Single-stranded molecular helical assembly from a self-complementary squaramide compound

Article abstract of DOI:10.1021/cg401639g

A new helical crystal structure of a disquaramide compound has been solved by means of direct methods from powder X-ray diffraction data. It contains a racemic mixture of alternating clock/anticlockwise rotating helices which are formed through an unprecedented combination of strong squaramide-squaramide and amine-phenol interactions, both in a head-to-tail fashion.

Full text of DOI:10.1021/cg401639g

Communication
pubs.acs.org/crystal
Single-Stranded Molecular Helical Assembly from a Self-
Complementary Squaramide Compound
Anna Portell† and Rafel Prohens*,†
†Unitat de Polimorfisme i Calorimetria, Centres Científics i Tecnolog
̀
ics, Universitat de Barcelona, Baldiri Reixac 10, 08028 Barcelona,
Spain
S
* Supporting Information
ABSTRACT: A new helical crystal structure of a disquaramide compound has been
solved by means of direct methods from powder X-ray diffraction data. It contains a
racemic mixture of alternating clock/anticlockwise rotating helices which are formed
through an unprecedented combination of strong squaramide−squaramide and
amine−phenol interactions, both in a head-to-tail fashion.
he helix is one of the most important structural motifs in
cyclic and (b) polymeric, which could give rise to helical
Tnature due to its ubiquitous presence, from the molecular assemblies (Figure 1). In order to study this possibility, the
level to the astronomical scale.1 Helicity shows relevant
asymmetric disquaramide 1 was synthesized through a two-step
selective condensation of N,N-dimethylethylenediamine and
tyramine with diethylsquarate in mild conditions (Figure 1a).11
Unfortunately, no crystals of 1 suitable for structure
determination by single-crystal XRD could be obtained.
Therefore, its crystal structure12 was solved from laboratory
X-ray powder diffraction data13 by means of direct space
methods using the computing program FOX.14
properties such as chirality and other geometric features
which have attracted the attention of the scientific community.2
Examples of helicity include the double-stranded DNA and the
assembly of linear proteins into multistranded complexes which
are responsible for the genetic information and diverse
biological functions.3 This fascinating natural motif has inspired
the design and synthesis from unnatural backbones of a broad
variety of artificial helices in the fields of supramolecular
chemistry, asymmetric catalysis, biomimetics, etc.4 Thus, the
use of synthetic building blocks for the supramolecular
assembling into helical polymers5 has been successfully
exploited in the past with metal-coordinated helical complexes6
or self-assembled spiral nanoarchitectures from barbituric acid,7
among many others.8 In this sense, hydrogen-bonding is a key
interaction due to its great directionality and strength which
can be used to design highly stable and selective building blocks
able to cooperatively drive the formation of polymeric
assemblies.9
Disecondary squaramides form head-to-tail structures in the
solid state thanks to the very strong self-complementary CO···
HN intermolecular interaction which has been exploited
recently by us to build self-assembling zwitterionic squaramides
in the solid state.10 With the objective of synthesizing hydrogen
bonded assemblies with new topological features, we designed
the nonsymmetrical squaramide compound 1 with both donor
and acceptor terminal groups able to establish self-comple-
mentary hydrogen bonding interactions.
The experimental powder diffraction diagram was indexed
with DICVOL04,15 and the space group (P21/c) was deduced
from the systematic absences. The presence of some impurities
in the diffractogram hindered the indexing procedure. In
accordance with the spectroscopic data (NMR-C, NMR-H)
together with DSC and TGA curves, these impurities could be
attributed to a squaramide ester generated in the first step of
the synthesis (Figure 1). The cell and space group were
validated with a Le Bail fit of the data using FullProf16
(goodness of fit: Chi2 = 2.83, Rwp: 12.4). The used background
(estimated from a set of experimentally read points and
interpolated) and the resulting cell, zero error and shape
parameters of the Le Bail fit were used in the structure solution
procedure with FOX. The structure was solved using the
parallel tempering algorithm implemented in FOX. The Z
matrix was created with an optimized model by using
SPARTAN,17 and FOX was instructed to treat cyclobutene
and phenol rings as rigid bodies. Three runs of two million
Received: November 2, 2013
Revised: December 13, 2013
Published: December 16, 2013
Assuming that the head-to-tail interaction can act as a
template, in principle two types of interactions are possible: (a)
© 2013 American Chemical Society
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Figure 1. Synthesis of 1 and the different schematic self-assembling modes.
Figure 2. Results of final Rietveld refinements of 1. Each plot shows
the experimental powder XRD profile (red + marks), the calculated
powder XRD profile (black solid line) and the difference profile (blue,
lower line).
Figure 3. Intermolecular H-bonds in the helix building block.
giving place to a head-to-tail motif which acts as a skeletal
template in the formation of peripheral amine−phenol
interactions. The most remarkable feature of the structure is
that discrete infinite helical assemblies are formed from this
repetitive building block running in the direction of the
squaramide dipole moment (Figure 3). The helices are formed
in an antiparallel orientation, compensating the strong dipole
moment of the squaramide ring in the crystal.
trials each were performed and lead rapidly to a low overall cost
function. The resulting structural models showed the same self-
assembled synthon, and the best resulting crystal structure was
the basis for subsequent Rietveld refinement18 with Fullprof
(see Figure 2).
X-ray crystallographic characterization revealed that 1
crystallizes in monoclinic system with space group P21/c and
one molecule in the asymmetric unit. As expected, the strong
CO···HN self-complementary interaction19 is established,
Helices are individually packed (following model a in Figure
1), connected to others through weak CH···π interactions
between the methylamino group and the aromatic ring,20 with
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Communication
Although helical assemblies from an achiral compound as 1
can a priori form chiral crystals, a racemic mixture of alternating
clock and anticlockwise spinning helices has been found
(Figure 6) and no polymorphism has been observed so far.
In summary, we have studied via X-ray crystallography an
unprecedented helix in a squaramide driven by a combination
of two different head-to-tail interactions, which is remarkable in
the field of crystal engineering and supramolecular chemistry.
The good geometrical and donor/acceptor complementarity
produces an optimal packing, which excludes the possibility of
cavity formation. However, the introduction of more suitable
substituents of the squaramide ring should permit the design of
new helical hydrogen-bonded nanotubes based on the same
strategy.
ASSOCIATED CONTENT
* Supporting Information
CIF file. This material is available free of charge via the Internet
Figure 4. Helix-packing motifs via CH···π interactions.
■
S
at http://pubs.acs.org.
AUTHOR INFORMATION
Corresponding Author
*E-mail: rafel@ccit.ub.edu.
■
Notes
The authors declare no competing financial interest.
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Crystal Growth & Design
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