Biasing positional change in interlocked and non-interlocked molecular machines
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Date
2010Author
Barrell, Michael Jack
Metadata
Abstract
This Thesis explores the topic of large amplitude motion within molecular machines
and the different mechanisms and molecular architectures that are exploited in order
to achieve control over the relative positions of submolecular components with
respect to one another. Chapter One provides a thorough survey of a vast range of
molecular switches and machines that have been developed during the last two
decades. The focus is on interlocked and non-interlocked systems that display highly
controlled large amplitude motion and the principles that govern their operation.
Initially, simple molecular switches and shuttles are described with the chapter
finally arriving at complex molecular machines such as motors, ratchets and walking
molecules. The importance of understanding the different mechanisms that dictate
the operation of switchable molecular machines and their fundamental differences
are highlighted throughout the chapter. Chapters Two to Four are devoted to
reporting the author’s contributions to novel switchable molecular systems. Chapter
Two describes the serendipitous discovery of an ion-pair template which has been
exploited in rotaxane formation and the operation of an orthogonal interaction
anion-switchable molecular shuttle. The macrocycle moves back and forth along the
thread between a cationic pyridinium station and a metal coordinating triazole motif
when chloride anions are bound and removed respectively from a palladium centre
which is located inside the cavity of the macrocycle. Excellent positional integrity
(>98%) of the ring at both stations is achieved due to the orthogonal binding modes
in the two states of the shuttle. Chapter Three presents a non-interlocked molecular
switch that operates through the manipulation of dynamic covalent chemistry. The
switch is comprised of a “two legged”, small organic molecule (a “walking unit”),
anchored to a three foothold track via one disulfide and one hydrazone bond. The
acid promoted hydrazone exchange allows a specific ratio of the two positional
isomers to be achieved at equilibrium. However, the system is also arranged in such
a manner that the ratio can be biased towards one positional isomer when the
hydrazone exchange is carried out alongside the photoisomerisation (Z E) of a
stilbene motif which is incorporated in the track. The isomerisation alters the relative
free energies of the products by increasing the ring strain of one positional isomer
with respect to the other, hence introducing bias into the system. The final chapter
reports the logical progression of the work presented in Chapter Three and describes
the pursuit of a four-station dynamic covalent energy ratchet, of which the net
position of the walker unit can be driven away from a steady state, minimum energy
distribution by orthogonal disulfide and hydrazone exchange and concomitant
stilbene isomerisation. The endeavour towards the successful synthesis of this rather
complex molecule is described alongside the principles for its proposed operation.
Chapter Two is presented in the form of an article that has already been published in
a peer-reviewed journal. No attempt has been made to rewrite this work other than a
slight alteration in the order of figures in the text to allow for easier reading and
re-formatting to ensure consistency of presentation throughout this thesis. The
original paper is reproduced, in its published format in the Appendix. Chapters Two,
Three and Four begin with a synopsis to provide a general overview of the work that
is presented in addition to a grateful acknowledgement of the contribution of my
fellow researchers.