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: oscar.castillo@ehu.es, antonio.luque@ehu.es

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.

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