Structural diversity in a copper(II)/isophthalato/9-methyladenine system. from one- to three-dimensional metal-biomolecule frameworks

Article abstract of DOI:10.1021/cg400458a

The synthesis, X-ray single crystal structure analyses, and physicochemical characterization of copper(II)-isophthalato coordination polymers containing the 9-methyladenine nucleobase {[Cu(μ-iso)(9Meade)(H₂O) ₂]}_n (1), {[Cu(μ-iso)(μ-9Meade)]}_n (2), {[Cu₂(μ₄-iso)₂(9Meade)₂] ·2H₂iso}_n (3), {[Cu₂(μ₃- iso)₂(μ-9Meade)(H₂O)]·H₂O} _n (4), and {[Cu₂(μ₃-iso)₂(μ- 9Meade)(H₂O)₂]·1.5H₂O}_n (5) (where iso = isophthalato and 9Meade = 9-methyladenine) are reported. Compound 1 contains neutral chains in which the isophthalato dianion acts as a bridging ligand, while the methylated nucleobase behaves as N7-coordinated terminal ligand. Compound 2 exhibits a two-dimensional network in which the aromatic dicarboxylate ligand and the nucleobase act as bidentate bridging ligands. Compound 3 is based on dimeric paddle-wheel shaped entities in which the copper(II) atoms are bridged by means of four isophthalato ligands to give a NO₄ chromophore with the N7 nitrogen atom of the 9-methyladenine filling the axial position. The linkage of the dimeric entities through the second carboxylate group of the dianions leads to covalent layers that are further connected to give a supramolecular three-dimensional pillared structure by means of hydrogen bonding and π-π interactions involving noncoordinated isophthalic acid molecules. Compounds 4 and 5 contain paddle-wheel [Cu ₂(μ-iso)₄(9Meade)₂] entities and [Cu(H ₂O)] or [Cu(H₂O)₂] units connected by means of the isophthalate and 9-methyladenine bidentate bridging ligands.

Full text of DOI:10.1021/cg400458a

Article
pubs.acs.org/crystal
Structural Diversity in a Copper(II)/Isophthalato/9-Methyladenine
System. From One- to Three-Dimensional Metal-Biomolecule
Frameworks
Sonia Perez-Yanez,* Garikoitz Beobide, Oscar Castillo,* Javier Cepeda, Antonio Luque,
́
́
̃
and Pascual Roman
́
Departamento de Química Inorgan
E-48080 Bilbao, Spain
́
ica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, UPV/EHU, Apartado 644,
S
* Supporting Information
ABSTRACT: The synthesis, X-ray single crystal structure
analyses, and physicochemical characterization of copper(II)-
isophthalato coordination polymers containing the 9-methyl-
adenine nucleobase {[Cu(μ-iso)(9Meade)(H2O)2]}n (1),
{[Cu(μ-iso)(μ-9Meade)]}n (2), {[Cu2(μ4-iso)2(9Meade)2]-
·2H2iso}n (3), {[Cu2(μ3-iso)2(μ-9Meade)(H2O)]·H2O}n (4),
and {[Cu2(μ3-iso)2(μ-9Meade)(H2O)2]·1.5H2O}n (5) (where
iso = isophthalato and 9Meade = 9-methyladenine) are
reported. Compound 1 contains neutral chains in which the
isophthalato dianion acts as a bridging ligand, while the
methylated nucleobase behaves as N7-coordinated terminal
ligand. Compound 2 exhibits a two-dimensional network in
which the aromatic dicarboxylate ligand and the nucleobase act as bidentate bridging ligands. Compound 3 is based on dimeric
paddle-wheel shaped entities in which the copper(II) atoms are bridged by means of four isophthalato ligands to give a NO4
chromophore with the N7 nitrogen atom of the 9-methyladenine filling the axial position. The linkage of the dimeric entities
through the second carboxylate group of the dianions leads to covalent layers that are further connected to give a supramolecular
three-dimensional pillared structure by means of hydrogen bonding and π−π interactions involving noncoordinated isophthalic
acid molecules. Compounds 4 and 5 contain paddle-wheel [Cu2(μ-iso)4(9Meade)2] entities and [Cu(H2O)] or [Cu(H2O)2]
units connected by means of the isophthalate and 9-methyladenine bidentate bridging ligands.
INTRODUCTION
■
Design of coordination frameworks via deliberate selection of
metals and multifunctional ligands, including biological relevant
molecules such as nucleobases,1 is one of the most attractive
topical areas of chemistry due to their fascinating structural
diversity and their development as new materials with tunable
properties.2 An essential part of coordination polymer design,
and the wider field of crystal engineering, is the use of building
blocks that combine the flexibility and necessary interconnec-
tion capability to achieve the desired dimensionality, but also
the sufficient strength to permit a predictable core which
maintains their structural integrity throughout the construction
of the solid. In this sense, [M2(μ-L)4X2] entities have been
known for a long time since the crystal structure of the [Cu2(μ-
acetato)4(H2O)2] compound was reported.3 The attractiveness
of the paddle-wheel (PW) motif is that structural and
functional changes can be achieved almost at will by simply
varying the metal cores, the bridging moieties, or the X-
Figure 1. Schematic representation showing the assembly process of
Received: March 27, 2013
paddle-wheel dimeric entities (circles) with (a) flexible dicarboxylate
(bent lines) and (b) rigid linear ligands (sticks).
Revised: May 27, 2013
© XXXX American Chemical Society
A
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recognition processes. The functional versatility of the
dinuclear PW motifs makes them particularly suitable as
secondary building units (SBUs) for the design and synthesis of
numerous crystalline materials ranging from zero-dimensional
(0D) species to three-dimensional (3D) coordination polymers
with interesting properties in areas such as magnetism,
medicine, catalysis, and gas storage.2,5,6
Continuing our previous work based on the use of dicopper
PW entities built up from adenine nucleobase and carboxylato
ligands, we have designed and synthesized five new compounds
employing 9-methyladenine as the nucleobase and benzene-1,3-
dicarboxylic acid (isophthalic acid) as the carboxylato ligand
precursor.
Aromatic spacers provide greater rigidity because their
geometric characteristics are limited, allowing restriction of
the structural variability. Furthermore, these ligands provide the
system the ability to modify or functionalize the channels
without altering the 3D framework. An example of this strategy
is the isoreticular diversity of the family of compounds derived
from the MOF-5, [Zn4O(benzene-1,4-dicarboxylate)3], wherein
the replacement of the dicarboxylic acid ligand by longer
spacers or the modification with different functional groups,
without modifying the disposition of the carboxylate groups,
allows an increase of the pore size and/or functionalization of
the walls thereof.7 Furthermore, the use of rigid aromatic
dicarboxylates in conjunction with adenine and different metals,
such as zinc or nickel, has demonstrated the suitability for
obtaining permanent porous structures.8 In the particular case
of PW shaped dimeric units, the use of aromatic dicarboxylic
ligands allows structures to be obtained ranging from isolated
clusters to porous 3D systems, as well as mono- and two-
dimensional (2D) systems.9
Figure 2. Structures based on [Cu2(μ-isophthalato)4] dimeric entities:
(a) non-centrosymmetric dimer giving rise to clusters and (b)
centrosymmetric dimer rendering layers.
ligands.4 These axial positions, usually occupied by solvent
molecules, can be replaced by nucleobase ligands, thus
increasing the ability of the systems to be involved in molecular
Taking advantage of the specific [Cu2(μ-dicarboxyla-
to)4(X)2] dimeric entity, it bears mentioning that when using
Table 1. Crystallographic Data and Structure Refinement Details of Compounds 1−5
a
b
1
2
3
4
5
empirical formula
formula weight
crystal system
space group
a (Å)
C14H15CuN5O6
412.85
C14H11CuN5O4
376.82
C44H34Cu2N10O16
1085.90
monoclinic
P21/a
C22H19Cu2N5O10
640.51
C22H19Cu2N5O11.5
667.53
monoclinic
P21/c
tetragonal
monoclinic
P21/a
triclinic
P42 c
P1
̅
̅
1
9.289(4)
10.210(5)
17.241(7)
90
16.6280(4)
16.6280(4)
11.0490(5)
90
13.458(2)
13.046(1)
13.826(2)
90
9.628(1)
19.315(1)
14.872(1)
90
9.2360(4)
12.4650(7)
23.2130(9)
90.297(4)
96.642(4)
104.656(4)
2566.5(2)
4
b (Å)
c (Å)
α (°)
β (°)
γ (°)
V (Å3)
99.938(3)
90
90
96.922(12)
90
108.705(3)
90
90
1611(1)
4
3054.9(2)
8
2409.9(6)
2
2619.6(2)
4
Z
ρcalcd (g cm−3
)
1.703
1.639
1.496
1.624
1.727
μ (mm−1
)
1.402
1.460
0.963
1.687
2.695
reflections collected
unique data/parameters
Rint
12192
10369
13662
40063
19325
3408/236
0.0471
3301/120
0.0404
4240/321
0.1358
7084/339
0.0343
9044/715
0.0828
c
goodness of fit (S)
0.929
1.071
0.894
1.041
0.951
d
e
R1 /wR2 [I > 2σ(I)]
0.0395/0.0932
0.0559/0.0979
0.1286/0.2582
0.1420/0.2662
0.1050/0.2571
0.2040/0.3001
0.0628/0.1621
0.0748/0.1688
0.0614/0.1566
0.0939/0.1736
d
e
R1 /wR2 [all data]
a
9-Methyladenine bridging ligand is disordered into two coplanar arrangements with inverted orientation regarding the coordination mode (μ-
b
1κN1:2κN7/μ-1κN7:2κN1). Nonmerohedral twin with a twin law of (1.0035 0.0019 0.0162/−0.0005 0.9996 0.0001/−0.1129 −0.0205 0.9941)
c
d
e
and a percentage of the minor domain of 29%. S = [∑w(F0 − Fc2)2/(Nobs − Nparam)]1/2. R1 = ∑∥F0| − |Fc∥/∑|F0|. wR2 = [∑w(F0 − Fc2)2/
2
2
∑wF0 ]1/2; w = 1/[σ2(F0 ) + (aP)2 + bP] where P = (max(F0 ,0) + 2Fc2)/3 with a = 0.0637 (1), 0.0001 (2), 0.1589 (3), 0.0809 (4), 0.1066 (5), and
2
2
2
b = 11.3145 (2).
B
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Figure 3. (a) Coordination environment and (b) polymeric chain in compound 1.
aliphatic dicarboxylic acids, the kinetics of the reaction makes
the system to evolve toward one-dimensional (1D) struc-
tures.10 To visualize this effect, we can just imagine two dimeric
entities linked by a unique bridging dicarboxylic ligand and
think about the behavior of a second dicarboxylic ligand: (i) it
can wait until getting close to a third dimeric unit and join it to
generate extended 2D or 3D structures, or (ii) it can connect to
the already linked second dimeric unit, as it happens in the
{[Cu2(μ4-glutarato/pimelato)2(methyladenine)2]}n compounds
previously reported by our group.10 The remaining ligands are
opposite oriented to the first and second ones, and, therefore,
they have no access to the second dimeric entity, so they must
wait until a third unit approximates, and once a dicarboxylato
ligand is bound, the next one will follow it. The repetition of
this process generates chains of dimeric units doubly bridged by
the dicarboxylic ligands, as it is schematized in Figure 1a.
When rigid aromatic ligands are used, they cannot twist
enough to establish a double bridge between the metal centers
and the structure evolves toward more complex architectures.
In particular for terephthalic acid, a typical example of a
bridging ligand in crystal engineering, the coplanar disposition
of the carboxylato groups at 180° generates a 2D structure
(Figure 1b). However, when this anion is functionalized in the
ortho position, for instance, the 2-chloroterephthalic ligand, the
steric hindrance of the substituents forces the carboxylato
groups to be arranged perpendicular, so the metal−organic
C
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polymer grows along the three dimensions leading to a porous
framework.11
RESULTS AND DISCUSSION
■
Crystal Structure of {[Cu(μ-iso)(9Meade)(H2O)2]}n (1).
Compound 1 contains neutral chains in which the isophthalic
With regard to the isophthalic acid, two dimeric entities with
different relative orientation of the ligands may coexist in
solution leading to (a) discrete clusters when the dimer is non-
centrosymmetric, with all uncoordinated carboxylate groups
pointing toward the same end of the dimer,12 or (b) infinite
layers when the dimeric entity is centrosymmetric, with free
carboxylate groups pointing toward both ends (Figure 2).13
Usually, discrete entities or crystal structures of lower
dimensionality are the kinetically favored product as they are
formed by the combination of a smaller number of constituents.
However, in order to isolate these kinetically favored structures,
they must be insoluble enough to precipitate, preventing the
system to evolve toward more extended structures that are
thermodynamically more stable.
Table 2. Selected Bond Lengths (Å) of Compound 1
Cu1−N7
Cu1−O11
Cu1−O21
2.030(3)
2.189(2)
2.724(2)
Cu1−O22
Cu1−O1w
Cu1−O2w
2.000(2)
1.963(2)
1.976(2)
In all these systems, if the apical position of the dimeric
entities is filled by a bridging ligand, the resulting structure
increases its connectivity achieving even a 3D coordination
network.14 In any case, it is well recognized that the crystal
engineering of coordination polymers with desired structures
and specific properties still remains a difficult challenge, since
there is a variety of factors influencing the self-assembly
process, such as the coordination geometry and the oxidation
state of the metal ions, metal-to-ligand ratio, solvents,
temperature, and/or counterions.
EXPERIMENTAL SECTION
■
Synthesis. A mixture of single crystals of compounds 1−5 was
obtained by slow diffusion of a methanolic solution (5 mL) of
Cu(NO3)2·3H2O (0.2 mmol, 0.0483 g) into an aqueous-methanolic
solution (1:1, 10 mL) of 9-methyladenine (0.2 mmol, 0.0307 g) and
isophthalic acid (0.2 mmol, 0.0336 g). The diffusion of the reactants
generates different concentrations and stoichiometric conditions,
which gives rise to a mixture of crystals stratified along the diffusion
tube after several weeks. The similar morphology and color of the
crystals of compounds 1−5 have prevented their manual separation.
All attempts to achieve pure samples of each compound have been
unsuccessful except for compound 1 which has been obtained by
direct mixture of reactants in aqueous-methanolic solution. Yield: 80−
90%. Anal. Calcd for {[Cu(μ-iso)(9Meade)(H2O)2]}n (1),
C14H15CuN5O6 (412.85 g/mol): C, 40.73; H, 3.66; N, 16.96; Cu,
15.39%. Found: C, 40.99; H, 3.41; N, 17.12; Cu, 15.11%. IR (cm−1,
KBr pellet): 3380m for ν(O−H); 3320m for (ν(NH2) + 2δ(NH2));
3120m for ν(C8−H + C2−H + NH2) + ν(C−H)iso; 2920m for
ν(CH3); 1688s for νas(O−C−O); 1602s for (ν(CC) + δ(NH2));
1583m for ν(C4−C5); 1550s for ν(N3−C4−C5); 1492w, 1475w,
1443w, 1431w for (δ(C2−H + C8−N9) + ν(C8−H)); 1415w for
δ(N1−C6−H6); 1387w, 1374m, 1338w for ν(C5−N7−C8); 1302w,
1272w, 1249w, 1238w for (ν(N9−C8 + N3−C2) + δ(C−H) + νs(O−
C−O)); 1188w, 1161w for (δ(C8−H) + ν(N7−C8)); 1068m, 1004w,
961w for τ(NH2); 931w, 908w, 897w for (ν(N1−C6) + τ(NH2));
836w, 794w, 762w, 737m, 727m, 721m for δ(O−C−O); 653w, 591m
for ring deformation; 572w, 539w, 519w, 467w, 440w, 416w for ν(M−
O + M−N).
X-ray Diffraction Data Collection and Structure Determi-
nation. Diffraction data of single crystals were collected at 100(2) K
on a STOE IPDS (1, 3, 4) and on an Oxford Diffraction Xcalibur (2)
diffractometer with graphite-monochromated Mo Kα radiation (λ =
0.71073 Å), and on a Supernova (5) diffractometer Cu Kα radiation (λ
= 1.5418 Å). The data reduction was done with the X-RED15 and
CrysAlis RED16 programs, respectively. Structures were solved by
direct methods using the SIR92 program17 and refined by full-matrix
least-squares on F2 including all reflections (SHELXL97).18 All
calculations were performed using the WINGX crystallographic
software package.19 Crystal data and details of the refinement
parameters of the compounds are given in Table 1.
Figure 4. (a) Layer of chains and (b) hydrogen bonding interactions
between Watson−Crick faces in compound 1.
a
Table 3. Selected Bond Lengths (Å) of Compound 2
Cu1−N1
Cu1−N7b
Cu1−O11a
2.140(11)
2.056(12)
2.660(9)
Cu1−O12a
Cu1−O21
Cu1−O22
1.784(12)
2.140(10)
2.119(11)
a
Symmetry codes: (a) y, −x + 2, −z; (b) y, −x + 1, −z.
ligand bridges two metal centers with a κ2O,O′:κO″
coordination mode, while 9-methyladenine acts as terminal
ligand (Figure 3). The copper(II) atom shows a distorted 4 + 1
+ 1 octahedral environment in which the basal plane consists of
the O22 oxygen atom of the isophthalic ligand, the imidazolic
N7 atom of the 9-methyladenine, and two water molecules in
trans arrangement. The metal coordination sphere is filled by
one of the oxygen atoms of each carboxylato group of the
isophthalic ligand (O11 and O21) through the axial positions
with Cu−O bond distances substantially longer than the
equatorial ones due to the Jahn−Teller distortion (Table 2). In
fact, the coordination bond distance involving O21 oxygen
atom is so long (2.724 Å) that the continuous shape
measurements20 result in a coordination geometry closer to a
square pyramid (SSPY = 0.58) than to an octahedron (SOh
=
4.55).
The asymmetric coordination of the two carboxylato groups
of the isophthalic ligand generates zigzag chains spreading
along the c axis, where the equatorial planes of two consecutive
chromophores are rotated 90°. The exocyclic amino group of
D
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Figure 5. (a) Cu(II) coordination environment and (b) coplanar disorder of the 9-methyladenine in compound 2.
Figure 6. (a) View of the rectangular layer throughout the crystallographic [001] direction and (b) stacking along the a axis showing the interactions
between the layers in compound 2.
the 9-methyladenine molecule forms an intramolecular hydro-
gen bonding interaction with the O21 oxygen atom of the
isophthalic ligand. Moreover, the O2w crystallization water
molecule also establishes an intramolecular hydrogen bond with
the noncoordinated O12 oxygen atom. The chains are linked
through hydrogen bonding interactions between the coordina-
tion water molecules and the O12 and O21 oxygen atoms of
the dicarboxylato, giving rise to layers that are spreading along
E
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between the aromatic rings of the 9-methyladenine and
isophthalato ligand (see Supporting Information).
Crystal Structure of {[Cu(μ-iso)(μ-9Meade)]}n (2).
Compound 2 is built up from the stacking of metal−organic
layers in which the copper atoms are bridged by bisbidentate
isophthalato dianions and bidentate 9-methyladenine ligands.
The copper(II) atom is hexacoordinated to four oxygen atoms
belonging to two carboxylato groups and two nitrogen atoms of
two 9-methyladenine molecules (Table 3) to give a cis-CuO4N2
donor set with a distorted octahedral geometry (SOh = 7.57)
due to the acute bite angle of the two chelating rings (ca. 55°).
As it is shown in Figure 5, the bridging 9-methyladenine ligand
is disordered into two coplanar positions showing the most
usual bidentate mode for this nucleobase, μ-κN1:κN7,21 but
with a reverse orientation, μ-1κN1:2κN7 and μ-1κN7:2κN1.
The coexistence of two bridging ligands results in a 2D
network with three metal−organic rings: (i) 10 Å × 10 Å
squares formed by four isophthalato ligands, (ii) 10 Å × 7 Å
rectangles built by two isophthalato ligands and two 9-
methyladenine molecules, and (iii) 7 Å × 7 Å squares with
four 9-methyladenine molecules (Figure 6a). This 2D arrange-
ment corresponds to the Shubnikov tetragonal sql topology,
the point symbol being (44.62).22 The offset stacking of these
layers along the [001] crystallographic direction is sustained by
means of π−π interactions involving the isophthalato and the 9-
methyladenine ligands with ···ABAB··· packing sequence
(Figure 6b).
Figure 7. Layers of compound 3 showing the isophthalic acid
molecules inserted among them.
Crystal Structure of {[Cu2(μ4-iso)2(9Meade)2]·2H2iso}n
(3). Compound 3, unlike compounds 1 and 2, is built from the
linkage of dimeric PW shaped entities. As described in Figure 2,
there are two types of possible structures with isophthalato
containing PW units: isolated octahedral clusters and infinite
2D systems. The coordination of the 9-methyladenine to the
apical position in the dimeric unit of compound 3 precludes the
formation of the octahedral cluster since it would imply the
presence of six of these nucleobases in the central cavity of the
hexamer with a diameter of ca. 10 Å, for which there is not
enough void. Therefore, the generated structure comprises
infinite layers among which noncoordinated isophthalic acid
molecules are inserted (Figure 7). Each dimeric entity, sited in
an inversion center, consists of four isophthalato ligands that
bridge the copper(II) atoms and two 9-methyladenine
molecules coordinated in the axial positions through the N7
nitrogen atom (Figure 8). The pentacoordinated copper(II)
atom shows a square pyramidal environment (SSPY = 0.39) with
equatorial distances of ca. 1.96 Å and a slightly greater axial
distance of 2.16 Å (Table 4).
Figure 8. Dimeric entity of compound 3.
The second carboxylato group of the isophthalato ligand
connects two adjacent dimeric entities to lead to a 2D network
of square rings, with a Shubnikov tetragonal sql topology and a
(44.62) point symbol, as it is shown in Figure 9a. For the
construction of this network, one of the carboxylato groups is
rotated ca. 40° with respect to the mean plane of the ring. This
rotation is transferred to the relative orientation between
adjacent dimeric entities so that the rings of the layer are not
planar but they acquire certain corrugation (Figure 9b).
The 9-methyladenine ligand forms an intramolecular N6−
H···O12 hydrogen bonding interaction, and it is disposed
outward the layer to interact with the solvate isophthalic acid
molecules which act as supramolecular linkers between the
layers. These inclusion molecules use one of the carboxylic
a
Table 4. Selected Bond Lengths (Å) of Compound 3
Cu1−N7
Cu1−O11
Cu1−O12a
2.161(10)
1.952(8)
1.975(8)
Cu1−O21b
Cu1−O22c
Cu1···Cu1a
1.948(8)
1.968(9)
2.682(3)
a
Symmetry codes: (a) −x, −y + 1, −z; (b) −x + 1/2, y + 1/2, −z; (c)
x − 1/2, −y + 1/2, z.
the bc plane, as it is shown in Figure 4. These layers are held
together by means of a double N6−H···N1 hydrogen bonding
interaction between the Watson−Crick faces of the terminal
nucleobases and a hydrogen bonding interaction between the
N3 atom of the 9-methyladenine and the O1w water molecule.
The crystal cohesiveness is reinforced by π−π interactions
groups to establish a R2 (8) hydrogen bonding ring with the
2
Watson−Crick face of a nucleobase, whereas the other one
F
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Figure 9. (a) 2D network showing the rotation of the carboxylato group and (b) relative disposition between the SBUs induced by the corrugation
of the isophthalato ligand in compound 3.
a
interacts with the N3 nitrogen atom of the 9-methyladenine
ligand that is anchored to the dimeric entity on the opposite
vertex of the square cavity. The supramolecular architecture is
reinforced by π−π interactions between the isophthalic acid
molecules and the nucleobases.
Crystal Structure of {[Cu2(μ3-iso)2(μ-9Meade)(H2O)]-
·H2O}n (4). The 3D network of 4 is formed by PW shaped
[Cu2(μ-iso)4(9Meade)2] dimeric entities and [Cu(H2O)] units
connected by means of the isophthalate anion and 9-
methyladenine. Table 5 gathers coordination distances of the
metal centers of both entities.
Table 5. Selected Bond Lengths (Å) of Compound 4
dimeric entity
Cu1−N1
Cu1−O11
Cu1−O12a
Cu1−O41b
Cu1−O42c
Cu1···Cu1a
monomeric entity
Cu2−N7
Cu2−O21d
Cu2−O22d
Cu2−O31
Cu2−O1w
2.191(4)
1.959(3)
1.958(3)
1.983(3)
1.994(3)
2.671(1)
2.032(4)
2.116(3)
1.970(3)
1.940(3)
2.167(4)
a
Symmetry codes: (a) −x + 3, −y + 1, −z + 2; (b) x + 1/2, −y + 1/2,
z; (c) −x + 5/2, y + 1/2, −z + 2; (d) x − 1/2, −y + 1/2, z − 1.
The copper atom of the dimeric entity exhibits a square
pyramidal coordination environment (SSPY = 0.36) in which the
Figure 10. (a, b) Structural entities in compound 4.
G
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Article
The copper(II) atoms of both dimeric entities (A and B)
present a square pyramidal environment (SSPY = 0.42 and 0.52,
respectively), and they are bridged by isophthalato ligands that
are asymmetrically coordinated to the monomeric entity: μ3-
κO:κO′:κ2O″,O‴ (bidentate-chelate) and μ3-κO:κO′:κO″ (bi-
dentate-monodentate). Both coordination modes coexist in
unit A, whereas in unit B the four ligands are bidentate−
monodentate ones. The monomeric C entity exhibits a
CuNO3Ow2 chromophore, (SOh = 5.66), while the D monomer
presents a square pyramidal CuNO2Ow2 chromophore (SSPY
=
0.93).
The bidentate 9-methyladenine bridging ligand inverts its
coordination mode with respect to compound 4, and the
nitrogen N7 atom occupies the axial position of the dimeric
entities, while the N1 atom completes the coordination sphere
of the monomeric centers. The Jahn−Teller effect is enhanced
in the momomer with square pyramidal geometry with a longer
axial Cu−N distance than in the dimeric entity (2.498 vs 2.205
Å). The 9-methyladenine coordination mode also allows the
establishment of a hydrogen bonding interaction between its
exocyclic amino group with the dimeric and monomeric
entities. The pyrimidinic N3 donor atom of the nucleobase is
hydrogen bonded to the coordination water molecules of the
[Cu(H2O)2] entities. π−π interactions between the aromatic
rings of the nucleobases complete the noncovalent interactions
of the crystal building (see Supporting Information).
Figure 11. Crystal packing of compound 4 showing the voids filled by
crystallization water molecules.
basal plane is occupied by oxygen atoms of four isophthalato
ligands. The apical position is filled by the N1 pyrimidinic atom
of a 9-methyladenine molecule. The PW entities are connected
to the monomeric units by the second carboxylic group of the
isophthalate and the imidazolic N7 atom of the nucleobase
which acts as bidentate bridging ligand. Two of the isophthalato
brigdes present a μ3-κO:κO′:κ2O″,O‴ coordination mode
(where the second carboxylato group chelates the monomeric
copper(II) atom), and the two other ones show a μ3-
κO:κO′:κO″ coordination mode with a free oxygen atom.
The different coordination modes are reflected in the C−O
bond distances which are equivalent for the chelating
carboxylato group (1.261, 1.267 Å) and different (1.284,
1.225 Å) for the monodentate carboxylate group. The NO3Ow
donor set in the monomeric entity (Figure 10) is completed
with a water molecule to give a distorted square pyramidal
geometry (SSPY = 2.34) due to the proximity of the two basal
oxygen atoms that form the chelating ring. The 3D binodal
network formed by the covalent interactions can be described
as a rutile type structure with (4.62)2(42.610.83) point symbol.
The 3D architecture is also reinforced by an extensive
hydrogen bonding network. The bidentate arrangement of the
nucleobase allows the formation of hydrogen bonding rings
between the exocyclic amino group and the oxygen atoms of
both complex entities. The coordination water molecule of the
monomeric entity establishes an O1w−H12w···O32a hydrogen
bond with the noncoordinated oxygen atom of the isophthalato
ligand and completes its hydrogen bonding scheme with the
crystallization water molecule (O1w−H11w···O2w). The
crystallization molecules occupy discrete voids within the
crystal structure that represents 14.8% of the unit cell volume
(Figure 11).
The overall covalent network also possesses a rutile topology,
although the discrete voids occupied by the crystallization water
molecules (Figure 13) represent a lower percentage of the total
volume than in compound 4 (6.6% vs 14.8%).
Comments on the CuII/Isophthalato/9-Methyladenine
System Diversity. The great structural diversity of this system
can be rationalized on the basis of two major factors: (a) the
versatility of coordination modes of isophthalato ligand when
coordinated to copper(II) metal centers (Figure 14) and (b)
the flexible coordination environment of copper(II) atom,
probably because of the Jahn−Teller effect, does not impose a
unique coordination geometry, and indeed, it can be easily
reorganized by slight displacements of the ligands. Moreover, a
perusal of the copper(II) containing coordination compounds
registered in the CSD shows a similar tendency toward
coordination numbers six, five, and four (43, 30, and 27%,
respectively).23 In the present case, both facts imply the
coexistence of a handful of coordination moieties in the
reaction media which can yield a variety of crystal structures
hindering the predictability.
The combination of these factors is evidenced along the
herein presented compounds, which is further transferred to
the coordination mode of the 9-methyladenine. In compound
1, which seems to be the kinetically favored one, the
isophthalato ligand exhibits a μ-κ2O,O′:κO″ coordination
mode giving rise to a 4 + 1 + 1 copper(II) environment. The
carboxylate groups only form a strong coordination bond with
the metal center through one of their oxygen atoms, whereas
the remaining ones are semicoordinated (O21) or remain free
(O12) due to the steric hindrance of the coordinated water
molecules. However, more prolonged crystallization times or
small temperature changes lead to the loss of the coordination
water molecules that induces a slight modification of the
coordination sphere giving rise to two four-member chelate
rings through its μ-κ2O,O′:κ2O″,O‴ coordination mode. This
new arrangement folds the copper(II)-isophthalato chains by
forcing consecutive isophthalato ligands to be perpendicular to
Crystal Structure of {[Cu2(μ3-iso)2(μ-9Meade)(H2O)2]-
·1.5H2O}n (5). The 3D structure of compound 5 also presents
PW shaped [Cu2(μ-iso)4(9Meade)2] dimeric entities linked to
[Cu(H2O)2] units, but it contains two crystallographically
independent dimeric entities and two monomeric ones.
Besides, the compound presents a higher hydration degree.
Figure 12 shows the ORTEP diagrams of the structural units,
and Table 6 gathers the bond distances of their coordination
environments.
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Crystal Growth & Design
Article
Figure 12. (a−d) Structural entities in compound 5.
a
Table 6. Selected Bond Lengths (Å) of Compound 5
each other. The 9-methyladenine can, in this way, coordinate
the metal centers of neighboring chains in a N1,N7-bidentate
fashion, which renders the 2D network of compound 2.
In compound 3, the isophthalato ligand adopts its most usual
μ4-κO:κO′:κO″:κO‴ coordination mode to give 2D layers built
up from PW entities in which the 9-methyladenine-κN7 ligand,
as predicted, occupies the apical position. The isophthalato
ligands, in compounds 4 and 5, adopt again nonsymmetric
coordination modes (μ3-κO:κO′:κ2O″,O‴ and μ3-κO:κO′:κO″)
which prevent the formation of PW entities solely, in such a
way that the PW entities are linked through monomeric ones.
This coordination scheme allows the 9-methyladenine to join
the building units together by the N1,N7-bidentate brigde.
At this point, it becomes evident that in the reaction media
the predicted [Cu2(μ-iso)4(9Meade)2] unit coexists with
different monomeric entities, whose combination leads to the
structural diversity herein reported. The segregation of the
kinetically favored compound 1 during the crystallization
process alters the concentration and ratio between the building
units giving access to the remaining crystal structures. In fact,
coordination environments in the dimeric entities
Cu2−N17
Cu2−O21
Cu2−O22a
Cu2−O31
Cu2−O32a
Cu2···Cu2a
2.205(5)
1.953(4)
1.957(4)
1.959(5)
1.970(5)
2.716(2)
Cu3−N27
Cu3−O61
Cu3−O62b
Cu3−O71
Cu3−O72b
Cu3···Cu3b
2.156(4)
1.961(4)
1.969(4)
1.974(4)
1.955(4)
2.670(1)
coordination environments in the monomeric entities
Cu1−N21
Cu1−O11
Cu1−O12
Cu1−O81c
Cu1−O1w
Cu1−O2w
2.373(4)
2.677(4)
1.936(4)
1.912(4)
2.060(5)
2.036(4)
Cu4−N11d
Cu4−O41
Cu4−O52e
Cu4−O3w
Cu4−O4w
2.498(5)
1.906(4)
1.941(4)
2.004(4)
1.980(4)
a
Symmetry codes: (a) −x + 1, −y, −z + 1; (b) −x + 2, −y, −z; (c) x, y
+ 1, z; (d) −x + 1, −y + 1, −z + 1; (e) −x + 2, −y + 1, −z + 1.
I
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Article
range from 1D to 3D frameworks. It becomes obvious that
there are many energetically available architectures for this
system based on the slight modifications of the CuII/
isophthalato/adenine ratio, temperature, and pH value that
take place both along the diffusion test tube and during the
experiment progress. It is also notorious that although the 9-
methyladenine nucleobase usually behaves as an N7-terminal
ligand, in some of these compounds (2, 4, and 5) it is also able
to bridge adjacent metal centers showing a μ-κN1:κN7-
coordination mode. Further work is in progress to achieve
analogous compounds with other benzenedicarboxylates such
as terephthalic, aminoterephthalic, and chloroterephthalic acids.
ASSOCIATED CONTENT
* Supporting Information
■
S
Tables and figures of noncovalent interactions, and crystallo-
graphic information files (CIF). This information is available
free of charge via the Internet at http://pubs.acs.org.
Figure 13. Crystal packing of compound 5 showing the voids occupied
by crystallization water molecules.
AUTHOR INFORMATION
Corresponding Author
*E-mail: sonia.perez@ehu.es (S.P.-Y.), oscar.castillo@ehu.es
(O.C.). Fax: (internat) +34-94601-3500.
■
Notes
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
Financial support from the Gobierno Vasco (IT477-10,
SAIOTEK S-PE12UN004) and the Universidad del Pais
■
́
Vasco/Euskal Herriko Unibertsitatea (UFI 11/53, postdoctoral
fellowship) is gratefully acknowledged. Technical and human
support provided by SGIker (UPV/EHU, MICINN, GV/EJ,
ESF) is also acknowledged.
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■
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