Extending helicity - Capturing the helical character of longer ortho-phenylene ethynylene oligomers

Article abstract of DOI:10.1039/b714237b

New ortho-phenylene ethynylene oligomers are shown to fold into helices of up to two full turns. Evidence of folding is shown by both 1D NMR, where π-π stacking is explored through both solvent and temperature titrations, as well as by 2D ROESY NMR which

Full text of DOI:10.1039/b714237b

New Journal of Chemistry
An international journal of the chemical sciences
www.rsc.org/njc
Volume 32 | Number 4 | April 2008 | Pages 557–744
ISSN 1144-0546
PAPER
Gregory N. Tew et al.
Extending helicity—capturing the helical character of longer ortho-phenylene
ethynylene oligomers

PAPER
www.rsc.org/njc | New Journal of Chemistry
Extending helicity—capturing the helical character of longer
ortho-phenylene ethynylene oligomersw
Ticora V. Jones, Morris M. Slutsky and Gregory N. Tew*
Received (in Gainesville, FL, USA) 14th September 2007, Accepted 19th December 2007
First published as an Advance Article on the web 25th January 2008
DOI: 10.1039/b714237b
New ortho-phenylene ethynylene oligomers are shown to fold into helices of up to two full turns.
Evidence of folding is shown by both 1D NMR, where p–p stacking is explored through both
solvent and temperature titrations, as well as by 2D ROESY NMR which confirmed folding but
also showed the dynamic nature of these helices through the flipping of the terminal TMS group
into and out of a hydrophobic pocket created when the helix forms.
Introduction
Results and discussion
Foldamers, and their implications for deciphering the com-
plexities of macromolecular biological systems, are of great
interest.1–4 Extending the helicity of newly synthesized folda-
meric systems is essential for discovering their utility as a new
class of molecular objects. Previous studies showed that short,
tetrameric ortho-phenylene ethynylene (o-PE) oligomers
adopted helical conformations in solution.2d This was con-
firmed using 1D solution NMR experiments to monitor the
influence of p–p stacking on the aromatic proton chemical
shifts and Rotating Frame Overhauser Spectroscopy
(ROESY)5 to determine through space interactions. In the
tetrameric oligomers, only the two terminal rings would be
involved in the p–p stacking of a helical conformation and
solvent titration experiments confirmed the protons on these
two rings shifted upfield as expected while the protons on the
two remaining central rings did not.2d At the same time, ROE
correlations confirmed through space interactions consistent
with helical conformations.
Deprotected monomers 9 and 10 were synthesized starting
from ethyl 4-amino benzoate as shown in Scheme 1. Oligomers
1, 2, and 3 were synthesized by a partially convergent strategy
of TMS-acetylene deprotection and Sonogashira couplings as
shown in Scheme 2. Coupling of deprotected acetylene mono-
mer 9 with iodide 10 gave dimer 11, which was taken on to
both iodide 12 and deprotected acetylene 13. Coupling of
monomer iodide 10 with dimer 13 gave trimer 14, which was
followed by another reaction cycle to yield tetramer 1. Penta-
mer 2 and hexamer 3 were produced by coupling dimer iodide
12 with the corresponding trimer or tetramer acetylene.
Fig. 1a shows that the three oligomers (1–3) studied here
contain four, five, and six o-PE repeats. The aromatic rings of
each oligomer are numbered consecutively beginning from the
silyl terminus so that 1 contains R1–R4. As the oligomer length
is extended from the tetramers, other folded conformations
besides a ‘correctly’ folded helix, with i, i + 4 residues p–p
stacking, become possible. For example, Fig. 1b highlights
some possible conformers for the hexamer, 3, starting with R1
and R4 folded via p–p stacking as was demonstrated pre-
viously in the tetramer. In this case, the other rings can all fold
into a helix as shown in the boxed structure, which is referred
This article reports the helical conformation of two new,
longer o-PE systems, including the hexamer, which forms a
helix with two full turns. The helical conformations are
examined in solution using NMR methods; two key titration
studies supported helix formation. These titration results were
complimented with ROESY experiments. In general, the
determination of a helical secondary structure for longer
o-PE oligomers has been more difficult to decipher compared
to their meta PE isomers in which UV and fluorescence
spectroscopy provided a convenient correlation between the
cisoid (folded) and transoid (unfolded) conformations.3a,b
Unfortunately this correlation appears to be absent for the
o-PE system, due to the electronic connectivity of the ortho vs.
the meta series.2d,6 However, solution NMR techniques con-
tinue to provide clear evidence supporting helical conforma-
tions in these o-PE systems.
Department of Polymer Science & Engineering, University of
Massachusetts, 120 Governors Drive, Amherst, MA 01003, USA.
E-mail: tew@mail.pse.umass.edu
w Electronic supplementary information (ESI) available: Synthesis for
1–3, NMR traces for data shown in Fig. 2 and 3, and ROESY data for
oligomers 1–3 See DOI: 10.1039/b714237b
Scheme 1 Synthesis of pivotal monomer and deprotected derivatives.
(i) I2, Ag2SO4, EtOH (ii) KOH, MeOH (iii) H2O, CH3CN, HCl,
NaNO2, HN(Et)2, K2CO3 (iv) DMAP, EDC, DCM, CH3(OCH2-
CH2)3OH (v) HCCSi(CH3)3, PdCl2(PPh3)2, CuI, TEA, THF (vi)
CH3I, I2 (vii) TBAF, THF.
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676 | New J. Chem., 2008, 32, 676–679

Fig. 1 (a) Tri-ethylene glycol substituted o-PE ester oligomers.
Tetramer 1 (n = 1), Pentamer 2 (n = 2), Hexamer 3 (n = 3). Each
ring (Rn) has three protons that are labeled respective to their
J-coupling and splitting pattern: a (8.4 Hz, d); b (2.1 Hz, d); and c
(8.4 Hz and 2.1 Hz, dd). (b) Four of the many potential conformations
of 3. The ‘correctly’ folded helical conformer is highlighted.
titration was 0 ppm, then the change in average ppm of the
protons on each ring (D ppm) during the titration was deter-
mined. Each point on the graph represents the average D ppm
value for the protons of each ring. Fig. 2a shows the protons on
rings R1,2,4,5 of 2 shift upfield as CD3CN is added, while only R3
remains at B 0 D ppm. Similarly, all six rings of 3 shift upfield as
CD3CN is added. These upfield shifts are in the opposite direction
of the natural tendency for these protons as model compounds
that cannot fold shift downfield when CD3CN is added to
CDCl3.2h Here, the results are consistent with p–p stacking and
the upfield shift caused by this interaction as the oligomers adopt a
helical conformation. The solvent titration results agree fully with
the expectations of a ‘correctly’ folded helical conformation for
both 2 and 3. As was the case with the previously reported
tetramers, these solvent titrations of 2 and 3 never flattened out as
the concentration of CD3CN approached 100% suggesting that
the solution always contained an equilibrium between folded and
unfolded oligomers. Since it was not possible to increase the
volume percent of CD3CN further, we decided to examine the
influence of temperature on the aromatic protons’ chemical shift.
It was speculated that if an equilibrium of folded and
unfolded structures coexisted in 100% CD3CN at room
temperature then cooling the solution would see an increased
upfield shift of the protons as the equilibrium was shifted
toward the folded structure. In contrast, heating the solution
would shift the protons back downfield as the equilibrium
moved toward the unfolded confirmation. As shown in Fig. 3a
and b, temperature titrations (À26 to 77 1C in CD3CN) were
performed to study these oligomers and are plotted as the
D ppm versus temperature. For oligomer 2, these temperature
titrations show that only the protons of R3 remain unshifted as
the temperature is changed by 100 1C while all the protons on
R1,2,4,5 shift. Starting from 25 1C, as the system is cooled the
protons shift upfield and as the system is heated the protons
shift downfield. Similarly, for 3 the temperature study makes it
very clear that all of the protons on R1–6 shift downfield during
heating from À26 to 77 1C. This change would only occur if all
the aromatic rings of 3 were associated intramolecularly via
p–p stacking of a compact helix in CD3CN. These observa-
tions support the boxed conformation shown in Fig. 1b as the
major conformer in solution and rule out the other possible
Scheme 2 Synthesis of oligomers 1, 2, and 3 by stepwise Sonagashira
couplings and deprotection steps. (i) PdCl2(PPh3)2, CuI, TEA, THF,
55 1C (ii) CH3I, I2, 110 1C (iii) TBAF, THF, 0 1C (iv) 10,
PdCl2(PPh3)2, CuI, TEA, THF, 55 1C (v) TBAF, THF, 0 1C/10,
PdCl2(PPh3)2, CuI, TEA, THF, 55 1C (vi, vii) TBAF, THF, 0 1C/12,
PdCl2(PPh3)2, CuI, TEA, THF, 55 1C.
to as the ‘correctly’ folded helix since this structure has all six
rings involved in p–p stacking. However, since this requires an
entropic penalty, the ability of this hexamer to adopt less ‘‘well-
folded’’ conformations such as those shown in Fig. 1b were
considered. Three other possible structures are illustrated in which
either R5 and/or R6 are not folded into the helical conformation.
As a result of this increasingly complicated landscape, it was
important to consider experimental methods that could distin-
guish between these partially folded structures and the ‘correctly’
folded helix shown in the box of Fig. 1b. This possibility of ‘‘mis-
folded’’ structures appeared important since computational cal-
culations showed that while longer o-PE helical conformations
were lower in energy, the energy difference between fully and
partially folded structures was relatively small.6b
Returning to the previous experimental observations that
confirmed folding of 1, in which only the terminal rings R1 and
R4 shifted upfield in CD3CN, it seemed reasonable that
‘correctly’ folded helical conformations of 2 and 3 would have
four and six rings, respectively, that experience upfield shifts
due to p–p stacking. More specifically, R1,2,4,5 of 2 and R1–6 of
3 would shift upfield leaving only R3 of 2 unshifted. Using
multiple NMR methods (COSY and HMBC), each aromatic
proton and its position in the oligomer has been assigned6c
allowing absolute tracking of each individual proton.
The 1D NMR results of solvent titrations (CDC13 to
CD3CN) for 2 and 3 are shown in Fig. 2a and b. The data
was normalized, as our previous report,2d so that the average
ppm of the protons on each ring at the beginning of the
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Fig. 2 Solvent titrations for oligomers 2 (a) and 3 (b) from CDCl3 to CD3CN (600 MHz, 1.25 mM from 0–100% CD3CN in CDCl3) at 298 K (2),
and 305 K (3).
Fig. 3 Temperature titrations for oligomers 2 (a) and 3 (b) in CD3CN from À26 to 77 1C (600 MHz, À26 to 77 1C, CD3CN, 1.25 mM).
conformers. Taken together, the solvent- and temperature-
dependent chemical shifts for the ring protons of 2 and 3
provide strong evidence for ‘correctly’ folded helical confor-
mations.
Fig. 4. For 3, two cross peaks are found between the terminal
TMS and aryl protons 2b and 5b (see Fig. 4a and b) corre-
sponding to calculated values of 3.4 and 3.5 A, respectively, in
good agreement with the model calculations of 3.5 A (2b) and
3.0 A (5b). These ROE correlations place the three groups
(TMS, R2 and R5) together locally in space, which is com-
pletely consistent with the compact helical structure expected
for the ‘correctly’ folded conformation. Due to the presence of
R5 in this larger oligomer, which is absent in 1, it appears that
a hydrophobic binding pocket is created for the TMS by the
stacking of R1,4 and R2,5. Pentamer 2 has similar ROE
correlations between the TMS and 2b, 5b, 4a (see Fig. 4c
and d) consistent with a helical conformation and the forma-
tion of a hydrophobic pocket. It also has a new cross peak
between the TMS and 3b, suggesting that the TMS can ‘flip’ to
the other side by a 1801 rotation around the R1,2 linkage. This
is shown in Fig. 4d with two TMS groups extending from R1
illustrating that the TMS interacts with both locations during
the ROE experiments. Similar cross peaks between the TMS
and 2b as well as 3b are observed for 1 (see ESIw) in addition
to those originally reported between the TMS and triazene.
These additional correlations observed for 1 and 2 are con-
sistent with the expected dynamic nature of short helices. It is
interesting to consider that hydrophobic packing of the TMS
end group may stabilize the helix analogously to end-capping
in short helix peptides where an acetyl is placed on the
N-terminus yielding an additional hydrogen bond to the
last turn.8
Although the 1D NMR evidence for helical folding of these
oligomers is strong, additional support from 2D NMR would
be reassuring. As a result, ROESY experiments were per-
formed on 1–3 and the results for 2 and 3 are shown in
Fig. 4 (a,c) ROESY spectra of 3 (a) and 2 (c) in CD3CN (600 MHz,
1.25 mM, 270 K, mixing time 0.3 s) (b,d) Energy minimized (MMFF)7
helical conformation highlighting the TMS cross peak protons
for 3 (b) and 2 (d), (d) shows both interactions of the TMS
by ‘flipping’ 1801.
Conclusions
In conclusion, helical folding in longer o-PE systems was
confirmed by their solvent- and temperature-dependent beha-
vior. ROE correlations confirm folding and the dynamic
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678 | New J. Chem., 2008, 32, 676–679

nature of the conformers (1 and 2) as the TMS ‘flips’ from one
side to the other and reveals a binding pocket for the TMS as
the oligomer length increases (2 and 3). While the lack of
baselines observed on NMR titration curves seems to indicate
a conformational equilibrium between unfolded and folded
states, examination of each ring within the oligomer provides
evidence for a ‘correctly’ folded helix and rules out partially
stacked conformers.
3 (a) J. C. Nelson, J. G. Saven, J. S. Moore and P. G.
Wolynes, Science, 1997, 277, 1793–1796; (b) R. B. Prince,
J. G. Saven, P. G. Wolynes and J. S. Moore, J. Am. Chem. Soc.,
1999, 121, 3114–3121; (c) L. H. Yuan, H. Q. Zeng, K. Yamato,
A. R. Sanford, W. Feng, H. S. Atreya, D. K. Sukumaran,
T. Szyperski and B. Gong, J. Am. Chem. Soc., 2004,
126, 16528–16537; (d) H. Jiang, J. M. Leger and I. Huc, J. Am.
Chem. Soc., 2003, 125, 3448–3449; (e) J. Q. Nguyen and B. L.
Iverson, J. Am. Chem. Soc., 1999, 121, 2639–2640; (f) T. Kim, L.
Arnt, E. Atkins and G. N. Tew, Chem.–Eur. J., 2006, 12,
2423–2427.
4 (a) K. Kirshenbaum, A. E. Barron, R. A. Goldsmith, P.
Armand, E. K. Bradley, K. T. V. Truong, K. A. Dill, F. E.
Cohen and R. N. Zuckermann, Proc. Natl. Acad. Sci. U. S. A.,
1998, 95, 4303–4308; (b) A. Hayen, M. A. Schnitt, F. N.
Ngassa, K. A. Thomasson and S. H. Gellman, Angew. Chem.,
Int. Ed., 2004, 43, 505–510; (c) D. Seebach and J. L.
Matthews, Chem. Commun., 1997, 21, 2015–2022; (d) R. P. Cheng,
S. H. Gellman and W. F. DeGrado, Chem. Rev., 2001, 101,
3219–3232.
Acknowledgements
T.V.J. thanks the Ford Foundation and G.N.T. thanks the
NSF-CAREER Award (CHE-0449663) for funding.
References
1 (a) R. P. Cheng, Curr. Opin. Struct. Biol., 2004, 14, 512–520; (b) D.
J. Hill, M. J. Mio, R. B. Prince, T. S. Hughes and J. S. Moore,
Chem. Rev., 2001, 101, 3893–4011; (c) M. S. Cubberley and B. L.
Iverson, Curr. Opin. Chem. Bio., 2001, 5, 650–653; (d) S. H.
Gellman, Acc. Chem. Res., 1998, 31, 173–180.
2 (a) R. H. Grubbs and D. Kratz, Chem. Ber./Recl., 1993, 126,
149–157; (b) S. Shotwell, P. M. Windschief, M. D. Smith and U. H.
F. Bunz, Org. Lett., 2004, 6, 4151–4154; (c) T. V. Jones, R. A.
Blatchly and G. N. Tew, Org. Lett., 2003, 5, 3297; (d) T. V. Jones,
M. M. Slutsky, R. Laos, T. F. A. de Greef and G. N. Tew, J. Am.
Chem. Soc., 2005, 127, 17235–17240; (e) A. Khan and S. Hecht, J.
Poly. Sci. A, 2006, 44, 1619–1627.
5 ROESY was found to be a better technique for these molecules
given the ambiguity of NOESY within the weight range of
oligomers 1–3.
6 (a) S. H. Seo, T. V. Jones, H. Seyler, J. O. Peters, T. H. Kim, J. Y.
Chang and G. N. Tew, J. Am. Chem. Soc., 2006, 128, 9264–9265;
(b) R. Blatchly and G. N. Tew, J. Org. Chem., 2003, 68, 8780–8785;
(c) M. M. Slutsky, T. V. Jones and G. N. Tew, J. Org. Chem., 2007,
72, 342–347.
7 Wavefunction, Inc.–Spartan 2004 software (Molecular mechanics
force field, MMFF minimization).
8 A. Chakrabartty, A. J. Doig and R. L. Baldwin, Proc. Natl. Acad.
Sci. U. S. A., 1993, 90, 11332–11336.
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