Solid state and solution conformation of 2-pyridinecarboxylic acid hydrazides: A new structural motif for foldamers

Article abstract of DOI:10.1016/S0040-4039(02)02881-2

X-Ray crystallography and NMR show a strong preference for trans conformers of N′-phenyl or N′-(2-pyridyl) 2-pyridinecarboxylic acid hydrazides, stabilized by an NH-N_pyr. intramolecular hydrogen bond both in the solid state and in solution. This allows us to extrapolate that oligomers of this unit should adopt extended linear conformations.

Full text of DOI:10.1016/S0040-4039(02)02881-2

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TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 44 (2003) 1421–1424
Solid state and solution conformation of 2-pyridinecarboxylic
acid hydrazides: a new structural motif for foldamers
Joachim Garric,a Jean-Michel Le´ger,b Axelle Grelard,a Masakazu Ohkitac and Ivan Huca,*
aInstitut Europe´en de Chimie et Biologie, 16 av. Pey Berland, 33607 Pessac Cedex, France
bLaboratoire de Pharmacochimie, Universite´ Victor Segalen Bordeaux II, 146 rue Le´o Saignat, 33076 Bordeaux, France
cDepartment of Applied Chemistry, Nagoya Institute of Technology, Nagoya 466-8555, Japan
Received 12 September 2002; revised 31 October 2002; accepted 19 December 2002
Abstract—X-Ray crystallography and NMR show a strong preference for trans conformers of N%-phenyl or N%-(2-pyridyl)
2-pyridinecarboxylic acid hydrazides, stabilized by an NHꢀNpyr. intramolecular hydrogen bond both in the solid state and in
solution. This allows us to extrapolate that oligomers of this unit should adopt extended linear conformations. © 2003 Elsevier
Science Ltd. All rights reserved.
Peptidomimetics are unnatural oligomers that adopt
stable conformations in solution, mimicking the struc-
tures and potentially the functions of peptides. Series of
aliphatic b-, g-, and d-homologues of a-peptides have
been reported, comprising various linkages such as
amides, sulfonamides, sulfoximines, N-oxo-amides,
ureas, or hydrazides.1,2 Several families of aromatic
oligoamides have also been shown to adopt stable
linear, bent, and helical conformations stabilized by
hydrogen bonds between amide groups and donors or
acceptors in the aromatic rings.1,3–5 In aromatic
oligoamides, unlike in most aliphatic peptidomimetics,
hydrogen bonds occur in a non-cooperative fashion
between consecutive units, which makes the folded struc-
tures particularly easy to predict. The conformational
behavior of a dimer or trimer can often be extrapolated
to longer strands. Aromatic amides can also be incor-
porated in aliphatic peptidomimetic sequences to tem-
plate their structures.6,7 These oligomers have been
based on various aromatic building blocks (e.g. pyridi-
nes, pyridine oxydes, pyrazines, anthranilic acids, 1,3-
dimethoxybenzenes…) but very few cases have made
use of a linkage other than the amide group.4,7
bonding to aromatic protons (Fig. 1(a)).5 Zimmerman
et al. have shown that 2-pyridyl-ureas exist as two
equilibrating cis and trans forms of the urea involving
We have previously investigated the structures of
oligoamides derived from 2-pyridinecarboxylic acids
and 2-aminopyridines, and shown that they adopt both
single and double helical conformations in the solid
state and in solution based on NHꢀNpyr. hydrogen-
bonding to pyridine nitrogens and COꢀH hydrogen-
Figure 1. Conformations of 2-pyridinecarboxamides (a) and
2-pyridyl-ureas (b), and possible conformations of 2-pyridine-
carboxylic acid hydrazides (c). Structures of 1–4 (d).
* Corresponding author.
0040-4039/03/$ - see front matter © 2003 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(02)02881-2

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J. Garric et al. / Tetrahedron Letters 44 (2003) 1421–1424
either a CO–H or an NH–Npyr. hydrogen bond (Fig.
1(b)).4 Here, we present a preliminary study of the
conformations of 2-pyridinecarboxylic acid hydrazides
in the solid state and in solution, in view of their
incorporation into oligomeric strands.
al.,10 which differs substantially from the expected
90°.7,8 The N% nitrogen of the hydrazide is distorted
pyramidal (defining three angles at 114.1, 110.3, and
115.8°). In the crystal lattice, the molecules are
arranged in linear tapes held by intermolecular hydro-
gen bonds involving both NH and N%H proton donors
12
,
,
Two intramolecular hydrogen bonds may be foreseen
between a pyridine nitrogen and an adjacent hydrazide
function, involving either the NH or the N%H proton.
Because of a more favorable orientation, the N%HꢀNpyr.
hydrogen bond in the cis conformer of the hydrazide is
expected to be stronger than the NHꢀNpyr. hydrogen
bond of the more stable trans conformer (Fig. 1(c)).
However, the hydrazide function is non-planar and
NꢀH and N%ꢀH bonds should define a dihedral angle
close to 90°,7,8 which might affect hydrogen-bonding
with the N%H. The conformations of benzoic acid N%-
phenylhydrazides bearing methoxy substituents have
been described.7 We searched for related compounds in
the CCDB but found no structures of 2-pyridinecar-
boxylic acid hydrazides where the N% nitrogen is neither
condensed in a hydrazone, nor acylated. Moreover,
although aliphatic hydrazinopeptides have been pre-
pared,9 experimental data on their structure are
scarce.8,10
(N%HꢀNpyr.: 3.32 A, 141.9°; NHꢀO: 2.62 A, 138.8).
Compound 3 was prepared with the idea that its addi-
tional pyridine nitrogen could be involved in
intramolecular hydrogen bonds with the NH or N%H
protons in the cis or the trans form and alter the
balance between them. Crystals were again grown from
CHCl3/n-hexane and yielded the structure in Figure 3,
which also shows a trans conformer of the hydrazide.13
The crystal parameters are very similar to those of 1
(same space group and unit cell dimensions)11,13 and the
two structures are practically superimposable. Linear
arrays of molecules are also found in the lattice involv-
ing intermolecular hydrogen bonds between the same
donors and acceptors as in the structure of 1. However,
the relative orientations of the molecules are different
which leads to different hydrogen bond distances and
,
,
angles (N%HꢀNpyr.: 3.07 A, 169.6°; NHꢀO: 2.76 A,
149.6°).12
Thus, when we started this work, it was not obvious
whether a more favorable hydrogen bond would bring
upon enough stabilization to favor the a priori less
stable cis isomer of the hydrazide, as is the case for the
urea.
Thus, 1 and 3 follow different packing modes in the
crystal. But the additional pyridine nitrogen in 3 does
not participate in any intra- or intermolecular hydrogen
bond, and does not even alter the torsion angles within
the molecule, suggesting a strong preference for that
particular conformer.
Compounds 1–4 (Fig. 1(d)) were prepared in one step
from 2- or 4-pyridinecarboxylic acid chlorides and
phenyl hydrazine or 2-hydrazinopyridine, in CH2Cl2 in
the presence of Et3N. Phenyl-hydrazide 1 gave crystals
suitable for X-ray analysis from CHCl3/n-hexane which
The conformations of 1 and 3 were also studied by
NMR in CDCl3 solutions. Both 1 and 3 feature a
strongly deshielded hydrazide proton (at 9.54 and 9.88
pmm, respectively) and a less deshielded hydrazide
proton (at 6.25 and 6.87 ppm, respectively). Their
assignment was made according to long range C/H
correlations in HMBC experiments. The more
deshielded proton correlates with the carbonyl carbon
revealed a trans conformation of the hydrazide (Fig.
12
2(a)).11 The NHꢀNpyr (2.74 A, 97.6°) intramolecular
,
hydrogen bond is far from being linear and similar to
those observed in amides.5 The NH–N%H torsion angle
is 131.5°, a value close to that reported by Aubry et
Figure 2. (a) X-Ray crystal structure of 1 showing the trans
form of the hydrazide and the NHꢀN intramolecular hydro-
gen bond; (b) linear array of molecules in the crystal involving
N%HꢀNpyr. and NHꢀO intermolecular hydrogen bonds; (c) top
view of the linear array.
Figure 3. (a) X-Ray crystal structure of 3 showing the trans
form of the hydrazide and the NHꢀNpyr. intramolecular
hydrogen bond; (b) linear array of molecules in the crystal
involving N%H–Npyr. and NHꢀO intermolecular hydrogen
bonds; (c) top view of the linear array.

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J. Garric et al. / Tetrahedron Letters 44 (2003) 1421–1424
1423
carboxylic acid was built (Fig. 6). Its structure is that of
an extended linear strand, the successive NꢀN linkages
being parallel and almost coaxial. The relative positions
of the pyridine rings is determined by the NHꢀN%H
torsion angles. In the structure shown in Fig. 6, these
and was assigned to the NH
correlates with the vicinal carbon of the phenyl or
2-pyridyl substituent and was assigned to the N%H (Fig.
6 , the less deshielded proton
6
4(a)). The large chemical shift difference between the
two protons (Dl=3.3 and 3.0 pmm for 1 and 3,
respectively) cannot be explained on the sole basis of
electron withdrawing effects of acyl versus aryl sub-
stituents and suggests that the NH proton is involved in
an intramolecular hydrogen bond with the pyridine
nitrogen as is found in the solid. However, this could
not be demonstrated by studying 1 and 3 directly. For
example, NOE-diff experiments on 1 show correlations
of NH6 and of N%H6 with protons of the phenyl ring (Fig.
5), but this is expected both in the trans and the cis
form of the hydrazide (Fig. 4(b)). That the NH protons
of 1 and 3 are indeed involved in an intramolecular
hydrogen bond is supported by the low dependence of
their chemical shift (Dl <0.05 ppm) upon addition of a
hydrogen bonding solvent (20% D6-DMSO) to the
CDCl3 solution, and upon increasing concentration or
decreasing temperature. On the other hand, the NH%
protons show a high chemical shift variation under
these conditions (Dl >0.72 ppm). Moreover, when the
nitrogen of the pyridinecarbonyl group is moved from
position 2 (in 1 and 3) to position 4 (in 2 and 4), the
chemical shift of N%H6 is almost unaffected (Dl <0.1
ppm), whilst the chemical shift of the NH is strongly
shifted upfield (Dl >1.38 ppm). The 4-pyridinecarbonyl
group has an electron withdrawing strength similar to
that of the 2-pyridinecarbonyl moiety, but it cannot
form an intramolecular hydrogen bond involving the
NH or the N%H proton.
Finally, NOE-diff experiments revealed that in 3, the
CH proton in position 3 of the 2-pyridyl group corre-
1
lates with the NH6 but not with N%H6 . This is consistent
Figure 5. Part of the 400 MHz H NMR spectra of 1 and 3
with the conformation of 3 observed in the crystal, and
in CDCl3. Top: spectrum of 1 and NOE-diff experiment at
25°C showing the signals of NH, N%H and H%3 after saturation
of the signal of H%2. Bottom: spectrum of 3 and NOE-diff
experiment at −45°C showing the signals of NH, H%6, and H4%
after saturation of the signal of H%3, and concomitantly of that
of H5%. For compound 3, NOEs are overcast by rapid
exchange between NH and N%H at higher temperatures.
shows that it also prevails in solution (Fig. 5).
In summary, both 1 and 3 show a strong preference for
a trans conformation in the solid and in solution and
no contribution of the cis conformer could be detected.
Assuming the preferred conformation of 3, a molecular
model of an oligohydrazide of 6-hydrazino-2-pyridine-
Figure 6. Structure, top view and side view of a molecular
model of an oligohydrazide of 6-hydrazino-2-pyridinecar-
boxylic acid, built by interconnecting three units of 3 as found
in the solid state. The NHꢀN%H torsion angles were manually
set at 131° (the parameters of most force fields are defined to
reach an energy minimum when this angle is 90°).
Figure 4. Relevant C/H correlations (a), and NOE correla-
tions (b), observed by NMR in 1 and 3.

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J. Garric et al. / Tetrahedron Letters 44 (2003) 1421–1424
angles are set at 131° and are arbitrarily chosen with
the same sign, which results in an helical arrangement
of the pyridyl groups. The synthesis and incorporation
of these pyridine hydrazide units in oligomers contain-
ing pyridine–amide monomers will be explored in the
sequel.
Khoury, R.; Lehn, J.-M. Chem. Eur. J. 2001, 7, 2798; (c)
Berl, V.; Huc, I.; Khoury, R.; Lehn, J.-M. Chem. Eur. J.
2001, 7, 2810; (d) Huc, I.; Maurizot, V.; Gornitzka, H.;
Le´ger, J.-M. Chem. Commun. 2002, 578.
6. (a) Nowick, J. S.; Lam, K. S.; Khasanova, T. V.; Kem-
nitzer, W. E.; Maitra, S.; Mee, H. T.; Lui, R. J. Am.
Chem. Soc. 2002, 124, 4972 and references cited therein;
(b) Zeng, H.; Yang, X.; Flowers, R. A.; Gong, B. J. Am.
Chem. Soc. 2002, 124, 2903.
Acknowledgements
7. Nowick, J. S.; Pairish, M.; Quen Lee, I.; Holmes, D. L.;
Ziller, J. W. J. Am. Chem. Soc. 1997, 119, 5413.
8. For computational studies, see: Gu¨nter, R.; Hofman,
H.-J. J. Am. Chem. Soc. 2001, 123, 247 and references
cited therein.
This work was supported by the CNRS, the University
of Bordeaux I, and by the region Aquitaine.
9. Guy, L.; Vidal, J.; Collet, A.; Amour, A.; Reboud-
Ravaux, M. J. Med. Chem. 1998, 41, 4833.
10. Aubry, A.; Bayeul, D.; Mangeot, J.-P.; Vidal, J.; Ste´rin,
S.; Collet, A.; Lecoq, A.; Marraud, M. Biopolymers 1991,
31, 793.
References
1. For reviews, see: (a) Gellman, S. H. Acc. Chem. Res.
1998, 31, 173; (b) Hill, D. J.; Mio, M. J.; Hughes, T. S.;
Moore, J. S. Chem. Rev. 2001, 101, 3893.
11. Crystal data for 1: C12H11N3O, M=213.24, monoclinic,
,
a=8.090(2), b=15.099(3), c=8.985(5) A, i=100.14(3)°,
2. For recent examples: (a) Woll, M. G.; Lai, J. R.; Guzei,
I. A.; Taylor, S. J. C.; Smith, M. E. B.; Gellman, S. H. J.
Am. Chem. Soc. 2001, 123, 11077; (b) Semetey, V.;
Rognan, D.; Hemmerlin, C.; Graff, R.; Briand, J.-P.;
Marraud, M.; Guichard, G. Angew. Chem., Int. Ed. 2002,
41, 1893; (c) Etezady-Esfarjani, T.; Hilty, C.; Wu¨thrich,
K.; Rueping, M.; Schreiber, J.; Seebach, D. Helv. Chim.
Acta 2002, 85, 1197.
3
,
V=1080.4(7) A , T=296(2) K, space group P21/c, Z=4,
m(Cu-Ka)=0.707 mm−1, 1837 reflections measured, 1837
unique. The final R indices were R1 (I>2|(I))=0.0437,
wR2 (all data)=0.1192. Crystallographic data (excluding
structure factors) have been deposited with the Cam-
bridge Crystallographic Database as supplementary pub-
lication no. CCDC 193207.
12. The distance is between the two heavy atoms, and the
angle is the NꢀHꢀ(N/O) angle.
3. Selected example: (a) Hamuro, Y.; Geib, S. J.; Hamilton,
A. D. J. Am. Chem. Soc. 1997, 119, 10587; (b) Delnoye,
D. A. P.; Sijbesma, R. P.; Vekemans, J. A. J. M.; Meijer,
E. W. J. Am. Chem. Soc. 1996, 118, 8717; (c) Gong, B.
Chem. Eur. J. 2001, 7, 4337 and references cited therein.
4. (a) Corbin, P. S.; Zimmerman, S. C. J. Am. Chem. Soc.
2000, 122, 3779; (b) Corbin, P. S.; Zimmerman, S. C.;
Thiessen, P. A.; Hawryluk, N. A.; Murray, T. J. J. Am.
Chem. Soc. 2002, 124, 10475.
13. Crystal data for 3: C11H10N4O, M=213.23, monoclinic,
,
a=8.087(1), b=15.079(1), c=8.822(1) A, i=99.20(1),
3
,
V=1061.95(19) A , T=296(2) K, space group P21/c,
Z=4, m(Cu-Ka)=0.750 mm−1, 1780 reflections measured,
1780 unique. The final R indices were R1 (I>2|(I))=
0.0467, wR2 (all data)=0.1323. Crystallographic data
(excluding structure factors) have been deposited with the
Cambridge Crystallographic Database as supplementary
publication no. CCDC 193206.
5. (a) Berl, V.; Huc, I.; Khoury, R.; Krische, M. J.; Lehn,
J.-M. Nature 2000, 407, 720; (b) Berl, V.; Huc, I.;