Synthesis of an amide cyclophane building block of shape-persistent triangular molecular wedges

Article abstract of DOI:10.1016/j.tetlet.2003.12.012

The synthesis of an amide cyclophane, which can be considered as the first generation of a family of triangular shape-persistent molecular wedges is described.

Full text of DOI:10.1016/j.tetlet.2003.12.012

Tetrahedron
Letters
Tetrahedron Letters 45 (2004) 1151–1153
Synthesis of an amide cyclophane building block of
shape-persistent triangular molecular wedges
Achim Amma and Thomas E. Mallouk*
Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, PA 16802, USA
Received 6 October 2003; revised 26 November 2003; accepted 3 December 2003
Abstract—The synthesis of an amide cyclophane, which can be considered as the first generation of a family of triangular shape-
persistent molecular wedges is described.
Ó 2003 Elsevier Ltd. All rights reserved.
Macromolecular, nanoscale building blocks suitable for
assembly to true hierarchical structures can be designed
using three characteristic features that are found in
proteins and are believed to enable their ability to work
as molecular machines.1 First, the building blocks
should be chemically precise in composition. Second,
they should posses a well defined, shape-persistent
structure. And third, they should be chemically asym-
metric. This asymmetry is the main difference between
biological macromolecules and many synthetic macro-
molecular assemblies obtained through molding and
replication techniques. As a consequence, assemblies
made from synthetic macromolecules tend to be highly
symmetric. We believe that in order to achieve a broader
class of functional hierarchical assemblies, it will be
necessary to have asymmetry introduced into the
building blocks, in addition to having control over their
size and shape.
asymmetry suitable for surface self-assembly. To mini-
mize conformational flexibility, a ring structure with
many sp2 centers was synthesized. The ring structure
consists of the symmetric units A3 (benzene-1,3,5-tri-
carboxylic acid) and B3 (1,3,5-triamino-benzene). With
the help of orthogonal protecting group chemistry,
selected functional groups on the A3 and B3 units can be
substituted with groups that could direct the surface-
assembly of the building blocks via weak noncovalent
interactions between molecules. For synthetic simplicity,
long alkyl chains have been used throughout the syn-
thetic protocol as shown in Figure 1. Other substituents
could be introduced in the same manner as the long
alkyl chains leading to a building block with more
asymmetry.
Earlier work on cyclic and planar building blocks has
reported predominantly symmetric structures.8–11 Equi-
lateral triangular,8 rectangular,9;10 and square shaped11
molecules have been studied and some have been used
for surface assembly. Still and co-workers have reported
low symmetry amide cyclophane structures, but the goal
of those studies was to design hosts for molecular rec-
ognition rather than building blocks for macromolecu-
lar assembly.8b;10b We describe here a building block for
isosceles triangular wedges. The synthesis of this first-
generation (G1) triangular wedge is outlined in Figure 1.
The synthesis was conducted in solution phase using
orthogonal protecting group chemistry. First, one me-
thyl ester of 1,3,5-benzene-tricarboxylic acid trimethyl
ester 1 was selectively hydrolyzed as described else-
where.12 The free carboxylic acid of compound 2 was
then reacted with di-tert-butyl-dicarbonate to yield the
tert-buytl ester 3. Selective hydrolysis of one methyl
ester of compound 3 yields compound 4.13 Best yields
An example of hierarchical assembly using these prin-
ciples was demonstrated by Whitesides and co-workers
with millimeter sized objects.2–7 Asymmetry was intro-
duced into polygons and polyhedra by chemically
modifying top, bottom, and selected edges of the ob-
jects. The objects could be assembled at liquid–liquid
interfaces and numerous assembly patterns could be
achieved.
Here, we present the synthesis of a planar, shape-
persistent macromolecular building block with built in
Keywords: Cyclophane; Shape persistent; Macromolecule.
* Corresponding author. Tel.: +1-814-863-9637; fax: +1-814-863-8403;
e-mail: tom@chem.psu.edu
0040-4039/$ - see front matter Ó 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2003.12.012

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A. Amma, T. E. Mallouk / Tetrahedron Letters 45 (2004) 1151–1153
O
O
O
O
O
O
O
O
a
c
b
O
O
O
O
O
O
O
O
O
OH
O
O
O
O
OH
O
2
3
1
4
O
O
O
HN (CH2)16CH3
HN (CH2)16CH3
NH2
Cl
(CH2)16CH3
d
e
O2N
NO2
H2N
NH2
O2N
NO2
5
6
7
O
(CH2)16CH3
O
O
f
H
N
HN
1 eq 4
O
8
O
O
O
H2N
HN (CH2)16CH3
O
O
H
N
O
O
O
O
HN
O
O
O
O
O
O
O
O
O
O
HN
O
NH
O
HN
NH
H3C(CH2)16
(CH2)16CH3
O
H3C(CH2)16
O
(CH2)16CH3
O
O
NH
N
NH
O
HN
O
N
g,h
O
i
j,k
N
NH
O
HN
O
N
H
H
H
2
H
2 eq 8
O
O
O
O
O
O
OH
OH
10
11
9
HN
O
HN
O
Figure 1. (a) NaOH (0.9 equiv), EtOH/H2O, 60%; (b) di-tert-butyl-dicarbonate, DMAP, THF, 91%; (c) NaOH (0.9 equiv), DMF/H2O; (d) THF, 2,6-
lutidine, 97%; (e) Pd (5%) on act. C, H2 (950 psi), quant.; (f) DCC, HOBT, DIEA, DMF, 50 °C, 34%; (g) 2,6-lutidine, DCC, HOBT, DMF, quant.;
(h) NaOH, DMF/H2O, 87%; (i) HOBT, DCC, DIEA, DMF, 50 °C 52%; (j) NaOH, DMF/H2O, 93%; (k) 7, HOBT, DCC, DIEA, DMF, 50 °C, 6%.
for this reaction were achieved by reacting a 23.9 mM
solution of compound 3 in DMF/H2O (70/1) with
0.9 equiv NaOH. Compound 4 has one free carboxylic
acid that can be used for an amide coupling reaction in
later synthetic steps. The other two carboxylic acids are
protected with orthogonal protecting groups.
mentioned above. The alloc protecting group can be
removed later with 1,3-dimethylbarbituric acid and
[(C6H5)3P]4Pd as a catalyst.
Compound 2 was coupled (DCC/HOBT) with aniline
and the two methyl esters were hydrolyzed to yield 9.
Aniline was chosen to simulate the attachment of A3 to
the solid phase resin. The two unprotected carboxylic
acids of 9 were coupled with 2 equiv of 8. Excess of DCC
(4.2 equiv) and HOBT (8.0 equiv) as well as moderate
heating (50 °C) had to be employed in order to obtain
10. After hydrolyzing the methyl esters of 10, compound
7 could be used to close the ring under dilution principle
conditions. As with 10, long reaction times and excess of
coupling reagents DCC (8 equiv) and HOBT (16 equiv)
were employed. Compound 10 and 7 were added in
millimolar concentrations to the coupling agents at
50 °C over the course of 20 h.15 The reaction had 6%
yield, which is not an untypical yield for ring closing
reactions of high membered rings.
3,5-Dinitro-aniline 5 was reacted with stearoyl chloride
to yield compound 6. The two nitro groups were
hydrogenated to afford di-amine 7. Compound 7 was
directly used in the next synthesis step due to its oxi-
dation lability. By coupling (DCC/HOBT) compound 7
with 1 equiv of compound 4, compound 8 (A3B3 unit)
was obtained.14 This reaction has low yield since com-
pound 4 can react with both amines of compound 7
resulting in a mixture of products that was separated by
column chromatography on silica. Alternatively, one
amine group of 7 was protected with an alloc protecting
group by reacting 7 with allyl chloroformate. This
reaction has low yield for the exact same reasons as

A. Amma, T. E. Mallouk / Tetrahedron Letters 45 (2004) 1151–1153
1153
Figure 2. Left: Structure of a second generation (G2) molecular wedge. Right: Energy-minimized (PC Macromodel) space filling model of the
building block.
9. Ariga, K.; Terasaka, Y.; Sakai, D.; Tsuji, H.; Kikuchi,
J.-.I. J. Am. Chem. Soc. 2000, 122, 7835.
10. (a) Kuehl, C. J.; Huang, S. D.; Stang, P. J. J. Am. Chem.
Soc. 2001, 123, 9634; (b) Weingarten, M. D.; Sekanina, K.;
Still, W. C. J. Am. Chem. Soc. 1998, 120, 9112.
11. Sugiura, K.; Tanaka, H.; Matsumoto, T.; Kawai, T.;
Sakata, Y. Chem. Lett. 1999, 1193.
12. Dimick, S. M.; Powell, S. C.; McMahon, S. A.; Moothoo,
D. N.; Naismith, J. H.; Toone, E. J. J. Am. Chem. Soc.
1999, 121, 10286.
The significance of synthesizing cyclophane 11 from 8 is
that the synthesis may in principle be extended, by
sequential coupling of suitably protected A3B3 units like
8, to make higher generation number wedges. To do
this, we are currently trying to improve the yield in the
ring closing step by synthesizing the molecule on solid
phase with stochiometric amounts of reactants at high
dilution. Our future plans are to extend the synthesis to
higher generation number isosceles triangular wedges as
illustrated in Figure 2.
13. 1H NMR (acetone-d6) d 8.80 (m, 3H, aromatic), 3.98 (s,
3H, methoxy), 1.65 (s, 9H, tert-butyl); 13C NMR (acetone-
d6) d [166.17, 165.92, 164.52] (ester carbons), [134.92,
134.68, 134.57, 134.08, 132.60, 132.17] (benzene carbons),
82.84 (tert-butyl carbon), 53.03 (methoxy carbon), 28.30
(methyl carbons); (APCI)ꢀ MS ([M)H]ꢀ ¼ 279.
Acknowledgements
We thank Prof. Raymond L. Funk for helpful discus-
sions, and the National Science Foundation for support
under grant CHE-0095394.
14. 1H NMR (THF-d8) d 9.56 (s, 1H, amide), 8.75 (s, 1H,
amide), 8.66 (m, 3H, aromatic), 7.30 (m, 1H, aromatic),
6.86 (m, 2H, aromatic), 4.52 (s, 2H, amine), 3.92 (s, 3H,
methoxy), 2.24 (t, J ¼ 7.5 Hz, 2H, methylene), 1.62 (s + m
overlaid, 9 + 2H, tert-butyl, methylene), 1.30 (s, 28H,
methylene), 0.88 (t, J ¼ 6.8 Hz, 3H, methyl); 13C NMR
(THF-d8) d [170.62, 165.48, 164.14, 163.90] (amide and
ester carbons), [149.48, 140.94, 140.32] (phenyl carbons
from 1,3,5-benzene-tricarboxylic acid), [137.62, 133.00,
132.77, 132.27, 131.07] (phenyl carbons from 1,3,5-triami-
nobenzene), [101.31, 100.02] (phenyl carbons from 1,3,5-
triamino-benzene), 81.73 (tert-butyl carbon), 52.00 (meth-
oxy carbon), [37.30, 32.30, 30.09, 30.03, 30.01, 29.78,
29.74, 27.69, 22.99] (methylene carbons), 13.87 (methyl
carbon); 2D HMQC NMR verifies structure; (APCI)þ MS
[M+H]þ ¼ 652.
References and notes
1. Alberts, B. Cell 1998, 92, 291–294.
2. Bowden, N.; Terfort, A.; Carbeck, J.; Whitesides, G. M.
Science 1997, 276, 233–235.
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G. M. J. Am. Chem. Soc. 1999, 121, 5373–5391.
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Lett. 1999, 75, 3222–3224.
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386, 162–164.
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Soc. 1998, 120, 8267–8268.
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Whitesides, G. M. Science 1999, 284, 948–951.
8. (a) Baas, T.; Gamble, L.; Hauch, K. D.; Castner, D. G.;
Sasaki, T. Langmuir 2002, 18, 4898; (b) Erickson, S. D.;
Simon, J.; Still, W. C. J. Org. Chem. 1993, 58, 1305.
15. 1H NMR (THF-d8) d 10.14 (m, 5H, amide), 9.81 (s, 1H,
amide), 9.30 (s, 4H, amide), 8.80 (m, 9H, aromatic), 8.47
(s, 3H, aromatic), 8.18 (s, 6H, aromatic), 7.85 (m, 2H,
aromatic), 7.34 (m, 2H, aromatic), 7.08 (m, 1H, aromatic),
2.35 (t, J ¼ 7.3 Hz, 6H, methylene), 1.66 (s + m overlaid,
18 + 6H, tert-butyl, methylene), 1.29 (s, 84H, methylene),
0.88 (m, 6H, methyl); (MALDI) MS calcd for
C
113H156N10O14 [M+Naþ] 1901.51, found 1901.49.