Crystal packing of a zinc(II)-azide complex with a N,N,S-tridentate thiosemicarbazone ligand: An experimental and computational study

Article abstract of DOI:10.1016/j.molstruc.2019.07.045

The aim of this study was to provide a crystallographic and electronic analysis of a zinc(II)-azide complex with a N,N,S-tridentate thiosemicarbazone ligand. The characterization was performed by single-crystal X-ray diffraction, elemental analysis and FT-IR spectroscopy. This compound showed a distorted square-planar structure and its crystal structure was in the triclinic space group P1ˉ with Z = 2. Based on the Hirshfeld surface analysis, the van der Waals forces, N???H hydrogen bonds and C–H???π are the main intermolecular interactions that stabilize the crystal packing assembly. In addition, the Density Functional Theory (DFT) was used to predict the electronic properties. DFT calculations estimated interaction energy of ?12.6 kcal mol^?1 required to form the dimer structure. Nevertheless, based on a Natural Bond Orbital (NBO) analysis, two hydrogen bonds between nitrogen atoms of the azide group and the hydrogen atom of the amine one (N–H???N) are the main interactions responsible for the stabilization of the dimer structure studied. In addition, we were also able to characterize other important intermolecular interactions as the Sulfur???Sulfur and the C–H???N formed between the azide groups and the aromatic rings performed with the Quantum Theory of Atoms in Molecules (QTAIM).

Full text of DOI:10.1016/j.molstruc.2019.07.045

Accepted Manuscript
Crystal packing of a zinc(II)-azide complex with a N,N,S-tridentate thiosemicarbazone
ligand: An experimental and computational study
Sinara F.F. dos Santos, Aline A. Oliveira, Genisson Reis, Ghodrat Mahmoudi, Farhad
A. Afkhami, Patrícia S. Santiago, Rommel B. Viana, Albérico B.F. da Silva, Regina
H.A. Santos
PII:
S0022-2860(19)30889-0
DOI:
https://doi.org/10.1016/j.molstruc.2019.07.045
MOLSTR 26798
Reference:
To appear in: Journal of Molecular Structure
Received Date: 29 October 2018
Revised Date: 7 July 2019
Accepted Date: 10 July 2019
Please cite this article as: S.F.F. dos Santos, A.A. Oliveira, G. Reis, G. Mahmoudi, F.A. Afkhami,
Patrí.S. Santiago, R.B. Viana, Albé.B.F. da Silva, R.H.A. Santos, Crystal packing of a zinc(II)-azide
complex with a N,N,S-tridentate thiosemicarbazone ligand: An experimental and computational study,
Journal of Molecular Structure (2019), doi: https://doi.org/10.1016/j.molstruc.2019.07.045.
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ACCEPTED MANUSCRIPT

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Crystal packing of a zinc(II)-azide complex with a N,N,S-tridentate
thiosemicarbazone ligand: an experimental and computational study
1
,2
3
1
4
Sinara F.F. dos Santos , Aline A. Oliveira , Genisson Reis , Ghodrat Mahmoudi , Farhad
5
6
1,7*
1*
A. Afkhami , Patrícia S. Santiago , Rommel B. Viana , Albérico B.F. da Silva , Regina
1
*
H.A. Santos .
1
. Instituto de Química de São Carlos, Universidade de São Paulo (USP), São Carlos-SP,
Brazil.
2
. Unidade de Estudos de Medicina Veterinária, Universidade Estadual do Maranhão
(UEMA), São Luiz-MA, Brazil.
3
. Escola de Artes, Ciências e Humanidades, Universidade de São Paulo (USP), São Paulo-
SP, Brazil.
4
5
6
7
. Department of Chemistry, Faculty of Science, University of Maragheh, Maragheh, Iran.
. Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
. Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Registro-SP, Brazil.
. Instituto de Química, Universidade de Alfenas (Unifal), Alfenas-MG, Brazil.
*
Corresponding author.
Emails: reginas@iqsc.usp.br (R.H.A. Santos); alberico@iqsc.usp.br (A.B.F. da Silva);
rommelbv@yahoo.com.br (R.B. Viana)
Av. Trabalhador São Carlense, 400 (caixa-postal: 780). Bairro: Centro. CEP: 13560-970.
São Carlos, SP – Brasil.

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ABSTRACT
The aim of this study was to provide a crystallographic and electronic analysis of a zinc(II)-
azide complex with a N,N,S-tridentate thiosemicarbazone ligand. The characterization was
performed by single-crystal X-ray diffraction, elemental analysis and FT-IR spectroscopy.
This compound showed a distorted square-planar structure and its crystal structure was in
ꢀ
the triclinic space group P1 with Z=2. Based on the Hirshfeld surface analysis, the van der
Waals forces, N⋅⋅⋅H hydrogen bonds and C−H⋅⋅⋅π are the main intermolecular interactions
that stabilize the crystal packing assembly. In addition, the Density Functional Theory
(DFT) was used to predict the electronic properties. DFT calculations estimated interaction
−1
energy of −12.6 kcal mol required to form the dimer structure. Nevertheless, based on a
Natural Bond Orbital (NBO) analysis, two hydrogen bonds between nitrogen atoms of the
azide group and the hydrogen atom of the amine one (N−H⋅⋅⋅N) are the main interactions
responsible for the stabilization of the dimer structure studied. In addition, we were also
able to characterize other important intermolecular interactions as the Sulfur⋅⋅⋅Sulfur and
the C−H⋅⋅⋅N formed between the azide groups and the aromatic rings performed with the
Quantum Theory of Atoms in Molecules (QTAIM).
Keywords: Thiosemicarbazone; pseudo-halide ligand; chalcogen-chalcogen interaction;
sulfur-sulfur.

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INTRODUCTION
Thiosemicarbazones are versatile multidentate ligands, valuable for the synthesize
of new metal-complexes with multiple pharmacological applications [1-4]. Among the
several biological applications investigated so far, metal-thiosemicarbazone complexes
have shown good antiretroviral [5,6] antitumor [7,8] and antimalarial activities [9,10], as
well as being an effective agent against Entamoeba histolytica [11,12], Mycobacterium
tuberculosis [13,14] and Trypanosoma cruzi [15,16]. Moreover, the synthesis of zinc-azide
complexes has also received extensive attention based on their wide variety of applications.
Das et al. [17] demonstrated their potential use as a chemical model for the corrosion
resistance that was enhanced by the azide ligand, which increased the adsorption capacity
on mild steel. The zinc-azide complexes can also be applied as potential therapeutic agents
against breast cancer cells [18] as well as Gram-positive and Gram-negative bacterial
strains [19-21]. Therefore, due to the increasing interest in the design of new metal
complexes and in the understanding of the chemistry of metal-azide thiosemicarbazone
compounds, it is imperative to characterize the spectroscopic and electronic properties of
any new structures in order to strengthen our knowledge of Schiff base metal-azide
complexes.
This study aims to characterize a Zn(II)-azide complex with the N,N,S-tridentate
thiosemicarbazone ligand. This thiosemicarbazone ligand was recently synthesized and
characterized by Ilies et al. [22] and was found to exhibit a good scavenging antioxidant
activity against free radicals. In this way, FTIR analysis, elemental characterization, single
crystal X-ray diffraction and the Density Functional Theory (DFT) were used to
characterize this metal complex. Moreover, a molecular Hirshfeld surface using the
diffraction data, Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules
(QTAIM) analyses were performed with the purpose of understanding the main
intermolecular interactions which stabilizes the crystal packing assembly.

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MATERIALS AND METHODS
Experimental procedure
Elemental analysis was carried out using an Elemental Vario EL III instrument. The
infrared region measurements were made using SHIMADZU (IRAffinity model) Fourier
−1
Transform Infrared spectrophotometer between 400 and 4000 cm using KBr pellets
The ligand was prepared using a modified methodology derived from Ilies et al.
[
22] 2-methylpyridine (0.107g, 1mmol) and a few drops of HCl was added slowly to a
.
solution of 4-phenylthiosemicarbazide (0.167g, 1mmol) in ethanol (30mL). The zinc
complex was synthesized by the reaction between the organic ligand, (0.026g, 0.10 mmol),
Zn(NO ) (0.10mmol) and sodium azide (0.065g, 1.0mmol) using a thermal gradient
3
2
method in a branched tube with ethanol (10 ml) as solvent. The tube was sealed and
immersed in an oil bath at 60 °C while the branched arm was kept at ambient temperature.
After five days, crystals were produced in the cooler arm and washed with acetone and
ether, and dried in air. (Anal. Calc. for C13
C, 43.06%; H, 3.41%; N, 26.73%. FT-IR (in cm ) selected bands (see Figure S1): 2058
(N )], 1280/1300, [ (N )], 1492-1602 [ν(C=C)], 1251 [ν(C-N)], 686 [ν(C-S)].
12 7
H N SZn: C, 42.93; H, 3.33; N, 26.96). Found:
−
1
[ν
a
3
ν
s
3
The appropriate size for the monocrystal was chosen using a polarized microscopy,
which was attached to a glass fiber and fixed to the diffractometer. The intensity data
collection was performed at 298 K using the diffractometer Bruker APEX-II and MoKα
(0.71073 Å) radiation. The cell parameters were constructed by all reflections using Bruker
SAINT [23] software included in the APEX2 [24] package. Data reduction and integration
were performed using Bruker SAINT [23] software.
The structure was elucidated using SHELXS-2013 [25], WinGX [26] and Olex−2
[27] software packages. The atoms were refined anisotropically, while the hydrogen atoms
were positioned according to the attached atoms. The molecule representation was
performed by ORTEP-3 [26], Mercury [28] and TOPOSPro [29] software packages. The
Platon [30] system was used in the geometrical and atomic interaction analyses, and
CrystalExplorer [31] software was applied in the exploration of intermolecular interactions.

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Quantum chemical methodology
Electronic calculations were performed using the GAUSSIAN 09 program [32].
Initially, it is worthy stressing that the geometries of the metal complexes with the
crystallographic coordinates were used as the starting point for the optimization procedure.
The stationary point on the potential energy surface was fully optimized, followed by
evaluations of the harmonic vibration frequencies. The absence of imaginary frequencies
indicated that the optimized structure was
a
true energy minimum. The
Perdew−Burke−Ernzerhof−Adamo functional (PBE0, also known as PBE1PBE) [33,34]
was used in the optimization procedure. The def2-TZVP basis set of Weigend and Ahlrichs
[35] was used for the zinc atom, and the 6-311++G(d,p) basis sets [36] were applied for the
other atoms. A tight convergence was used in the optimization procedure and in the self-
consistent field for each simulation, as well as using an ultrafine grid. The Mayer bond
index [37] was carried out to define the bond order indexes on the coordination sphere,
while natural population analysis (NPA) [38] was employed to predict the atomic charge
distribution. For the Natural Bond Orbital (NBO) analysis, the NBO6 program [39] was
used. The Quantum Theory of Atoms and Molecules (QTAIM) was applied in the topology
analysis of the electronic density, which was performed in the AIMALL program [40].

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RESULTS AND DISCUSSIONS
Examining the vibrational spectrum (see Figure S1), the N asymmetric stretching
3
-1
band is present at 2058 cm as a strong absorption peak, identifying the azide group. These
values are in good agreement with the literature, which detected the N asymmetric
stretching band in the range 2042-2105 cm [41-44]. Also, the N symmetric stretching
3
−1
3
−1
vibration mode was assigned at 1280/1300 cm as a medium band. The frequencies in the
−1
region 1492-1602 cm were attributed to the C=C bonds, while the C−N bond was
−1
assigned at 1251 cm . Taking a glance at the C−S bond, it can be noted that the carbon-
−1
sulfur stretching absorption may be detected at 774 cm in the spectrum of the free
−1
thiosemicarbazone ligand, which shifts to 686 cm after the zinc complexation, confirming
the coordination of the thiolate sulfur [22,45]. In the case of the analogous platinum-,
copper- and nickel-halogen structures, a blue shift is detected in the C−N stretching for
−1
high values in the range of 1542-1602 cm [22,46,47]. whereas the C−S band shifts to 519
−1
cm in the copper complexes synthesized by Iles et al. [22]. These differences in C−N and
C−S stretching bands among other metal complexes [22,46,47] assign the influence of
metal-ligand interactions.
The ORTEP [26] representation of the Zn−complex is shown in Figure 1a,
while a summary of key crystal parameters data is shown in Table 1. As one can see in
Figure 1b, the Zn(II) center is four-coordinated by the Schiff base, which acts as a
tridentate chelating ligand through the N S−donor set completing the coordination sphere
2
with one nitrogen atom of the azide anion. Moreover, X-ray diffraction of the crystal
structure showed that it crystallizes in the triclinic system with two molecules in the unit
ꢀ
cell showing a space group P1. It is interesting to note that the discrepancy between the
experimental and DFT geometries was very small, although the DFT calculations were
performed with the molecule in the isolated phase (i.e., in a vacuum) and the experimental
results were obtained from the crystal data, which is influenced by crystal packing (see
Figure 1c). Looking at the superposition among the experimental and DFT results, one can

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see that the most significant differences occur on the azide group position and on the Zn−S,
Zn−N
1
and C12−C13 (in the aromatic ring) bonds.
Table 2 shows the bond lengths and angles obtained by X-ray diffraction and DFT
methods. The experimental Zn−S bond exhibited a length of 2.151 Å, while a slight
increase of 0.07 Å was reported by Iles et al. [22] in the case of the analogous copper-
halogen complexes indicating the small influence from the metal substitution. In contrast,
the Zn−S bond length determined here is shorter than in other Zn−thiosemicarbazone
complexes, where the bond lengths ranged 2.357−2.488 Å [48-55]. Based on the Mayer
bond order indexes, results close to 1 are indicative of σ-bond and those results close to 2
and 3 refers to double and triple π-bonds, respectively. Then, Zn−S bond can be
characterized as a σ-bond based on the bond order value of 0.7. The largest bond index in
the coordination sphere was predicted for the Zn−N bond involving the azide ligand,
4
which showed an experimental bond length of 1.888 Å. In contrast, the Zn−N bond length
1
was 1.934 Å, which predicted a bond order five times smaller than the Zn−N
corroborating with the small covalent character of the Zn−N bond involving the pyridine
moiety. In the azide ligand, the character of N −N is calculated to be closer to a s σ−bond
while N −N is closer to a π−bond, even though the experimental bond lengths are quite
4
bond index;
4
5
5
6
close to each other with bond lengths of 1.180 and 1.160 Å, respectively. Additional
calculations with B3LYP [56,57], B3P86 [56,58], B3PW91 [56,59], M05 [60], M06 [61]
and wB97XD [62] DFT methods were also applied with the purpose of evaluating and
comparing the performance of different functionals to predict the geometry of the zinc
complex (see Table S1). Although the PBE0 functional showed the greater accuracy among
the DFT methods for estimating the geometry, a similar performance was seen in
comparative with the B3LYP, B3P86, and B3PW91 functionals, whereas the mean absolute
errors (MAEs) among them were lower than 2%. The worst performance was assigned by
the M05 and wB97XD functionals.
It is worth mentioning that a careful choice for a methodology is necessary due to
several indexes that can underestimate the bond order values, which would lead to a
misinterpretation of the results [63-65]. Therefore, in order to explain this issue, four
additional indexes that were successfully employed to different systems [66-69] will be

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applied here to compare the results. For this task, we employed Wiberg (bo ) [70], the
wib
atom−atom overlap natural localized molecular orbitals/natural population analysis (bonlmo
)
[71], atom–atom overlap natural atomic orbital (bo ) [38] and bond delocalization (bdi)
nao
[72] indexes (see Table S2). Compared to other bond indexes, bonlmo underestimates the
zinc−ligand bond orders by almost an order of magnitude indicating ionic bonding
character instead of the more covalent bonding suggested by the other bond indexes. On the
other hand, bonao and bdi show similar results to the bowib index.
Additional analyses were also devoted to calculating the energy gap between the
optimized structures with different multiplicities (triplet and quintet ones), even though the
singlet structure was the most stable one. The triplet-singlet energy difference showed a
−1
−1
value of 38 kcal mol , while the quintet-singlet energy gap was 115 kcal mol . These
results were also in accordance with other DFT methods (see Table S3). This large gap in
comparison with other first-row transition metal complexes [73-75] only emphasizes the
low-spin state of the zinc-azide structure studied here. Moreover, similar electric dipole
moment values were observed among the DFT methods, ranging from 8.79-9.15 Debye
(see Table S4).
Turning the attentions to the frontier molecular orbitals (see Figure 2a), we can see
a delocalized contribution from the nitrogen and sulfur lone-pair electrons as well as a
minor contribution from the Zn d-orbitals to the highest occupied molecular orbital
*
(
HOMO). In contrast, the lowest unoccupied molecular orbital (LUMO) showed a π nature
*
comprising the π orbitals from the pyridine ring and the carbon-nitrogen bonds in the
coordination sphere. The contribution of zinc d-orbitals between H-1 and H-8 are also
found in all these orbitals except for H-2 which shows a delocalized contribution along the
thiosemicarbazone ligand (see Figure S2). The HOMO-LUMO (HL) energy gap was
estimated at 3.5 eV. It is noteworthy to comment that previous studies calculated HL gaps
ranging from 2.9 to 3.7 eV among zinc complexes [76-78], which is in good accordance
with that shown in Figure 2. In contrast, larger values can be seen when both frontier
molecular orbitals are mainly composed of π-orbitals [79] and lower by an order of
magnitude when the metal complexes exhibited a high conjugation effect, which may
improve the electron transport and then reducing the HL energy difference [80]. Moreover,

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only a small increase lower than 1 eV in HL gap is noted examining HOMO and LUMO of
the thiosemicarbazone ligand, whereas HOMO is composed by sulfur lone pair electrons
*
and LUMO is mainly π in nature with small contributions from sulfur and nitrogen lone
pair electrons (see Figure S3).
Moreover, the molecular electrostatic potential (MEP) maps have been applied to
characterize the chemical reactivity of the molecules through the charge distribution by
defining regions with the highest negative and positive potential, thus enabling a qualitative
interpretation of the potential targets for electrophilic and nucleophilic reactions in
biological systems [81]. Figure 2 also shows the MEP map where the regions in blue and
red indicated positive and negative potentials, respectively. Thereby, red regions show the
potential areas for electrophilic attacks which are delocalized around the azide group and
on the aromatic rings. In contrast, the highest positive potentials are located close to the
zinc atom and distributed along the hydrogen atoms in the aromatic rings.
An important tool to understand the main intermolecular interactions responsible for
the stabilization of the crystal packing is the Hirshfeld surface analysis (Figure 4), which is
based on the partitioning of the electron density calculated as the average electron density
of the spherical atoms [82-84]. In the shape index surface plots, the red regions are
associated with the stronger interatomic contact, while the blue ones show the areas where
the weakest interatomic interactions are located. In this way, the red areas are distributed
along the aromatic rings indicating π⋅⋅⋅π interactions and additional red spots can also be
observed in the aromatic C−H bonds pointing out the C−H⋅⋅⋅π intermolecular interactions.
Nevertheless, the decomposing of the fingerprint plots indicated that the van der Waals
forces (H⋅⋅⋅H contacts; 32.5%), N⋅⋅⋅H hydrogen bonds (24.3%) and C−H⋅⋅⋅π (15.8%)
stacking interactions play the major role in the cohesion of the supramolecular motif.
Examining the crystalline arrangement, it can be noted that the unit cell is composed
of two zinc-azide thiosemicarbazone complexes indicating that discrete units are distributed
in parallel into the unit cell (see Figure 3). Thereby, we will focus hereafter our
computational efforts in to elucidate some interesting non-covalent interactions in this self-
assembled dimer structure. The first step was to calculate the interaction energy, which was
based in the subtraction of the dimer motif energy by two times the energy obtained for the

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monomer structure. The DFT calculation estimated a modest interaction energy of −12.6
−1
kcal mol . This self-assembled dimer is mainly stabilized by two hydrogen bonds between
the nitrogen atoms of the azide group and the hydrogen atom of the amine one (N−H⋅⋅⋅N).
The experimental calculated N−H⋅⋅⋅N bond distance is 2.180(7) Å (see Table 2), which is in
good agreement with the optimized one for the dimeric structure, 2.019 Å. Performing the
second order perturbation theory analysis of the Fock matrix in NBO basis (E
2
) in the
N−H⋅⋅⋅N hydrogen bond, we predict a charge transfer from the nitrogen lone pair electrons
*
*
−1
into the σ N−H bond [N →σ
] with an energy of 9.1 kcal mol .
N−H
LP
A question that may arise concerns the contribution of Sulfur⋅⋅⋅Sulfur intermolecular
interaction to stabilize the dimer formation, which may be a difficult task for the Hirshfeld
surface analysis to resolve in some cases [85]. A S⋅⋅⋅S distance of 3.39 Å was observed in
the the unit cell for the dimer structure, instead the DFT calculation showed a larger value
than the experimental one with 3.76 Å. The experimental value for the S⋅⋅⋅S distance is in
accordance with other metal-thiosemicarbazone complexes observed in the range of 3.19-
3
.64 Å [86,87]. It is noteworthy to mention that a maximum distance of 3.9-4.2 Å was
reported by Shukla and Chopra [88] for the C═S···S═C interactions based in the
Cambridge Structural Database. Moreover, a charge transfer from the sulfur lone pair
*
*
electrons into the σ C−S bond [S →σ
] was predicted based on the NBO E analysis,
C−S 2
LP
2
though with a weak contribution to the dimer stability. In the dimer structure, an E energy
−1
value of 0.4 kcal mol was estimated for the S⋅⋅⋅S interaction, which is lower than that
reported in the literature for organic molecules [88-90]. This difference is caused by the
*
charge transfer from sulfur into the Zn atom and then weakening the S →σ
charge
C−S
LP
transfer process.
Further insights into the nature of the intermolecular interactions can be also
provided by performing QTAIM topological analysis. Bond critical points shown in Figure
5
correspond not only to N-H···N and S···S interactions but also to C-H···N intermolecular
interactions between the azide groups and the aromatic rings (see Table S5). It is important
to keep in mind that hydrogen bonds show electronic densities [ρ(r)] values between 0.002
and 0.034 a.u. [91], which is in accordance with each interaction predicted here. A
comparative analysis involving p(r) results showed that the N−H⋅⋅⋅N value is almost three

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times greater than the S⋅⋅⋅S and C−H⋅⋅⋅N intermolecular ones. Nevertheless, when we
examine other parameters such as the Laplacian distribution of the electronic charge density
2
[
∇ ρ(r)] and the total energy density [H(r)], we observed a different picture from the
2
character of each interaction in the dimer. The ∇ ρ(r) predicted positive values to each
interaction, which is an indicative of charge depletion [92]. This is corroborated with the
results of H(r) that are also positive in each case, characterizing these interactions as ionics
[90]. Another parameter that reinforces these previous results is the relationship between
the modulus of the local potential energy and the local energy density [|V(r)|/G(r)]. In this
case, |V(r)|/G(r) showed values less than one, thus characterizing these interactions as ionic
ones which can be seen elsewhere [93-95].
CONCLUSION
In summary, we reported here the characterization of a Zn(II)-azide complex with a
thiosemicarbazone ligand. This metal complex presented the Zn(II) center four-coordinated
by a N,N,S-tridentate chelating ligand with one nitrogen atom of the azide anion. The
crystal framework is a triclinic system with two molecules in the unit cell and a space group
ꢀ
P1. Based on the Hirshfeld surface plots, the van der Waals forces (H⋅⋅⋅H contacts; 32.5%),
N⋅⋅⋅H hydrogen bonds (24.3%) and C−H⋅⋅⋅π (15.8%) stacking interactions play the major
role in the cohesion of the supramolecular motif. Based on QTAIM parameters, the
N−H⋅⋅⋅N, S⋅⋅⋅S and C−H⋅⋅⋅N intermolecular interactions show ionic characters
.
Acknowledgments
S.F.F. dos Santos acknowledges FAPEMA (Fundação de Amparo à Pesquisa e ao
Desenvolvimento Científico e Tecnológico do Maranhão) for the Ph.D. fellowship, while
G. Reis and A.A. Oliveira are grateful to CNPq (Conselho Nacional de Desenvolvimento
Científico e Tecnológico) for Ph.D. and pos-doc fellowship, respectively. R.B. Viana is
thankful to CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) for
the previous research fellowship. This research was supported by resources supplied by the
Center for Scientific Computing (NCC/GridUNESP) of the São Paulo State University
(UNESP)

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Appendix A. Supplementary material
CCDC: 1510456 contains the supplementary crystallographic data for this work. These data
can be obtained free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html [or from the
Cambridge Crystallographic Data Centre (CCDC), 12 Union Road,Cambridge CB2 1EZ,
UK; fax: +44 (0)1223 336033.
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Figure caption:
Figure 1. (a) Representation with 50% probability for the Zn(II)-azide thiosemicarbazone.
(b) Polyhedron showing the molecular structure. (c) Superposition of the structures
obtained by X-ray diffraction (in blue) and calculated ones with the PBE0 (in red)
functional.
Figure 2. HOMO and LUMO representations (isovalue=0.05 a.u.) for the Zn(II)-azide
thiosemicarbazone complex in the left side. In the right side is showed the molecular
electrostatic potential (MEP) of the structure (isovalue=0.001 a.u.), whereas the down side
panel shows the front of the solid surface and the up side view shows the back of the
surface and the molecular disposition.
Figure 3. (a) The unit cell representation showing the N−H⋅⋅⋅N intermolecular interactions.
(b) The representation of crystal packing assembly of the Zn(II)-azide thiosemicarbazone.
Figure 4. The shape index (A) and the Hirshfeld surface map (B) of the Zn(II)-azide
thiosemicarbazone complex. In the shape index surface plots, the red regions show the
greater interatomic contact, while the blue ones are associated with the weakest interatomic
interactions. (C) The 2D fingerprint plots decomposing the main intermolecular interactions
for the cohesion of the supramolecular motif.
Figure 5. Contour maps of the Laplacian distribution of the electronic charge density
2
2
[
∇ ρ(r)] for the dimer structure. The blue lines refer to ∇ ρ>0, and the red ones indicate
2
∇
ρ< 0, while the green points represent the bond critical points (BCP) and red points
indicate ring critical ones (RCP).

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Table 1. Main crystallographic data summary for the Zn(II)-azide thiosemicarbazone
Chemical formula
Formula weight
Crystal system
Space group
a (Å)
C H N SZn
13 12 7
362.74
Triclinic
ꢀ
P1
6.822(5)
8.068(5)
b (Å)
c (Å)
α (°)
β (°)
γ (°)
13.362(5)
97.115(5)
96.895(5)
99.021(5)
2
Z (molecules/unit cell)
V (Å)
Calculated Density (mg.m ) 1.689
3
713.4(7)
-3
F(000)
368
Crystal size (mm)
Wavelength (λ(Å))
0.06 x 0.02 x 0.01
0.71073
θ
̸
mín (°); θ
̸
máx (°)
3.1; 27.5
Limiting indices
Temperature (K)
N ; N
-8 ≤ h ≥7; -10 ≤ k ≥10; -17 ≤ l ≥17
293
3259; 200
ref
par
Nobs (I>2.0σ(I))
R; wR ; S
2896
2
0.0774; 0.2302; 1.07

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o
Table 2. Comparison of bond length (in Å) and angles (in ) between experimental (X-ray)
and calculated geometries with the PBE0 functional, as well as the bond order index (BO)
employing Mayer method
Bond length Exp
PBE0
BO
1.10
0.67
0.22
0.69
1.32
1.93
0.87
1.20
Zn-N
Zn-S
Zn-N
4
1.888(4) 1.925
2.151(1) 2.331
1.934(4) 2.165
1.848(4) 2.126
1.180(6) 1.206
1.160(7) 1.140
1.751(4) 1.747
1.390(5) 1.329
1
Zn-N2
-N
N -N6
N
4
5
5
7
C -S
N -N3
2
Bond angles
S-Zn-N1
170.1(1) 145.2
S-Zn-N
S-Zn-N4
-Zn-N
N -Zn-N4
2
86.7(2)
96.2(1) 120.7
83.5(2)
93.7(2)
80.8
N
1
2
75.5
91.6
1
N
2
-Zn-N
4
176.3(2) 149.9
95.4(1) 94.6
128.8(3) 125.2
Zn-S-C7
Zn-N -C
1
1
Zn-N -C5 111.7(3) 113.9
1
Zn-N
2
-N
3
125.9(3) 121.4
Zn-N -C6 117.5(3) 117.3
2
Zn-N
4
-N
5
124.3(4) 127.2
175.6(5) 176.3
N -N -N
4
5
6
Table 3. Geometry of the intermolecular interactions in the Zn(II)-azide thiosemicarbazone
complex
D−B⋅⋅⋅A interaction N -H ⋅⋅⋅N
C -H⋅⋅⋅N6 C -S⋅⋅⋅S
7
6
6
13
7
d(D−B / in Å)
d(B⋅⋅⋅A / in Å)
a(D-B⋅⋅⋅A/ in °)
Symmetry
1.016(5)
2.180(7)
174(4)
1.082(8)
2.700(6)
139(3)
1.760(6)
3.400(7)
164(4)
-x, -1-y, 1-z -x, -1-y, 1-z -x, -1-y, 1-z

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Figure 1.

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Figure 2.

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Figure 3.

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Figure 4.

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Figure 5.

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•
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Toward a crystallographic and electronic analysis
Electronic properties of a zinc(II)-azide complex with a thiosemicarbazone
ligand
•
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N−H⋅⋅⋅N, C−H⋅⋅⋅N and Sulfur⋅⋅⋅Sulfur intermolecular interactions
Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital
NBO) analysis
(