From 7-azaindole to adenine: Molecular recognition aspects on mixed-ligand Cu(ii) complexes with deaza-adenine ligands

Article abstract of DOI:10.1039/c2dt32191b

For a better understanding of the versatile behaviour of adenine as a ligand, a series of 10 ternary copper(ii) complexes with deaza-adenine ligands [7-azaindole (1,6,7-trideaza-adenine, H7azain), 4-azabenzimidazole (1,6-dideaza-adenine, H4abim), 5-azabenzimidazole (3,6-dideaza-adenine, H5abim), and 7-deaza-adenine (H7deaA)] have been synthesised and characterised by X-ray diffraction. Likewise, all the compounds studied have been analysed by spectral and thermal methods. The proton tautomers and donor capabilities of the above-mentioned deaza-adenine ligands have been calculated by DFT. We conclude that the increasing presence of N-donors in deaza-adenine ligands favours the proton tautomerism and their versatility as co-ligands. Notably, H7azain consistently uses the same tautomer, H4abim uses two different tautomers but is not protonated by the pentadentate H₂EDTA^2- ligand, and H(N1)5abim displays the μ₂-N7,N9 mode, whereas H(N9)7deaA binds Cu(ii) by N3 in cooperation with an intra-molecular N9-H...O interaction or using the unprecedented bidentate μ₂-N1,N3 bridging mode.

Full text of DOI:10.1039/c2dt32191b

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From 7-azaindole to adenine: molecular recognition aspects on mixed-
ligand Cu(II) complexes with deaza-adenine ligands
Alicia Domínguez-Martín,*a Duane Choquesillo-Lazarte, b Jose A. Dobado,c Isaac Vidal,c Luis Lezama,d
Josefa María González-Pérez,a Alfonso Castiñeirase and Juan Niclós-Gutiérreza
5
Received (in XXX, XXX) Xth XXXXXXXXX 200X, Accepted Xth XXXXXXXXX 200X
DOI: 10.1039/b000000x
For a better understanding of the versatile behaviour of adenine as a ligand, a series of 10 ternary
copper(II) complexes with deazaꢀadenine ligands [7ꢀazaindole (1,6,7ꢀtrideazaꢀadenine, H7azain), 4ꢀ
azabenzimidazole (1,6ꢀdideazaꢀadenine, H4abim), 5ꢀazabenzimidazole (3,6ꢀdideazaꢀadenine, H5abim),
10 and 7ꢀdeazaꢀadenine (H7deaA)] have been synthesised and characterised by Xꢀray diffraction. Likewise,
all the compounds studied have been analysed by spectral and thermal methods. The proton tautomers
and donor capabilities of the aboveꢀmentioned deazaꢀadenine ligands have been calculated by DFT. We
conclude that the increasing presence of Nꢀdonors in deazaꢀadenine ligands favours the proton
tautomerism and their versatility as coꢀligands. Notably, H7azain consistently uses the same tautomer,
15 H4abim uses two different tautomers but is not protonated by the pentadentate H2EDTA2ꢀ ligand, and
H(N1)5abim displays the ꢁ2ꢀN7,N9 mode, whereas H(N9)7deaA binds Cu(II) by N3 in cooperation with
an intraꢀmolecular N9ꢀHꢂꢂꢂO interaction or using the unprecedented bidentate ꢁ2ꢀN1,N3 bridging mode.
within some gas mixtures which could be used for gas storage or
Introduction
catalysis.4 Alternatively, it is known that 7ꢀdeazapurine ligands
50 are electrochemically oxidizable at carbon electrodes at less
positive potentials compared to any natural building block of
DNA. Thus, 7ꢀdeazaꢀadenine, incorporated into DNA, could be
useful as an electroꢀactive label for easily monitoring PCR
amplification.3c
Over recent decades, supramolecular chemistry has become a
20 matter of current interest. The design and development of new
bioꢀmaterials as well as molecular frameworks has increased
rapidly, addressing the coordination chemistry of biologically
related ligands.1 In this sense, nucleic acids and especially purineꢀ
like ligands such as adenine, are outstanding because of their rich,
25 versatile behaviour.2 The inꢀdepth understanding of the molecular
recognition patterns of different nucleobases and their derivatives
and/or analogues has been devoted to rationalizing biochemical
processes, leading to promising physicoꢀchemical developments,
i.e. molecular probes or sensors, or further pharmaceutical
30 approaches. Indeed, therapeutical and biotechnological
applications are extensively documented for a large variety of
purineꢀlike ligands and/or purineꢀlike metal complexes.3 For
instance, regarding deazaꢀadenine ligands, Jose Ruiz et al.3b have
reported two ternary Pt(II) complexes with 7azaindolate,
35 according to the formula [Pt(dmba)(7azain)(L’)] (dmba is N,Nꢀ
dimethylbenzylamineꢀkN,kC, 7azain is 7ꢀazaindolate and L’ is
DMSO or PPh3), which are able to form adducts with DNA
showing in vitro cytotoxicity. These latter compounds are active
in the subꢀmicromolar range towards the cisꢀplatin resistant
40 human breastꢀcancer cell line T47D and the epithelial ovarian
carcinoma cells A2780 and A2780cisR. Likewise, research has
been fruitful in the synthesis and characterization of zeolitic
imidazolate frameworks, involving purineꢀlike ligands.3e The
55
As part of our research, we have been working on ternary
Cu(II) complexes having deazaꢀadenine ligands. The relevance of
deazaꢀadenine ligands is related to fact that 7ꢀazaindole (H7azain
= 1,6,7ꢀtrideazaꢀadenine), 4ꢀ and 5ꢀazabenzimidazole (H4abim =
1,6ꢀdideazaꢀadenine and H5abim
=
3,6ꢀdideazaꢀadenine,
60 respectively) or 7ꢀdeazaꢀadenine (H7deaA), among others, can be
considered as bioisosteres of the purine moiety (Scheme 1). Note
that all the ligands mentioned herein have at least one Nꢀ
heterocyclic donor atom in each cycle. Hence, the study of
ternary complexes involving deazaꢀadenine ligands is
65 challenging, since it could provide new insights into how
restrictions on the Nꢀheterocyclic donor atoms affect the relative
basicity order of the Nꢀdonors in the purine moiety and therefore
the coordination abilities of such ligands. In this context, it should
be remarked that, in the study of molecular recognition, work on
70 mixedꢀligand complexes, singleꢀcrystal Xꢀray diffraction (XRD),
and density functional theory (DFT) calculations offers useful
tools by providing reliable information on the metalꢀbinding
pattern as well as on the nonꢀcovalent interligand interactions (Hꢀ
bonds, pi,piꢀstacking, CꢀH/piꢀinteractions, etc).
complexes
{[Zn(ꢁ2ꢀ5azabenzimidazolate)2]ꢂDMF0.75ꢂ(H2O)2}n
have proved
75
45 and {[Zn(ꢁ2ꢀ4azabenzimidazolate)2]ꢂ(H2O)0.25
}
n
< Scheme 1 >
useful as gas adsorbents for H2, CH4, CO2 or Ar. A notable
property of these materials is also their selective gas adsorption
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Results and discussion
< Figure 1 >
1. DFT Calculations
Tautomers for the isolated deaza-adenine ligands
60 For the Cu(II)/MIDA chelate, H7azain shows a coordination
preference via N3, with a ꢃGr difference of 3.5 kcalꢂmolꢀ1 respect
to the 9p3 metalꢀbinding mode.§. In addition, this difference is
also observed for the complex Cu(II)/NBzIDA/H7azain.
Structurally, the most significant features of these mononuclear
65 complexes are the following: (i) the chelating ligands MIDA and
NBzIDA display a merꢀNO2 conformation and the distances of
the coordination bonds NꢂꢂꢂCu and OꢂꢂꢂCu are close to 2.0 and 1.9
Å, respectively. The latter bond becomes slightly larger
(increasing in 0.2 Å) when the oxygen atom is involved in Hꢀ
70 bonds (see Figure 1 and Table S2); (ii) they show an intraꢀ
molecular interaction with values of approx. 1.79 Å and 140º for
the NꢂꢂꢂO distance and <NꢀHꢂꢂꢂO angle, respectively. Moreover,
the chelating ligand and the deazaꢀadenine are coplanar (dihedral
angle close to 2º). As we will discuss in the crystallographic
75 section, the theoretical results agreed well with the experimental
ones.
To explore the relative stability of the corresponding hydrogen
tautomers of the aboveꢀmentioned deazaꢀadenine ligands, we
calculated the gas phase and solventꢀeffect Gibbs energies, these
being summarized in Table 1. As expected, the H(N9) tautomers
are the most stable ones in the gas phase and also when the
solvent effect is included. Note that H5abim, in the gas phase,
5
10 shows a small difference of only 0.3 kcalꢂmolꢀ1 with respect to the
next stable tautomer, H(N7), which remains almost the same once
the solvent effect (0.6 kcalꢂmolꢀ1) is considered. For H7azain and
H7deaA ligands, the second tautomer in terms of energy is the
H(N3), with values close to 12 kcalꢂmolꢀ1.
15
< Table 1 >
Only one study is available on the experimental and theoretical
tautomers of H4abim.5 In accordance with our results, the most
20 stable tautomer is reportedly the H(N9) form among the four
possible tautomers. In that study, the electronic relative energies
(Er) were reported, yielding values of 4.14 and 4.19 kcalꢂmolꢀ1 for
the H(N7) tautomer, at very accurate B3LYP/6ꢀ
The structures of H4abim with the chelates Cu(II)/MIDA and
Cu(II)/CBIDA also adopt a merꢀNO2 coplanar conformation,
yielding similar geometrical data (see Table S2). However, the
80 H2EDTA ligand has different coordination preferences.
A
restricted search for EDTA(4ꢀ) and Cu(II) in the Cambridge
Structural Database (CSD) reported mostly pentadentate
coordination of this former ligand. Hence, we performed
theoretical models for the Cu(II)/H2EDTA complex behaving as
85 tetraꢀ or pentadentate ligand, resulting in the calculations the
tetradentate form the most stable due to the existence of two
intraꢀmolecular Hꢀbonds. In this former complex, H4abim was
not coplanar with H2EDTA but formed a dihedral angle close to
10º. However, in the presence of a deprotonated Nꢀatom (i.e. in
90 the 3p7 or 9p7 forms) this dihedral angle significantly increases
to approx. 60º. In energy terms, the most stable complexes of
H4abim are the 3p9 species, similar to H7azain. The following in
terms of energy are the 9p3 for MIDA and CBIDA in approx. 3.0
kcalꢂmolꢀ1. This situation changes significantly when we consider
95 the H2EDTA ligand. In this case, the next stable structure is the
3p7 within 1.1 kcalꢂmolꢀ1. It is remarkable that for MIDA and
CBIDA ligands the ꢃGr of the 3p7 conformation were approx.
10.0 kcalꢂmolꢀ1. This means that the H2EDTA chelating ligand
allows more coordination versatility due to a significant decrease
100 of the protonation barrier (p7 and p9).
311++G**//B3LYP/6ꢀ311++G**
and
QCISD/ccꢀ
25 pVDZ//B3LYP/6ꢀ311++G** theoretical levels, respectively. Our
results are in good agreement with those previously reported,
although in the present study we report ꢃGr values of 3.9
kcalꢂmolꢀ1. However, it bears mentioning that when the solvent
effect is included in the calculations, this difference is reduced
30 significantly to 0.2 kcalꢂmolꢀ1. Therefore, although the most
stable tautomer for H4abim and H5abim is the H(N9), the next
tautomer in energy is the H(N7) within a narrow range of approx.
0.5 kcalꢂmolꢀ1.
35 Mononuclear copper(II) complexes
To estimate the coordination abilities of the Nꢀheterocyclic
donors of H7azain, H4abim, H5abim, and H7deaA, we selected
different model systems which consist of ternary copper(II)
complexes
having
the
chelating
ligand
Nꢀmethylꢀ
40 iminodiacetate(2ꢀ) (MIDA). The Cu(II)/MIDA chelate was tested
for all the purineꢀlike ligands. Calculations were also extended to
other iminodiacetateꢀlike ligands such as Nꢀbenzylꢀ and Nꢀ(pꢀ
Cu(II)/MIDA/H5abim
and
Cu(II)/NBzIDA/H5abim
chlorobenzyl)ꢀiminodiacetate(2ꢀ)
or
ethyleneꢀ
complexes also show similar geometries compared to the aboveꢀ
mentioned H7azain and H4abim complexes. Nevertheless, the
energetics and theoretical coordination preferences differ. In the
105 present study, the 1p7 mode is the most stable one but, as
opposed to aforementioned cases, we can also find the 1p9, 9p7
or 7p9 modes within a narrow range of 1.5 kcalꢂmolꢀ1 (see Table
S2). This indicates that such coordination alternatives are
plausible as well as a bidentate role (vide infra ꢀ dinuclear
110 copper(II) complexes section). The geometrical DFT results of
diaminotetraacetate(2ꢀ) anions (NBzIDA, CBIDA or H2EDTA,
45 respectively).
As discussed above, the free nucleobases here presented
exhibit the tautomer H(N9) in neutral form (see Table 1).
However, for the model systems, we also calculated all the
protonation alternatives for the mononuclear Cu(II) complexes
50 since the presence of copper could alter these tautomeric
preferences. Figure 1 depicts the structures of the most stable
mononuclear Cu(II) complexes calculated at the B3LYP/6ꢀ
31+G**//B3LYP/6ꢀ31+G** theoretical level. Besides, Table S2
(see Supporting Material) summarizes the relative Gibbs energy
55 (ꢃGr) for the different coordination and proton tautomer
complexes, together with some selected geometrical parameters.
those
complexes
concerning
the
Cu(II)/MIDA and
Cu(II)/NBzIDA chelates and H7deaA are very similar to those
previously reported for H7azain and H4abim. Thus, the energy
again favours the 3p9 mode. Nevertheless, the second most stable
2
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mode is the 1p9,with ꢃGr values of 2.8 and 2.3 kcalꢂmolꢀ1 for
MIDA and NBzIDA, respectively.
= 0.10 for Cu(1) and τ = 0.12 for Cu(2)). The N10, O11, and O21
donors of the tridentate merꢀNO2 FBIDA chelator and the N3
atom from H7azain satisfy the basal coordination plane. It seems
60 that the tautomerizable proton, placed on N9, could be involved
in a weak bifurcated Hꢀbonding interaction: one intraꢀmolecular
and the other interꢀmolecular (see Table S5.3). The apical donor
is the O12 atom from the bridging carboxylate group of an
adjacent FBIDA ligand (Fig. 3). Again, the dihedral angle is
65 higher than expected [49.76º for Cu(1) and 47.33º for Cu(2)].
Note that despite the molecular (1) and polymeric (2) nature of
the two novel compounds, the dihedral angles are quite similar.
Furthermore, it is noteworthy that, among the 26 firstꢀrow
transition metal complexes containing H7azain referred to in the
70 CSD, only three have a polymeric structure.
Dinuclear copper(II) complexes
5
In the previous section, we discussed that the H5abim complexes
presented energy in a range of approx. 1.5 kcalꢂmolꢀ1 for the
different coordination modes. Moreover, we also synthesised and
crystallized Cu(II) complexes where H5abim coordinate as a
bidentate ligand. Consequently, we carried out DFT calculations
10 of different dinuclear Cu(II) model system with H5abim, which
are depicted in Figure 2. It is notable that the preferred
protonation site changed to p1, as opposed to the mononuclear
models, which pointed out p7 (see Figure 1).‡ Nonetheless, these
results are not contradictory, since the energy range for these
15 proton tautomers is very small, approx. 1.2 and 0.6 kcalꢂmolꢀ1, for
MIDA and NBzIDA, respectively. Therefore, the theoretical
< Figure 3 >
results support the experimental findings of
a bidentate
The results from theoretical and crystallographic methods
75 support the general molecular recognition pattern described for
monodentate neutral 7ꢀazaindole, which consists of an MꢀN3
bond in cooperation with an intraꢀmolecular interligand
interaction involving the N9ꢀH group. Indeed, previous results
from our group support the aforementioned molecular recognition
80 pattern.11 The stability of the H(N9) tautomer appears to be
related with the large difference in basicity between the two Nꢀ
donor atoms in H7azain. There is a known exception that is found
in three aluminium complexes where H7azain and 7azain are
involved in metal binding. In these complexes, H7azain shows
85 the rare tautomer H(N3)7azain and coordinates via N9 in
cooperation with an intraꢀmolecular N3ꢀHꢂꢂꢂN3 Hꢀbond.12
coordination mode. In terms of geometries, the dinuclear
complexes yielded geometrical parameters similar to the
20 mononuclear ones (see Table S2).
< Figure 2 >
2. X-Ray-diffraction Studies
25 Compounds with 7-azaindole
The ligand 7ꢀazaindole is structurally rich. The structure of the
neutral ligand, H(N9)7azain, has been reported,6 as well as
several metal complexes where H7azain shows the MꢀN3 bond,
usually reinforced by an intraꢀmolecular Hꢀbonding interaction
30 N9ꢀHꢂꢂꢂA.7 Alternatively, metal complexes with the 7ꢀazaindolate
anion typically display the monodentate MꢀN9 or the bridging ꢁ2ꢀ
N3,N9 modes;8 although η2ꢀN3,N9 and ꢁꢀN3,η2ꢀN9 roles are also
known.9
Compounds with 4-azabenzimidazole
The structural information concerning H4abim is rather limited;
90 indeed the crystal structure of the ligand remains unknown.
Concerning metal complexes, H4abim is found in three different
Cu(II) paddlewheelꢀlike compounds in which a ꢁ2ꢀN3,N9 mode is
displayed.13 Alternatively, the 4abim(1ꢀ) anion is present in two
compounds serving as a ꢁ2ꢀN7,N9 bridge.4,14
35 Compound 1 [Cu(TEBIDA)(H7azain)(H2O)]ꢂ3H2O consists of a
complex molecule and water molecules. The copper(II) atom
exhibits a 4+1 coordination polyhedron where the four closest
donor atoms correspond to the tridentate IDAꢀlike chelating
ligand (N10, O11, O21) and the N3(purineꢀlike) donor of
95
The crystal of compound 3, {[Cu(CBIDA)(H4abim)]ꢂ2H2O}n,
consists of polymeric chains that extend parallel to b axis and
40 H7azain. Thus, the TEBIDA ligand adopts
a merꢀNO2
water molecules. The metal exhibits
a 4+1 coordination
conformation. One aqua ligand occupies the apical position. In
this complex, the Cu(II) coordination environment is close to a
squareꢀbased pyramidal coordination, according to the Addison
parameter,10 τ = 0.21. It bears noting that the ligands TEBIDA
45 and H7azain are not coplanar as expected (dihedral angle <OꢀCuꢀ
NꢀC is 46.88º), considering the previous theoretical information.
Hence, the Hꢀbonding interaction N9ꢀHꢂꢂꢂO21(coord. carboxy) is
weakened, this being related essentially to those packing forces
present within the crystal (see Table S4.3 and Figure and
50 comments in S4.4).
polyhedron where the four closest donor atoms are supplied by
100 the tridentateꢀchelating CBIDA ligand (N10, O11 and O21) and
H4abim via N7. Hence, the tautomer H(N9)4abim cannot
reinforce the CuꢀN7 bond with an intraꢀmolecular Hꢀbond.
However, the N9ꢀH group is involved in interꢀmolecular
interactions of building 2D layers (see Table S6.3 and Figure and
105 comments in S6.4). This fact may contribute to the value of the
dihedral angle (<OꢀCuꢀNꢀC 49.86º). In addition, the CBIDA
ligand, in merꢀNO2 conformation, displays a ꢁ2ꢀbridging role by
means of a synꢀanti carboxylate group, occupying the apical
position in the Cu(II) surrounding. In this compound, the Addison
110 parameter τ = 0.007 reveals a nearly regular squareꢀbased
pyramidal coordination.
The crystal of 2, {[Cu(FBIDA) (H7azain)]ꢂ2H2O}n, is based on
a coordination polymer built by the synꢀantiꢀbridging carboxylate
group of FBIDA ligand. The two copper(II) atoms are not
55 crystallographically equivalent. They both exhibit a squareꢀbased
pyramidal coordination, type 4+1, with a slight basal distortion (τ
Compound
4
agrees
with
the
formula
[Cu(H2EDTA)(H4abim)]ꢂ0.5H2O. The asymmetric unit consists
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of a complex molecule (Fig. 4) and half water molecule. The
copper(II) atom shows a 4+1+1 coordination polyhedron. The
H2EDTA chelator acts as a pentadentate ligand, occupying three
of the four closest sites around the metal centre (N10, O11, O21)
plus the two apical positions (N20 and O16). Note that the
60
Compound 5 {[Cu2(IDA)2(ꢁ2ꢀN7,N9ꢀH5abim)]ꢂH2O}n consists
of a coordination polymer built by dinuclear units. Such units
extend, leading to a 3D network by means of the synꢀanti
bridging role of two carboxylate groups from the IDA moiety
(see Figure and comments in S8.4). The copper(II) centres are
5
longest coordination bond corresponds to
a coordinated
carboxylic group (see Table S7.2). This is worth mentioning 65 equivalent and exhibit a 4+2 coordination. Three donor atoms
because it means that the carboxylic group has not been able to
transfer its proton to H4abim, which is coordinated via N9 as the
10 tautomer H(N7)4abim. Thus, no intraꢀmolecular Hꢀbond is
possible in this configuration. However, the N7ꢀH group is
from the tridentate merꢀNO2 IDA chelator and the N7 or N9 atom
from H5abim are the closest Cu(II) donors. The apical donors are
the O12 and O22 from the bridging carboxylate groups of
adjacent IDA ligands. The ꢁ2ꢀN7,N9 role forces the
involved in interꢀmolecular interactions that help to stabilise the 70 tautomerizable proton to shift to N1, thus no intraꢀmolecular Hꢀ
multiꢀstacked 1D chains within the crystal (see Table S14.2 and
Figure and comments in S7.4).
bonds are involved in the metalꢀbinding pattern. The dihedral
angle is higher than expected (<OꢀCuꢀNꢀC 52.68º). It should be
noted that a mirror plane is located in the middle of H5abim
ligand, and then the ligand is delocalised over two positions, with
75 an occupancy factor of 0.5.
15
< Figure 4 >
In compound 3, H4abim acts as a monodentate ligand through
N7. This molecular recognition pattern has previously been
The
crystal
of
6,
[Cu2(NBzIDA)2(ꢁ2ꢀN7,N9ꢀ
20 reported by our group, referring to a close polymer with the
chelating ligand Nꢀbenzylꢀiminodiacetate.11 In both compounds,
H5abim)(H2O)2]ꢂH2O, consists of a centroꢀsymmetric dinuclear
complex molecule plus nonꢀcoordinated water. The metal
the proton is tightly bonded to N9 (the most basic Nꢀheterocyclic 80 exhibits
a squareꢀbased pyramidal coordination, type 4+1
donor atom), and thus coordination takes place via the secondꢀ
most basic Nꢀdonor. Alternatively, compound 4 reveals a new
25 monodentate coordination role for neutral H4abim. Herein, the
tautomer H(N7)4abim is first reported and this implies that N9 is
(Addison parameter τ = 0.003), built by the N10, O11, and O21
donors of the tridentate NBzIDA chelator (merꢀNO2
conformation) and the N7 or N9 atom of H5abim. The apical
position is occupied by one aqua ligand. Again, H5abim acts as a
now available for coordination. These patterns are not the same 85 bridging ligand, between the two metal centres, displaying a ꢁ2ꢀ
as those observed as ‘preferred’ in the theoretical results (see
‘Mononuclear copper(II) complexes’ section). However, the
30 discrepancy is acceptable, taking into account the driving forces
of the crystal packing and the small protonation barrier between
N7,N9 role (Fig. 5) and showing the H(N1) tautomer. Likewise, a
binary axe is located in the middle of H5abim ligand, so that it is
again delocalized at 50%. The two Nꢀbenzyl moieties of the
NBzIDA ligand and the water molecule are also disordered over
the p9 and p7 tautomers (see Table 1). Moreover, if we consider 90 two alternative positions with an occupancy factor of 0.52/0.48
H4abim as a 1,6ꢀdideazaꢀadenine, the formation of a CuꢀN7 bond
is according to the assumed sequence of basicity of adenine (N9
35 > N1 > N7 > N3 >> 6NH2). Indeed, these former molecular
recognition patterns have previously been reported for
and 0.69/0.31, respectively. This fact should be considered in the
analysis of interꢀmolecular interactions and crystal packing (see
Figure and comments in S9.4). Within the dinuclear units, a
bifurcated nonꢀclassical Hꢀbond is observed between H5abim and
mononuclear metal complexes with neutral Hade and 95 the Oꢀcarboxy atoms from the two NBzIDA moieties (see Table
iminodiacetateꢀlike ligands,15 as well as other related chelating
ligands.16 The use of the chelating ligand H2EDTA(2ꢀ) in
40 compound 4 was based on the idea of synthesising compounds
containing the H24abim(1+) cation. In fact, the transfer of the
proton from a carboxylic group of H2EDTA(2ꢀ) to adenine has 100
formerly been described.17 The reason why H4abim remained in
its neutral form could be related to the crystal packing or the
45 relative acidity of the protons.
S9.3). This probably influences the rather close shape of the
dinuclear motifs and might contribute to the low value of the
dihedral angle according to the theoretical model (<OꢀCuꢀNꢀC
11.16º).
< Figure 5 >
It bears remarking that, regardless of the molecular or
Furthermore, irrespective of the vagaries of compounds 3 and
polymeric nature of the compounds (6 and 5, respectively), both
4, it should be noted that the coordination versatility of H4abim 105 display the same molecular recognition pattern: ꢁ2ꢀN7,N9. This
has increased noticeably with respect to H7azain. This fact may
be related to the addition of one Nꢀheterocyclic donor atom.
50 Thus, the difference of basicity between the Nꢀdonors in the
heterocycle is shorter, this promoting tautomerism phenomena.
latter role has previously been mentioned regarding the 4abim
and 5abim anions.4 Moreover, this metal binding has also been
described for Hade and ade ligands18ꢀ19. For instance, our group
reported the dinuclear complex [Cu2(NBzIDA)2(ꢁ2ꢀN7,N9ꢀ
110 H(N3)ade)(H2O)2]H2O.18 Therein, both coordination bonds were
assisted by the corresponding N6ꢀHꢂꢂꢂO and N3ꢀHꢂꢂꢂO Hꢀbonds,
respectively. By contrast, the reported complexes show the
H(N1)5abim tautomer and therefore reinforcement is not
possible. The fact that both Nꢀligands are able to display the same
115 molecular recognition pattern, despite their Nꢀrestrictions,
supports the idea of using these kinds of deazaꢀadenine ligands as
Compounds with 5-azabenzimidazole
55 A recent search in the CSD reveals that, to date, there is no
structure reported for neutral H5abim. However, one Zn(II)
polymeric compound has been reported for 5abim(1ꢀ), displaying
the bridging ꢁ2ꢀN7,N9 mode.4
4
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models to study the versatility and metalꢀbinding patterns of
purine ligands. The reason why N1 is not involved in
coordination in these sorts of complexes remains unknown. Note
that the absence of the exocyclic amino group could have
encouraged the coordination abilities of N1. However, no
coordination was observed. It is remarkable that this recognition
60
The polymeric compounds 9 [Cu(NBzIDA)(H7deaA)]n and 10
[Cu(MEBIDA)(H7deaA)]n give very similar crystals. These 1D
polymers extend throughout the c axis by means of the synꢀantiꢀ
bridging carboxylate group of NBzIDA or MEBIDA ligands,
respectively. The metal exhibits a 4+1 coordination polyhedron,
5
pattern is clearly favoured in terms of energy (vide supra – 65 with a slight basal distortion (τ = 0.052 in 9 and τ = 0.075 in 10).
dinuclear copper(II) complexes section). In addition, crystal
packing features should also be considered, since the N1ꢀH group
10 appears to play a relevant role regarding intermolecular Hꢀ
bonding interactions (see Figure and comments in S8.4 and S9.4).
The four closest Cu(II) donor atoms are supplied by the
tridentateꢀchelating IDAꢀlike ligands (N10, O11 and O21) and
the N3 donor atom of H(N9)7deaA ligand. The apical position is
occupied by one Oꢀcarboxylate bridging atom. The dihedral
70 angles (<OꢀCuꢀNꢀC) are 36.12º in 9 or 41.49º in 10. This fact
could be related to the bifurcated character of the Hꢀbond tied to
the tautomerizable proton. Thus, N9ꢀH would be involved both in
the reinforcement of the CuꢀN3 bond [N9ꢀHꢂꢂꢂO21(coord.
carboxy)] and in an interꢀmolecular interligand Hꢀbond [N9ꢀ
75 HꢂꢂꢂO11(coord. carboxy)] (Fig. 7). In the crystal, the exocyclic
amino group plays a key role connecting adjacent polymeric
chains (see Figure and comments in S12.4 and S13.4)
Compounds with 7-deazaadenine
15 In accordance to their pharmaceutical interest, the structures of
tubercidine (7ꢀdeazaadenosine) and closely related synthetic
nucleosides have been reported.20 Nevertheless, no other
structural information is available on 7ꢀdeazaꢀadenine.
20
Compound 7 [Cu(IDA)(H7deaA)(H2O)]ꢂ2H2O consists of a
complex molecule and two water molecules. The copper(II) atom
exhibits a 4+1 coordination polyhedron, where the four closest
donor atoms correspond to the tridentate IDA chelating ligand
(N10, O11, O21) and the N3 donor of H7deaA. Thus, IDA ligand
< Fig. 7 >
80
In all the described 7ꢀdeazaꢀadenine derivatives, the Nꢀ
heterocyclic ligand exists as its most stable tautomer
H(N9)7deaA. This is consistent with the theoretical results and
the basicity order of adenine, which highlights N9 as the most
85 basic Nꢀdonor atom. In three of the four compounds studied,
H7deaA shows a similar molecular recognition pattern to
H7azain, despite that H7deaA offers more Nꢀheterocyclic donors
available for coordination. Why N3 is preferred over N1 for a
monodentated coordination seems to be related to the possibility
90 of establishing the MꢀN3 bond assisted by an intraꢀmolecular
interligand Hꢀbond N9ꢀHꢂꢂꢂO. This reinforcement would form a
sixꢀmembered ring with an angle close to 136º. In principle, the
N1 donor is also able to assist the CuꢀN1 bond with an intraꢀ
molecular interaction N6ꢀHꢂꢂꢂO. However, this reinforcement has
95 a much lower angle, close to 119º. Moreover, the CuꢀN1
coordination is partially hindered due to the negative contribution
of the electronic and steric effects of the exocyclic amino group.
It should be noted that, according to solutions studies made by H.
Sigel, B. Lippert et al. with adenineꢀlike ligands,21 the N3ꢀ
100 metalation significantly alters the basicity of N1, thus turning it
into a poorer metalꢀbinding site. Nonetheless, these former
hindrances per se are not enough to avoid coordination via N1.
Indeed, in compound 8, H(N9)7deaA exhibits an unique ꢁ2ꢀ
N1,N3 coordination role. The relevance of this new coordination
105 mode is tied not only to its novelty but to the metalꢀbinding
pattern consequences of the absence of N7. Thus, the restriction
on the N7(purine) donor enhances mostly the coordination
abilities of the sixꢀmembered ring in the purine moiety and drives
the coordination through N3 and, furthermore, promotes the
110 coordination role of N1. In this context, the N7 vs. N1 dichotomy
can also be analysed in terms of geometry. Although both N1 and
N7 coordination can be assisted by an Hꢀbonding interaction N6ꢀ
HꢂꢂꢂA, the N7 reinforcement forms a sevenꢀmembered ring with
an angle of close to 130º, in contrast to the aboveꢀmentioned sixꢀ
115 membered ring with an angle of close to 119º. Also, no relevant
hindrances could be expected for the N7 donor atom. Therefore,
25 adopts a merꢀNO2 conformation. One aqua ligand occupies the
apical position. The stability of the ternary complex is reinforced
by the intraꢀmolecular interligand Hꢀbonding interaction N9ꢀ
HꢂꢂꢂO21(coord. carboxy – see Table S10.3). The dihedral angle
(<OꢀCuꢀNꢀC) is nearly 40º, probably because of the influence of
30 pi,piꢀstacking interactions between adjacent H7deaA ligands
within the crystal (see Figure and comments in S10.4). In this
complex, the Cu(II) coordination environment is fairly close to a
regular squareꢀbased pyramidal coordination, according to the
Addison parameter τ = 0.02.
35
Compound 8 [Cu2(MIDA)2(ꢁ2ꢀN1ꢀN3ꢀH7deaA)(H2O)2]ꢂ5H2O
is an asymmetrical dinuclear complex having the unique ꢁ2ꢀ
N1,N3 bridging mode (Fig. 6). The copper(II) atoms exhibit a
squareꢀbased pyramidal coordination, type 4+1, built by three
40 donor atoms from the MIDA chelator in
a merꢀNO2
conformation, one Nꢀdonor from H7deaA and one apical aqua
ligand. There is a small difference in the distortion of the two
Cu(II) centres: τ = 0.021 for Cu(1) and τ = 0.008 for Cu(2) as
well as in the dihedral angles <OꢀCuꢀNꢀC 40.06º and 54.39º for
45 Cu1 and Cu2, respectively. To the best of our knowledge, the ꢁ2ꢀ
N1,N3 bridging mode has never been reported for any metal
complex having purineꢀlike bases. This pattern uses the most
stable tautomer H(N9)7deaA. Although,
a
priori, both
coordination bonds have the possibility of being reinforced by an
50 intraꢀmolecular Hꢀbond, experimental data indicate that only the
CuꢀN1 bond is assisted with the intraꢀmolecular N6ꢀ
H6AꢂꢂꢂO21(coord. carboxy ꢀ see Table S11.3) Hꢀbond whereas
the CuꢀN3 bond is not reinforced since the N9ꢀH group is
involved in interꢀmolecular N9ꢀHꢂꢂꢂO interactions, highly
55 influenced by the crystal packing (see Figure and comments in
S11.4).
< Figure 6 >
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in the presence of N7, this latter donor constitutes a richer metalꢀ 55 followed, using H2FBIDA acid (0.5 mmol, 0.120 g) instead of
binding site compared to N1, regardless of their difference of
basicity. Nevertheless, when N7 is removed, N1 turns into a more
competitive metalꢀbinding site; this tendency has also been
observed, for instance, with other purineꢀlike ligands.22
H2TEBIDA acid. In two days, needleꢀlike crystals were obtained.
The reaction yielded 65%. Elemental analysis (%): Calc. for
C18H21CuFN3O9: C 49.15, H 4.35, N 9.55; Found: C 49.33, H
6.28, N 9.48. FTꢀIR (KBr, cmꢀ1) νas(H2O) 3434, νs(H2O) shoulder
60 3257, ν(NꢀH) overshadowed, νas(CH2) 2927, νs(CH2) 2852,
δ(H2O) overlapped 1620, νas(COO) 1620, δ(NꢀH) 1512, νs(COO)
1384, π(CꢀH)ar 731 (H7azain), π(CꢀH)ar 793 (FBIDA). The
UV/Vis spectrum shows an asymmetric dꢀd band with λmax at 681
nm (νmax 14680 cmꢀ1). The EPR spectrum in the Xꢀband shows a
5
Experimental section†
Materials
Bluish Cu2CO3(OH)2 was purchased from Probus. Iminodiacetic 65 quasiꢀisotropic shape (g1 2.18, g2 2.14 and g3 2.09) corresponding
10 acid (H2IDA) was supplied by AlfaꢀAesar and Nꢀmethylꢀ
iminodiacetic acid (H2MIDA) was supplied by Across.
Ethylendiaminotetraacetic acid (H4EDTA), 7ꢀazaindole, 4ꢀ
azabenzimidazole, 5ꢀazabenzimidazole and 7ꢀdeazaadenine were
to a Cu(II) centre in dx2ꢀy2 ground state. Under airꢀdry flow, the
sample lost part of the nonꢀcoordinated water molecule. Hence,
the sample started the TG experiment with formula
{[Cu(FBIDA)(H7azain)]ꢂ 0.55H2O}. The thermal behaviour was
purchased from sigmaꢀAldrich. All the above reagents were used 70 divided into four steps. The sample lost the former 0.55 H2O
15 without further purification. Nꢀ(pꢀtBu)ꢀ, Nꢀbenzylꢀ, Nꢀ(pꢀ
methylbenzyl)ꢀ, Nꢀ(pꢀfluorobenzyl)ꢀ and Nꢀ(pꢀchlorobenzyl)ꢀ
iminodiacetic acids (H2TEBIDA, H2NBzIDA, H2MEBIDA,
H2FBIDA and H2CBIDA, respectively) were synthesised in their
acid form as reported in refs. 14a and 23.
molecules during the first step (Calc. 2.30%; Found 2.60%),
according to the evolved gasses. Three additional pyrolytic steps
produced H2O, CO2, CO, and Nꢀoxide gasses (N2O, NO, NO2) to
reach a final CuO residue (480ºC, Calc. 18.42%; Found 19.45%).
75
20
{[Cu(CBIDA)(H4abim)]·2H2O}n (3)
Syntheses of the complexes
A synthetic procedure similar to that of compound (1) was
followed, using Cu2CO3(OH)2 (0.25 mmol, 0.055 g), H2CBIDA
acid (0.5 mmol, 0.128 g), and H4abim (0.5 mmol, 0.060 g). In
[Cu(TEBIDA)(H7azain)(H2O)]·3H2O (1)
Cu2CO3(OH)2 (0.25 mmol, 0.055 g) was reacted in 80 mL of
distilled water with H2TEBIDA acid (0.5 mmol, 0.095 g) in a
25 Kitasato flask, heating (50ºC ) and stirring under moderate
vacuum. Once a clear blue solution was obtained, H7azain was
added (0.5 mmol, 0.059 g). The reacting mixture was stirred for 1
h until the ligand was completely dissolved. Afterwards, the
resulting blue solution was filtered, without a vacuum, in a
30 crystallization device and allowed to stand at room temperature,
covered with a plastic film to control the evaporation. After
several weeks, parallelepiped crystals suitable for XRD purposes
were collected. The yield was ca. 70ꢀ75%. Elemental analysis
(%): Calc. for C15H27CuN3O8: C 40.86, H 6.17, N 9.53; Found: C
35 40.73, H 6.32, N 9.59. FTꢀIR (KBr, cmꢀ1) νas(H2O) 3456, νs(H2O)
3250, ν(NꢀH) 3163, νas(CH3) 2985, νs(CH3) 2854, νas(CH2) 2964,
νs(CH2) 2825, δ(H2O) 1633, νas(COO) 1608, δ(NꢀH) 1507,
νs(COO) 1384, π(CꢀH)ar 725. The UV/Vis spectrum showed an
asymmetric dꢀd band with λmax at 677 nm (νmax 14770 cmꢀ1). The
40 EPR spectrum in the Xꢀband shows an axial shape (g1 2.26, g2
2.10 and g3 2.04) corresponding to a Cu(II) centre in dx2ꢀy2 ground
state. Under airꢀdry flow, the sample lost the nonꢀcoordinated
water molecules, and thus the TG experiment started with an
average formula [Cu(TEBIDA)(H7azain)(H2O)]. The thermoꢀ
45 gravimetric curve showed three steps. The first step corresponded
to the loss weight of the apical aqua ligand (Calc. 4.66%; Found
4.56%). Indeed, only H2O was found in the evolved gasses during
the first step. The following pyrolytic steps yielded a final residue
of CuO (425ºC , Calc. 20.56%; Found 21.45%). The evolved
50 gasses during the pyrolysis involved H2O, CO2, CO and two Nꢀ
oxide gasses (N2O and NO).
80 approximately three weeks, needleꢀlike crystals were collected.
The reaction yielded 81%. Elemental analysis (%): Calc. for
C17H19ClCuN4O6: C 43.04, H 4.04, N 11.81; Found: C 42.85, H
3.98, N 11.93. FTꢀIR (KBr, cmꢀ1) νas(H2O) 3418, νs(H2O) 3258,
ν(NꢀH) 3132, two different νas(CH2) 2971 and 2927, two different
85 νs(CH2) 2872 and 2818, δ(H2O) shoulder 1625, νas(COO)bridging
1614, νas(COO)monodentate 1600, δ(NꢀH) 1539, νs(COO)bridging 1399,
νs(COO)monodentate 1388, π(CꢀH)ar 780 (H4abim), π(CꢀH)ar 677
(CBIDA). The UV/Vis spectrum shows an asymmetric dꢀd band
with λmax at 677 nm (νmax 14770 cmꢀ1). The EPR spectrum in the
90 Xꢀband shows an axial shape (g1 2.24, g2 2.08 and g3 2.07)
corresponding to a Cu(II) centre in dx2ꢀy2 ground state. Under airꢀ
dry flow, the sample lost 1.5 nonꢀcoordinated water molecules,
and hence the TG experiment started with an average formula
{[Cu(CBIDA)(H4abim)]ꢂ0.5H2O}.
The thermoꢀgravimetric
95 curve was divided into four steps. The first step corresponded
only to the loss of 0.5 H2O molecules (Calc. 2.01%; Found
1.94%). Pyrolysis of the organic ligands was conducted in three
consecutive steps, in which H2O, CO2, CO, N2O, NO, and NO2(t)
were evolved. At the end, a CuO residue was obtained (530ºC,
100 Calc. 17.78%; Found 17.88%).
[Cu(H2EDTA)(H4abim)]·0.5H2O (4)
A synthetic procedure similar to that of compound (3) was
followed, using H4EDTA acid (0.5 mmol, 0.146 g) instead of
105 H2CBIDA acid. Four weeks later, suitable crystals for XRD
purposes were collected. Yield is ca. 75ꢀ80%. Elemental analysis
(%): Calc. for C16H20CuN5O8.5: C 39.88, H 4.18, N 14.53; Found:
C 40.01, H 4.23, N 14.26. FTꢀIR (KBr, cmꢀ1) νas(H2O) 3435,
νs(H2O) shoulder 3259, ν(NꢀH) 3136, two different νas(CH2) 2929
110 and 2919, two different νs(CH2) 2879 and 2857, ν(C=O)free ꢀCOOH
1727, δ(H2O) 1617, νas(COO) 1568, δ(NꢀH) overshadowed,
{[Cu(FBIDA)(H7azain)]·H2O}n (2)
A synthetic procedure similar to that of compound (1) was
6
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combined mode ν(CꢀO)+δ(OꢀH) shoulder 1412, νs(COO) 1384,
δ(OꢀH) 1116, π(OꢀH) 733, π(CꢀH)ar 783. The UV/Vis spectrum
an asymmetric dꢀd band with λmax at 675 nm (νmax 14815 cmꢀ1).
The EPR spectrum in the Xꢀband shows an axial shape (g1 2.24,
shows an asymmetric dꢀd band with λmax at 675 nm (νmax 14810 60 g2 2.08 and g3 2.06) corresponding to a Cu(II) centre in dx2ꢀy2
cmꢀ1) and a shoulder at λ 1050 nm (νsh 9480 cmꢀ1). The EPR
spectrum in the Xꢀband shows an axial shape (g1 2.31, g2 2.09
and g3 2.05) corresponding to a Cu(II) centre in dx2ꢀy2 ground
state. Under airꢀdry flow, the sample lost all the nonꢀcoordinated
ground state. Under airꢀdry flow, the sample lost all the water
content. The thermal behaviour was divided into two steps. The
TG experiment started at 190ºC when the sample directly
underwent pyrolysis up to 455ºC, when the CuO residue was
5
water molecule. The thermoꢀgravimetric curve was divided into 65 measured (Calc. 20.16%; Found 21.42%). The pyrolysis of
three steps. In the TG experiment, the sample directly underwent
[Cu2(NBzIDA)2(H5abim)] produced H2O, CO2, CO, N2O, NO
and NO2(t).
10 pyrolysis, from 170ºC to 525ºC, when the CuO residue was
measured (Calc. 16.82%; Found 18.29%). The pyrolysis of
[Cu(H2EDTA)(H4abim)] produced H2O, CO2, CO, and Nꢀoxide
gasses (N2O, NO, and NO2).
[Cu(IDA)(H7deaA)(H2O)]·2H2O (7)
70 A synthetic procedure similar to that of compound (1) was
followed, using Cu2CO3(OH)2 (0.25 mmol, 0.055 g), H2IDA acid
(0.5 mmol, 0.067 g), and H7deaA (0.5 mmol, 0.067 g). In two
weeks, greenish needleꢀlike crystals were collected. The reaction
yielded 75%. However, the easy ageing of the crystals prevented
15 {[Cu2(IDA)2(µ2-N7,N9-H5abim)]·H2O}n (5)
A synthetic procedure similar to that of compound (1) was
followed, using Cu2CO3(OH)2 (0.25 mmol, 0.055 g), H2IDA acid
(0.5 mmol, 0.067 g), and H5abim (0.5 mmol, 0.060 g). However, 75 the successful Xꢀray data collection. To avoid this problem, we
only extremely thin needleꢀlike crystals, useless for XRD
20 purposes, resulted. Hence, the synthesis was redesigned.
Cu2CO3(OH)2 (0.06 mmol, 0.013 g) was reacted in 5 mL of
distilled water with H2IDA acid (0.125 mmol, 0.016 g) in a small
grew the crystals in a gel medium to preserve their integrity, as
described here. H7deaA (0.02 mmol, 0.0027 g) was added as a
solid powder to a vial. Afterwards, 2 mL of an 0.5% agar solution
of [Cu(IDA)(H2O)2] 0.01M was added to the same vial, stirring
Erlenmeyer flask, heating (50ºC) and stirring. Once the reaction 80 the solution in a water bath (gentle heating) until the reaction
was completed, an aliquot (3 mL) of such blue solution was
25 moved to a vial. Separately, H5abim (0.125 mmol, 0.017 g) was
took place. Then, the solution, properly capped, was left gel at
room temperature. The vial stood at room temperature where
better crystals appeared within four weeks. One of these crystals
was removed and successfully used for XRD purposes. Elemental
dissolved in
5 mL of DMF and slowly added to the
aforementioned blue solution. The vial was properly capped and
the solution left to evaporate at 120ºC. After two days, good 85 analysis (%): Calc. for C10H17CuN5O7: C 31.37, H 4.48, N 18.29;
parallelepiped crystals were obtained. The reaction yielded 65%.
30 Elemental analysis (%): Calc. for C14H17Cu2N5O9: C 31.94, H
3.26, N 13.30; Found: C 32.09, H 3.46, N 13.21. FTꢀIR (KBr, cmꢀ
1) νas(H2O) 3478, νs(H2O) 3205, ν(NꢀH) 3131 (H5abim), ν(NꢀH)
Found: C 31.49, H 4.53, N 18.15. FTꢀIR (KBr, cmꢀ1) νas(H2O)
3421, νas(NH2) 3346, νs(NH2) 3272, νs(H2O) 3228, ν(NꢀH) 3134
(H7deaA and IDA overlapped), νas(CH2) 2943, νs(CH2)
overshadowed, δ(H2O) 1652, δ(NH2) 1604, νas(COO) 1586, δ(Nꢀ
3100 (IDA), νas(CH2) 2925, νs(CH2) 2829, δ(H2O) overlapped 90 H) 1514, νs(COO) 1392, π(CꢀH)ar 734. The UV/Vis spectrum
1618, νas(COO) 1618, δ(NꢀH) 1547, νs(COO) 1382, π(CꢀH)ar 641.
35 The UV/Vis spectrum shows an asymmetric dꢀd band with λmax at
687 nm (νmax 14555 cmꢀ1). The EPR spectrum in the Xꢀband
shows an axial shape (g1 2.24, g2 2.10 and g3 2.07) corresponding
shows an asymmetric dꢀd band with λmax at 726 nm (νmax 13755
cmꢀ1). The EPR spectrum in the Xꢀband shows an axial shape (g1
2.27, g2 2.06 and g3 2.06) corresponding to a Cu(II) centre in dx2ꢀ
ground state. Under airꢀdry flow, the sample lost only part of
y2
to a Cu(II) centre in dx2ꢀy2 ground state. The absence of enough 95 the nonꢀcoordinated water molecule. Hence, the sample started
highꢀquality samples allowed us to analyse the TG experiment
40 only in a qualitative way. The TG curve was divided into four
steps. In the first step (to 230ºC), only the water content was lost
according to the evolved gasses. Successive pyrolytic steps
with a TG formula [Cu(IDA)(H7deaA)(H2O)]ꢂ1.5H2O. The
thermal behaviour was divided into four steps. The entire water
content was lost during the first step (Calc. 12.05%; Found
12.16%), according to the evolved gasses – only H2O. Three
produced H2O, CO2, CO, NO2, and NO gasses, yielding a 100 additional pyrolytic steps produce H2O, CO2, CO, NH3, and Nꢀ
possible CuO residue (440ºC).
oxide gasses (N2O, NO, NO2) to reach a final CuO residue
(550ºC , Calc. 21.27%; Found 21.39%).
45
[Cu2(NBzIDA)2(µ2-N7,N9-H5abim)(H2O)2]·H2O (6)
[Cu2(MIDA)2(µ2-N1,N3-H7deaA)(H2O)2]·5H2O (8)
A synthetic procedure similar to that of compound (1) was
followed, using Cu2CO3(OH)2 (0.25 mmol, 0.055 g), H2NBzIDA 105 A synthetic procedure similar to that of compound (1) was
acid (0.5 mmol, 0.112 g), and H5abim (0.5 mmol, 0.060 g). Six
followed, using Cu2CO3(OH)2 (0.25 mmol, 0.055 g), H2MIDA
acid (0.5 mmol, 0.073 g), and H7deaA (0.5 mmol, 0.067 g). After
two months, very thin needleꢀlike crystals were collected. Yield
was ca. 70ꢀ75%. Elemental analysis (%): Calc. for
50 weeks later, parallelepiped crystals suitable for XRD purposes
were collected. Yield is ca. 65ꢀ70%. Elemental analysis (%):
Calc. for C28H33Cu2N5O11: C 45.28, H 4.48, N 9.43; Found: C
45.06, H 4.31, N 9.57. FTꢀIR (KBr, cmꢀ1) νas(H2O) 3427, νs(H2O) 110 C16H34Cu2N6O15: C 28.36, H 5.06, N 12.40; Found: C 28.26, H
3269, ν(NꢀH) 3126, two different νas(CH2) 2983 and 2937, two
55 different νs(CH2) 2872 and 2835, δ(H2O) overlapped 1629,
νas(COO) 1629, δ(NꢀH) 1538, νs(COO) 1384, π(CꢀH)ar 644
(H5abim), π(CꢀH)ar 708 (NBzIDA). The UV/Vis spectrum shows
4.88, N 12.56. FTꢀIR (KBr, cmꢀ1) νas(H2O) 3470, νas(NH2) 3401,
νs(NH2) 3236, νs(H2O) overlapped 3236, ν(NꢀH) shoulder 3120,
νas(CH3) 2975, νas(CH2) 2934, νs(CH3) 2858, νs(CH2) 2859,
δ(H2O) 1639, δ(NH2) overlapped 1614, νas(COO) 1614, δ(NꢀH)
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1512, νs(COO) 1391, π(CꢀH)ar 738. The UV/Vis spectrum shows
an asymmetric dꢀd band with λmax at 696 nm (νmax 14370 cmꢀ1).
49.82, H 4.26, N 16.14. FTꢀIR (KBr, cmꢀ1) νas(NH2) 3365,
νs(NH2) 3280, ν(NꢀH) 3195, νas(CH3) 2942, νas(CH2) 2922,
The EPR spectrum in the Xꢀband shows an axial shape (g1 2.24, 60 νs(CH3) 2859, νs(CH2) 2822, δ(NH2) 1637, νas(COO) 1596, δ(Nꢀ
g2 2.09 and g3 2.06) corresponding to a Cu(II) centre in dx2ꢀy2
ground state. Under airꢀdry flow, the sample lost part of the nonꢀ
coordinated water molecules. The TG experiment started with an
average formula [Cu2(MIDA)2(H7deaA)(H2O)2]ꢂ2.3H2O. The
H) 1513, νs(COO) 1390, π(CꢀH)ar 739 (H7deaA), π(CꢀH)ar 808
(MEBIDA). The UV/Vis spectrum shows an asymmetric dꢀd
band with λmax at 710 nm (νmax 14085 cmꢀ1). The EPR spectrum
in the Xꢀband shows an axial shape (g1 2.22, g2 2.10 and g3 2.07)
5
thermoꢀgravimetric curve was divided into four steps. The first 65 corresponding to a Cu(II) centre in dx2ꢀy2 ground state. The
step agreed with the loss of 4.3 H2O molecules, which
thermal behaviour was divided into three steps. Since the sample
had no water content, the compound directly followed three
pyrolytic steps, producing H2O, CO2, CO, and Nꢀoxide gasses
(N2O, NO, NO2) to form a final CuO residue (470ºC, Calc.
10 corresponded to 2.3 nonꢀcoordinated plus two apical aqua ligands
(Calc. 12.32%; Found 12.42%). Pyrolysis of the organic ligands
was conducted in three consecutive steps, in which H2O, CO2,
CO, NH3, trimethylꢀamine, N2O, and NO were evolved. Note that 70 18.33%; Found 18.04%).
trimethylꢀamine is a typical gas present in the pyrolysis of MIDA
15 ligand. In the end, a CuO residue was obtained (450ºC, Calc.
23.48%; Found 23.78%).
Conclusions
In the ternary iminodiacetateꢀcopper(II) complexes studied in this
[Cu(NBzIDA)(H7deaA)]n (9)
work, we found a general trend to use different tautomers and to
75 diversify the metalꢀbinding patterns of the deazaꢀadenines
studied. It was notable that, although H(N9) was the most stable
tautomer of all the purineꢀlike ligands, tautomerism phenomena
are possible within the metal complexes, i.e. H4abim and
H5abim, where the tautomers H(N9) and H(N7) were very close
80 in terms of energy. We found that the absence of N7 in
H(N9)7deaA encouraged the formation of the rare CuꢀN1 bond in
cooperation with an intraꢀmolecular interligand N6ꢀHꢂꢂꢂO Hꢀ
bond. Overall, a remarkable and broad agreement was observed
between the molecular structures and the reported DFT
85 calculations.
A synthetic procedure similar to that of compound (8) was
20 followed, using H2NBzIDA acid (0.5 mmol, 0.112 g) instead of
H2MIDA acid. The day after, microꢀcrystals covered the
crystallization device and the solution was filtered with the aim of
obtaining larger crystals. Two weeks later, crystals reached an
appropriate size but Xꢀray data collection was not successful. The
25 reaction yielded 65%. Hence, crystallization on gel medium was
performed to improve the size and the quality of the crystals:
H7deaA (0.01 mmol, 0.0013 g) was added as a solid powder into
a
vial. Afterwards, 2 mL of an 0.5% agar solution of
[Cu(NBzIDA)(H2O)2] 2.5 mM was added to the same vial,
30 stirring the solution in a water bath (gentle heating) until the
reaction took place. Then, the solution was left to gel at room
temperature. Once the solution was a proper gel, 200 ꢁL of
MeOH was added as an antiꢀsolvent and the vial was capped. The
vial stood at room temperature, and suitable crystals appeared
35 within four weeks. One of these crystals was removed and
successfully used for XRD purposes. Elemental analysis (%):
Calc. for C17H17CuN5O4: C 48.74, H 4.09, N 16.72; Found: C
48.79, H 4.09, N 16.69. FTꢀIR (KBr, cmꢀ1) νas(NH2) 3304,
νs(NH2) 3270, ν(NꢀH) 3190, two different νas(CH2) 2959 and
40 2928, two different νs(CH2) 2888 and 2863, δ(NH2) shoulder
1605, νas(COO) 1593, δ(NꢀH) 1509, νs(COO) 1399, π(CꢀH)ar 746
(H7deaA), π(CꢀH)ar 710 (NBzIDA). The UV/Vis spectrum shows
an asymmetric dꢀd band with λmax at 731 nm (νmax 13680 cmꢀ1).
The EPR spectrum in the Xꢀband shows a quasiꢀisotropic shape
45 (g1 2.21, g2 2.14 and g3 2.07) corresponding to a Cu(II) centre in
dx2ꢀy2 ground state. The thermal behaviour was divided into three
steps. Since the sample did not have any water content, the
compound directly followed three pyrolytic steps, producing
H2O, CO2, CO, and Nꢀoxide gasses (N2O, NO, NO2) to reach a
50 final CuO residue (, 440ºC Calc. 18.99%; Found 20.81%).
Acknowledgements
Financial support from Research Groups FQMꢀ283 and FQMꢀ
174 (Junta de Andalucía) and MICINNꢀSpain (Project
90 MAT2010ꢀ15594) is gratefully acknowledged. The project
‘Factoría de Cristalización, CONSOLIDER INGENIOꢀ2010’
provided Xꢀray structural facilities for this work. We thank the
“Centro de Servicios de Informática y Redes de Comunicaciones”
(CSIRC), Universidad de Granada, for providing computing time.
95 Financial support from ERDF Funds and Junta de Andalucía to
acquire the FTꢀIR spectrophotometer Jasco 6300 is gratefully
acknowledged. ADM thanks MEꢀSpain for a FPU Ph.D contract.
Notes and references
100 a Department of Inorganic Chemistry, Faculty of Pharmacy, University of
Granada, Campus Cartuja s/n, 18071 Granada, Spain. Fax: +34 958
246219; Tel: +34 958 243853; E-mail: adominguez@ugr.es
b Laboratorio de Estudios Cristalográficos, IACT, CSIC-University of
Granada, Avenida de las Palmeras 4, 18100 Armilla (Granada), Spain.
105 c Grupo de Modelización y Diseño Molecular, Department of Organic
Chemistry, University of Granada, Severo Ochoa s/n, 18071 Granada,
Spain.
[Cu(MEBIDA)(H7deaA)]n (10)
d Department of Inorganic Chemistry, Faculty of Science and Technology,
University of Basque Country, E-48080 Bilbao, Spain.
A synthetic procedure similar to that of compound (8) was
followed using H2MEBIDA acid (0.5 mmol, 0.120 g) instead of
55 H2MIDA acid. Two weeks later, suitable parallelepiped crystals
were collected. Yield is ca. 70ꢀ75%. Elemental analysis (%):
Calc. for C18H19CuN5O4: C 49.94, H 4.42, N 16.18; Found: C
110 e Department of Inorganic Chemistry, Faculty of Pharmacy, University of
Santiago de Compostela, 15782 Santiago de Compostela, Spain.
8
| Journal Name, [year], [vol], 00–00
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14 S.J. Rettig, V. Sánchez, A. Storr, R.C. Thompson, J. Trotter, J. Chem.
Soc., Dalton Trans. 2000, 3931.
† Electronic Supplementary Information (ESI) available: Experimental
details are provided in S1. Additional data about DFT calculations are
provided in S2 and S3. Additional crystal data, formula and structural
plots of all the compounds reported in this work are included in the
supporting information (S4 to S14). CCDC 881136 ꢀ 881145. FTꢀIR, UVꢀ
Vis and EPR spectra of all the reported compounds are provided in S15,
S16 and S17, respectively. As an example, the analysis of thermal
15 (a) E. BugellaꢀAltamirano, D. ChoquesilloꢀLazarte, J.M. Gonzálezꢀ
Pérez, M. J. SánchezꢀMoreno, R. MarínꢀSánchez, J.D. Martínꢀ
Ramos, B. Covelo, R. Carballo, A. Castiñeiras and J. Niclósꢀ
Gutiérrez, Inorg. Chim. Acta, 2002, 339, 160; (b) A. C. Morel, D.
ChoquesilloꢀLazarte, C. AlarconꢀPayer, J. M. GonzálezꢀPerez, A.
Castiñeiras, J. NiclósꢀGutiérrez, Inorg. Chem. Commun., 2003, 6,
1354; (c) M. P. BrandiꢀBlanco, B. DumetꢀFernandes, J. M. Gonzálezꢀ
Perez, D. ChoquesilloꢀLazarte, Acta Crystallogr., 2007, E63, m1598.
16 (a) M. J. Zaworotko, H. H. Hammud, A. Kabbani, G. J. McManus, A.
M. Ghannoum, M. S. Masoud, J. Chem. Cryst., 2009, 39, 853; (b) J.
P. GarcíaꢀTerán, O. Castillo, A. Luque, U. GarcíaꢀCouceiro, G.
Beobide, P. Román, Dalton Trans., 2006, 902.
85 17 E. SerranoꢀPadial, D. ChoquesilloꢀLazarte, E. BugellaꢀAltamirano,
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2002, 21, 1451.
18 P. X. RojasꢀGonzález, A. Castiñeiras, J. M. GonzálezꢀPérez, D.
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5
75
80
stability of compound
DOI: 10.1039/b000000x/.
8
is also provided in S18. See
10 Additional thermal analyses (TGA) have been carried out for all the
reported compounds. For further information, please contact the
corresponding author.
§ Notation for the Nꢀatom coordinated to Cu(II) and the N atom
protonated, i.e. 9p3 means coordination via N9 and the dissociable proton
15 bounded to N3 of the deazaꢀadenine ligand.
‡ There is another possibility of dinuclear coordination: 1,7p9. This
former conformation has been intentionally discarded due to the
distortions arising from the proximity of both chelating ligands (see, for
example, the dihedral angles in Table S2).
20
90
6190.
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Scheme 1. Adenine and related deaza-adenine ligands (purine conventional notation is used throughout
this work despite the IUPAC notation of these N-ligands).
Figure 1. DFT (B3LYP/6-31+G**//B3LYP/6-31+G**) most stable coordination modes and proton
tautomers for the mononuclear copper(II) complexes with nucleobases (H7azain, H4abim, H5abim and
H7deaA) and the chelating ligands (MIDA, CBIDA, NBzIDA and H2EDTA).
Figure 2. DFT (B3LYP/6-31+G**//B3LYP/6-31+G**) two most stable coordination modes and proton
tautomers of the dinuclear copper(II) complexes with H5abim and the chelating ligands MIDA and
NBzIDA.
Figure 3. Fragment of the coordination polymer {[Cu(FBIDA)(H7azain)]·2H2O}n (2) and numbering of
the coordination environment.
Figure 4. Molecular structure of [Cu(H2EDTA)(H4abim)]·0.5H2O (4) and numbering of the coordination
environment.
Figure 5. Molecular structure of [Cu2(NBzIDA)2(µ2-N7,N9-H5abim)(H2O)2]·H2O (6) and numbering of
the coordination environment.
Figure 6. Molecular structure of [Cu2(MIDA)2(µ2-N1,N3-H7deaA)(H2O)2]·5H2O (8) and numbering of
the coordination environment.
Figure 7. Fragment of the coordination polymer [Cu(NBzIDA)(H7deaA)]n (9) and numbering of the
coordination environment.

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6
6
NH2
NH2
7
N
7
N
1
1
1
N
N
N
N
H
N
N
H
9
9
N
3
N
3
9
N
3
H
Purine
(Hpur)
Adenine
(Hade)
7-deaza-adenine
(H7deaA)
7
N
7
N
1
N
N
N
H
N
H
N
3
9
9
9
N
3
H
4-azabenzimidazole
1,6-dideaza-adenine
5-azabenzimidazole
7-azaindole
3,6-dideaza-adenine 1,6,7-trideaza-adenine
(H5abim)
(H7azain)
(H4abim)

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Table 1: DFT Gas phase and solvent (water) relative Gibbs energies (ꢀGrel) for the
different tautomers of diazadenine ligands, calculated at the B3LYP/6ꢁ
31+G**//B3LYP/6ꢁ31+G**
and
PCMꢁB3LYP/6ꢁ31+G**//PCMꢁB3LYP/6ꢁ31+G**
theoretical levels, respectively.
TautomerꢀH1
ꢁGrel
(Kcal/mol)
TautomerꢀH9
ꢁGrel (Kcal/mol)
TautomerꢀH7
ꢁGrel (Kcal/mol)
TautomerꢀH3
ꢁGrel (Kcal/mol)
Compound a
I-p9 / I-p3
(H7azain)
II-p9 / II-p7 / II-p1
(H5abim)
III-p9 / III-p7 / III-p3
(H4abim)
0.0
0.0
0.0
0.0
-
12.5 (9.7)
-
-
0.3 (0.6)
3.9 (0.2)
-
7.8 (3.8)
-
9.6 (6.1)
11.2 (8.5)
IV-p9 / III-p3 / III-p1
(H7deaA)
22.6 (12.5)
a. The Latin numbers refer to the deaza-adenine ligand (i.e. I is 7-azaindole; II is 4-azabenzimidazole; III is 5-
azabenzimidazole and IV is 7-deaza-adenine). Values in parentheses correspond to the solvent effect PCM (water). The
number after the ‘p’ indicates where the tautomerizable proton is located, i.e. p9.

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mononuclear Cu(II) complexes
UM06-L/ 6-31G*//UM06-L/6-31G*
H7azain
Ia-3p9
Cu(MIDA)(H7azain)
Ib-3p9
Cu(NBzIDA)(H7azain)
H4abim
IIc-3p9
Cu(CBIDA)(H4abim)
IId-3p9
Cu(H2EDTA)(H4abim)
IIa-3p9
Cu(MIDA)(H4abim)
H5abim
IIIa-1p7
Cu(MIDA)(H5abim)
IIIb-1p7
Cu(NBzIDA)(H5abim)
H7deaA
IVb-3p9
Cu(NBzIDA)(H7deaA)
IVa-3p9
Cu(MIDA)(H7deaA)

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dinuclear Cu(II) complexes
UM06-L/ 6-31G*//UM06-L/6-31G*
H5abim
Va-p1
Cu2(MIDA)2(H5abim)
Gr = 0.0
Va-p7
Cu2(MIDA)2(H5abim)
Gr = 1.2
Vb-p1
Cu2(NBzIDA)2(H5abim)
Gr = 0.0
Vb-p7
Cu2(NBzIDA)2(H5abim)
Gr = 0.6

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Fragment of the coordination polymer {[Cu(FBIDA)(H7azain)]—2H2O}n (2) and numbering of the
coordination environment.

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Molecular structure of [Cu(H2EDTA)(H4abim)]—0.5H2O (4) and numbering of the coordination environment.

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Molecular structure of [Cu2(NBzIDA)2(ꢀ2ꢁN7,N9ꢁH5abim)(H2O)2]—H2O (6) and numbering of the
coordination environment.

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Molecular structure of [Cu2(MIDA)2(ꢀ2ꢁN1,N3ꢁH7deaA)(H2O)2]—5H2O (8) and numbering of the
coordination environment.

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Fragment of the coordination polymer [Cu(NBzIDA)(H7deaA)]n (9) and numbering of the coordination
environment.