Acid-induced molecular-structural transformation of N-methyl aromatic oligoamides bearing pyridine-2-carboxamide

Article abstract of DOI:10.1016/j.tetlet.2015.11.058

Amide oligomers composed of pyridine-2-carboxamide as the repeating unit were synthesized in a stepwise manner and their structures were examined by means of ¹H NMR, NOE measurements, and DFT calculations. All the synthesized oligomers adopted a folded conformation, but became partially unfolded at the C-terminal upon addition of acid. A characteristic long-range hydrogen bond, which stabilizes local folding, was present in oligomers with a long main chain.

Full text of DOI:10.1016/j.tetlet.2015.11.058

Tetrahedron Letters 57 (2016) 56–59
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Acid-induced molecular-structural transformation of N-methyl
aromatic oligoamides bearing pyridine-2-carboxamide
⇑
Ryu Yamasaki, Saori Fujikake, Ai Ito, Kentaro Migita, Nobuyoshi Morita, Osamu Tamura, Iwao Okamoto
Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan
a r t i c l e i n f o
a b s t r a c t
Article history:
Amide oligomers composed of pyridine-2-carboxamide as the repeating unit were synthesized in a step-
wise manner and their structures were examined by means of 1H NMR, NOE measurements, and DFT cal-
culations. All the synthesized oligomers adopted a folded conformation, but became partially unfolded at
the C-terminal upon addition of acid. A characteristic long-range hydrogen bond, which stabilizes local
folding, was present in oligomers with a long main chain.
Received 7 October 2015
Revised 13 November 2015
Accepted 20 November 2015
Available online 30 November 2015
Ó 2015 Elsevier Ltd. All rights reserved.
Keywords:
Pyridine-2-carboxamide
Foldamer
Acid-induced conformational alteration
Amide oligomer
Stepwise elongation
Introduction
such as 1, altered the predominant conformation from anti-cis to
syn-trans (Fig. 1).11 These conformational features are different from
Foldamers and folding mechanisms have attracted intense
attention in connection with studies to comprehend and imitate
the structures and functions of biological relevant molecules, such
as peptides, proteins, and nucleic acids.1 The past several decades
have witnessed an enormous expansion of this field, and one of
the hottest topics is the development of stimulus-responsive fold-
ing/unfolding transformation systems.2 Indeed, many proteins,
such as receptors and channels, change their structure in response
to various external stimuli, such as ligands, ions, and acid.3
Although there are many reports concerning foldamers whose con-
formational behavior is controlled by ligands or anions, there are
only a few examples of acid-induced conformational switching
systems.4,5
Among reported stimulus-responsive folding/unfolding systems,
oligo aromatic amides are particularly attractive, mainly because of
their potential for structure-based molecular design.6–10 We have
developed pyridine-containing aromatic amides as acid-responsive
molecular switching units.4,11 In general, aromatic amide com-
pounds, such as benzanilide and acetanilide, exist predominantly
in trans conformation. However, their conformational preference is
dramatically switched by N-methylation, and most N-methylated
aromatic amides favor cis conformation.12 We found that addition
of acid to compounds bearing an N-methyl-N-(2-pyridyl) moiety,
those of other related foldamers containing hydrogen-bonding net-
works of N–H protons in amide functionalities,8 and the dynamical
behavior has unique characteristics. In the previous study, we dis-
covered the unique folding and unfolding behavior of an N-methyl
amide compound containing five pyridine rings (2) (Fig. 2); specifi-
cally, the structure changed from layered to spiral to flat form in
response to addition of acid.4 It is noteworthy that this folding nat-
ure emerges as a result of oligomerization of multiple amide bond
units, and does not simply represent the sum of the behaviors of
the individual amide units. Because of the Cs symmetry of com-
pound 2, N-methyl amide was grouped into only two types, which
limits dynamic behavior. In order to investigate the nature of longer
and less symmetric pyridyl oligoamides, we designed head-to-tail
type 2-pyridyl oligo amides containing continuous non-equivalent
N-methyl amide bonds. In this Letter, we describe the synthesis of
2-pyridyl amides 3–5 (Fig. 2) and their conformational changes
induced by the addition of acid.
Results and discussion
Aromatic oligoamides 3–5 were synthesized as shown in
Schemes 1 and 2, featuring 2-nitrobenzenesulfonyl (Ns) as a pro-
tecting group.13 The main chain was elongated by means of
repeated deprotection and coupling cycles of compound 6, simi-
larly to peptide synthesis, as shown in Scheme 1. Compound 6
was coupled with N-methyl-2-pyridine using thionyl chloride as
⇑
Corresponding author. Tel.: +81 42 721 1569; fax: +81 42 721 1570.
E-mail address: iokamoto@ac.shoyaku.ac.jp (I. Okamoto).
http://dx.doi.org/10.1016/j.tetlet.2015.11.058
0040-4039/Ó 2015 Elsevier Ltd. All rights reserved.

R. Yamasaki et al. / Tetrahedron Letters 57 (2016) 56–59
57
Figure 1. Conformational transformation of pyridyl aromatic amide 1 elicited by
acid.
CH3 H3C
CH3 H3C
O
O
O
O
N
N
N
N
N
N
N
N
N
2 (see ref. 4)
O
CH3
O
CH3
Scheme 2. Synthesis of oligoamides 3–5.
N
N
N
N
N
n
The structures of the oligoamides 3–5 in solution were analyzed
by means of 1H NMR measurements in CD2Cl2 (Fig. 3). As already
mentioned, N-methyl-N-2-pyridyl amide has cis conformational
preference, which is a general preference of secondary aromatic
amide compounds.11 These pyridyl amides also showed cis confor-
mational preference, compared with simple pyridyl amide com-
pounds; the signal of aromatic protons at the ortho position was
shifted to a higher field, which is a typical feature of cis aromatic
amides.11b
3 (n=1)
4 (n=2)
5 (n=3)
Figure 2. Cs symmetric aromatic oligoamides 2, and 3–5 bearing pyridine-2-
carboxamide.
To obtain further insights into the folding structures of these
oligomers, NOE experiments were performed. Most signals were
assigned by means of spin population transfer (SPT) experiments
(see Supplementary data), and the results are shown in Figure 4.
Irradiation of each N-methyl proton of 3 revealed correlations with
aromatic protons of N-terminal pyridine, indicating that the whole
molecular skeleton adopts a zigzag shape, not the cage-like syn con-
formation observed in sterically hindered oligo-m-benzanilide.14
This result can be rationalized in terms of both cis-amide prefer-
ence and the dipole relationship between carbonyl and nitrogen
at pyridine. Since similar trends can be found in pyridine tetramer
4 and pyridine pentamer 5, adaptation of a zigzag shape appears to
be
a general trend of these head-to-tail types of N-methyl
oligopicolinamides.
To examine acid-induced conformational alterations in solu-
tion, oligoamides 3–5 were exposed to acidic conditions and
observed by 1H NMR. Figure 3 shows the 1H NMR spectra of the
aromatic region of oligoamides 3–5 in the absence (upper) and
presence of excess trifluoroacetic acid-d (TFA-d, 150 equiv) (lower,
expressed as 3H–5H). In our previous studies,4,11b the use of TFA-d
allowed us to partially protonate the pyridine nitrogen atom; only
the C-terminal and N-terminal pyridines are protonated, whereas
the central pyridine nitrogen atom is not protonated even when
an excess amount of TFA-d is used. In the cases of 3 and 5, the
lower field shift of aromatic protons upon addition of TFA-d indi-
cates protonation at the terminal pyridine nitrogen. In contrast,
addition of acid to a solution of 4 broadened the whole 1H NMR
spectrum, which precluded detailed analysis. In the cases of oligo-
mers 3H and 5H, all proton signals were assigned by means of SPT
experiments (see Supplementary data), and the observed NOE
enhancement of oligoamides by excess TFA-d is illustrated in
Figure 5. In addition, the changes in the chemical shifts of oligoamides
3 and 5 elicited by acid are summarized in Figure 6. The conforma-
tional behavior of oligomers 3 and 5 was quite similar to that of the
model compound 1 (vide infra).11
Scheme 1. Elongation cycles of pyridine-2-carboxamide.
an activating reagent to afford 7 in good yield. The Ns group was
removed in the presence of anionic thiol and the resultant sec-
ondary amine, 8, was reacted with activated 6 to afford amide
dimer 9. This deprotection and elongation cycle was repeated to
afford amide trimer 11 and the corresponding amine 12 in a good
overall yield.
The designed oligoamides 3–5 were synthesized by capping free
secondary amines with picolinic acid (13) activated with
ethylchloroformate or isobutylchloroformate, in moderate to good
yields (Scheme 2).

58
R. Yamasaki et al. / Tetrahedron Letters 57 (2016) 56–59
Figure 3. 1H NMR spectra of 3–5 (upper) and 3H–5H (lower) in CD2Cl2 Assignment was given based on the structures in Fig. 4.
by 0.3–1.0 ppm upon acidification; these large shifts are inter-
preted as being due to conformational inversion from cis-amide
to trans-amide, as well as protonation at pyridine nitrogen. This
conformational alteration is also supported by the results of NOE
enhancement experiments (Figs. 4 and 5). The enhancement
observed for N-methyl protons of the central pyridine and aro-
matic protons of N-terminal pyridine (3), or the second N-methyl
protons from the N-terminal and the aromatic protons of N-terminal
pyridine (5) disappeared in 3H and 5H. This conformational alter-
ation is reasonable, taking 6-membered-ring hydrogen bonding of
the pyridinium proton and amide carbonyl into account.
1.1%
11
1.5%
1.7%
O
O
10
1.0%
CH3
2.9%10
CH3
CH3
O
9
4
1
N
9
N
N
5.0%
6.7%
N
14
N
8
3
2
8
N
O
N
4
N
11
12
N
5
5
N
N
CH3
4.8%
3
2.1%
N
6
13
CH3
1
2
6
7
7
O
2.4%
3.9%
O
1.4%
3
4
1.3%
2.5%
Many of the 1H NMR changes induced by TFA-d were common
to 3 and 5, but a notable difference emerged with elongation of the
amide chain. Oligoamide 5 showed unique behavior of the central
pyridine ring, which exhibited higher field shifts (À0.4 ppm for
3-position and À0.1 ppm for 5-position) upon addition of TFA-d
(Fig. 6). This is unusual, since protonation on pyridine nitrogen
generally causes a lower field shift of pyridine aromatic proton
peaks. Presumably the shift resulted from an aromatic ring current
effect due to local folding. Considering the observed NOE correla-
tion between the N-methyl group attached to the central pyridine
and the C6-proton of C-terminal pyridine (0.6%), involvement of a
hydrogen bond between the carbonyl attached to central pyridine
and the C-terminal pyridinium proton seems likely (Fig. 7). The
NOE correlation between the third N-methyl group from the
C-terminal and the C-5 proton of the central pyridine unit (3.0%)
implies syn conformation of the central pyridine unit, supporting
the long-range hydrogen bonding. This long-range intramolecular
hydrogen bond would contribute to stabilization of the local fold-
ing. In contrast, the stabilization by intramolecular hydrogen bond-
ing would be weak for 4H because of competition with the more
stable six-membered hydrogen bonding between the N-terminal
pyridinium proton and the corresponding carbonyl (Fig. 7).4 This
O
2.1% 10
CH3
16
CH3
15
N
17
3.7%
4.1%9
N
4
3
14
N
8
N
N
N
6.6%
CH3
11
N
5.1%
5
6
2
1
N
12
N
13
CH3
2.3%
7
O
O
5
Figure 4. Observed NOE correlations of oligoamides 3–5.
In the C-terminal pyridine unit of 3H and 5H, the peak of the
proton at the 3-position was relatively unchanged, compared to
the other protons of the corresponding pyridine ring. This can be
attributed to the conformational alteration from anti to syn, which
is the same as in the case of 1.11 On the other hand, the values of
the chemical shifts of all of N-terminal pyridine protons increased
O
CH3
6.2%
H
N
H3C
N
N
N
2.0%
N
O
1.5%
3H
H
O
O
CH3
CH3
N
N
N
N
N
+0.7
+0.9
+0.3
+0.8
CH3
3.0%
+0.1
+0.3
+0.8
O
N
+0.7
H
+0.7
Center
3
+0.8
C-terminal
5.1%
+1.0
O
N-terminal
16.0%
N
CH3
CH3
N
N
N
N
N
12.8%
O
CH3
O
CH3
CH3
O
CH3
O
N
N
N
N
2.1%
N
O
N
N
N
3.8%
CH3
N
N
N
+0.6
+0.8
+0.6
C-terminal
+0.3
+0.8
H
-0.4
+0.5
-0.1
+0.4
O
+0.5
-0.2 +0.5
+0.7
+1.0
+0.4
+0.1
Center
5
+0.5
5H
0.6%
C2
N2
N-terminal
Figure 5. Observed NOE correlations of protonated oligoamides 3H and 5H.
Figure 6. Change of 1H NMR chemical shift induced by the addition of acid.

R. Yamasaki et al. / Tetrahedron Letters 57 (2016) 56–59
59
In conclusion, we synthesized oligoamides composed of pyri-
dine 2-carboxamide by stepwise elongation of up to five pyridine
units. The oligomer having five pyridine units exhibited a drastic
conformational transformation from the folded form to the par-
tially unfolded form, which is considered to be exhibit long-range
hydrogen bonding that stabilizes the local folding. Four successive
amide linkages were required for the emergence of this hydrogen
bonding. The observed long-range hydrogen bonding is similar to
that in the Cs symmetric oligoamide 2,4 but the conformational
behavior is different, presumably due to the loss of symmetry.
Our findings may be applicable for the design of pH-responsive
conformation-switching foldamers.
N
H
O
N
H
O
CH3
CH3
N
N
N
N
N
CH3
O
4H
CH3
O
N
H
O
N
CH3
CH3
N
N
N
N
N
N
Acknowledgments
O
N
H
CH3
This work was supported by JSPS KAKENHI Grant No. 26460154
and by a grant from Hoansha Foundation.
O
5H
Figure 7. Plausible intramolecular hydrogen bonding scheme to promote tight
folding of aromatic amides 4H and 5H.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.tetlet.2015.11.
058.
References and notes
1. Foldamers: Structure, Properties and Applications; Hecht, S., Huc, I., Eds.; Wiley-
VCH: Weinheim, 2007. Goering, B. K. Ph.D. Dissertation, Cornell University,
1995.
3
3H
2. For reviews, see: (a) Juwarker, H.; Jeong, K. S. Chem. Soc. Rev. 2010, 39, 3664–
3667; (b) Zhang, D. W.; Zhao, X.; Li, Z. T. Acc. Chem. Res. 2014, 47, 1961–1970;
(c) Knipe, P. C.; Thompson, S.; Hamilton, A. D. Chem. Sci. 2015, 6, 1630–1639.
95.
3. Goto, Y.; Calciano, L. J.; Fink, A. L. Proc. Nat. Acad. Sci. U.S.A. 1990, 87, 573–577.
4. Okamoto, I.; Nabeta, M.; Hayakawa, Y.; Morita, N.; Takeya, T.; Masu, H.;
Azumaya, I.; Tamura, O. J. Am. Chem. Soc. 2007, 129, 1892–1893.
5. Dolain, C.; Maurizot, V.; Huc, I. Angew. Chem., Int. Ed. 2003, 42, 2738–2740.
6. Zhang, D. W.; Zhao, X.; Hou, J. L.; Li, Z. T. Chem. Rev. 2012, 112, 5271–5316.
7. Kudo, M.; Tanatani, A. New J. Chem. 2015, 39, 3190–3196.
4
4H
8. (a) Sebaoun, L.; Maurizot, V.; Granier, T.; Kauffmann, B.; Huc, I. J. Am. Chem. Soc.
2014, 136, 2168–2174; (b) Sebaoun, L.; Kauffmann, B.; Delclos, T.; Maurizot, V.;
Huc, I. Org. Lett. 2014, 16, 2326–2329; (c) Singleton, M. L.; Pirotte, G.;
Kauffmann, B.; Ferrand, Y.; Huc, I. Angew. Chem., Int. Ed. 2014, 53, 13140–
13144; (d) Lautrette, G.; Aube, C.; Ferrand, Y.; Pipelier, M.; Blot, V.; Thobie, C.;
Kaufmann, B.; Dibreuil, D.; Huc, I. Chem. Eur. J. 2014, 20, 1547–1553; (e) Kudo,
M.; Maurizot, V.; Kauffmann, B.; Tanatani, A.; Huc, I. J. Am. Chem. Soc. 2013, 135,
9628–9631.
5
5H
9. Kortelainen, M.; Suhonen, A.; Hamza, A.; Pápai, I.; Nauha, E.; Yliniemelä-Sipari,
S.; Nissinen, M.; Pihko, P. M. Chem. Eur. J. 2015, 21, 9493–9504.
10. Sun, C.; Liu, Y.; Liu, J.; Lu, Y.-J.; Yu, L.; Zhang, K.; Zeng, H. J. Org. Chem. 2014, 79,
2963–2973.
Figure 8. Optimized structures of 3–5 and 3H–5H obtained by DFT calculation.
11. (a) Okamoto, I.; Terashima, M.; Masu, H.; Ono, K.; Morita, N.; Katagiri, K.;
Azumaya, I.; Tamura, O. Tetrahedron 2011, 67, 8536–8543; (b) Okamoto, I.;
Nabeta, M.; Minami, T.; Nakashima, A.; Morita, N.; Takeya, T.; Masu, H.;
Azumaya, I.; Tamura, O. Tetrahedron Lett. 2007, 48, 573–577.
12. Itai, A.; Toriumi, Y.; Tomioka, N.; Kagechika, H.; Azumaya, I.; Shudo, K.
Tetrahedron Lett. 1989, 30, 6177–6180.
13. Kan, T.; Fukuyama, T. Chem. Commun. 2004, 353–359.
14. Chabaud, L.; Clayden, J.; Helliwell, M.; Page, A.; Raftery, J.; Vallverdú, L.
Tetrahedron 2010, 66, 6936–6957.
15. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.;
Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.;
Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.;
Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.;
Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao,
O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken,
V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A.
J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G.
A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.;
Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.;
Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.;
Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.;
Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe,
M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A.
Gaussian 03, Revision E.01; Gaussian: Wallingford, 2004.
would lead to instability of local folding and might account for the
peak broadening in the 1H NMR spectrum of 4H (Fig. 3).
Unfortunately, attempts to obtain suitable crystals for X-ray
crystallography of those oligomers have not been successful to
date. Therefore, to obtain insights into the structures of the oligomers
(3, 3H, 4, 4H, 5, and 5H), DFT calculations at the B3LYP/6-31G⁄ level
were performed.15 Optimized structures of those oligomers before
and after addition of acid are illustrated in Figure 8. The layered
(folded) structures of protonation-free oligomers were supported
by DFT calculations. The partially unfolded structures of the
protonated oligomers, supported by the 1H NMR spectra, are also
presented. Conformations of amide bonds in those oligomers are
cis–trans (3H), cis–cis–trans (4H), and cis–cis–cis–trans (5H) from
the C-terminal to the N-terminal. The observed long-range
intramolecular interaction, indicated by 1H NMR, was also
supported by the DFT calculation, and the distance between the
C-terminal pyridinium proton and the corresponding carbonyl
was 1.95 Å for 4H and 1.76 Å for 5H.