On justification of Cu(II) environment in mononuclear complexes: Joint X-ray and AIM studies

Article abstract of DOI:10.1016/j.poly.2011.04.002

Interaction of copper(II) acetate with benzoic acid (benzene-1,3,5- tricarboxylic acid = H₃-btc and 3,5-dinitro-benzoic acid = H-dnb) and pyridine (Py) resulted in two mononuclear square-planar complexes with the compositions [Cu(H₂-btc)₂(Py)₂] (1) and [Cu(dnb)₂(Py)₂] (2). The recrystallization of 2 from dimethylsulfoxide (DMSO) yielded the square-bipyramidal complex [Cu(dnb) ₂(DMSO)₂(H₂O)₂] (3). Crystal structures of 1-3 were determined by single crystal X-ray diffraction at 100 K. The square-planar Cu(II) geometry with the Cu-O and Cu-N distances of 1.924(2), 1.925(2) and 2.024(3) and 2.025(3) in 1, and 1.930(4) and 2.033(5) in 2 was found. The extended H-bonding system in 1 built on the robust carboxylic synthons is giving rise to the high-ordered porous layered structure. Insight into metal center environment and stabilizing intramolecular short interactions is obtained through quantum theory of atoms in molecules (QTAIM). As revealed by QTAIM, in octahedral complex 3 Cu-dnb and Cu-DMSO bonds are stronger than Cu-N bonds in 1 and 2.

Full text of DOI:10.1016/j.poly.2011.04.002

Polyhedron 30 (2011) 1710–1717
Contents lists available at ScienceDirect
Polyhedron
journal homepage: www.elsevier.com/locate/poly
On justification of Cu(II) environment in mononuclear complexes: Joint X-ray
and AIM studies
Alexandr Fonari a, , Evgeniya S. Leonova a,b, Mikhail Yu. Antipin a,b
⇑
a New Mexico Highlands University, Las Vegas, NM 87701, USA
b A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991 Moscow, Russian Federation
a r t i c l e i n f o
a b s t r a c t
Article history:
Interaction of copper(II) acetate with benzoic acid (benzene-1,3,5-tricarboxylic acid = H3-btc and 3,5-
dinitro-benzoic acid = H-dnb) and pyridine (Py) resulted in two mononuclear square-planar complexes
with the compositions [Cu(H2-btc)2(Py)2] (1) and [Cu(dnb)2(Py)2] (2). The recrystallization of 2 from
dimethylsulfoxide (DMSO) yielded the square-bipyramidal complex [Cu(dnb)2(DMSO)2(H2O)2] (3). Crys-
tal structures of 1–3 were determined by single crystal X-ray diffraction at 100 K. The square-planar
Cu(II) geometry with the Cu–O and Cu–N distances of 1.924(2), 1.925(2) and 2.024(3) and 2.025(3) Å
in 1, and 1.930(4) and 2.033(5) Å in 2 was found. The extended H-bonding system in 1 built on the robust
carboxylic synthons is giving rise to the high-ordered porous layered structure. Insight into metal center
environment and stabilizing intramolecular short interactions is obtained through quantum theory of
atoms in molecules (QTAIM). As revealed by QTAIM, in octahedral complex 3 Cu-dnb and Cu-DMSO
bonds are stronger than Cu–N bonds in 1 and 2.
Received 11 January 2011
Accepted 4 April 2011
Available online 12 April 2011
Keywords:
Cu(II) square-planar geometry
Extended H-bonding system
X-ray
Quantum theory of atoms in molecules
Ó 2011 Elsevier Ltd. All rights reserved.
1. Introduction
generation of multinuclear and polymeric Cu(II)-carboxylic net-
works [6]. The diversity of the networks built from the similar
Metal–organic building blocks as a prototype to highly porous
metal–organic frameworks [1] continue to be an active research
field because of the large variety of metal–ligand combinations.
The d9 configuration of the Cu(II) cation favors either a square-
planar, square-pyramidal or square-bipyramidal geometries.
Mono- and polycarboxylic acids are by far the most widely used
organic ligands for the synthesis and crystal engineering of
compounds that exhibit highly ordered 2D or 3D networks. Among
them benzene-1,3,5-tricarboxylic acid (H3-btc, also known as
trimesic acid) occupies a special place, as it is a polyfunctional car-
boxylic acid with 3-fold symmetry comprising a phenyl ring and
three identical carboxyl end groups in the same plane [2]. Starting
from the seminal Science paper [3] which reported a highly porous
metal coordination polymer [Cu3(btc)2(H2O)3]n various open
frameworks with the fascinated supramolecular architectures
containing Cu(II) as a metal center and polycarboxylic aromatic
acids as linkers were described. In particular, benzene-1,3,5-tricar-
boxylic acid was explored either as a unique ligand for construction
of Cu(II)-based carboxylate networks [4] or in combination with
different amines as auxiliary ligands [5]. Along with H3-btc, its
nitro- and dinitro-analogs with the same positions of the substitu-
ents in the aromatic core, have been successfully applied so far for
components and explained by the possibility of different coordina-
tion environment of Cu(II), different modes of carboxylic groups
coordination, and different degree of deprotonation of starting acid
was found using X-ray analysis of the structure of such compounds.
An additional insight into metal center environment can be
obtained through quantum theory of atoms in molecules (QTAIM).
The topological analysis, based on the QTAIM [7,8], is a useful
tool to justify the metal coordination environment as well as to
estimate the stabilizing impact of short intramolecular interactions
in such complexes. Recently a number of papers describing differ-
ent bonding aspects of pure organic molecules as well as coordina-
tion complexes were published using QTAIM approach. Analysis of
the local electron density properties at bond critical points (BCPs)
allows qualitative and quantitative classification of the metal–
ligand bonds. Using this approach Firme et al. compared the stabil-
ity of the titanium complexes based on the number of BCPs found
between metal and ligands [9]. Cukrowski and co-workers esti-
mated the stabilizing effect of Hꢀ ꢀ ꢀH close contacts in Zn(II) and
Ni(II) complexes [10]. As the correct assignment of the primary
coordination sphere for Cu(II) still remains a challenge [11,12]
the modern computational approaches such as QTAIM demon-
strate their facilities in solving this problem. For example, consid-
eration of a number of topological indicators by Farrugia with
co-workers for Cu(II) 3-amino-propanolato complexes containing
weakly coordinated anions provided an insight into the differing
electrostatic and covalent contributions to the chemical bonds
⇑
Corresponding author. Tel.: +1 5056522245.
E-mail addresses: alexandr.fonari@gmail.com (A. Fonari), mishan@nmhu.edu
(M.Yu. Antipin).
0277-5387/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.poly.2011.04.002

A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
1711
Table 3
Intermolecular hydrogen bonding in 1–3. Distances are in (Å) and angles in (°).
D–Hꢀ ꢀ ꢀA
d(D–H)
d(Hꢀ ꢀ ꢀA)
d(Dꢀ ꢀ ꢀA)
\DHA
Compound 1
C(7)–H(7A)ꢀ ꢀ ꢀO(9)#1
C(19)–H(19A)ꢀ ꢀ ꢀO(3)#2
O(3)–H(3)ꢀ ꢀ ꢀO(8)#1
O(6)–H(6)ꢀ ꢀ ꢀO(11)#3
O(9)–H(9)ꢀ ꢀ ꢀO(2)#2
O(12)–H(12)ꢀ ꢀ ꢀO(5)#4
Compound 2
0.95
0.95
0.81(2)
0.97(7)
0.82(5)
0.81(2)
2.27
2.28
1.89(2)
1.65(7)
1.86(5)
1.97(8)
3.184(4)
3.200(4)
2.671(3)
2.605(3)
2.663(4)
2.628(3)
162
163
165(5)
165(7)
169(5)
137(11)
C(11)–H(11A)ꢀ ꢀ ꢀO(2)#5
C(11’)–H(11B)ꢀ ꢀ ꢀO(2’)#6
C(9’)–H(9’A)ꢀ ꢀ ꢀO(3)#1
Compound 3
0.95
0.95
0.95
2.57
2.54
2.51
3.206(8)
3.164(8)
3.145(8)
124
123
124
Scheme 1.
O(1w)–H(1w)ꢀ ꢀ ꢀO(2)
0.84(3)
0.75(3)
1.83(3)
1.99(3)
2.617(2)
2.724(2)
156(2)
167(3)
[13], while Robertazzi et al. successfully employed QTAIM calcula-
tions on copper phenanthroline complexes to show the decrease in
strength of Cu–N bond when water molecule is included into
copper coordination [14].
With the aim to study the electron density topology of the Cu-
center environment we fulfilled the synthesis of two novel
O(2w)–H(2w)ꢀ ꢀ ꢀO(7)#7
Symmetry transformation used to generate equivalent atoms: #1 = 1 + x, y, z;
#2 = x ꢁ 1, y, z; #3 = 1 + x, y, 1 + z; #4 = x ꢁ 1, y, z ꢁ 1; #5 = ꢁ1 ꢁ x, 1 ꢁ y, ꢁz;
#6 = 1 ꢁ x, ꢁy, 1 ꢁ z; #7 = ꢁx, ꢁy, ꢁz.
Table 1
Selected crystal data, details of data collection and structure refinement for 1–3.
Compound
1
2
3
Empirical formula
Formula weight
T (K)
C
28H20CuN2O12
C24H16CuN6O12
643.97
100(2)
C18H22CuN4O16S2
678.06
100(2)
640.00
100(2)
Crystal system
Space group
a (Å)
b (Å)
c (Å)
monoclinic
P21/c
12.9247(10)
13.9421(11)
16.8693(10)
90
114.691(4)
90
2761.9(3)
4
triclinic
P1
monoclinic
P21/n
10.6242(14)
5.2823(6)
22.573(3)
90
91.932(4)
90
1266.1(3)
2
ꢀ
5.5818(13)
10.327(2)
21.550(5)
86.350(4)
87.059(4)
89.504(4)
1238.0(5)
2
a
(°)
b (°)
c
(°)
V (Å3)
Z
Dcalc (g cmꢁ3
)
1.539
0.861
1.727
0.965
1.779
1.116
l
(mmꢁ1
)
F(0 0 0)
1308
654
694
Reflections collected/unique
Data/restraints/parameters
Goodness-of-fit on F2
32073/4869
4869/2/414
0.976
4344/4344
4344/0/392
1.120
5634/2218
2218/0/197
1.050
R1, wR2 (I > 2
R1, wR2 (all data)
r
(I))
0.0407, 0.0995
0.0704, 0.1201
0.0678, 0.1940
0.0803, 0.2034
0.0252, 0.0639
0.0295, 0.0666
Table 2
Selected experimental and calculated geometric parameters of the described structures. Distances are in (Å) and angles in (°).
Parameters
1
1c
2
2’
2ca
3
3ca,b
Cu(1)–O(1)
1.924(2)
2.900(2)
1.925(2)
2.929(2)
–
2.025(3)
2.024(3)
1.283(4)
1.231(4)
1.275(4)
1.245(4)
–
1.987
2.596
1.987
2.596
–
2.080
2.080
1.300
1.240
1.300
1.240
–
–
–
90.0
90.0
90.0
90.0
1.930(4)
3.001(5)
–
–
1.934(4)
2.796(5)
–
–
1.994
2.604
1.994
2.604
–
2.068
2.068
1.296
1.239
1.296
1.239
–
–
–
90.0
90.0
90.0
90.0
1.968(1)
3.298(2)
2.371(1)
–
1.971(2)
–
–
1.269(2)
1.243(2)
–
–
93.4(1)
92.8(1)
87.7(1)
1.988
3.283
1.988
3.283
2.071
–
–
–
–
–
–
90.8
93.3
86.1
–
–
–
Cu(1)ꢀ ꢀ ꢀO(2)
Cu(1)–O(7)
Cu(1)ꢀ ꢀ ꢀO(8)
Cu(1)–O(1w)
Cu(1)–N(1)
–
–
2.033(5)
–
1.285(8)
1.223(8)
–
–
–
–
2.042(5)
–
1.272(8)
1.228(8)
–
–
–
–
Cu(1)–N(2)
C(1)–O(1)
C(1)–O(2)
C(13)–O(7)
C(13)–O(8)
O(1)–Cu(1)–O(7)
O(1)–Cu(1)–O(1w)
O(7)–Cu(1)–O(1w)
O(1)–Cu(1)–N(1)
O(1)–Cu(1)–N(2)
O(7)–Cu(1)–N(1)
O(7)–Cu(1)–N(2)
–
–
–
–
89.7(1)
90.3(1)
90.0(1)
90.0(1)
90.9(2)
90.2(2)
–
–
–
–
–
–
–
–
–
–
–
a
When possible, same labeling convention as in 1 is obeyed.
Due to inversion center pseudosymmetry only half of the molecular geometry is listed.
b

1712
A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
Cu(II)-carboxylate complexes, [Cu(H2-btc)2(Py)2] (1) and
[Cu(dnb)2(Py)2] (2) obtained by the reaction of copper(II) acetate
with pyridine, and two geometrically similar benzoic acids, ben-
zene-1,3,5-tricarboxylic acid (H3-btc), and 3,5-dinitro-benzoic acid
(H-dnb) (Scheme 1). Complex [Cu(dnb)2(DMSO)2(H2O)2] (3) previ-
ously reported as a product of interaction of copper sulfate with
3,5-dinitrobenzoate of piperidine in DMSO [15] was obtained by
recrystallization of 2 from DMSO. The low temperature single crys-
tal X-ray study along with the comparative QTAIM evaluation for
1–3 is reported herein.
1.1. Synthesis
Fig. 1. ORTEP plot of 1 with the numbering scheme. Thermal ellipsoids are shown
with the 50% probability level. The major position is shown for the disordered O(10)
atom.
Compounds 1 and 2 were obtained following the synthetic pro-
cedure described in [16] by mixing of copper acetate monohydrate,
Fig. 2. H-bonded layer in 1 viewed along b (a) and c (b) axes; crystal packing with the voids shown in brown (c). (For interpretation of the references to colour in this figure
legend, the reader is referred to the web version of this article.)

A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
1713
Fig. 5. ORTEP plot of 3 with the numbering scheme. Thermal ellipsoids are shown
with the 50% probability level.
Fig. 3. ORTEP plot of 2 with the numbering scheme. Thermal ellipsoids are shown
with the 50% probability level.
1.3. Computational methodology
pyridine, and corresponding acid in anhydrous methanol. In both
cases, light blue plate-like crystals suitable for single crystal X-
ray analysis were found upon evaporation. Crystals of 3 were ob-
tained upon recrystallization of 2 from aqueous DMSO.
All calculations were carried without any symmetry restriction
in the doublet ground state, for isolated molecule, using the
GAUSSIAN09 program [20]. Geometry optimizations were performed
using B3LYP [21–23] functional and 6-31G⁄⁄ basis set for C, H, N
and O atoms, and effective core potential basis set LANL2DZ for
Cu atom [24] (tail c is added for calculated structures). Single point
energies were calculated in gas phase starting from optimized
geometries at the B3LYP/6-31++G⁄⁄ level of theory for all atoms.
Resulting wave functions were used for further studies of the
electron density using topological approach of the QTAIM with
AIMALL (Version 10.12.08) [25].
1.2. X-ray investigations
Single crystal X-ray diffraction experiments for 1–3 were car-
ried out with a Bruker SMART APEX II diffractometer with CCD area
detector
(graphite
monochromated
Mo
K
a
radiation,
k = 0.71073 Å),
x
-scans with a 0.5° step in x at 100 K. Semi empir-
ical method SADABS [17] was applied for absorption correction for all
three compounds. Compound 2 was pseudomerohedrally twinned.
By running the TWINROTMAT program within the PLATON [18] package
the twinned matrix (ꢁ1 0 0 0 1 0 0 0 ꢁ1) was obtained for the min-
or component (38%). From the total number of 4350 reflections 750
were removed from the hkl file and SHELX HKLF 5 format file was gen-
erated for the refinement. The structure solution and refinement
preceded similarly using SHELX-97 program package for all struc-
tures [19]. The structures were solved by direct methods and re-
fined by the full-matrix least-squares technique against F2 with
the anisotropic temperature parameters for all non-hydrogen
atoms. The hydrogen atoms on the carboxylic groups in 1, and in
water molecule in 3 were located from the Fourier electron density
map and refined isotropically. All C-bound hydrogen atoms were
refined within the riding model. Data reduction and further calcu-
lations were performed using Bruker SAINT+ and SHELXTL NT [19] pro-
gram packages. The X-ray data and details of the refinement for 1–
3 are summarized in Table 1, the selected geometric parameters
are given in Table 2, the hydrogen bonding geometry is given in
Table 3.
2. Results and discussion
2.1. X-ray structures
X-ray structural analysis revealed that complexes 1 and 2, in
contrast with previously published results [16], where authors
used the similar synthetic procedure, do not contain water mole-
cules in Cu coordination sphere. Complex [Cu(H2-btc)2(Py)2] (1)
crystallizes in the monoclinic centrosymmetric P21/c space group
with an entire molecule in the asymmetric unit (Fig. 1). The Cu(II)
center adopts a square-planar geometry by coordinating to two
pyridine molecules in trans-position at Cu–N distances of
2.024(3) and 2.025(3) Å, and two trans-carboxylate O atoms
of two monodeprotonated (H2-btc)ꢁ ligands, at C–O distances of
1.924(2) and 1.925(2) Å with cis-angles ranging from 89.7(1) to
90.3(1)° for the metal center (Table 2).
Trans-coordinated ligands are arranged essentially in the same
planes, the dihedral angle between the average planes through
the Py molecules is equal to 0.5(2)°, and between two H2-btc
Fig. 4. Crystal packing of 2 viewed along a-axis (a) one stack held by weak hydrogen bonds (b).

1714
A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
moieties is equal to 3.3(1)°. So, the mutual arrangement of the dis-
tinctive ligands which are almost perpendicular can be character-
ized by two, practically planar fragments, plane PA that includes
all non-H atoms from two H2-btc residues, (excluding the disor-
dered O(10) atom), and plane PB that contains two pyridine mole-
cules, dihedral angle PA/PB being equal to 89.2(1)°.
It was reported that free H3-btc assembles in diverse supramo-
lecular structures due to the trigonal exodentate functionality, and
the most common motif is a planar honeycomb network structure
formed through the dimerization of the carboxyl groups [2]. The
reported examples reveal different degree of H3-btc deprotonation
in the Cu(II)-based networks, where the hydrogen bonds arising
from the COOH carboxylic groups contribute to the structure
robustness [26]. In 1, each of two (H2-btc)ꢁ anions use only one
carboxylate group for the monodentate coordination to the Cu(II)
center. Four other carboxylic groups generate the planar extended
system of hydrogen bonding parallel to the (0 1 0) plane, built on
the robust R88(8) and R88(16) carboxylic patterns [27], the latter rep-
resents the combination of three shared molecular patterns, R22(7),
R22(10), R22(7) (Table 3). These interactions acting in the concerted
way result into honeycomb network with the 8.6 ꢂ 16.9 Å cavities
(Fig. 2a) partially filled by the pillared Py molecules from adjacent
Fig. 6. Bond length distribution in four-coordinated Cu(II) environment: Cu–O coordination bonds (a); Cu–N coordination bonds (b); Cuꢀ ꢀ ꢀO non-coordination distances (c);
0
All distances are given in ÅA. Red rectangle marks range of the bond lengths in 1 and 2. (For interpretation of the references to colour in this figure legend, the reader is referred
to the web version of this article.)

A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
1715
Table 4
Topological properties of the electron density (
q
) at the selected BCPs: Laplacian of the electron density (r2qBCP), total energy density (H), kinetic energy density (G) and the
potential energy density (V). Densities are measured in e Åꢁ3, Laplacian of the electron density in e Åꢁ5 and energies in Hartree Åꢁ3. Refer to the ORTEP plots for the labeling
convention.
2q
Bond
q
H
G
V
r
1c
2c
3c
1c
2c
3c
1c
2c
3c
1c
2c
3c
1c
2c
3c
Cu(1)–O(1)
Cu(1)–O(7)
Cu(1)–N(1)
Cu(1)–N(2)
Cu(1)–O(1w)
Cu(1)–O(1’)a
Cu(1)–O(7’)
Cu(1)–O(1w’)
0.084
0.084
0.076
0.076
–
–
–
–
0.083
0.083
0.078
0.078
–
–
–
–
0.084
0.084
–
0.322
0.322
0.228
0.228
–
–
–
–
0.314
0.314
0.235
0.235
–
–
–
–
0.370
0.370
–
ꢁ0.028
ꢁ0.028
ꢁ0.025
ꢁ0.025
–
0.109
0.109
0.085
0.085
–
–
–
–
0.106
0.106
0.088
0.088
–
–
–
–
0.118
0.118
–
ꢁ0.137
ꢁ0.134
ꢁ0.144
ꢁ0.144
–
ꢁ0.028
ꢁ0.028
ꢁ0.137
ꢁ0.134
ꢁ0.028
ꢁ0.030
ꢁ0.113
ꢁ0.118
–
–
ꢁ0.028
ꢁ0.030
–
–
ꢁ0.113
ꢁ0.118
–
0.076
0.084
0.084
0.076
0.305
0.370
0.370
0.305
–
–
–
–
–
–
–
–
ꢁ0.024
ꢁ0.026
ꢁ0.026
ꢁ0.024
0.100
0.118
0.118
0.100
–
–
–
–
–
–
–
–
ꢁ0.124
ꢁ0.144
ꢁ0.144
ꢁ0.124
a
Related by inversion center pseudosymmetry.
layers. The partially interdigitated layers are packed with the gen-
eration of small voids (40 Å3) (Fig. 2b and c) [18].
Complex [Cu(dnb)2(Py)2] (2) crystallizes in the triclinic centro-
ꢀ
symmetric P1 space group with two symmetrically independent
complexes (2 and 20) in the asymmetric unit. Both of them reside
on inversion centers, with structural parameters similar to those
in 1 (Fig. 3 depicts complex 2). In both complexes the centrosym-
metric N2O2-coordination core is formulated by two dnb residues
that coordinate in a monodentate mode, Cu(1)–O(1) 1.930(4) Å in
2 and 1.934(4) Å in 20, and two molecules of pyridine, Cu(1)–N(1)
being 2.032(5) Å in 2, and 2.042(5) Å in 20. The O(2) atom evidently
does not coordinate to the metal center, as suggested by long
Cu(1)–O(2) separations in both complexes, and differentiated
C–O distances for the coordinated and non-coordinated oxygen
atoms in carboxylic groups. The regular square-planar geometry
of the metal center is supported by the practically equal
N–Cu(1)–O syn-angles close to 90° (Table 2). The similar square-
planar Cu(II) geometry has been registered for example in
trans-bis(2-amino-5-methyl-1,3,4-thiadiazole-N)-bis(3,5-dica-
rboxybenzoato-O)-copper(II) [26a], and catena-[bis(l2-5-nitroi-
sophthalato)-tetrakis(benzimidazole)-di-copper] [28].
The dnb residues are characterized by the planar skeletons with
the carboxylic and nitro-groups being practically coplanar with the
aromatic core. The dihedral angle PA/PB is equal to 70.6(1)° in 2
being somewhat smaller than 81.0(1)° in 20 (as for 1, PB contains
atoms from pyridine molecule).
In the crystal, complexes 2 and 2’ generate uniform chains
(Fig. 4) along the shortest crystallographic a-axis (Table 1) with
the parallel alignment of Py and dnb moieties, and held by similar
weak hydrogen bonds with involvement of O(2) oxygen atom of
carboxylic groups, C(11)–H(11A)ꢀ ꢀ ꢀO(2) (ꢁ1 ꢁ x, 1 ꢁ y, ꢁz)
3.205(8) Å for 2, and C(110)–H(11A)ꢀ ꢀ ꢀO(20)(1 ꢁ x, ꢁy, 1 ꢁ z)
3.164(8) Å for 20 (Fig. 4). The chains are held via C(90)–
H(90A)ꢀ ꢀ ꢀO(3)(1 + x, y, z) 3.146(8) Å interactions with participation
of nitro group as H-bond acceptor. All these weak hydrogen bonds
are in the range of Hꢀ ꢀ ꢀO standard distances (Table 3) [29].
The recrystallization of 2 from DMSO yielded the square-
bipyramidal complex [Cu(dnb)2(DMSO)2(H2O)2] (3) with the
substitution of two Py molecules by four solvate species including
two water and two DMSO molecules. Complex 3 resides on the
center of symmetry (Fig. 5). Two dnb residues, and two water mol-
ecules are displayed in the equatorial plane, Cu–O(car-
boxyl) = 1.968(1), and Cu–O(H2O) = 1.971(2) Å, while two DMSO
molecules occupy the axial positions, Cu–O(DMSO) = 2.371(1) Å.
The distribution of distances related to metal–ligand interactions
in 3 is similar to 1 and 2 and may serve as an additional proof
for monodentate mode of carboxylic group coordination in 1 and
2. The decrease of the unit cell volume in 3 by 60 Å3 was observed,
comparing to the room temperature experiment reported in [15].
Fig. 7. Molecular graph of 1c (a), 2c (b) and 3c (c) showing C-Hꢀ ꢀ ꢀO bond paths with
dashed lines. Bond critical points (BCPs) are marked with small green spheres, ring
critical points (RCPs) are marked with small orange spheres. (For interpretation of
the references to colour in this figure legend, the reader is referred to the web
version of this article.)

1716
A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
Table 5
Structural and nonstructural rings revealed by QTAIM. Densities are measured in e Åꢁ3, Laplacian of the electron density in e Åꢁ5. Refer to the ORTEP plots for the labeling
convention.
2qBCP
Rings
q
r
1c
2c
3c
1c
2c
3c
C(2)–C(3)–C(4)–C(5)–C(6)–C(7)
C(14)–C(15)–C(16)–C(17)–C(18)–C(19)
N(1)–C(8)–C(9)–C(10)–C(11)–C(12)
N(2)–C(20)–C(21)–C(22)–C(23)–C(24)
Cu(1)–N(1)–C(8)–H(8)–O(1)
Cu(1)–N(1)–C(12)–H(12)–O(7)
Cu(1)–N(2)–C(20)–H(20)–O(1)
Cu(1)–N(2)–C(24)–H(24)–O(7)
Cu(1)–O(1w)–H(1w)–O(2)–C(1)–O(1)
Cu(1)–O(1w0)–H(1w0)–O(20)–C(10)–O(10)
Cu(1)–O(7)–S(1)–C(8)–H(8c)–O(20)
Cu(1)–O(70)–S(10)–C(80)–H(8c0)–O(2)
0.021
0.021
0.022
0.022
0.011
0.011
0.011
0.011
–
0.021
0.021
0.022
0.022
0.011
0.011
0.011
0.011
–
0.021
0.021
–
–
–
–
–
–
0.014
0.014
0.003
0.003
0.161
0.161
0.175
0.175
0.054
0.054
0.054
0.054
–
0.162
0.162
0.175
0.175
0.052
0.052
0.052
0.052
–
0.162
0.162
–
–
–
–
–
–
0.064
0.064
0.011
0.011
–
–
–
–
–
–
–
–
–
–
–
–
The bond lengths distribution in the metal coordination core for
four-coordinated Cu(II) compounds that include aromatic carbox-
ylic group and N-base as coordinating species, has been augmented
using the CSD data [30]. The CSD search (CSD version 5.31) resulted
in 159 hits (excluding disordered and repeated structures, no
experimental temperature specification) for which the histograms
(Fig. 6) were generated using Vista software. The histograms
clearly demonstrate that the coordination Cu–O and Cu–N bonds
in 1 and 2 correspond to the frequently reported values.
geometry of Cu(II) (Fig. 7). Furthermore, QTAIM analysis revealed
four intramolecular C–Hꢀ ꢀ ꢀO interactions between pyridine and car-
boxylate residues similar for 1c and 2c, which do not obey ‘‘geomet-
rical criteria’’ of hydrogen bonding [29] (CHO angle around 113°).
These interactions are described by the presence of BCP, and the
bond path that connects CH-donor and O-acceptor atoms. Values
of the electron density and Laplacian of the electron density at the
BCPs (averaged
q
BCP = 0.013(1) e Åꢁ3 and
r
2qBCP = 0.040(1) e Åꢁ5
)
lie within normal range of contacts describing hydrogen bonds
[33–35] (Table 5), thus bringing further stabilization for metal envi-
ronment. Due to intramolecular interactions, four nonstructural
rings are formed, with values of the electron density at the ring crit-
2.2. Quantum chemical calculations
ical points(qRCP) twice lower than in benzene and pyridine rings (Ta-
ble 5). Topological analysis of 3c supports crystallographic data on
intramolecular hydrogen bonding, local density properties of O–
Geometries obtained from DFT calculations are in good agree-
ment with the XRD data. Overall relaxation of the geometry is ob-
served (Table 2), which can be explained by absence of crystalline
intermolecular interactions. For both 1c and 2c similar trends in
geometry were observed. Geometries of 2 and 20 arrive in the same
true minima (2c) on the potential energy surface as revealed by fre-
quency analysis performed for optimized structures. Both optimized
structures gained regular square-planar conformation (Table 2).
Dihedral angle PA/PB arrived to the ideal value of 90.0°. Optimized
geometry of 3c does not arrive to the ideal square-bipyramidal coor-
dination, which can be explained by several intramolecular interac-
tions detected by QTAIM. As suggested by QTAIM calculations Cu–O
and Cu–N bonds in all three calculated structures can be classified as
dative, intermediate between closed-shell and shared interactions.
Hꢀ ꢀ ꢀO bonds are described by:
q
BCP = 0.060 e Åꢁ3 and
r
2qBCP = 0.156 e Åꢁ5. Due to the mentioned interactions two non-
structural rings are formed: Cu(1)–O(1w)–H(1w)–O(2)–C(1)–O(1)
and Cu(1)–O(1w0)–H(1w0)–O(20)–C(10)–O(10), with the local density
properties:
nonstructural rings are formed because of C–H(DMSO)ꢀ ꢀ ꢀO(car-
boxyl) intramolecular contacts and
BCP = 0.010 e Åꢁ3
q
BCP = 0.014 e Åꢁ3, and
r
2qBCP = 0.064 e Åꢁ5. Other two
(
q
r
2qBCP = 0.031 e Åꢁ5) describedwiththedrastically decrease of qRCP
value compared to the benzene rings: 0.003 versus 0.021 e Åꢁ3, sug-
gesting weak Hꢀ ꢀ ꢀO interaction (Table 5).
Dative bonds are characterized by: (1) electron density (
q) value ly-
3. Conclusions
ing in range 0.050–0.150 au, being intermediate between values for
ionic and covalent interactions; (2) positive value of the Laplacian of
Two
novel
mononuclear
Cu-carboxylate
complexes
the electron density (
r
2q > 0); (3) small negative value of the total
[Cu(H2-btc)2(Py)2] and [Cu(dnb)2(Py)2] were obtained by reaction
of copper(II) acetate with pyridine (Py) and two similar benzoic
acids, benzene-1,3,5-tricarboxylic (H3-btc), and 3,5-dinitro-ben-
zoic acid (H-dnb) in anhydrous medium. Recrystallization of
[Cu(dnb)2(Py)2] from DMSO resulted in octahedral complex
[Cu(dnb)2(DMSO)2(H2O)2]. Low temperature single crystal X-ray
structural study and topological analysis of the theoretical electron
densities according to the quantum theory of atoms in molecules
are in agreement for these three complexes. Consideration of a
number of local electron density properties at the bond critical
energy density (H), defined as a sum of kinetic energy density (G),
and the potential energy density (V) at the bond critical point
(BCP) [7,31]. For 1c–3c the coordination Cu–O(carboxyl) bonds are
the strongest as suggested by the qBCP values (Table 4). The values
of the electron density at the BCPs of Cu–N(Py) are equal to 0.076
and 0.078 e Åꢁ3 for 1c and 2c, respectively, and 0.076 e Åꢁ3 of Cu–
O(H2O) for 3c are similar, implyingthe same strength of these bonds.
Noteworthy that metal–dnb and metal–DMSO bonds in 3c are de-
scribed with the same qBCP value, larger then Cu–N bonds in 1c
and 2c, suggesting substitution of pyridine with DMSO. No decrease
points (BCPs) including qBCP
,
r
2qBCP and total electron energy
in
qBCP of Cu–O(carboxyl) was observed upon increasing of the metal
density H provided insight into metal center environment and
stabilizing intramolecular short interactions. The square-
planar primary coordination sphere in [Cu(H2-btc)2(Py)2] and
[Cu(dnb)2(Py)2] is augmented by a long distance with the second
O atom of the coordinated carboxylic group which participates in
short homomeric H2-btcꢀ ꢀ ꢀH2-btc intermolecular contacts in
[Cu(H2-btc)2(Py)2], and heteromeric dnbꢀ ꢀ ꢀPy intermolecular
contacts in [Cu(dnb)2(Py)2] in the crystal. The absence of the bond
coordination number. Topologicalfeaturesofthemetalcoordination
environment are reflected in the geometrical features, the greater
values of qBCP correspond to the shorter bond lengths. The obtained
energy density properties: H, G and V for the dative bonds of 1c, 2c
and 3c are in good agreement with the results reported in the liter-
ature [32,14]. The absence of bond paths between carbonyl oxygen
atoms [O(2) and O(8)] and metal centers confirms the square-planar

A. Fonari et al. / Polyhedron 30 (2011) 1710–1717
1717
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and metal centers confirms the square-planar geometry of Cu(II).
Furthermore, QTAIM analysis revealed four intramolecular C–
Hꢀ ꢀ ꢀO interactions between pyridine rings and carboxylate resi-
dues in complexes 1 and 2, which bring additional stabilization
to the metal environment. Topological analysis of octahedral com-
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intramolecular hydrogen bonding, and reveals two other nonstruc-
tural rings formed because of C–H(DMSO)ꢀ ꢀ ꢀO(carboxyl) intramo-
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Acknowledgments
We thank Prof. T.V. Timofeeva for fruitful discussions. This work
was supported by the NSF-DMR grant 0934212. The authors are
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Appendix A. Supplementary data
CCDC 806864, 806865, and 806866 contains the supplementary
crystallographic data for this paper. These data can be obtained
free of charge via http://www.ccdc.cam.ac.uk/conts/retriev-
ing.html, or from the Cambridge Crystallographic Data Centre, 12
Union Road, Cambridge CB2 1EZ, UK; fax: (+44) 1223-336-033;
or e-mail: deposit@ccdc.cam.ac.uk.
[19] (a) SAINT+, Version 6.2a, Bruker Analytical X-ray System, Inc., Madison, WI,
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