Folding of coordination polymers into double-stranded helical organization

Article abstract of DOI:10.1002/chem.200800056

Self-assembling coordination polymers based on Pd^II and Cu ^II metal ions were prepared from complexation of a bent-shaped bispyridine ligand and a corresponding transition metal. These coordination polymers were observed to self-assemble into supramolecular structures that differ significantly depending on the coordination geometry of the metal center. The polymer based on Pd^II self-assembles into a layer structure formed by bridging bispyri dine ligands connected in a trans-position of the square-planar coordination geometry of metal center. In contrast, the polymer based on Cu^II adopts a double-helical conformation with regular grooves, driven by interstranded, copper-chloride dimeric interaction. The double-stranded helical organization is further confirmed by structure optimization from density functional theory with aromatic framework, showing that the optimized double-helical structure is energetically favorable and consistent with the experimental results. These results demonstrate that weak metal-ligand bridging interactions can provide a useful strategy to construct stable double-stranded helical nanotubes.

Full text of DOI:10.1002/chem.200800056

FULL PAPER
DOI: 10.1002/chem.200800056
Folding of Coordination Polymers into Double-Stranded Helical
Organization
Ho-Joong Kim,[a] Eunji Lee,[a] Min GyuKim, [b] Min-Cheol Kim,[a] Myongsoo Lee,*[a] and
Eunji Sim*[a]
Abstract: Self-assembling coordination
polymers based on PdII and CuII metal
ions were prepared from complexation
of a bent-shaped bispyridine ligand and
a corresponding transition metal. These
coordination polymers were observed
to self-assemble into supramolecular
structures that differ significantly de-
pending on the coordination geometry
of the metal center. The polymer based
dine ligands connected in a trans-posi-
tion of the square-planar coordination
geometry of metal center. In contrast,
the polymer based on CuII adopts a
double-helical conformation with regu-
lar grooves, driven by interstranded,
copper–chloride dimeric interaction.
The double-stranded helical organiza-
tion is further confirmed by structure
optimization from density functional
theory with aromatic framework, show-
ing that the optimized double-helical
structure is energetically favorable and
consistent with the experimental re-
sults. These results demonstrate that
weak metal–ligand bridging interac-
tions can provide a useful strategy to
construct stable double-stranded helical
nanotubes.
Keywords: coordination polymers ·
helical structures · self-assembly ·
supramolecular chemistry
on PdII self-assembles into
a layer
structure formed by bridging bispyri-
Introduction
can be constructed by the complexation of two oligomeric li-
gands twisted around metal ions,[4] attractive p–p interac-
tions between two single strands,[5] and complementary in-
teractions between two different strands.[6]
One of the most significant recent highlights in the field of
supramolecular polymer chemistry is the development of
folded helical structures, which are important modules in
the engineering of functional nano-sized objects, such as
nanotubes, nanowires, and chiral materials.[1] In most cases,
however, the supramolecular interactions lead to the forma-
tion of polymeric strands that fold into single helical confor-
mations.[2] Because only a few supramolecular polymers
have been reported to form infinite double-stranded heli-
ces,[3] the development of supramolecular double helices
structurally comparable to those of DNA is a challenging
topic of current research. Double-stranded helical structures
Previous publications from our laboratory have shown
that extended polymeric chains formed from complexation
between bent-shaped ligands and silver cations with a linear
coordination geometry can give rise to a helical secondary
structure depending on the size of the counter anion.[7] In
addition, these helical polymers showed the dynamic confor-
mational change from the nonfluorescent compressed state
to the fluorescent stretched state, triggered by tempera-
ture.[8] One can envision that the coordination geometry of
the metal center has influence on the secondary structure of
coordination polymers.[9] With this in mind, we have pre-
pared coordination polymers based on PdII and CuII ions,
which are known to adopt a square-planar coordination ge-
[a] H.-J. Kim, E. Lee, M.-C. Kim, Prof. Dr. M. Lee, Prof. Dr. E. Sim
Center for Supramolecular Nano-Assembly and
Department of Chemistry
AHCTREUNG
Yonsei University, Seoul 120-749 (Korea)
Fax : (+82)2-393-6096
E-mail: mslee@yonsei.ac.kr
stranded helical structure from coordination polymers,
driven by interstranded metal–ligand dimeric interactions.
The coordination polymers are based on PdII (1) and CuII
(2) metal ions, prepared from complexation of a conforma-
tionally flexible, meta-linked bispyridine ligand containing a
flexible dendritic side group and a corresponding transition
metal. The polymer based on PdII self-assembles into an un-
esim@yonsei.ac.kr
[b] Dr. M. G. Kim
Pohang Accelerator Laboratary
Pohang University of Science and Technology
Pohang 790-784 (Korea)
Supporting information for this article is available on the WWW
under http://www.chemeurj.org/ or from the author.
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folded zigzag conformation that organizes into a layered
structure. In contrast, the polymer based on CuII adopts a
double-helical conformation that organizes into a two-di-
mensional lattice, even though the coordination geometry of
Cu complex is an essentially similar square-planar structure
to that of Pd complex.
Results and Discussion
Synthesis and characterization: The synthesis of a bispyri-
dine ligand containing a dendritic side chain started with a
stepwise fashion according to the procedures described pre-
viously.[7] The resulting ligand
was treated with [PdCl2-
(PhCN)2] or CuCl2 to afford the
PdII (1) or CuII (2) coordination
polymers, respectively. They
were characterized by 1H and
13C NMR spectroscopy, elemen-
tal analysis, and matrix-assisted
laser
desorption
ionization
Figure 1. Top: X-ray diffraction pattern of 1. Bottom: TEM image of an
ultramicrotomed film of 1 revealing layered structures of alternating
light-colored dendritic, and dark aromatic layers.
time-of-flight (MALDI-TOF)
mass spectrometry and were
shown to be in full agreement
with the structures presented.
Both polymers were birefrin-
gent waxy solids that are readi-
ly soluble in common organic
solvents such as CH2Cl2, THF, EtOH and water. The solid-
state structures of the polymers were investigated by X-ray
scattering. Small-angle X-ray scattering (SAXS) measure-
ments of 1 showed several sharp reflections corresponding
to a 1D lamellar structure with in-plane 2D order with a
layer thickness of 3.6 nm (Figure 1, top). This structural
identification was further confirmed by transmission elec-
tron microscopy (TEM) experiments that showed dark or-
ganized aromatic layers with a lattice dimension of approxi-
mately 4 nm (Figure 1, bottom). The lamellar structure with
this dimension indicates that the coordination polymer back-
bone of 1 adopts an unfolded zigzag conformation that or-
ganizes into a layered structure (Figure 2). Bridging bispyri-
dine ligands connected in the trans-position of the square-
planar coordination geometry of PdII generates unfolded po-
lymer chains.[9a,11]
Figure 2. Schematic representation for the formation of the lamellar
structure of 1.
information on the structural dimensionality of 2 was ob-
tained by 2D X-ray diffraction with a sheared sample exhib-
iting macroscopic orientation. As shown in Figure 4, the re-
flections at wide angles were diffracted at an angle of 708
with respect to the SAXS scattering, indicative of the pres-
ence of a periodicity together with an additional order along
the direction of the column axis.
To further corroborate the structural features of the coor-
dination polymer, extended X-ray absorption fine structure
(EXAFS) experiments were performed with 2 at ambient
temperature. As shown in Figure 5, the profile revealed sev-
eral peaks at 2.2, 3.5, and 4.4 Š, that can be indexed as
In great contrast to polymer 1, CuII coordination polymer
2 self-assembles into a 2D oblique columnar structure with
lattice constants of a=4.9 nm, b=4.2nm and g=1228, as
identified by SAXS patterns (Figure 3, top). The evidence
for the formation of the 2D oblique columnar structure was
also provided by a TEM image that shows a 2D array of
dark domains in a matrix of light aliphatic segments with di-
mensions of 4 and 5 nm, which is consistent with the results
obtained from the SAXS (Figure 3, bottom). Another inter-
esting point to be noted is the presence of two sharp reflec-
tions at the wide angles, corresponding to d-spacings of 0.88
and 0.55 nm, respectively (Figure 3, top inset). Additional
À
À
À
Cu(1) Cl(1), Cl(1) Cu(2), and Cu(1) Cu(2) scatterings, re-
À
spectively. In particular, the Cu Cu distance at 4.4 Š was
also identified by the WAXS pattern.[12] All of these scatter-
ing peaks are consistent with the values for the pseudo-
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Chem. Eur. J. 2008, 14, 3883 – 3888

Coordination Polymers
FULL PAPER
square-planar, chloro-bridged dimers formed through weak
axial coordination to one copper center by a chloride ligand
located at the adjacent copper atom.[13] It is worth noting
À
that, considering the Cl(1) Cu(2) distance (0.35 nm) togeth-
er with the WAXS peak at 0.88 nm associated with a pitch,
an additional X-ray diffraction peak at 0.55 nm can be de-
scribed as the width of a groove along the direction of
column axis. From the lattice constants and the density, the
number of repeating units per pitch was calculated to be
4.2units. [7a,14] Considering the interstrand, copper–chloride
dimeric interactions, this calculated number indicates that
the columns are based on double-stranded helical chains.
On the basis of the results described thus far, it can be
concluded that the CuII coordination polymer chains adopt a
double-stranded helical conformation with a regular pitch of
0.94 nm (deduced from 0.88 nm/sin 708) together with a
groove of 0.55 nm in width (Figure 6). Subsequently, the
Figure 3. Top: X-ray diffraction patterns of 2. Bottom: TEM image of ul-
tramicrotomed film of 2 revealing 2D oblique columnar array of aromatic
core.
Figure 6. Schematic representation of the double-stranded helical struc-
ture of 2.
double-stranded helices self-organize into a 2D oblique col-
umnar structure. These results show how the complexation
of the bent-shaped bispyridine ligand with a CuII metal ion
and a pseudo-square-planar coordination geometry could
lead to folded double-stranded helical polymers through
complementary dimeric interactions. Considering that in the
absence of the metal–chloride bridging interactions com-
pound 1 self-assembles into a layered structure consisting of
an unfolded zigzag conformation, the dimeric association
through metal–chloride bridging interactions in the CuII co-
ordination polymer seems to be essential for the formation
of a double-stranded helical structure. Indeed, inspection of
CPK models revealed that a cisoid double-helical conforma-
tion of two polymer chains maximizes these dimeric interac-
tions (see Figure S4 in the Supporting Information).
Figure 4. 2D X-ray diffraction patterns of 2. The inset image shows the
2D small angle X-ray diffraction pattern.
In an effort to provide further evidence for the key influ-
ence of the dimeric association on the formation of a
double-helical structure, we synthesized homologous CuII
complex 3 containing a methyl group on the ortho-position
of pyridyl unit that is expected to prevent the copper–chlo-
Figure 5. EXAFS profile of 2 and the peak assignments.
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M. Lee, E. Sim et al.
ride dimeric association due to steric crowding (Figure 7).[15]
In contrast to 2, the resulting coordination polymer showed
to self-assemble into a layered structure (Figure 7 and
complex 4.[16] It should be noted that, similar to 2, the model
complex exhibited the three strong reflections at the wide
angles, corresponding to helical pitch of 0.88, groove width
of 0.55, and p–p stacking distance of 0.35 nm, respectively,
demonstrating that model complex 4 also adopt a double-
helical conformation with the same dimensions as those of 2
(Figure 9). Structural modeling was performed by density
Figure 7. Molecular structure and X-ray diffraction patterns of 3.
Figure 8, bottom), suggesting that the coordination geome-
try of CuII consists of a separated square-planar structure.
Furthermore, the EXAFS profile showed no peak corre-
Figure 9. Molecular structure and X-ray diffraction pattern of 4.
functional theory (DFT) by using SIESTA (Spanish Initia-
tive for Electronic Simulation of Thousands of Atoms).[17]
To mimic periodic structure, the computation unit cell was
chosen to contain two turns of double-stranded helix com-
posed of eight monomers with 296 atoms. Atom-centered
and strictly confined numerical functions were used as a
basis set for solving the Kohn–Sham equations.[18] Norm-
conserving pseudopotentials were constructed within im-
proved Troullier-Martins scheme.[19] The electron configura-
tions of used pseudopotentials with pseudoionization radii
are given in Table 1 (given in Bohr). We used a double-z
Table 1. Pseudoionization radii used for pseudopotentials.
Atom
Pseudoionization radius [Bohr]
Cu
Cl
C
4s1 (2.05) 4p0 (2.30) 3d10 (2.05) 4f0 (2.05)
3s2 (1.74) 3p5 (1.74) 3d0 (1.74) 4f0 (1.74)
2
2
2 (1.25) 2p2
2 (1.24) 2p3
C
s
s
N
basis set for all atoms except Cu and Cl. While double-z po-
larization orbitals were used for both Cu and Cl, relativistic
effects were taken into account only for Cu. The exchange-
correlation was treated in GGA-PBE.[20] We performed a
full optimization of the double-stranded helical structure by
means of conjugate gradients allowing unit cell variation.
The optimized structure is consistent with the double-strand-
ed helical conformation predicted experimentally as shown
in Figure 10. Table 2shows that the geometric parameters
for the double-helical system obtained from our simulations
are in good agreement with the experimental profiles. In
Figure 8. Top: EXAFS profile of 3 and the peak assignments. Bottom:
TEM image of ultramicrotomed film of 3 revealing layered structures of
alternating light dendritic, and dark aromatic layers.
À
sponding to a Cu(1) Cl(2) scattering at 3.5 Š (Figure 8,
top). These results further support that the double-helical
conformation is attributed to the metal–chloride bridging di-
meric association.
À
particular, the Cu(1) Cl(2) dimeric interaction distance was
À
Computational structure modeling: To provide further infor-
mation on the formation of a double-stranded helical organ-
ization, computational modeling was performed with model
reproduced excellently as well as the Cu(2) Cu(1)’ groove
with respect to the values obtained from the X-ray diffrac-
tion pattern given in Figure 9.
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Coordination Polymers
FULL PAPER
AHCTREUNG
Techniques: 1H NMR spectra were recorded in CDCl3 on a Bruker AM
250 spectrometer. The purity of the products was checked by thin-layer
chromatography (TLC; Merck, silica gel 60); visualization was achieved
with UV light and iodine vapor. A Nikon optical polarized microscopy
(magnification: 100) equipped with a Mettler FP 82hot-stage and a Met-
tler FP 90 central processor was used to observe the thermal transitions
and to analyze anisotropic texture. Microanalyses were performed with a
Perkin Elmer 240 elemental analyzer at Organic Research Center,
Sogang University. X-ray scattering measurements were performed in
transmission mode with synchrotron radiation at the 3C2and 10C1 X-ray
beam line at the Pohang Accelerator Laboratory (Korea). The scattered
X-rays were detected on imaging plates for better 2D-XRD resolution.
The orientationally ordered domain of complex 2 was obtained by shear-
ing the sample on a kapton film. The long axis of resulting columns was
aligned in the direction of shear. To reduce air-scattering, a vaccum
chamber made of kapton film was placed between sample and detector.
Extended X-ray absorption fine structure (EXAFS) spectra were per-
formed at the 7C1 beam line at the Pohang Accelerator Laboratory
(Korea). MALDI-TOF mass spectra were performed on Perceptive Bio-
systems Voyager-DE STR by using a 2,5-dihydroxy benzoic acid matrix.
The transmission electron microscope (TEM) was performed at 120 kV
using JEOL-JEM 2010. Ultrathin sectioning of specimens was performed
by cryoultramicrotomy using a RMC PowerTome-XL. Before the ultra-
thin sectioning, the samples were aligned by annealing at 808C for 10 h.
Figure 10. Left: Optimized structure of double-stranded helix unit cell
(Cl atoms are not shown for clarity). Right: dimeric unit of 4.
Table 2. Comparison of relevant geometrical parameters [Š].
Bond length
Calculated[a] [Š]
Experimental [Š]
À
Cu(1) N(1)
1.8
2.1
4.4
3.4
5.3
1.9
2.2
4.4
3.5
5.5
À
Cu(1) Cl(1)
À
Cu(1) Cu(2)
À
Cu(1) Cl(2)
À
Cu(2) Cu(1)’
[a] Average values.
Thin sections of the specimen were transferred to
a carbon-coated
copper grid. Compounds were synthesized according to the procedure de-
scribed Scheme S1 and S2in the Supporting Information and then puri-
fied by silica gel column chromatography and preperative HPLC (Japan
Analytical Instrument). CPK models were computed with Materials
Studio Modeling 3.0 (Accelrys Inc.) software.
Conclusion
A bent-shaped bipyridine ligand containing a dendritic ali-
phatic side chain has been synthesized and forms complexes
with PdII and CuII through a self-assembly process. These
complexes were observed to self-assemble into ordered
structures that differ significantly depending on the coordi-
nation geometry of the metal center in the solid state. The
polymer based on PdII self-assembles into layer structure
formed by bridging bispyridine ligands connected in a trans-
position of the square-planar coordination geometry of
metal center. In contrast, the polymer based on CuII adopts
double-helical conformations with regular grooves along the
helical axis, through the metal–chloride dimeric interactions.
These notable conformations are attributed to the pseudo-
square-planar chloro-bridged dimers formed through weak
axial coordination to one copper center by a chloride ligand
located at the adjacent copper atom. It is also notable that
the double-stranded helices self-organize into a 2D colum-
nar structure in the bulk state. These results represent a
unique example that weak metal–ligand bridging interac-
tions can provide a useful strategy to construct stable
double-stranded helical nanotubes.
Acknowledgements
This work was supported by the National Creative Research Initiative
Program of the Korean Ministry of Science and Technology. Partial sup-
port was provided by the Korea Science and Engineering Foundation
(KOSEF-R01-2007-000-11831-0, E.S.). E.L. thanks the Seoul Science Fel-
lowship Program, H.-J.K. and E.L. acknowledge a fellowship of the
BK21 program from the Ministry of Education and Human Resources
Development.
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Received: January 11, 2008
Published online: April 7, 2008
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