Molecular Assemblies of Metal Complexes via Base-Pairing of Nucleic Acids in the Crystalline State

Article abstract of DOI:10.1002/chem.201700593

The nature of the molecular assemblies formed in the crystalline state by cobalt(II) terpyridine (terpy) complexes incorporating appended adenine (A) or thymine (T) bases was found to be controlled by which bases are present. Single-crystals of the cobalt(II) complexes [Co(A-C6-terpy)₂](BF₄)₂ (1) and [Co(T-C6-terpy)₂](BF₄)₂ (2) have needle and block habits, respectively. Subsequent mixing of 1 and 2 in MeOH resulted in isolation of [Co(A-C6-terpy)_1.5(T-C6-terpy)_0.5](BF₄)₂ (3) as plate-like crystals. A 3D network structure is present in 1 that incorporates 1D chains, whereas 2 adopts a 2D stacked structure constructed from ladder-type assemblies. For 3, “dimer-rings” consisting of [Co(A-C6-terpy)₂]²⁺ and [Co(A-C6-terpy)(T-C6-terpy)]²⁺ units are generated by means of base-pairing between A and T. Notably, 3 displays the first crystal structure of a heteroleptic cobalt(II) complex of [Co(A-C6-terpy)(T-C6-terpy)](BF₄)₂. These assembly differences involving the terpyridine cobalt(II) complex units in 1–3 affect the cooperativities influencing their spin crossover (SCO) behavior. The influence of the terminal nucleobases on the resulting assembly has been probed by investigating the co-crystallization of [Co(terpy)₂](BF₄)₂ (4) with [Co(C6-terpy)₂](BF₄)₂ (5) and 1 with 5.

Full text of DOI:10.1002/chem.201700593

A Journal of
Accepted Article
Title: Molecular Assemblies of Metal Complexes via Base Pairing of
Nucleic Acids in the Crystalline State
Authors: Manabu Nakaya, Ryo Ohtani, Kunihisa Sugimoto, Masaaki
Nakamura, Leonard F Lindoy, and Shinya Hayami
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To be cited as: Chem. Eur. J. 10.1002/chem.201700593
Link to VoR: http://dx.doi.org/10.1002/chem.201700593
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Molecular Assemblies of Metal Complexes via Base Pairing of
Nucleic Acids in the Crystalline State
Manabu Nakaya,[a] Ryo Ohtani,[a] Kunihisa Sugimoto,[b] Masaaki Nakamura,[a] Leonard F Lindoy,[c] and
Shinya Hayami*[a, d]
Abstract: The nature of the molecular assemblies formed in the
crystalline state by cobalt(II) terpyridine complexes incorporating
appended adenine (A) or thymine (T) bases was found to be
controlled by which bases are present. Single-crystals of the
cobalt(II) complexes [Co(A-C6-terpy)2](BF4)2 (1) and [Co(T-C6-
terpy)2](BF4)2 (2) have needle and block habits, respectively.
Subsequent mixing of 1 and 2 in MeOH resulted in isolation of
[Co(A-C6-terpy)1.5(T-C6-terpy)0.5](BF4)2 (3) as plate-like crystals. A 3-
D network structure is present in 1 that incorporates 1-D chains,
while 2 adopts a 2-D stacked structure constructed from ladder-type
assemblies. For 3, “dimer-rings” consisting of [Co(A-C6-
terpy)2](BF4)2 and [Co(A-C6-terpy)(T-C6-terpy)](BF4)2 units are
generated via base-pairing between A and T. It is noteworthy that 3
displays the first crystal structure of a heteroleptic cobalt(II) complex
of [Co(A-C6-terpy)(T-C6-terpy)](BF4)2. These assembly differences
involving the terpyridine cobalt(II) complex units in 13 affect the
cooperativities influencing their SCO behaviour. The influence of the
terminal nucleobases on the resulting assembly has been probed by
investigating the co-crystallization of [Co(terpy)2](BF4)2 (4) with
[Co(C6-terpy)2](BF4)2 (5) and 1 with 5.
macroscopic supramolecular structures such as DNA origami
have been constructed;[1] functional materials for active release
of drugs[2] and chemical sensing devices have also been
obtained.[3] Related approaches to the construction of metal-
coordinated systems have demonstrated a precise control of
metal ion arrays in solution.[4] The molecular recognition
between individual nucleobases provides a potential driving
force for assembling metal complex molecules, not only in
solution but also in the solid state, thus providing a strategy for
controlling metal complex structure/function properties in the
crystalline state. Application of this strategy involves three steps:
1) the introduction of nucleobases such as A and T into organic
ligands as terminal substituents, 2) formation of corresponding
metal complexes and 3) subsequent mixing of these complexes
to yield mixed ligand species incorporating, in the above case,
both A and T ligand derivatives. The latter product was
anticipated to exhibit different assembly behaviour to those
occurring in the respective single component crystals. Although
metal complexes incorporating nucleobase functional groups
have been synthesized previously,[5] investigation of their co-
crystallization with spontaneous base pairing has been limited.[6]
The present approach provides a facile route to a new class of
interesting metal-complex based crystalline materials.
Introduction
In this study, the A and T bases modified with attached alkyl
chains are present as substituents on the terpyridine cobalt(II)
complexes. The alkyl chains act as flexible spacers. Related
long-chain terpyridine complex and other terpyridine complex
derivatives have been shown to display interesting new physical
properties such as spin crossover (SCO) phenomena,[7] redox
activities[8] and photo luminescence[9] that depend on both the
metal ion species involved and the nature of the substituent
groups present. In particular, the SCO behaviour of cobalt(II)
ions is sensitive to a difference in cooperativity associated with
the intermolecular interactions present in crystals. In the
discussion that follows the effects of assembly changes due to
the presence of different combinations of A and T base pairs on
the cooperativity is presented in terms of their different SCO
behaviour.
Cobalt(II) complexes of type [Co(R-C6-terpy)2](BF4)2 (R = A (1)
and T (2), C6-terpy = 4’-hexyloxy-2,2’:6’,2”-terpyridine) (see
Scheme 1) were synthesized and, subsequently, a co-crystal of
type [Co(A-C6-terpy)1.5(T-C6-terpy)0.5](BF4)2 (3) was obtained by
recrystallization of a 1:1 mixture of 1 and 2 from MeOH. Single
crystal X-ray structural analysis on this product showed that the
terminal nucleobases of 13 are connected via hydrogen
The DNA nucleobases adenine (A), thymine (T), cytosine (C)
and guanine (G) have attracted much attention in both biology
and chemical biology. In biological systems, partner bases
recognize each other so as to form beautiful helixes via
intermolecular hydrogen bonding and  -  stacking. By means
of artificial programming of their sequences, micro- or
[a]
M. Nakaya, Dr. R. Ohtani, Dr. M. Nakamura, Prof. S. Hayami
Department of Chemistry
Graduate School of Science and Technology
Kumamoto University, 2-39-1, Kurokami, Chuo-ku
Kumamoto 860-8555 (Japan)
E-mail: Hayami@sci.kumamoto-u.ac.jp
Dr. K. Sugimoto
[b]
Research & Utilization Division,
Japan Synchrotron Radiation Research Institute
1-1-1, Kouto, Sayo-cho, Sayo-gun
Hyogo 679-5198 (Japan)
[c]
[d]
Prof. L. F. Lindoy
School of Chemistry
The University of Sidney
NSW 2006 (Australia)
Prof. S. Hayami
Institute of Pulsed Power Science (IPPS)
Kumamoto University, 2-39-1, Kurokami, Chuo-ku
Kumamoto 860-8555 (Japan)
bonding and
 -  interactions. The different assembly
arrangements were found to impact on the cooperativity
influencing their SCO behaviour (as revealed by regular solution
models). Clarification of the role of the nucleobase substituents
in these systems was probed by investigating the co-
Supporting information for this article is given via a link at the end of
the document. CCDC-1496071, -1496072, -1497324 contain the
supplementary crystallographic data.
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crystallization of [Co(terpy)2](BF4)2 (4) with [Co(C6-terpy)2](BF4)2
(5) and 1 with 5.
Å (Figure 2(b)). The form of this base pair is categorized as a
Hoogsteen base pairing model.[11] These N---H interaction
networks resulted in formation of a 1-D chain incorporating
terpyridine units of 1 (Figure 2(b)). The 1-D chains extend along
the a axis (green structures in Figure 2(c)) and b axis (red
structures in Figure 2(c)). There is inter-chain  -  interactions
between adenine substituents with a separation of 3.34 Å
(Figure 2(c)). Moreover, the respective (green and red) chains
are inter-locked at their crossover points to produce a 3-D
network assembly structure (Figure 2(d)).
R =
Adenine (A)
Thymine (T)
R-C6-terpy
Scheme 1. A-C6-terpy and T-C6-terpy ligands.
(a)
N15
N7
N9
Co
N1
N16
N8
N10
Results and Discussion
N2
N3
N11
The two terpyridine ligand derivatives, A-C6-terpy and T-C6-
terpy, were prepared using minor modifications of previously
reported literature methods[10] (See Supporting Information: SI).
[Co(A-C6-terpy)2](BF4)2 (1) and [Co(T-C6-terpy)2](BF4)2 (2) were
synthesized by mixing Co(BF4)2·6H2O with A-C6-terpy for 1 and
with T-C6-terpy for 2 in MeOH. Needle and block shape crystals
of 1·0.5H2O·MeOH and 2·3H2O were obtained, respectively,
following recrystallization from MeOH (Figure 1). Subsequently,
methanol solutions of a 1:1 mixture of 1 and 2 were mixed and
(b) o
c
c
2.36 Å
b
H5
N16
H10
N8
2.36 Å
(c) o
(d)
c
c
3.34 Å
stirred at 60 ̊C for a few minutes resulting in formation of co-
a
crystals of type [Co(A-C6-terpy)1.5(T-C6-terpy)0.5](BF4)2 (3).
Orange plate-like crystals of 3 were obtained on recrystallization
of the initial product from MeOH (Figure 1). These compounds
were fully characterized by elemental analyses, MS spectra and
single crystal X-ray diffraction (XRD) measurements.
Figure 2. (a) Molecular structure of 1·0.5H2O·MeOH. (b) 1-D chain structure of
1·0.5H2O·MeOH and hydrogen bonding between adenine moieties. (c)
Packing structure of 1·0.5H2O·MeOH. Green indicates the 1-D chain along the
a axis and red indicates the chain along the b axis. (d) Schematic figure
showing the packing structure of 1·0.5H2O·MeOH. Hydrogen atoms, counter
anions and solvent molecules are omitted for clarity. Colour code: Magenta,
Co; red, O; blue, N; grey, C.
1 (needle)
2 (block)
3 (plate)
2·3H2O crystallized in the monoclinic space group P21/c. The
molecular structure of 2 is shown in Figure 3(a). The Co-N bond
lengths are Co-N(1) = 2.157(4) Å, Co-N(2) = 1.994(3) Å, Co-N(3)
= 2.172(4) Å, Co-N(6) = 2.084 (4) Å, Co-N(7) = 1.969(3) Å and
Co-N(8) = 2.075(4) Å, respectively. Terpyridine complexes in 2
are dimerized via a hydrogen bond (1.93 Å, NH - O) between the
respective terminal thymine substituents (Figure 3(b)). This form
of thymine pair is categorized as a reverse Watson and Crick
(W-C) base pairing model.[11] Such dimers are assembled along
the a axis via inter-dimer hydrogen bonds (2.65 Å) between NH
and CH3 groups in adjacent thymine molecules as well as by  -
 interactions (3.49 Å) between pyridine rings on adjacent
terpyridine ligands (Figure 3(b)), resulting in the formation of
ladder-type assembly structures in the ab plane (Figure 3(b)).
These ladders are stacked along the c axis through CH - 
interactions between alkyl chain CH groups and pyridine rings
(2.80 Å) together with hydrogen bonds (2.50 Å) between the
Figure 1. Crystal images of 1, 2 and 3.
Single crystal XRD measurements for 1·0.5H2O·MeOH and
2·3H2O were performed at 100 K, while the structural analysis of
3·3H2O was carried out at 90 K. Crystal parameters for the three
compounds are shown in Table S1 (Supporting Information: SI).
1·0.5H2O·MeOH crystallized in the tetragonal space group
P41212. The molecular structure of 1 is shown in Figure 2(a).
The Co-N bond lengths are Co-N(1) = 2.080(5) Å, Co-N(2) =
1.931(4) Å, Co-N(3) = 2.075(5) Å, Co-N(9) = 2.118(5) Å, Co-
N(10) = 1.940(4) Å and Co-N(11) = 2.091(5) Å. Two terminal
adenine substituents are oriented in the same direction as
shown in Figure 2(a), and their NH2 groups face in the opposite
direction. Each of these NH2 groups interact with a NH2 group
from a neighbouring complex by intermolecular N---H interaction
with distances of N(8)---H(10) = 2.36 Å and N(16)---H(5) = 2.36
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thymine CH3 substituents and the O atoms linking the alkyl
chains to the terpyridine units (Figure 3(c) and (d)).
for crystals of 3 resulted in the incorporation of A-C6-terpy and
T-C6-terpy ligands into the co-crystals with a ratio of 1:1. Their
conflicting results indicate that a different co-crystal of [Co(A-C6-
terpy)0.5(T-C6-terpy)1.5](BF4)2 also precipitated at the same time
as the formation of 3. It is noteworthy that [Co(A-C6-terpy)(T-C6-
terpy)](BF4)2 in the dimer ring is the first crystal structure of a
heteroleptic cobalt(II) complex.
(a)
O3
N1
Co
N5
N6
O2
N7
N2
N8
N3
O5
O6
Disordering of adenine (A)
and thymine (T)
N10
(a)
(b)
o
b b
adenine (A)
1.93 Å
a
N1
N9
3.49 Å
3.49 Å
2.65 Å
N10
N2
Co
N3
N11
(b)
A
A
1.93 Å
2.65 Å
T
(c)
(d)
o
b
A
b
c
(c)
(d)
b
o
c
a
・
・
・
=
・
・
・
Figure 3. (a) Molecular structure of 2·3H2O. (b) Ladder type assembly
structure of 2·3H2O. (c) Packing structure of 2·3H2O. (d) Schematic figure
showing the packing structure of 2·3H2O. Hydrogen atoms, counter anions
and solvent molecules are omitted for clarity. Colour code: Magenta, Co; red,
O; blue, N; grey, C.
Figure 4. (a) Molecular structure of 3·3H2O. (b) “Dimer ring” in 3. (c) 2-D
structure of 3. (d) Schematic figure showing the packing structure of 3.
Hydrogen atoms, counter anions and solvent molecules are omitted for clarity.
Colour code: Magenta, Co; red, O; blue, N; grey, C.
The different molecular assemblies in 13 affect the
cooperativity influencing their SCO behaviour. Magnetic
susceptibility measurements for 13 were performed using
SQUID (Figure 5). In order to estimate the cooperativity of SCO
behaviour, the experimental χmT versus T curves (χm; molar
magnetic susceptibility, T; temperature) were simulated by
applying the regular solution model (see experimental
section).[12] The simulated parameters are shown in Table 1. The
calculated cooperativity factor (C) are 0.34 for 1, 0.48 for 2, and
0.017 for 3, respectively. These different values reflect the
different assembly arrangements of the terpyridine units in the
respective structures. As mentioned previously, in the case of 1
the 3-D network structure is composed of 1-D chains, while 2
In the X-ray structure determination of 3·3H2O, terminal
substituents were found to be disordered. The assembly
crystalizes in the triclinic space group P-1, which is different from
that obtained for 1 and 2. The molecular structure of 3 is shown
in Figure 4(a). One terpyridine ligand is A-C6-terpy, while the
other is displayed as the disordered model incorporating A-C6-
terpy and T-C6-terpy at a ratio of 1:1. The terpyridine units in 3
are dimerized by an intermolecular interaction between terminal
substituents, resulting in formation of a “dimer ring” that consists
of respective [Co(A-C6-terpy)2](BF4)2 and [Co(A-C6-terpy)(T-C6-
terpy)](BF4)2 complexes as shown in Figure 4(b). Both base
pairs of AA and AT are categorized as a W-C base pairing
model.[11] These dimer rings are assembled in turn to form 2-D
structures that stack with a half-phase shift (Figures 4(c) and (d)).
Unlike this X-ray structural analysis for 3, an elemental analysis
has
a stacked structure of 2-D ladders, with the latter
incorporating intermolecular interactions between terpyridine
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cores, giving rise to a higher cooperative SCO behaviour than
occurs for 1. On the other hand, the extended structure of 3
involves “dimer rings” with no inter-terpyridine core interactions
being observed, thus resulting in the smallest value of the
cooperativity factor among 13.
MS data clearly ligand-exchange between 4 and 5 occurs in
MeOH in a similar manner to that described earlier for a mixture
of 1 and 2.
In the case of a mixture of 1 and 5 in MeOH, peaks for the 1+
and 2+ ions of a heteroleptic complex, [Co(A-C6-terpy)(C6-
terpy)](BF4)2 (7), were observed at m/z 945 and 858,
respectively (Figure S1(c)). Unlike the result for the solid product
obtained from a mixture of 4 and 5 following solvent removal, a
sample of the solid product obtained for 1 and 5 showed a
different PXRD pattern that was not consistent with the presence
of either 1 or 5; however, it was in keeping with the presence of
a new phase incorporating both A-C6-terpy and C6-terpy (Figure
S3). Unfortunately, single crystals of this product suitable for an
X-ray structure determination were not obtained.
2.5
2.0
1.5
1.0
From the above results, clearly ligand exchange equilibria occur
in MeOH in all cases (Scheme 2). However, co-crystallization for
heteroleptic complexes is seen to require intermolecular
interactions between terminal substituents on the respective
bound ligands. Thus 4 without substituents when co-crystallized
with 5 only yielded crystals of 4 and 5. Nevertheless, under
similar conditions 5 incorporating C6 alkyl chains was expected
to interact with 1 through inter-chain interactions to yield a
“mixed phase”. A PXRD study confirmed the co-crystallization of
1 and 5 to form such a mixed phase; however, once again single
crystals of the product suitable for an X-ray structure
determination were not obtained.

○
□
△
１
２
３
0.5
0.0
― fitting
100
200
300 400
Temperature / K
Figure 5. Magnetic behaviour for (a) 1 (circle), (b) 2 (square) and (c) 3
(triangle). Black solid lines indicate fitting by the regular solution models.
Table 1. H, S, T1/2, and C values, obtained by the regular solution model
1
2
3
ΔH (J mol-1)
ΔS (J K-1)
T1/2 (K)
C
4066.63
10.90
373
4278.24
12.62
339
5061.86
17.45
290
Adenine
Thymine
In MeOH
In MeOH
In MeOH
Crystallization
0.34
0.48
0.017
1
2
Crystalsof 3
We have also investigated the self-assembly and co-
crystallisation processes associated with the formation of base-
pairs in 3 (that incorporates the two different ligand derivatives,
A-C6-terpy and T-C6-terpy). MS-spectra and Powder X-ray
diffraction (PXRD) measurements together with control
experiments using [Co(terpy)2](BF4)2 (4) and [Co(C6-
terpy)2](BF4)2 (5) have been undertaken to corroborate the role
of the terminal nucleobases. The MS-spectrum for 3 in MeOH
showed peaks resulting from {[Co(A-C6-terpy)2](BF4)}+ and
deprotonated molecule [Co(A-C6-terpy)2(-H)]+ at m/z 1078 and
991, and of [Co(T-C6-terpy)2](BF4)2 at m/z 1060 and 973,
corresponding to 1 and 2, respectively (Figure S1(a)). Moreover,
the peaks arising from heteroleptic species in 3, [Co(A-C6-
terpy)(T-C6-terpy)](BF4)2, were present at m/z 1069 and 982,
respectively. These results are in accord with 1, 2 and 3
occurring in equilibrium in MeOH via ligand-exchange.
Crystallization
4
5
Respective Crystals of 4 and 5
Crystallization
No crystals
1
5
Scheme 2. Self-assembly and crystallization of terpyridine cobalt(II)
complexes incorporating alkylated adenine, alkylated thymine, and alkyl
chains as terminal substituents.
Conclusions
The MS-spectrum of a mixture of 4 and 5 in MeOH showed
peaks for the 1+ and 2+ ions at m/z 712 and 625 in accord with
the formation of the heteroleptic complex, [Co(terpy)(C6-
terpy)](BF4)2 (6) (Figure S1(b)) together with the homoleptic
compounds 4 and 5. Nevertheless, fractional crystallization of a
MeOH solution of a 1:1 mixture of 4 and 5 initially gave rise to
single crystals of 5 followed by single crystals of 4. Following
isolation of the crystals, the solution was taken to dryness. The
resulting powder proved to be a mixture of 4 and 5, as confirmed
by a PXRD measurement (Figure S2). Nevertheless, from the
In this study, we have demonstrated that the molecular
assembly behaviour of [Co(terpy)2]2+ complexes incorporating
the terminal nucleobases, A (1) and/or T (2), can be altered by
varying which combination of these base pairs is present. For
example, mixing 1 and 2 led to the co-crystals, [Co(A-C6-
terpy)1.5(T-C6-terpy)0.5](BF4)2 (3). The base pairing of the
terminal nucleobase substituents was shown to play a crucial
role in the co-crystallization and formation of single crystals of 3.
Crystalline 1 has a 3-D network structure consisting of 1-D
chains, while 2 displays a stacked structure of 2-D ladders. In
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[4]
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(a) G. Chen, D. Liu, C. He, T. R. Gannett, W. Lin, Y. Weizmann, J. Am.
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the case of 3, “dimer rings” that consist of homoleptic [Co(A-C6-
terpy)2](BF4)2
and
heteroleptic
[Co(A-C6-terpy)(T-C6-
terpy)](BF4)2 result from the co-crystallization of 1 and 2. These
differences in the respective molecular assemblies are shown to
affect the cooperativity influencing the corresponding SCO
behaviour.
We believe that our strategy of introducing nucleobases as
terminal substituents provides a useful means for combining two
different metal complex species and obtaining their co-crystals
via base pairing of the respective nucleobases.
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Acknowledgements
This work was supported by JSPS Grant-in-Aid for Young
Scientists (B) JP15K17833 and JSPS Grant-in-Aid for Scientific
Research on Innovative Areas (Dynamical Ordering & Integrated
Functions) JP16H00777. This work was also supported by
KAKENHI Grant-in-Aid for Scientific Research (B) JP26288026.
This work was partially supported by the Cooperative Research
Program of ‘Network Joint Research Centre for Materials and
Devices’. M.N. is grateful to JSPS Research Fellowships for
Young Scientists (No. JP15J11333). The authors thank Dr. H.
Sato (Rigaku) and Dr. T. Kikuchi (Rigaku) for technical support
for the X-ray single crystal structural analysis. We also thank
Professor Hayato Ishikawa (Kumamoto University) for support
with the measurement of MS-spectra.
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Keywords: nucleobase • supramolecular chemistry • cobalt
complex • self-assembly • spin crossover
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