Chemical Physics Letters 651 (2016) 172–177

Contents lists available at ScienceDirect

Chemical Physics Letters

journal homepage: www.elsevier.com/locate/cplett

Complex modes of bonding: NCI/ELI-D vs. DORI surface analyses of

hapticities and hydrogen–hydrogen contacts in zincocene related
compounds
Stefan Mebs
Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany

a r t i c l e i n f o a b s t r a c t

Article history: Atoms-in-molecules (AIM) topology is prone to wrong/ambiguous bond assignments (lacking bond crit-
Received 28 January 2016 ical points) in areas of low electron densities (ED), e.g. for hydrogen–hydrogen contacts, and flat density
In final form 18 March 2016 gradients, e.g. for metal–ring contacts (hapticities), both in experimental and computed ED. Within this
Available online 24 March 2016
study, two ED-derived bonding indicators are applied to a set of zincocene related compounds: non-
covalent interactions (NCI) surfaces are combined with electron localizability indicator (ELI-D) surfaces
and compared to density overlap regions indicator (DORI) surfaces. Both methods (NCI/ELI-D, DORI)
result in spatial deconvolution of covalent and non-covalent interactions and unravel weak interactions
not observed in the AIM topology.
© 2016 Elsevier B.V. All rights reserved.

1. Introduction of molecular orbitals (MO), complementary topological analysis

Metallocenes are frequently used catalysts in organometallic
synthesis, e.g. in polymerization reactions [1]. The most prominent
examples, such as ferrocene, include central first row transi-
tion metals (groups V–VIII) and in principle exhibit symmetric
molecular structures. Unfortunately, their tendency for rotational
fluctuations can hamper unambiguous determination of the pre-
cise solid-state, solution, or gas-phase molecular geometry by
XRD, NMR, DFT, and other experimental and/or computational
approaches [2,3]. In contrast, metallocenes with early transition
metals, e.g. titanium or zirconium, form molecular structures
with bent (pentamethyl)cyclopentadienyl (Cp( *) ) arrangements. In
these cases the molecular geometries are determined not only by
metal–ligand (M Cp( *) ) connectivities (hapticities; ␩n , n = 1–5) but
also by weaker inter-ligand interactions comprising dispersion or
Van-der-Waals forces, or steric repulsion. The largest structural
diversity, however, is observed for main group elements [4] and
zincocene related compounds [5–11], which cover the whole range
from ␩1 (␴- or ␲-dominated) to ␩5 (␲-dominated) M Cp( *) bond-
ing and exhibit numerous weak intra- and inter-ligand contacts.
Since complex modes of bonding, especially asymmetric
␩2 –␩4 M Cp( *) hapticities and weak non-covalent H· · ·H con-
tacts, cannot straightforwardly be characterized by inspection
E-mail address: stefan.mebs@fu-berlin.de
of the corresponding electron densities (ED) according to the
atoms-in-molecules (AIM) [12] space-partitioning scheme may be
performed. AIM provides a bond paths motif including bond criti-
cal points (bcp), which typically resembles the molecular structure.
The ED can be extracted both from high-resolution XRD studies
and from quantum chemical calculations, which caused a wide dis-
tribution of this approach in the last two decades [13]. However,
once applied to different metallocenes, it turned out that the topo-
logical AIM approach also fails to provide a reliable picture of the
non-trivial atom–atom interactions in terms of bond paths. Firstly,
the cone-shaped ED accumulation connecting the central metal
atom (located at the tip of the cone) with the Cp( *) ring (located
at the base of the cone) is characterized by a flat ED-gradient so
that typically not all expected M Cp( *) bcp are observed, neither
in experiment, nor in theory, see reference [14] and references
therein. Secondly, according to a recent analysis of the non-covalent
interactions (NCI) index [15], which is a surface-based bonding
indicator derived from the ED (see below), AIM stationary point
(or topological) analysis is found to be too restrictive in the assign-
ment of weak non-covalent interactions including intra-molecular
hydrogen bonds, thus underestimating the number of such contacts
[16].
In recent computational studies on zincocene related com-
pounds, we could trace back the topologies of the ED, the
corresponding virial field (VF; potential energy density field), and
the electron-pair densities within the framework of the electron
localizability indicator (ELI-D) [17] to the molecular geometries

http://dx.doi.org/10.1016/j.cplett.2016.03.046
0009-2614/© 2016 Elsevier B.V. All rights reserved.
 S. Mebs / Chemical Physics Letters 651 (2016) 172–177
[18–20]. As a result, a Zn Cp* contact is formed for Zn CCp* dis-
tances below 2.32 Å. Another important aspect of the cited work
is that not the H(1)· · ·H(2) distances but the absolute and relative
C(1) H(1)· · ·H(2) C(2) angles (␶CHHC ) are the major determinants
for the formation of a H· · ·H saddle point (sp) in the considered
fields; ELI-D, ED, and VF: for an averaged ␶CHHC being larger than
ca. 97◦ a H· · ·H ELI-D sp is formed. If the value exceeds ca. 110◦ an
additional ED bcp appears. Only at very large angles of ca. 125◦ an
additional VF sp is observed. Although exceptions from these trends
could be explained by the effect of several weak contacts to the ED
of one single H atom, the question remains how to reliably estimate
the number and kind of weak intra- and inter-ligand contacts.
The recently introduced non-covalent interactions (NCI) index
[15], which is based on an analysis of the reduced electron den-
sity gradient, s(r) = [1/2(3␲2 )1/3 ]||/4/3 , promises to fill the gap
between AIM and ELI-D topology. In contrast to AIM, which uncov-
ers covalent as well as non-covalent bonding, NCI solely unravels
(extended) areas in space where non-covalent interactions take
place, which is in accordance with the non-directional charac-
ter of these interactions. It thus greatly complements the ELI-D
approach, since iso-surface representations of the latter are closely
related to covalent/directional bonding. Moreover, by mapping the
ED multiplied by the sign of the second eigenvalue of the Hessian
(sign(2 )) on iso-surfaces of s(r), different contact types including
steric/repulsive (2 > 0), Van-der-Waals like (2 ≈ 0), and attractive
(2 < 0) can be distinguished, which is not possible within the AIM
framework.
The recently introduced density overlap regions indicator
(DORI) [21] is another scalar field, which like NCI is derived from
the ED and its derivatives: (r) = (((r)/(r))2 )2 /((r)/(r))6 .
Since (r) becomes infinite at bonding regions a transformation
(r) = (r)/(1 + (r)) is applied to obtain values between zero and
one. It does not probe electron localization but geometrical fea-
tures of the ED in terms of deviations from single-exponentiality.
Free atoms and molecules have exponential ED tails where DORI
vanishes. DORI uncovers regions in space where the ED of adja-
cent atoms overlap, causing a local perturbation in the total ED. The
magnitude of the ED does not matter as deviations are measured on
the scale given by the local wavevector. Accordingly, DORI simul-
taneously uncovers regions of covalent as well as strong and weak
non-covalent interactions. Non-interacting lone pairs are, however,
not visible within DORI. Like NCI, DORI may be color-coded with
sign(2 ) in order to distinguish weak attractive from non-bonding
and repulsive atom–atom contacts.
Our previous systematic DFT-study on zincocene related com-
pounds [20] included all possible variations with ethyl (Et), Cp*,
and Cp*2/3N (C5 Me4 (CH2 )2/3 NMe2 ) ligands resulting in the fol-
lowing Zn-complexes: ZnEt2 (1), ZnEtCp* (2) [22], ZnEtCp*2N (3)
[10], ZnEtCp*3N (4) [11], ZnCp*2 (5) [8], ZnCp*Cp*2N (6) [10,11],
ZnCp*Cp*3N (7) [11], Zn(Cp*2N )2 (8) [10], Zn(Cp*2N Cp*3N ) (9, both
ligands are bidentate) [11], Zn(Cp*2N Cp*3N ) (10, Cp*2N is monoden-
tate), Zn(Cp*2N Cp*3N ) (11, Cp*3N is monodentate), and Zn(Cp*3N )2
(12, one Cp*3N ligand is monodentate) [11]. Within the present
study, hapticities as well as hydrogen–hydrogen interactions are
investigated in terms of NCI surface analysis supported by sur-
face and topological ELI-D analysis. The results are compared to
the DORI analysis.
2. Theoretical calculations
For all 12 compounds the gas-phase molecular structures had
been optimized at the BP86/TZVP [23,24] level of theory with
gaussian 09 [25] in the previous study [20]. In the present study,
the resulting wavefunction (wfn) files were utilized for a subse-
quent NCI analysis applying NCIplot (grid step size = 0.1 bohr) [26].
DORI was extracted from a modified NCIplot version, which was
173
provided by the authors of reference [21]. For compounds 2, 5,
6, and 8, ELI-D grids of identical size and orientation were gener-
ated with DGRID [27] for graphical superposition of NCI and ELI-D.
The NCI and ELI-D cube files were fused by the in-house software
addfaze.pl programmed by Dr. Christian Hübschle. For topological
analysis of the ELI-D, additional grids with 0.05 bohr step size were
generated. Topological electron localization function (ELF) [28,29]
analysis of hydrogen bonds is well established [30]. However, since
the localization values are related to the uniform electron gas of the
very same compound, ELF results are not comparable between dif-
ferent molecules. This disadvantage was overcome by introduction
of ELI-D, which was used here. All figures are displayed with MolIso
[31].
3. Results and discussion
Figure 1 displays ELI-D(1.3)/NCI(0.5) iso-surface representations
for the relaxed gas-phase molecular structures of ZnEtCp* (2),
ZnCp*2 (5), ZnCp*Cp*2N (6) and Zn(Cp*2N )2 (8). As anticipated,
(polar) covalent C H, C C, C N, and CEt Zn bonding is well rep-
resented by the ELI-D approach. The description of Zn Cp*(2/3N)
bonding, however, is not trivial, as Zn CCp*(2/3N) basins are formed
for Zn C distances closer than ca. 2.3 Å. Additionally, the formerly
bisynaptic V2 (C,C) basins (C C bonds) of the free Cp*(2/3N) ligands
are in parts transformed into trisynaptic V3 (C,Zn,C) basins [18,20].
Within ELI-D, non-covalent H· · ·H contacts result in flattened pro-
tonated monosynaptic valence basins (V1 (C,H); in other words: H
atoms), best visible in the corresponding localization domain rep-
resentations [19]. Moreover, H· · ·H saddle points are observed in
the ELI-D for averaged ␶CHHC values larger than ca. 97◦ [19,20],
see red dots in Figure 1. The dark blue NCI surfaces in Figure 1
cover areas in space complementary to the ELI-D localization
domains indicating spatial deconvolution of covalent and non-
covalent bonding aspects; a topic of recent publications [21,32,33].
Notably, this separation is not only observed between molecules
or ligands but also within polarized covalent interactions: The fun-
nel (␩5 ) or horse-shoe (␩<5 ) shaped NCI surfaces surrounding the
Zn Cp*(2/3N) interaction axes indicate non-covalent contributions,
even more so for the dative Zn N bonds for which prominent disk-
shaped NCI areas are observed ‘connecting’ the Zn core with the N
atoms lone pair (LP) localization domain, resulting in the following
arrangement: N(core)–N(LPELI-D )–NCI area–Zn(core). Extended but
flat NCI surfaces are observed for the inter-ligand H· · ·␲ contacts in
6 and 8, while H· · ·H contacts are characterized by quite localized
NCI areas.
Close inspection of NCI surfaces and ELI-D topology unravels
that for most H· · ·H NCI areas a corresponding ELI-D sp is observed.
ELI-D topology thus equally well represents ‘simple’ covalent bond-
ing (such as C C, C H, by 3,−3 critical points; attractors) and
non-covalent bonding (by 3,−1 critical points; ELI-D sp). As pre-
viously observed, NCI as well as ELI-D suggest that conventional
AIM topology is too restrictive in the assignment of weak non-
covalent contacts [16,19,20]. All intra- and inter-ligand H· · ·H ELI-D
sp are characterized by low ELI-D values (Y = 0.4–0.6) and highly
positive Laplacians (2 (Y) = 36–57 eÅ−5 ). The ratios of the potential
over kinetic energy density are below 1 (|V|/G = 0.6–0.8) resulting
in positive total energy densities (H = 0.002–0.004 a.u.) for the ELI-
D. With few exceptions, the ellipticities at the H· · ·H ELI-D sp are
low as well (ε < 1). Within AIM topology similar relations (low ED
value, positive Laplacian and total energy density) are related to
non-covalent/ionic bonding in the ED.
Considering the hapticities, the number of ELI-D attractors
(black dots in Figures 1 and 2) is lower than expected for highly
delocalized Zn Cp* contacts (␩3-5 ), compare compounds 2 and 5
and discussion in reference [20]. Here, the number of ‘proto-basins’
174 S. Mebs / Chemical Physics Letters 651 (2016) 172–177

Figure 1. Spatial deconvolution of covalent and non-covalent atom–atom interactions for 2, 5, 6, and 8 by graphical superposition of ELI-D (Y = 1.3) and NCI (s = 0.5) iso-
surfaces. NCI is given as dark blue surface, ELI-D colors change according to basin size; from light blue (small) to light green (large). For clarity, hydrogen atoms are given in
transparent mode. ELI-D attractors are given as black dots, saddle points as red dots. (For interpretation of the references to colour in this figure legend, the reader is referred
to the web version of this article.)

as visible in the localization domain representations are a more
reliable estimate of the hapticity.
Figure 2 displays again the NCI areas of compounds 2, 5, 6, and
8, but now sign(2 ) is mapped on the surfaces, which facilitates
discrimination of repulsive (2 > 0), attractive (2 < 0), and non-
bonding (2 ≈ 0) forces. The corresponding results for compounds
1, 3, 4, 7, and 9–12 are collected in Figure S1 in the supporting
information. The 2 distribution unravels additional attractive
(blue) non-covalent forces for the polarized covalent Zn C bonds.
Interestingly, for ␩3-5 -type of bonding (compounds 2 and 5) the
blue areas are ring-shaped at the inner part of the NCI-funnel
(pointing at the Zn atom) but separated into five localized areas
at the outer part (pointing at the five C atoms of the Cp* rings).
For reduced hapticities the corresponding NCI area becomes much
thinner, increasingly horse-shoe shaped, and also the inner parts
now show localized blue areas pointing along the Zn C axes. As
expected, non-covalent Zn CCp*2/3N bonding aspects become less
important with increasingly localized/directional Zn C bonding.
Like for the Zn C bonds, the attractive disk- or ring-shaped NCI
areas of the dative Zn N bonds are surrounded by red areas
of electron–electron repulsion. As anticipated, repulsion is also
observed at the centers of the Cp*2/3N rings [15].
All intra- and inter-ligand H· · ·H contacts are green colored and
thus fall into the regime of Van-der-Waals interactions. The lack
of inter-ligand NCI surfaces uncover areas of increased structural
flexibility, compare for example compounds 2 and 8. As the former
may show free rotation of the ethyl group in the gas-phase, hardly
any ligand–ligand reorientation seems possible for the latter. The
increasing number and size of inter-ligand NCI areas in the order of
increasing ligand sizes (2 < 5 < 6 < 8) is of course related to increased
steric crowding, resulting in increased AIM valence densities [20]
as well as increasingly red colored Zn C contact areas.
The corresponding DORI surfaces are compiled in Figure 3. The
corresponding results for compounds 1, 3, 4, 7, and 9–12 are
collected in Figure S2. Apparently, there are strong similarities
between the NCI/ELI-D and the DORI spatial separation of covalent
and non-covalent interactions, although the latter are seemingly
more pronounced in the DORI scheme for the common iso-surface
values s(r) = 0.5, (r) = 0.9 (the choice of the iso-value is of course
arbitrary). Like for NCI, Zn C single bonds are characterized by a
 S. Mebs / Chemical Physics Letters 651 (2016) 172–177 175

Figure 2. Iso-surface representations of the non-covalent interactions (NCI) index for compounds 2, 5, 6, and 8. sign(2 ) is mapped onto the reduced density gradient
iso-surface (s(r) = 0.5). Blue surface parts refer to attractive forces, red to repulsive forces. Green indicates non-bonding interactions. ELI-D attractors are given as black dots,
saddle points as red dots. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

disk-shaped DORI surface, whereas ␩5-1 -type of hapticities exhibit
funnel to horse-shoe shaped surfaces. Extended regions of weak
inter-ligand contacts become visible, which are becoming domi-
nant in the steric crowded compound 8, see Figure 3d. The increased
crowding in 8 is reflected in the pronounced coloring of the inter-
ligand surface. Both for NCI and DORI large and flat interaction areas
are typically related to weak contacts, whereas stronger contacts
show more localized surface areas. Like NCI/ELI-D, DORI confirms
that AIM bond topology is not able to detect all weak contacts. In
contrast to the NCI/ELI-D approach it is not always straightforward
to identify the nature of polarized or dative contacts, such as Zn Cp
and Zn N, within the DORI scheme – if they are basically covalent or
non-covalent in nature (for NCI/ELI-D both bonding aspects are sep-
arately visible). However, DORI is much easier accessible compared
to the NCI/ELI-D approach and solely relies on the ED, which make
this real-space bonding indicator (RSBI) appealing both for compu-
tational as well as experimental analysis of all types of atom–atom
interactions.
Notably, NCI and DORI also show similar behavior against vari-
ation of the iso-values, but in an inverse manner, see Figure S3.
Increasing (decreasing) the NCI (DORI) iso-values leads to the
formation of a molecular surface, which shows similarities to
conventional electron density iso-surfaces (e.g. the 0.001 a.u. ED
surface). In contrast to such ED surfaces, adjacent ligands as well as
different chemical groups within one ligand (e.g. adjacent methyl
groups in the Cp* ligands) are separated by surface areas (green)
which may be interpreted as possible areas of non-covalent inter-
actions.
In real-space, bond formation becomes first observable in terms
of small changes in the gradient of the electron density, which is
exploited by tools like NCI and DORI, and in the topology of local-
ization functions like ELF and ELI-D. Subsequently, bond critical
points are observed in the electron density and in the virial field,
which makes the atom–atom contacts also ‘visible’ within the AIM
approach. Especially for complex modes of bonding only the com-
bination of different RSBI, including topological approaches (AIM,
ELF, ELI-D) as well as surface-based approaches (NCI, DORI, aspher-
ical stockholder fragments (ASF) [18], Hirshfeld surfaces (HS)
[34,35]) renders more or less unambiguous determination of intra-
and inter-molecular contact numbers, strengths, and characters
176 S. Mebs / Chemical Physics Letters 651 (2016) 172–177
Figure 3. Iso-surface representations of the density overlap regions indicator (DORI; (r) = 0.9) for compounds 2, 5, 6, and 8. sign(2 ) is mapped onto the surface.
possible. Since both NCI and DORI are based on the electron density
and its gradients it would be of great benefit if DORI would be imple-
mented in software used to extract experimental high-resolution
XRD electron densities, such as XD2006 [36]. For NCI first applica-
tions to experimental electron densities are published [37–40]. A
recent NMR/DFT analysis on conformational isomers of an amino
acid building block included AIM, ELF, NCI, and DORI [41].
4. Conclusion
Covalent as well as non-covalent atom–atom interactions are
manifesting themselves in a gradual way, affecting first the gradient
of the electron density, which apparently contradicts the exclu-
sive use of a topological approach relying on the (non-)existence
of stationary points in the underlying electron density. NCI and
DORI are easily computed real-space bonding indicators derived
from the electron density and its gradients. Since NCI describes
exclusively non-covalent bonding aspects, it was combined in this
study on zincocenes with ELI-D – representing covalent bonding
aspects – in order to uncover the complex bonding patterns found
in these structures, including Zn Cp hapticities and H· · ·H contacts.
The results were complemented by DORI analysis, which unravels
areas in space where electron densities of different atoms clash,
thus simultaneously providing a picture of covalent as well as non-
covalent interactions. Both approaches give reliable estimates of
the hapticities and unravel weak H· · ·H contacts not observed in
AIM.
Acknowledgements
Piotr de Silva and Clemence Corminboeuf are acknowledged for
providing the modified NCIplot code, Christian Hübschle for sup-
port with addfaze and MolIso, Jens Beckmann and Julian Henn for
helpful discussions.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.cplett.2016.03.046.
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