Documente Academic
Documente Profesional
Documente Cultură
By
Taylor A. Murie
Submitted to
April 2016
Abstract
Progress has been made on the coordination of silver(I) to various 4,4-bithiazole (4-Tz)
characterized using NMR and IR spectroscopy. Coordination to silver was attempted, however,
preferred coordination of silver(I) to 4-Tz. The rotational profile of 4-Tz has been determined
and it has allowed us to begin to optimize the lowest energy states of 4-Tz.
Acknowledgements
First, I would like to thank my supervisor, Dr. Craig MacKinnon for showing me the world
of synthetic chemistry. This experience has been very eye-opening for me and has helped me
develop an appreciation for research. I consider myself lucky to have had the opportunity to
I would also like to thank my committee members Dr. Greg Spivak and Dr. Robert
Mawhinney for assisting me throughout this project. This project would not have been possible
without their help and guidance. Dr. Justin Jiang also assisted with this project on multiple
occasions and I would like to thank him for his assistance with various syntheses and
mechanisms.
I would also like to thank the MacKinnon lab members, Marnie Merchant and Joep
Trijbels. They have both been a great help in completing this project and it has been a pleasure
The faculty and staff in the chemistry department also deserve a special mention as they
all played a part in the completion of this thesis throughout their assistance over the last four
years.
Lastly, I would like to thank my friends and family for their support and guidance.
i
Contents
Acknowledgements.........................................................................................................................i
Contents..........................................................................................................................................ii
List of Figures.................................................................................................................................iv
List of Tables...................................................................................................................................v
List of Schemes...............................................................................................................................vi
Abbreviations................................................................................................................................vii
1. Introduction..............................................................................................................................1
3. Experimental...........................................................................................................................10
ii
4. Results and Discussion............................................................................................................13
4.1.1. 1,4-dibromo-2,3-butanedione..............................................................................13
4.1.2. 1,4-dibromo-2,3-pentanedione............................................................................14
4.2.1. 2,2-dimethyl-4-Tz.................................................................................................14
4.2.2. 2,2-diamino-4-Tz..................................................................................................16
5. References..............................................................................................................................23
2,2-diamino-4-Tz IR.................................................................................................24
iii
List of Figures
Figure 1. Molecular structures of linear (A), bent (B) and off-axis linear (C) ligands.
Figure 3. The dihedral angle of 4-Tz, to be rotated about in the rotational profile analysis.
iv
List of Tables
Table 1. Amounts of ligand, metal salt and solvent used in silver(I) coordination attempts.
v
List of Schemes
vi
Abbreviations
bipy = 2,2-bipyridine
H = Hartree
hr = time in hours
IR = infrared
Me = methyl group
S = singlet
Tz = bithiazole
2-Tz = 2,2-bithiazole
4-Tz = 4,4-bithiazole
vii
1. Introduction
1.1 General Introduction to Coordination Chemistry
predictable solid state structures based on the preferred geometry of the ligand and metal
centre [1]. Transition metals with a d10 electron configuration, like silver(I), do not have a
preferred geometric structure, meaning they can coordinate in any configuration ranging from
linear to octahedral. d10 transition metals have full, spherically shaped outer shells. This leads to
no preferred ligand field stabilization energy, and therefore no preferred geometric structure.
When attempting to engineer a crystal structure, small changes like solvent, stoichiometry, or
counterions also need to be taken into account as they can have a large impact on the
geometric configuration of the resulting coordination compound. For example, changing the
stoichiometry of ligand to metal cation when crystal engineering with a d10 transition metal can
effectively change the crystal structure from a linear structure to a more complex one. As a
whole, our research group is particularly interested in heterocyclic ligands as the heteroatoms
compete for coordination sites in the corresponding crystal structure. This could lead to new
There are three possible conformations of planar cyclic bidentate ligands: linear, off axis
linear, and bent. Each conformation can lead to a different crystal structure [1].
1
In Figure 1, a linear ligand, 2,2-bipyridine (bipy) is shown. Linear ligands like compound A can
form coordination complexes ranging from linear to three dimensional diamondoid structures
[2]. Bent ligands exhibiting the same structure as compound B generally lead to chelation with a
metal, and therefore can lead to new and interesting crystal structures that have not been seen
before [1]. Compounds in an off axis linear configuration could potentially lead to extended
crystal structures, also making them interesting to investigate [1]. As a research group, we are
particularly interested in bent and off-axis linear bidentate cyclic ligands containing
heteroatoms.
A B C
Figure 1. Molecular structures of linear (A), bent (B) and off-axis linear (C) ligands.
In bithiazole complexes, there are a number of ways coordination to a metal can occur.
Coordination can occur via an interaction at the sulfur group, chelation at the nitrogen groups
or coordination to a substituent present on the ring (R in Figure 2). Focus will be on 2,2-
bithiazole (2-Tz) and 4,4-bithiazole (4-Tz) as these isomers can lead to a chelation interaction.
2-Tz has been extensively researched by prior laboratory members in our group. Based
on the previous results of the coordination of 2-Tz with silver(I) from our lab and from others
work, we anticipate that the preferred interaction between 4-Tz and silver(I) will be chelation at
the nitrogen groups, potentially in addition to interaction with ring substituents (R), should such
substituents be present [3,4]. From the conjugation in the ring, it can be seen that there is only
one lone pair present on each nitrogen in contrast to each sulfur which has two lone pairs.
Based on the hybridization of the nitrogen, we anticipate that the lone pair will be planar and
lie within the plane of the compound. The sulfur is sp3 hybridized so we anticipate that the lone
pairs will lie above and below the plane of the compound [5]. With the sulfur lone pairs in this
configuration, it becomes difficult for a metal to form a strong chelation system as the angles
are not favourable. In comparison to the nitrogen, the sulfur is not a good donor, making a
chelation interaction more favourable at the nitrogen groups. Although Tz contains the
unfavourable donor sulfur groups, these compounds have the ability to chelate due to the ring
3
1.3 Potential Applications of Bithiazole Complexes
complexes, soft magnetic metals and polymers [6]. Bleomycin is an anticancer drug that has
bithiazole in the active portion of the compound. The bithiazole moiety binds to the DNA of
malignant cells via intercalation, and effectively inhibits further synthesis and replication
[6,7,8]. Bithiazole derivatives have also found application as soft ferromagnets [8].
one of the most widely utilized inorganic ligands, bipy. Due to the difference in bite angle
between 4-Tz and bipy, 4-Tz may have a greater selectivity for specific metals. In the literature,
bithiazole complexes are usually coordinated with larger or heavier (late) metals [6,8,9]. For
reactions where bite angle is not an issue, bipy and 4-Tz may be able to be used
interchangeably. 2-Tz has shown to have selectivity towards larger and heavier metals at least
in the set of Group 10 d10 transition metals, and we anticipate that 4-Tz will demonstrate this
same characteristic. If this is the case, there is potential for these compounds to be used in
situations that need to test for (sense) or remove heavy metals from a material, like drinking
4
1.4 Comparison to Other Inorganic Ligands
4-Tz can be compared to other chelating ligands, namely the ubiquitous inorganic ligand
bipy. The two complexes share a few similar characteristics. 4-Tz can also be compared to its
First, to compare to bipy, both ligands have the capability of chelating and acting as a
bidentate ligand. Bipys primary mode of coordination is via a chelation interaction, which is
Comparing the regioisomers 2-Tz and 4-Tz, they display many of the same superficial
characteristics. The difference between the two isomers is the placement of the sulfur groups
within the ring system. This placement has a large impact on the sterics of the compound. The
location of the sulfurs in 2-Tz are sites that could potentially be substituted in 4-Tz. Substituting
with a large R group at those sites (5 and 5 in 4-Tz) would be quite challenging in comparison to
substituting 2-Tz at its open sites. This steric hindrance in the 5 and 5 sites drastically
changes the sterics of this ligand and could lead to new crystal structures with greater porosity
Having different substituents can cause a change in the electronics and sterics of a
ligand, which would allow for new potential bonding pockets and/or differences in electron
richness. Previous members of our group have worked on derivatives of the ligand 2-Tz,
5
however, no one in our group has looked at the geometric isomer 4-Tz. Both are made by a
double ring closing reaction, but it is much easier to generate asymmetrically substituted 4-Tz.
In the synthesis of 4-Tz, when using an asymmetric diketone, the product would selectively be
the asymmetrically substituted 4-Tz. In the synthesis of 2-Tz, on the other hand, two
equivalents of a monoketone are used. Hence, two different ketones, R1(CO)CH2Br and
R2(CO)CH2Br, would have to be added to the reaction mixture to obtain an asymmetric product,
which would then necessitate separation as there would be a mixture of products, R1R12-Tz,
R1R22-Tz, and R2R22-Tz. The ease with which an asymmetric species is made is clearly seen
As can be seen in the mechanism in Scheme 2, the sulfur group from the thio complex C
has a zwitterionic resonance structure. The existence of this resonance structure allows attack
from the sulfur to the carbon alpha to the ketone. Bromine departs, combining with a proton
lost from the amino group of the thio complex, producing hydrobromic acid as a by-product. In
6
the next step, the intramolecular ring closing occurs via attack of the nitrogen lone pair at the
carbon of the ketone, pushing electron density towards the oxygen, forming a zwitterionic
complex. Next, a tautomerization occurs, moving the hydrogen from the nitrogen to the oxygen
to balance out the charges. A hydroxyl group and a proton eliminate producing conjugation in
the ring with the loss of a water molecule. This leaves behind half of 1,4-dibromo-2,3-
butanedione. The mechanism repeats again in a stepwise fashion to form the other ring.
Previous work done showed the isolation of a single ring species, demonstrating that this
7
1.6 Computational Chemistry
Two programs, Gaussian and AimALL, will be used in order to perform the
computational DFT calculations for this project. The aim of the computational work is to
provide insight on the electron density around each heteroatom in various substitutions of 4-Tz
The first step in this process is to determine the rotational profile of each variation of 4-
Tz in order to determine the lowest energy conformation of the ligand about a predefined
Figure 3. The dihedral angle of 4-Tz, to be rotated about in the rotational profile analysis,
Based on the analysis of the rotational profile, a geometry optimization and computation of
force constants and the resulting vibrational frequencies can then be run on the lowest energy
state(s). The rotational profile can also help determine the amount of energy required to form a
certain conformation of a compound. The optimized lowest energy conformation(s) can then be
transferred into AimAll, where the electron density can be determined at each atom within a
molecule and the bite angle of the dihedral angle can be calculated. From this information, it
8
can be determined where the bonding of a specific ligand is preferred to occur to a metal as
well as whether or not there is specificity for chelation with heavier or larger metals.
The intent of this research project was to determine the bonding capabilities of 4-Tz to
silver(I) and to compare with known 2-Tz ligands previously investigated in our laboratory. This
was to be done through two parts: laboratory work and computational chemistry.
For the laboratory work, the goal was to synthesize variations of 4-Tz, coordinate them
to silver(I) and isolate the crystals. The next step of the laboratory work was to obtain a crystal
structure of the coordination complex. The computational portion was to perform an analysis
of each substituted 4-Tz (synthesized in the laboratory portion) to determine the theoretical
results for the locations of the electron density and lone pairs of each heteroatom present in 4-
Tz. This would lead to the calculation of the bite angle of the chelating nitrogen groups and
allow comparison to bipy. It could also allow for determination of the selectivity of 4-Tz towards
These two related goals would allow for the determination of the electronic structure
and relative donor abilities of the lone pairs of 4-Tz, which can be compared to 2-Tz.
Comparison of the computational results with the synthetic results will be evaluated to validate
The rationale behind this project leads back to crystal engineering. These heterocyclic
ligands are of interest to us as they create competition for coordination sites in the
9
corresponding crystal structures. This could lead to discoveries of new applications for such
ligands.
3. Experimental
The reactions used in the preparation of the ligands were performed under an inert
atmosphere of N2 unless otherwise stated. All of the reagents used for the syntheses were of
analytical grade and were used as received from Aldrich without further purification. NMR
spectra were recorded on a Varian Unity Inova 500 MHz spectrometer at 499.99 MHz for 1H.
Chemical shifts are reported in ppm relative to the internal standard of TMS. IR spectra
Computational results were obtained with Gaussian Suite 03 [12] using the PBE1PBE
hybrid density functional and the 6-31++G(d,p) basis set [13,14]. Gaussian Suite was used to
complete DFT calculations and AimALL will be used to complete electron density analysis [15].
AimAll allows users to perform an analysis on individual atoms within a molecule, and
10
determine electron density on and around those atoms. AimALL is based on the QTAIM,
Using Gaussian, the initial attempts to calculate the rotational profile for unsubstituted
4-Tz were not converging and the application was failing. It was then decided that we would
run the calculations at stationary angles using 10o increments instead of running the entire
calculation at once.
slowly from a dropping funnel into a solution of Br2 (10.55g, 66.02 mmol) in chloroform (4 mL)
at room temperature. Once the addition was finished, the mixture was heated to 48oC and
allowed to stir over 3 hrs. The mixture was then placed into an ice bath for approximately 2 hrs
and then the light yellow precipitate was filtered. The yield for this reaction was 32%. 1H NMR
were dissolved in dry methanol (10 mL). The mixture was then allowed to reflux for 3 hrs. The
resulting solution was added to approximately 100 mL of H2O and then neutralized using
11
aqueous Na2CO3. Excess solvent was removed using a rotary evaporator and the precipitate
filtered to yield a light yellow-brown solid. The yield for this reaction was 86%. 1H NMR (499.9
MHz, CDCl3): 3.76 (s, 6H, CH3), 7.58 (s, 2H, Tz) [7].
were added to ethanol (20 mL). The resultant mixture was allowed to reflux in air under
atmospheric conditions for 6 hrs. It was then poured into approximately 40 mL of H2O and
neutralized using aqueous NH4OH. The white, crystalline solid was then filtered. The yield for
this reaction was 57%. IR: 3446, 3296, 3153, 3127, 1596, 1522, 1298, 1025, 773, 704 cm-1 [17].
12
4. Results and Discussion
4.1.1 1,4-dibromo-2,3-butanedione
This synthesis was based on a literature preparation using acetic acid and urea for the
bromination of a monoketone (2-octanone), however the NMR spectrum of the product from
this reaction was not promising [18]. Another literature preparation of this precursor was found
and the reaction worked well, this time using CHCl3 as the solvent [16]. The 1H NMR spectrum is
13
The large peak at 4.34 ppm corresponds to all four protons present in this compound. This
4.1.2. 1,4-dibromo-2,3-pentanedione
The purpose of this reaction was a proof of concept reaction demonstrating the
asymmetric substitution of 4-Tz. Unfortunately, this reaction was unsuccessful in the initial
bromination step. The bromination of pentanedione was completed using the same procedure
as was done for the butanedione [16]. The NMR spectrum showed no significant peaks
demonstrating that a bromination had taken place and therefore the reaction was deemed
unsuccessful. In the future, this reaction could be attempted using another solvent,
brominating agent, or possibly be allowed to heat for a longer period of time to allow the
reaction to occur.
4.2.1 2,2-dimethyl-4-Tz
The synthesis of methyl substituted 4-Tz was one of our most successful reactions. This
synthesis utilized the previously synthesized brominated butanedione and was a very
14
straightforward reaction. This reaction was taken from a literature preparation [7]. The product
precipitated out of solution readily and the 1H NMR spectrum was easy to characterize.
The larger peak at 3.76 ppm integrated for all six protons from the two methyl groups on the 4-
Tz and the other peak at 7.58 ppm integrated for two protons, and were in the aromatic range
indicating the protons directly substituted on the bithiazole. These peaks corresponded to
15
4.2.2 2,2-diamino-4-Tz
compound was acquired in order to compare it with the paper. All peaks matched between the
two papers, and therefore it could be concluded that the synthesis was successful.
An initial trial was run in order to see if there would be any interaction between a
silver(I) salt and 2,2-dimethyl-4-Tz. This was done using small masses of AgNO3 and 2,2-
Three attempts were made to coordinate the 2,2-dimethyl-4-Tz to silver(I) using varying
amounts of ligand, metal and solvent. The three silver compounds that were used in this
endeavor were AgBF4, AgPF6 and AgClO4; these salts were chosen based on successes
Table 1. Amounts of ligand, metal salt and solvent used in silver(I) coordination attempts.
Metal Salt Mass of Salt (mg) Mass of Ligand (mg) Solvent Volume (mL)
16
Each reaction vessel tube was filled with the masses and volumes of the metal salt, ligand and
solvent as shown in Table 1. These tubes were then placed under vacuum and frozen by placing
the tube in a liquid nitrogen bath. Once frozen, the tubes were sealed under vacuum. These
tubes were then placed in an oven overnight at 100oC. The reaction conditions and
temperatures used for this reaction were identical to those used for successful coordination of
2-Tz, however, these same conditions did not work for 4-Tz. Black precipitate was formed when
heated for all three attempts, which is characteristic of a silver precipitate rather than
coordination. In the future, other stoichiometric ratios and solvents could be used in order to
The first step of the computational calculations was to perform a rotational profile
analysis of the unsubstituted 4-Tz as well as the methyl substituted, amino substituted and
asymmetrically trimethyl substituted 4-Tz compounds. Research is still ongoing in this area as
only the unsubstituted 4-Tz rotational profile has been successful at this point.
17
Rotational Profile of 4-Tz
-1136.23
-1136.232
Energy (Hartrees)
-1136.234
-1136.236
-1136.238
-1136.24
-1136.242
-1136.244
0 20 40 60 80 100 120 140 160 180 200
Dihedral Angle (degrees)
This rotational profile demonstrates two energy barriers and two minima, indicating
that there are two points of rotation where the compound is most stable. The two minima
correspond to approximately 35o and 180o, meaning that the conformation with the nitrogen
groups trans to one another is very stable, as well as a conformation where the molecule is
slightly off-planar. This 35o minimum is likely due to the steric hindrance at the 5 and 5 sites of
the 4-Tz.
As can be seen in Figure 7, bipy has a very similar rotational profile to 4-Tz. It is
important to note that the rotational profile of bipy seems to be a mirror image of that of 4-Tz,
however this is because the Ramana Rao research group determined the rotational profile had
opposite dihedral angle starting points than we did (i.e. our 0o conformation was their 180o
18
Figure 7: The B3LYP/6-31++G(d,p) rotational profile of bipy.
Because of the synthetic methodology of 4-Tz, the 2 and 2, and 5 and 5 sites can be
readily substituted with various R groups. For the rotational profile calculations thus far, all R
groups are hydrogens. The 5 and 5 sites are very sterically hindered sites in 4-Tz. Even having
just hydrogen in the 5 and 5 sites affects the rotational profile, indicating that even hydrogen
groups are large enough to create a steric barrier to rotation, as seen by the local maximum at
0o in Figure 6. Bipy also has hydrogens in the same relative positions as 4-Tz. This leads to very
similar rotational profile, where the cis conformation is again a local maximum.
Further work could include performing analyses of the rotational profiles of substituted
4-Tz compounds as well as substituted 2-Tz compounds and comparing the differences. The
optimization and frequency calculations for each minimum would need to be run for each
variation of Tz. These optimized compounds can then be transferred into AimALL to perform an
19
analysis on the electron density and lone pairs at the heteroatoms in the ring system. This
butanedione was then used to synthesize successfully the methyl substituted 4-Tz as well as the
amino substituted 4-Tz. The 1H NMR spectrum for the methyl substituted 4-Tz demonstrated
that the synthesis was successful and the IR for the amino substituted 4-Tz also showed that
In summary of the laboratory work, two 4-Tz ligands have been synthesized, namely
2,2-dimethyl-4-Tz and 2,2-diamino-4-Tz. Both were created using the synthesized precursor
In terms of computational work, the rotational profile for 4-Tz was found through the
use of Gaussian Suite 03. It could then be compared to other ligands, like 2-Tz and bipy. This
comparison demonstrated a steric barrier to rotation present in 4-Tz that we do not expect to
be present in 2-Tz due to lack of steric hindrance, but that is present in bipy. This information is
20
4.6 Future Work
Future work could include synthesizing more variations of 4-Tz, including ones that have
different substituents in the 5 and 5 positions of the compound. Finding a general synthesis to
dibromoketones that would allow synthesis of a variety of different substituents on 4-Tz would
also be beneficial.
part of the future work as well, making modifications to the previously attempted
stoichiometric ratios of ligand to metal and changing the solvent or reaction temperature.
Through trial and error, we anticipate that it should be possible to obtain crystals of the
In terms of the computational work, building other variations of 4-Tz and running a
addition, completing the optimization and frequency calculations for each variation of 4-Tz
would also be required in order to transfer the lower energy states of these compounds into
AimALL. A QTAIM analysis using AimALL would also need to be done in order to determine the
electron density around each heteroatom and to determine the location of the lone pairs of the
sulfur and nitrogen on 4-Tz. This would lead to an accurate determination of the bonding mode
of 4-Tz to the metal that could then be compared to work in the laboratory.
Once the above work is completed, these complexes could then be tested for their
selectivity for larger and heavier metals and the bite angle of each variation could also be
determined. Depending on their selectivity, this could open up new applications of these
21
complexes to sense for, or even potentially remove larger or heavier metals in substances
This is just a small indication of where this work could take these compounds. Future
research will be required to determine the potential of these ligands for other applications.
22
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6. Appendix A: Spectroscopic Data
2,2-diamino-4-Tz IR
24