyethers etc., and (ii) host molecules that NMR data were collected on a Bruker AC400 instru-
can form inclusion through packing in a lattice in such a ment at 25
C.
way that cavities, channels, or layers are being occupied
by guest molecules. The inclusion compounds obtained Synthesis
from the first type of host molecules are also called
1,3,5-Triazine,2,2¢-[2-methyl-1,3-phenylenebis(oxy)]bis
* Author for correspondence. E-mail: kaftory@tx.technion.ac.il (4,6-dichloro)(1)Æ1/2(ethyl acetate). To a stirred mixture
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of 1.84 g (10 mmol) of cyanuric chloride in 20 ml of Crystal structure determination

acetone, cooled in an ice bath, was added dropwise over
10 min, 0.62 g (5 mmol) of 2-methylresorcinol in 5 ml of Relevant details of data collection and refinement of the
acetone and 1.33 g (5 mmol) of 2,4,6-collidine. A mix- crystal structures of (1)Æ(ethyl acetate) and (2)Æ(acetone)2
ture was stirred at 0
C for two hours. The mixture was are collected in Table 1. The crystal stuctures were
filtered from collidine chloride, the solution was diluted solved and refined with SHELXL93 [10], using aniso-
with 20 ml of ice water. The solution was treated with tropic displacement parameters for non-hydrogen
chloroform to extract the product. The solution was atoms. All H atoms were located from difference Fou-
dried over MgSO4. The resulted mixture was allowed to rier maps and refined isotropically. The ethyl acetate is
remain at room temperature overnight. The chloroform disordered and was refined isotropically without the
extract was filtered and concentrated to dryness in hydrogen atoms.
vacuo. Cream-white solid was purified by silica gel
chromotography with CH2Cl2 and isolated in 66 %
yield. Recrystallization from ethyl acetate gave the Results and discussion
inclusion complex (guest-ethyl acetate, m.p. 178
C, 1H
NMR (CDCl3) d 7.41 (t, H), 7.13 (d, 2H), 2.02 (s, 3H). Crystallographic data for the two inclusion compounds
1,3-Benzenediamine,N,N¢-bis(4,6-dichloro-1,3,5-tria- 1Æ2(acetone), and 2Æ1/2(ethyl acetate) are summarize in
zine-2-yl)(2)Æ2(acetone). To a cooled 20 ml of water in Table 1. The molecular structures of 1 and 2 with the
an ice bath was added boiled mixture of 1.84 g atomic numbering are shown in Figures 1, and 2,
(10 mmol) of cyanuric chloride in 15 ml of acetone, the respectively. The two host molecules adopt different
mixture was cooled in an ice bath at 0
C. 1.08 g conformations. Comparison of similar molecules shows
(10 mmol) of 1,3-phenylenediamine was added dropwise that they adopt one of three main conformations, crown,
over 10 min. The mixture was stirred at 0
C for 1.5 h butterfly, and propeller as shown in Scheme 1 with their
and after 0.5 h at room temperature. The mixture was Cambridge Crystallographic Data Center refcodes [11].
diluted with 100 ml of ice water. The cream-white solid The distinction between the three types of conforma-
was filtered. Recrystallization from mixture of (1:1) tions is based on the torsion angles about the bonds
ethyl acetate and acetone gave the product in 76.1% C–X (Scheme 1) where X is C, N, O, or S. In the
yield, m.p. 210
C, 1H NMR (CDCl3) d 8.1 (s, H), 7.45 conformation crown, the absolute value of the torsion
(d, 2H), 7.38 (t, H). angles C3–C2–X–R2, and C5–C6–X–R2 (Scheme 1) are

Table 1. Crystal data and structure refinement for 1 and 2

1 2

Formula C12H6Cl4N8•2(C3H6O) C13H6Cl4N6O2•1/2(C4H8O2)

Mr 520.20 454.05
Crystal color, habit Colorless Colorless
Crystal dimensions 0.30 · 0.30 · 0.15 0.51 · 0.18 · 0.15
Crystal system Monoclinic Orthorhombic
Space Group C2/c Pna21
a [Å] 7.950(1) 7.510(1)
b [Å] 19.450(3) 16.902(3)
c [Å] 15.370(3) 15.286(3)
b [o] 92.18(3) 90.00
V [Å3] 2374.9(7) 1940.3(6)
Z 4 4
Dcalc [g cm)3] 1.455 1.554
l(MoKa) [cm)1] 0.0531 0.0639
2(h max [o] 50.98 50.08
Reflection collected 3255 1782
Independent reflections 1973 1782
Observed reflections 679 1568
Largest difference peak [eÅ)3] 0.162 0.286
Largest difference hole [eÅ)3] )0.170 )0.190
No. of parameters 149 250
Ra 0.0395 0.0490
WRa 0.0708 0.1300
GOFb 0.666 1.148
 155

in the range of 158.2–176.2o. The range of the absolute

values of the same torsion angles is 1.3–34.8o in the
butterfly conformation. In the propeller conformation
the absolute value of one of the torsion angles is above
90o, the other below 90o. 1,3-Benzenediamine,N,N¢-
bis(4,6-dichloro-1,3,5-triazine-2-yl) (1) occupies the 2-
fold crystallographic special position and adopts the
crown conformation. 1,3,5-Triazine,2,2¢-[2-methyl-1,3-
phenylene bis(oxy)]bis(4,6-dichloro) (2) on the other
hand adopts the propeller conformation.
The packing of the two inclusion compounds is
different. 1,3-Benzenediamine,N,N¢-bis(4,6-dichloro-1,3,
5-triazine-2-yl) (1) crystallizes with two molecules of
acetone and are bonded to the guest molecules via N4–
Figure 1. Molecular structure of 1. H4N O1 hydrogen bonds (H4N O1 distance is 2.029 Å
and N4–H4N O1 angle is 170.0o). 1,3,5-Triazine,2,2¢-[2-
methyl-1,3-phenylene bis(oxy)]bis(4,6-dichloro) (2)
crystallizes with half a molecule of ethyl acetate (also
with methanol and ethanol). The guest molecule is
disordered. It is interesting to note that ethyl acetate is
found to be disordered in 132 crystal structures out of
277 crystal structures that include ethyl acetate and are
deposited in the Cambridge Crystallographic Data
Center [11]. The host molecules form dimers between
molecules related by translation along the c axis with
short Cl N and Cl O distances as shown in Figure 3. The
geometry of the short contacts are: Cl3 N6 3.175(6) Å,
Figure 2. Molecular structure of 2.
C11–Cl3 N6 170.9(5)o, Cl1 N3 3.340(6) Å, C2– Cl1 N3
155.1(5)o, Cl1 O1 3.157(7) Å, and C2– Cl1 O1 164.6(6)o.
Similar short intermolecular contacts between chlorine
R2 R2 atom and nitrogen and oxygen separated by one atom
R1 R2 was found in only three other compounds (for refcodes
S S AHEGEZ [17] NH2 p-Tol
QAMNEX [18] NH2 p-ClPh see reference [11]).
N N QAMPOJ [19] NH2 Ph Tetrachlorothiophene-N-ethoxycarbonylimide-S-oxide
crown XULTUT [20] Cl o-OMePh (FIZGOK) [12], and Tetradecahydro-dipyrrolo(1,2-a:2,1-
R1 i)-1,4,7,10-tetra-azacyclotetradecine-4,9,14,17-tetrone chl-
oroform solvate (QENZOY) [13]. The Cl N distances
X 1 X R1 R2 X
R2 6 2 R2
DAKGAX [21] NO2 Ph S
are 3.415, 3.471, and 3.403 Å in the three compounds
5 3 DPMPAM [22] H Ph NH respectively. The Cl O distances are 3.224, 3.188, and
Butterfly 4 MIRNAC [23] H PhOPhPh CO 3.195 Å in the three compounds, respectively.
R1
PUBWAK [24] H o-dinitroPh NH
P,P¢-bis(Tetrachloro-catecholato-O,O¢)-2,4,6,8-tetram-
ethyl-2,4,6,8-tetra-aza-1,5-diphosphabicyclo(3.3.0)octane-
R1 R2
3,7-dione dichloromethane solvate (BIFHON) [14], The
R2 R1 R2 X
channels formed by the packing of the host molecules in the
TELRIL [25] OH Ph CO crystal lattice have different cross-sections, while the cross-
Propeller section in the lattice of the inclusion compounds of 1 is
R1 rectangular with edges of 7.2 · 10.8 Å (Figures 3, 4 and 5),
Scheme 1. the cross-section of the channel made up by 2 has a trape-
zoid shape with the size of 10.8 · 6.6 Å (Figure 6). The
walls of the channel in 1Æ2(acetone) are made up of chlorine
Cl N Cl atoms that build the narrower wall boundary of the rect-
Cl N Cl Cl N Cl
angle, and the face of the phenyl ring which form the wider
N N
N N N N Me wall boundary of the rectangle. The inner wall of the rect-
Cl N O O
angle is therefore, rich of electrons. The walls of the channel
H
N N
H
in 2Æ1/2(ethyl acetate) are made up from four dichlorotri-
N N azine moieties that may be described as two twizers of dif-
ferent opening angle which provides a space between them
Cl (2)
(1) of a trapezoid shape. It is interesting to note that there are
Scheme 2. other examples where halo-substituted phenyls may act as
156

Figure 3. The structure of a dimer of 1,3,5-Triazine,2,2¢-[2-me-

thyl)1,3-phenylene bis(oxy)]bis(4,6-dichloro) (2).

Figure 5. View of the rectangular channel cross-section made of host

molecules of 1 (drawn in space-filling style) with the guest molecules
(drawn in stick style).

Figure 4. Side view of the channel in 1. The guest molecules are drawn
in stick style and the host molecules are drawn in space-filling style.

host in the formation of channel inclusion compounds. For

example the hexagon nanoporous host structure based on
2,4,6-tri-4-(halo-phenoxy)-1,3,5-triazines [15], that crystal-
lize with various substituted benzenes. Another example is
the host molecule tetrakis(N-(p-Tolyl)-tetrachlocopha-
thalimide [16], that forms channels of elipsoid cross-section
with a width of 3.5 Å which can accommodate only aro-
Figure 6. View of the trapezoid channel cross-section made of host
matic compounds as guests. molecules of 2 (drawn in space-filling style) with the guest molecules
(drawn in stick style).
Supporting information available

The crystallographic data for the two inclusion com- Graphical Contents entry
pounds have been deposited with the Cambridge
Structural Database in CIF format (CCDC-246138 and The structure of new host molecules that form channel
CCDC-246139). These data can be obtained free of inclusion compounds
charge at www.ccdc.cam.ac.uk/conts/retrieving.html [or Natalia Fridman, Moshe Kapon, Yana Sheynin and
from the Cambridge Crystallographic Center, 12, Union Menahem Kaftory
Road, Cambridge, CB2 1EZ, UK; fax: (internat.) +44- Department of Chemistry, Technion-Israel Institute
1223/336-033; E-mail: deposit@ ccdc.cam.ac.uk]. of Technology, Haifa, 32000, Israel
 157

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