Molecular basis for water-promoted supramolecular chirality inversion in helical rosette nanotubes

Article abstract of DOI:10.1021/ja0706192

Helical rosette nanotubes (RNTs) are obtained through the self-assembly of the G∧C motif, a self-complementary DNA base analogue featuring the complementary hydrogen bonding arrays of both guanine and cytosine. The first step of this process is the format

Full text of DOI:10.1021/ja0706192

Published on Web 04/07/2007
Molecular Basis for Water-Promoted Supramolecular Chirality
Inversion in Helical Rosette Nanotubes
Ross S. Johnson,†,‡ Takeshi Yamazaki,†,# Andriy Kovalenko,†,# and
Hicham Fenniri*,†,‡
Contribution from the National Institute for Nanotechnology, Department of Chemistry, and
Department of Mechanical Engineering, UniVersity of Alberta, 11421 Saskatchewan DriVe,
Edmonton, Alberta, T6G 2M9, Canada
Received January 27, 2007; E-mail: hicham.fenniri@ualberta.ca
Abstract: Helical rosette nanotubes (RNTs) are obtained through the self-assembly of the G∧C motif, a
self-complementary DNA base analogue featuring the complementary hydrogen bonding arrays of both
guanine and cytosine. The first step of this process is the formation of a 6-membered supermacrocycle
(rosette) maintained by 18 hydrogen bonds, which then self-organizes into a helical stack defining a
supramolecular sextuple helix whose chirality and three-dimensional organization arise from the chirality,
chemical structure, and conformational organization of the G∧C motif. Because a chiral G∧C motif is
predisposed to express itself asymmetrically upon self-assembly, there is a natural tendency for it to form
one chiral RNT over its mirror image. Here we describe the synthesis and characterization of a chiral G∧C
motif that self-assembles into helical RNTs in methanol, but undergoes mirror image supramolecular chirality
inversion upon the addition of very small amounts of water (<1% v/v). Extensive physical and computational
studies established that the mirror-image RNTs obtained, referred to as chiromers, result from thermody-
namic (in water) and kinetic (in methanol) self-assembly processes involving two conformational isomers
of the parent G∧C motif. Although derived from conformational states, the chiromers are thermodynamically
stable supramolecular species, they display dominant/recessive behavior, they memorize and amplify their
chirality in an achiral environment, they change their chirality in response to solvent and temperature, and
they catalytically transfer their chirality. On the basis of these studies, a detailed mechanism for
supramolecular chirality inversion triggered by specific molecular interactions between water molecules
and the G∧C motif is proposed.
Introduction
oligomeric systems (e.g., polymers, biopolymers). While there
is literature precedent for solvent-induced chirality inversion,
most of these reports dealt with host-guest complexes,2
polymers,3 biopolymers,4 liquid crystalline phases,5 or thin
polymer films,3a,g,i and provided limited mechanistic insight as
to the role of solvent at the intermolecular level. The system
Supramolecular chirality (SC)1 is the expression of absolute
molecular chirality at the macromolecular level and generally
results from the self-assembly of multiple copies of one or more
chiral components or from the self-organization of chiral
† National Institute for Nanotechnology.
(2) (a) Borovkov, V. V.; Hembury, G. A.; Inoue, Y. Angew. Chem., Int. Ed.
2003, 115, 5468-5472. (b) Boiadjiecv, S. E.; Lightner, D. A. J. Am. Chem.
Soc. 2000, 122, 378-383.
‡ Department of Chemistry.
# Department of Mechanical Engineering.
(1) (a) Green, M. M.; Peterson, N. C.; Sato, T.; Teramoto, A.; Cook, R.; Lifson,
S. Science 1995, 268, 1860-1866. (b) Ferringa, B. L.; van Delden, R. A.
Angew. Chem., Int. Ed. 1999, 38, 3419-3438. (c) Yashima, E.; Maeda,
K.; Nishimura, T. Chem.sEur. J. 2004, 10, 42-51. (d) Hill, D. J.; Mio,
M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S. Chem. ReV. 2001, 101,
3893-4011. (e) Borovkov, V. V.; Hembury, G. A.; Inoue, Y. Acc. Chem.
Res. 2004, 37, 449-459. (f) Hof, F.; Craig, S.-L.; Nuckolls, C.; Rebek, J.,
Jr. Angew. Chem., Int. Ed. 2002, 41, 1488-1508. (g) Kikuchi, Y.;
Kobayashi, K.; Aoyama, Y. J. Am. Chem. Soc. 1992, 114, 1351-1358.
(h) Yashima, E.; Maeda, K.; Okamato, Y. Nature 1999, 399, 449-451. (i)
Prins, L. J.; De Jong, F.; Timmerman, P.; Reinhoudt, D. N. Nature 2000,
408, 181-184. (j) Lauceri, R.; Raudino, A.; Scolaro, L. M.; Micali, N.;
Purello, R. J. Am. Chem. Soc. 2002, 124, 894-895. (k) Huck, N. P. M.;
Jager, W. F.; de Lange, B.; Feringa, B. L. Science 1996, 273, 1686-1688.
(l) Ribo´, J. M.; Crusats, J.; Sague´s, F.; Claret, J.; Rubires, R. Science 2001,
292, 2063-2066. (m) Zahn, S.; Canary, J. W. Science 2000, 288, 1404-
1407. (n) de Jong, J. J. D.; Lucas, N. L.; Kellogg, R. M.; van Esch, J. H.;
Feringa, B. L. Science 2004, 304, 278-281. (o) Goto, H.; Yashima, E. J.
Am. Chem. Soc. 2002, 124, 7943-7949. (p) Holmes, A. E.; Barcena, H.;
Canary, J. W. AdV. Supramol. Chem. 2002, 8, 43-78. (q) Sakurai, S.;
Okoshi, K.; Kumaki, J.; Yashima, E. J. Am. Chem. Soc. 2006, 128, 5650-
5651.
(3) (a) Satrijo, A.; Meskers, S. C. J.; Swager, T. M. J. Am. Chem. Soc. 2006,
128, 9030-9031. (b) Goto, H.; Okamoto, Y.; Yashima, E. Macromolecules
2002, 35, 4590-4601. (c) Langeveld-Voss, B. M. W.; Christiaans, M. P.
T.; Janssen, R. A. J.; Meijer, E. W. Macromolecules 1998, 31, 6702-
6704. (d) Price, C. C.; Osgan, M. J. Am. Chem. Soc. 1956, 78, 4789-
4790. (e) Furukawa, J. In Optically ActiVe Polymers; Se´le´gny, E., Ed.; D.
Reidel Publishing Co.: Dordrecht, The Netherlands, 1979; pp 317-330.
(f) Pu, L. Acta Polym. 1997, 8, 116-141. (g) Bouman, M. M.; Meijer, E.
W. AdV. Mater. 1995, 7, 385-387. (h) Bidan, G.; Guillerez, S.; Sorokin,
V. AdV. Mater. 1996, 8, 157-160. (i) Kajitani, T.; Okoshi, K.; Sakurai,
S.; Kumaki, J.; Yashima, E. J. Am. Chem. Soc. 2006, 128, 708-709. (j)
Sakurai, S.; Okoshi, K.; Kumaki, J.; Yashima, E. J. Am. Chem. Soc. 2006,
128, 5650-5651. (k) Lam, J. W. Y.; Tang, B. Z. Acc. Chem. Res. 2005,
38, 745-754. (l) Fujiki, M.; Koe, J. R.; Motonaga, M.; Nakashima, H.;
Terao, K.; Teramoto, A. J. Am. Chem. Soc. 2001, 123, 6253-6261. (m)
Nakako, H.; Nomura, R.; Masuda, T. Macromolecules 2001, 34, 1496-
1502. (n) Cheuk, K. K. L.; Lam, J. W. Y.; Chen, J.; Lai, L. M.; Tang, B.
Z. Macromolecules 2003, 36, 9752-9762. (o) Maeda, K.; Mochizuki, H.;
Watanabe, M.; Yashima, E. J. Am. Chem. Soc. 2006, 128, 7639-7650. (p)
Okoshi, K.; Sakurai, S.; Ohsawa, S.; Kuwaki, J.; Yashima, E. Angew.
Chem., Int. Ed. 2006, 45, 1-5. (q) Nakashima, H.; Fujiki, M.; Koe, J. R.;
Motonaga, M. J. Am. Chem. Soc. 2001, 123, 1963-1969.
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J. AM. CHEM. SOC. 2007, 129, 5735-5743
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A R T I C L E S
Johnson et al.
Scheme 1. Line Structures of Compounds 1-3 and Synthesis of
Compound 3a
Figure 1. Self-assembly of G∧C base derivatives 1-3 in water and
methanol. Letters D and A denote donor/acceptor of H-bonds. Compounds
1 and 2 self-assemble into mirror image helical rosette nanotubes (RNTs)
in both water and methanol, with no change in the CD profile. The SC
inversion observed with 3 could result from its self-assembly into left- or
right-handed helical RNTs, to which we refer here as W-chiromer (in water)
and M-chiromer (in methanol).10 Note that the only difference between 1
and 3 is the exocyclic NHCH3 group. Because of this structural difference,
3 could in principle engage in two additional H-bonds (silver arrows),
whereas 1 and 2 cannot for steric reasons.
a Conditions: (a) 4, POCl3, DMF, 70%; (b) 5, allylamine, DCM, -78
°C, 79%; (c) 6, NH4OH, EtOH, 0 °C, 65%; (d) 7, BnOH, NaH, THF, reflux,
76%; (e) 8, Boc2O, DMAP, Et3N, THF, room temp, 72%; (f) 9, NH2OH-
HCl, pyridine, room temp; (g) 10, TFFA, THF, reflux, 89% (two steps);
(h) 11, N-chlorocarbonyl isocyanate, DCM, 0 °C, 62%; (i) 12, NH3/MeOH
(7 M), room temp, 77%; (j) 13, Boc2O, DMAP, Et3N, THF, room temp,
74%; (k) 14, OsO4, NMMO, THF/t-BuOH then NaIO4, DCM/H2O, room
temp, 54%; (l) 15, 16, NaBOAc3H, DIEA, 1,2-DCE, room temp, 65%; (m)
17, thioanisole/TFA (6%), room temp, 78% (based on 3‚3.5TFA‚1.5H2O).
described here deals with the hierarchical self-assembly of a
small molecule whose SC crosses the mirror plane upon specific
interaction with water molecules. These studies led us to propose
novel mechanisms for SC inversion and catalytic transfer.
in 64% (three steps). Reaction with N-chlorocarbonyl isocyanate
under basic conditions followed by cyclization in a concentrated
methanolic solution of ammonia yielded a key intermediate in
the preparation of G∧C base derivatives, 1,2-dihydropyrimido-
[4,5-d]pyrimidine (13) in 48% yield (two steps). Boc protection
of the free amino group followed by Lemieux-Johnson
conversion of the allyl group to the corresponding aldehyde gave
15 in 40% yield (two steps). Reductive amination with the
partially protected lysine 16 followed by deprotection in 5%
thioanisole/trifluroacetic acid yielded the final product 3 in 51%
(two steps).
Solvent-Induced SC Inversion. G∧C derivatives 1 and 2
(Figure 1) undergo hierarchical self-assembly to form a six-
membered supermacrocycle maintained by 18 H-bonds,6-9
which then self-organizes into remarkably stable,6,7 autocata-
lytic,8 helical rosette nanotubes (RNTs) in water and methanol.6-8
In agreement with basic SC principles,1,6-8 compound 1 and
its mirror image D-isomer 2 self-assemble into nanotubular
architectures with opposite helicities in water or methanol
(Figure 1A,B). While compounds 1 and 2 featured CD spectra
whose sign and profile were not altered in both water and
methanol (Figure 2A,B), compound 3 underwent mirror image
CD inversion upon switching the solvent from methanol to water
Results
Synthesis. Compounds 1, 2, and 56-8were prepared according
to previously reported procedures. Compound 3 was prepared
in 13 steps and 72% average stepwise yield (Scheme 1). First,
barbituric acid was converted in 70% yield to 2,4,6-trichloro-
pyrimidine-5-carbaldehyde (5). Three consecutive nucleophilic
aromatic substitutions on this compound afforded compound 8
in 39% yield (three steps). Selective protection of the primary
amine followed by oxime synthesis and dehydration yielded 11
(4) (a) Pohl, F. M.; Jovin, T. M. J. Mol. Biol. 1972, 67, 375-396. (b) Cosstick,
R.; Eckstein, F. Biochemistry 1985, 24, 3630-3638. (c) Okamoto, Y.;
Nakano, T.; Ono, E.; Hatada, K. Chem. Lett. 1991, 525-528. (d) Steinberg,
I. Z.; Harrington, W. F.; Berger, A.; Sela, M.; Katchalski, E. J. Am. Chem.
Soc. 1960, 82, 5263-5279. (e) Blout, E. R.; Carver, J. P.; Gross, J. J. Am.
Chem. Soc. 1963, 85, 644-646. (f) Gratzer, W. B.; Rhodes, W.; Fasman,
G. D. Biopolymers 1963, 1, 319-330. (g) Letsinger, R. L. Proc. Robert A.
Welch Found. Conf. Chem. Res. 1985, 29, 459. (h) McIntosh, L. P.;
Zielinski, W. S.; Kalish, B. W.; Pfiefer, G. P.; Sprinzl, M.; van de Sande,
J. H.; Jovin, T. M. Biochemistry 1985, 24, 4806-4814. (i) Pu, Y.-M.;
McDonagh, A. F.; Lightner, D. A. J. Am. Chem. Soc. 1993, 115, 377-
380.
(5) (a) Celebre, G.; De Luca, G.; Maiorino, M.; Iemma, F.; Ferrarini, A.;
Pieraccini, S.; Spada, G. P. J. Am. Chem. Soc. 2005, 127, 11736-11744.
(b) Slaney, A. J.; Nishiyama, I.; Styring, P.; Goodby, J. W. J. Mater. Chem.
1992, 2, 805-810. (c) Loubser, C.; Wessels, P. L.; Styring, P.; Goodby, J.
W. J. Mater. Chem. 1994, 4, 71-79. (d) Radley, K.; McLay, N. J. Phys.
Chem. 1994, 98, 3071-3072.
(6) (a) Fenniri, H.; Deng, B. L.; Ribbe, A. E.; Hallenga, K.; Jacob, J.;
Thiyagarajan, P. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (suppl. 2), 6487-
6492. (b) Fenniri, H.; Mathivanan, P.; Vidale, K. L.; Sherman, D. M.;
Hallenga, K.; Wood, K. V.; Stowell, J. G. J. Am. Chem. Soc. 2001, 123,
3854-3855.
(7) Moralez, J. G.; Raez, J.; Yamazaki, T.; Motkuri, R. K.; Kovalenko, A.;
Fenniri, H. J. Am. Chem. Soc. 2005, 127, 8307-8309.
(8) Fenniri, H.; Deng, B. L.; Ribbe, A. E. J. Am. Chem. Soc. 2002, 124, 11064-
11072.
(9) (a) Lawrence, D. S.; Jiang, T.; Levett, M. Chem. ReV. 1995, 95, 2229-
2260. (b) Ducharme, Y.; Wuest, J. D. J. Org. Chem. 1988, 53, 5787-
5789. (c) Zerkowski, J. A.; Seto, C. T.; Whitesides, G. M. J. Am. Chem.
Soc. 1992, 114, 5473-5475. (d) Zimmerman, S. C.; Duerr, B. F. J. Org.
Chem. 1992, 57, 2215-2217. (e) Bonazzi, S.; De Morais, M. M.; Gottarelli,
G.; Mariani, P.; Spada, G. P. Angew. Chem., Int. Ed. 1993, 32, 248-250.
(f) Yang, J.; Marendaz, J.-L.; Geib, S.-J.; Hamilton, A. D. Tetrahedron
Lett. 1994, 35, 3665-3668. (g) Prins, L. J.; Timmerman, P.; Reinhoudt,
D. N. Pure Appl. Chem. 1998, 70, 1459-1468. (h) Davis, J. T. Angew.
Chem., Int. Ed. 2006, 43, 668-698. (i) Marsh, A.; Silvestri, M.; Lehn,
J.-M. Chem. Commun. 1996, 1527-1528. (j) Mascal, M.; Hext, N. M.;
Warmuth, R.; Moore, M. H.; Turkenburg, J. P. Angew. Chem., Int. Ed.
1996, 35, 2204-2206.
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Chirality Inversion by Water Molecules
A R T I C L E S
Figure 2. CD spectra of 1-3 in water and methanol. The CD spectra of 1 (6.8 × 10-5 M, black) and 2 (6.8 × 10-5 M, pink) in water (A) and MeOH (B)
grew over time reaching their maximum intensity over a period of 1 month at 20 °C. The higher ellipticity in methanol reflects the formation of much longer
RNTs in this solvent. The CD spectra of 3 (4.0 × 10-5 M) in water (blue, W-chiromer) and methanol (green, M-chiromer) were recorded after aging the
water stock solution (1.3 × 10-3 M, 1 mg/mL) for 840 h and the methanol stock solution (1.3 × 10-3 M, 1 mg/mL) for 5 h, at 20 °C (C).
(and vice versa). Although unexpected, this observation was
critical in developing a molecular model and a mechanism for
this solvent-induced SC inversion (vide infra). The methanol
chiromer10 (M-chiromer) in Figure 2C shows two minima
(-39.4 mdeg at 289 nm, -31.1 mdeg at 244 nm), and one
maximum (19.6 mdeg at 229 nm), whereas the water chiromer
(W-chiromer) gave a mirror image profile (37.7 mdeg at 290
nm, 32.0 mdeg at 244 nm, -22.8 mdeg at 228 nm).
Time-dependent CD experiments established that this is not
a random process (Supporting Information Figure S1), and
variable temperature CD experiments (Figure S2) established
that the observed chirality is supramolecular in nature as it
disappears upon heating and is restored upon cooling. Since
the absolute chirality of 3 cannot reversibly invert upon
switching solvents, it was logical to postulate that the conforma-
tion of 3 within the supramolecular architecture is such that
circularly polarized light interacts with chromophores in mirror
image spaces in water and methanol, respectively, regardless
of the absolute molecular chirality of 3.
The Chiromers Display the Same Hierarchical Organiza-
tion. The hypothesis of a conformationally-driven chirality
inversion implies that the chiromers maintain the same hierar-
chical organization and that 3 self-assembles into a rosette
supermacrocycle, which in turn self-organizes into pseudomirror
image tubular stacks in water and methanol. As a result, we
anticipated the chiromers to display similar NMR spectra and
physical dimensions. NOESY NMR experiments established
that compound 3 does indeed form key H-bonds6,7 characteristic
of the rosette assembly in 90% H2O/D2O and in CD3OH
(Figure 3).
As shown in Figure 4 (and Figure S3-S11) tapping mode
AFM, TEM, and SEM imaging of 3 established the formation
of RNTs with identical outer diameters in water and methanol:
3.6 nm by AFM and 3.8 nm by TEM, in agreement with the
calculated van der Waals diameter of 3.7 nm. UV-vis spectra
of 3 in water and methanol featured essentially the same profiles.
A hypochromic effect (20%) and a small red shift (7 nm) were
noted in methanol, indicating advanced aggregation in this
solvent (Figure S12).6 These results confirm that the supramo-
lecular architectures in water and methanol have the same
hierarchical organization, dimensions, and shape. Therefore, the
observed chirality inversion is associated with stable, solvent-
dependent conformational states, to which we refer here as
W-chiromer (in water) and M-chiromer (in methanol).10 To
better define these states, the effect of solvation free energy
was investigated first to identify the dominant/recessive chi-
romer. Second, the ability of the chiromers to memorize1h their
SC was established. Third, the effect of temperature was
investigated to establish the kinetic/thermodynamic pathways
leading to the chiromers. Finally, the ability of the thermody-
namic (dominant) chiromer to catalytically transfer its chirality
to the kinetic (recessive) one was demonstrated.
Water Leads to the Formation of the Dominant Chiromer.
This experiment consisted in preparing nine samples of 3 (1
mg/mL, 1.3 × 10-3 M) varying in water (methanol) content
from 100% (0%) to 0% (100%) and monitoring their CD spectra
over time. After 24 h (and over a period of 672 h), it was clear
that water, even at 1% of the total volume, was the dominant
solvent (Figures 5A, S13). The opposite SC appeared when
methanol exceeded 99% (v/v). Particularly noteworthy, is the
accelerating effect of methanol on the formation of the RNTs
as can be inferred from the faster growth of the CD profile
between 0-95% methanol (Figures S13, S14). Time-dependent
dynamic light scattering (Figure 5B) and SEM studies (Figures
S6-S11) established that the accelerating effect of methanol is
associated with the formation of longer RNTs. In summary this
study (a) has shown that very small amounts of water (1% v/v)
induced SC inversion of the M-chiromer thereby suggesting a
specific role for this solvent and confirmed (b) that chiromerism
is not a random process and (c) that there are two chiromers
with opposite chiroptical properties, whose formation is con-
trolled by their solvation free energy, as well as by the kinetics/
thermodynamics of RNT self-assembly. These results also
suggest that the formation of the M-chiromer is under kinetic
control.
Chiromerism Results from Conformational Memory. This
experiment was designed to test the ability of the chiromers to
memorize their SC in a solvent that induces the opposite
chirality. Thus, compound 3 (1.3 × 10-3 M, 1 mg/mL) was
dissolved in methanol and water and allowed to equilibrate (672
h) before an aliquot (62.5 µL) from each solution was transferred
to the solvent that induces opposite SC (1937.5 µL, 97% final
volume). The SC of the water/methanol (3:97) sample of 3 (4.0
× 10-5 M) decreased initially over 168 h, then increased
significantly, well beyond the initial value (Figure S16), thus
(10) The term chiromerism was introduced to express the notions of chirality
and chimerism. That is the ability of a single chiral molecule to express
multiple, yet thermodynamically stable, supramolecular chirality outputs
as a result of preferred conformational states under a set of physical
conditions. Chiromers are supramolecular conformational isomers that (a)
are thermodynamically stable, (b) can memorize their chirality, and (c)
can amplify their chirality in an achiral environment.
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A R T I C L E S
Johnson et al.
Figure 3. One-dimensional 1H NMR and section of the NOESY spectrum in 90% H2O/D2O (A) and in CD3OH (B) showing evidence of the formation of
the proposed H-bond network (C). The NOESY spectra show NOEs between HA and HB (dark bars in C). Since these protons are too far apart to display
any intramodular NOEs, the observation of an NOE between them confirms the existence of intermodular H-bonds. In addition, no other NOEs or imino
proton signals resulting from nonassembled 3 or nonspecific aggregates thereof were observed. These results are diagnostic of the formation of the rosette
assembly.6,7
confirming the ability of the W-chiromer to memorize its SC.
The initial decrease in SC is possibly the result of a small
amount of nonassembled 3 in the parent water stock solution,
which upon dilution in methanol, undergoes self-assembly into
the M-chiromer, thus attenuating the system’s overall SC.
Subsequent growth of the CD profile beyond the initial phase
confirms the accelerating effect of methanol on RNT growth
and suggests a catalytic interconversion of chiromers (vide
infra).
While the M-chiromer (4.0 × 10-5 M) maintained its SC in
methanol/water (3:97), the intensity of the CD profile decreased
steadily over the course of the experiment (Figure S16),
eventually disappearing after 8 weeks with no restoration or
inversion even after 7 months. The fact that the CD profile of
the M-chiromer disappears over time suggests an equilibrium
for chiromer interconversion involving unassembled 3 as an
intermediate species, since the latter does not self-assemble at
CD concentration. However, when 90% of the solvent was
evaporated, the residue aged for 2 weeks, then rediluted in water
(4.0 × 10-5 M), its CD profile was not only restored, but was
indeed that of the W-chiromer. These experiments confirm that
(a) W-chiromer is the thermodynamic product whereas the
M-chiromer is the kinetic product, (b) W-chiromer is kinetically
and thermodynamically stable, (c) water is the dominant solvent,
(d) methanol accelerates RNT growth, and (e) chiromerism is
the result of two distinct, “mirror image”, stable, and solvent-
dependent conformational states.
Kinetic versus Thermodynamic Control of Hierarchical
Self-Assembly. Solutions of 3 (1.3 × 10-3 M, 1 mg/mL) in
methanol and in water were each split into two equal-volume
samples, the first was kept at 20 °C while the other was refluxed
for 3 s. Aliquots (62.5 µL) from the water and methanol
solutions were diluted in the same solvents (1937.5 µL, [3]final
) 4.0 × 10-5 M) after 24, 120, 168, and 336 h and their CD
spectra were recorded. The heated water samples showed a large
increase (300-400%) in the CD intensity and no change in
profile over a period of 336 h (Figure S16). Conversely, the
heated methanol samples adopted the opposite SC (Figure 5C).
This thermally-induced chirality inversion was found to take
place only for stock solutions aged for less than 72 h. Samples
aged for more than 72 h became stereochemically locked (Figure
S18). Regardless of the age and thermal treatment, SEM imaging
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Chirality Inversion by Water Molecules
A R T I C L E S
Figure 4. TM-AFM (A, B), TEM (C-F), and SEM (G-J) images of W-chiromer (A, C, D, G, H) and M-chiromer (B, E, F, I, J) establishing their identical
dimensions and hierarchical organization. TM-AFM images show that the chiromers have very similar outer diameter, 3.58 for W-chiromer (A) versus 3.63
for M-chiromer (B). The TEM images of the W-chiromer (C, D) and M-chiromer (E, F) stained with nano-W gave the same outer diameter for both
chiromers (3.8 nm). SEM images of the W-chiromer (G, H) and M-chiromer (I, J) show the formation of long nanotubes after aging for 1 month at 1.3 ×
10-3 M (1 mg/mL) and then diluting to 0.33 × 10-3 M (0.25 mg/mL). Scale bars are 40 nm for C-F and 250 nm for G-J.
Figure 5. Experiments establishing the kinetic and thermodynamic pathways leading to the M- and W-chiromers. (A) Binary solvent study showing that
the W-chiromer of 3 is the dominant supramolecular isomer. The blue/green bars show the growth after 24 h at 290 nm and the black extensions show the
additional growth recorded after 672 h. (B) Time-dependent hydrodynamic diameter of the W-chiromer (blue trace) and M-chiromer (green trace) monitored
by DLS. (C) Thermally-induced SC inversion of the M-chiromer. The CD profiles of the heated (red traces) and nonheated (black traces) were monitored after
24 and 120 h. (D) SC inversion of M-chiromer catalyzed by W-chiromer (green/blue traces). The W-chiromer was replaced with water in the control
experiment (black trace). Free energy trajectories of RNTs #1, #2, #163, and #515 relative to the most stable RNT at N ) 1 (#163) in water (E) and methanol
(F). Although RNT #515 is more stable than RNT #2 for N > 4, it does not form in methanol because it must overcome a significant energy barrier (gray
box) during the early stages of self-assembly.
showed the formation of RNTs in all samples (Figure S11),
although significantly longer in the heated samples, in agreement
with DLS data (Figure S15). These studies confirmed that (a)
W-chiromer and M-chiromer are one species that exists in two
mirror-image, interconvertible, conformational states, (b) M-
chiromer is the kinetic product and W-chiromer is the thermo-
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A R T I C L E S
Johnson et al.
Scheme 2. Catalytic and Thermodynamic Pathways for Chiromer Formation and Interconversion in Methanol (Left) and Water (Right)a
a Upon dissolution of compound 3 in water or methanol, both chiromers can form during the early stages of self-assembly. However, depending on the
solvent and thermodynamic conditions used, only one chiromer will grow preferentially.
dynamic product, and (c) M-chiromer can cross the mirror plane
before becoming kinetically and conformationally locked.
Catalytic Transfer of Conformational Chirality. Since the
W-chiromer memorizes its SC, grows faster in the presence of
methanol, and is the thermodynamic product, we tested its ability
to catalyze the SC inversion of the M-chiromer. Thus, catalytic
amounts of W-chiromer (10 mol %) were added to the
M-chiromer and the reaction was monitored by CD. As shown
in Figure 5D (and Figure S19), the M-chiromer underwent
complete inversion of chirality, whereas the control experiment
(without W-chiromer) underwent, as expected, an attenuation
of the CD profile.
153 RNTs consisting each of 11 rosettes, with the top and
bottom 2 rosettes as well as all the G∧C bases fixed to reduce
end effects. The central rosette in each of the 153 RNTs was
taken to finally construct RNTs composed of N ) 1-10 rosettes.
Finally, to obtain a detailed microscopic insight into the
organization of solvent molecules around the RNTs and their
role in nanotube formation, we applied the 3D-RISM-KH
theory7,11 to the 153 RNTs composed of N rosettes (N ) 1-10)
in water or methanol and in the presence of Cl- counterions.
The free energy of a given RNT conformer was obtained as a
sum of the internal energy and the solvation free energy. Figures
S22-S29 present the free energy trajectories, relative to the
most stable RNT at N ) 1 (RNT #163).
The Chiromers Are Solvent-Stabilized Supramolecular
Conformational Isomers. Based on our experimental results,
it is clear that the chiromers self-assemble into pseudomirror
image RNTs. It is also clear that the water and methanol
chiromers correspond to the thermodynamic and kinetic prod-
ucts, respectively. To uncover the structural basis for these
results we carried out a conformational search in water and
methanol, with the solvation structure and thermodynamics
obtained by the three dimensional molecular theory of solvation
(section M, Supporting Information).7,11 The first step consisted
in carrying out a conformational search around compound 3.
This motif was minimized, then 648 conformations were
generated by varying dihedral angles around six bonds as shown
in Figure S21. The second step consisted in arranging each of
these conformations to form 6-fold symmetry rosettes main-
tained by 18 H-bonds. The rosettes were then stacked in a
tubular fashion with an interplanar separation of 4.5 Å and a
rotation angle of 30° per rosette along the main axis.6-8 Because
of severe steric constraints, only 153 of the 648 conformers
could be assembled into RNTs. The third step consisted in
minimizing the energy of the 153 RNTs using Macromodel 8.5/
Maestro 6.0 with OPLS-AA force field.12 The PRCG energy
minimization in implicit GB/SA water was then applied to the
From these calculations two families of RNTs were identified,
typified by (a) right-handed RNT #515, as a global thermody-
namic minimum corresponding to the W-chiromer, and (b) left-
handed RNT #2, as a kinetic product corresponding to the
M-chiromer (Figures 1 and S30). To further substantiate this
hypothesis, we have also carried out electronic structure
calculations to obtain theoretical CD spectra for helically
arranged motifs derived from stable RNT #515 (W-chiromer)
and #2 (M-chiromer) as shown in Figures S31 and S32. The
system described here is the first in which mirror-image
supramolecular chirality outputs were unambiguously connected
to a kinetic Versus thermodynamic control of hierarchical self-
assembly. Such control results from the self-assembly of
preferred conformational states of a single homochiral molecule.
Discussion
A Mechanism for Chiromer Formation and Catalytic
Interconversion. On the basis of the above experimental results
and computational studies, the following mechanism for chi-
romer formation, growth, and interconversion may be envisioned
(Scheme 2, Figure 6). Dissolution of compound 3 in water leads
most likely to the formation of a large population of chiromers,
typified by left- and right-handed short RNTs. However, because
RNT growth is significantly slower in water, and because the
initial energy barriers to formation of left- and right-handed
(11) Kovalenko, A. In Molecular Theory of SolVation; Hirata, F., Ed.; Kluwer
Academic Publishers: Dordrecht, The Netherlands, 2003; pp 169-275.
(12) Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. J. Am. Chem. Soc.
1996, 118, 11225-11235.
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Chirality Inversion by Water Molecules
A R T I C L E S
Figure 6. Proposed templated supramolecular chain reaction mechanism for the catalytic transfer of conformational chirality from W-chiromer to M-chiromer.
Table 1. Free Energy (kCal/mol) of Binding of Water Molecules in
Unique Arrangements (W1-W3) and Methanol Molecules in
Unique Arrangements (M1, M2) in the First Solvation Shell around
a Single Motif in W-Chiromer (RNT #515) and M-Chiromer (RNT
#2) in Water, Water-Methanol (50/50), and in Methanol
H2O
H2O/MeOH (50/50)
MeOH
Chiromer
W
M
W
M
W
M
W1
W2
W3
∑Wn
-5.03
-6.01
-5.36
-16.4
-5.47
-5.62
-4.59
-15.7
-5.51
-6.34
-6.25
-18.1
-6.60
-6.22
-4.72
-17.5
M1
M2
∑Mn
-4.46
-5.74
-10.2
-5.60
-4.29
-9.9
-5.45
-7.73
-13.2
-7.53
-5.37
-12.9
RNTs are similar (Figure 5E), right-handed RNTs will form
preferentially because their free energy trajectory is steeper,
leading as a result to the W-chiromer (right-handed, thermo-
dynamic product). Dissolution of 3 in methanol should also lead
to the formation of both left- and right-handed short RNTs.
However, because there is no energy barrier to the formation
of left-handed RNTs in methanol (Figure 5F), and because
methanol accelerates RNT self-assembly regardless of handed-
ness, the left-handed population of RNTs will grow faster
(kinetic pathway) and take over the SC of the system, leading
as a result to the M-chiromer (left handed, kinetic product). It
is also important to point out that the right-handed W-chiromer
can be induced to form and grow faster in methanol if heat is
applied to the solution to overcome the initial energy barrier.
This heat-induced SC inversion is indeed possible if the sample
is heated within 72 h of preparation. Beyond 72 h, conversion
of M-chiromer into W-chiromer does not take place because
(a) all traces of W-chiromer that could act as a catalyst for
interconversion were converted to long and kinetically stable
M-chiromer, and (b) inverting the chirality of mature M-
chiromer would require overcoming its very large solvation free
energy.
A simple mechanistic pathway for the conversion of M-
chiromer into W-chiromer could be targeted equilibrium shifting
toward the thermodynamic product, a supramolecular variation
on Le Chaˆtelier’s principle (Table S2). Alternatively, an active
role for the W-chiromer may also be envisioned, possibly
involving: (a) the formation of a hybrid M/W-chiromer through
end-to-end fusion followed by (b) cooperative transfer of
conformational information from the W-chiromer to the M-
chiromer via a templated supramolecular chain reaction8 mech-
Figure 7. Hydrogen-bond network generated in the first solvation shell
with W-chiromer (A, C) and M-chiromer (B, D) in water (A, B) and in
methanol (C, D).
anism (Figure 6). The latter mechanism is more likely since (a)
the formation of the M-chiromer proceeds much faster (Figure
5B), and (b) the M-chiromer used in this experiment was aged
beyond the stage for interconversion (i.e., conformationally
locked, Figures S18, S19).
Achiral Solvent Molecules Play the Role of a Supramo-
lecular Chirality Switch. One important point we had to
address, however, is the profound effect of an apparently small
structural difference between compound 1 and 3 (a methyl
group) on the RNTs’ chiroptical and physical properties. The
absence of the methyl group in 3 not only eliminates a
hydrophobic patch, but also opens access to the pyrimidinic
nitrogens thus creating two new H-bond donor/acceptor sites
(see Figure 1). This triple effect should allow for a deeper
penetration of solvent molecules into the walls of the RNTs
where they could establish strong H-bonds. This hypothesis was
probed computationally and solvation models were obtained
(section N, Supporting Information). The solvation models
resulted in three unique arrangements of water molecules (W1-
W3) and two for methanol (M1, M2) around the chiromers (Table
1, Figure S41). As expected, most of these solvent molecules
are within H-bond distances from the exocyclic amino group
and/or the pyrimidinic nitrogen (Figure 7).
The proposed mechanism for chiromer formation rests on the
hypothesis that W- and M-chiromers coexist in solution during
the early stages of the self-assembly process and that one grows
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A R T I C L E S
Johnson et al.
preferentially depending on the solvent used. Comparison of
columns 2/3 versus 6/7 in Table 1, and the extensive hydrogen
bond network in Figure 7A,B versus Figure 7C,D, show that
both chiromers are preferentially solvated by water. However,
the unique water cluster identified (W1-W3) binds significantly
more strongly to the W-chiromer than to the M-chiromer (4.32
kcal/mol per rosette, compare column 2 versus 3, Table 1),
leading to a preferential stabilization of the W-chiromer in water.
Methanol was found to bind more strongly to the W-chiromer,
indicating that the latter is also more stable in methanol (1.68
kcal/mol per rosette, compare column 6 versus 7, Table 1).
However, as shown in Figure 5F, W-chiromer must overcome
an energy barrier in methanol, whereas M-chiromer does not.
As a result, the latter forms preferentially in methanol as a
kinetic product.
organization but expressed mirror-image SC. They were also
shown to be thermodynamically stable supramolecular species
yet displayed dominant/recessive behavior. Solvent and tem-
perature were shown to play a critical role in determining the
dominant chiromer. We have shown that the chiromers memo-
rize and amplify their chirality in an achiral environment, change
their chirality in response to the environment (solvent, temper-
ature), and catalytically transfer their SC according to a novel
mechanism, thus demonstrating that molecular conformational
information can be stored and catalytically propagated.
Extensive experimental and theoretical studies established that
the chiromers are solvent-stabilized supramolecular conforma-
tional isomers. The solvation models revealed unique arrange-
ments of solvent molecules around the chiromers involved in
an extensive network of H-bonds with the exocyclic amino
group and/or the pyrimidinic nitrogen of the G∧C base. On the
basis of these interactions a mechanism was proposed for SC
inversion in which achiral solvent molecules (water) play the
role of SC switches. These studies have also demonstrated that
methanol acts as a cocatalyst that accelerates RNT self-assembly,
whereas contrary to the conventional wisdom in the field, water
enhances RNT’s relative thermodynamic stability and controls
its SC.
Changes in free energy of binding upon transfer from one
solvent to the mixture agree with water being the dominant
solvent and W-chiromer being the dominant conformational
isomer. In effect, transfer of W-chiromer from water to 50/50
methanol/water, results in a strengthening of free energy of
binding of water molecules (10.2 kcal/mol per rosette, compare
columns 2 and 4, Table 1). On the other hand, transfer of
M-chiromer from methanol to 50/50 methanol/water, results in
a weakening of the binding energy of methanol molecules (18.1
kcal/mol per rosette, compare columns 5 and 7, Table 1). This
trend suggests a mechanism whereby water molecules play the
role of a supramolecular chirality switch involving: (a) water
penetration in the RNT grooves and displacement of methanol
molecules, (b) establishment of a H-bond network with the
exocyclic amino group and pyrimidinic nitrogen, (c) confor-
mational change of the self-assembling module by rotation
around the side chain’s CH2-CH2-N(R)H2-C(R)H dihedral
angle leading to the formation of the thermodynamic W-
chiromer. These results demonstrate that methanol acts as a
cocatalyst that accelerates RNT self-assembly, whereas contrary
to the conventional wisdom in the field, water enhances RNT’s
relative thermodynamic stability and controls its SC.
Finally, while absolute molecular chirality guarantees some
form of macromolecular chirality, its profile and amplitude are
determined by thermodynamic and kinetic parameters defined
by the environment in which self-assembly and self-organization
took place. SC may thus be viewed as the result of conforma-
tional memory.
Materials and Methods
All circular dichroism spectra were recorded on a JASCO J-810
spectropolarimeter. Samples were scanned from 350-200 nm at a rate
of 100 nm/min. Sample preparations and concentrations are indicated
in the figure captions and in the Supporting Information section. Nuclear
magnetic resonance experiments were conducted at 5 °C on a Varian
Inova-800 spectrometer equipped with either a 5 mm triple axis gradient
HCN probe or a 5 mm HCN-Zaxis-gradient cold probe. Atomic force
microscopy measurements were performed in tapping mode (TM-AFM)
at a scan rate of 2 Hz per line using a Digital Instruments/Veeco
Instruments MultiMode Nanoscope IV equipped with an E scanner.
Silicon cantilevers (MikroMasch USA, Inc.) with spring constants of
40 N/m were used. TEM imaging was performed on a JEOL 2010
microscope operating at 200 kV. The samples were negatively stained
with either 1% uranyl acetate or nano-W (methylamine tungstate,
Nanoprobes Inc.). All SEM images were obtained without negative
staining, at 5 kV accelerating voltage and a working distance of 3.0
mm on a high-resolution Hitachi S-4800 cold field emission SEM. UV-
vis spectra were recorded on an Agilent 8453. Dynamic light scattering
(DLS) experiments were performed on a Malvern Zetasizer Nano S
working at a 90° scattering angle at 25 °C. This instrument is equipped
with a 40 mW He-Ne laser (λ ) 633 nm) and an avalanche photodiode
detector. Size distributions were calculated using an inverse Laplace
transform algorithm, and the hydrodynamic radii were calculated using
the Stokes-Einstein equation.
Supramolecular Chirality Is the Result of Conformational
Memory. It is clear from these investigations and earlier
reports1-8 that absolute molecular chirality guarantees some
form of SC, but certainly not its profile. The latter is determined
by thermodynamic and kinetic parameters defined by the
environment in which self-assembly and self-organization took
place. Thus, through their hierarchical and conformational states
and chiroptical outputs, chiral supramolecular architectures may
be viewed as a manifestation of their physical/chemical environ-
ment. An important corollary of this statement is that any chiral
supramolecular assembly could in principle express multiple
chiroptical outputs depending on its physical environment. This,
as a result, leads to the conclusion that SC is nothing but an
expression of conformational memory.
Conclusion
We have shown that a single chiral molecule can express
mirror image chiroptical outputs upon self-assembly into
pseudomirror image supramolecular conformational isomers
(chiromers). This system is also the first in which mirror-image
SC outputs were unambiguously connected to kinetic versus
thermodynamic control of a hierarchical self-assembly process.
The chiromers were shown to have identical hierarchical
Acknowledgment. We thank NSERC, NRC Canada, and the
University of Alberta for supporting this program. We thank
the Canadian National High Field NMR Centre (NANUC) for
their assistance and use of the facilities. Operation of NANUC
is funded by the Canadian Institutes of Health Research, the
Natural Science and Engineering Research Council of Canada,
and the University of Alberta. The computations were supported
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5742 J. AM. CHEM. SOC. VOL. 129, NO. 17, 2007

Chirality Inversion by Water Molecules
A R T I C L E S
by the Centre of Excellence in Integrated Nanotools at the
University of Alberta. We thank Dr. J. G. Moralez for help with
AFM imaging.
studies; DLS measurements; chiral memory experiments; ther-
mally-induced chirality inversion experiments; catalytic transfer
of SC experiments; theory and modeling methods and results;
solvation models and associated methods and results. This
material is available free of charge via the Internet at
http://pubs.acs.org.
Supporting Information Available: Synthetic procedures for
the preparation and characterization of compound 3; time-
dependent CD and VT-CD; 1D and 2D NMR procedures; AFM,
TEM and SEM imaging; UV-vis spectroscopy; binary solvent
JA0706192
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J. AM. CHEM. SOC. VOL. 129, NO. 17, 2007 5743