Reverse-CD mimics with flexible linkages offer adaptable cavity sizes for guest encapsulation

Article abstract of DOI:10.1039/c3cc47734g

Reverse-CD mimics with adaptable cavity sizes have been synthesized. The adaptability has been demonstrated through single crystal structure determination and guest binding studies.

Full text of DOI:10.1039/c3cc47734g

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Reverse-CD mimics with flexible linkages offer
adaptable cavity sizes for guest encapsulation†‡
Cite this: DOI: 10.1039/c3cc47734g
Atchutarao Pathigoolla and Kana M. Sureshan*
Received 8th October 2013,
Accepted 29th October 2013
DOI: 10.1039/c3cc47734g
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Reverse-CD mimics with adaptable cavity sizes have been synthesized.
The adaptability has been demonstrated through single crystal structure
determination and guest binding studies.
Cyclodextrins (CDs) are toroidal shaped natural a-1,4-cyclo-
oligoglucopyranosides with the ability to encapsulate hydro-
phobic guest molecules in their hydrophobic cavities.1 CDs
consisting of six (a-CD), seven (b-CD) and eight (g-CD) glucose
units are naturally abundant and are rigid with cavity diameters
of approximately 5 Å, 7 Å and 8 Å, respectively. CDs and their
derivatives2–4 are widely used in molecular recognition,5 molecular
reactors,6 catalysis,7 drug delivery,8 polymers,9 etc. The main draw-
backs of natural CDs and their derivatives are their fixed size of
the cavity, fixed polarity of the cavity and rigid structure which
limits the class of guests that can be encapsulated. Though many
CD-analogs10 with non-glycosidic linkages have been synthesized,
in all these analogs, as in the natural CDs, the a-face of the
pyranoses makes the inner wall of the cavity, which is responsible
for the guest recognition (Fig. 1A). Fernandez et al. introduced the
concept of reverse-CDs (R-CDs), wherein the b-face of the pyranoses
forms the inner wall.11 A few R-CD mimics viz. cyclotrehaloses (CTs,
Fig. 1B) have been tactically synthesized by the head-to-head (6,60)
linkage of the C2-symmetric disaccharide (trehalose) derivative.
However, an ideal R-CD will have b-1,4-linkages (head-to-tail)
between pyranoses with b-oriented 4-OH (e.g. D-galactopyranose)
such that the endocyclic oxygens and the hydroxymethyl groups
will orient inward the cavity (Fig. 1C). Though this will modify
Fig. 1 Structural comparison of (A) CDs, (B) CTs, (C) R-CDs and (D) R-CD mimics.
(E) Possible conformational freedoms for triazolylmethyl linkages.
the polarity of the cavity, they are expected to be rigid, like CDs, their variable cavity sizes through crystallography and guest
due to the glycosidic linkages. We herein report flexible reverse- binding profiles.
CD analogs with adaptable cavity sizes and provide evidence for
As the glycosidic linkages impart rigidity to the R-CDs, we
planned to introduce flexible linkages between sugar units, which
can impart conformational freedom to the macrocycle. Such con-
formationally flexible reverse-CD analogs can orchestrate diverse
cavity sizes by adopting different conformations and consequently
encapsulate guests of different sizes.12 We planned to replace
alternate b-(1,4)-galactopyranosyl units in R-CDs by flexible
triazolylmethyl groups (Fig. 1D), which can adopt multiple
conformations either through rotation of the triazolyl ring around
the single bonds or through adoption of different conformation of
School of Chemistry, Indian Institute of Science Education and Research,
Thiruvananthapuram, CET campus, Thiruvananthapuram-695016, Kerala, India.
E-mail: kms@iisertvm.ac.in
† Dedicated to Dr Suresh Das on his 60th Birthday.
‡ Electronic supplementary information (ESI) available: Experimental proce-
dures, characterization data for all new compounds, computational and binding
studies of compounds 2–4 and crystallographic data for compound 3. CCDC
960369. For ESI and crystallographic data in CIF or other electronic format see
DOI: 10.1039/c3cc47734g
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Fig. 3 ORTEP diagram of trimer 3 showing conformers A and B. Water molecules
are omitted for clarity.
tetramer 4 suggested conformational flexibility of these macro-
cycles in solution too, as evident from the slight downfield shift
of H-2 and the up-field shift of triazolyl protons upon increasing
temperature.
Scheme 1 Synthesis of R-CD analogs: (a) NaOAc, Ac2O, 60 1C, 12 h, 90%;
(b) Me3SiN3, SnCl4, DCM, rt, Ar, 12 h, 95%; (c) (i) NaOMe, MeOH, rt, (ii) PhCH(OMe)2,
TsOH, MeCN, rt, Ar, 24 h, 83% (2 steps); (d) BnBr, NaH, DMF, 0 1C-rt, 3 h, 90%;
(e) Et3SiH, CF3COOH, (CF3CO)2O, DCM, 0 1C-rt, 5 h, 78%; (f) propargyl bromide, NaH,
DMF, ꢀ15 1C, 2 h, 87%; (g) CuI, DIPEA, THF, Ar, rt, 24 h, 90%; (h) Pd/C (w/w 10%),
HCOONH4, EtOAc : EtOH : H2O (v/v/v 2 :2:1), 50 1C, 20 h (>90%).
The trimer 3 crystallized as colorless plate-like rectangular
crystals from a mixture of ethanol and chloroform (7 : 3 v/v). Single
crystal XRD analysis of these crystals revealed that the asymmetric
unit has two conformers A and B along with nine water molecules
(Fig. 3 and ESI‡). This is the first report on the crystal structure of a
triazole-linked CD mimic. Interestingly, in support of our hypo-
thesis of adaptability, the cavity sizes of these two conformers were
found to be different. The inner diameter of conformer A is B5 Å
and that of conformer B is B5.4 Å, whereas the natural a-CD has a
diameter of 5.8 Å (Table 1). Thus we could show that the trimer 3
can adopt at least three stable conformations (two XRD structures
and one DFT) with different cavity sizes due to its flexibility. This
suggests that the higher analogs, due to their increased flexibility,
might have many conformations of varying cavity sizes.
A comparison of the crystal structure of 3 with known crystal
structures of a-CD revealed a clear difference in their hydration.
While 3 crystallized with 4.5 water molecules per molecule of 3, a-CD
usually crystallizes with 6–7 molecules of water. Though 3 and a-CD
have similar cavity sizes, the former encapsulates only a single water
molecule in its cavity (crystal), but the latter entraps three molecules
of water in its cavity (crystal). This suggests that the R-CD analogs
have different cavity properties, and hence guest binding ability than
the natural CDs. Such a comparative analysis of crystal structure of
CD-analogs with natural CDs has not been reported earlier.
Inclusion properties of these R-CD analogs were investigated
with different guest molecules using 1H NMR spectroscopy and
isothermal titration calorimetry (ITC). As expected, dimer 2
the sp3 hybridized –O–CH2– linkages (Fig. 1E). Also, the alternate
aromatic triazolyl motifs in the host might render different guest
selectivity for these reverse-CD analogs than the natural CDs.
We have synthesized 2,3,6-tri-O-benzyl-4-O-propargyl-b-D-galacto-
sylazide (1) from D-galactose in seven steps in an overall yield of
43% as reported.13 Among the various CuAAC14 reaction conditions
attempted, compound 1 underwent cyclooligomerization upon
treatment with CuI and N,N-diisopropylethylamine in THF giving a
mixture of cyclooligomers. Chromatographic separation of the
oligomers afforded cyclic dimer 10 (15%), cyclic trimer 11 (28%),
cyclic tetramer 12 (15%) and cyclic pentamer 13 (3%). Debenzylation
of compounds 10–12 gave R-CD analogs 2–4 respectively (Scheme 1).
Though the monomer undergoes topochemical oligomerization to
linear oligomers in the solid state,13 no linear oligomers were
formed in solution. It is interesting to note the formation of the
strained cyclic dimer, which has not been observed previously.10j
In order to get a clear insight into the conformation of these
R-CD analogs, we have optimized the compounds 2, 3 and 4 using
DFT. We have used B3LYP and M05-2X functionalities with basis set
6-311+G(d,p). The relative stabilities of these molecules followed the
same trend in both the methods. The dimer 2 adopted a rigid
conformation with a slightly distorted chair conformation for the
pyranose ring and showed no cavity space for guest encapsulation
as anticipated (Fig. 2A). The trimer 3 showed a bowl shaped
symmetrical cavity with an internal diameter of B6 Å (Fig. 2B).
But the tetramer 4 adopted a saddle-like conformation with a
diameter of 5.5 Å (Fig. 2C). VT-NMR studies of trimer 3 and
Table 1 Comparison of cavity sizes of R-CD analogs with CDs
CD/R-CD analog
Diameter of the cavitya (Å)
Dimer 2b
2.8
6.0
5.0
5.4
5.4
5.8
7.4
9.2
Trimer 3b
Trimer 3 (conformer A)c
Trimer 3 (conformer B)c
Tetramer 4b
a-Cyclodextrinc
b-Cyclodextrinc
g-Cyclodextrinc
a
The cavity diameter was measured using UCSF Chimera by consider-
ing the atoms distances from the centroid of the cyclic molecule.15
Fig. 2 Minimum energy (DFT-M05-2X) structures of (A) dimer 2, (B) trimer 3 and
(C) tetramer 4.
b
c
DFT. Crystal structure.
c
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association constant of B30 000 Mꢀ1, which is of the order of the
Ka of b-CD:benzoic acid binding (Fig. 4B). This also supports the
guest-dependent adaptability of these R-CD analogs (Table 2).
In conclusion, for the first time we have synthesized R-CD
analogs with flexible triazolylmethyl linkages through CuAAC click
reaction of 4-O-propargyl-b-galactosyl azide. To the best of our
knowledge, this is the first report on b-(1,4)-galactopyranosyl linked
R-CD analogs. This is also the first report on the head-to-tail linked
R-CD analog synthesized from a monosaccharide derivative. DFT
calculations and single crystal X-ray crystallography provided proof-
of-concept for (i) the polarity difference between R-CD and normal
CD and (ii) cavity-size adaptability of R-CD analogs. Inclusion
studies of these R-CD analogs also confirmed that they bind guests
of different sizes supportive of the adaptable nature of their cavity
size. Flexible R-CDs offer a new class of CD analogs with a different
cavity property and adaptable cavity sizes.
Fig. 4 1H NMR titration (A) and ITC (B) of benzoic acid with tetramer 4.
could not encapsulate even small organic molecules like ethanol
or propargyl alcohol. As the conformational analysis of 3 suggested
variable cavity sizes, ranging from cavity size smaller than that of
a-CD to a size intermediate between the cavity sizes of a-CD and
b-CD, it is expected to bind guests of varying sizes. 1H NMR titration
experiments suggested the binding of trimer 3 with small
organic molecules such as 1-propanol, 1-butanol, propargyl alcohol
and but-3-yn-1-ol (ESI‡), as evident from the down-field shift
(0.02–0.01 ppm) of the guest protons. The ITC experiments also
confirmed the guest binding. It is noteworthy that the alkynes
showed better binding than the corresponding alkanes. For
instance, propargyl alcohol and but-3-yn-1-ol bound better than
1-propanol and 1-butanol respectively. The plausible CHꢁ ꢁ ꢁp
hydrogen bonding between the acidic triazolyl protons and the
alkyne might be responsible for the slightly improved binding
of alkynes over alkanes. Interestingly, trimer 3 also showed
guest binding with bigger guests, such as aromatic molecules. For
instance, it binds with benzoic acid with an association constant (Ka)
of 3550 Mꢀ1 (ESI‡) which is intermediate between the Kas of benzoic
acid binding with a-CD (1000 Mꢀ1) and b-CD (64 500 Mꢀ1).5 These
results suggest that 3 could attain a cavity size better than that of
a-CD for binding relatively large guests. Thus the binding of 3 with
small and large organic guests provides proof of concept for the
adaptability of these R-CD analogs.
A.P. thanks CSIR-India for Senior Research Fellowship assis-
tance. K.M.S. thanks the Department of Science and Technology
(DST, India) for a Ramanujan Fellowship. This work was made
possible by financial support from DST and CSIR.
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Guest
a-CD
b-CD
3
4
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Benzoic acid
But-3-yn-1-ol
1-Butanol
1000
NR
80
64 500
NR
15
3550
30 000
ND
ND
7
3
5
Propargyl alcohol
NR
NR
ND
NR: not reported; ND: not determined.
c
This journal is The Royal Society of Chemistry 2013
Chem. Commun.