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Accepted Manuscript
Supramolecular architectures of metal-oxalato complexes containing purine nu‐
cleobases
Sonia Pérez-Yá ñez, Oscar Castillo, Javier Cepeda, Juan P. García-Terán,
Antonio Luque, Pascual Román
PII: S0020-1693(10)00604-3
DOI: 10.1016/j.ica.2010.09.012
Reference: ICA 13754
To appear in: Inorganica Chimica Acta
Received Date: 27 July 2010
Revised Date: 3 September 2010
Accepted Date: 10 September 2010
Please cite this article as: S. Pérez-Yá ñez, O. Castillo, J. Cepeda, J.P. García-Terán, A. Luque, P. Román,
Supramolecular architectures of metal-oxalato complexes containing purine nucleobases, Inorganica Chimica
Acta (2010), doi: 10.1016/j.ica.2010.09.012
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Supramolecular architectures of metal-oxalato complexes containing
purine nucleobases
Sonia Pérez-Yáñez, Oscar Castillo*, Javier Cepeda, Juan P. García-Terán, Antonio
Luque*, Pascual Román
Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad
del País Vasco, Apartado 644, E–48080 Bilbao, Spain
A B S T R A C T
The reaction of purine nucleobases (adenine, 3-methyladenine and 9-methylguanine) with a metallic salt in the presence of potassium oxalate yields three compounds with formulae {[Cd(µ-ox)(H2O)(Hade)]·H2O}n (1), {[Cu(µ-ox)(H2O)(3Meade)]·H2O}n (2) and [Cu(ox)(H2O)2(9Megua)]·2.5H2O (3). Crystal structures of compounds 1–2 consist of one-dimensional zig-zag chains in which cis-[M(H2O)(nucleobase)]2+ fragments are linked by bis-bidentate oxalato ligands. In compound 1, the nucleobase is coordinated through the minor groove N3 atom, and the resulting non-canonical 7H-adenine tautomer is stabilized by non-covalent interactions involving more basic N9 and N7 sites. In compound 2, the mutagenic 3-methyladenine is attached to the metal atoms by means of the imidazole N7 atom. The dissimilar binding pattern of the nucleobases produces significant differences in the supramolecular architectures of compounds 1 and 2 which are essentially governed by an extensive network of non-covalent interactions such as hydrogen bonded adenine-adenine base pairs, hydration of the nucleobases, carboxylato-nucleobase associations, and face-to-face ð–ð stacking. The stacking. The model 9-methylguanine nucleobase of compound 3 exhibits its usual coordination mode through the major groove N7 atom to form two monomeric [(Cu(ox)(H2O)2(9Megua)] units which are held together by means of Watson-Crick like hydrogen bonds between the guanine moieties and the inorganic frameworks generating almost planar tetrameric metal-organic aggregates. The three dimensional packing of the complex entities affords an open structure containing voids which are filled by decameric (H2O)10 clusters. Variable-temperature magnetic susceptibility measurements of compound 2 show the occurrence of antiferromagnetic intrachain interactions in good agreement with the structural features of its 1D metal-oxalato framework.
Keywords: Adenine, guanine, oxalato, X-ray diffraction, supramolecular chemistry, structure-magnetism relationships * Corresponding author. E-mail: [email protected], [email protected]
Graphical abstract
Three new bioinorganic complexes have been prepared and X-ray structurally
characterized by exploiting the high efficiency of the metal-oxalato frameworks to
anchor a wide diversity of purine nucleobases (adenine, 3-methyladenine and 9-
methylguanine) by means of a combination of coordinative bonds, hydrogen bonds and
�–� interactions
1. Introduction
Over the past decades, there has been a substantial research effort on rational design
and elaboration of biomimetic systems [1] based on the interaction of nucleic acids and
their building units with a wide range of both organic and inorganic frameworks [2].
The interest of these systems not only stems from the desire to understand better the
complex interactions often present in a great diversity of molecular biorecognition
processes [3], but also to afford a powerful tool for the improvement of pharmaceutical
agents [4] and the development of artificial receptors used as specific nucleotide sensors
or even for the determination of low concentrations of biological and therapeutic agents
[5]. On the other hand, the molecular architecture of coordination compounds
containing nucleobases has proven very useful, giving several molecular geometric
shapes and high-dimensional architectures [6].
In addition to the coordinative bonds, one of the most useful strategies for preparing
extended structures with metal building blocks is based on the use of intermolecular
forces such as hydrogen bonds and/or �-� interactions [7]. In that sense, nucleobases
provide interesting building blocks to form extended structures, not only by the multiple
ways in which bases may interact by H-bonds, but also for the possible �-stacking
between them [8]. Coordination of metal ions to nucleobases can modify the usual H-
bond interactions between bases allowing new arrangements and stabilizing certain
types of base-base associations [9].
Our group has recently studied the high efficiency of several metal-dicarboxylato
(oxalato and malonato) systems to act as receptors of adenine and cytosine (neutral,
cationic and supramolecuar aggregates) by means of the covalent anchoring of
nucleobases to the metal centres and/or by the establishment of complex hydrogen-
bonding recognition patterns between the organic and inorganic frameworks [10]. Now,
in a continuation of our research program on molecular recognition processes between
nucleobases and inorganic frameworks, we have succeeded in demonstrating that the
metal-oxalato entities also act as good receptors for a wider diversity of nucleobases and
we report herein the synthesis and supramolecular structures of compounds {[Cd(�-
ox)(H2O)(Hade)]·H2O}n (1), {[Cu(�-ox)(H2O)(3Meade)]·H2O}n (2) and
[Cu(ox)(H2O)2(9Megua)]·2.5H2O (3) containing the non-modified adenine nucleobase
(Hade), the 3-methyladenine (3Meade) and the model 9-methylguanine (9Megua) which
act as monodentate ligands. 3-methyladenine is highly cytotoxic and mutagenic as a
result of its ability to block DNA replication since the N3-methyl group protrudes into
the minor groove of the DNA double helix and thereby stops replication [11]. So that,
the design and structural analyses of coordination compounds containing this
methylated adenine can supply useful information to understand the conformational
damages induced by the N-alkylation of nucleobases in biological systems and the
molecular recognition processes to repair them.
2. Experimental
All chemicals were of reagent grade and were used as commercially obtained.
Elemental analyses (C, H, N) were performed on an Euro EA (EuroVector) Elemental
Analyzer. Metal content was determined by absorption spectrometry performed on a
Perkin-Elmer Analyst 100. The IR spectra (KBr pellets) were recorded on a FTIR
8400S Shimadzu spectrometer in the 4000–400 cm–1 spectral region. Magnetic
measurements were performed on polycrystalline samples of the complexes taken from
the same uniform batches used for the structural determinations with a Quantum Design
SQUID susceptometer covering the temperature range 5–300 K at a magnetic field of
5000 G. The susceptibility data were corrected for the diamagnetism estimated from
Pascal's Tables [12], the temperature-independent paramagnetism and the magnetization
of the sample holder.
Diffraction data were collected at 293(2) K on Oxford Diffraction Xcalibur
diffractometer with graphite-monochromated Mo-Kα radiation (λ = 0.71073 Å). The
data reduction was done with the CrysAlis RED [13]. Structures were solved by direct
methods using the SIR92 program [14] and refined by full-matrix least-squares on F2
including all reflections (SHELXL97) [15]. All calculations were performed using the
WINGX crystallographic software package [16]. During the data reduction process it
became clear that the crystal specimen of compound 1 was a non-merohedric twin with
a twin law: (1 0 0 / 0 –1 0 / 0.7993 0.2987 1). The final result showed a percentage of
twinned component of 24.5%. Crystal parameters and details of the final refinements of
compounds 1–3 are summarized in Table 1.
Table 1
All the quantum mechanical calculations of geometry optimizations have been carried
out in gas phase using the density functional theory with Becke’s three-parameter
exchange functional [17] along with the Lee-Yang-Parr nonlocal correlation functional
(B3LYP) [18]. The standard 6-31G(d) basis set was used as implemented in the
Gaussian 03 program [19]. It is well known that although the B3LYP functional method
might not be suitable for the consistent study of the whole range of the DNA base
interactions due to its insufficiency in describing the dispersion interactions, it predicts
reliable interaction energies for hydrogen-bonded systems [20]. The initial geometry of
the models was built up from the experimental crystal structures.
2.1. Synthesis of {[Cd(�-ox)(Hade)(H2O)]·H2O}n (1)
The slow diffusion of an aqueous-methanolic solution (40 mL, 3:1 ratio) containing
CdCl2 (0.03 g, 0.16 mmol) and adenine (0.0655 g, 0.49 mmol) over an aqueous solution
(35 mL) of potassium oxalate (0.0302 g, 0.16 mmol) gave rise to colourless X-ray
quality single-crystals after two months in 60% yield (based on metal). Anal. Calc. for
C7H9CdN5O6 (Formula mass: 371.60 g/mol): C, 22.63; H, 2.44; N, 18.85; Cd, 30.25.
Found: C, 23.15; H, 2.18; N, 19.06; Cd, 30.15%. Main IR features (cm–1, KBr pellet):
3416s for �(O–H); 3222s for (�(NH2) + 2�(NH2)); 3026s for �(C8–H + C2–H); 1702s
for �as(O–C–O); 1652w for (�(C=C) + �(NH2)); 1556vs for (�(C4–C5) + �(N3–C4–C5));
1448m for (�(C2–H + C8–N9) + �(C8–H)); 1412m for �(N1–C6–H6); 1364m for �(C5–
N7–C8); 1275m for (�(N9–C8 + N3–C2) + �(C–H) + �s(O–C–O)); 1234m, 1191m,
1117w for (�(C8–H) + �(N7–C8)); 993m for �(NH2); 941m, 886m for (�(N1–C6) +
�(NH2)); 799m, 742m for �(O–C–O); 709m, 644w, 617w for ring deformation; 560m,
539m, 520m, 458w for �(M–O + M–N)
2.2. Synthesis of {[Cu(�-ox)(3Meade)(H2O)]·H2O}n (2)
An aqueous-methanolic solution (12 mL, 1:1 ratio) of 3-methyladenine was added
dropwise to an aqueous mixture of K2[Cu(ox)2]·H2O (0.0495 g, 0.14 mmol) and
K2(ox)·H2O (0.0258 g, 0.14 mmol) with continuous stirring at 50 ºC. The resulting
solution was allowed to evaporate at room temperature. Light-green single crystals of
compound 2 were obtained after two months in 75% yield (based on metal). Anal. Calc.
for C8H11CuN5O6 (Formula mass: 336.77 g/mol): C, 28.53; H, 3.29; N, 20.80; Cu,
18.87. Found: C, 28.13; H, 3.08; N, 21.15; Cu, 19.02%. Main IR features (cm–1, KBr
pellet): 3533s, 3490sh, 3354s, for (�(NH2) + 2�NH2)); 3202m, for (�(C8–H + C2–H) +
(�(NH2)); 3105w, 2960w, 2922w, for (�(CH3)); 1685s, for (�as (O–C–O)); 1634sh,
1600s, for (�(C=C) + (�NH2)); 1520w, 1463m, for (�(C2–H + C8–N9) + �(C8–H));
1415m, for �(N1–C6–H6); 1308m, for (�(N9–C8 + N3–C2) + �(C–H) + �s(O–C–O));
1263w, 1208m, for (�(C8–H) + �(N7–C8)); 1052w, for τNH2); 1008w, 936w, 908w, for
(�(N1–C6) + �(NH2)); 800m, for �(O–C–O); 716w, 641m, for ring deformation; 505m,
460m, for �(M–O + M–N).
2.3. Synthesis of [Cu(ox)(H2O)2(9Megua)]·2.5H2O (3)
Green single crystals of 3 were grown by the slow diffusion of an aqueous-methanolic
(1/1) solution (15 mL) of Cu(NO3)2·3H2O (0.06 mmol) and 9-methylguanine (0.06
mmol) into an aqueous solution (5 mL) of K2(ox)·H2O (0.06 mmol). Yield: 30% (based
on metal). Anal. Calc. for C8H16CuN5O9.5 (Formula mass: 397.81 g/mol): C, 28.53; H,
3.29; N, 20.80; Cu, 18.87. Found: C, 28.13; H, 3.08; N, 21.15; Cu, 19.02%. Main IR
features (cm–1, KBr pellet): 3389s, for (í(NH(NH2) + í(N(N1–H) + í (O(O–H)); 3164s, 2955m,
for (í (CH(CH3)); 1678vs, for (ías (O–C–O)); 1641s for (í (C=C) + (äNH(C=C) + (äNHNH2)); 1599m, 1556m,
for (í (C(C4–C5) + (N3–C4–C5)); 1494m for (ä(C(C8–N9) + í (C(C8–H)); 1426m, for (ä (N(N1–C6–
H6); 1383m, 1347w, (í ((C5–N7–C8) + ä (CH(CH3)); 1282m for (í (N(N9–C8 + N3–C2) + ä (C(C8–
H) + í s(O–C–O)); 1224w, 1180m, 1126w for (ä (C(C8–H) + í (N(N7–C8)); 1088w, 1063w for
ô (NH2); 1023w, 972w, 889w for (í (N(NH2); 1023w, 972w, 889w for (í (N(N1–C6) + ô (NH(NH2)); 795m, for (í (C=O) + ä (O(C=O) + ä (O(O–C–
O)); 731m, for (í (C=O); 694m, 626m for ring(C=O); 694m, 626m for ring deformation; 542w, 526w, 477w, 417w
for í (M(M–O + M–N).
The purity and homogeneity of the samples employed for the physical
characterization of these compounds have been checked by means of X-ray powder
diffraction.
3. Results and discussion
3.1. Crystal structure of {[Cd(�-ox)(Hade)(H2O)]·H2O}n (1)
Compound 1 contains one-dimensional zig-zag chains running along the [110]
direction in which cis-[Cd(H2O)(Hade)]2+ units are sequentially bridged by two
centrosymmetric bis-bidentate oxalato ligands (ox1 and ox2) with a Cd···Cd distance of
5.981(1) Å and a Cd…Cd…Cd angle of 113.7º (Fig. 1). The dihedral angle between two
consecutive oxalato bridging ligands is of 76.7º and the adenine ligand is almost
perpendicular to the propagation plane of the metal-oxalato chains with a dihedral angle
between the adenine moiety and the oxalato ligands of 78.5º (ox1) and 75.1º (ox2),
respectively. The metal atoms (placed on a general position) exhibit a distorted
octahedral coordination formed by four oxygen atoms from two oxalato ligands, one
water molecule, and one endocyclic nitrogen atom of the adenine, resulting in a NO4Ow
donor set. Selected bond lengths for the coordination polyhedron are gathered in Table
2. The Cd–O bond distances range from 2.270 to 2.338 Å and they are similar to those
previously reported for polymeric cadmium-oxalato complexes [21]. The adenine
nucleobase is bound via the pyrimidine N3 atom with a substantially longer Cu–N bond
distance [2.282(4) Å] than that found (2.193 Å) in the compound [CdL(ade)]ClO4 (L:
tris(2-aminoethyl)amine-N,N',N'',N'''), the only structurally characterized Cd-complex
with the non-substituted adenine nucleobase as terminal ligand registered in the
Cambridge Structural Database (CSD, May 2010 release) in which the coordination of
the adeninato anion takes place through the most basic N9 nitrogen atom [22]. In
biological systems, the highly toxic cadmium metal coordinates to major groove N7 of
adenine owing to the attachment of the sugar-phosphate backbone to the N9 atom and
the steric hindrance of the neighbouring N3 site [23].
Figure 1
Table 2
In the polymeric chains of compound 1, the adenine ligands are oriented in such a
way to permit the formation of an intramolecular hydrogen bond involving the
coordinated water molecule (donor) and the N9 atom (acceptor) which reinforces the
observed metal-binding pattern of the nucleobase. Furthermore, the proton transfer from
N9 to N7 to give the 7H-adenine tautomer favors the formation of a hydrogen-bonded
R21(7) ring between the Hoogsteen face [N6H, N7H] of the nucleobase as donor and a
crystallization water molecule as acceptor with asymmetric N···O distances of 3.132(5)
and 2.788(5) Å. These values are in the range reported in experimental and theoretical
studies performed to analyse the key role that hydration processes of the nucleobases
play on the structural features and properties of artificial and biological systems [10d,
24]. As can be seen in Fig. 2, the polymeric chains are cross-linked by a pair of N6–
H···N1 hydrogen bonding interactions between the Watson-Crick faces of two
nucleobases and by an O1w–H11w···O3 interaction between the coordinated water
molecule and the oxalato ligand belonging to one adjacent chain. Additionally, the
crystallization water molecule occupies the interstitial space between the neutral chains
and displays O1···H21w–O2w–H22w···O4 hydrogen contacts to the carboxylate-oxygen
atoms of two neighbouring chains. Table 3 lists the structural parameters of the non-
covalent interactions between the building units in compound 1.
Figure 2
Table 3
It is interesting to note that 3D supramolecular structure does not show the presence
of face-to-face or edge-to-face interactions between the ð–systems of the adenine rings
due to the long distance (9.5 Å) found between two nucleobases attached to the same
side of the polymeric chains. This is in clear contrast to what occurs in the Co(II) and
Zn(II) complexes with formula {[M(µ-ox)(H2O)(Hade)]·2(Hade)·(H2O)}n [10e]. These
compounds contain similar polymeric chains but the smaller radii of the first-row
transition metals produces a different arrangement of the ligands around the metallic
centres. As a consequence, the adenine is present as the canonical 9H-amino tautomer,
the 1D chain exhibits a bulkier corrugated conformation with a dihedral angle between
the nucleobase and the ox2 bridging ligand of ca 25º, and the distance between two
adjacent nucleobases is only 7.5 Å. This last parameter permits the inclusion of the
solvation 9H-adenine molecules among the coordinated nucleobases establishing ð–ð
stacking interactions with them (Fig. 3).
Figure 3
3.2. Crystal structure of {[Cu(�-ox)(3Meade)(H2O)]·H2O}n (2)
X-ray analysis of compound 2 showed the presence of zig-zag chains growing along
the crystallographic c-axis which are also comprised of cis-[Cu(H2O)(3Meade)]2+
fragments joined by bis-bidentate oxalato ligands. The separation of the metals along
the chain is 5.365(1) Å, the Cu···Cu···Cu angle is 101.5º, and the dihedral angle between
two consecutive oxalato bridging ligands is 64.3º. The oxalato bridging ligand is not
planar, since the carboxylate groups show a rotation of approximately 15º between
them. Fig. 4 shows a view of the polymeric chain together with the coordination
environment of the copper atom. Each metal centre exhibits a tetragonally elongated
CuNO4Ow chromophore in which the equatorial plane is defined by three oxygen atoms
of two oxalato ligands and the imidazole N7 atom of the 3-methyladenine, the usual
binding site observed in the complexes of this mutagenic purine base. The apical
positions of the octahedral coordination are filled by the remaining O1 oxygen atom of
the oxalato bridging ligand and the O1w coordinated water molecule with metal-ligand
bond distances (Table 4) substantially longer than the equatorial ones (< 2.04 Å).
Figure 4
Table 4
3-methyladenine ligands are perpendicularly arranged respect to the growing plane
of the metal-oxalato framework with an interplanar distance of 7.05 Å between two
consecutive parallel adenine moieties in the same side of the polymeric chain. This
value facilitates the insertion of the adenine molecules belonging to adjacent chains
giving rise to 2D zipper-like layers that spread out the crystallographic bc–plane (Fig.
5). This arrangement permits the establishment of face-to-face ð–ð interactions between
adjacent pyrimidinic rings with a centroid···centroid distance of 3.76 Å and a lateral
offset of 1.29 Å.
Figure 5
The layers of polymeric chains are held together by an intricate network of
hydrogen bonding interactions (Table 5). The Watson-Crick face of the nucleobases
from a layer is hydrogen bonded to the adjacent ones by means of a N6–H62···O4
interaction between the exocyclic amino group and the oxalato ligand, and by a weak
C8–H8···N1 base-base association. Additionally, the N9 nitrogen atom of the imidazole
ring acts as acceptor of a hydrogen bonding interaction with the coordination water
molecule of a neighbouring chain (Fig. 6a). The hydrogen-bonding scheme is completed
by an intramolecular N6–H61···O2 hydrogen bond. The overall three-dimensional
crystal packing of the polymeric chains generates channels along the [001] direction,
with dimensions of ca. 4 x 6 Å2, which are occupied by crystallization water molecules
hydrogen bonded to two carboxylato O atoms and to a coordinated water molecule (Fig.
6b).
Table 5
Figure 6
3.3. Crystal structure of [Cu(ox)(H2O)2(9Megua)]·2.5H2O (3)
The crystal structure determination of compound 3 has revealed the presence of two
distinct [(Cu(ox)(H2O)2(9Megua)] units, which are shown in Fig. 7. Selected bond
lengths for the coordination polyhedra of both complex units are gathered in Table 6.
The metal centres adopt a distorted square pyramidal coordination in which the basal
plane is occupied by two oxygen atoms from a bidentate oxalato ligand, one water
molecule, and the N7 site of the nucleobase that is the most frequent coordination metal
binding pattern for the 9-methylguanine ligand [25]. The apical positions are occupied
by water molecules with Cu–Ow distances [2.341(2) and 2.369(2) Å for units A and B,
respectively] longer than those of the basal planes [< 2.00 Å]. The most significant
difference between the two complex units stems from the orientation of the nucleobase
with respect to the plane defined by the oxalato ligand. Thereby, the dihedral angles
between the mean planes of both ligands are 28.6º in unit A and 2.9º in unit B.
Figure 7
Table 6
To get a deeper insight into the structural features of the [(Cu(ox)(H2O)2(9Megua)]
entities we have realized DFT analysis using the atomic positions of the B unit as
starting point. The optimized structure shows the distortion of the coordination
polyhedra toward to a trigonal bipyramid geometry and the pyramidalization of the
exocyclic amino group of the nucleobase. Moreover, the entity shows a dihedral
oxalato-nucleobase angle of 36.7º, similar to that observed for the A entity (28.6º), but
clearly far from the planarity observed in the B entity (2.9º), as shown in Fig. 8. This
fact seems to indicate that non-covalent interactions (Table 7) involving the molecular
units play an important role in their conformations.
Figure 8
Table 7
The Watson-Crick face of the nucleobase belonging to A unit establishes a triple
hydrogen bonding interaction with three oxygen atoms of the B entity, one from the
coordinated water molecule and the other ones from a carboxylate group of the oxalato
ligand. This interaction forms two different R22(8) rings which resembles the
complementary guanine-cytosine molecular recognition pattern found in biological
systems. Nevertheless, the keto group of the guanine ligand from the B unit establishes
an intramolecular hydrogen bond with the coordinated water molecule, whereas the
N1H and N2H sites are connected to the non-coordinated oxygen atoms from an
adjacent A unit to form a hydrogen-bonded R22(9) motif. The above-described hydrogen
bonding scheme between the complex units gives rise to centrosymmetric metal-organic
quartets which resembles the homonucleobase tetrameric aggregates (G4) presented in
the guanine-rich zones of the multistranded nucleic acid structures. The almost planar
metal-organic tetrads in 3 are interconnected by means of R22(8) rings formed by a
doubly N2B–H2B1···N3B hydrogen bonding interaction [26] between two guanine
moieties of neighbouring quartets which gives rise to infinite tapes spreading out the
crystallographic ac-plane (Fig. 9). The 3D supramolecular packing of these tapes
sustained by N–H···Ow and Ow–H···O hydrogen bonds exhibits a porous structure with
voids occupied by crystallization water molecules.
Figure 9
The embedded water molecules O5w–O9w are arranged in centrosymmetric discrete
(H2O)10 aggregates with Ow···Ow distances ranging from 2.845 to 3.090 Å. Each
aggregate is formed by a cyclic tetramer with the four free hydrogen atoms in an up-up-
down-down (uudd) disposition [27] joined to two acyclic (H2O)3 units (Fig. 10a).
Although the uudd configuration is energetically less stable compared to the energy
minimum udud configuration, it has been observed in the crystalline solids of metal
complexes [28]. The water molecules presented in the aggregates complete their
hydrogen-bonding environments establishing Ow–Hw···O interactions in which oxygen
atoms from the coordination water molecules and the oxalato ligands act as acceptors.
Structural and theoretical investigations of hydrogen-bonded water clusters has caused
intensive attention due to their relevance in many chemical and biological systems [29].
Among these water clusters, decamers are common forms, although present a great
diversity of topologies because (H2O)10 aggregates seem to be very dependent on the
surrounding environment [28, 30]. Indeed, our DFT calculations performed to an
isolated decameric aggregate have shown that it evolves towards another (H2O)10 cluster
in which two coplanar (H2O)4 cycles are joined by two water molecules placed in a
perpendicular plane (Fig. 10b).
Figure 10
3.4. Magnetic properties
The ÷ MT and ÷ M vs T curves (where ÷ M is the magnetic susceptibility per copper atom)
for compound 2 are shown in Fig. 11. The ÷ MT value is 0.412 cm3mol–1 K at room
temperature, which is higher than the expected for an uncoupled paramagnetic S = ½
centre (0.375 cm3 mol–1 K, g = 2.0). This value remains almost constant until 100 K,
after which it suffers a sharp decrease upon cooling. The thermal evolution of the
magnetic susceptibility shows the presence of a maximum around 30 K and an increase
below 10 K due to paramagnetic impurities. This behaviour is indicative of
antiferromagnetic interactions between the Cu(II) atoms.
Figure 11
The experimental data were least-squares fitted with a numerical expression [31] for
an antiferromagnetic copper(II) uniform chain [the Hamiltonian being H = –JÓ iSi·Si+1].
The best fit parameters obtained are J = –34.0 cm–1, g = 2.1 and ñ = 3% (paramagnetic = 3% (paramagnetic
impurity percentage) with the agreement factor R = 7.22 x 10–9. This J value is in good
accordance with the perpendicular topology of the magnetic orbital observed in this
compound [32, 33]. The oxalato bridging ligand forms two short Cu–O bonds at one
copper atom and one short and one long at the other copper atom, so that, one of the
metal-centred magnetic orbital (a dx2–y2 type orbital in an elongated octahedral
geometry) is coplanar with the oxalato bridge, whereas the other one is perpendicular to
it. A few copper-oxalato examples with this topology have been previously reported
where the magnetic exchange coupling J values range from –22 to –75 cm–1 [32]. A J
value around –90 cm–1 has been postulated using density functional theory and ab initio
approaches [33] for this topology, although it has been experimentally found that the
magnetic coupling is weakened by the metal-metal separation, the displacement of the
metal out of the basal plane, the dihedral angle between the planes containing the
magnetic orbitals and the oxalato group, the distortion of the metal chromophore, the
non-planarity of the oxalato bridge and the nature of terminal ligands.
4. Conclusions
In the present work three new metal(II)-oxalato-nucleobase compounds have been
synthesized and structurally characterized. In this way we have demonstrated that the
metal-oxalato frameworks act as receptors of different nucleobases (adenine, 3-
methyladenine and 9-methylguanine). The selection of the metal seems to be crucial as
it can be observed when replacing Co or Zn by Cd. It originates a different arrangement
of the ligands to give rise a more efficient packing of the polymeric chains in the
cadmium complex. On the other hand, modifications such as the N-methylation of the
nucleobases offers an alternative to study the supramolecular interactions that take place
in these compounds. Finally, the overall antiferromagnetic behaviour of compound 2
and the value of the magnetic coupling constant are in good agreement with the orbital
topology of the copper-oxalato-copper framework.
Acknowledgement
This work was supported by the Ministerio de Ciencia e Innovación (MAT2008-
05690/MAT) and the Gobierno Vasco (IT477-10). Sonia Pérez-Yáñez
(PIFA01/2007/021) and Javier Cepeda thank Universidad del País Vasco/Euskal
Herriko Unibertsitatea for a predoctoral fellowship. Technical and human support
provided by SGIker (UPV/EHU, MICINN, GV/EJ, ESF) is gratefully acknowledged.
Appendix A. Supplementary material
CCDC 779251, 779252, 779253 contain the supplementary crystallographic data for 1,
2 and 3. These data can be obtained free of charge from The Cambridge
Crystallographic Data Center via www.ccdc.cam.ac.uk/data_request/cif.
Tables
Table 1
Single-crystal data and structure refinement details for compounds 1–3.
1 2 3
Formula C7H9CdN5O6 C8H11CuN5O6 C8H16CuN5O9.5
Weight (g mol–1) 371.60 336.77 397.81
Crystal system triclinic monoclinic triclinic
Space group P� P21/c P�
a (Å) 5.4910(6) 7.886(2) 9.1279(9)
b (Å) 9.5929(11) 20.759(3) 11.7372(11)
c (Å) 11.2825(14) 8.312(2) 14.2862(10)
α (°) 94.834(10) – 81.324(7)
β (°) 99.573(10) 115.60(2) 80.271(7)
γ (°) 102.687(10) – 78.677(8)
V (Å3) 567.19(12) 1227.1(5) 1468.2(2)
Z 2 4 4
ρcalcd (g cm–3) 2.176 1.823 1.800
µ (mm–1) 1.960 1.816 1.550
Reflections collected 8396 7425 15008
Unique data/parameters 8396/173 3293/182 8495/426
Reflections with I � 2σ(I) 6941 2209 4669
Goodness of fit (S) [a] 1.140 0.920 1.045
R1[b] /wR2 [c] [I � 2σ(I)] 0.0453 / 0.1420 0.0480 / 0.1166 0.0452 / 0.1040
R1/wR2 [all data] 0.0535 / 0.1468 0.0792 / 0.1255 0.0894 / 0.1132
[a] S = [�w(F02 – Fc
2)2 / (Nobs – Nparam)]1/2 [b] R1 = �||F0|–|Fc|| / �|F0| [c] wR2 = [�w(F0
2 – Fc2)2 / �wF0
2]1/2; w = 1/[2(F02) + (aP)2 + bP] where P =
(max(F02,0) + 2Fc2)/3 with a = 0.0840 (1), 0.0542 (2), 0.0521 (3) and b = 0.2349 (1).
Table 2
Selected bond lengths (Å) for compound 1.
Cd1–N3 2.282(4) Cd1–O3 2.296(3)
Cd1–O1 2.292(3) Cd1–O4b 2.338(3)
Cd1–O2a 2.270(3) Cd1–O1w 2.285(3)
Symmetry codes: (a) –x, –y, –z + 1; (b) –x + 1, –y + 1, –z + 1.
Table 3
Hydrogen-bond geometry (Å, deg) in compound 1.
D–H···A H···A D···A D–H···A
N6–H6A···N1a 2.24 3.098(6) 175
N6–H6B···O2w 2.31 3.132(5) 161
N7–H7···O2w 1.97 2.788(5) 158
C2–H2···O2b 2.22 3.070(6) 151
O1w–H12w···N9 1.94 2.757(5) 148
O1w–H11w···O3c 1.86 2.693(4) 163
O2w–H21w···O1d 2.08 2.937(4) 160
O2w–H22w···O4e 2.04 2.893(4) 167
Symmetry codes: (a) –x + 2, –y, –z + 2; (b) –x + 1, –y, –z + 1; (c) x – 1, y, z; (d) x, y, z + 1; (e) –x + 2, –y + 1, –z + 2.
Table 4
Selected bond lengths (Å) for compound 2.
Cu1–N7 1.989(3) Cu1–O3a 2.030(2)
Cu1–O1 2.383(3) Cu1–O4 2.039(3)
Cu1–O2a 1.984(3) Cu1–O1w 2.224(3)
Symmetry code: (a) x, –y – 1/2, z – 1/2.
Table 5
Hydrogen-bond geometry (Å, deg) in compound 2.
D–H···A H···A D···A D–H···A
N6–H61···O2a 2.01 2.816(5) 156
N6–H62···O4b 2.20 3.031(4) 162
C8–H8···N1c 2.81 3.600(5) 144
O1w–H11w···N9d 1.98 2.823(4) 172
O1w–H12w···O2w 1.91 2.751(5) 173
O2w–H21w···O3e 2.05 2.903(5) 177
O2w–H22w···O1f 2.03 2.870(5) 171
Symmetry codes: (a) x, –y – 1/2, z – 1/2; (b) x + 1, y, z; (c) x – 1, y, z; (d) –x + 1, –y, –z + 2; (e) x, y, z – 1; (f) x – 1, y, z – 1.
Table 6
Selected bond lengths (Å) for both complex units of compound 3.
Cu1A–N7A 1.997(2) Cu1B–N7B 2.008(2)
Cu1A–O1A 1.955(2) Cu1B–O1B 1.944(2)
Cu1A–O2A 1.941(2) Cu1B–O2B 1.960(2)
Cu1A–O1Aw 1.946(2) Cu1B–O1Bw 1.919(2)
Cu1A–O2Aw 2.341(2) Cu1B–O2Bw 2.369(2)
Table 7
Hydrogen-bond geometry (Å, deg) in compound 3.
D–H···A H···A D···A D–H···A
N1A–H1A···O2Ba 2.05 2.903(3) 174
N2A–H2A2···O3Ba 2.02 2.877(3) 173
N2A–H2A1···O2Bwb 2.17 2.952(3) 152
N1B–H1B···O3Ac 1.92 2.731(3) 156
N2B–H2B2···O4Ac 2.04 2.883(3) 168
N2B–H2B1···N3Bd 2.22 3.080(3) 177
O1Aw–H1A2w···O6A 1.77 2.606(3) 169
O2Aw–H2A2w···O4Be 1.96 2.775(3) 167
O1Bw–H1B2w···O6B 1.75 2.568(3) 158
O1Bw–H1B1w···O6Aa 1.80 2.631(3) 168
O2Bw–H2B1w···N3Af 2.12 2.959(3) 172
Symmetry codes: (a) –x + 1, –y + 1, –z; (b) –x, –y + 1, –z; (c) x – 1, y, z + 1; (d) –x – 1, –y + 1, –z; (e) –x + 1, –y + 1, (f) x, y + 1, z.
Figure Captions
Fig. 1. (a) Coordination environment of the metal and (b) polymeric chain in compound 1.
Fig. 2. Hydrogen bonding interactions in the crystal packing of compound 1.
Fig. 3. Crystal packing of {[M(�-ox)(H2O)(Hade)]·2(Hade)·(H2O)}n compounds [M(II) = Co and Zn] showing �–� stacking of the adenine molecules (dashed lines).
Fig. 4. (a) Coordination environment of the metal centre and (b) polymeric chain of compound 2.
Fig. 5. View of a layer of compound 2 sustained by �–� interactions (dashed lines).
Fig. 6. (a) Hydrogen bonding interactions among the structural units of compound 2. (b) View of crystal packing in the crystallographic ab–plane.
Fig. 7. Complex units (A and B) in compound 3.
Fig. 8. Superposition of units A and B, and the optimized model (black).
Fig. 9. Infinite tapes of metal-organic quartets in compound 3.
Fig. 10. (H2O)10 aggregates (a) experimental and (b) after the geometric optimization.
Fig. 11. Thermal dependence of MT (�) and M (�) for compound 2. (–) best theoretical fit (see text). Inset: perpendicular orbital topology of the Cu–ox–Cu framework.
References
[1] B. Lippert, Chem. Biodiversity 5 (2008) 1455.
[2] (a) M. Byres, P. J. Cox, G. Kay, E. Nixon, CrystEngComm 11 (2009) 135; (b) M. A.
Galindo, A. Houlton, Inorg. Chim. Acta 362 (2009) 625; c) B. Lippert, D. Gupta,
Dalton Trans. (2009) 4619; (d) J. A. R. Navarro, B. Lippert, Coord. Chem. Rev. 222
(2001) 219.
[3] M. J. Hannon, Chem. Soc. Rev. 36 (2007) 280.
[4] (a) M. Legraverend, D. S. Grierson, Bioorg. Med. Chem. 14 (2006) 3987; (b) S.
Sikova, S. J. Rowan, Chem. Soc. Rev. 34 (2005) 9.
[5] (a) K. Ghosh, T. Sen, R. Fröhlich, Tetrahedron Letters 48 (2007) 7022; (b) F.
Zamora, M. Kunsman, M. Sabat, B. Lippert, Inorg. Chem. 36 (1997) 1583.
[6] (a) J. An, S. J. Geib, N. L. Rosi, J. Am. Chem. Soc. 132 (2010) 38; (b) S. Verma, A.
Kumar-Mishra, J. Kumar, Acc. Chem. Res. 43 (2010) 79; (c) J. Kumar, S. Verma,
Inorg. Chem. 48 (2009) 6350; (d) F. Zamora, M. P. Amo-Ochoa, P. J. Sanz-Miguel, O.
Castillo, Inorg. Chim. Acta 362 (2009) 691; (e) J. P. García-Terán, O. Castillo, A.
Luque, U. García-Couceiro, P. Román, L. Lezama, Inorg. Chem. 43 (2004) 4549.
[7] (a) I. Dance, M. Scudder, J. Chem. Soc., Dalton Trans. (1998) 1341; (b) J. C. M.
Rivas, L. Brammer, New J. Chem. 22 (1998) 1315; (c) A. S. Batsanov, P. Hubberstey,
C. E. Russell, P. H. Walton, J. Chem. Soc., Dalton Trans. (1997) 2667.
[8] (a) D. Choquesillo-Lazarte, M. P. Brandi-Blanco, I. García-Santos, J. M. González-
Pérez, A. Castineiras, J. Niclós-Gutiérrez, Coord. Chem. Rev. 252 (2008) 1241; (b) A.
Houlton, J. Inorg. Biochem. 86 (2001) 58.
[9] J. A. R. Navarro, B. Lippert, Coord. Chem. Rev. 186 (1999) 653.
[10] (a) S. Pérez-Yáñez, O. Castillo, J. Cepeda, J. P. García-Terán, A. Luque, P. Román,
Eur. J. Inorg. Chem. (2009) 3889; (b) J. P. García-Terán, O. Castillo, A. Luque, U.
García-Couceiro, G. Beobide, P. Román, Cryst. Growth Des. 7 (2007) 2594; (c) J. P.
García-Terán, O. Castillo, A. Luque, U. García-Couceiro, G. Beobide, P. Román, Inorg.
Chem. 46 (2007) 3593; (d) J. P. García-Terán, O. Castillo, A. Luque, U. García-
Couceiro, G. Beobide, P. Román, Dalton Trans. 7 (2006) 902; (e) J. P. García-Terán, O.
Castillo, A. Luque, U. García-Couceiro, P. Román, F. Lloret, Inorg. Chem. 43 (2004)
5761.
[11] M. D. Wyatt, J. M. Allan, A. Y. Lau, T. E. Ellenberger, L. D. Samson, BioEssays
21 (1999) 668.
[12] A. Earnshaw, Introduction to Magnetochemistry, Academic Press, London, 1968.
[13] CrysAlis RED, version 1.170; Oxford Diffraction: Wroclaw, Poland, 2003.
[14] A. Altomare, M. Cascarano, C. Giacovazzo, A. Guagliardi, J. Appl. Crystallogr. 26
(1993) 343.
[15] G. M. Sheldrick, SHELXL97, Program for the Solution of Crystal Structures,
Universitat of Göttingen: Germany, 1997.
[16] L. J. Farrugia, J. Appl. Cryst. 32 (1999) 837.
[17] A. D. Becke, J. Chem. Phys. 98 (1993) 5648.
[18] (a) C. Lee, W. Yang, R. G. Parr, Phys. Rev. B37 (1988) 785; (b) B. Miehlich, A.
Savin, H. Stoll, H. Preuss, Phys. Lett. 157 (1989) 200.
[19] M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R.
Cheeseman, J. A. Jr. Montgomery, T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam,
S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.
A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M.
Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P.
Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E.
Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y.
Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S.
Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K.
Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J.
Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L.
Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M.
Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, J. A.
Pople, Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
[20] (a) A. K. Rappe, E. R. Bernstein, J. Phys. Chem. A 104 (2000) 6117; (b) O. S.
Sukhanov, O. V. Shiskin, L. Gorb, Y. Podolyan, J. Leszczynskii, J. Phys. Chem. B 107
(2003) 2846; (c) A. V. Morozov, T. Kortemme, K. Tsemekhman, D. Baker, Proc. Natl.
Acad. Sci. U.S.A. 101 (2004) 6946.
[21] See for example: (a) M. C. Das, S. K. Ghosh, E. C. Sanudo, P. K. Bharadwaj,
Dalton Trans. (2009) 1644; (b) U. García-Couceiro, O. Castillo, A. Luque, J. P. García-
Terán, G. Beobide, P. Román, Eur. J. Inorg. Chem. (2005) 4280; (c) I. Imaz, G. Bravic,
J. P. Sutter, Dalton Trans. (2005) 2681.
[22] M. A. Salam, H. Q. Yuan, T. Kikuchi, N. A. Prasad, I. Fujisawa, K. Aoki, Inorg.
Chim. Acta 362 (2009) 1158.
[23] Z. Hossain, F. Huq, J. Inorg. Biochem. 90 (2002) 97.
[24] (a) S. Urashima, H. Asami, M. Ohba, H. Saigusa J. Phys. Chem. A 2010, DOI:
10.1021/jp102918k; (b) D. M. Close, C. E. Crespo-Hernández, L. Gorb, J. Leszczynski,
J. Phys. Chem. A 112 (2008) 12702; (c) C. E. Crespo-Hernández, B. Cohen, P. M.
Hare, B. Kohler, Chem. Rev. 104 (2004) 1977.
[25] (a) P. Brandi-Blanco, P. J. Sanz-Miguel, B. Müller, E. Gil-Bardaji, M. Willermann,
B. Lippert, Inorg. Chem. 48 (2009) 5208; (b) B. Lippert, Coord. Chem. Rev. 200-202
(2000) 487.
[26] See for example: (a) E. Corral, H. Kooijman, A. L. Spek, J. Reedijk, New J. Chem.
31 (2007) 21; (b) P. Amo-Ochoa, M. I. Rodríguez- Tapiador, S. S. Alexandre, C. Pastor,
F. Zamora, J. Inorg. Biochem. 99 (2005) 1540; (c) M. S. Luth, E. Freisinger, F. Glahe,
B. Lippert, Inorg. Chem. 37 (1998) 5044.
[27] (a) X. D. Zhang, C. H. Ge, F. Yu, Q. T. Liu, M. L. Zhu, Acta Crystallogr. C63
(2007) m519; (b) L. S. Long, Y. R. Wu, R. B. Huang, L. S. Zheng, Inorg. Chem. 43
(2004) 3798; (c) J. M. Ugalde, I. Alkorta, J. Elguero, Angew. Chem. Int. Ed. 39 (2000)
717.
[28] N. H. Hu, Z. G. Li, J. W. Xu, H. Q. Jie, J. J. Niu, Cryst. Growth Des. 7 (2007) 15.
[29] (a) M. Mascal, L. Infantes, J. Chisholm, Angew. Chem., Int. Ed. 45 (2006) 32; (b)
L. Infantes, J. Chisholm, S. Motherwell, CrystEngComm 5 (2003) 480; (c) L. Infantes,
S. Motherwell, CrystEngComm 4 (2002) 454.
[30] Y. Xie, J. Ni, F. Zheng, Y. Cui, Q. Wang, S, Weng-Ng, W. Zhu, Cryst. Growth
Des. 9 (2009) 118.
[31] J. Bonner, M. E. Fisher, Phys. Rev. 135 (1964) A640.
[32] (a) O. Castillo, A. Luque, M. Julve, F. Lloret, P. Román, Inorg. Chim. Acta 315
(2001) 9; (b) O. Castillo, A. Luque, F. Lloret, P. Román, Inorg. Chem. Commun. 4
(2001) 350; (c) S. Kitagawa, T. Okubo, S. Kawata, M. Kondo, M. Katada, H.
Kobayashi, Inorg. Chem. 34 (1995) 4790; (d) M. Julve, M. Verdaguer, A. Gleizes,
Inorg. Chem. 23 (1984) 3808.
[33] (a) J. Cabrero, N. B. Amor, C. de Graaf, F. Illas, R. Caballol, J. Phys. Chem. A 104
(2000) 9983; (b) J. Cano, P. Alemany, S. Alvarez, M. Verdaguer, E. Ruiz, Chem. Eur. J.
4 (1998) 476 and references therein.