Self-Assembly of Non-Biological Polymeric Strands Undergoing Enforced Helical Self-Organization

Article abstract of DOI:10.1002/hlca.200390286

The polycondensation of a dihydrazino-pyrimidine (5 and 6) with a pyrimidine-dicarbaldehyde (7 and 8b) provides an efficent access to helical polymeric strands based on the formation of hydrazone connections between the pyrimidine groups. The folding into a helical structure is enforced by the helicity codon defined by the (hydrazone-pyrimidine) sequence. The polymers obtained have been characterized by mass spectrometry, indicating molecular weights up to ca. 12000 Da. Electronic spectra display specific absorption and emission features. These helical polymers present a core diameter of ca. 20 A, a pitch of 3.5 A, and, for a molecular weight around 9000 Da, a height of ca. 42 A with 12 turns. The self-assembled helical polymers obtained represent stable frameworks for the lateral attachment of functional residues in a helical disposition. Such entities may possess a range of novel chemical as well as biological properties.

Full text of DOI:10.1002/hlca.200390286

Helvetica Chimica Acta Vol. 86 (2003)
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Self-Assembly of Non-Biological Polymeric Strands Undergoing Enforced
Helical Self-Organization
by Jean-Louis Schmitt and Jean-Marie Lehn*
¬
ISIS-ULP-CNRS UMR 7006, 8, allee Gaspard Monge, BP 70028, F-67083 Strasbourg cedex
(phone: 0390245145; fax 039024 5140; e-mail: lehn@isis.u-strasbg.fr)
Dedicated to Professor Dieter Seebach
The polycondensation of a dihydrazino-pyrimidine (5 and 6) with a pyrimidine-dicarbaldehyde (7 and 8b)
provides an efficent access to helical polymeric strands based on the formation of hydrazone connections
between the pyrimidine groups. The folding into a helical structure is enforced by the helicity codon defined by
the (hydrazoneÀpyrimidine) sequence. The polymers obtained have been characterized by mass spectrometry,
indicating molecular weights up to ca. 12000 Da. Electronic spectra display specific absorption and emission
features. These helical polymers present a core diameter of ca. 20 ä, a pitch of 3.5 ä, and, for a molecular
weight around 9000 Da, a height of ca. 42 ä with 12 turns. The self-assembled helical polymers obtained
represent stable frameworks for the lateral attachment of functional residues in a helical disposition. Such
entities may possess a range of novel chemical as well as biological properties.
Introduction. The precise control of structure generation determines function and
is, thus, of prime importance in biology as well as in materials science and
nanotechnology on both the molecular and the supramolecular levels. It rests on
self-organization processes [1 3], leading to complex molecular and supramolecular
architectures, and is directed both by the structural and conformational information
encoded in the molecule, acting through the patterns of non-covalent intermolecular
interactions between components. Adequate programming of the generation of a well-
defined structure requires the orchestration of multiple interactional features, thus
directing a molecular strand to spontaneously adopt a specific geometry by a self-
folding process. It requires a detailed analysis of the geometrical and interactional
features that determine the generation of a given three-dimensional architecture from a
biological or synthetic molecular strand [2] as output of a suitably instructed,
programmed chemical system [3][4]. This is, in particular, the case for the highly
complex factors and pathways involved in protein folding [5][6].
Supramolecular architectures result from the self-assembly of the molecular
components under the control of patterns of intermolecular, non-covalent interactions.
Similarly, it may be possible to generate precise molecular architectures by self-
assembly from suitable components connected through reversible covalent bonds. Such
control requires the recognition and implementation of structuration codons on the
molecular and supramolecular levels. Thus, specific H-bonding patterns [7 9] may
yield either linear [10] or circular [11][12] supramolecular assemblies. The folding of a
molecular strand into a well-defined geometrical entity is a problem whose importance
is matched by its complexity. This applies of course first to protein folding, but also to

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synthetic, non-biological molecular strands, whose arrangement into a given geo-
metrical pattern has been subject of intense investigation in recent years [2]. One may
note in particular that −folding diseases× (e.g., Alzheimer and prion diseases) result from
conformational states and changes of proteins [13].
Principles for the Generation of Self-Folding Helical Strands. Helical molecular
entities are of special interest in view of their characteristic geometrical features as well
as their role in biology, where H-bonding, stacking interactions, and conformational
effects contribute to the stabilization of the a-helix of polypeptides and the double
helix of DNA. Helical folding of a chain may be driven by stacking or electrostatic
interactions and solvophobic effects [2][14 17], as well as by H-bonding (for recent
examples see, e.g. [18 21]). In our laboratory, specific arrays of H-bonding sites have
been used to induce helicity in heterocyclic-polyamide strands [22][23], which may
dimerize into double helices by stacking of two helical strands [22][24]. H-bonding
interaction with an appropriate template has also been used to induce folding of a
molecular strand [25]. The induction of helicity by helical programing [2][26] is, thus,
being actively investigated. On the other hand, helical self-organization of multi-
subunit ligand strands into inorganic double helices, the helicates, is induced by binding
of metal ions of appropriate coordination geometry [3][27].
In an another approach, in an earlier work from our group, it has been shown that
suitable sequences of directly connected heterocyclic units impose a specific geometry
on a polyheterocyclic strand by virtue of the marked conformational preference for a
transoid orientation around the connecting bonds. In particular, the (2,4')-pyridine-
pyrimidine (py-pym) sequence represents a helicity codon that has been shown to
enforce helical wrapping of a molecular (py-pym)n strand [28 30]. Control of the
geometrical properties may be achieved by appropriate modifications. Thus, replacing
the pyrimidine group by a pyridazine unit leads to helices of larger diameter that stack
into extended fibers [31]. Furthermore, it was shown that the pyridine group could be
replaced by an isomorphic hydrazone (hyz) unit, which preserves the strong preference
for a transoid orientation in the (hyz-pym) sequence [32].
As a consequence, imine formation, e.g., in hydrazones, provides a very efficient
synthesis of helical strands by molecular self-assembly through amineÀcarbonyl
condensation. Furthermore, since the reaction is reversible, the entities generated may,
in principle, undergo the exchange and selection processes characteristic of dynamic
combinatorial chemistry [33][34]. Imine functionalities have recently been introduced
into m-phenylene-ethynylene foldamers to connect the subunits [35][36]. A logical
extension of our earlier work was to replace all pyridine groups in a (py-pym)n strand
by hydrazone units so as to form (hyz-pym)n strands representing helical oligomers and
polymers. A process such as the formation of a helical superstructure via hydrazone
formation combines a number of features of general interest: 1) the generation of an
oligomeric or a polymeric strand by molecular self-assembly through imine formation;
2) the isomorphic pyridine ! hydrazone replacement, which results in a facile synthetic
procedure to give efficient, fast, and controlled access to the products, and to allow
stepwise condensation to yield discrete oligomers as well as polycondensation to
polymeric materials, in this case of helical type; 3) the control of the folding of a
molecular strand through interactional patterns defining structuration codons; in this

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case, a helicity codon, but other geometries may be induced; 4) the reversibility of the
self-assembly reaction, conferring constitutional dynamic capacity [1] and generating
folded structures, in this case, carbonylÀamine (hydrazine) condensations yielding
dynamic molecular helices capable, in principle, of incorporating, decorporating, and
exchanging components; 5) within the general framework of dynamic chemistry
[1][37], the generation of dynamic materials, in particular, dynamic polymers
(−dynamers×) [38][39]; presenting reversibility, healing, adjustability (adaptation)
through reversible covalent connections, conferring to molecular entities and the
dynamic features of supramolecular materials [1][33][36 40].
We have reported earlier the synthesis of a number of oligomeric molecular strands
based on (hyz-pym)n units (n ˆ 1 9; up to 10 hyz groups) and described their helical
structures, displaying up to 31³3 turns [41]. We now present the synthesis, character-
ization, and some properties of the polymers 1-H, 1-Me, 2-H, 2-Me, 3-Me, and 4-Me
generated from the polycondensation of the dihydrazino-pyrimidines 5 and 6 with the
pyrimidine-dicarbaldehydes 7 and 8b.
Synthesis of the Polymeric Strands 1 and 2. Two methods were employed for the
synthesis of the polymers 1 4 depending upon whether the monomer used was a
dihydrazino-pyrimidine (5-H and 6-H) or a bis(methylhydrazino) derivative (5-Me and
6-Me). In the case of the dihydrazino compounds, the conditions for polymer formation
were optimal when a one-to-one equiv. of 5-H or 6-H, and dicarbaldehyde 7 or 8b in a
CHCl3/MeOH solution were treated with a catalytic amount of AcOH. In the case of
the bis(methylhydrazino)-pyrimidines 5-Me and 6-Me, the presence of AcOH and
MeOH were unnecessary.
Characterization and Properties of the Helical Strands 1 4. The polymers 1 and 2
are yellow solids, stable over several months upon storage below 08. The N-methylated
polymers 1-Me and 2-Me were soluble in a wide range of organic solvents such as
CHCl3, CH2Cl2, THF, and DMSO. The unmethylated polymers 1-H and 2-H, on the
other hand, were only poorly soluble in CHCl3/MeOH 9 :1 mixture.
Analysis of the Polymers 1 and 2 by Mass Spectrometry. Extensive investigations of
the polymers 1 and 2 were performed by MALDI-TOFand FAB mass spectrometry.
The spectra revealed the presence of species between 1000- and 12000-Da molecular
weight, displaying regular mass distribution over the whole domain (Figs. 1 and 2).
These molecular weights cover a range of oligomers to polymers from 6 to 50 residues.
Mass peaks were present at alternating intervals corresponding, respectively, to
polymers differing by a bis(methylhydrazino)-pym unit or a diformyl-pym unit (see
Figs. 1 and 2). The chains may be terminated either by two bis(methylhydrazino)-pym
units, two diformyl-pym units, or by one unit of each type.
Interestingly, the FAB mass spectra gave mass peaks displaying association of the
‡
‡
different polymers with Na and K ions present in the matrix. The chains terminated
‡
by amine functional groups were found to associate preferentially with Na , while those
terminated by aldehyde groups bound preferentially K . Macrocycles were detectable
‡
in all mass spectra, but only those containing 4 and 6 heterocyclic rings and an
equivalent amount of both monomers.

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1H-NMR Spectra of the Polymers 1-Me and 2-Me. The polymers 1-Me and 2-Me
1
gave H-NMR spectra displaying extensive line-broadening even at higher temper-
atures. They could not be used for structural characterization, and it was not possible to
unambiguously assign the NOE cross-peaks for determining interproton interactions.
Electronic Absorption and Fluorescence Spectra of the Polymers 1-Me and 2-Me.
The electronic absorption and the fluorescence spectra of the polymer 1-Me are shown
in Figs. 3 and 4, respectively, together with corresponding spectra of the oligomers 9a

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Fig. 1. MALDI-TOF Mass spectrum of polymer 1-Me
and 9b, described earlier [41], for comparison purposes. The UV absorption spectrum
of polymer 1-Me presents two broad bands with maxima around 300 and 260 nm, the
latter being somewhat more intense. The first may arise from the terminal pyridines,
and the second from the pyrimidine and/or hydrazone units. Such an assignment would
agree with the relative intensities of the bands observed at similar wavelengths in the
oligomers 9, which display a higher pyridine-to-pyrimidine ratio than the polymers, i.e.,
a more intense band at 300 than at 260 nm [41].
The emission spectra display more distinctive features. Thus, the polymer 1-Me
shows a strong, very broad (200-nm-wide) and featureless emission centered at ca.
470 nm, as compared to ca. 430 nm for the oligomers 9 (Fig. 4). The shift to longer
wavelength by ca. 30 nm in the polymer with respect to the longest oligomer 9b is in line
with earlier results on helical (py-pym) strands, indicating such a shift with increasing
length of the strand [29][30]. This is in agreement with a more intense excimer
emission as the number of stacked pyrimidines increases with the chain length in the
polymers.
Helical Structure and Geometric Features of the Polymers 1 4. On the basis of the
helical form of the oligomers 9 and related compounds [41], one may confidently assign
a helical structure to the polymers 1 4. All spectral data available agree with such a
formulation. Thus, polycondensation of the dihydrazino-pyrimidines 5 and 6, and
pyrimidine-dicarbaldehydes 7 and 8b yields polymers presenting a strongly enforced

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Fig. 2. MALDI-TOF Mass spectrum of polymer 2-H
Fig. 3. Electronic absorption spectra of the oligomers 9a, 9b, and of the polymer 1-Me

Helvetica Chimica Acta Vol. 86 (2003)
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Fig. 4. Fluorescence emission spectra of the oligomers 9a, 9b, and of the polymer 1-Me in CH2Cl2 under excitation
at 310 nm
helical structure, as represented by 10. A long polymeric strand of 1-Me of molecular
weight ca. 9000 Da, as found in the mass spectrum, is expected to correspond to a helix
containing ca. 12 turns. Using the pitch of 3.5 ä found in the crystal structure of the
oligomers 9 [41], the core of this helix may be inscribed in a cylinder with a diameter of
20 ä and a height of 42 ä, as shown in Fig. 5.
Physicochemical Properties of Polymers 1 4. Molecular strands generated by
multiple hydrazineÀcarbonyl condensations may, in principle, be dynamic, in view of
the reversibility of the reaction. Such reversibility would make the strands chemically
unstable, but allow, potentially, the exchange of the components forming the strand, a
property characteristic of constitutionally dynamic systems [1][4][38 40]. In the case
of the oligomers 9 as well as of the polymer 1-Me, addition of the bis(methylhy-
drazino)-trimethoxyphenyl-pyrimidine 6-Me (in various organic solvents, in absence or
presence of acid) did not lead to any exchange. This result indicates that the tight
stacking within the helices, as seen in the crystal structures of the related oligomers
[41], hinders access of an external reagent to the hydrazone functions, thus precluding
component exchange. As a result, the self-assembled helices obtained are chemically
resistant. Replacing the hydrazone groups by imines might allow component exchange,
rendering the helical structures dynamic. Such studies are being persued.
Conclusion. The present results extend the earlier work on the induction of helical
folding to polymeric strands on the basis of a helicity codon defined by the (hyz-pym)
sequence. Hydrazone formation allows the facile self-assembly of such extended helical
entities. Their chemical stability, resulting probably from the tight packing within the

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Fig. 5. Schematic representation of the core helix of the polymeric helical strands 1 4 inscribed in a cylinder of
20-A diameter. The height indicated corresponds to a polymer of ca. 9000 Da presenting 12 turns; substituents
on the helix omitted for clarity.
spiral, makes them attractive frameworks for the helical arrangement of lateral
functional groups. On the other hand, it may be possible to introduce reversibility in the
self-assembly process by appropriate modification of the connecting groups, leading to
dynamic helical strands capable of assembling, dissociating, and exchanging compo-
nents, thus opening helical folding processes to constitutional dynamic chemistry [1].
¡
This work was supported by a doctoral fellowship from the Ministere de la Jeunesse, de la Recherche et de la
Technologie (J.-L.S.). We thank Dr. Franz J. Mayer-Posner (Bruker Daltonik GmbH) for help in mass-
spectroscopic measurements.

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Experimental Part
General. TLC: Polygram Sil G/UV254 pre-coated plastic sheets. Flash chromatography (FC): 230 400-mesh
silica-gel particles supplied by Merck. M.p.: B¸chi B-540 melting-point apparatus, uncorrected. 1H (200 or
400 MHz) and 13C-NMR spectra (50 or 100 MHz) were recorded on Bruker AC-200 or Avance-400
spectrometers, respectively; CDCl3 as solvent, unless otherwise noted, chemical shifts d are in ppm with a
residual solvent 1H peak as reference. Electron-ionization, fast-atom-bombardment mass spectra (FAB-MS)
¬
were recorded by the Service d×Analyse de l×Universite Louis Pasteur; MALDI-MS was carried out on a Bruker
Autoflex or on a Perseptive Biosystems Voyager Pro DE with dithranol as matrix.
4,6-Dimethyl-2-(3,4,5-trimethoxyphenyl)pyrimidine (8a). A soln. of 3,4,5-trimethoxybenzamidine hydro-
chloride (4 g, 16.2 mmol), acetylacetone (2.9 ml, 27.5 mmol), an K2CO3 (7.12 g, 51.5 mmol) in 25 ml of H2O was
stirred for 30 min and then left to stand for 3 d. The white precipitate was filtered, washed with H2O, dissolved in
1
CH2Cl2, and dried (MgSO4) to yield 8a (2.5 g, 56%). White solid. H-NMR (CDCl3, 400 MHz): 7.76 (s, 2 H);
6.92 (s, 1 H); 4.01 (s, 6 H); 3.93 (s, 3 H); 2.55 (s, 6 H). 13C-NMR (CDCl3, 100 MHz): 166.6; 163.5; 153.2; 133.6;
‡
117.8; 105.3; 60.9; 56.2; 32.41. FAB-MS: 275.2 (100, [M ‡ H] ).
2-(3,4,5-Trimethoxyphenyl)pyrimidine-4,6-dicarbaldehyde (8b). A soln. of 8a (0.50 g, 1.8 mmol) and SeO2
(0.44 g, 0.40 mmol) was refluxed in dioxane (15 ml) for 1 h under an Ar atmosphere. The hot soln. was filtered
and cooled, the solvent was then removed under reduced pressure, and the residue was purified by
chromatography (SiO2; CHCl3) to give 8b (50 mg, 9%). Yellow solid. M.p. 1658. 1H-NMR (CDCl3, 400 MHz):
10.20 (s, 2 H); 8.10 (s, 1 H); 7.91 (s, 2 H); 4.02 (s, 6 H); 3.96 (s, 3 H). 13C-NMR (CDCl3, 100 MHz): 192.1; 160.2;
‡
155.9; 153.6; 109.6; 105.8; 105.30; 61.0; 56.3. FAB-MS: 303.1 (100, [M ‡ H] ).
Synthesis of the Polymeric Strand 1 4. The same general procedures have been used for the synthesis of the
six polymeric strands 1 4, with a slight difference in the conditions for the N-H and the N-Me derivatives.
Typical procedures are described below.
Polymer 1-H. A soln. of 2-phenylpyrimidine-4,6-dicarbaldehyde (7; 50 mg, 0.23 mmol) and 4,6-dihydra-
zino-2-(3,4,5-trimethoxyphenyl)pyrimidine (6-H; 72 mg, 0.23 mmol) in 20 ml of CHCl3/EtOH 70 :30 (v/v) was
stirred at r.t. for 4 d. The soln. was concentrated to 10 ml, MeOH was added, and the precipitate was filtered and
washed with MeOH.
Polymer 1-Me. A soln. of 7 (50 mg, 0.23 mmol) and 4,6-bis(1-methylhydrazino)-2-(3,4,5-trimethylphenyl)-
pyrimidine (5-Me; 56 mg, 0.23 mmol) in 20 ml of CHCl3 was stirred at r.t. for 4 d. The soln. was concentrated to
10 ml, MeOH was added, and the precipitate was filtered.

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Received July 18, 2003