A simple peptidomimetic that self-associates on the solid state to form a nanoporous architecture containing chiral π-channels

Article abstract of DOI:10.1039/b922172g

The crystal structure of a simple peptidomimetic compound, derived from phenylalanine, shows the formation of a nanoporous architecture containing monodimensional π-channels with the aromatic rings as the exclusive components of the chiral channel walls. The Royal Society of Chemistry 2010.

Full text of DOI:10.1039/b922172g

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COMMUNICATION
www.rsc.org/crystengcomm | CrystEngComm
A simple peptidomimetic that self-associates on the solid state to form
a nanoporous architecture containing chiral p-channels†‡
Jorge Becerril,a Michael Bolte,b M. Isabel Burguete,a Jorge Escorihuela,a Francisco Galindoa
and Santiago V. Luisa
Received 22nd October 2009, Accepted 30th January 2010
First published as an Advance Article on the web 23rd February 2010
DOI: 10.1039/b922172g
of a large number of aromatic residues, leading to the proposal of the
important role of p-interactions in defining the structure in those
regions, and for the transport mechanisms,6 as confirmed in the case
of an ammonia channel.7
The crystal structure of a simple peptidomimetic compound, derived
from phenylalanine, shows the formation of a nanoporous archi-
tecture containing monodimensional p-channels with the aromatic
rings as the exclusive components of the chiral channel walls.
A large number of pseudopeptidic structures have been designed in
recent years for multiple purposes, and we have been recently
involved in the preparation and study of minimalist pseudopeptides
containing the general structure 4. These compounds can be prepared
very efficiently in three steps (ca. 80% overall yields) starting from
commercially available N-Cbz protected amino acids (1) through the
initial formation of their activated N-hydroxysuccinimide esters (2),
coupling with a variety of diamines and final N-deprotection
(Scheme 1).8 C2 pseudopeptides 4 can be used as building blocks for
the construction of macrocyclic structures.9 Some of them are able to
display organogelating properties,10 acting as ‘in vivo’ fluorescent pH
probes,11 as selective receptors for substrates of biological relevance,12
as minimalistic molecular machines,12a,c or acting as ligands for the
efficient enantioselective addition of dialkylzinc to aromatic alde-
hydes.13 Recently, we have reported on the crystal structure of three
pseudopeptidic macrocycles that display ‘‘knobs into holes’’ hydro-
phobic interactions between aliphatic side chains.14
Building nanometric molecular devices with applications in different
fields is a major challenge for researchers.1 An important milestone
for the study of nanoporous materials was their observation in bio-
logical systems.2 Transport through membranes is an essential
process in living beings that, predominantly, use channels with
porosities at the nanometre scale.3 From the possible strategies to
build up nanoporous structures, the supramolecular approach based
on the self-organization of low molecular weight components is the
most attractive. This target has been achieved by assembling metal–
organic structures,4 or, less frequently, by the exclusive use of organic
components, usually macrocyclic peptidic structures.5 Moreover, the
analysis of proteins in transmembrane channels revealed the presence
a
´
ꢀ
ꢀ
Departamento de Quımica Inorganica y Organica, Universidad Jaume I,
Avenida Sos Baynat s/n, Castelloꢀn, Spain. E-mail: luiss@qio.uji.es; Fax:
+34-964-728-214; Tel: +34-964-728-239
NMR analysis of compounds 4 revealed a strong tendency of the
amide group to form hydrogen bonds either intramolecularly or
intermolecularly.8 Attempts to crystallize those compounds were
carried out in order to gain information on the nature of the
hydrogen-bonding network formed. This could contribute to explain
their folding properties, as well as to understand the behavior of
related systems as receptors and as strong organogelators. Crystalli-
zation was first assayed in CH2Cl2 and it was observed that the
product derived from (S)-phenylalanine containing an aliphatic
spacer with two methylene groups (4a, n ¼ 0) gave place to the
formation of crystals suitable for X-ray analysis, while only a partial
bInstitut fu€r Anorganische Chemie, J. W. Goethe-Universita€t, Frankfurt,
Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
† Electronic supplementary information (ESI) available: Crystal data for
4c. CCDC reference numbers 279709, 738995 and 739838. For ESI and
crystallographic data in CIF or other electronic format see DOI:
10.1039/b922172g
‡ Crystallographic data for compound 4a (CCDC-279709): C20H26N4O2.
ꢁ
ꢁ
1/3C4H10O, M ¼ 379.15, hexagonal, a ¼ 16.994(2) A, c ¼ 6.2966(7) A, V ¼
3
ꢁ
1574.8(3) A , T ¼ 173 K, space group P64 (No. 172), Z ¼ 3, 14595
reflections measured, 2348 unique (Rint ¼ 0.028) which were used in all
calculations. Final wR2 ¼ 0.0853 and R1 ¼ 0.0348 for data with I > 2s (I).
Due to the absence of anomalous scatterers, Friedel pairs were merged.
Compound 4a0 (CCDC-739838): C20H26N4O2$1/2CH2Cl2, M ¼ 396.91,
3
ꢁ
ꢁ
ꢁ
hexagonal, a ¼ 16.9390(10) A, c ¼ 6.2865(5) A, V ¼ 1562.12(18) A , T ¼
173 K, space group P64 (No. 172), Z ¼ 3, 15134 reflections measured, 2305
unique (Rint ¼ 0.061) which were used in all calculations. Final wR2
¼
0.1183 and R1 ¼ 0.0519 for data with I > 2s (I). Since the absolute structure
could not be determined reliably, Friedel pairs were merged.
Compound 4a-meso (CCDC-738995): C20H26N4O2, M ¼ 354.45, mono-
ꢁ
ꢁ
ꢁ
clinic, a ¼ 8.327(2) A, b ¼ 12.216(3) A, c ¼ 9.643(3) A, b ¼ 98.648(6), V ¼
3
ꢁ
969.8(4) A , T ¼ 298 K, space group P21/c (No. 14), Z ¼ 2, 7836 reflections
measured, 2894 unique (Rint ¼ 0.027) which were used in all calculations.
Final wR2 ¼ 0.1389 and R1 ¼ 0.0541 for data with I > 2s (I).
For compound 4c the presence of some disorder in the chain atoms
precluded an accurate and complete analysis, and only a partial deter-
mination of the structure could be achieved: C22H30N4O2, M ¼ 382.50,
ꢁ
ꢁ
ꢁ
monoclinic, a ¼ 5.5416(11) A, b ¼ 43.066(9) A, c ¼ 8.7604(18) A, b ¼
ꢀ
3
ꢁ
90.01(3) , V ¼ 2090.7(7) A , T ¼ 293 K, space group P21 (No. 4), Z ¼ 4,
20001 reflections measured, 4019 unique (Rint ¼ 0.072) which were used
in all calculations. Final wR2 ¼ 0.206 and R1 ¼ 0.085 for data with I >
2s (I).
Scheme 1 Synthesis of chiral bis(amino amide) ligands. Reagents: (i)
DCC, N-hydroxysuccinimide, THF, r.t.; (ii) H2NCH2(CH2)nCH2NH2,
DME, r.t.; (iii) HBr/AcOH; (iv) NaOHaq
.
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determination of the structure for the compound with four methylene
groups (4c, n ¼ 2) was achieved, because of the disorder present for
some atoms of the aliphatic spacer.
The results obtained suggest the formation of very different
patterns as a function of the length of the spacer. For compound 4a
the molecules show a folded structure (Fig. 1) while 4c molecules
present an extended conformation (Fig. 2) that seems to assemble
into a b-sheet-like structure.15
On the contrary, compound 4a assembles in the solid state to form
a very unique architecture with crystallographic two-fold symmetry.
Surprisingly, the structure obtained for compound 4a (Fig. 3) is
highly porous, (channels represent a 14.4% of the total volume) and
Fig. 4 (A) Schematic representation of the parameters for describing
edge-to-face interactions, where d1 is the distance between ring centroids,
d2 is the distance between hydrogen and the ring plane, d3 is the offset
from the ring centroid, d4 is the distance between the ring centroid and
hydrogen and q is the angle formed by planes that contain the rings. (B)
Ball and stick representation of the edge-to-face interactions in
compound 4a.
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contains channels of about 5.3 A. One of the most remarkable
features of this unique structure is that the walls of such channels are
formed by the aromatic rings of the side chains of the phenylalanine
moieties that interact through a complex network of tilted edge to
face interactions.16
The critical parameters for such interactions (Fig. 4) are q ¼ 57.7ꢀ,
aromatic rings gives place to a chiral helical structure of the walls,
forming a double helix. The diameter of the channels is almost in the
range of the diameter found, for instance, in the central part of the K+
channel.18 It is interesting to consider that the 1 nm scale also
corresponds to the size of the cavities found in single wall carbon
nanotubes (SWCN), but with the noteworthy difference that in our
case the p-electronic cavities are formed through a non-covalent self-
assembly. In this regard, a report showed how discrete graphitic
nanotubes with diameters one order of magnitude larger (14 nm)
than those of carbon nanotubes can self-assemble from amphiphilic
hexa-perihexabenzocoronene.19
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ꢁ
ꢁ
d1 ¼ 5.491 A, d2 ¼ 3.013 A, d3 ¼ 1.405 A, d4 ¼ 3.472 A and
correspond well with the values observed in other organic systems
and in proteins,17 where, as mentioned above, this kind of interaction
can play an important role. The result is the formation of a channel
whose walls are exclusively shaped by the aromatic rings that
completely wrap the cavity formed. The relative orientation of the
Six different aromatic rings belonging to six phenylalanine residues
of different molecules are required to complete every layer of the
channel walls. Accordingly, the structure looking on the ab-plane can
be described in terms of a honeycomb architecture similar to those
observed in many metal–organic systems. Besides the p–p interac-
tions, an extensive network of intramolecular and intermolecular
hydrogen bonds is observed. It can be seen that intramolecular
hydrogen bonds between the nitrogen of the NH2 group and the
amido hydrogen atom along with intramolecular CH–p interactions
(see Fig. 1 A) contribute to stabilize an U-turn conformation, a situ-
ation that had been postulated to be important for explaining the
excellent yields observed for macrocyclization reactions for
compounds 4.8 According to this folded conformation, the two
phenyl groups of the phenylalanine side chains point out in opposite
directions, and are involved in the formation of the walls of two
contiguous channels.
Fig. 1 Molecular structure of compound 4a present in its X-ray struc-
ture.
Fig. 2 Molecular structure of compound 4c present in its X-ray struc-
On the other hand, each single molecule in the structure is connected
with four additional molecules by hydrogen bonds. Each phenylala-
nine residue present in 4 is bound to two vicinal molecules. As can be
seen in Fig. 3, molecules are arranged around a single channel in six
columns. Within each column, molecules are disposed in a completely
parallel arrangement. Two contiguous columns are connected through
hydrogen bonds between the oxygen of the carbonyl groups of the
phenylalanine moiety and one of the hydrogen atoms of amino groups
of molecules in the second column. In this arrangement, the C]O
groups point downwards whilst the NH2 groups point upwards, so
that the hydrogen bond is formed between two molecules located at
a different height in the columns. Accordingly, as schematized in
Fig. 5a, those C]O / H–NH hydrogen bonds are arranged around
the periphery of the channel forming a sextuple helix. On the other
hand, every two of the columns are connected to a third column not
ture (one single conformer is shown).
Fig. 3 (A) Front view (CPK) of one of the channels highlighting the six
molecules involved. (B) Side view of one of the channels. (C) View of the
ab plane in the crystal structure.
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a situation that is very unusual for crystal structures where packing
forces always try to minimize those void spaces.
The stability of the porous structure was confirmed by their ability
to incorporate and release additional guests.20 Thus, when crystals of
4a were stored in a recipient with I2 for 10 h, the colour of the crystals
changed from colourless to dark brown, showing that I2 can enter the
channels, and the process was shown to be reversible (see Fig. 6).
The spacer is not the only structural factor playing a key role to
determine the nature of the self-assembling in the crystal structure.
The configuration of the stereogenic center is also critical. Thus, when
the meso compound related to 4a was synthesized, the crystalline
structure obtained revealed to be very different (Fig. 7). The packing
does not present any porosity and the crystalline structure is formed
by layers of pseudopeptidic molecules interacting through a 2D
network of hydrogen bonds. Aromatic rings protude at both sides of
the layer with alternate orientations. Each aromatic ring of a given
layer is intercalated between two other benzene subunits from
a contiguous layer. In the final structure, all the aromatic rings are
Fig. 5 (A) and (B) Schematic representation of the helical arrangement
of hydrogen bonds in the crystal structure. Arrows indicate the sense of
the hydrogen bond (C]O / H–NH). (C) Representation of a channel
filled with CH2Cl2 molecules.
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parallel at a distance of 3.65 A. Thus, the crystal structure alternates
polar and non-polar layers (Fig. 7).
In summary, we report on the crystal structure of three peptido-
mimetics derived from (S)-phenylalanine. The structure of compound
4a represents a unique situation in which pseudopeptidic molecules
assemble in the crystalline state to form a highly porous crystal
containing monodimensional channels. One of the most singular
features of the structure is the fact that the walls of the channel are
exclusively formed by the aromatic rings of the side chains of the
phenylalanine moieties of which the peptidomimetic structure is built
up. The molecular architecture here presented represents the first
example of peptidic-like compounds able to self-assemble through
the aromatic side chains to form p-electronic channels. Chirality in
the structure, including the channels, is provided not only by the
stereogenic centers originating at the phenylalanine residues, but also
involved in that channel, again through C]O / H–NH hydrogen
bonding. In this case the C]O/H–NH hydrogen-bonding network
defines (see Fig. 5B) a triple helix. Thus, for a given phenylalanine
residue, the oxygen of the amido carbonyl group is hydrogen bonded
to one of the hydrogens of the NH2 group of a second neighbouring
molecule, while its amino group is connected by a hydrogen bond to
the oxygen of a carbonyl group of a third molecule. Finally, the
hydrogen atom of each amino group not involved in the former bonds
is hydrogen bonded to the carbonyl group of the molecule lying above
in the same column.
A detailed study of diffraction data showed the presence of some
residual electron density that must be attributed to solvent molecules.
Unfortunately, these solvent molecules are heavily disordered and, as
a result of that, no valid model could be found. Therefore, the
contribution of the solvent to the diffraction data was suppressed.
This led us to consider the possibility that those solvent molecules
could act as a template favoring the formation of the channels or
preventing their collapse. This could be in good agreement with the
ability of this kind of solvents to participate in H–p-interactions.16
Accordingly, crystallization of this compound was attempted using
different solvents and conditions. Suitable crystals were also obtained
in a CH2Cl2–Et2O mixture, but the structural parameters were
essentially identical. The new crystals also contained some residual
CH2Cl2 molecules in the channels. Moreover, an analysis of the
potential positions for the solvent molecules (CH2Cl2) in the channels
reveals that the chiral helical arrangement of the walls provides
a significant chiral environment for the guests. This is seen in Fig. 5C
that shows a channel filled with CH2Cl2 molecules that need to be
organized in a double helix arrangement.
Fig. 6 Dry 4a crystal (left) and after treatment with I2 (right).
Additionally, suitable crystals were also obtained from toluene.
This solvent was selected considering that its size was much less
appropriate to be kept in the channels and that it could also interfere
with the p–p network. The same structure was again obtained with
essentially no modification in the structural parameters, but no
solvent molecules were found in the channels. This reveals the
secondary role played by the solvent molecules in other cases and the
stability of this structure containing up to 14.4% of void space,
Fig. 7 View of the cb plane in the crystal structure (left) and spacefill
representation (right) of the meso structure.
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from the helical arrangement of the edge to face p–p interactions and
hydrogen bonds. A detailed analysis of this structure opens the way
for a better understanding of the role of aromatic residues in bio-
logical channels as well as for the design of novel families of nano-
porous and tubular structures and artificial channels.
Acknowledgements
ꢀ
Financial support from Ministerio de Ciencia e Innovacion
(CTQ2009-14366-C02-01) is gratefully acknowledged. J. E. thanks
ꢀ
UJI for a contract under the program: Pla de promocio de la
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