Design, synthesis, and structure of novel cesium receptors

Article abstract of DOI:10.1023/A:1024269812003

The podand, bis(2-methoxyphenoxy)w-xylene (1), was designed and synthesized as a potential host for the cesium ion. Its structure was determined by single crystal X-ray diffraction. It crystallizes in P2 ₁/c with cell dimensions: a = 8.5723(7)

Full text of DOI:10.1023/A:1024269812003

C
Journal of Chemical Crystallography, Vol. 33, Nos. 5/6, June 2003 ( 2003)
Design, synthesis, and structure of novel cesium receptors
Jeffrey C. Bryan,1, Benjamin P. Hay,2 Richard A. Sachleben,3 Cassandra T. Eagle,4
Cungen Zhang,2 and Peter V. Bonnesen5
Received July 1, 2002
The podand, bis(2-methoxyphenoxy)m-xylene (1), was designed and synthesized as a
potential host for the cesium ion. Its structure was determined by single crystal X-
˚
ray diffraction. It crystallizes in P21/c with cell dimensions: a = 8.5723(7) A, b =
3
˚
˚
˚
8.3931(14) A, c = 25.2879(26) A, = 96.224(9) , and V = 1808.7(4) A . A crown
derivative, tribenzo-21-crown-6 (2), was also prepared and structurally characterized. It
˚
˚
also crystallizes in P21/c with cell dimensions: a = 15.5825(13) A, b = 15.8648(16) A,
3
˚
˚
c = 8.8266(7) A, = 95.247(6) , and V = 2172.9(3) A . The structures exhibit hydrogen
bonding, and are evaluated in terms of complementarity and preorganization for cesium
binding.
KEY WORDS: Crystal structure; synthesis; conformation; cesium; crown ether; design.
Introduction
significant energy will need to be applied to re-
orient the ligand to a conformation suitable for
binding a cation.3–5
Single-crystal structures of large, uncom-
plexed, crown ether molecules tend to exhibit con-
formations that are not suitable for efficient bind-
ing of guest cations. In fact, they appear as if they
have collapsed in on themselves, filling the cen-
tral void with portions of the crown ring.1 The
motivation for doing so is evidently the filling
of what would be empty space, and the forma-
As part of our ongoing effort to understand
the structural factors that influence the relative
ability to bind large cations,6–8 we sought to de-
sign a crown ether molecule that would be well
suited to bind cesium and would adopt an open,
low-energy free ligand structure. Recent publica-
tions have described the extraordinarily cesium-
selective calix[4]arene-crown-6 molecules, and
their success, in part, appears to be due to the rigid
calix[4]arene, which lends a degree of preorgani-
zation to the crown ring, and to the formation of
cesium– bonds.9,10 Inspired by these successes,
we decided to build a crown ring, using m-xylene
as a donor group. This paper describes the design,
synthesis, and structure of tribenzo-21-crown-6,
a ligand that can be thought of as dibenzo-21-
crown-7 with one oxygen atom replaced by an
m-xylyl group.
---
tion of weak, intramolecular, C H O hydrogen
bonds.2 If these free-ligand structures represent a
low-energy conformation, then it is possible that
(1) Chemistry Department, University of Wisconsin-La Crosse, 1725
State Street, La Crosse, Wisconsin 54601.
(2) Pacific Northwest National Laboratory.
(3) Solvias, Inc.
(4) Appalachian State University.
(5) Oak Ridge National Laboratory.
To whom correspondence should be addressed. E-mail: bryan.
jeff@uwlax.edu
349
C
1074-1542/03/0600-0349/0 2003 Plenum Publishing Corporation

350
Bryan et al.
Experimental
Crystallography
Syntheses
A summary of crystallographic data is given
in Table 1. Complete crystallographic data are
available as supplementary material. Intensity
data were obtained using a Nonius CAD4 diffrac-
tometer fitted with a 1.1-mm collimator using
Bis(2-methoxyphenoxy)m-xylene
(1). A
mixture of guaiacol (1.0 g, 8.1 mmol), 1,3-
bisbromomethylbenzene (1.0 g, 3.8 mmol), and
K2CO3 (3 g, 0.02 mol) was heated at reflux
with stirring under argon overnight (12–16 h).
The solvent was evaporated in vacuo and the
residue was partitioned between dichloromethane
(20 mL) and water (20 mL). The organic phase
was washed twice with 1 N NaOH (5 mL) and
once with NaHCO3 (5 mL), dried over sodium
sulfate, and evaporated in vacuo to obtain 1.27 g
˚
Mo K radiation ( = 0.71073 A)and an Oxford
Cryosystems 600 series low-temperature device.
Calculations were carried out using XCAD411
(data reduction), SHELXTL12 (absorption correc-
tion, structure solution/refinement, and molecular
graphics), andPLATON13 (structureanalysis). All
non-hydrogen atoms were refined anisotropically.
Except as noted below, each H atom was placed
in a calculated position, refined using a riding
model, and given an isotropic displacement pa-
rameter equal to 1.2 (CH, CH2) or 1.5 (CH3) times
the equivalent isotropic displacement parameter
of the atom to which it is attached. When war-
ranted, methyl H atomic positions were allowed to
1
(95%) of 1 as white crystals. mp 117 C; H
NMR (400.13 MHz, CDCl3, 23 C, CHCl3):
= 3.88 (6 H, s), 5.15 (4 H, s), 6.80–6.96
(8 H, m), 7.32–7.42 (3 H, m), 7.50 (1 H, s); 13C
NMR (100.613 MHz, CDCl3, 23 C, CDCl3):
= 55.93, 70.91, 111.88, 114.24, 120.78,
121.47, 126.01, 126.72, 128.81, 137.58, 148.11,
149.67.
---
rotate about the adjacent C C bond. Full-matrix
Tribenzo-21-crown-6 (2). A mixture of
bis(o-hydroxyphenoxyethoxy)ethane (1.67 g,
5.0 mmol), , -dibromo-m-xylene (1.32 g,
Table 1. Crystal Data and Structure Refinement
0
Compound
CCDC deposit no.
Color/shape
1
2
5.0 mmol), Cs2CO3 (4.9 g, 15 mmol), and CsI
(0.26 g, 1.0 mmol) in 25-mL argon-sparged
acetonitrile was heated with stirring in a sealed
flask at 85–90 C for 6 days. The solvent was
evaporated in vacuo and the residue was parti-
tioned between dichloromethane (40 mL) and
water (40 mL). The organic phase was washed
twice with 0.5 N NaOH (20 mL) and once with
saturated NaHCO3 (20 mL), dried over anhydrous
magnesium sulfate, and evaporated in vacuo to
obtain 1.95 g (89%) of crude 2 as a yellow waxy
solid. Colorless needles were obtained from slow
evaporation from dichloromethane. mp 110 C;
1H NMR (400.13 MHz, CDCl3, 23 C, CHCl3):
= 3.79 (4H, s), 3.90 (4H, dd), 4.16 (4H, dd),
5.11 (4 H, s), 6.87–7.01 (8 H, m), 7.39 (3 H, m),
7.61 (1 H, s); 13C NMR (100.613 MHz, CDCl3,
23 C, CDCl3): = 69.52, 71.47, 71.63, 113.67,
115.93, 121.25, 122.00, 126.78, 127.21, 128.34,
137.74, 148.58, 149.48.
201718
Colorless/
prism
C22H22O4
350.4
100(2)
Monoclinic
P21/c
8.5723(7)
8.3931(14)
25.2879(26)
96.224(9)
1808.7(4)
4
1.29
0.088
2.3–26.0
13699
3544 (Rint
0.035)
3544/0/259
1.03
0.034
201719
Colorless/
fragment
C26H28O6
436.5
100(2)
Monoclinic
P21/c
15.5825(13)
15.8648(16)
8.8266(7)
95.247(6)
2172.9(3)
4
Chemical formula
Formula weight
Temperature, K
Crystal system
Space group
˚
a, (A)
˚
b, (A)
˚
c, (A)
, ( )
3
˚
V, (A )
Z
3
Dcalc (g cm
Absorption coefficient (mm
range ( )
Reflections measured
Independent reflections
)
1.33
0.094
2.5–27.5
11379
4985(Rint
1
)
=
=
0.039)
Data/restraints/parameters
Goodness of fit on F2
R1 [I > 2 (I)]
4985/0/289
1.02
0.040
wR2 (all data)
0.094
0.109

Design, synthesis, and structure of novel cesium receptors
351
2
Results and discussion
leastsquares refinement against |F| of the quan-
P
tity w(Fo2 Fc2)2 was used to adjust the refined
parameters.
Arationalfirststepinthesearchforimproved
host architectures is to identify connectivity that
yields complementary three-dimensional arrays
for groups of potential binding sites. The ability
to recognize such architectures requires a defini-
tion of the optimal geometry for the interaction
between each binding site and the metal ion. Prior
investigations have identified the geometry, illus-
trated in Fig. 1, that gives the strongest interaction
between cesium and the simple chelating binding
sites offered by 1,2-dimethoxybenzene (DMB).16
Bis(2-methoxyphenoxy)m-xylene (1). The
crystals were grown by slow evaporation of
an acetonitrile solution. Cell constants and an
orientation matrix were obtained from a crystal
measuring 0.80 0.60 0.25 mm3, by least-
squares refinement, using the setting angles of
25 reflections in the range 16.5 < < 20.7 . The
highest peak in the final difference map measured
3
˚
0.21 e/A .
Tribenzo-21-crown-6 (2). The crystals were
---
At the experimental average Cs O distance of
grown by slow evaporation of an acetonitrile so-
lution. Cell constants and an orientation matrix
were obtained from a crystal measuring 0.51
0.48 0.24 mm3, by least-squares refinement,
using the setting angles of 24 reflections in the
range 10.2 < < 14.6 . The crown portion of the
molecule appears to be disordered between C16
and C18. Modeling these atoms as simple twofold
disorder gives occupancy factors of roughly 95:5.
Because of this high ratio, and because the met-
rical parameters of the minor disorder component
are chemically unreasonable, attempts to model
the putative disorder were abandoned. The high-
˚
3.22 A, the geometry of this complex has Cs sym-
metry. The cesium cation lies on the mirror plane,
but is displaced to one side of the arene plane.
An obvious strategy for the design of a cesium
host containing two DMB binding sites is to iden-
tify architectures that allow both chelate rings to
maintain the optimal geometry with respect to the
cation.
The deliberate design of host structures
by assembling sets of disconnected binding
sites in three dimensions is not a trivial
task. Inspired by approaches used in de novo
est peak in the final difference map measured
3
˚
0.59 e/A .
Molecular modeling
Molecular mechanics (MM) calculations
were performed using the MM3(96) program(6)
with an extended parameter set for the treat-
ment of cesium interactions with ether binding
sites.3,6,14–16 Cation– interactions were included
by applying the Hill function between the cesium
ion and each arene carbon atom17 using the fol-
lowing parameters:r = 3.87, ε = 3.46 kcal/mol.
Conformer searches were performed using the
stochastic search option of the MM3 program.
(6)MM3(96). The program may be obtained from Tripos Associates,
1699 S. Hanley Road, St. Louis, MO 63144, by commercial
users, and it may be obtained from the Quantum Chemistry Pro-
gram Exchange, Mr Richard Counts, QCPE, Indiana University,
Bloomington, IN 47405, by noncommercial users.
Fig. 1. Optimal geometry for an isolated cesium-DMB com-
---
plex with Cs O distances fixed at the experimental average
˚
value of 3.22 A.

352
Bryan et al.
it serves as a -donor to the cesium cation,19–21
thereby providing further stabilization to the com-
plex. The MM3 Optimized geometry of the ce-
sium complex with 1 is shown in Fig. 2.
One method to evaluate the degree of struc-
tural complementarity in a host architecture in-
volves calculating the difference in steric energy,
1Ucomp, between the bound form of the host
and the binding conformer of the host, in other
words, the strain in the host that is caused by
guest complexation.4,5,22–27 Complementary archi-
tectures should give small 1Ucomp values. Strain
energy analysis for the cesium complexed form of
1 gives a 1Ucomp value of 2.28 kcal/mol indicat-
ing that this podand (1) structure exhibits a high
degree of complementarity for cesium.
Thecrystalstructureofthemetal-freeformof
1 is illustrated in Fig. 3. Selected dihedral angles
Fig. 2. MM3 optimized structure of the cesium complex
with 1.
structurebased drug design, a new computer pro-
gram, HostDesigner,18(7) has been developed to
address this issue. HostDesigner generates can-
didate structures by combining molecular frag-
ments and scores the resulting structures with
respect to their complementarity for the tar-
geted guest. This program was used to search
for cesium hosts composed of two DMB com-
ponents. After examination of 221, 387 pos-
sible candidates, HostDesigner identified bis(2-
methoxyphenoxy)m-xylene (1), as an architecture
that provides a complementary arrangement of the
two DMB binding sites. In addition, the arene con-
necting the two DMB groups is oriented such that
(7)HostDesigner, Version 1.0, was developed by B. P. Hay and
T. K. Firman in the William R. Wiley Environmental Molecular
Sciences Laboratory at the Pacific Northwest National Lab-
oratory under partial sponsorship of Chemical Sciences, Of-
fice of Basic Energy Sciences, Office of Science, U.S. Depart-
ment of Energy under Contract No. DE-AC06-76RL01830. The
software can be obtained at no charge from the following website:
http://hostdesigner.emsl.pnl.gov.
Fig. 3. Crystal structure of 1 showing 50% probability
displacement ellipsoids.

Design, synthesis, and structure of novel cesium receptors
353
Table 2. Selected Torsion Angles ( )
1obs
1calc
Cs-1calc
2obs
2calc
Cs-2calc
---
---
---
O(1) C(8) C(9) O(2)
1.2(2)
168.6(1)
0.0
178.6
0.5
174.8
1.5(2)
177.8(1)
167.5(1)
80.6(1)
169.0(1)
83.4(2)
93.4(2)
174.3(1)
177.3(1)
74.4(1)
155.9(1)
169.3(1)
6.1(2)
175.4(1)
172.2(1)
97.2(1)
60.0(2)
169.9(1)
177.7(1)
0.3
168.9
178.8
76.0
157.7
77.6
5.3
172.0
168.0
66.0
160.0
177.0
66.5
164.8
72.8
64.9
165.2
165.0
3.5
168.0
174.9
87.4
84.0
168.9
178.2
--- --- ---
C(8) C(9) O(2) C(14)
--- --- ---
C(9) O(2) C(14) C(15)
--- --- ---
O(2) C(14) C(15) O(3)
--- --- ---
C(14) C(15) O(3) C(16)
--- --- ---
C(15) O(3) C(16) C(17)
--- --- ---
O(3) C(16) C(17) O(4)
--- --- ---
77.0
C(16) C(17) O(4) C(18)
--- --- ---
173.0
171.0
75.9
178.7
172.0
0.0
177.7
178.6
86.9
C(17) O(4) C(18) C(19)
--- --- ---
O(4) C(18) C(19) O(5)
--- --- ---
C(18) C(19) O(5) C(20)
--- --- ---
C(19) O(5) C(20) C(21)
--- --- ---
178.1(1)
0.3(1)
174.9(1)
178.7(1)
61.8(1)
104.2(1)
175.3(1)
174.4(1)
179.4
0.0
179.4
179.0
65.9
107.3
180.0
178.0
175.0
0.4
174.0
180.0
84.7
84.9
179.7
174.0
O(5) C(20) C(21) O(6)
--- --- ---
C(20) C(21) O(6) C(26)
--- --- ---
C(21) O(6) C(26) C(3)
--- --- ---
O(6) C(26) C(3) C(2)
--- --- ---
C(2) C(1) C(7) O(1)
--- --- ---
79.2
179.0
175.6
C(1) C(7) O(1) C(8)
--- --- ---
C(7) O(1) C(8) C(9)
are presented in Table 2. The conformation ob-
served in the crystal structure differs from the
predicted binding conformation shown in Fig. 2
the crystal is not significantly distorted by pack-
ing forces.
Examination of the observed metal-free form
with the bound form of 1 reveals that only small
structural changes are required to complex ce-
sium. The main difference in the structures is
---
in that the C1 C7 bond is rotated from 85 in the
binding conformer to 104 in the crystal structure.
The central area of molecule 1 is not empty as
Fig. 2 suggests, but is filled by a methoxy group
---
that the two bonds to the -bound arene, C1 C7
---
(O2 C14) of a symmetry equivalent molecule.
The slightly electropositive hydrogen atoms on
C14 are surrounded by regions of electron den-
sity from the oxygen lone pairs and the cen-
tral ring’s -cloud on the symmetry equivalent
molecule. Despite this, only one hydrogen bond
with suitable metrical parameters is observed
a
˚
Table 3. Hydrogen Bond Geometry (A, )
b
6
---
---
H
D
H
A
H⊥
H
A D
A
D
A
O(5)i
Cg1ii
Cg1ii
2.48 3.449(2)
169
121
92
165
138
161
149
162
158
---
1 C(14) H(14c)
1 C(7) H(7a)
---
1 C(7) H(7b)
---
2.66 2.74 3.362(1)
3.03 3.18 3.362(1)
Cg3iii 3.07 3.26 4.230(2)
2.59 3.390(2)
2.55 3.497(2)
2.71 2.79 3.672(2)
Cg3iv 2.95 2.96 3.908(2)
---
(Table 3). Additional C H
interactions are
---
---
---
1 C(26) H(26a)
2 C(18) H(18a)
2 C(18) H(18b)
---
2 C(7) H(7b)
O(3)iv
O(6)iv
Cg1v
observed and presented in Table 3. These interac-
tions originate from methylene groups adjacent to
an ether oxygen atom, thus making the methylene
hydrogen atoms more electropositive.1,2 MM3
optimization starting from the crystal structure
coordinates yields a very similar structure. The
average difference in selected torsion angles is
only 3.7 (see Table 2), and superposition of the
crystal structure on the MM3 optimized structure
yields a root-mean-squared displacement of only
---
---
2 C(17) H(17a)
2 C(22) H(22)
Cg1vi
2.90 2.90 3.804(2)
aNo su’s are given for some parameters because the positional pa-
rameters of those H atoms involved were not refined. CgX refers to
---
---
the calculated centroid of the arene rings (X = 1, C1 6;2, C8 13;
---
3, C20 25). Symmetry codes are as follows: (i) 1 x, 1 y, 1
1
2
y,
1
2
1
2
1
2
z (ii) x, y, 1 z (iii) x,
+ y,
z (iv) x,
y, + z
1
1
2
(v) 1 x, 1 y, z (vi) x,
+ z.
2
b H⊥ is the perpendicular distance between the H atom and the arene
˚
0.08 Asuggesting that the geometry observed in
plane.

354
Bryan et al.
---
and C3 C26, are rotated approximately 20 (see
Table 2). The crystal structure conformation is
only slightly lower in energy, 0.03 kcal/mol, than
the predicted cesium binding conformer, show-
ing that there is not a substantial penalty to
reorganize 1 for cesium complexation. The cal-
culations and data suggest that 1 is both comple-
mentary and preorganized to bind cesium.
The next step in this design process was to
incorporate the architecture offered by 1 within
a macrocyclic framework. Visual inspection
of the cesium complex with 1 showed that
the two terminal methyl carbon atoms are
˚
6.25 A apart, a distance that can be bridged
---
--- --- --- --- ---
by
a CH2O CH2 CH2 O CH2 chain.
Performing this operation yields the novel
macrocycle tribenzo-21-crown-6 (2). A con-
former search of the cesium complex with 2
yields the global minimum geometry shown
in Fig. 4. Strain energy analysis of the cesium
Fig. 5. Crystal structure of 2 showing 50% probability
displacement ellipsoids.
complexed form of 2 gives a 1Ucomp value of
3.47 kcal/mol, a value which is comparable
with 2.0–2.5 kcal/mol calculated for the ce-
sium complexes with tribenzo-21-crown-73 and
3.3 kcal/mol calculated for the cesium complex
with tetrabenzo-24-crown-8.6
The crystal structure of the metal-free form
of 2 is illustrated in Fig. 5. Selected dihedral
angles are presented in Table 2. Like the po-
dand 1, the crown has a relatively open struc-
ture. This is somewhat unusual, as large crown
ethers typically collapse in on themselves to fill
the void and form weak hydrogen bonds.1,2 As
with the podand, the apparent cavity within the
ring is filled with part of an adjacent (symme-
try equivalent) crown ether molecule. Intermolec-
ular interactions are formed between the hydro-
gen atoms attached to C18 and oxygen atoms
on a neighboring molecule. Additionally, one
hydrogen atom on C17 interacts with the
---
-
Fig. 4. The global minimum structure for the cesium complex
with 2 located by MM3 conformational analysis.
cloud of the benzo group composed of C1 6,

Design, synthesis, and structure of novel cesium receptors
355
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---
---
tween C20 25 and C1 6. Metrical parame-
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Table 3.
Unlike the podand 1, MM3 optimization
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does not well reproduce the crystal structure.
The average difference in selected torsion an-
gles is 9.2 with the largest discrepancies occur-
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---
---
ring for O5 C19 (25.4 ), O1 C7 (19.2 ), and
---
O5 C20 (18.7 ) (see Table 2). Superposition of
thecrystalstructureandtheMM3optimizedstruc-
ture yields a root-mean-squared displacement of
˚
0.47 A. These differences suggest the geometry
observed in the crystal to be distorted by pack-
ing forces such as those detailed in the previous
paragraph and in Table 3.
Examination of the observed metal-free form
with the bound form of 2 reveals that signifi-
cant structural changes are required to get to the
---
binding conformer; the O3 C16 bond goes from
---
gauche( ) to anti, the C16 C17 bond goes from
---
gauche( ) to gauche(+), and the O4 C18 bond
goes from anti to gauche(+). These structural
changes do not entail a large difference in energy,
however, and the metal-free conformation is only
0.88 kcal/mol lower in energy than the predicted
cesium binding conformer. Thus, the energy re-
quired for conformational reorganization of 2 is in
the range of that observed for tribenzo-21-crown-
7 (1.1–1.5 kcal/mol)3 and tetrabenzo-24-crown-8
(0 kcal/mol).6 Given the degree of complementar-
ity, preorganization, and the fact that the cesium–
interaction is almost identical in strength to the
cesium–ether interaction,20,21 the results of this
study suggest that 2 may be expected to complex
cesium as well as tribenzo-21-crown-7.
26. Hay, B.P.; Dixon, D.A.; Vargas, R.; Garza, J.; Raymond, K.N.
Inorg. Chem. 2001, 40, 3922.
References
27. Lumetta, G.J.; Rapko, B.M.; Garza, P.A.; Hay, B.P.; Gilbertson,
R.D.; Weakley, T.J.R.; Hutchison, J.E.J. Am. Chem. Soc. 2002,
124, 5644.
1. Bryan, J.C.; Marchand, A.P.; Hazlewood, A. Acta Crystallogr.
Sect. E 2001, 37, o13–o15; and references therein.