Self-Assembly of Dinuclear Complexes Featuring Aromatic and Aliphatic Walls

192 Pages·2013·13.75 MB·English

by  Kristina Stevenson

Self-Assembly of Dinuclear Complexes
Featuring Aromatic and Aliphatic Walls

by

Kristina Aramantha Stevenson

A thesis submitted to the Department of Chemistry
In conformity with the requirements for
the degree of Master of Science

Queen’s University
Kingston, Ontario, Canada
(September, 2013)

Copyright ©Kristina Stevenson, 2013
Dedicated to my Grandpa

“We cannot direct the wind, but we can adjust the sails”
ii
Abstract
The objective of my MSc thesis is to study the self-assembly process of macrocyclic complexes,
as well as the properties that affect the obtained supramolecular architectures. The possibility of substrate
recognition within the cavity of these complexes is also of interest. Preparation of three new ligands based
on the triazole-pyridine chelating units connected through variable spacer groups, as well as the
complexes formed with octahedral metal ions, are described herein.
The first ligand contained a naphthalene spacer region, which was longer than the previously
examined xylene spacer. This extension increases the distance between metal ions in the complex, as well
as the size of the cavity. More work is required to obtain the unsaturated double-stranded complex, which
could potentially bind substrate molecules within its cavity. The triple-stranded saturated complexes with
[Fe(H O) ](BF ) and [Ni(H O) ](BF ) both gave insight into the process of self-assembly.
2 6 4 2 2 6 4 2
The next two ligands were designed to probe the effect that increasing the length of an aliphatic
spacer had on complex self-assembly. Both ethyl and propyl spacer units had been previously studied, so
butyl and pentyl spacer groups were the natural next step to analyze. The length of the alkyl spacer was
found to be very important in the nature of the obtained complex. As the length of the alkyl chain, and the
corresponding flexibility increased, so too did the complexity of the resulting supramolecular
architectures.

iii
Acknowledgements
I would first like to express my utmost gratitude and appreciation to my supervisor, Dr. Anne
Petitjean. Her enthusiasm and expertise in the area provided me with a wealth of knowledge and the
experience was invaluable. The guidance and support I received throughout my Master’s degree was
second to none and it was truly a pleasure to work and learn from her.
I am grateful for the contributions from the Queen’s faculty and staff in the Department of
Chemistry. Sincere thanks are given to my committee members, Dr. David Zechel, Dr. Ralph Whitney
and Dr. Michael Baird. Your wonderful insights and devotion of time are greatly appreciated.
Furthermore, I would like to thank Dr. Ruiyao Wang for his X-ray crystallographic analyses and Dr.
Françoise Sauriol for her expertise in NMR spectroscopy.
During my two years working in the Petitjean lab I had the opportunity to work with a number of
devoted colleagues, mentors and friends. Dr. Yi Yan, Weiwen, Huan, Caitlin and Mona, your insights and
advice were extremely helpful, and I sincerely believe my Master’s wouldn’t have been as enjoyable
without your kind support and friendship.
Most importantly I’d like to thank my family, because without their constant love and support I
wouldn’t be where I am today. I am extremely fortunate to have such wonderful parents; you’ve given me
everything I could have hoped for. Last, but certainly not least, I owe a huge thanks to my sister Tori. As
far as sisters go I’d say I’m pretty lucky. To my mom, dad and Tori, your encouraging words and ongoing
support were there when I needed them most, and I could not have made it through my academic career
thus far without you.

iv
Statement of Originality
I hereby certify that all of the work described within this thesis is the original work of the author under
the supervision of Dr. Anne Petitjean at Queen’s University. Exceptions include the X-ray
crystallography data, which were collected and solved by Dr. Ruiyao Wang; MS spectroscopy data,
which were provided by Dr. Jiaxi Wang and James Wei. Further exceptions include:
Chapter 2: The UV-vis titrations of [Fe(H O) ](BF ) /[Ni(H O) ](BF ) into N1 and corresponding Job
2 6 4 2 2 6 4 2
plots were performed by Dr. Anne Petitjean.
Chapter 3: The UV-vis titrations of [Fe(H O) ](BF ) /[Ni(H O) ](BF ) into C4 and the corresponding
2 6 4 2 2 6 4 2
Job plots were performed by Dr. Anne Petitjean. Dr. Petitjean performed the same titration and Job plot
experiments with C5 as well. St

Any published (or unpublished) ideas and/or techniques from the work of others are fully
acknowledged in accordance with the standard referencing practices.

v
Table of Contents
ABSTRACT .............................................................................................................................................. III
ACKNOWLEDGEMENTS ...................................................................................................................... IV
STATEMENT OF ORIGINALITY ......................................................................................................... V
LIST OF TABLES ..................................................................................................................................... X
LIST OF ABBREVIATIONS ................................................................................................................. XV
CHAPTER 1: INTRODUCTION .............................................................................................................. 1
1.1 SELF ASSEMBLY: A BRIEF INTRODUCTION ......................................................................................... 1
1.1.1 Hydrogen Bond Directed Self-Assembly ..................................................................................... 1
1.1.2 Metal-Directed Self-Assembly ..................................................................................................... 2
1.2 METALLOMACROCYCLES .................................................................................................................... 4
1.2.1 Directional-Bonding Approach ................................................................................................... 5
1.2.2 Symmetry-Interaction Approach ................................................................................................. 6
1.2.3 Helicates and Mesocates ............................................................................................................. 7
1.2.4 Helicates vs. Mesocates – The ‘Even-Odd’ Principle ................................................................. 9
1.3 METALLORECEPTORS ........................................................................................................................ 10
1.4 CLICK CHEMISTRY – AN OVERVIEW ................................................................................................. 13
1.4.1 Copper-Catalyzed Azide-Alkyne Cycloaddition (CuAAC) ........................................................ 15
1.4.2 ‘Click-Triazole’: Applications ................................................................................................... 15
1.4.2.1 Triazole-Pyridine: Applications ...................................................................................................... 17
1.5 PREVIOUSLY STUDIED LIGANDS ....................................................................................................... 17
1.5.1 Previously Studied: X1 Ligand ................................................................................................. 18
1.5.2 Previously Studied: C3 Ligand ................................................................................................. 21
1.5.2.1 Spin Crossover – A Brief Introduction .......................................................................................... 23
1.5.2.2 Previously Studied: C3 Magnetism Results ................................................................................... 24
1.6 RESEARCH OBJECTIVES ..................................................................................................................... 25
1.6.1 Synthesis of Aromatic Spacers and Metal Complexes .............................................................. 25
1.6.2 Synthesis of Aliphatic Spacers and Metal Complexes ............................................................... 26
1.7 REFERENCES ...................................................................................................................................... 28
CHAPTER 2 .............................................................................................................................................. 32
2.1 INTRODUCTION: FEATURES OF AROMATIC SPACERS ........................................................................ 32
2.1.1 Increasing Spacer Length - Using Aromatic Functionalities .................................................... 33
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2.1.2 Variation in Naphthalene Substitution Pattern ......................................................................... 33
2.1.3 Previous Ligand: Containing a p-xylyl Spacer ......................................................................... 34
2.1.4 Ligand Components ................................................................................................................... 35
2.2 LIGAND SYNTHESES .......................................................................................................................... 36
2.2.1 Synthesis of N1 Ligand .............................................................................................................. 36
2.2.1.1 Synthesis of 2,6-bis(hydroxymethyl)naphthalene (2.1) ................................................................. 37
2.2.1.2 Synthesis of 2,6-bis(bromomethyl)naphthalene (2.2) .................................................................... 37
2.2.1.3 Synthesis of N1 – ‘Click Reaction’ .................................................................................................. 38
2.2.2 Synthesis of [7-[(2-Chloroacetyl)oxy]naphthalen-2-yl 2-chloroacetate]] (2.3) ....................... 38
2.3 FORMATION OF METALLOMACROCYCLES WITH OCTAHEDRAL METAL IONS .................................. 39
2.3.1 Synthesis of [Fe (N1) ](BF ) ................................................................................................... 39
2 3 4 4
2.3.2 Synthesis of [Ni (N1) ](BF ) .................................................................................................... 40
2 3 4 4
2.3.3 Complex Formation of N1 with [Fe(H O) Cl ] ........................................................................ 40
2 4 2
2.3.3.1 Previous Work with Coordinating Anions .................................................................................... 40
2.3.4 Complex Formation of N1 with [Ni(H O) (OAc) ] ................................................................... 41
2 4 2
2.4 RESULTS AND DISCUSSION ................................................................................................................ 42
2.4.1 Characterization of N1 Ligand ................................................................................................. 42
2.4.1.1 NMR Analysis of N1 ........................................................................................................................ 42
2.4.1.2 Mass Spectrometry and Elemental Analysis of N1 ....................................................................... 43
2.4.2 Characterization and Analysis of [Fe (N1) ](BF ) ................................................................. 44
2 3 4 4
2.4.2.1 NMR Analysis of [Fe (N1) ](BF ) .................................................................................................. 45
2 3 4 4
2.4.2.2 Single Crystal X-Ray Structure of [Fe (N1) ](BF ) ..................................................................... 46
2 3 4 4
2.4.2.3 Molar Absorptivity Determination of [Fe (N1) ](BF ) ................................................................ 50
2 3 4 4
2.4.2.4 UV-vis Titration of N1 with [Fe(H O) ](BF ) ............................................................................... 51
2 6 4 2
2.4.3 Characterization of [Ni (N1) ](BF ) ....................................................................................... 53
2 3 4 4
2.4.3.1 UV-vis Spectroscopy Analysis of [Ni (N1) ](BF ) ........................................................................ 54
2 3 4 4
2.4.3.2 Molar Absorptivity Determination of [Ni (N1) ](BF ) ................................................................ 55
2 3 4 4
2.4.4 Characterization of N1 with [Fe(H O) Cl ] ............................................................................. 57
2 4 2
2.4.4.1 NMR Analysis of N1 with [Fe(H O) Cl ] ........................................................................................ 57
2 4 2
2.4.4.2 UV-vis Analysis of N1 with [Fe(H O) Cl ] ...................................................................................... 59
2 4 2
2.4.5 Characterization of N1 with [Ni(H O) (OAc) ] ......................................................................... 62
2 4 2
2.4.5.1 UV-vis Analysis of N1 with [Ni(H O) (OAc) ] ............................................................................... 62
2 4 2
2.4.6 Towards the N2 Ligand ............................................................................................................. 64
2.5 CONCLUSIONS .................................................................................................................................... 65
2.6 NOTES AND REFERENCES .................................................................................................................. 66
vii
2.7 REFERENCES ...................................................................................................................................... 67
CHAPTER 3 .............................................................................................................................................. 69
3.1 INTRODUCTION: PREVIOUS ALIPHATIC SPACERS .............................................................................. 69
3.1.1 Increasing the Length of the Spacer .......................................................................................... 70
3.2 LIGAND SYNTHESES: BUTYL (C4) AND PENTYL (C5) - ALKYL SPACERS ......................................... 70
3.3 FORMATION OF METALLOMACROCYCLES WITH OCTAHEDRAL METAL IONS .................................. 72
3.3.1 Synthesis of [Fe (C4) ](BF ) and [Fe (C5) ](BF ) ................................................................ 72
2 3 4 4 2 3 4 4
3.3.2 Synthesis of [Ni (C4) ](BF ) and [Ni (C5) ](BF ) ................................................................. 73
2 3 4 4 2 3 4 4
3.4 RESULTS AND DISCUSSION ................................................................................................................ 73
3.4.1 Characterization of C4 Ligand ................................................................................................. 73
3.4.1.1 NMR Analysis of C4 ........................................................................................................................ 74
3.4.1.2 Mass Spectrometry and Elemental Analysis of C4 ....................................................................... 75
3.4.2 Characterization of C5 Ligand ................................................................................................. 76
3.4.2.1 NMR Analysis of C5 ........................................................................................................................ 76
3.4.3 Characterization of [Fe (C4) ](BF ) ....................................................................................... 77
2 3 4 4
3.4.3.1 NMR Characterization of [Fe (C4) ](BF ) ................................................................................... 78
2 3 4 4
3.4.3.2 UV-vis Titration of C4 with [Fe(H O) ](BF ) ............................................................................... 80
2 6 4 2
3.4.3.3 Molar Absorptivity Analysis of [Fe (C4) ](BF ) and [Fe (C5) ](BF ) ...................................... 83
2 3 4 4 2 3 4 4
3.4.3.4 Models of [Fe (C4) ]4+ ...................................................................................................................... 85
2 3
3.4.4 Characterization of [Fe (C5) ](BF ) ....................................................................................... 86
2 3 4 4
3.4.4.1 NMR Characterization of [Fe (C5) ](BF ) ................................................................................... 86
2 3 4 4
3.4.4.2 UV-vis Titration of [Fe (C5) ](BF ) ............................................................................................... 90
2 3 4 4
3.4.4.3 of [Fe (C5) ]4+ ................................................................................................................................... 91
2 3
3.4.5 Characterization of [Ni (C4) ](BF ) and [Ni (C5) ](BF ) ..................................................... 92
2 3 4 4 2 3 4 4
3.4.5.1 UV-vis Analysis of [Ni (C4) ](BF ) and [Ni (C5) ](BF ) ............................................................ 93
2 3 4 4 2 3 4 4
3.4.5.2 Molar Absorptivity Values for [Ni (C4) ](BF ) and [Ni (C5) ](BF ) ........................................ 96
2 3 4 4 2 3 4 4
3.5 CONCLUSIONS .................................................................................................................................... 97
3.6 REFERENCES ...................................................................................................................................... 99
CHAPTER 4 ............................................................................................................................................ 101
4.1 GENERAL METHODS ........................................................................................................................ 101
4.2 EXPERIMENTAL DETAILS ................................................................................................................. 102
4.2.1 2,6-Bis(hydroxymethyl)naphthalene (2.1) ............................................................................... 102
4.2.2 2,6-Bis(bromomethyl)naphthalene (2.2) ................................................................................. 102
viii
4.2.3 [2-{1-[(6-{[4-(Pyridin-2-yl)-1,2,3-triazol-1-yl]methyl}naphthalen-2-yl)methyl]-1,2,3-triazol-
4-yl}pyridine]] (N1) .......................................................................................................................... 103
4.2.4 Metallomacrocycles Formed with Ligands Containing Aromatic Spacer Units .................... 104
Non-Coordinating Anions ........................................................................................................................... 104
4.2.4.1 [Fe (N1) ](BF ) Complex .............................................................................................................. 104
2 3 4 4
4.2.4.2 [Ni (N1) ](BF ) Complex .............................................................................................................. 105
2 3 4 4
Coordinating Anions .................................................................................................................................... 105
4.2.4.3 3 [N1] + 2 [Fe(H O) Cl ] ............................................................................................................... 105
2 4 2
4.2.5 [2-(1-{4-[4-(Pyridin-2-yl)-1,2,3-triazol-1-yl]butyl}-1,2,3-triazol-4-yl)pyridine]] (C4) ........ 105
4.2.6 [2-(1-{5-[4-(Pyridin-2-yl)-1,2,3-triazol-1-yl]pentyl}-1,2,3-triazol-4-yl)pyridine]] (C5) ....... 106
4.2.7 Metallomacrocycles Formed with Ligands Containing Aliphatic Spacer Units ..................... 107
Non-Coordinating Anions ........................................................................................................................... 107
4.2.7.1 [Fe (C4) ](BF ) Complex .............................................................................................................. 108
2 3 4 4
4.2.7.2 [Ni (C4) ](BF ) Complex .............................................................................................................. 108
2 3 4 4
4.2.7.3 [Fe (C5) ](BF ) Complex .............................................................................................................. 108
2 3 4 4
4.2.7.4 [Ni (C5) ](BF ) Complex .............................................................................................................. 109
2 3 4 4
4.2.8 [7-[(2-Chloroacetyl)oxy]naphthalen-2-yl 2-chloroacetate]] (2.3) ......................................... 109
4.3 REFERENCES .................................................................................................................................... 110
CHAPTER 5 ............................................................................................................................................ 111
5.1 SUMMARY AND CONCLUSION ......................................................................................................... 111
5.2 FUTURE DIRECTIONS ....................................................................................................................... 112

ix
List of Tables
Table 2.1: Metal-metal distances within helicate complexes (‘intramolecular’ distances) and between
complexes through head-to-tail stacking (‘intermolecular’ distances) ...................................................... 50
Table 3.1: Summary of ε (M-1cm-1) and log ε values for [Fe (C4) ](BF ) and [Fe (C5) ](BF ) complexes.
2 3 4 4 2 3 4 4
..................................................................................................................................................................... 84
x