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Kamal Albdeery Final 23919.Pdf Abiogenically Relevant Self- Assembly Processes Within Silica Hydrogels KAMAL GASIM SHAALAN ALBDEERY Submitted in accordance with the requirements for the degree of Doctor of Philosophy The University of Leeds School of Chemistry September 2019 i The candidate confirms that the work submitted is his own, except where work which has formed part of jointly-authored publication has been included. The contribution of the candidate and the other authors to this work has been explicitly indicated below. The candidate confirms that appropriate credit has been given within the thesis where reference has been made to the work of others. Further details of the jointly-authored publication and the contributions of the candidate and the other authors to the work should be included below this statement. This copy has been supplied on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. The right of Kamal Gasim Shaalan Albdeery to be identified as Author of this work has been asserted by him in accordance with the Copyright, Designs and Patents Act 1988. © 2019 The University of Leeds and Kamal Gasim Shaalan Albdeery Reference for jointly authored publication 1. Gorrell, I.B., Henderson, T.W., Albdeery, K., Savage, P.M., Kee, T.P., Chemical Transformations in Proto-Cytoplasmic Media. Phosphorus Coupling in the Silica Hydrogel Phase. Life 2017, 7(4), 45. This paper contains material from Chapter 2 of this thesis. Specifically in includes some results from scanning electron microscopy, BET surface area measurements and dynamic light scattering studies on silica hydrogels that had been prepare for analysis via critical point drying. All the phosphorus chemistry in this paper was performed by IBG, TWH & PMS. TPK wrote the manuscript. 2. Amphiphilic Self-Assembly in the Silica Hydrogel Phase. Implications for Abiogenesis (based on material in chapter 3). K. Albdeery, S. Alanazi and T. P. Kee. Manuscript in preparation, to be submitted to Life 3. Molecular Diffusional Behaviour of Condensed Phosphates in the Silica Hydrogel Phase (based on material in chapter 5) K. Albdeery, George Hodgin and T. P. Kee. Manuscript in preparation, to be submitted to Life. ii Dedicated to… My dear mother Mrs Fatima Alsafi (may Allah bless her soul), your voice left me with tears since the early stage of my PhD journey but your soul will be with me forever. You were my first mentor and your words still touching my heart when remembers and may Allah give me strength and faith to hold what you learn me. I will always remember how you gently held my hand and help me to write my first letter ever. Thank you, mom, for everything and wish to gather in heaven. iii Acknowledgements I would like to express my sincere gratitude to my supervisor Dr Terence P. Kee for his time, patient, helping, encouragement, guiding and advice during my research time. I could not achieve this work without his unlimited support. Thanks are due to the Government of Iraq, Ministry of Higher Education and Scientific Research for their financial support of this work. The Iraqi cultural attaché in London for their support during my research time. I would like to thank my co-supervisor Dr Paul Thornton for his valuable advices, helping, support and efforts during my research time more especially when he spends hours to revise my previous reports. I would like to thank the love of my life, Mrs Anaam Alrakhat my wife and the mother of my three angels Ridha, Jaffar and Ayah, for her continuous support and unconditional love during my dark times. I would like to thank my dad, my brothers and my sisters for their unconditional love, support, and encouragement. My dear family, day after day, I realize how much you both sacrificed to give us a better life. I love you all from the bottom of my heart. I would like to thank Prof. Dejian Zhou and Prof. Patrick McGowan for them valuable corrections and feedback on my transfer report. In addition I would thank Mr Martin Fuller for helping me in critical point drying, Mr Stuart Micklethwaite for helping to perform scanning electron microscopy, Mr David Fogarty for help and support on the UV and Fluorescence spectroscopy instruments (and for reminding me to wear my lab coat and safety specs), Dr Algy Kazlauciunas for training on dynamic light scattering and performing the thermal analysis, Dr Angela Bejarano-Villafuerte and Dr Alex Kulak for helping in the SEM images, BET and EDX and Dr Mark Howred, Dr Mathias Nilsson, Dr Laura Castanar acedo and Gabriel Rossetto for their combined technical expertise in performing DOSY experiments. Finally, I would like to thank Mrs A. Luty and all staff members at the University of Leeds. iv Abstract In this thesis are presented studies which are aimed at elucidating the effects, if any, that the hydrogel phase has in influence chemical processes of relevance to abiogenesis over the aqueous phase. The significance of this is set in the light of the hydrogel hypothesis which suggests that the most primitive organisms would have emerged within a hydrogel environment rather than purely an aqueous one. Chapter 1 provides an introduction to the fundamental principles of interest to this work, discusses hydrogels, their synthesis, properties, applications and especially their potential role in abiogenesis. Also discussed are the concepts of amphiphilic self-assembly and molecular diffusions which are two molecular behaviours that have been looked at in most detail here. This chapter then concludes with some discussion of the analytical techniques used within the project. Chapter 2 describes the preparation of silica hydrogels (the main hydrogel used in this work) along with methods for isolating the silica matrix and surface analyses using electron microscopy and associated techniques (BET, EDX). This section also includes the results of dynamic light scattering and thermogravimetric studies on silica hydrogels. Chapter 3 outlines how amphiphilic self-assembly of a probe molecule, sodium dodecylsulphate (SDS), behaviour differs between the aqueous and silica hydrogel phases. This is achieved through measurements of critical micelle concentrations in both phases using UV-VIS spectrophotometry and colorimetric reporter dyes (merocyanine 540 and pinacyanol chloride). The key outcome being that CMC’s are definitively reduced in the salt-containing silica hydrogel over the pure aqueous phase. Chapter 4 describes investigations into a decolourisation phenomenon observed with the merocyanine 540 dye which says it complete colour bleach at high silicate concentrations of the hydrogel. Whilst the investigations did not produce a definitive answer to this issue it did highlight a protective role for amphiphiles in the decolourisation and also led, indirectly, to observations allowing us to probe gelation times using simple light scattering. Chapter 5 discusses the use of diffusion order spectroscopy (DOSY) as a technique for measuring and comparing molecular diffusion coefficients in both aqueous and silica hydrogel phases. Molecules of prebiotic significance such as the adenosine phosphates and condensed phosphates, AMP, ADP, ATP as well as the sugar d-ribose. Results suggest that direct measurements of v diffusion coefficients in the silica hydrogel phase is effective and offers a potentially useful tool for probing more complex diffusional behaviours. Chapter 6 contains the experimental details from Chapters 2-5 and Chapter 7 offers a summary, conclusions and future work perspective. Abbreviations ˚C degrees Celsius µL microliter µm micrometre 3D three dimensions Abs absorption ADP adenosine diphosphate AMP adenosine monophosphate ATP adenosine triphosphate BET Brunauer-Emmett-Teller (surface area analysis) CAC critical aggregation concentration CHC critical hydrogen-bonding concentration CMC critical micelle concentration CMC critical micelle concentration CP/MAS cross polarization and magic-angle spinning CPD critical point drying CVC critical vesicle concentration D2O deuterium water DLS dynamic light scattering; Z-average, size average DOSY diffusion-ordered spectroscopy DSC differential scanning calorimetry DTG differential thermogravimetry eV electron volts EXD energy dispersive X-ray vi FID Fourier Transformation of the imported GNAT general NMR analysis toolbox Gw Gaussian HR high resolution Hrs hours Hz hertz I intensity ICTAC The International Confederation for Thermal Analysis and Calorimetry K Kelvin LEMAS Leeds Electron Microscopy and Spectroscopy Centre lw Lorentzian M molar (moles per litre) MC540 merocyanine 540 MCs* excited singlet merocyanine 540 MHz megahertz Min minute mM millimoles per litre mS milliSiemens NIR near infrared nm nanometre NMR nuclear magnetic resonance PAH polycyclic aromatic hydrocarbon PC pinacaynol chloride PFG pulsed field gradient ppm part per million vii RF radio frequency SAXS small angle X-ray scattering SDS sodium dodcecylsulphate SEM scanning electron microscopy SGHs silica hydrogels SMO singlet molecular oxygen SOP standard operating protocol ST.Dev standard deviation STE stimulated echo TA thermal analysis TEM transition electron microscopy TGA thermogravimetric analysis UV-Vis UV-Visible WAXS wide angle X-ray scattering vii Table of Contents Chapter 1 Introduction and Background ................................................... 1 1.1 Hydrogels ......................................................................................... 1 1.1.1 Applications of silica hydrogels(SHGs) ..................................
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