Cytosine-substituted nitronylnitroxide radical: A key component for bio-inspired molecule-based magnetics

Article abstract of DOI:10.1021/jp046621m

A cytosine-substituted nitronylmtroxide radical (1) was synthesized. The nucleobase moiety plays a primary role in molecular packing in the crystal. It has been found from X-ray structure analyses and magnetic susceptibility measurements that the intermolecular magnetic interactions in the crystal are propagated by orbital overlaps between the phenylnitronylndtroxide moieties of the adjacent molecules, whereas the relative arrangement of the molecules are governed by the hydrogen bonding of the nucleobase moiety, giving a doubled chain structure. The hydrogen-bonded aggregation of the cytosine-substituted radical molecules can be a useful element for molecular assembly of bio-inspired molecule-based magnets in terms of crystal engineering for nucleobase- substituted radicals.

Full text of DOI:10.1021/jp046621m

16606
J. Phys. Chem. B 2004, 108, 16606-16608
Cytosine-Substituted Nitronylnitroxide Radical: A Key Component for Bio-Inspired
Molecule-Based Magnetics
Daisuke Shiomi,*,†,‡ Mikito Nozaki,† Tomoaki Ise,†,‡ Kazunobu Sato,† and Takeji Takui*,†
Departments of Materials Science and Chemistry, Graduate School of Science, Osaka City UniVersity,
Sumiyoshi-ku, Osaka 558-8585, Japan, and PRESTO, Japan Science and Technology Agency (JST),
4-1-8 Honcho Kawaguchi, Saitama 332-001, Japan
ReceiVed: July 29, 2004; In Final Form: September 12, 2004
A cytosine-substituted nitronylnitroxide radical (1) was synthesized. The nucleobase moiety plays a primary
role in molecular packing in the crystal. It has been found from X-ray structure analyses and magnetic
susceptibility measurements that the intermolecular magnetic interactions in the crystal are propagated by
orbital overlaps between the phenylnitronylnitroxide moieties of the adjacent molecules, whereas the relative
arrangement of the molecules are governed by the hydrogen bonding of the nucleobase moiety, giving a
doubled chain structure. The hydrogen-bonded aggregation of the cytosine-substituted radical molecules can
be a useful element for molecular assembly of bio-inspired molecule-based magnets in terms of crystal
engineering for nucleobase-substituted radicals.
Molecule-based magnetism has witnessed a rapid develop-
ment in the past decades.1 In the molecule-based magnetics,
full control of molecular packing, or relative arrangement of
open-shell molecules in a crystalline solid state, has been an
unresolved, long-standing issue that has a crucial relationship
to magnetic properties of molecular assemblages such as
ferromagnetism. Biomolecule-based architecture such as a DNA
duplex with nucleobase pairing is fascinating from the viewpoint
of magnetic materials. Introduction of electron spins to the
biomolecule-based nanostructure should bring about further
developments in spin-mediated nanotechnology as well as in
molecule-based magnetics. In this paper, we propose a control
of the molecular packing of organic open-shell compounds by
employing nucleobases as a structure-determining element in
crystalline solids.
SCHEME 1: Synthesis of Cytosine-Substituted
Radical 1a
a Steps: (a) 2,3-Bis(hydroxylamino)-2,3-dimethylbutane (1 equiv)
in methanol; (b) PbO2 (7 equiv) in dichloromethane; (c) cytosine (1
equiv), K2CO3 (1 equiv), and KI (1 equiv) in acetonitrile.
Hydrogen-donating and accepting molecules other than
naturally found nucleobases, such as phenol, carboxylic acid,
and pyridine derivatives, have been introduced to the stable
radical family of nitroxide and imino- or nitronylnitroxide.2 The
magnetic properties of these compounds have been examined
in view of hydrogen-bonded assemblage of the open-shell
building blocks.2 Tetrathiafulvalene cation radicals with nucleo-
base substituents3 and paramagnetic transition metal complexes
embedded in a DNA duplex4 have been reported as well. To
our knowledge, however, there have been only two examples
of stable, neutral organic radicals with well-characterized crystal
structure, to which a naturally found nucleobase moiety has been
introduced;5 one is 5-uradinyl and the other is 6-uradinyl
substituted imino- or nitronylnitroxide. For the 5-uradinyl
nitronylnitroxide, magneto-structural correlation has not been
fully clarified.5a The 6-uradinyl iminonitroxide has been found
to exhibit intermolecular antiferromagnetic interaction to give
a molecular dimer in a singlet (S ) 0) ground state.5b An
Figure 1. ORTEP drawings of 1 with the thermal ellipsoids of 50%
probability. The hydrogen atoms are omitted for clarity.
extended doubled chain structure is reported in this paper for a
new nitronylnitroxide radical 1 (Scheme 1), which has a cytosine
group serving as the structure-determining element. The syn-
thesis, X-ray crystallography, and magnetic susceptibility of 1
are described.
The cytosine-substituted radical 1 was synthesized by a direct
coupling of cytosine with the 3-(bromomethyl)phenyl derivative
of nitronylnitroxide 2 (Scheme 1). The precursor 2 was prepared
by following the reported method.6 Single crystals of 1 were
obtained by recrystallization from methanol. The crystalline solid
of 1 was stable under aerated conditions at room temperature.
In Figure 1 is depicted the molecular structure of 1.7 The
unit cell contains two crystallographically independent mol-
ecules, A and B. Molecule B has a positional disorder of atoms
in the phenylnitronylnitroxide moiety.8 The phenyl and the
cytosine rings have large dihedral angles in both A and B (93.7°
in A, 86.2° and 88.2° in B) around the methylene bridges. It is
expected that the delocalization of unpaired electron spin in 1
* Corresponding authors. Telephone: +81-6-6605-3149. Fax: +81-6-
6605-3137. E-mail: D.S., shiomi@sci.osaka-cu.ac.jp; T.T., takui@sci.osaka-
cu.ac.jp.
† Osaka City University.
‡ Japan Science and Technology Agency.
10.1021/jp046621m CCC: $27.50 © 2004 American Chemical Society
Published on Web 09/30/2004

Letters
J. Phys. Chem. B, Vol. 108, No. 43, 2004 16607
the molecules in the crystalline solid state. The intermolecular
short contacts around O2 should be responsible for the antifer-
romagnetic interaction. The decrease in øpT gets less steep
around 10 K, and the øpT value goes down again below 5 K.
The stationary behavior of øpT indicates the occurrence of
additional weak antiferromagnetic interactions. The temperature
dependence of øpT was analyzed with
2
NAg2µB
1
2
3
3
4
øp )
+
(1)
[
]
3kB(T - θAB
)
3 + exp(-2JA/kBT)
where the first term in the bracket represents the ground-state
singlet dimer of molecule A with the antiferromagnetic interac-
tion JA attributed to the short contacts around O2. The second
term corresponds to molecule B. Weak intermolecular inter-
actions other than JA are approximated by the mean field θAB
in eq 1. The observed øpT was reproduced by eq 1 with the
parameters JA/kB ) -19.0 ( 0.3 K, θAB ) -1.5 ( 0.1 K. The
g-factor g is fixed as g ) 2.006, which was observed in an
ESR spectrum of a dichloromethane solution. A simple Curie-
Weiss model with the single parameter Θ ) -7.5 K fails to
reproduce the low-temperature øpT values as shown in Figure
3. The stationary behavior of øpT around 10 K corresponding
to half moles of S ) 1/2 spin is ascribed to the formation of the
ground-state singlet dimer of molecule A.
Figure 2. Doubled chain of 1 in the crystal. The thin solid lines
represent the intermolecular hydrogen bonds between the cytosine
moieties. The hydrogen bond lengths are 2.953(9) Å (N5H-O3),
2.963(9) Å (N11H-O7), 2.988(9) Å (N5H-N10), and 2.968(9) Å
(N11H-N4). The methyl groups are omitted for clarity.
Cytosine has been found to be an efficient building block
for organization of open-shell molecules in a crystalline solid
state, exemplifying that the hydrogen-bonded aggregation of the
cytosine-substituted radical molecules can be a useful element
for molecular assembly of bio-inspired molecule-based magnets
in terms of crystal engineering for nucleobase-substituted
radicals. Syntheses of guanine-substituted nitronylnitroxide
radicals and their molecular complexes with 1 are in progress.
Heteromolecular complexation based on complementary nucleo-
base pairing will lead to molecule-based heterospin magnetics
such as organic molecule-based ferrimagnetics.13
Figure 3. Paramagnetic susceptibility øp of 1 measured on a SQUID
magnetometer with B ) 0.1 T in the øpT vs T plot. In the inset are
shown the øpT values at low temperatures. The solid line denote the
calculated values from eq 1 (JA/kB ) -19.0 K, θAB ) -1.5 K), and
the dashed line represents the simple Curie-Weiss law with Θ )
-7.5 K.
Acknowledgment. This work has been supported by Grants-
in-Aid for Scientific Research from the Ministry of Education,
Sports, Culture, Science and Technology, Japan. Financial
support from PRESTO of Japan Science and Technology
Agency (JST) is also acknowledged.
is truncated at the methylene bridge. It was found from DFT
calculations that the cytosine moiety has little spin density,9
supporting the truncation of π-conjugation. Thus, the cytosine
group in 1 plays a role primarily in determining the molecular
packing instead of propagating intermolecular magnetic inter-
actions.
As shown in Figure 2, the molecular packing of 1 features
in intermolecular hydrogen bonds between the nucleobase
substituents. The lengths of the intermolecular hydrogen bonding
are very close to those of pristine cytosine.10 The relative
arrangement of the molecules is governed by the hydrogen
bonding of the cytosine moiety. Molecules A and B are
assembled to form chains A and B, respectively. The two
parallel chains are related by inversion symmetry in the motif
of ‚‚‚-A-B-B-A-A-B-‚‚‚ in the crystal.11
Supporting Information Available: Crystallographic data
(CIF file), ORTEP drawings, and table of atomic spin densities
calculated by the DFT methods. This material is available free
of charge via the Internet at http://pubs.acs.org.
References and Notes
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1
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indicating that antiferromagnetic interactions dominate between

16608 J. Phys. Chem. B, Vol. 108, No. 43, 2004
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The R value being larger than 0.1 results from the disorder as described in
the text.
(8) A lowered symmetry with the doubled number of independent
molecules, i.e., space group P1 or a doubled cell parameter along the a
axis, has not improved the refinement, retaining the disorder. On the final
difference Fourier map, density peaks were found around the disordered
rings of molecule B with the maximum and minimum of +0.93 and -0.48
e/Å3, respectively. The refinement including the residual peaks was
unsuccessful, resulting in divergence of the least-squares calculation.
(9) The spin density distribution of molecule A was calculated with
the unrestricted density functional theory at the UB3LYP/6-31+G(d,p) level
using a program package Gaussian98 (Revision A.9, Gaussian, Inc.,
Pittsburgh, PA, 1998). The molecular geometry was taken from the X-ray
crystal structure.
(10) (a) Jeffrey, G. A.; Kinoshita, Y. Acta Crystallogr. 1963, 16, 20.
(b) McClure, R. J.; Craven, B. M. Acta Crystallogr. 1973, B29, 1234. (c)
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(d) Barker, D. L.; Marsh, R. E. Acta Crystallogr. 1964, 17, 1581. (e)
McClure, R. J.; Craven, B. M.; Acta Crystallogr. 1973, B29, 1234.(f)
Eisenstein, M. Acta Crystallogr. 1988, B44, 412.
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Chem. Soc. 1972, 94, 7049.
(7) The crystal structure was solved by direct methods using a program
package CrystalStructure (ver.3.60) by Rigaku/Molecular Structure Cor-
poration. Crystallographic data: C36H44N10O6, M ) 712.81, 0.05 × 0.1 ×
0.4 mm3, Mo KR, 193 K, triclinic, space group P1h, a ) 6.9780(1) Å, b )
14.529(1) Å, c ) 20.034(1) Å, R ) 78.023(8)°, â ) 75.20(2)°, γ )
78.00(2)°, V ) 1895.0(2) Å3, Z ) 2, Dcalc ) 1.249 g cm-3. R ) 0.127, Rw
) 0.214 (GOF ) 1.00) for 4180 reflections (I > 2σ(I)) and 515 parameters.
(11) The ORTEP drawings for nearest-neighbor molecules and tables
of interatomic distances are provided as Supporting Information.
(12) Bondi, A. J. Phys. Chem. 1964, 68, 441.
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