metal-ligand self-assembly and dissipative assembly by Andrew Krisjanis Damb

476 Pages·2013·10.75 MB·English

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Explorations in synthetic ion channel research: metal-ligand self-assembly and
dissipative assembly

by

Andrew Krisjanis Dambenieks
Master of Science, The University of Western Ontario, 2006
Bachelor of Science, The University of Western Ontario, 2004

A Doctoral Dissertation Submitted in Partial Fulfillment
of the Requirements for the Degree of

DOCTOR OF PHILOSOPHY

in the Department of Chemistry

 Andrew Krisjanis Dambenieks, 2013
University of Victoria

All rights reserved. This dissertation may not be reproduced in whole or in part, by
photocopy or other means, without the permission of the author.
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Supervisory Committee

Explorations in synthetic ion channel research: metal-ligand self-assembly and
dissipative assembly
by
Andrew Krisjanis Dambenieks
Master of Science, The University of Western Ontario, 2006
Bachelor of Science, The University of Toronto, 2004

Supervisory Committee
Dr. Thomas Fyles, Department of Chemistry
Supervisor

Dr. Natia L. Frank, Department of Chemistry
Departmental Member

Dr. Fraser Hof, Department of Chemistry
Departmental Member

Dr. Francis E. Nano, Department of Biochemistry
Outside Member
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Abstract

Supervisory Committee
Dr. Thomas Fyles, Department of Chemistry
Supervisor
Dr. Natia L. Frank, Department of Chemistry
Departmental Member
Dr. Fraser Hof, Department of Chemistry
Departmental Member
Dr. Francis E. Nano, Department of Biochemistry
Outside Member

This thesis explores fundamental design strategies in the field of synthetic ion
channel research from two different perspectives. In the first part the synthesis of
complex, shape persistent and thermodynamically stable structures based on metal-
ligand self-assembly is explored. The second part examines transport systems with
dynamic transport behavior in response to chemical inputs which more closely mimic
the dissipative assembly of Natural ion channels.
In part one, two model systems, the ethylenediamine palladium(II) - 4,4’-
bipyridine squares of Fujita and the trimeric bis(terpyridine) - iron(II) hexagonal
macrocycles of Newkome, were targeted for structural modification towards becoming
transport competent systems via improving the membrane partitioning characteristics
of the final coordination compounds by increasing their lipophilicity.
Modifications of the Fujita system involved the generation of two lipophilic 4,4’-
bipyridines with addition of lipophilic groups of 13 and 17 carbon long alkyl chains
respectively at the 3 and 3’ positions. After pursuing multiple unsuccessful synthetic
routes the successful syntheses afforded the final lipophilic 4,4’-bipyridines in overall
yields of 19 to 21% over two synthetic steps. Mixtures of the newly generated lipophilic
4,4’-bipyridines with a known lipophilic ethylenediamine palladium(II) “corner”
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exhibited evidence of self-assembly from NMR spectroscopy experiments however
attempts at further characterization by ESI-MS and X-ray crystallography were
unproductive. The putative self-assembled structures were inactive in HPTS vesicle
assays but showed erratic conductance activity in bilayer clamp experiments. However,
the magnitude of the conductance observed was not indicative of the passage of ions
through the internal pore of the square complex.
Modifications to the Newkome hexagons were aimed at generating overall
neutral assemblies with external lipophilic groups. These modifications involved
imparting a net -2 charge to the ligand via modifications to the terminal tridentate
ligands so that upon coordination to octahedral metal centers in the +2 oxidation state
the overall hexagonal complex would be neutrally charged. Two bis-polydentate ligands
were generated; a dissymmetric molecule comprising one terpyridine and one
dipicolinate tridentate ligand (TERPY-DPA) and a symmetrical molecule comprising two
2,2’-bipyridine-6-carboxylate tridentate ligands (BIPYA-BIPYA). The successful syntheses
provided the desired trimethylsilylethyl ester protected compounds in yields of 9.2 and
7.5 % over 6 and 8 total synthetic steps for TERPY-DPA and BIPYA-BIPYA respectively. A
new approach to metal-ligand complex formation by concomitant fluoride deprotection
and assembly was demonstrated with a monomeric complex. Polymetallic complexes
formed with a variety of transition metals based on colorimetric changes but the
products were very intractable and resisted full structural or transport characterization.
Part two develops a system potentially capable of exhibiting dissipative assembly of
active transporters. A library of six thioester containing compounds structurally related
to known active oligoester compounds was synthesized. The successful syntheses
provided the desired compounds in overall yields of 1.0 to 17.7% over 11 to 13 total
synthetic steps. The intramolecular cyclization - truncation and thioester exchange
reactions central to the dissipative assembly strategy were explored using a model
compound. The full length compounds showed transport activity via the HPTS vesicle
assay that was significantly below that of the lead compound. Bilayer clamp
experiments however, revealed significant transport activity for both the full length as
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well as the truncated thiol molecules. In the case of the latter the transport events had
exceedingly high conductivity for such a small molecule. This unexpected activity for
both the full length and truncated compounds, although different, prevented a full
implementation of dissipative assembly of transport.
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Table of Contents

Supervisory Committee .......................................................................................................ii
Abstract ............................................................................................................................... iii
Table of Contents ................................................................................................................ vi
List of Tables ..................................................................................................................... viii
List of Figures ...................................................................................................................... ix
List of Schemes.................................................................................................................. xxi
List of Abbreviations ...................................................................................................... xxvii
List of Numbered Compounds ......................................................................................... xxx
Acknowledgements ........................................................................................................... xlii
1 Introduction ................................................................................................................ 1
1.1 Summary ............................................................................................................. 1
1.2 Origins - The Lipid Bilayer Membrane ................................................................ 1
1.3 The Challenge - Ion Transport ............................................................................. 6
1.3.1 Natural Ion Channels .................................................................................... 11
1.3.2 Synthetic Ion Channels.................................................................................. 12
1.4 Studying Ion Channel Activity ........................................................................... 15
1.4.1 Vesicle Based Transport Activity Experiments.............................................. 16
1.4.2 Planar Lipid Bilayer Based Transport Activity Experiments .......................... 19
1.5 New Challenges of Synthetic Ion Channel Research ........................................ 24
1.5.1 Supramolecular Chemistry and Non-Covalent Interactions ......................... 26
1.5.2 The Hydrophobic Effect ................................................................................ 29
1.5.3 Metal - Ligand Interactions ........................................................................... 31
1.5.4 Reversible Covalent Bonds ........................................................................... 33
1.6 Molecular Recognition Strategies ..................................................................... 34
1.6.1 Complementarity .......................................................................................... 34
1.6.2 Preorganization ............................................................................................. 39
1.7 Designing Synthetic Self-Assembled Supramolecular Systems in Water ......... 44
1.7.1 Existing Synthetic Ion Channels Incorporating Metal-Ligand Self-Assembly 45
1.8 Outline of the Thesis ......................................................................................... 49
2 Thermodynamic Metal - Ligand Self-Assembly of Semi-Rigid Macrocycles ............. 51
2.1 Conceptual Ion Channel Motifs ........................................................................ 51
2.2 Macrocycles and Supramolecular Self-Assembly ............................................. 53
2.3 The Fujita Square .............................................................................................. 54
2.4 Previous Work - First Generation Modified Fujita Squares .............................. 54
2.5 Design Considerations for Second Generation Modified Fujita Squares ......... 56
2.6 Target Molecules and Retrosynthetic Analysis ................................................. 58
2.7 Synthesis ........................................................................................................... 59
2.8 NMR Studies of the Self-Assembly of Second Generation Lipophilic Fujita
Squares .......................................................................................................................... 76
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2.9 Vesicle Based Studies on the Self-Assembly and Ion Transport Properties of
Second Generation Lipophilic Fujita Squares ............................................................... 85
2.10 Bilayer Clamp Studies on the Self-Assembly and Ion Transport Properties of
Second Generation Lipophilic Fujita Squares ............................................................... 90
2.11 Interpretations and Hypotheses on the Failure of the Modified Fujita System92
2.12 New Scaffold for Generation of Self-Assembling Ion Channels ....................... 93
2.13 Design Considerations for a Modified Newkome L M Hexagon ..................... 96
3 3
2.14 Considerations for Hexagonal Complexes from the Modified Newkome Ligands
99
2.15 Speciation Simulation for the Terpyridine-Dipicolinate Ligand System ......... 101
2.16 Synthesis of modified Newkome bis-tridentate ligands ................................. 114
2.17 Complexation of Bis-Tridentate ligands with Transition Metals .................... 139
2.18 Trial Transport Assays - TERPY-DPA + Co2+ Mixture ....................................... 142
2.19 Lessons Learned and Potential Future Directions .......................................... 143
3 Dissipative Assembly of Transport Active Systems ................................................ 146
3.1 Thermodynamic vs. Dissipative Assembly ...................................................... 146
3.2 Design Considerations for a Channel Exhibiting Dissipative Assembly .......... 148
3.3 Design Elements for the Dissipatively Assembling Ion Channel ..................... 151
3.4 Dissipative Assembling Ion Channel Synthetic Target .................................... 153
3.5 Retrosynthetic Analysis of Target Molecules ................................................. 161
3.6 Synthesis ......................................................................................................... 163
3.7 Vesicle Based HPTS Studies............................................................................. 179
3.8 Fluorescence Based Assay of Compound Partitioning ................................... 181
3.9 HPLC Studies on the Stabilities of the Full Length Compounds ...................... 186
3.10 Model NMR Studies of Truncation and Thioester Exchange Reactions ......... 191
3.11 Bilayer Clamp Based Transport Activity Studies ............................................. 205
3.12 Conclusions and Future Work: Systems Using Dissipative Assembly ............. 217
References ...................................................................................................................... 222
Appendix 1: Experimental Details ................................................................................... 234
Appendix 2: Crystallographic Data .................................................................................. 289
Appendix 3 - NMR Spectra .............................................................................................. 319
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List of Tables

Table 1-1: Non-covalent interactions prevalent in supramolecular chemistry with
associated bonding strengths and schematic examples of each where appropriate. ..... 27

Table 2-1: Summary of the required stepwise association processes, their notation and
literature logK values for their association with copper(II) ions. In the graphical
representation to the processes the DPA and TERPY binding sites of the TERPY-DPA
ligand are represented by the red and blue termini respectively. ................................. 106

Table 2-2: Naming convention, derivation and values of equilibrium constants for
individual species as well as for species with the same stoichiometry used for the
speciation study of TERPY-DPA (2-42) self assembly in the presence of Cu2+ cations. .. 107

Table 3-1: Summary of synthesized compounds with associated numbers and naming
conventions. .................................................................................................................... 178
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List of Figures

Figure 1-1: The chemical structures of some representative phospholipid molecules. ... 2

Figure 1-2: The idealized 2-D structure of a lipid bilayer membrane composed entirely
of the phospholipid 1,2-dihexadecanoyl-sn-glycero-3-phosphocholine and a 3-D
representation of a small section of a lipid bilayer membrane.......................................... 3

Figure 1-3: The three dimensional volumes associated with the shape parameter S, a
structure of a representative for each class and their preferred arrangement within a
bent bilayer structure. The pink surface of the shapes indicates the polar head group
end of the molecule. A) Lipids with S < 1 represented by N-(hexadecanoyl)-sphing-4-
enine-1-phosphocholine, B) lipids with S = 1 represented by 1,2-diphytanoyl-sn-glycero-
3-phosphocholine and C) lipids with S > 1 represented by 1,2-dihexadecanoyl-sn-
glycero-3-phosphoethanolamine. ...................................................................................... 5

Figure 1-4: Cartoon representations of bilayer membrane environments and simplified
curves of potential energy versus position associated with the passage of a membrane
impermeable ionic species from one side of the lipid bilayer to the other in the case
where A) equal concentrations of the species are present on either side of the bilayer
and B) there is a concentration gradient from one side of the bilayer to the other. ........ 7

Figure 1-5: Simplified illustration of the effect of a representative ion transporter in this
case depicted as a transmembrane ion channel, on the shape of the potential energy
versus position profile for the movement on ions across the lipid bilayer membrane. .... 8

Figure 1-6: Some representative ion channels from literature; A) Tabushi’s original
amphiphilic β-cyclodextrin channel 23, B) Gokel’s 4,13-diaza-18-crown-6 containing
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hydraphiles 30, C) Cragg’s calixarene based channels 31, D) Fyles’ oligoester amphiphiles
32, E) Matile’s Pi slides 33, F) aplosspans also from Gokel 34, 35 and G) bola-amphiphiles
also from Fyles 36. .............................................................................................................. 14

Figure 1-7: Diagram representing the series of events involved in a vesicle based assay
using an entrapped ion sensitive fluorescent dye as the reporter as well as an associated
graph of transport data to demonstrate observations made at each stage of the
experiment. ....................................................................................................................... 17

Figure 1-8: Structure of 8-hydroxypyrene-1,3,6-trisulfonate in both its protonated and
deprotonated forms with associated wavelengths of maximum excitation and emission.
........................................................................................................................................... 18

Figure 1-9: Simplified diagram of the experimental set up of the bilayer clamp
experiment as well as corresponding current versus time recordings associated with
applied potentials at each of the stages of the set-up. .................................................... 19

Figure 1-10: The open duration versus conductance activity grid and representative ion
transport behaviors with associated colour code as developed by Fyles et al. for the
cataloging ion transport activities as obtained from bilayer clamp experiments 43. ....... 22

Figure 1-11: Sample activity grid analysis of a bilayer trace. By breaking down a trace
into smaller segments along the time axis individual or small collections of signals can be
systematically processed manually or using a computer program to generate activity
grids for each segment. The number of different events for the entire trace can then be
tallied and each square of the summary activity grid can be coloured the appropriate
colour and intensity to reflect the types and frequencies of observed activity. ............. 23