Allosteric regulation of the conformational dynamics of a cavitand receptor

Article abstract of DOI:10.1021/ol0612760

Inspired by allostery in nature, we synthesized cavitand 1 and investigated regulation of its conformational dynamics. Quantitative ¹H NMR studies have revealed that the rate of the conformational isomerization of 1 can be modulated using the e

Full text of DOI:10.1021/ol0612760

ORGANIC
LETTERS
2006
Vol. 8, No. 17
3697-3700
Allosteric Regulation of the
Conformational Dynamics of a Cavitand
Receptor
Zhiqing Yan, Yuning Chang, Dennis Mayo, Veselin Maslak, Shijing Xia, and
Jovica D. Badjic´*
Department of Chemistry, The Ohio State UniVersity, 100 West 18th AVenue,
Columbus, Ohio 43210
badjic@chemistry.ohio-state.edu
Received May 25, 2006
ABSTRACT
Inspired by allostery in nature, we synthesized cavitand 1 and investigated regulation of its conformational dynamics. Quantitative 1H NMR
studies have revealed that the rate of the conformational isomerization of 1 can be modulated using the external addition of acid. As 1
maintains its vase-like conformation in an acidic environment, ample opportunities for controlling the kinetics of molecular recognition, and
thus reactivity, in this and related receptors have arisen.
The conformational dynamics of biological molecules is of
prime importance in regulating their molecular recognition
and activity.1 Mechanisms have been proposed,1c and they
include propagating conformational changes in addition to
stochastic modulation of the binding site entry. As adapted
to supramolecular chemistry, this concept will allow the
preparation of receptors capable of controlling the kinetics
of molecular encapsulation and reactivity in an unnatural
setting.2 The conformational dynamics of artificial receptors
has long been recognized as an essential parameter in the
thermodynamics of molecular recognition.3,4 The dynamic
nature of receptors5,6 has been considered in elucidating the
mechanisms of molecular encapsulation. In the study pre-
sented herein, we report on the preparation and the confor-
mational behavior of the cavitand 1 (Figure 1); in particular,
we directed our efforts toward understanding the allosteric
regulation of the kinetics of its conformational change using
a strong acid as a stimulus. It was originally demonstrated
by Cram et al. that resorcin[4]arene-based cavitands akin to
1 assume either vase or kite conformations, for which the
equilibrium can be set by varying the external conditions.7
Additionally, Diederich and others have shown that the vase/
kite thermodynamic equilibrium can be perturbed if the four
pyrazine-based units are to interact with an external source
of acid or a transition metal cation.8
(2) (a) Mogck, O.; Pons, M.; Boehmer, V.; Vogt, W. J. Am. Chem. Soc.
1997, 119, 5706-5712. (b) Beno, B. R.; Sheu, C.; Houk, K. N.; Warmuth,
R.; Cram, D. J. Chem. Commun. 1998, 3, 301-302. (c) Vysotsky, M. O.;
Thondorf, I.; Bohmer, V. Angew. Chem., Int. Ed. 2000, 39, 1264-1267.
(d) Yoshizawa, M.; Takeyama, Y.; Kusukawa, T.; Fujita, M. Angew. Chem.,
Int. Ed. 2002, 41, 1347-1349. (e) Davis, A. V.; Yeh, R. M.; Raymond, K.
N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4793-4796. (f) Zhong, Z.;
Anslyn, E. V. Angew. Chem., Int. Ed. 2003, 42, 3005-3008. (g) Kaanu-
malle, L. S.; Gibb, C. L. D.; Gibb, B. C.; Ramamurthy, V. J. Am. Chem.
Soc. 2004, 126, 14366-14367. (h) Davis, J. T.; Kaucher, M. S.; Kotch, F.
W.; Iezzi, M. A.; Clover, B. C.; Mullaugh, K. M. Org. Lett. 2004, 6, 4265-
4268. (i) Fiedler, D.; Bergman, R. G.; Raymond, K. N. Angew. Chem., Int.
Ed. 2004, 43, 6748-6751. (j) Purse, B. W.; Gissot, A.; Rebek, J., Jr. J.
Am. Chem. Soc. 2005, 127, 11222-11223. (k) Zuccaccia, D.; Pirondini,
L.; Pinalli, R.; Dalcanale, E.; Macchioni, A. J. Am. Chem. Soc. 2005, 127,
7025-7032. (l) Purse, W. P.; Rebek, J., Jr. Proc. Natl. Acad. Sci. U.S.A.
2005, 102, 10777-10782. (m) Maslak, V.; Yan, Z.; Xia, S.; Gallucci, J.;
Hadad, C. M.; Badjiæ, J. D. J. Am. Chem. Soc. 2006, 128, 5887-5894. (n)
Hooley, R. J.; Van A.; Hillary, J.; Rebek, J., Jr. J. Am. Chem. Soc. 2006,
128, 3894-3895.
(1) (a) McCammon, J. A.; Northrup, S. H. Nature 1981, 293, 316-317.
(b) Wlodek, S. T.; Clark, T. W.; Scott, L. R.; McCammon, J. A. J. Am.
Chem. Soc. 1997, 119, 9513-9522. (c) Gunasekaran, K.; Buyong, M.;
Nussinov, R. Proteins 2004, 53, 433-443.
10.1021/ol0612760 CCC: $33.50
© 2006 American Chemical Society
Published on Web 07/26/2006

Figure 3. (a) N-H stretching region of the infrared spectra for
5.4 mM CHCl3 solution of 1 (red line) and 11.2 mM CHCl3 solution
of 2 (blue line). (b) Chemical structure of model cavitand 3.
counted the possibility of intermolecular aggregation. The
observed diffusion coefficients of 1 remained almost a
constant value of (5 ( 2) × 10-6 cm2 s-1 for concentrations
of 0.7-6.9 mM of 1 in CDCl3.9 The VPO measurements,
3.0-8.9 mM CDCl3 solutions of 1, showed that the observed
molecular weight (Mwobs ) 1210 ( 120) is about 50% lower
than the value calculated for the monomeric 1 (Mw ) 2339).
The discrepancy is significant; however, additional experi-
ments with model compounds were consistent in showing
nonideal behavior of this class of molecules.10 The 1H NMR
spectrum of 1 at 328 K revealed a set of well-defined
resonances corresponding to a molecule with average C4
symmetry (Figure 2a). At 258 K, however, each resonance
was clearly split into two signals with equal intensities, so
Figure 1. Chemical structures of cavitand 1 and model compound
2. Energy minimized (AMBER) enantiomeric forms 1a and 1b of
C2 symmetrical 1 as vase-like conformers.
Cavitand 1 was designed to contain four identical pyrazine-
based “flaps”, with each flap having a benzene unit func-
tionalized with an acetamide and a methoxy group (Figure
1). The acetamides were predisposed to act as donors (but
may also be acceptors!) and the methoxy groups as acceptors
of hydrogen bonding, so that 1 can develop a vase-like
geometry with a seam of intramolecular hydrogen bonds
along its upper rim.5c As the vase structure is maintained
via hydrogen bonding, the pyrazine units were foreseen to
act as basic sites to, upon reacting with an external acid,
promote change in the conformational dynamics of 1.
The preparation of 1 and model compounds 2 and 3
(Figure 3) is described in the Supporting Information. The
(3) (a) Gutsche, C. D.; Bauer, L. J. Tetrahedron Lett. 1981, 22, 4763-
4766. (b) Groenen, L. C.; Van Loon, J. D.; Verboom, W.; Harkema, S.;
Casnati, A.; Ungaro, R.; Pochini, A.; Ugozzoli, F.; Reinhoudt, D. N. J.
Am. Chem. Soc. 1991, 113, 2385-2392. (c) Blixt, J.; Detellier, C. J. Am.
Chem. Soc. 1994, 116, 11957-11960. (d) Ikeda, A.; Shinkai, S. Chem.
ReV. 1997, 97, 1713-1734. (e) Ma, S.; Rudkevich, D. M.; Rebek, J., Jr.
Angew. Chem., Int. Ed. 1999, 38, 2600-2602. (f) Jasat, A.; Sherman, J. C.
Chem. ReV. 1999, 99, 931-967. (g) Naumann, C.; Patrick, B. O.; Sherman,
J. C. Tetrahedron 2002, 4, 787-798. (h) Gibb, C. L. D.; Li, X.; Gibb, B.
C. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 4857-4862. (i) Kang, S.-W.;
Castro, P. P.; Zhao, G.; Nunez, J. E.; Godinez, C. E.; Gutierrez-Tunstad,
L. M. J. Org. Chem. 2006, 71, 1240-1243.
(4) Cram, D. J. Science 1988, 240, 760-767.
(5) (a) Houk, K. N.; Nakamura, K.; Sheu, C.; Keating, A. E. Science
1996, 273, 627-629. (b) Rudkevich, D. M.; Hilmersson, G.; Rebek, J., Jr.
J. Am. Chem. Soc. 1997, 119, 9911-9912. (c) Rudkevich, D. M.;
Hilmersson, G.; Rebek, J., Jr. J. Am. Chem. Soc. 1998, 120, 12216-12225.
(d) Wang, X.; Houk, K. N. Org. Lett. 1999, 1, 591-594. (e) Palmer, L. C.;
Rebek, J., Jr. Org. Biomol. Chem. 2004, 2, 3051-3059.
(6) (a) Hiraoka, S.; Harano, K.; Shiro, M.; Shionoya, M. Angew. Chem.,
Int. Ed. 2005, 44, 2727-2731. (b) Davis, A. V.; Raymond, K. N. J. Am.
Chem. Soc. 2005, 127, 7912-7919. (c) Zuccaccia, D.; Pirondini, L.; Pinalli,
R.; Dalcanale, E.; Macchioni, A. J. Am. Chem. Soc. 2005, 127, 7025-
7032. (d) Davis, A. V.; Fiedler, D.; Seeber, G.; Zahl, A.; Van E. R.;
Raymond, K. N. J. Am. Chem. Soc. 2006, 128, 1324-1333.
(7) (a) Moran, J. R.; Karbach, S.; Cram, D. J. J. Am. Chem. Soc. 1982,
104, 5826-5828. (b) Moran, J. R.; Ericson, J. L.; Dalcanale, E.; Bryant, J.
A.; Knobler, C. B.; Cram, D. J. J. Am. Chem. Soc. 1991, 113, 5707-5714.
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1992, 57, 4608-4612.
(8) (a) Skinner, P. J.; Cheetham, A. G.; Beeby, A.; Gramlich, V.;
Diederich, F. HelV. Chim. Acta 2001, 84, 2146-2153. (b) Azov, V. A.;
Diederich, F.; Lill, Y.; Hecht, B. HelV. Chim. Acta 2003, 86, 2149-2155.
(c) Azov, V. A.; Jaun, B.; Diederich, F. HelV. Chim. Acta 2004, 87, 449-
462. (d) Frei, M.; Marotti, F.; Diederich, F. Chem. Commun. 2004, 12,
1362-1363. (e) Lagugne-Labarthet, F.; An, Y. Q.; Yu, T.; Shen, Y. R.;
Dalcanale, E.; Shenoy, D. K. Langmuir 2005, 21, 7066-7070. (f) Azov,
V. A.; Schlegel, A.; Diederich, F. Angew. Chem., Int. Ed. 2005, 44, 4635-
4638.
Figure 2. 1H NMR spectra (500 MHz) of 1 (1.50 mM) in dry
CDCl3 recorded at (a) 328 K, (b) 300 K, and (c) 258 K.
1H NMR spectrum of 1 at 300 K (Figure 2b) showed a set
of broad signals, indicating the existence of either ill-defined
intermolecular aggregates or conformational isomers ex-
1
changing at intermediate rates on the H NMR time scale.
(9) For a review, see: Cohen, Y.; Avram, L.; Frish, L. Angew. Chem.,
Int. Ed. 2005, 44, 520-554.
(10) For further discussion, see Supporting Information.
Diffusion NMR spectroscopy (HR-DOSY) in combination
with vapor pressure osmometry (VPO) measurements dis-
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Org. Lett., Vol. 8, No. 17, 2006

that the 1H NMR spectrum of 1 corresponded to a molecule
with average C2 symmetry (Figure 2c). Clearly, dynamic
conformational changes occurred in 1 as the temperature of
its CDCl3 solution was varied.11 With the help of 2D ROESY
and EXSY NMR spectroscopic methods, we assigned all of
the signals in the 1H NMR spectrum of 1, as shown in Fig-
ure 2. The resonance for the methine proton Ha is positioned
at 5.6 ppm and shifted insignificantly with temperature
(∆δ/∆T ) 1.4 × 10-3 ppm/K), indicating the dominance of
the vase conformer at all temperatures.7 With this information
in hand, we contemplated that the geometry of the low-
temperature C2 symmetrical 1 incorporates two aromatic flaps
which can interact in pairs to form hydrogen bonds via
acetamide groups, thereby leaving all of the methoxy units
free and uncomplexed (1a/b in Figure 1).12 In this way, two
amide protons in 1 stay hydrogen bonded, and two remain
free. This mode of intramolecular association superseded our
originally anticipated and, at least on paper, reasonable mode
of interaction with the full occupancy of all hydrogen
Figure 4. 1H NMR chemical shifts for the methine Ha proton in
1 (2, 2.84 mM) and 3 (9, 1.20 mM) in dry CDCl3 as a function of
molar equivalents of (a) DMSO-d6, and (b) trifluoroacetic acid
(TFA), incrementally added to their solutions.
of 1 did not affect the vase/kite conformational balance; that
is, the equilibrium remained heavily weighted toward the
vase conformer (Figure 4b). On the contrary, addition of TFA
to a CDCl3 solution of 3 (Figure 4b) affected its vase/kite
equilibrium, favoring the kite conformer.8 The results of the
titration experiments corroborated our contention that in-
tramolecular hydrogen bonding is indeed present in 1, even
when this cavitand is dissolved in CDCl3 containing a great
excess of TFA.13 This noncovalent interaction reinforced the
vase conformer, which proved to be (a) highly receptive to
the presence of a strong hydrogen bond acceptor solvent
(DMSO), and (b) thermodynamically stable in the presence
of a great excess of TFA.
1
bonding sites. In the H NMR spectrum of 1 (Figure 1c),
two N-H singlets were positioned at 6.77 and 4.34 ppm,
and according to the proposed structure would correspond
to a pair of hydrogen bonded and free N-H protons,
respectively. Inspection of a CPK molecular model of C2
symmetrical 1 revealed that the “free” N-H protons are in
fact positioned above the neighboring benzene rings and are
possibly involved in the polar π interactions (N-H‚‚‚π)
(Figure 1). These N-H protons are thus each in the shielding
zone of the neighboring benzene, which rationalizes their
high-field resonance at 4.34 ppm.
Since 1 retained the vase-like structure in an acidic
environment, we investigated the effect that acid would have
on its conformational dynamics. C2 symmetrical 1 is inher-
ently chiral and exists as a pair of enantiomers, 1a and 1b
(Figure 1). The molecule flutters between two enantiomeric
forms, as the hydrogen bonding pattern oscillates from the
clockwise to the counterclockwise arrangement; this inter-
conversion leads to the exchange of 1H NMR signals of the
proton nuclei experiencing different chemical environments.14
Dynamic NMR methods, 2D EXSY or the classic total band-
shape analysis, provide quantitative data about the kinetics
of chemical exchange processes.14 The resonance for the Hb
proton in 1 was, at a high temperature, observed as a singlet
at 8.11 ppm (Figure 2a). This proton, residing in two
chemically different environments in 1a and 1b, exchanged
The results of infrared spectroscopic analysis of 1 provided
additional support for its C2 symmetrical geometry (Figure
3a). The FT-IR spectrum of 1 revealed two concentration
independent N-H stretching vibrations at 3435 and 3398
cm-1. The model compound 2, however, revealed a concen-
tration independent N-H band at 3436 cm-1; this vibration
can be ascribed to the free N-H, due to the low propensity
of 2 for intermolecular association. Accordingly, the 3435
cm-1 vibrational band in 1, observed at a nearly identical
frequency, is consistent with the free N-H. The low
wavenumber peak at 3398 cm-1 would thus be congruent
with the hydrogen bonded N-H groups.
An incremental addition of a strong hydrogen bond
acceptor DMSO-d6 to a CDCl3 solution of 1 promoted a
complete vase to kite conformational change (Figure 4a), as
indicated by the methine Ha resonance shift, 5.6 to 3.3 ppm.7
Cavitand 3 incorporates nitro instead of acetamide groups,
and it is incapable of hydrogen bonding (Figure 3b). 3 mostly
assumed a vase conformation in CDCl3, methine proton δ
) 4.50 ppm,7 which proved to be rather insensitive to the
presence of DMSO-d6 (Figure 4a). Interestingly, incremental
addition of trifluoroacetic acid (TFA) to a CDCl3 solution
1
its positions slowly on the H NMR time scale at low
temperature, which resulted in the appearance of two distinct
singlets at 8.32 and 7.77 ppm (Figure 2c). From the
temperature dependence of Hb’s resonance line shape, we
calculated the apparent first-order rate constant kapp for the
1a/1b interconversion.10 Subsequently, we titrated a CDCl3
solution of 1 with TFA, and upon each increment of the
1
added acid, variable temperature H NMR spectra were
acquired and the kinetic parameters evaluated. Outstandingly,
the apparent rate constant, kapp, for the 1a/1b interconversion
(11) Hindered rotation about the (O)C-N bond in the acetamide group
of 1, in the examined range of temperatures, was discounted by the fact
that the conformational isomerism was not observed in parallel experiments
with the model compound 2.
(12) Preliminary computational studies (MM, PM3) have suggested other
plausible C2 symmetrical conformations. The proposed geometry is in
agreement with the available experimental results.
(13) In principle, TFA may compete for hydrogen bonds. 1H NMR
chemical shifts for NH protons in 1a/b (δ ) 6.77 and 4.34 ppm; 253 K,
CDCl3) changed, but not dramatically, upon addition of TFA (δ ) 6.43
and 4.45 ppm; 253 K, CDCl3). Rather low affinity of TFA for amides in 1
is thus evident.
(14) (a) Jesson, J. P.; Meakin, P. Acc. Chem. Res. 1973, 6, 269-275.
(b) Perrin, C. L.; Dwyer, T. J. Chem. ReV. 1990, 90, 935-967.
Org. Lett., Vol. 8, No. 17, 2006
3699

was discovered to be highly affected by the presence of
exogenous acid (Figure 5). The more acidic the solution of
Table 1. Activation Parameters for 1a/b Interconversion in
CDCl3, with and without Trifluoroacetic Acid (TFA)
TFA
(molar equiv)
∆Hq
(kcal/mol)a
∆Sq
(cal/molK)a
∆Gq
(kcal/mol)b
0
17 ( 1
14 ( 1
17 ( 2
23 ( 2
20 ( 2
22 ( 2
9 ( 1
2.6 ( 0.1
11 ( 1
30 ( 3
18 ( 3
26 ( 3
13.3 ( 0.2
13.6 ( 0.2
14.8 ( 0.2
14.8 ( 0.2
15.0 ( 0.2
15.0 ( 0.2
0.3
1.0
3.0
7.0
17.0
a Calculated from an Eyring plot of log(kapp/T) versus 1/T, over the
temperature range of 258-328 K. b Calculated directly from the Eyring
equation using kapp at 300 K.
Figure 5. Apparent first-order rate constants, kapp, for the 1a/b
interconversion in CDCl3 as a function of trifluoroacetic acid (TFA)
at 318 K (9), 308 K (2), 300 K (b), and 288 K (1, inset).
In summary, we discovered that the conformational
dynamics of our newly designed cavitand 1 can, in principle,
be operated at multiple levels using an exogenous source of
acid. To obtain more insight into the mechanism of the 1a/b
interconversion, we are currently utilizing computational
chemistry approaches to understand the dynamics in this
system. The allosteric regulation of the kinetics of molecular
recognition in 1 and similar receptors is also under experi-
mental investigation in our laboratory.
1 in CDCl3, the slower the obserVed interconVersion of the
enantiomers! This allosteric effect, expressed by an acid, is
more pronounced at higher than at lower temperatures. TFA
is a strong acid (pKa ) -0.25) that is known to protonate
pyrazine nitrogen atoms (pKa ) 0.36)15 of cavitands analo-
gous to 1.8 On the basis of that, it is reasonable to assume
that the [1‚‚‚TFA] interaction played a role in augmenting
the activation energy barrier for the 1a/1b interconversion.
Activation parameters for the 1a/1b interconversion were
calculated from an Eyring plot (Table 1). As a result of the
inherent correlation that arises between ∆Hq and ∆Sq, as both
are computed from the same data set and usually masked
by dominant statistical compensation patterns,16 we refrain
from conducting any in-depth analysis. However, for the
transition state of the rate-limiting step in the 1a/1b inter-
conversion, both the activation enthalpy and entropy are
positive regardless of whether the acid is present in the
system. The positive value of ∆Hq (14-23 kcal/mol) points
to the absence of intramolecular hydrogen bonding interac-
tions. That is to say, for 1a to switch into 1b the intramo-
lecular hydrogen bonds need to be broken. The positive ∆Sq
(2-30 cal/molK) refers to a disordered transition state, which
is consistent with 1 lacking hydrogen bonds.
Acknowledgment. We thank Professor Christopher M.
Hadad of the Ohio State University for useful suggestions.
This work was financially supported with funds obtained
from the Ohio State University.
Supporting Information Available: Detailed descrip-
tions of experimental methods and synthetic procedures. This
material is available free of charge via the Internet at
http://pubs.acs.org.
OL0612760
(15) Brown, H. C. In Determination of Organic Structures by Physical
Methods; Braude, E. A., Nachod, F. C., Eds.; Academic Press: New York,
1955.
(16) (a) Krug, R. R.; Hunter, W. G.; Grieger, R. A. Nature 1976, 261,
566-567. (b) McBane, G. C. J. Chem. Educ. 1998, 75, 919-922.
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