A new five-coordinated CuIP2NO2 system: XRD structure of 6-acetyl-1,3,7-trimethyl-pteridine-2,4(1H,3H)-dione and its Cu(i) (N5,O61,O4)-tridentate complex with triphenylphosphine. An AIM study of the nature of metal-ligand bonds

Article abstract of DOI:10.1039/b807634k

The second example of a five-coordinated Cu^IP₂NO ₂ system, [Cu(DLMAceM)(PPh₃)₂]ClO₄ (DLMAceM = 6-acetyl-1,3,7-trimethyl-pteridine-2,4(1H,3H)-dione), is reported. The structural characterization of both the DLMAceM ligand and the Cu(i) compound has been achieved by IR, ¹³C and ¹H NMR and XRD methods. The metal is coordinated to the PPh₃ molecules (Cu-P 2.224(2) and 2.258(2) ) and the pyrazine N(5) atom (Cu-N(5) 2.058(6) ) in a trigonal planar arrangement; two additional semi-coordinated atoms (Cu...O(4) 2.479(5) and Cu...O(61) 2.559(5) ) can be observed, forming an intermediate SP/TBP polyhedron. To define the nature of the metal-ligand bonds for the Cu(i) compound, especially in regards to the semi-coordinated oxygen atoms, a topological analysis of the electron density ρ_b within the framework provided by the quantum theory of atoms in a molecule (QTAIM) using Hartree-Fock and DFT(B3LYP) levels of theory has been performed. Five bond critical points (BCP) have been found, whose associated bond paths connect the Cu metal with the atoms P(1), P(2), O(4) O(61) and N(5). The type of interaction between the Cu and ligand binding sites has been characterized in terms of the Laplacian of the electron density, ?²ρ _b, the total energy density, H_b, and the delocalization index, δ_AB.

Full text of DOI:10.1039/b807634k

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PAPER
www.rsc.org/dalton | Dalton Transactions
A new five-coordinated CuIP2NO2 system: XRD structure of
6-acetyl-1,3,7-trimethyl-pteridine-2,4(1H,3H)-dione and its Cu(I)
(N5,O61,O4)-tridentate complex with triphenylphosphine. An AIM study of
the nature of metal–ligand bonds†
Francisco Hueso-Uren˜a,a Sonia B. Jime´nez-Pulido,a Maria P. Ferna´ndez-Liencres,b Manuel Ferna´ndez-Go´mezb
and Miguel N. Moreno-Carretero*a
Received 6th May 2008, Accepted 31st July 2008
First published as an Advance Article on the web 9th October 2008
DOI: 10.1039/b807634k
The second example of a five-coordinated CuIP2NO2 system, [Cu(DLMAceM)(PPh3)2]ClO4
(DLMAceM = 6-acetyl-1,3,7-trimethyl-pteridine-2,4(1H,3H)-dione), is reported. The structural
characterization of both the DLMAceM ligand and the Cu(I) compound has been achieved by IR, 13
C
and 1H NMR and XRD methods. The metal is coordinated to the PPh3 molecules (Cu–P 2.224(2) and
˚
˚
2.258(2) A) and the pyrazine N(5) atom (Cu–N(5) 2.058(6) A) in a trigonal planar arrangement; two
˚
additional semi-coordinated atoms (Cu ◊ ◊ ◊ O(4) 2.479(5) and Cu ◊ ◊ ◊ O(61) 2.559(5) A) can be observed,
forming an intermediate SP/TBP polyhedron. To define the nature of the metal–ligand bonds for the
Cu(I) compound, especially in regards to the semi-coordinated oxygen atoms, a topological analysis of
the electron density rb within the framework provided by the quantum theory of atoms in a molecule
(QTAIM) using Hartree–Fock and DFT(B3LYP) levels of theory has been performed. Five bond
critical points (BCP) have been found, whose associated bond paths connect the Cu metal with the
atoms P(1), P(2), O(4) O(61) and N(5). The type of interaction between the Cu and ligand binding sites
2
has been characterized in terms of the Laplacian of the electron density, — rb, the total energy density,
Hb, and the delocalization index, dAB
.
knowledge (search of the CCDC database), only one similar
CuIP2NO2 coordinating system has been previously reported by
Kaim et al.9 in the CuI complex with 2¢,7¢,9¢-trimethylester of
pyrroloquinoline-quinone. As in this example, the geometrical
arrangement of the organic ligand DLMAceM in the title complex
allows us to suggest the establishment of Cu–O interactions longer
Introduction
Lumazines (2,4-dioxo-(1H,3H)-pteridines) are biologically rel-
evant heterocycles that occur as natural products e.g. in the
biosynthesis of the flavin co-enzymes.1,2 The binding of metal
complex fragments to these heterocycles usually occurs through
the O(4)–N(5) chelating sites.3 This coordination produces a five-
membered ring containing an unsaturated p-carbonylimino func-
tion, which can act as a p-acceptor towards a bound p-electron rich
metal center such as rhenium(I). Low-valent metal compounds,
including [Re(CO)3Cl(DML)] (DML = 1,3-dimethyllumazine)
have been reported.4 Upon trying to extend the coordinative
properties of lumazine, the six position of the pyrazine ring has
been functionalized with an acetyl group to give the title ligand
(DLMAceM), however, there are not any examples where this
substituent is involved in the coordination, but it has been reported
in the complex [Re(CO)3Cl(DMLAceM)].5 In the present work,
we describe the structure of the DLMAceM itself and its five-
˚
than 2.48 A, cited many times within the literature. This also
allows us to describe, in an ambiguous and qualitative fashion,
semi-coordination.10 To know whether the atoms at such long
distances are linked by a true chemical bond, the second part
of this work has been devoted to the characterization of, by
means of theoretical calculations, the nature of these long metal–
ligand interactions.
Experimental
Synthesis
+
coordinated complex with the Cu(PPh3)2 moiety. It should be
noted that five-coordinated Cu(I) complexes are very rare,6–8 in
contrast with the Cu(II) five-coordinated complexes and, to our
Synthesis of DLMAceM. 6-acetyl-1,3,7-trimethyllumazine
was obtained by reacting 6-amino-1,3-dimethyl-5-nitrosouracil
with acetylacetone following reported methods.11 The yellow
prismatic crystals, suitable for XRD, were isolated by slow
evaporation of the filtrate solution. Yield = 90%. Analytical data
(%): found C 53.33, H 4.83, N 22.50; calcd for C11H12N4O3 C 53.22,
H 4.87, N 22.57. IR data/cm-1: n(C–H) 3065 w, 3000 w, 2963 w,
aDepartamento Qu´ımica Inorga´nica y Orga´nica, Universidad de Jae´n,
Campus Las Lagunillas B3, 23071 Jae´n, Spain. E-mail: mmoreno@ujaen.es;
Fax: +34 953 211 876; Tel: +34 953 212 738
bDepartamento Qu´ımica F´ısica y Anal´ıtica, Universidad de Jae´n, Campus
Las Lagunillas B3, 23071 Jae´n, Spain
=
=
=
=
=
n(C O) 1725 m, (C61 O) 1694 s, (C2 O) 1679 s, (C4 O), n(C N)
† CCDC reference numbers 675523 (DLMAceM) and 645170
([Cu(DLMAceM)(PPh3)2]ClO4). For crystallographic data in CIF or other
electronic format see DOI: 10.1039/b807634k
1599 s, 1559 s, n(C C) + n(C–N) 1494 m, 1455 m, 1288 m. 13C
=
NMR data (d/ppm, TMS): 198.9 (C61), 159.0 (C4), 157.9 (C7),
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150.5 (C2), 147.8 (C8A), 141.3 (C6), 124.3 (C4A), 29.1 (C1), 28.4
(C3), 27.4 (C71), 24.2 (C62). H NMR data (d/ppm, TMS): 3.5
(N1–CH3), 3.3 (N3–CH3), 2.8 (C71–CH3), 2.6 (C62–CH3).
using a Bruker-Nonius KappaCCD apparatus with graphite-
1
˚
monochromated MoKa radiation (l = 0.71073 A). Lorentz
polarization and multi-scan absorption corrections were applied
2
with SADABS.15 Weighting scheme w-1 = s (Fo2) + (0.1210P)2,
Synthesis of [Cu(DLMAceM)(PPh3)2]ClO4. Yellow-reddish
crystals of [Cu(DLMAceM)(PPh3)2]ClO4, suitable for XRD anal-
ysis, were isolated after refluxing 0.5 mmol DLMAceM, 0.5 mmol
Cu(ClO4)2·6H2O and 0.5 mmol PPh3 in EtOH (50 mL) for
several hours. (CAUTION! Perchlorate salts are explosive and
must be handled carefully.) Yield = 31%. Analytical data (%):
found C 59.99, H 4.40, N 5.75; calcd for C47H42ClCuN4O7P2 C
60.32, H 4.52, N 5.99. IR data/cm-1: n(C–H) 3054 w, 3004 w,
2
2
where P = 1/3(Fo + 2Fc ). Final R and wR [I > 2s(I)] were
0.0717 and 0.1701, data-to-parameter ratio = 17.6, GOF = 1.049,
-3
˚
max. and min. Dr were 0.851 and -0.847 e A . Flack parameter =
0.01(2).
Computational details
In order to get the electron wave function to be used in the
QTAIM topological analysis of the Cu–ligand bonds, we used
the X-ray crystal structure as the initial point to optimize by
using Gaussian0316 running on an ia64HP server rx 2600. We
performed two optimizations at the DFT/B3LYP17–19 level using
the well-known Pople’s basis set 6–31 + G*20 first, and then the
SDDall21 basis sets, which uses the Dunning-Huzinaga D95V basis
set for all atoms up to Ar and applies Stuttgart pseudo potentials
on Cu, N, P, C and O atoms. Within the isolated molecule
approximation, the optimization arrives at a Cu–O(6) distance
=
=
=
=
2955 w, n(C O) 1717 m (C61 O), 1693 s (C2 O), 1661 s (C4 O),
=
=
n(C N) 1574 s, 1547 s, n(C C) + n(C–N) 1481 m, 1435 m, 1291
m, perchlorate bands 1093 s, 623 m, PPh3 bands 750 m, 694 s, 520
m. 13C and 1H NMR spectra are virtually coincident with those of
the free ligand and also show signals from PPh3.
Apparatus
C, H and N microanalyses were performed on a Fisons EA1108
apparatus. IR spectra were measured using a Perkin-Elmer FT-
IR 1760-X (KBr pellets, 4000–400 cm-1) and a FT-IR Bruker
Vector-22 spectrophotometer (polyethylene pellets, 600–220 cm-1).
1H and 13C NMR spectra were recorded using a Bruker DPX-300
apparatus (DMSO-d6 solutions).
˚
noticeably shortened (ca. 0.3 A) when compared with the initial
value, while for the remaining Cu–X distances, the attained final
values keep on the same order than the experimental values. This
points out that solid-state effects are strong enough to make the
isolated molecule approximation invalid. This is the main reason,
along with computational limitations, why we decided to obtain
the electron wave function from a single point calculation on the
experimental X-ray crystal structure. Thus, topological properties
were obtained from the electron wave function at DFT/B3LYP
with the standard 6–311 + G(2d,2p)21 and HF/6–311 + G(d,p)21
basis sets as levels of calculations from the X-Ray data, using the
program AIM2000.22 An integration of the atomic properties over
the atomic basins have been performed in natural coordinates,
with a tolerance of 10-4 per integration step. The radius of the beta
sphere used for the integration of the atomic properties was at the
default value of 0.5 a.u.
Crystallographic studies
Both structures were solved by direct methods and refined using
SHELXL97 program12 inside the WinGX package13 employing
full-matrix least-squares methods on F2. All non H atoms were
refined anisotropically and the hydrogen atoms were placed in
calculated ideal positions following riding models. All calculations
and graphics were carried out with PLATON.14
X-Ray crystal structure data for DLMAceM. C11H12N4O3,
Mr = 248.24 g mol-1, monoclinic, space group P21/c, unit cell
˚
parameters a = 16.030(2), b = 4.4861(6), c = 15.7288(9) A, b =
◦
3
˚
97.716(8) , V = 1120.9(2) A , T = 293 K, Z = 4; Dcalcd = 1.471 Mg
m-3, F(000) = 520, yellow prisms (0.27 ¥ 0.20 ¥ 0.13 mm3), m =
0.111 mm-1; q range = 3.0–27.5◦, -20 < h < 20, -5 < k < 5,
-20 < l < 20, 25 969 measured reflections, 2575 independent,
1802 with I > 2s(I) used in the refinement (Rint = 0.047). The
data were collected using a Bruker-Nonius KappaCCD apparatus
Results and discussion
Crystallographic work
The molecular structure of DLMAceM is displayed in Fig. 1.
The free-metal pteridine moiety is almost planar (dihedral angle
between pyrimidine and pyrazine mean planes, 1.5(1)◦) and is
angled with the mean plane of the acetyl substituent (C(6)–C(61)–
C(62)–O(61)) by 12.9(1)◦. In the crystal structure, the molecules
are arranged as columns along the b axis with the pteridine planes
parallel to each other and roughly perpendicular to the [311]
direction. The columns are built through a partial p-stacking
interaction between the pyrimidine and the pyrazine rings of
consecutive pteridines (Fig. 2) with the centroids of adjacent
˚
with graphite-monochromated MoKa radiation (l = 0.71073 A).
Lorentz polarization and multi-scan absorption corrections were
2
applied with SADABS.15 Weighting scheme w-1 = s (Fo2) +
(0.0617P)2 + 1.1017P, where P = 1/3(Fo + 2Fc ). Final R and
wR [I > 2s(I)] were 0.0548 and 0.1300, data-to-parameter ratio =
2
2
-3
˚
15.8, GOF = 1.039, max. and min. Dr were 0.440 and -0.249 e A .
X-Ray crystal structure data for [Cu(DLMAceM)(PPh3)2]ClO4.
C47H42ClCuN4O7P2, Mr = 935.78 g mol-1, monoclinic, space group
Cc, unit cell parameters a = 10.3034(7), b = 27.145(1), c =
˚
rings separated by 3.543(1) A with a, b, and g angles, calculated
◦
15.387(1) A, b = 94.071(7) , V = 4292.9(5) A , T = 293 K,
Z = 4, Dcalcd = 1.448 Mg m-3, F(000) = 1936, yellow-reddish
prisms (0.56 ¥ 0.32 ¥ 0.19 mm3), m = 0.704 mm-1, q range =
3.0–27.5◦, -13 < h < 13, -35 < k < 35, -19 < l < 19, 29 259
measured reflections, 9678 independent, 5316 with I > 2s(I)
used in the refinement (Rint = 0.076). The data were collected
with PLATON, of 1.5, 19.0 and 18.5◦, respectively. The slippage
3
˚
˚
˚
between both rings is ca. 1.1 A and the ring–plane overlap are
is ca. 45%.23 Also, the analysis with PLATON indicates the
existence of s ◊ ◊ ◊ p-ring interactions (Y–X ◊ ◊ ◊ Cg) contributing to
the stabilization of the crystal structure: C(2)–O(2) ◊ ◊ ◊ pyrimidine
(x, y + 1, z) and C(61)–O(61) ◊ ◊ ◊ pyrazine (x, y - 1, z), with
6462 | Dalton Trans., 2008, 6461–6466
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Fig.
1
ORTEP plot with labelling scheme for 6-acetyl-1,3,7-
trimethyllumazine (DLMAceM) (ellipsoids at 50% probability).
Fig. 3 View of the cationic unit [Cu(DLMAceM)(PPh3)2]+, displaying
˚
atom numbering (ellipsoids at 50% probability). Bond distances (A) and
angles (◦) around the metal: Cu–P(1) = 2.224(2), Cu–P(2) = 2.258(2),
Cu–N(5) = 2.058(6), Cu ◊ ◊ ◊ O(4) = 2.479(5), Cu ◊ ◊ ◊ O(61) = 2.559(5),
P(1)–Cu–P(2) = 131.38(7), P(2)–Cu–N(5) = 106.7(2), N(5)–Cu–P(1) =
121.9(2), O(4) ◊ ◊ ◊ Cu ◊ ◊ ◊ O(61) = 143.4(2), O(4) ◊ ◊ ◊ Cu–P(1) = 103.4(1),
O(4) ◊ ◊ ◊ Cu–P(2) = 91.3(1), O(4) ◊ ◊ ◊ Cu–N(5) = 74.1(2), O(61) ◊ ◊ ◊ Cu–
P(1) = 88.0(1), O(61) ◊ ◊ ◊ Cu–P(2) = 107.1(1), O(61) ◊ ◊ ◊ Cu–N(5) = 70.5(2).
enough (43.3 kJ mol-1, RHF-PM3) to avoid the formation of M–
L bonds, despite the steric hindrances between the C(62) and
C(71) methyl groups. In addition to the rearrangement of the
acetyl group, the geometry of coordinated DLMAceM exhibits
only minor differences with the metal-free structure one. The most
important changes are the opening of the C(7)–C(6)–C(61) angle
(4.9◦) and the consequent closing of N(5)–C(6)–C(61) (2.1◦) and
N(5)–C(6)–C(7) (2.9◦), due to the above-cited rearrangement of
the acetyl substituent.
Due to the steric requirements of the Cu(I) complex (Fig. 3),
both rings of the pteridine moiety are slightly angled (7.0(3)◦).
The two five-membered chelates are also angled to each other
by 11.3(3)◦. They are not planar and their shape, following the
Cremer and Pople’s ring puckering analysis,24 can be described as
half-chair-twisted on N(5)–Cu (Cu–N(5)–C(4A)–C(4)–O(4), f =
165.2 and k = 4.09) and an envelope on C(61) (Cu–N(5)–C(6)–
C(61)–O(61), f = 253.5 and k = 7.04). The metal is trigonal-
planar three-coordinated with atoms P(1), P(2) and N(5). The
metal center lies only slightly out of the plane defined by the three
Fig. 2 View along the [203] direction for the O(2) ◊ ◊ ◊ pyrimidine ◊ ◊ ◊
pyrazine ◊ ◊ ◊ O(61) column-like intermolecular arrangement in the crystal
structure of DLMAceM. Hydrogen atoms are omitted for clarity.
˚
X ◊ ◊ ◊ Cg distances of 3.260(2) and 3.188(2) A and Y–X ◊ ◊ ◊ Cg
angles of 100.3(1) and 89.9(1)◦, respectively. The unit cell contains
no residual solvent-accessible voids.
donor atoms (0.032 A) and despite bond angles around the metal
˚
deviating a little from the ideal value (120◦), their sum is 360◦. The
lumazine ligand is arranged in a roughly perpendicular fashion
(80.6◦) to the above mentioned trigonal plane, the metal ion lying
The structure of [Cu(DLMAceM)(PPh3)2]ClO4 consists of
isolated [Cu(DLMAceM)(PPh3)2]+ cations (Fig. 3) and unco-
ordinated and disordered perchlorate anions. With the relative
arrangement of the acetyl group and the pteridine moiety (N(5)–
C(6)–C(61)–O(61) torsion, 166.5(2)◦), the free DLMAceM is not
able to act as a tridentate ligand through the O(4), N(5) and
O(61) atoms; however, the energy difference between the metal-
free conformation and the Cu(I)-coordinated conformation (N(5)–
C(6)–C(61)–O(61) torsion, 32(1)◦), in which the acetyl mean plane
is turned off by 128.0◦ around the C(6)–C(61) bond, is not large
˚
0.455 A out of this plane. In this plane, there are two additional and
˚
very long Cu ◊ ◊ ◊ O(4) and Cu ◊ ◊ ◊ O(61) (2.479(5) and 2.559(5) A,
respectively), which define an intermediate TBP/SP-shaped poly-
hedron (Fig. 4), whereas the Addison’s t criterion25 describes the
polyhedron as a distorted square-pyramid (t = 0.2, apical atom
N(5)), Muetterties and Guggenberger’s calculations26 show that
the polyhedron is best described as a distorted trigonal-bipyramid
(D = 0.2) with an P(1)/P(2)/N(5) equatorial plane and a skewed
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p-stacking.23 The unit cell contains no residual solvent-accessible
voids.
Topological analysis
The structure of Cu(DLMAceM)(PPh3)2]+ displays values of
˚
˚
2.224(2) and 2.258(2) A for Cu–P and 2.058(6) A for Cu–
N bonds, respectively, while Cu–O distances are in the range
˚
2.479(5)–2.559(5) A. Thus, we can formulate doubt about the
˚
covalent nature of bonds as long as 2.56 A. Although the bonding
in transition metal complexes is usually rationalized upon an
extended molecular orbital scheme, an alternative description that
uses local topological analysis of the electron density can be used to
get a deeper insight into this matter. The quantum theory of atoms
in molecules, developed by Bader,29,30 which is widely recognized
for its utility in the analysis of chemical bonding, provides such
Fig. 4 A detailed view of the metallic coordination environment, showing
the quasi-planar O(4)–P(1)–N(5)–O(61) face (dihedral angle over the
P(1)–N(5) edge, 157.5◦).
2
a scheme wherein electron density rb, Laplacian — rb, density of
the total energy Hb at the bond critical point (BCP) as well as
delocalization index d, are searched for.
Critical points (CP) of the charge distribution are classified
by their rank and sign analyzing the Hessian matrix of rb.
Accordingly, four kinds of CP can be characterized. Those with
three non-zero eigenvalues li, two of them negative (l1, y, l2) and
the remaining positive (l3) are named bond critical points (3, -1).
The first two eigenvalues li, (i = 1, 2) measure the curvature of rb
along the interatomic surface and the latter eigenvalue provides
curvature along the atomic interaction line. Thus, a covalent bond
is characterized by the charge density exhibiting two large negative
curvatures perpendicular to the bond and a relatively small positive
curvature along the bond at the position of the (3,-1) critical point.
At the BCP, the gradient of the density vanished, —rb = 0 and the
O(61)–Cu–O(4) axis due to the restricted bite of the tridentate
DLMAceM. The disappointment can be easily explained by the
different points of view of both calculation methods. Whereas
Addison’s t is based only on the two bigger bond angles over
the metal without taking into account the steric array of the
donor atoms, Muetterties and Guggenberger’s D describes the
external shape of the polyhedron from the relative position of
the donor atoms and, consequently, the dihedral angles between
the contiguous faces, without considering the position of the metal
inside the polyhedron. A similar contradiction on evaluating the
coordination polyhedron shape has been previously reported.9
Despite the geometrical data of the previously reported
CuIP2NO2 coordination environment9 is very similar to those of
the Cu(I) title compound, a closer analysis indicates that the last
one shows slightly more unsymmetrical PPh3 groups with a P(2)
atom occupying a somewhat more apical position than P(1), thus,
2
sum of the three li yields the Laplacian, — rb.
The type of pairwise atomic interactions is characterized by the
sign of the Laplacian of the electron density at the BCP. If electrons
2
are locally concentrated in the BCP (— rb < 0), the electron
density is shared then by both nuclei (pure covalent shared–shared
the difference between both Cu–P bond lengths in the title complex
interaction). Otherwise, the electrons are concentrated in each
of the atomic basins separately (— rb > 0) and the interaction
9
2
˚
˚
(0.034 A) is higher than those reported by Kaim (0.014 A). In
addition to this, whereas the exocyclic carbonyl Cu–O distances
belongs to the closed-shell type (partially covalent shared–closed
interaction; the closed–closed one is of a van der Waals or ionic
nature).31 In this latter case, the difference between them is the
sign of Hb, which is positive for the closed–closed interaction and
negative for the other. Several studies32–34 have shown that bonds
involving metals present characteristics associated with closed-
˚
are similar (2.559(5) and 2.579(4) A), the endocyclic distances are
˚
quite different (2.479(5) and 2.254(4) A), the very weak O(4)–
DLMAceM semi-coordinative behaviour being in accord with
previously reported results for analogous lumazine derivatives.27,28
On the other hand, a comparison between the structure of the Cu(I)
title compound with the previously reported Re(I)–DLMAceM
complex,5 in which the exocyclic O61 carbonylic oxygen is not
coordinated, indicates a great difference in the N(5)–C(6)–C(61)–
O(61) torsion (Re(I) complex 106(1)◦, Cu(I) complex 32(1)◦), the
steric coupling of the acetyl group with the fac-tricarbonyl ligands
over the Re(I) being the main reason of the uncoordination.
The analysis of the short ring interactions in the crystal structure
does not indicate the existence of any significant p-stacking
interactions. Only the interaction between both pyrimidine and
pyrazine rings from DLMAceM and the U phenyl ring from
PPh3 could be cited, but despite distances between the centroids
2
shell type interactions: rb is small, l3 dominates and — rb is
positive, while Hb is negative and close to zero, showing, therefore,
2
features typical of ionic (rb and — rb) and covalent (Hb) bonds.
Bianchi et al.34 have proposed a set of indicators, related to the
mentioned topological parameters, enabling an assignment in
terms of the different subclasses of the shared and closed-shell
interactions, thus the metal–ligand interactions can be classified
as intermediate between ionic and covalent bonds and they are
included as belonging to closed-shell type interactions.
Although the presence of a bond path provides a universal
indicator of bonding, the criteria based solely on electron density,
however, look too restrictive for the large variety of bonds
found in transition metal compounds.35 Thus, the delocalization
index d(A ◊ ◊ ◊ B) seems to be a more sensitive probe at this aim.
According to Fradera et al.,36 the delocalization index, defined as
˚
(3.616(4) and 3.867(4) A), which lie within the range accepted for
23
˚
these interactions (3.4–4.6 A), the interplanar dihedral angles
a (12.2 and 12.6◦, respectively) clearly show both rings of each
couple are far to be parallel enough to consider the existence of
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Table 1 Bond lengths and topological properties of the electron density at the critical points of Cu–ligand bonds in the cation [Cu(DLMAceM)(PPh3)2]+
-3
2
-5
-3
-3
-3
˚
˚
˚
˚
˚
˚
Bond (X ◊ ◊ ◊ Y)
R
XY/A
rb/e A
— r/e A
dAB
Gb/hartree A
Vb/hartree A
Hb/hartree A
HF/6–311 + G(p,d)
Cu ◊ ◊ ◊ O(4)
Cu ◊ ◊ ◊ O(61)
Cu ◊ ◊ ◊ P(1)
Cu ◊ ◊ ◊ P(2)
Cu ◊ ◊ ◊ N(5)
2.480
2.559
2.257
2.244
2.058
0.0259
0.0217
0.0821
0.0872
0.0718
0.1059
0.0878
0.1994
0.2154
0.3879
0.131
0.106
0.616
0.582
0.346
0.0294
0.0236
0.0766
0.0830
0.1066
-0.0323
-0.0252
-0.1033
-0.1121
-0.1163
-0.0029
-0.0016
-0.0267
-0.0291
-0.0097
B3LYP/6–311 + G(2d,2p)
Cu ◊ ◊ ◊ O(4)
Cu ◊ ◊ ◊ O(61)
Cu ◊ ◊ ◊ P(1)
Cu ◊ ◊ ◊ P(2)
Cu ◊ ◊ ◊ N(5)
2.480
0.0286
0.0243
0.0838
0.0890
0.0762
0.0979
0.0822
0.1425
0.1546
0.3276
0.174
0.145
0.690
0.733
0.444
0.0279
0.0224
0.0667
0.0723
0.0980
-0.0313
-0.0243
-0.0978
-0.1059
-0.1141
-0.0034
-0.0019
-0.0311
-0.0336
-0.0161
2.559
2.257
2.244
2.058
Fig. 5 Molecular graph determined by the topology of the electron density in the planes containing Cu centers and the donor atoms. Positions of the
bond CPs are denoted by the cross.
dij = 2(NjNk - Njk) (Ni being the numbers of electrons in a
particular atomic basin and Nij being the number of the electron
pairs involved in two atomic basins), turns out to be the covalent
bond order when a single-determined wave function is used, as
is the case.37 Large values of d(A ◊ ◊ ◊ B) are indicative of electron
shared interactions while low d(A ◊ ◊ ◊ B) values characterize closed-
shell interactions.
The molecular graph for the Cu complex reproduces the bond
path corresponding to the Cu–P(1), Cu–P(2), Cu–O(4), Cu–O(61)
and Cu–N(5) bonds (see Fig. 5). The results of the topological
analysis are given in Table 1. The bond critical points along
Cu–X (X = N, O, P) bonds are characterized by a low rb
and a positive Laplacian, which indicates a weakly closed-shell
interactions, while the energy density, Hb, which is the sum of
the kinetic and potential energies at the critical point, is slightly
negative, indicating a bond that is weakly covalent. All this, as
well as small values for the delocalization index, point out that the
bonding involving Cu is more of a partially covalent shared–closed
interaction type, regardless of the atom that Cu is linked to. The
delocalization indices computed from the HF wave function are
slightly smaller than those obtained from B3LYP as Poater et al.38
already pointed out, indicating a slightly enhanced covalency
of DFT as compared to HF.39 As can be seen, the magnitude
of Hb parallels the increase in the values of rb and — rb. The
delocalization index for bonded interactions also increases along
2
with the values of rb.
The charge densities at the Cu–P BCPs, as for those in other
cases,40 have a reverse trend with respect to the corresponding
-3
˚
bond distance, are close to zero (0.085 e A average) and their
-3
˚
Laplacian are small and positive (0.2 and 0.15 e A average with
HF and B3LYP methods, respectively). The charge densities at the
Cu–O BCPs are also small, although lower than those calculated
for Cu–P, and their Laplacian values are positive and even smaller
(ca. 50% average) than those for Cu–P bonds, indicating that they
are dative bonds in character according to the QTAIM signatures
of the dative bonds.34 Thus, in other words, it could be stated that
the Cu–O bond is weaker and more polarized than the Cu–P bond.
By virtue of the Gb and |Vb| values of the Cu–P bonds, which
are almost comparable, |Vb| prevailing, the resulting energy
densities Hb have small negative values. On the other hand, the
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d(Cu–O) indices are lower than the d(Cu–P) values and this
is related to the higher covalent character of the Cu–P bonds
versus the Cu–O interactions, with the Cu–N interaction being
intermediate between both.
14 A. L. Spek, Acta Crystallogr., Sect. A: Found. Crystallogr., 1990, 46,
C34.
15 G. M. Sheldrick, SADABS, Program for area detector adsorption
correction, Institute for Inorganic Chemistry, University of Go¨ttingen,
Germany, 1996.
16 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. Robb,
A. J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C.
Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci,
M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M.
Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T.
Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E.
Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo,
R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi,
C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth,
P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D.
Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K.
Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S.
Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz,
I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y.
Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W.
Chen, M. W. Wong, C. Gonzalez and J. A. Pople, Gaussian 03, Revision
C.01, Gaussian, Inc., Wallingford, CT, 2004.
Conclusions
The structure of the second example of a five-coordinated
CuIP2NO2 system, [Cu(DLMAceM)(PPh3)2]ClO4 (DLMAceM =
6-acetyl-1,3,7-trimethyl-pteridine-2,4(1H,3H)-dione), is reported.
The metal is coordinated to the PPh3 molecules and the pyrazine
N(5) atom in a trigonal planar arrangement and long-distanced
˚
interactions (> 2.48 A) with two semi-coordinated oxygen atoms
can be observed, designing an intermediate SP/TBP polyhedron.
The nature of the metal–ligand bonds, especially in regards to
the semi-coordinated oxygen atoms, has been defined using topo-
logical analysis of the electron density rb within the framework
provided by the quantum theory of atoms in molecules (QTAIM).
The results point out that the Cu–X (X = N, O, P) bonds are
characterized by a low rb and a positive Laplacian, which indicates
a weakly closed-shell interaction, while Hb is slightly negative,
indicating a bond that is weakly covalent. All this, as well as
small delocalization index values, point out that bonding involving
copper is more of a partially covalent shared–closed interaction
type, regardless of the atom to which Cu is linked.
17 A. D. Becke, J. Chem. Phys., 1993, 98, 5648.
18 C. Lee, W. Yang and R. G. Parr, Phys. Rev. B: Condens. Matter Mater.
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Acknowledgements
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We thank the Junta de Andaluc´ıa (research teams FQM-273 and
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