Can a single pyridinedicarboxylic acid be ample enough to nucleate supramolecular double helices in enantiomeric pseudopeptides?

Article abstract of DOI:10.1039/c3ce26912d

Two enantiomeric pseudopeptides I & II, comprising a single pyridinedicarboxylic acid and a flexible dipeptidyl fragment H-Xaa-mABA-OMe (Xaa: l-Ala, pseudopeptide I; d-Ala, pseudopeptide II, mABA: meta aminobenzoic acid), have been synthesized using Boc chemistry. X-ray crystallographic analysis reveals that in the solid state, both the enantiomers form a dimeric unit stabilized by intermolecular hydrogen bonding interactions. Interestingly, these dimeric subunits self-assemble to form a supramolecular double helical architecture using various noncovalent interactions. To date, significant examples are documented in the literature where DNA analogues/derivatives or several rigid templates have been employed as synthons for double helical self assembly. However, to the best of our knowledge, this novel example represents one of the very few reports of a supramolecular double helix design resulting from the self assembly of a flexible dimeric peptidyl unit, solely nucleated by the conformational features, of the peptides. Concentration and temperature dependant NMR experiments were performed for pseudopeptide I (one of the enantiomers) to decipher the existence of the dimeric unit in solution. Pseudopeptide II (one of the enantiomers) was subjected to iodine and gas absorption studies, which demonstrates its candidature in the design of nanoporous materials. The Royal Society of Chemistry 2013.

Full text of DOI:10.1039/c3ce26912d

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PAPER
Can a single pyridinedicarboxylic acid be ample enough
to nucleate supramolecular double helices in
enantiomeric pseudopeptides?3{
Cite this: CrystEngComm, 2013, 15,
2466
Anita Dutt Konar*
Two enantiomeric pseudopeptides I & II, comprising a single pyridinedicarboxylic acid and a flexible
dipeptidyl fragment H-Xaa-mABA-OMe (Xaa: L-Ala, pseudopeptide I; D-Ala, pseudopeptide II, mABA: meta
aminobenzoic acid), have been synthesized using Boc chemistry. X-ray crystallographic analysis reveals that
in the solid state, both the enantiomers form a dimeric unit stabilized by intermolecular hydrogen bonding
interactions. Interestingly, these dimeric subunits self-assemble to form a supramolecular double helical
architecture using various noncovalent interactions. To date, significant examples are documented in the
literature where DNA analogues/derivatives or several rigid templates have been employed as synthons
for double helical self assembly. However, to the best of our knowledge, this novel example represents one
of the very few reports of a supramolecular double helix design resulting from the self assembly of a
flexible dimeric peptidyl unit, solely nucleated by the conformational features, of the peptides.
Concentration and temperature dependant NMR experiments were performed for pseudopeptide I
(one of the enantiomers) to decipher the existence of the dimeric unit in solution. Pseudopeptide II (one of
the enantiomers) was subjected to iodine and gas absorption studies, which demonstrates its candidature
in the design of nanoporous materials.
Received 24th November 2012,
Accepted 12th January 2013
DOI: 10.1039/c3ce26912d
www.rsc.org/crystengcomm
approach of nucleating double helical assembly.7 Gabriel and
Iverson are known for their substantial input into double
Introduction
The mimicry of helical entities into double or triple strands
has emerged as a focal point of bioorganic and medicinal
chemistry.1 Since the inspirational discovery of the DNA
double helix by Watson and Crick in natural systems, chemists
have been motivated to design hybridization patterns that
possess the ability to intertwine into multiple helices.2 Over
the past few years, considerable progress has been devised in
stabilizing dimeric ensembles, mainly from DNA analogues or
their derivatives.3 However, the design of non-DNA moieties as
synthons for supramolecular double helix formations is much
less evolved and is of current research interest to the scientific
community.4 In this context, Yashima and his co-workers are
extensively recognized for their contribution to double helix
stabilization by intermolecular salt-bridge formations5 and p–
p interactions.6 The twisting of supramolecular polymeric
ladders reported by Sada and his group represents another
helical stabilization by alternating the stacking of electron rich
and electron poor aromatic systems.8 The double helical
stabilization by a self-complementary array of hydrogen bond
donors and acceptors by Wisner and his group is noteworthy.9
Apart from these, the design of artificial oligoamides
constitutes another class of synthons in supramolecular
double helix stabilization. In this context, the pioneering
contribution of Lehn and his co-workers in studying the
dynamic exchange of aromatic oligoamides into single and
double stranded helicates needs special mention.10 A careful
search shows that Huc and his group have made novel
contributions in the design of supramolecular double helices
using several aromatic heterocycles or their derivatives.11
As part of the investigation into determining the motifs for
supramolecular double helix stabilization from suitable
building blocks, this project aims to utilize a single pyridinyl
unit i.e. 2,6 pyridinedicarboxylic acid coupled with H-Xaa-
mABA-OMe (where Xaa is L-Ala, Peptide I; D-Ala, Peptide II)
using Boc chemistry (Fig. 1). The design of the double helical
complex was approached based on the hydrogen bonding
interaction between a planar six-membered heterocycle con-
taining nitrogen based donor/acceptor groups that are
connected sequentially in a 1,3 manner (pyridine). As a further
design element, a simple dipeptidyl sequence, comprising
Dept of Chemical Sciences, Indian Institute of Science Education and Research,
Bhopal, ITI Gas Rahat Building, Govindpura, Bhopal 462023, India.
E-mail: anita@iiserb.ac.in; Fax: +91 7554092392; Tel: +91 7554056278
Dedicated to Professor Animesh Pramanik, University of Calcutta, for his
3
significant contribution in the field of peptidomimetics.
{ Electronic supplementary information (ESI) available: NMR, mass and CIF
files of peptides I and II respectively. CCDC 894165 and 894166. For ESI and
crystallographic data in CIF or other electronic format see DOI: 10.1039/
c3ce26912d
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Synthesis of the peptides
Pseudopeptides I & II containing two terminal methoxy
carbonyls were synthesized using conventional solution phase
methodology, with racemization free techniques, followed by a
fragment condensation strategy (Scheme 1).13 The t-butylox-
ycarbonyl and methyl ester groups were used for the amino
and carboxyl protections respectively and dicyclohexylcarbo-
diimide (DCC) and 1-hydroxy benzotriazole (HOBT) were used
as coupling agents for the synthesis of the dipeptides. Methyl
ester hydrochlorides of mABA were prepared by the thionyl
chloride–methanol procedure.12 All the intermediates
obtained were checked for purity by thin layer chromatography
(TLC) on silica gel and used without further purification. All
the final pseudopeptides were purified by column chromato-
graphy using silica gel (100–200 mesh) as the stationary phase
and ethyl acetate and petroleum ether mixture as the eluent.
The reported pseudopeptides I & II were fully characterised by
X-ray crystallography, NMR and mass spectrometry.
Fig. 1 Schematic representation of pseudopeptides I & II.
naturally occurring amino acids and conformationally biased
meta amino benzoic acid (*: although pseudopeptides I and II
are enantiomers, their different chemical formula in Table 1
reflects the presence of disordered solvent molecules which we
are unable to resolve) having b-sheet forming propensity, was
chosen.12 The idea was to decipher whether the dipeptidyl
fragments present in enantiomeric pseudopeptides I and II are
ample enough to nucleate double helical assembly when
coupled to a single pyridine 2,6 dicarboxylic acid unit.
Concentration and temperature dependant NMR experiments
were performed for pseudopeptide I (one of the enantiomers)
to decipher the existence of the dimeric unit in solution.
Pseudopeptides II (one of the enantiomers) was subjected
to iodine and gas adsorption studies to explore its candidature
in the design of nanoporous materials.
Boc-L-Ala-mABA-OMe (1). Ref. 12b.
Boc-D-Ala-mABA-OMe (2). The methyl m-aminobenzoate
(1.52 g, 10 mmol), obtained from its hydrochloride (3.76, 20
mmol) was added to an ice-cool solution of Boc-D-Ala-OH (1.9
g, 10 mmol) in 10 ml of DCM. Then DCC (2 g, 10 mmol; 1,3-
dicyclohexylcarbodiimide) was added to the cooled mixture,
which was stirred for a day at room temperature. The residue
was then added into ethyl acetate (50 ml) and the DCU
(N,N-dicyclohexylurea) was filtered off. The organic layer was
washed with 2 M HCl (3 6 50 ml), 1 M sodium carbonate (3 6
50 ml) and brine (2 6 50 ml), dried over anhydrous sodium
sulfate and evaporated in vacuo to yield a solid material. The
crude peptide was used without further purification.
Yield: 2.98 g (9.22 mmol, 92%). Mp: 145u; 1H NMR 400 MHz
(CDCl3; d ppm): 1.24–1.25 (3H, d), 1.45 (9H, s), 3.85 (3H, s),
4.43–4.47 (1H, m), 5.42–5.60 (1H, m), 7.62–8.10 (4-Ar–Hs),
9.14–9.16 (1H, m); 13C NMR 100 MHz (CDCl3; d ppm): 17.8,
28.6, 50.2, 52, 80.4, 120.7, 124.1, 125.3, 128.9, 130.7, 138.2, 156,
167, 172.1.
Peptide I. Trifluoroacetic acid (5 ml) was added to Boc-L-Ala-
mABA-OMe (1) (1.5 g, 4.65 mmol) at 0 uC and stirred at room
temperature. The removal of the Boc group was monitored by
TLC. After 6 hours, the trifluoroacetic acid was removed under
reduced pressure to afford the crude trifluoroacetate salt. The
residue was taken up in water and washed with diethyl ether.
The pH of the aqueous solution was adjusted to pH 8 with
Experimental
Abbreviations
Aib, a-aminoisobutyric acid; TFA, trifluoroacetic acid; mABA,
m-amino benzoic acid; Boc, tertiary butyloxy carbonyl; OMe,
methoxy carbonyl; DCC, dicyclohexylcarbodiimide; HOBt,
1-hydroxy benzotriazole.
Table 1 Crystallographic refinement details for pseudopeptides I and II
Pseudopeptide I
Pseudopeptide II
Chemical formula*
Formula weight (g)
Crystal system
Space group
a (Å)
b (Å)
c (Å)
2(C29 H29N5 O8),C2O
1191.16
Tetragonal
P41212
13.627(4)
13.627(4)
36.416(12)
90
90
90
6763(4)
4
2(C29 H29N5 O8),C4O
1215.18
Tetragonal
P43212
13.5368(6)
13.5368(6)
36.4665(15)
90
90
90
6682.3(5)
4
a(u)
b (u)
c (u)
V (Å3)
Z
Collected reflections
Unique reflections
c (Mo–Ka)(Å)
T (K)
7129
3099
0.71073
296(2)
0.0907
0.2331
7415
5753
0.71073
296(2)
0.0717
R1
wR2[I . 2s(I)]
0.2208
Scheme 1 Synthetic strategy of pseudopeptide I and II.
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sodium bicarbonate and extracted with ethyl acetate. The
extracts were pooled, washed with saturated brine, dried over
sodium sulphate and concentrated to a highly viscous liquid
that gave a positive ninhydrin test. DMF and DIPEA (3.2 ml,
13.98 mmol) was added to a well stirred and ice-cooled
solution of the obtained free base. To this mixture, a freshly
prepared solution of pyridine 2,6 dicarbonyldichloride (0.44 g,
2.33 mmol) in 10 ml of DMF was added over a period of
0.5 hours and the mixture continued to stir at room
temperature for 2 days. The solvents were evaporated in vacuo,
the residue was dissolved in ethyl acetate and washed
sequentially with 1 M HCl (3 6 30 ml), a 1 M Na2CO3 solution
(3 6 30 ml) and again with water. The solvent was then dried
over anhydrous Na2SO4 and evaporated in vacuo, giving a light
yellow solid. Purification was done using silica gel as the
stationary phase and an ethyl acetate–petroleum ether mixture
as the eluent. Single crystals were grown from an acetone–
petroleum ether mixture (90 : 10) by slow evaporation and
were stable at room temperature.
Yield: 0.52 g (40.0%, 0.93 mmol). Mp = 150–152 uC; IR (KBr):
1273, 1400, 1531, 1672, 1723, 3436 cm21 1H NMR 400 MHz
;
(CDCl3, d ppm): 1.62–1.63 (6H, m, Ala(1) CbHs), 3.93 (6H, s,
methoxy H’s), 4.58–4.62 (2H, m, Ala(1) CaHs), 7.42–7.43 (1H,
m, Hc (m-ABA(2)), 7.82 (2H, d, J = 4 Hz, Hb (m-ABA(2)), 7.91
(2H, d, J = 4 Hz, Hd (m-ABA(2)), 8.12–8.09 (1H, m, py Ha), 8.14
(2H, s, Ha (m-ABA(2)), 8.27 (2H, s, py Hb), 8.40 (2H, d, J = 8 Hz,
Ala(1) NH), 8.75 (2H, d, J = 8 Hz, mABA(2)NH); 13C NMR 100
MHz (CDCl3, d ppm): 17.7, 50.2, 52.2, 120.9, 124.4, 125.4,
125.5, 129.1, 130.7, 138.2, 139.2, 148.4, 164, 166.7, 170.9,; HR–
MS C29H29N5O8 (M + Na+) = 598.197, Mcalcd C29H29N5O8 (M +
Na)+ = 598, C58H58N10O16 (M + Na+) = 1173.3756, Mcalcd
C29H29N5O8 (M + Na)+ = 1173.
X-ray crystallography
Data collection of the compounds was performed at 296 K on a
Bruker Apex II diffractometer with Mo–Ka (l = 0.71073 Å)
radiation. Data reduction and cell refinement were performed
with the SAINT program and the absorption correction
program SADABS14 was employed to correct the data for
absorption effects. The crystal structures were solved by direct
methods and refined with full-matrix least-squares (SHELXTL-
97)15 with atomic coordinates and anisotropic thermal
parameters for non-hydrogen atoms. The atoms of the
disordered solvent molecules were refined isotropically. As
the quality of the crystals was poor, the data obtained was also
poor, which finally resulted in large ADP values for some non-
solvent hydrogen atoms in 1. Higher experimental tempera-
tures (296 K) could be another reason for this. The crystal-
lographic data are summarized in Table 1. The SHELXTL,
Mercury and Diamond software were used to visualize the
structures.
Yield: 0.65 g (50.0%, 1.16 mmol). Mp = 192–193 uC; IR (KBr):
1292, 1442, 1540, 1655, 1724, 3291 cm21 1H NMR 400 MHz
;
(CDCl3, d ppm): 1.66 (6H, d, J = 8 Hz, Ala(1) CbHs), 3.89 (6H, s,
methoxy H’s), 4.93–4.98 (2H, m, Ala(1) CaHs), 7.34 (2H, t, J = 8
Hz, Hc (m-ABA(2)), 7.74 (2H, d, J = 8 Hz, Hb (m-ABA(2)), 7.95
(2H, d, J = 8 Hz, Hd (m-ABA(2)), 8.04 (1H, t, J = 8 Hz, py Ha),
8.12 (2H, s, Ha (m-ABA(2)), 8.37 (1H, d, J = 8 Hz, py Hb), 8.9
(2H, d, J = 8 Hz, Ala(1) NH), 9.2 (2H, s, mABA(2) NH); 13C NMR
100 MHz(CDCl3, d ppm): 17.8, 50.2, 52.2, 120.9, 124.4, 125.3,
125.5, 129.0, 130.7, 138.2, 139.2, 148.4, 164.01, 166.71, 171.11;
HR–MS C29H29N5O8 (M + Na+) = 598.195, Mcalcd C29H29N5O8 (M
+ Na)+ = 598, C58H58N10O16 (M + Na+) = 1173.3736, Mcalcd
C29H29N5O8 (M + Na)+ = 1173.
Peptide II. Trifluoroacetic acid (5 ml) was added to Boc-D-
Ala-mABA-OMe (2) (1.5 g, 4.65 mmol) at 0 uC and stirred at
room temperature. The removal of the Boc group was
monitored by TLC. After 6 hours, the trifluoroacetic acid was
removed under reduced pressure to afford the crude trifluor-
oacetate salt. The residue was taken up in water and washed
with diethyl ether. The pH of the aqueous solution was
adjusted to pH 8 with sodium bicarbonate and extracted with
ethyl acetate. The extracts were pooled, washed with saturated
brine, dried over sodium sulphate and concentrated to a
highly viscous liquid that gave a positive ninhydrin test. DMF
and DIPEA (3.2 ml, 13.98 mmol) was added to a well stirred
and ice-cooled solution of the obtained free base. To this
mixture, a freshly prepared solution of pyridine 2,6 dicarbonyl
dichloride (0.44 g, 2.33 mmol) in 10 ml of DMF was added over
a period of 0.5 hours and the mixture continued to stir at room
temperature for 2 days. The solvents were evaporated in vacuo
and the residue was dissolved in ethyl acetate and washed
sequentially with 1 M HCl (3 6 30 ml), a 1 M Na2CO3 solution
(3 6 30 ml) and again with water. The solvent was then dried
over anhydrous Na2SO4 and evaporated in vacuo, giving a light
yellow solid. Purification was done using silica gel as the
stationary phase and an ethyl acetate–petroleum ether mixture
as the eluent. Single crystals were grown from an acetone–
petroleum ether mixture (90 : 10) by slow evaporation and
were stable at room temperature.
Gas adsorption studies
N2 absorption studies at 77 K with dehydrated samples
prepared at 373 K under a high vacuum were carried out
using a fully computer-controlled volumetric Belsorp-Max
surface area analyzer. The nitrogen gas used for the measure-
ments was of scientific/research grade with 99.999% purity.
The dead volume of the sample cell was measured using
helium gas of 99.999% purity. Non-ideal corrections were
made by applying virial coefficients at the measurement
temperature.
Results and discussion
Solid state conformational analysis
Single crystals suitable for X-ray diffraction were obtained
from a mixture of acetone and petroleum ether after slow
evaporation. Both the enantiomeric pseudopeptides I and II
crystallize with one molecule in the asymmetric unit. The
crystallographic parameters for both the pseudopeptides are
reported in Table 1.
The solid state structure of enantiomeric pseudopeptides I
and II reveal a bent conformation near the central aromatic
system and an overall extended structure around the dipepti-
dyl fragment, where the aromatic units are in edge-to-face and
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Table 3 Intermolecular hydrogen bonding parameters of pseudopeptides I and
II
…
…
…
…
D–H
A
H
A/Å
D
A/Å
D–H A/u
Pseudopeptide I
a
…
N3–H4A O3
2.13
2.18
2.02
2.95
3.00
2.87
155.2
160.5
162.7
a
…
N4–H1A O8
a
…
N2–H5A O9
Pseudopeptide II
a
…
N1–H15A O4
2.24
2.08
1.97
2.86
2.99
2.95
163.5
155.4
156.8
a
…
…
N3–H3A O3
a
N6–H6A O2
a
Symmetry equivalent x, y, z.
…
…
…
mABA NH (N4–H1A O8, 2.18 Å; N4 O8, 3.00 Å; N4–H1A O8
160.5u; x, y, z) and molecule 1 Ala NH forms a hydrogen bond
…
…
to molecule 2 Ala CO (N3–H4A O3, 2.13 Å, N3 O3, 2.95 Å,
N3–H4A O3, 155.2u, x, y, z), to stabilize the dimeric structure
…
Fig. 2 Crystal Structure of (a) pseudopeptide I (b) pseudopeptide II with an
(Table 3). A similar type of dimeric moiety is also formed by
two molecules of the enantiomeric pseudopeptide II (N3–
atom numbering scheme.
…
…
…
H3A O3, 2.08 Å, N3 O3, 2.99 Å, N3–H3A O3 155.37u, x, y, z);
…
…
…
(N6–H6A O2, 1.97 Å, N6 O2, 2.95 Å, N6–H6A O2, 156.83u, x,
y, z) (Table 3). The crystal structure of both the pseudopeptides
reveal the presence of a C2 symmetric axis.
face-to-face contact with the central pyridine ring (Fig. 2). The
torsion angles and hydrogen bonding parameters of both the
pseudopeptides are presented in Table 2 and 3 respectively.
Each molecule of pseudopeptide I and II first forms a dimeric
entity (molecule 1 and 2 of the same pseudopeptide; molecule
1 is shown as a capped stick and molecule 2 as a ball and
stick), where the two central pyridine rings slightly inter-
digitate with each other and the two arms of the dipeptidyl
fragment are in a mirror image relationship connected by two
intermolecular hydrogen bonds (Fig. 3a: pseudopeptide I,
Fig. 4a: pseudopeptide II). In pseudopeptide I, the molecule
1pyridinyl CO forms a hydrogen bond with the molecule 2
Interestingly, each dimeric entity of the enantiomeric
pseudopeptides I and II are then regularly stacked one on
top of the other, maintaining a proper registry to form an
intermolecular hydrogen bonded helical strand along the
crystallographic a-axis.
There is a single intermolecular hydrogen bond between
molecule 1 mABA NH and molecule 2 pyridinyl CO of another
…
…
…
…
dimeric set (N2–H5A O9, 2.09 Å N2 O9, 2.87 Å, N2–H5A O9,
…
162.7u, x, y, z for peptide I and N1–H15A O4, 2.24 Å, N1 O4,
2.86 Å, N1–H15A O4, 163.5u; x, y, z peptide II, Table 3) (Fig. 3b
…
Table 2 Selected torsion angles (u) for pseudopeptides I and II
Pseudopeptide I
C10–N1–C9–C11
N1–C9–C11–N3
C9–C11–N3–C13
C11–N3–C13–C8
N3–C13–C8–N2
C13–C8–N2–C19
C8–N2–C19–C20
N2–C19–C20–C28
C19–C20–C28–C26
C20–C28–C26–O1
Pseudopeptide II
C17–N4–C13–C12
N4–C13–C12–N6
C13–C12–N6–C10
C12–N6–C10–C9
N6–C10–C9–N1
C10–C9–N1–C7
C9–N1–C7–C8
177.8(5)
2.9(7)
173.2(5)
88.4(6)
2162.5(4)
2165.7(4)
161.1(5)
180.0(5)
176.7(5)
171.8(6)
C9–N1–C10–C12
N1–C10–C12–N6
C10–C12–N6–C18
C12–N6–C18–C14
N6–C18–C14–N4
C18–C14–N4–C21
C14–N4–C21–C16
N4–C21–C16–C30
C21–C16–C30–C23
C16–C30–C23–C30
2179.5(5)
0.3(7)
2173.2(4)
259.8(6)
230.2(6)
2173.8(5)
23.7(9)
2179.5(5)
2178.7(6)
27(1)
2178.4(3)
22.9(4)
2174.6(3)
288.2(4)
163.1(3)
167.0(3)
2160.3(3)
179.2(3)
C13–N4–C17–C18
N4–C17–C18–N2
C17–C18–N2–C19
C18–N2–C19 –C21
N2–C19 –C21–N3
C19 –C21–N3–C22
C21–N3–C22–C27
N3–C22–C27–C26
C22–C27–C26–C28
C27–C26–C28–O7
2179.8(3)
0.2(4)
172.1(3)
60.2(4)
29.9(4)
174.6(3)
2.4(5)
2178.0(8)
177.9(4)
6.7(6)
Fig. 3 Schematic representation of the stepwise supramolecular double helix
formation from pseudopeptide I a) Dimeric entity; Single helical strand b)
without sidechains and nonhydrogen bonded atoms; c) with sidechains and all
atoms; d) double helical assembly along the crystallographic a-axis. (Hydrogen
bonded atoms are shown as dotted lines.)
N1–C7–C8–C3
C7–C8–C3–C2
C8–C3–C2–O8
2176.1(3)
2173.5(3)
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Fig. 4 Schematic representation of the stepwise supramolecular double helix
formation from pseudopeptide II a) Dimeric entity; Single helical strand b)
without sidechains and nonhydrogen bonded atoms; c) with sidechains and all
atoms; d) double helical assembly along the crystallographic a-axis. (Hydrogen
bonded atoms are shown as dotted lines.)
Fig. 5 The formation of the supramolecular double helical assembly of a)
pseudopeptide I and b) pseudopeptide II, as observed along the crystal-
lographic c-axis in a spacefilling model.
and 4b) which is responsible for creating a single strand of the
double helix along the crystallographic a-axis, respectively.
These individual helical strands are then tethered via non-
covalent interactions to form the supramolecular double
Fig. 7 500 MHz 1H NMR spectra of (aromatic and NH region) pseudopeptide I a)
34 mM; b) 8 mM; c) 2 mM; d) 0.5 mM in CDCl3 at different temperatures. Ala(1)
NH (round) and mABA(2) NH are marked as rounded squares.
Fig. 6 Mass spectra of pseudopeptide I.
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helical superstructure along the crystallographic a-axis (Fig. 3c
and 4c). The torsion angle around the central pyridinyl moiety
plays a crucial role in dictating the overall double helical
structural features. Fig. 3 and 4 represents a schematic
diagram of the stepwise formation of the supramolecular
double helix starting from the dipeptidyl building blocks as
subunits for both the pseudopeptides. Fig. 5 also depicts a
clear view of the supramolecular double helical assemblage of
both the enantiomeric pseudopeptides I and II, respectively in
a spacefilled model, as is observed along the crystallographic
c-axis. It is interesting to note that the mABA units present in
each duplex are engaged in multiple intraduplex interstrand
face-to-face and edge-to-face interactions at various angles,
which may be responsible for the overall stabilization of these
motifs.
not simply reflect the relative amounts of the species in
solution as it is affected by many experimental parameters.
Therefore, concentration and temperature dependant NMR
studies in CDCl3 were carried out to substantiate the MS
results.
The spectra of the pseudopeptides were recorded at several
concentrations and temperatures. A comparison of the proton
chemical shifts of pseudopeptide I in concentrated and dilute
solutions is presented in Fig. 7. The NMR analysis reveals that
at a particular concentration, the amide protons of alanine
and meta amino benzoic acid moieties exhibit higher
resonance frequencies with a decrease in the temperature,
which may be attributed to the hydrogen-bonding interactions
predicted in the dimeric assembly. Conversely, all the aromatic
protons shift upfield as a consequence of the p–p interactions
and ring currents exerted by them. In order to determine
whether the hydrogen bonds are intra or intermolecular,
dilution experiments were performed.17 The NH resonances
reveal considerable shifts with a change in concentration,
suggesting the presence of intermolecular hydrogen bonding
within the pseudopeptides. Had it been intramolecular, there
would be a negligible change in their chemical shifts with
Solution conformational analysis
In order to explore the solution conformational features of
enantiomeric pseudopeptides I and II, ESI-MS and NMR
studies were performed. The enantiomeric pseudopeptides I
and II reveal signals of m/z 2M + Na (I:1173.3736; II:1173.3956)
in the ESI-MS analysis (Fig. 6), supporting the formation of
dimers in MeOH.16 However, the relative signal intensities do
Fig. 8 500 MHz ROESY spectrum of pseudopeptide I in CDCl3 exhibiting the NOE intensities responsible for the intermolecular hydrogen bonding interactions
between the aromatic and NH protons (marked with arrows).
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Table 4 Initial weight of the sample = 41.4 mg. Weight loss of the I2 exposed
sample of pseudopeptide II in air
Time (min) Wt of the sample (mg) Wt increase (mg) % Wt increased
0
10
20
30
40
50
60
120
180
45.70
41.56
37.47
33.38
33.38
33.38
33.38
33.38
33.38
33. 38
4.30
4.14
4.09
4.01
4.01
4.01
4.01
4.01
4.01
4.01
10.4
10.1
9.9
9.7
9.7
9.7
9.7
9.7
9.7
9.7
24 hours
Fig. 9 TGA of pseudopeptide II. (It is evident that the compound exhibits no
decomposition, phase transition or mass loss up to 325 uC, which is much higher
than its melting point (152 uC).)
nature of the absorption, the crystals of pseudopeptide II after
iodine exposure were crushed. The color inside the crystals
was found to be dark brown for pseudopeptide II, indicating
uniform absorption (Fig. 10). To affirm our results, further
surface area measurement studies were performed.21 The
evacuated samples of pseudopeptide II indicate that they
exhibit a type-III absorption isotherm (Fig. 11). The pore size
distribution curve of pseudopeptide II showed a peak maxima
at 1.88 nm at 77 K and 1 atm pressure.
dilution. Moreover, the NOESY intensities between the
aromatic protons in the ROESY spectrum further affirms the
presence of intermolecular hydrogen bonding between the
aromatic protons (Fig. 8).
Absorption studies
Owing to the ecofriendly nature of peptides, they are
considered to be attractive targets for the design of nanopor-
ous materials.18 Inspired by the guest molecule adsorption
properties in the architecture of a double helix,19 the author
aims to explore the candidature of the enantiomeric pseudo-
peptides in the design of nanoporous materials. Since
enantiomers exhibit identical properties, only one of the
enantiomers (pseudopeptide II) was subjected to guest
molecule encapsulation studies.
The TGA experiments of pseudopeptide II reveal that the
supramolecular double helices have significant thermal
stability. It showed no decomposition, phase transitions or
mass loss up to 325 uC, which is much higher than the melting
point (Fig. 9).
Conclusions
In summary, this report reflects that in the solid state, two
enantiomeric pseudopeptides I and II, comprising a single
pyridinedicarboxylic acid and a flexible dipeptidyl fragment
H-Xaa-mABA-OMe (Xaa: L-Ala, pseudopeptide I; D-Ala, pseudo-
peptide II, mABA: meta aminobenzoic acid), displays supra-
molecular double helical assemblage by employing dimeric
The exposure of the sample was carried out in a closed
chamber for 24 h, where iodine vapours were generated by
warming the chamber at regular time intervals.20 It was
observed that colorless crystals of pseudopeptide II turned
dark brown (Fig. 10) (Table 4) (9.7 wt%). The crystals of
pseudopeptide II after iodine absorption were not suitable for
diffraction so we are unable to comment on the cell
parameters of the iodine absorbed crystals. To verify the
Fig. 10 Photograph of a) a single crystal of pseudopeptide II; b) after exposure
to iodine vapours; c) showing the uniform absorption of iodine vapours in the
crystal after crushing.
Fig. 11 N2 adsorption–desorption isotherm of pseudopeptide II at 77 K and 1
atm pressure. Red square: sorption; red circle: desorption.
2472 | CrystEngComm, 2013, 15, 2466–2473
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Commun., 2011, 47, 2092; (e) S. K. Maity, S. Maity, P. Jana
and D. Haldar, Chem. Commun., 2012, 48, 711.
subunits as building blocks. To date, significant examples are
documented in the literature where DNA analogues/derivatives
or several rigid templates have been employed as synthons for
double helical self assembly. However, to the best of our
knowledge, this novel example represents one of the very few
reports of supramolecular double helix design resulting from
the self assembly of a flexible dimeric peptidyl unit, solely
nucleated by the conformational features, of the peptides and
stabilized by non-covalent interactions (H-bonding and p–p
interactions) as the driving force. Concentration and tempera-
ture dependant NMR experiments and ESI-MS analysis also
supported the existence of the dimeric unit in solution of
pseudopeptide I (one of the enantiomers). Pseudopeptide II
(one of the enantiomers) was subjected to iodine and gas
absorption studies, which demonstrates their candidature in
the design of nanoporous materials.
This report further reveals that careful engineering of
flexible amino acid/peptidyl fragments coupled with a single
pyridinedicarboxylic acid for the design of supramolecular
double helical assemblage with large pore diameters, to
display successful adsorption properties, is currently under
investigation. This path may open a new avenue for scientists
to tailor environmentally benign peptide based nanoporous
materials.
5 (a) Y. Tanaka, H. Katagiri, Y. Furusho and E. Yashima,
Angew. Chem., Int. Ed., 2005, 44, 3867; (b) Y. Furusho,
Y. Tanaka and E. Yashima, Org. Lett., 2006, 8, 2583.
6 H. Goto, H. Katagiri, Y. Furusho and E. Yashima, J. Am.
Chem. Soc., 2006, 128, 7176.
7 T. Sugimoto, T. Suzuki, S. Shinkai and K. Sada, J. Am.
Chem. Soc., 2007, 129, 270.
8 G. J. Gabriel and B. L. Iversion, J. Am. Chem. Soc., 2002, 124,
15174.
9 (a) J. Li, J. A. Wisner and M. C. Jennings, Org. Lett., 2007, 9,
3267; (b) H. Bo, B. P. Mudraboyina, J. Li and J. A. Wisner,
Chem. Commun., 2010, 46, 7343; (c) H. B. Wang, B.
P. Mudraboyina and J. A. Wisner, Chem.–Eur. J., 2012, 18,
1322.
10 (a) V. Berl, I. Huc, R. G. Khoury, M. J. Krische and J.
M. Lehn, Nature, 2000, 407, 720; (b) E. Kolomiets, V. Berl
and J. M. Lehn, Chem.–Eur. J., 2007, 13, 5466.
11 (a) D. Haldar, H. Jiang, J. A. Leger and I. Huc, Angew.
Chem., Int. Ed., 2006, 45, 5483; (b) B. Baptiste, J. Zhu,
D. Haldar, B. Kauffmann, J. M. Leger and I. Huc, Chem.–
Asian J., 2010, 5, 1364; (c) H. Jiang, J. M. Leger and I. Huc, J.
Am. Chem. Soc., 2003, 125, 3448; (d) Q. Gan, Y. Ferrand,
C. Bao, B. Kauffmann, A. Grilard, H. Jiang and I. Huc,
Science, 2011, 331, 1172; (e) A. M. Kendhale, L. Poniman,
Z. Dong, K. L. Reddy, B. Kauffmann, Y. Ferrand and I. Huc,
J. Org. Chem., 2011, 76, 195.
12 (a) A. Dutt, M. G. B. Drew and A. Pramanik, Org. Biomol.
Chem., 2005, 2250; (b) S. K. Kundu, P. A. Mazumdar, A.
K. Das, V. Bertolasi and A. Pramanik, J. Chem. Soc., Perkin
Trans., 2002, 1602; (c) P. Koley and A. Pramanik, Soft
Matter, 2012, 8, 5364; (d) P. Koley and A. Pramanik, Adv.
Funct. Mater., 2011, 21, 4126.
13 M. Bodanszky and A. Bodanszky, The Practice of Peptide
Synthesis, Springer-Verlag, New York, 1984, p. 1.
14 SADABS, G. M. Sheldrick, Program for Absorption Correction
of Area Detector Frames, BRUKER AXS Inc., 5465 East Cheryl
Parkway, Madison, WI 53711- USA.
Acknowledgements
The author wishes to thank DST, New Delhi, India, for
financial support (Project No. SR/FT/CS-025/2010) and IISER
Bhopal for providing the infrastructures. The author is very
grateful to Dr. Sanjit Konar for their assistance in the X-ray
crystallography and valuable advice. Mr. Amit Adhikary, Mr.
Javeed Ahmad Sheikh, Mr. Suresh Sanda, Mr. Soumyabrata
Goswami, Mr Sajal Khatua, Mr. Soumava Biswas and Mr. P.
Sreenivasulu are sincerely acknowledged for various measure-
ments for this work.
15 (a) G. M. Sheldrick, Acta Crystallogr., Sect. A: Fundam.
Crystallogr., 1990, 46, 467; (b) G. M. Sheldrick, SHELXL 97
Program for Crystal Structure Refinement, University of
References
¨
Gottingen, Germany, 1997.
1 (a) M. M. Cox and D. L. Nelson, Principles of Biochemistry,
W. H. Freeman and Company, New York, 2008; (b)
A. Bruce, Molecular Biology of the Cell, Garland Science,
New York, 2008.
16 D. Haldar, H. Jiang, J. M. Leger and I. Huc, Tetrahedron,
2007, 63, 6322.
17 K. Wuthrich, in NMR of Proteins and Nucleic Acids, Wiley:
New York, 1986, p. 192.
2 J. D. Watson and F. C. H. Crick, Nature, 1953, 171, 737.
3 (a) B. Petersson, B. B. Nielsen, H. Rasmussen, I. K. Larsen,
M. Gajhede, P. E. Neilsen and J. S. Kastrup, J. Am. Chem.
Soc., 2005, 127, 1424; (b) R. W. Wanger, Nature, 1994, 372,
333; (c) M. Egli, P. S. Pallan, R. Pattanayek, C. J. Wilds,
P. Lubini, G. Minasov, M. Dobler, C. J. Leuman and
A. Eschenmoser, J. Am. Chem. Soc., 2006, 128, 10847; (d)
M. Tarkoy and C. Leumann, Angew. Chem., Int. Ed., 1993,
32, 1432.
4 (a) A. D. Konar, CrystEngComm, 2012, 14, 6689; (b) C.
H. Gorbitz, Chem.–Eur. J., 2007, 13, 1022; (c) S. Guha, M. G.
B. Drew and A. Banerjee, Org. Lett., 2007, 9, 1347; (d)
P. Jana, S. Maity, S. K. Maity and D. Haldar, Chem.
¨
18 (a) C. H. Gorbitz, Chem.–Eur. J., 2007, 13, 1022; (b) C.
¨
H. Gorbitz, M. Nilsen, K. Szeto and L. W. Tangen, Chem.
Commun., 2005, 4288; (c) C. H. Gorbitz, CrystEngComm,
2005, 7, 670.
¨
19 P. Jana, S. Maity, S. K. Maity and D. Haldar, Chem.
Commun., 2011, 47, 2092.
20 (a) L. Dobrzanska, G. O. Lloyd, H. G. Raubenheimer and L.
J. Barbour, J. Am. Chem. Soc., 2005, 127, 2937; (b) L. Rajput,
V. V. Chernyshev and K. Biradha, Chem. Commun., 2010,
46, 6530.
21 D. Chandra and A. Bhaumik, J. Mater. Chem., 2009, 19,
1901.
This journal is ß The Royal Society of Chemistry 2013
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