Polyhedron 25 (2006) 2559–2564

www.elsevier.com/locate/poly

DFT studies of copper complexes with biphenyldiimino dithioether

II. Mechanical strain
Martin Breza *, Jozef Kožı́šek
Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia

Received 14 October 2005; accepted 1 March 2006

Available online 24 March 2006

Abstract

The geometries of tetrahedral and square-planar Cu(bite)q complexes, q = +1 or +2, as well as of the macrocyclic bite ligand,
bite = tetrabenz[a,e,g,k]-15,18-dithia-9,24-diaza-cyclohexadeca-9,23-diene, have been optimized using the DFT method. The reorganiza-
tion and strain energy values of Cu(bite)+/2+ complexes are comparable with analogous DFT/MM data for tetracoordinate copper com-
plexes with monodentate imidazole and thiolate ligands that are used as model systems for blue copper proteins.
 2006 Elsevier Ltd. All rights reserved.

Keywords: Blue copper protein model compounds; DFT method; Optimal geometry; Strain energy; Reorganization energy

1. Introduction The gated behavior might be of exceptional importance

The relationship between the geometry of the copper site
in redox-active enzymes and their resultant rate of electron
transfer has long been a subject of especial interest in cop-
per chemistry. Electron transfer in copper(II/I) systems
involves an unusually large change in coordination geome-
try. The change in conformation can itself become rate-
limiting under specific circumstances so that the reactions
become first order, independent of the counter reagents, a
condition known as ‘‘gated’’ electron transfer [1]. When
this limiting condition is reached, further increases in the
reaction driving force may result in a switch to an alterna-
tive mechanistic path so that the overall mechanism can be
described as a dual-pathway square scheme (Fig. 1). In this
scheme, CuIIL (O) and CuIL (R) (L is a multidentate
ligand) are the thermodynamically stable species while
CuIIL (Q) and CuIL (P) are metastable intermediates in
which the coordination geometry more nearly resembles
that of the thermodynamically stable species of the oppo-
site oxidation state.
*
Corresponding author. Tel.: +421 2 59325 482; fax: +421 2 52493198.
E-mail address: breza@cvt.stuba.sk (M. Breza).
in biological systems [1] where conformational constraints
could control the ultimate rate of redox reactions. Confor-
mational gating should occur in only one direction for ther-
modynamically favorable processes. These constraints
might account for the very rapid electron-transfer kinetics
of blue copper proteins. The copper sites in these systems
are essentially either trigonal pyramidal (plastocyanins)
or trigonal bipyramidal (azurins) and their rapid electron-
transfer kinetics have been attributed to the effects of this
distorted geometry.
Based on high-level quantum mechanical calculations of
Cu complexes with simple monodentate ligands, Ryde and
co-workers [2] claim that, in a low molecular weight ana-
logue of blue copper proteins, cysteine thiolate and methi-
onine thioether ligands lower the reorganization energy
accompanying Cu(II/I) electron transfer by flattening the
potential surfaces and stabilizing a nearly tetrahedral struc-
ture for the oxidized state. Thus, they have concluded that
the blue copper site is virtually strain free.
Flanagan and co-workers [3] published the synthesis, X-
ray structure, spectral and electrochemical studies of two
macrocyclic compounds of Cu(I) and Cu(II) with a biphe-
nyldiimino dithioether type ligand (bite), tetrabenz[a,e,g,k]-

0277-5387/$ - see front matter  2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.poly.2006.03.005
2560 M. Breza, J. Kožı́šek / Polyhedron 25 (2006) 2559–2564
Path A
kA2
ARed + Cu(II)L (O) Cu(I)L (P) + AOx
k2A
kQO kOQ kRP kPR
kB2
ARed + Cu(II)L (Q) Cu(I)L (R) + AOx
k2B
Path B
Fig. 1. The dual-pathway square scheme [1].
15,18-dithia-9,24-diaza-cyclohexadeca-9,23-diene, possible
model systems of blue copper proteins. [CuI(bite)](BF4)
(Fig. 2) reveals a distorted tetrahedral N2S2 coordination
about copper, with highly unequal Cu–S distances
(2.194(2) and 2.323(2) Å). The distortions from perfect C2
symmetry may be related to the unusually high redox
potential of the [CuI/II(bite)]+/2+ couple. [CuII(bite)](BF4)2
reveals an approximately square-planar CuN2S2 structure
of C2 symmetry (Fig. 3) with two distant axial BF4 anions
(Cu–F distance of 2.546(4) Å) in the solid state. However,
the spectral data indicate the existence of only four-
coordinate [CuI/II(bite)]+/2+ complexes in acetone and
dichloromethane solutions [3].
Cyclic voltammetry experiments [3] of the [CuI/II-
(bite)](BF4)1,2 redox couple in acetonitrile show only quasi-
reversible behavior with wide peak-to-peak separation.
Copper(I/II) electron self-exchange kinetics measured by
1
H NMR line broadening of [CuI(bite)]+ in the presence
Fig. 2. The structure of quasi-tetrahedral Cu(bite)+ (H atoms omitted) [3].
Fig. 3. The structure of quasi-square planar Cu(bite)2+ (H atoms omitted)
[3].
of [CuII(bite)]2+ reveal an overall first-order process with
a rate constant of 21.7 ± 1.9 s 1 at 295 K in acetone-d6,
which corresponds to fully gated electron transfer [3].
Electron-transfer kinetics of the [Cu(bite)]+/2+ redox
couple with Co(II), Ru(II) and Fe(III) complexes in aceto-
nitrile has been studied by UV–Vis stopped-flow methods
and explained in terms of a dual-pathway square mecha-
nism (Fig. 1). All of the cross-reactions proceed through
the same intermediate, and the outer-sphere self-exchange
reaction should fulfill a second-order rate law with a rate
constant of 0.01 M 1 s 1 [4].
The preferable electron transfer to the pseudo-tetrahe-
dral [CuI(bite)]+ as an initial step in the anodic oxidation
of [CuI(bite)]+ has been observed by in situ ESR/UV–
Vis–NIR cyclovoltammetry at different temperatures in
various solutions [5]. Domination of the more stable
square-planar [CuII(bite)]2+ structure, observed during
the oxidation of [CuI(bite)]+ even at 230 K, indicates very
fast transformation of metastable tetrahedral [CuII(bite)]2+
to square-planar [CuII(bite)]2+. In dichloromethane, where
no adsorption phenomena arise, the rate constant for het-
erogeneous electron transfer, k = 2 · 10 4 cm s 1, has been
estimated.
In the first part of this study [6] the geometry and cor-
responding electronic structure parameters of DFT opti-
mized tetrahedral and square-planar Cu(bite)q complexes,
q = +1 and +2, have been investigated and compared
with experimental data. A simple change of the cation
charge does not cause a qualitative change of Cu
coordination, which indicates an energy barrier for the
 M. Breza, J. Kožı́šek / Polyhedron 25 (2006) 2559–2564 2561

tetrahedral M square-planar coordination transition dur-
ing oxidation. Substantial differences in Cu–S bond
lengths, observed in the tetrahedral reduced complex,
are of intrinsic origin (mechanical strain of the bite
ligand). Due to the plasticity of the central Cu atom,
the energy effects implied by mechanical strain are low
but the geometry deformations of the Cu coordination
polyhedron may substantially change the composition
as well as the relative energy of the frontier molecular
orbitals and thus decrease the Franck–Condon barrier.
The first order rate constant (21.7 ± 1.9 s 1 at 295 K in
acetone-d6) obtained by 1H NMR line broadening kinetic
studies [3] corresponds to oxidation in the tetrahedral
geometry (path B of Fig. 1).
Many experts (such as most referees of biochemical and
biophysical journals) denote the macrocyclic compounds as
very poor model systems of blue copper proteins (blue cop-
per proteins cannot be modelled by strained complexes,
their electronic structure is quite different, their electron
transfer rate is very low, etc.). One of their arguments is
the large mechanical strain in comparison with real blue
copper proteins. The aim of this study is to evaluate the
strain and reorganization energy in the [Cu(bite)]+/2+ sys-
tem and to compare them with analogous data for tetraco-
ordinate copper complexes with monodentate imidazole
and thiolate ligands that are used as model systems for blue
copper proteins [2].
2. Calculations
As in the first part of this study [6], the standard DFT
method of quantum chemistry (Amsterdam Density
Functional – ADF program package) [7] with Vosko–
Wilk–Nussair parameterization for the local density
approximation (LDA), and Becke exchange and Perdew
correlation gradient corrections has been used in order to
find the optimal geometries of tetrahedral and square-
planar Cu(bite)q, q = +1 or +2 (denoted as R/Q and P/O
structures, respectively – see Table 1 and Figs. 1–3) as well
as of the bite ligand alone (tetrahedral T and square-planar
S structures). No symmetry restrictions were applied.
Cu(II) systems were treated within the unrestricted formal-
ism. The geometries of the individual model systems start-
ing from experimental structures were optimized until the
maximum and the root-mean-squared gradients were
below 0.01 and 0.007 Hartree/Å and the maximum and
root-mean-squared changes in geometry were below 0.01
and 0.007 Å, respectively. For H, C, N and S atoms, stan-
dard basis sets III (of DZP type) from the ADF library
have been used (with the 1s orbitals of C, N and S and

Table 1
Selected structure data (DFT optimized geometries)
Tetrahedral geometry Square-planar geometry
+ 2+ 0
Compound Cu(bite) Cu(bite) Bite Cu(bite)+ Cu(bite)2+ Bite0
Geometry notation R Q T P O S
Interatomic distances (Å)
Cu–S1 2.278 2.271 2.443 2.341
Cu–S2 2.347 2.279 2.445 2.344
Cu–N1 1.943 1.964 2.023 2.022
Cu–N2 1.944 1.968 2.025 2.020
S1–S2 3.481 3.380 3.413 3.350 3.279 3.171
N1–N2 3.252 3.263 3.185 3.158 3.054 3.261
S1–N1 3.277 3.205 3.024 3.051 3.007 2.949
S1–N2 3.788 3.810 3.473 4.454 4.354 4.381
S2–N1 3.717 3.802 3.442 4.454 4.361 4.321
S2–N2 3.235 3.206 2.998 3.054 2.999 2.921
Angles ()
S1–Cu–S2 97.6 95.9 86.5 88.8
S1–Cu–N1 101.5 98.1 85.6 86.8
S1–Cu–N2 127.3 127.9 170.9 173.6
S2–Cu–N1 119.8 127.2 170.9 174.1
S2–Cu–N2 97.4 97.7 85.6 86.5
N1–Cu–N2 113.5 112.2 102.5 98.2
S1–S2–N1–N2 87.3 91.7 81.3 171.2 172.1 174.2
Distances from phenyl plane 1 (Å)
Cu 0.645 0.603 1.563 1.417
S1 0.165 0.194 0.091 0.189 0.202 0.117
N1 0.320 0.192 0.012 0.525 0.485 0.527
Distances from phenyl plane 2 (Å)
Cu 1.041 0.728 1.551 1.423
S2 0.178 0.180 0.106 0.207 0.214 0.111
N2 0.489 0.256 0.110 0.520 0.485 0.500
2562 M. Breza, J. Kožı́šek / Polyhedron 25 (2006) 2559–2564

and and co-workers [3], higher non-equivalence of Cu-

Cu(bite)2+
phenyl non-planarity (such as higher differences in Cu dis-
Cu(bite)2+ bite
ox
tances from the phenyl plane) in Cu(I) systems than in
Cu(II) ones implies that the origin of this ligand geometry
E E perturbation is in mechanical strain caused by the larger
Estr Cu(I) ion in the same macrocyclic bite ligand. Thus, we
described the Cu volume by the surrounding S2N2 tetrahe-
Cu(bite)+ dron dimensions (Table 1) and compared them with these
Cu(bite)+ bite dimensions in the optimized geometry of the free bite mol-
red ecule. The resulting bite geometry is different for starting
tetrahedral and square-planar S2N2 arrangements. It may
R Q R or Q T be expected that the edges of the S2N2 tetrahedron in the
Geometry: free bite molecule (i.e., without the central copper atom)
P O P or O S
are shorter than in the corresponding Cu(bite)q complexes
Fig. 4. Schematic illustration of reorganization (kox, kred) and strain (Estr) but this relation has many exceptions (see the S1–S2, N1–
energies. N2 and S1–N2 distances in Table 1) . Analogously, these
edges need not be longer for Cu(I) than for Cu(II) in
the 2p orbitals of the S atoms frozen). For copper, a similar quasi-tetrahedral systems. Such a behavior is reflected by
(IV) type basis set (containing only 4p polarization func- bond angles, too. The extent of non-planarity of the phenyl
tions) has been enhanced with 4d and 4f functions (with rings bonded to S atoms (Cu, S and N atoms distances
frozen 2p orbitals) with exponent values of 1.70 (4d) and from phenyl planes) in the free bite ligands may substan-
1.05 (4f) , respectively [8]. tially differ from the corresponding Cu complexes (up to
For the sake of simplicity, the values of the total energy 0.11 Å in the T model versus over 0. 18 Å in R and Q
of the molecule, Etot, are related to the total energy of the models).
most stable tetrahedral R conformation of Cu(bite)+ com- As mentioned in the first part of this study [6], the most
plex cation , DEtot = Etot Etot(R). Using the Etot values of stable reduced structure is tetrahedral (R) whereas the most
the individual systems under study, some energy character- stable oxidized one is square-planar (O) in agreement with
istics of the Cu(bite)+/2+ redox system are estimated [2]. the dual-pathway square scheme [1]. The total energy of the
The inner-sphere reorganization energy for the oxidized quasi-tetrahedral R conformation of Cu(bite)+ is taken as
complex, kox, is calculated as the difference in energy of the the reference energy value in Table 2.
Cu(II) system at its optimal geometry and at the optimal Calculated values of reorganization and strain energies
geometry of the reduced complex. Likewise, the reorgani- are presented in Table 3. The total inner-sphere reorganiza-
zation energy for the reduced complex, kred, is calculated tion energy is higher within quasi-tetrahedral conforma-
as the energy of the Cu(I) system at its optimal geometry tions (28.3 kJ/mol) in comparison with the square-planar
minus the energy of the Cu(I) complex calculated at the ones (23.5 kJ/mol). If the tetrahedral M planar structural
geometry optimal for the Cu(II) complex (see Fig. 4). change is accounted for, the reorganization energy
The total inner-sphere reorganization energy for a self- increases ca. 3–4 times (93.7 kJ/mol). A similar increase
exchange reaction, ki, is the sum of kox and kred. of the strain energy is not observed, its highest value corre-
The strain energy, Estr, is the energy of the ligand mole- sponds to the tetrahedral Cu(I) system (36.5 kJ/mol). It
cule (i.e., without the Cu ion) in the optimal geometry of
Table 2
the complex related to the optimal geometry of the ligand Calculated energy data of Cu(bite)q cations and bite ligands (for geometry
alone (see Fig. 4) [2]. notation see Table 1, energy data are related to the total energy of the R
conformation of Cu(bite)+)
3. Results and discussion Compound Geometry Charge q DEtot (kJ/mol)
Cu(bite)q tetrahedral R +1 0.0
As mentioned in [6], the results of the geometry optimi- R +2 967.6
zation of Cu(bite)+ (R and P structures), Cu(bite)2+ (Q and Q +1 3.2
O structures) and bite0 (T and S structures) starting from Q +2 942.5
experimental quasi-tetrahedral and quasi-planar geome- square-planar P +1 33.5
P +2 930.9
tries (Table 1) exhibit no qualitative changes in the starting O +1 45.5
S2N2 polyhedron. This indicates an energy barrier for the O +2 919.4
tetrahedral M square-planar coordination transition. The
Bite tetrahedral R 0 106.6
geometry and electronic structure of the tetrahedral and Q 0 111.3
square-planar Cu(bite)q complexes has been discussed in T 0 143.1
the first part of this study [6]. Substantial differences in square-planar P 0 112.2
Cu–S bond lengths may be observed in the tetrahedral O 0 109.1
S 0 126.1
reduced (R) complex only. As proposed by Flanaghan
 M. Breza, J. Kožı́šek / Polyhedron 25 (2006) 2559–2564 2563

Table 3 should decrease the above quantities also for Cu(bite)+,2+

The calculated reorganization and strain energy data model systems.
Transition Reorganization energy Strain energy The inner-sphere reorganization energy ki in the real
(kJ/mol) (kJ/mol) proteins azurin and plastocyanin has been estimated to
kred kox ki Cu(I) Cu(II) 19 kJ/mol [9] and 18 kJ/mol [10], respectively. It is evident
Tetrahedral M tetrahedral 3.2 25.0 28.3 36.5c
31.8c that our ki results for the case of the preserved coordination
Planar M planar 12.0 11.5 23.5 13.9d 17.1d polyhedra type (28.3 kJ/mol for tetrahedral M tetrahedral
Tetrahedral M planar 45.5a 48.2b 93.7 30.9c 34.0c and 23.5 kJ/mol for square-planar M square-planar coor-
19.6d 14.9d
dination transitions in vacuo, see Table 3, should be low-
a
O–R energy difference for Cu(bite)+. ered in the above mentioned environments, too) agree
b
R–O energy difference for Cu(bite)2+.
c
Related to the tetrahedral T geometry.
very well with these experimental data as well. It might
d
Related to the square-planar S geometry. be an indirect proof that the Cu coordination polyhedron
type is preserved during the oxidation/reduction of blue
copper proteins. Nevertheless, it must be kept in mind that
means that Cu(I) in this system causes the largest deforma- the self-exchange reactions of Cu(II)/Cu(I) model com-
tion of the bite ligand (evaluated in energy units) that plexes, in general, tend to have large inner-sphere reorgani-
should increase the reactivity of this system as a whole. zation barriers in comparison with copper proteins just
Table 4 presents similar data for some copper protein owing to the different geometric preferences of the two oxi-
model systems with monodentate imidazole (Im) and thio- dation states [11].
late (SCH3 and S(CH3)2) ligands in vacuo [2d] or in which
a substantially larger environment has been included by
QM/MM treatment at the B3LYP level of theory [2e]. It 4. Conclusions
may be seen that Cu(bite)+,2+ reorganization energies
within the same coordination type (24–28 kJ/mol) in vacuo Our results indicate that the reorganization and strain
are comparable with those for Cu(Im)2(SCH3)(S(CH3)2)0/+ energy of the macrocyclic bite ligand are comparable with
in various environments (27–57 kJ/mol) and are signifi- simple monodentate ligands of blue copper proteins model
cantly lower than these ones in vacuo (62–78 kJ/mol). Only systems. This may be explained by the plasticity of the cen-
the Cu(bite)+,2+ reorganization energy for the tetra- tral copper atom. On the contrary to monodentate imidaz-
hedral M planar transition is higher (94 kJ/mol). The strain ole and thiolate ligands where the ligand positions are
energy data calculated for Cu(bite)+,2+ (14–37 kJ/mol) determined by the central atom properties and to a lower
are comparable or lower than for Cu(Im)2(SCH3)- extent by the mutual ligands repulsion, the mechanical
(S(CH3)2)0/+ in various environments (34–66 kJ/mol). It strain in the bite ligand forces the N and S atoms to adopt
may be expected that the environment effect inclusion such positions that are determined prevailingly by the
ligand sterical demands and are only influenced to a lower
extent by the central Cu atom. It may result in unusual
Table 4
Cu–S bond lengths, bond angles deformations as well as
Comparison of the reorganization and strain energy data of
Cu(Im)2(SCH3)(S(CH3)2)0/+ in various environments [2d] significant changes of molecular orbitals. The deformations
of the electronic structure of the active center may be cru-
Environment Environment Reorganization Strain energy
type fixation energy (kJ/mol) (kJ/mol) cial for the electron transfer. Consequently, thermal vibra-
tions with minimal energy demands may lead to the active
kred kox ki Cu(I) Cu(II)
center geometry possessing molecular orbitals with energies
Trigonal symmetry
and symmetry properties suitable for oxidation/reduction
Vacuo 32.7 28.8 61.5
Reduced yes 23.4 3.7 27.2 50.6 36.1 and thus reducing the Franck–Condon energy barrier.
plastocyanin As mentioned above, many experts denote the macrocy-
no 25.7 0.4 29.7 44.7 34.7 clic compounds as very poor model systems of blue copper
Oxidized yes 18.9 19.0 37.9 58.2 36.0 proteins due to many reasons. The aim of this study cannot
plastocyanin
be the polemics with them. Nevertheless, our results indi-
no 26.0 5.1 31.1 46.8 32.6
cate that large mechanical strain cannot be the argument
Tetragonal symmetry against these model systems.
Vacuo 37.7 39.8 77.5
Nitrite reductase yes 21.9 9.2 31.1 58.6 40.7a
no 28.9 5.2 34.1 53.8 40.6a Acknowledgments
Cucumber yes 18.4 8.2 26.6 51.0 33.8b
basic protein
no 15.4 41.5 57.0 66.4 44.9b We thank Prof. P. Coppens (SUNY at Buffalo, USA)
a
The tetragonal structure obtained in vacuo with the
for helpful discussions and valuable suggestions. This work
Cu(Im)2(SH)(S(CH3)2)+ model. has been supported by National Science Foundation, USA
b
The structure intermediate between trigonal and tetragonal that can- (Project No. NSF-CHE9981864) and by Slovak Grant
not be found in vacuo. Agency, Slovakia (Project Nos. 1/2449/05 and 1/3566/
2564 M. Breza, J. Kožı́šek / Polyhedron 25 (2006) 2559–2564
06). Computational support has been provided by the
Center for Computational Research of SUNY-Buffalo,
USA, which is supported by grant DBI9871132 from the
US National Science Foundation.
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