Préparation, caractérisation structurale et physico-chimique de nouveaux composés de coordination des métaux zinc et cuivre

Basdouri, Zeineb
Lawrence Rocco Falvello (dir.) ; Mohsen Graia (dir.)

Universidad de Zaragoza, 2020

Resumen: We summarize here the most important aspects of the work carried out in this Thesis and
described in the previous chapters, together with its conclusions. The thesis, entitled
"Preparation, structural and physicochemical characterization of novel coordination
compounds of zinc and copper" is based on the study of coordination compounds, formed on
the one hand by zinc with the hexamethylenetetramine ligand and on the other hand by copper
with the orotate ligand. This work has been divided into six chapters for a clearer exposition of
the results obtained.
In the first chapter, we present general information on coordination chemistry in order to reprise
some basic concepts, followed by a brief review of the intermolecular interactions that provide
the stability and cohesion among the entities in the solids reported in this thesis. A bibliographic
study is also presented, based on the complexes formed by the metals and ligands used in this
work for the development of new coordination compounds. This begins with a brief
introduction to coordination chemistry followed by a definition of a coordination complex and
the entities that form it. We also focus on the geometries that can be found in coordination
complexes as well as the steps to follow in order to name such a complex. The text continues
with an overview of the phenomena of crystallization and polymorphism followed by a
description of Ostwald’s rule of stages. In the remainder of this chapter, intermolecular
interactions such as hydrogen bonds, Van der Waals forces and - interactions, which are
responsible for the cohesion and stability of our synthesized materials, are discussed. Regarding
the bibliographic study, we present in the rest of this chapter the principal characteristics of zinc
and copper as well as the ligands hexamethylenetetramine and orotic acid, accompanied by
some examples of the complexes synthesized previously, as drawn from the literature with their
crystallographic characteristics.
In the second chapter, the different characterization techniques used in this work as well as the
associated experimental devices are described. After a brief introduction, the principles and
practical implementation of X-ray structure analysis are presented. This technique is the
mainstay of our work. After a suitable crystal has been chosen and mounted for single crystal
X-ray diffraction, the analysis is carried out in three steps. The first step is to determine the
crystal lattice, then perform the data collection and finally solve the structure. For our
compounds, we have used two types of diffractometers; one is an Enraf-Nonius CAD-4 with
FR590 X-ray generator, and the other is a Rigaku/Oxford Diffraction Xcalibur/Sapphire 3. The
thesis describes in detail the different steps for the two diffractometers. Subsequently, the text
describes the principle of Hirshfeld surface analysis, which allowed us to study the
intermolecular interactions in our synthesized compounds. The principle of X-ray powder
diffraction is described; this analysis allowed us to ensure the purity of our compounds using
the Rietveld method, which is described later. In the rest of this chapter, we also describe the
principle and the equipment of infrared absorption spectroscopy, used to study the vibrations
of the different functional groups in our synthesized materials. This chapter ends with
background on thermal analysis and especially thermogravimetric analysis (TGA) to study the
stability and thermal behavior of our materials.
The third chapter is focused on the study of organic-inorganic hybrid compounds based on zinc
and hexamethylenetetramine. A brief introduction is followed by a description of the synthetic
procedure and the strategy for preparing crystals. This chapter presents a study of three hybrid
zinc compounds. These are prepared by slow evaporation of solvent at room temperature; two
of the new products emerge from the same preparation. The detailed structural study as well as
the Hirshfeld surface analysis of two anhydrous complexes, [hmtaH]ZnCl3 and
(hmtaCH2OH)ZnCl3, are presented. The first compound, of formula (C6H13N4)ZnCl3,
crystallizes in the orthorhombic system, space group Pnma. Its structure is formed by
[hmtaH]ZnCl3 molecules. These entities arrange in layers parallel to the (101) plane. The
cohesion between the molecules is ensured by N-H...Cl and C-H...Cl hydrogen bonds within
layers and by van der Waals interactions between layers. The second compound, of formula
(C7H15N4O)ZnCl3, crystallizes in the triclinic system, space group P-1. Its structure is formed
of discrete [(C7H15N4O)ZnCl3] molecules, which in the crystal form a compact bimolecular
aggregate. O-H...Cl hydrogen bonds connect neighbouring molecules, forming an unbounded
chain of dimers. The cohesion of the structure is maintained by Van der Waals interactions
between neighbouring chains of dimers. The Hirshfeld surface analysis confirms the type of
intermolecular interactions responsible for the structural stability of these compounds. The
remainder of this chapter deals with the structural, comparative and physicochemical study of
the hemihydrate compound [Zn(H2O)6][{(CH2)6N4}ZnCl3]2·0.5H2O. The structural study
establishes that it crystallizes in the trigonal system, space group P-3c1. Its structure can be
described as consisting of stacks parallel to the crystallographic c axis: Firstly, cationic
Zn1(O1WH2)6 octahedra and disordered unligated water molecules line up along the three-fold
symmetry axis at x = 0, y = 0; secondly, the anionic complexes are arranged along the threefold
axes at (1/3, 2/3, z) and (2/3, 1/3, z). The stability of this arrangement is governed by O-H…N and O-H…Cl hydrogen bonding interactions between cation and anion chains, with a lesser contribution within the cation/water chains from O-H…O H-bonds with the partially
occupied free water as receptor. It is noted that this material is the second hydrate synthesized
in this system. The relationship between the packing in the new structure and that of the
previous hexahydrate [Zn(H2O)6][{(CH2)6N4}ZnCl3]2·6H2O, which was reported by Thomas
C. W. Mak in 1986, is described. The comparative study showed that the two structures differ
essentially in the proportion and arrangement of the water of hydration. The purity of this
compound was checked by X-ray powder diffraction analysis using the Rietveld method. Then,
for the vibrational study of our material, a theoretical semi-empirical calculation of the infrared
spectrum using the Cache program was carried out in order to compare the different bands in
the theoretical spectrum with those in the experimental spectrum. The thermal stability of this
hemihydrate compound was subsequently studied by TGA-DTG. Finally, Hirshfeld surface
analysis and fingerprint plots were applied to confirm the existence of weaker intermolecular
interactions in the crystal.
In the fourth chapter, we present the study of two copper orotates of formulas
(Cs)2[Cu(orotate)2(H2O)2]·4H2O and (Cs)2[Cu(orotate)2]·2H2O, which were synthesized from
the same starting solution. The first compound is not stable and it changes over time to give rise
to crystals of the second phase. These two compounds crystallize in the triclinic system, space
group P-1. The structure of the (Cs)2[Cu(orotate)2(H2O)2]·4H2O compound is formed by layers
of [Cu(HOr)2(H2O)2]2- anions parallel to the (001) plane. The layers are linked to each other by
hydrogen bonds involving the H2O2W and H2O3W water molecules. The cesium cations are
located in the inter-layer space and also contribute to the cohesion between layers. As for the
structure of (Cs)2[Cu(orotate)2]·2H2O, it presents a layer of double chains of bimolecular
complex aggregates parallel to (010). N3-H3 ... O14 and N13-H13 ... O4 hydrogen bonds ensure
cohesion and progression in a chain. The hydration water molecules as well as the Cs+ cations
are located in the inter-layer space and ensure cohesion between layers. Subsequently, the
comparative study of Cs2[Cu(orotate)2(H2O)2]·4H2O with its isomorph of the previously
studied analogous nickel compound, namely Cs2[Ni(HOr)2(H2O)2]·4H2O, has been conducted.
In fact, the two structures have a clear resemblance and some points of difference. However,
this is due to the Jahn-Teller effect, which is present only in the copper compound. The
transformation of crystals of the first compound into crystals of the second compound involves
the egress of four water molecules per formula unit accompanied by the modification of the
coordination about the copper center from octahedral six-coordinate to distorted square
pyramidal [4+1]. Both compounds have also been characterized by infrared absorption
spectroscopy followed by thermal analysis, TGA-DTG, for the (Cs)2[Cu(orotate)2]·2H2O
In the fifth chapter, we describe the study of a new copper orotate with the organic cation
guanidinium, of formula, (CH6N3)2[Cu (orotate)2]·2H2O. This complex has been synthesized
by slow evaporation of solvent at room temperature. Its structure is formed by layers of the
[Cu(HOr)2]2- anion and hydration water molecules parallel to the (001) plane. Between these
layers, the guanidinium cations (CH6N3)+ are located; they are all linked together via hydrogen
bonding interactions. Analysis of the Hirshfeld surfaces aids in the interpretation of the
intermolecular interactions. Thermal analysis has shown that this compound is stable at
temperatures ≤ 100°C. The comparative study with Cs2[Cu(HOr)2]·2H2O shows the effect of
the change of counterion on the structure and non-covalent interactions. It is noted that the
compound (CH6N3)2[Cu(HOr)2]·2H2O is more stable than the analogue with the Cs+ cation;
this can be explained by the capacity of the guanidinium cation (CH6N3)+ to form hydrogen
bonds, which enhances its contribution to maintaining the stability of the compound.
In the sixth and last chapter, we have identified a crystallization process showing a neat
solution-mediated single crystal to single crystal transformation between two conformational
polymorphs of (nBu4N)2[Cu(orotate)2]·2H2O, with the co-existence of both forms in the same
experimental conditions for an extended period of time; on this basis they might be considered
concomitant polymorphs. However, the crystal transformation process obeys Ostwald’s rules
of stages with superposition of the corresponding domains. The two polymorphs can be
distinguished by their difference in colour and their morphologies. The crystals of form I
develop as blue green needles while those of form II are blue-purple blocks. The square planar
geometry around the Cu2+ ion for polymorph I is distorted while in polymorph II it is flat. The
geometry calculated by the program SHAPE has a deviation of 5.08% compared to an ideal
square-planar coordination and 16.01% compared to an ideal tetrahedral coordination for form
I and a 0.41% deviation from an ideal square-planar coordination and 33.61% compared to an
ideal tetrahedral coordination for form II. Polymorph I of (nBu4N)2[Cu(orotate)2]·2H2O
crystallizes in the monoclinic system, space group P21/n; as for polymorph II, it crystallizes in
the same crystal system, with space group P21/c. The structures of these two polymorphs are
constituted by anionic ribbons formed by [Cu(HOr)2]2- anions and uncoordinated water
molecules extending along the a axis. The cohesion within a ribbon is ensured by hydrogen
bonds. The inter-ribbon space is filled by nBu4N+ cations. The cohesion between the anionic
ribbons and the organic cations is maintained by van der Waals interactions. The contributions
of the interactions observed on the Hirshfeld surface (dnorm) and the corresponding 2D
fingerprints plots for the two polymorphs are very similar. X-ray powder diffraction analysis
allowed us to confirm the purity of the two compounds using the le Bail method. Detailed
vibrational study by infrared absorption spectroscopy and thermal analysis by TGA-DTG were
conducted. IR spectroscopy analysis showed the decrease of symmetry in form I compared to
form II. This results in a splitting of the vibration bands. According with the TGA data, both
crystals lose their water molecules below 90°C with the water molecules of form I being lost at
a slightly lower temperature (DTGmax = 72.35°C), which could indicate that the hydrogenbonding
system is a bit stronger in the final planar compound (form II, DTGmax = 80.14°C).
Additionally, the final compound has a slightly larger volume (>2.5%, 1262.8 Å3/mol) than the
first one (1228.3 Å3/mol), which could be related to the entropy of the systems. After the loss
of water, the TGA curves are not identical, which indicates that they do not evolve towards the
same compound upon heating. DFT calculations on the complex anion realized by Dr. Miguel
Baya García reveal a slight energetic advantage for the distorted conformation, from which
the conclusion is drawn that crystals of form II, which according to Ostwald's Rule of Stages
are more stable than those of form I, are energetically favored as a result of the hydrogen

Resumen (otro idioma): 

Pal. clave: cristalografia ; estructura cristalina ; quimica del estado solido ; compuestos coordinados

Titulación: Programa de Doctorado en Química Inorgánica
Plan(es): Plan 493
Nota: Presentado: 25 09 2020
Nota: Tesis-Univ. Zaragoza, , 2020

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