The Scope of the Bis-Urea Macrocycle Assembly Motif

258 Pages·2014·7.84 MB·English

by  Michael F. Geer

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Theses and Dissertations
1-1-2013
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Michael F. Geer
University of South Carolina
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Geer, M. F.(2013). The Scope of the Bis-Urea Macrocycle Assembly Motif. (Doctoral dissertation).
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THE SCOPE OF THE BIS-UREA MACROCYCLE ASEMBLY MOTIF

by

Michael F. Geer

Bachelor of Science
Clarion University of Pennsylvania, 2008

Submitted in Partial Fulfillment of the Requirements
For the Degree of Doctor of Philosophy in
Chemistry
College of Arts and Sciences
University of South Carolina
2013
Accepted by:
Linda S. Shimizu, Major Professor
Brian Benicewicz, Chairman, Examining Committee
Stanley Angel, Committee Member
Christopher Williams, Committee Member
Lacy Ford, Vice Provost and Dean of Graduate Studies
©Copyright by Michael F Geer, 2013
All Rights Reserved

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DEDICATION

This work is dedicated to my wife Dee and my three children, Schuyler, Devon and
Alexis, without whose unwavering support this could not have been possible.

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ACKNOWLEDGEMENTS

I would like to take the opportunity to thank all those who contributed and helped
me in my path to this thesis. First to Dr. Linda Shimizu whose leadership and teaching
helped me to become the scientist I am today. Also, whose patience and compassion
proved invaluable during my growth. Also, to the Shimizu group members who proved to
be great friends and peers, including Yeuwen, Sandipan, and Kinkini, who’s involved
debates I will miss. To Weiwei and Sahan who have proven to be good friend I wish all
the luck with their futures.
I would also like to thank the University of South Carolina’s Dean’s Dissertation
Fellowship and the NSF (CHE-1012298, CHE-0718171 and CHE-1048629
(computational center)) for their financial support.
I would like to thank my Family, my mom and dad who have been great support
and inspiration to strive to be great at all I do. Finally and most importantly to my wife
and children who have sacrificed a lot to allow me to follow my dream and allow me the
time I needed to be successful.

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ABSTRACT

From the formation of rock candy crystals, to the functionality of DNA in the cell,
to the cosmic dust throughout the universe, supramolecular chemistry has a great impact
and importance in the world around us. In this thesis, we explore the supramolecular
interactions and self-assembly of bis-urea macrocyclic systems and investigate how their
structure and assembly influences bulk properties and functionality. Specifically, in
chapter one, we review the factors that guide, limit, and define supramolecular structures
from the atomic to the centimeter scale.
In chapter two, we investigate the incorporation of benzophenone, a well known
triplet sensitizer, within a bis-urea macrocycle and its effects on the photophysical
properties. Bis-urea macrocycles consist of two urea groups and two C-shaped spacers.
We observe upon self-assembly that the benzophenone bis-urea macrocycle generates a
host with an unusually stable radical, which was detected by Electron Paramagnetic
Resonance spectroscopy (EPR). The host crystals are porous structures that are able to
absorb guests including alkenes and aromatics in the interior channel. UV-irradiation of
the benzophenone macrocycle in oxygenated solvents resulted in the generation of singlet
oxygen. Solid complexes of the host and 2-methyl-2-butene or cumene facilitated
selective oxidation of the guest in good conversion when irradiated under an oxygen
atmosphere.
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In chapter three, we investigate the synthesis and assembly of macrocyclic
systems that employ expanded aryl spacers. Incorporation of 2,7-dimethyl naphthalene
resulted in a macrocycle that had a unique “bowl shaped monomer with an unusual
parallel urea conformation that disrupted the typical urea self-assembly. The
incorporation of 1,3-dimethyl and 4-bromo-1,3-dimethyl naphthalene spacers showed the
formation of macrocycles that display favorable conformations for the assembly into
columnar structures. The bromo analog shows a propensity for halogen bonding
interactions.
Finally, in chapter four, we explore the co-crystallization of a pyridyl bis-urea
macrocycle with halogenated compounds in order to examine the ability of this
macrocycle to act as a Lewis base in the formation of halogen bonds. The macrocycle
was co-crystallized with a series of halogen bond donors. X-ray quality crystals were
obtained by slow evaporation of the host with iodopentafluoro benzene and
diiodotetrafluoro ethane from methylene chloride solutions. The crystal structures of
these complexes show very strong halogen bonds with R-X•••B distances from 2.179-
2.745 Å that are of an average only 78 % of the sum of the Van der Waals radii for iodine
and oxygen. These halogen bonds were also analyzed through DFT calculations, and we
estimate the association energies to be 7.381 kcal mol-1 for iodopentafluoro benzene and
10.331 kcal mol-1 for diodotetrafluoro ethane. These results suggest that the pyridyl
hosts will be a strong organizing motif for co-crystallizing electrophilic halides. In the
future, we plan to explore the application of this motif for organizing molecules with
important optical and electronic properties.

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TABLE OF CONTENTS
DEDICATION ......................................................................................................................... ii
ACKNOWLEDGEMENTS ................................................................................................... iii
ABSTRACT.............................................................................................................................. v
LIST OF TABLES ..................................................................................................................xi
LIST OF FIGURES ............................................................................................................... xii
LIST OF SCHEMES .......................................................................................................... xviii
CHAPTER 1. SUPRAMOLECULAR CHEMISTRY: ASSEMBLY AND SELF-
ORGANIZATION.................................................................................................................... 1

1.1. Abstract ...................................................................................................................... 1
1.2. Introduction ................................................................................................................. 2
1.3. Key Players in Self-assembly .................................................................................... 4
1.4. Assembly in Solution to Yield Discrete Structures ................................................ 12
1.5. Summary and Conclusions ....................................................................................... 24
1.6. References ................................................................................................................. 27

CHAPTER 2. SELF-ASSEMBLED BENZOPHENONE BIS-UREA
MACROCYCLES FACILITATE SELECTIVE OXIDATIONS BY
SINGLET OXYGEN ..................................................................................................... 40

2.1. Abstract ..................................................................................................................... 40
2.2. Background ............................................................................................................... 41
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2.3. Structural Analysis of Host 2.1 ................................................................................ 46
2.4. Photophysical Characterization of Host 2.1 ............................................................ 47
2.5. Production of Singlet Oxygen .................................................................................. 55
2.6. Absorption of Small Molecules by Host 2.1 Crystals ............................................ 56
2.7. Oxidation of Host 2.1•Guest Complexes ................................................................ 61
2.8. EPR Experiments ...................................................................................................... 67
2.9. Future Work .............................................................................................................. 74
2.10. Conclusions ............................................................................................................. 78
2.11. Experimental ........................................................................................................... 80
2.12. References ............................................................................................................... 94

CHAPTER 3. SYNTHESIS, CHARACTERIZATION AND CRYSTAL
ENGINEERING OF NAPHTHALENE BIS-UREA MACROCYCLES. ................105

3.1. Abstract ...................................................................................................................105
3.2. Background .............................................................................................................106
3.3. Analysis of the bis-Urea Building Block and Design of New
Macrocycles ............................................................................................................112

3.4. Synthesis of 2,7-Dimethyl Naphthalene bis-Urea Macrocycle
(3.12) .......................................................................................................................115

3.5. Crystal Structure Characterization of 2,7-Dimethyl Naphthalene
Bis-Urea Macrocycle (3.12) ...................................................................................116

3.6. Synthesis of 1,3-Dimethyl Naphthalene Bis-Urea Macrocycle
(3.13) .......................................................................................................................120

3.7. Crystal Structure Characterization of 1,3-Dimethyl Naphthalene
Bis-Urea Macrocycle [C H N O ] (3.13). ..........................................................122
38 46 6 2
3.8. Synthesis of 4-Bromo-1,3-Dimethyl Naphthalene Bis-Urea
Macrocycle (3.14) ...................................................................................................125
3.9. Crystal Structure Characterization of 4-Bromo-1,3-Dimethyl
Naphthalene Bis-Urea Macrocycle (3.14) .............................................................126
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3.10. Conclusions ...........................................................................................................129

3.11. Summary and Future Work ..................................................................................129

3.12. Experimental .........................................................................................................131

3.13. References .............................................................................................................152

CHAPTER 4. CO-CRYSTALLIZATION THROUGH HALOGEN
BONDING WITH PYRIDYL BIS-UREA MACROCYCLE....................................156

4.1. Abstract ...................................................................................................................156

4.2. Background .............................................................................................................157

4.3. Design of Experiments ...........................................................................................165

4.4. Examining the Pyridyl Bis-Urea Macrocycle by Computational
Methods ...................................................................................................................167

4.5. Evaluation of the Oxygen Lone Pair in the Pytidyl Bis-Urea
Macrocycle (4.2) as a Halogen Bond Acceptor ....................................................168

4.6. Ionic Salts of the Pyridyl Bis-Urea Macrocycle. ..................................................174

4.7. Computational Examination of the Halogen Bonds .............................................178

4.8. Solid-to-Solid Transformations and Analyzing the Uptake of
Ethylene Glycol ......................................................................................................184

4.9. Future Work ............................................................................................................186
4.10. Summary and Conclusions ...................................................................................188
4.11. Experimental .........................................................................................................189
4.12. References .............................................................................................................201
BIBLIOGRAPHY ................................................................................................................205

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