Ultrafast Excited State Reaction Dynamics in Light Driven

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Declaration, I declare that the work contained in this thesis submitted by me for the degree of Doctor of. Philosophy is my work except where due reference is made to other authors and has not. previously been submitted by me for a degree at this or any other university. Jamie Conyard,Acknowledgements, Firstly I would like to thank my supervisor Prof Steve Meech for his constant guidance and. support over the duration of my time at UEA as both a postgraduate and undergraduate. Without Steve s influence I do not believe I would have had the confidence to even. undertake a PhD I am also indebted to Dr Ismael Heisler for teaching me the background of. ultrafast spectroscopy from the very basics for his constant help with the experimental set. ups and data analysis and for his general support with all aspects of my PhD studies A huge. thanks is also owed to Dr Andras Lukacs for teaching me the transient absorption set up and. his continued support with the system long after he left UEA. I also extend my thanks to all members of the Meech research group past and present Kiri. Francesca Kamila Ismael Andras Leo Minako and Mike for their friendship and support. over the past 4 years, I thank our collaborators on the molecular motor project Prof Ben Feringa and his research. group with special thanks to Arjen Cnossen for the synthesis of the samples and Dr Wesley. Browne for his advice and support on all aspects of the project I also thank our collaborators. on the GFP project Dr Kyril Solntsev and his research group with special thanks to. Anthony Baldridge for the synthesis of the HBDI samples. Finally I am infinitely grateful to my family and friends for their encouragement and support. in everything that I do In particular my parents and sister I would not have made it through. the last few months of my studies without them, Excited state dynamics on an ultrafast timescale can provide insight into primary events in. photochemical and photobiological processes In this work excited state dynamics of two. important systems are characterized unidirectional molecular rotary motors and HBDI. derivatives synthetic chromophores of the green fluorescent protein GFP In both cases. the excited state is selectively probed by ultrafast fluorescence up conversion with a time. resolution better than 50 fs, Molecular motors have biphasic sub picosecond and picosecond fluorescence decays and.
oscillations attributed to excitation of coherently excited vibrational modes The fluorescence. data were contrasted with excited state decay and ground state recovery kinetics recorded. using ultrafast transient absorption Combining these experimental data with substituent. dependence and solvent dependence studies as well as existing calculations we proposed a. coupled two state model for dynamics on the excited state potential energy surface These. data have implications for the design and optimisation of optically driven molecular motors. A molecular propeller was also studied and shown to be more sensitive to medium friction. than the motor, The GFP experiments focused on determining the effect of alkyl substitution upon excited. state dynamics of HBDI HBDI in solution exhibits a very low quantum yield compared to. the chromophore in its protein environment Large alkyl substituents were found to shift the. spectra but to exhibit only small retardation effects upon the excited state decay time even in. highly viscous solvents This supports an assignment of a volume conserving isomerization. mechanism promoting radiationless decay Substituents which distort the planar structure of. the chromophore lead to an enhanced radiationless decay This provides further evidence for. a link between radiationless decay of the excited state and twisting of HBDI. 1 Introduction 1,1 1 Molecular Motors and Machines 1. 1 2 The Green Fluorescent Protein 6,1 3 Excited State Structural Dynamics 9. 1 3 1 Excited State Isomerisation 9, 1 3 2 Solvent Friction Effects upon Photoisomerization 12. 1 3 3 Solvation Dynamics 16,1 3 4 Vibrational Coherence 18.
1 4 References 21,2 Experimental 27, 2 1 Ultrafast Time resolved Fluorescence Up conversion 27. 2 2 Ultrafast Transient Absorption 31,2 2 1 White Light Continuum Generation 32. 2 2 2 CCD Detection 33,2 2 3 Data Readout 36, 2 2 4 CCD Calibration for Conversion of Pixel Column to Wavelength 38. 2 3 Data Analysis 39,2 3 1 Fluorescence Up conversion 39. 2 3 1 1 Fluorescence Decay Fitting 39,2 3 1 2 Error Analysis 43.
2 3 1 3 Time Dependent Fluorescence Spectra 45,2 3 2 Transient Absorption 51. 2 3 2 1 Coherent Artefact 53,2 3 2 2 Fitting of Time Domain Data 55. 2 3 2 3 Error Analysis 56,2 4 Sample Preparation 58. 2 4 1 Molecular Motors 58,2 4 2 HBDI Derivatives 58. 2 5 References 58, 3 Excited State Dynamics of a Unidirectional Molecular Rotary Motor 61.
3 1 Introduction 61,3 2 Experimental 65,3 3 Results and Discussion 68. 3 3 1 Steady State Spectroscopy 68,3 3 2 Ultrafast Fluorescence Up conversion 71. 3 3 2 1 Time Dependent Emission Spectra 77,3 3 2 2 Bi modal Fluorescence Decay 80. 3 3 2 3 Coherent Oscillation 81,3 3 3 Transient Absorption Spectroscopy 85. 3 3 4 Solvent Dependence 89,3 4 Conclusion 99,3 5 References 100.
4 Excited State Dynamics of Substituted Unidirectional Molecular. Rotary Motors 103,4 1 Introduction 103,4 2 Experimental 106. 4 3 Results and Discussion 107,4 3 1 Steady State Spectroscopy 107. 4 3 2 Ultrafast Fluorescence Up Conversion Spectroscopy 110. 4 3 3 Ultrafast Transient Absorption Spectroscopy 123. 4 3 3 1 Stimulated Emission 131, 4 3 4 A One Dimensional Model for Substituent Dependent Motor Dynamics 135. 4 3 5 Model Scheme of Excited State Relaxation and Solution of Kinetic Rate. Equations 139,4 3 6 Solvent Dependence 143,4 4 Conclusion 155. 4 5 References 157, 5 Excited State Dynamics of a tri phenylacetylene Substituted Molecular.
5 1 Introduction 159,5 2 Experimental 160,5 3 Results and Discussion 161. 5 3 1 Steady State Spectroscopy 161, 5 3 2 Ultrafast Fluorescence Up conversion Spectroscopy 162. 5 3 3 Ultrafast Transient Absorption Spectroscopy 169. 5 4 Conclusion 176,5 5 References 177, 6 Excited State Dynamics of 9 9 bifluorenylidene 179. 6 1 Introduction 179,6 2 Experimental 181,6 3 Results and Discussion 181. 6 3 1 Steady State Spectroscopy 181, 6 3 2 Ultrafast Fluorescence Up conversion Spectroscopy 182.
6 3 3 Transient Absorption Spectroscopy 188,6 4 Conclusion 199. 6 5 References 201, 7 Photodynamics of Alkyl Substituted Derivatives of the GFP. Chromophore 203,7 1 Introduction 203,7 2 Experimental 208. 7 3 Results 209, 7 3 1 Steady State Absorption of HBDI derivatives 209. 7 3 2 Steady State Fluorescence 214,7 3 3 Ultrafast Time Resolved Fluorescence 217.
7 3 3 1 Emission Wavelength Dependence 221,7 3 3 2 Viscosity Dependence 223. 7 3 4 DFT Calculations 227,7 4 Conclusion 229,7 5 References 231. 8 Summary and Outlook 203,1 Introduction, In this thesis we describe the excited state dynamics of two molecular systems a synthetic. molecular motor and the chromophore of a photoactive protein Photoisomerization. underpins the excited state dynamics of both of these systems It is the aim of this work to. gain a better understanding of the molecular dynamics on the excited state potential energy. surface which facilitate isomerization in each system To do so ultrafast time resolved. spectroscopy is employed,1 1 Molecular Motors and Machines. Significant breakthroughs in molecular biology over the past two decades have revealed that. biological motors drive numerous modes of movement throughout nature For example. muscle contraction 1 2 intracellular transport3 and the movement of some bacteria Flagella. motor 4 5 are just a small number of the processes in which biological motors are key These. motors typically convert chemical energy into mechanical energy thus fuelling movement at. the molecular level One of the most important motors is ATP synthase 6 7 This protein acts as. a biological molecular rotary motor and is intimately involved in the synthesis and hydrolysis. of ATP which is the primary method for storing and releasing chemical energy throughout. nature 8 A schematic representation of the motor function of ATP synthase is shown in Figure. 1 1 reproduced from Reference 9 Such discoveries have prompted extensive attempts to. design synthetic systems capable of replicating the controllable molecular motion which is so. elegantly employed by nature Clearly this is very challenging not least because it requires an. input of energy into the system which selectively drives only specific motions out of the. numerous possible degrees of freedom 10 Despite these significant difficulties remarkable. progress has been made in this field over the past decade. Figure 1 1 A schematic representation of the functioning of ATP synthase The rotational. motion facilitates conformational changes which allow sequential substrate binding ATP. formation and ATP release This figure is reproduced from Reference 9. Numerous synthetic systems have been designed in which controllable molecular motion is. achieved and functioning molecular switches shuttles and motors have been developed 11. Molecular switches use input energy to undergo a selectively reversible structural change. between two forms 12 Light has proven to be the most commonly used source of energy for. molecular switches Photochromism the light driven reversible change of a chemical species. between two forms with different absorption spectra13 is the key principle behind the. functionality of such switches Photoisomerization is one of the key processes which. facilitates photochromism in such molecular devices 14 If each form of the switch exhibits a. well resolved absorption spectrum the irradiation wavelength can be tuned in order to. selectively induce a photoisomerization reaction of one form to the other Ideally the reaction. occurs with a high photochemical quantum yield and is reversible so that the switch can be. reset Light activated molecular switches have a number of potential applications including. sensors and data storage Numerous examples of molecular switches driven by light have. been described 12 14 16 Particular success has been found with switches based on the. photoisomerization of azobenzene 12 17 18 In this system it has been demonstrated that energy. input can be harnessed to fuel controllable and reversible mechanical motion on a molecular. Molecular shuttles are supramolecular structures which use input energy to transfer cargo. molecules ions or electrons from one location of the structure to another 19 Although a. variety of energy sources have been demonstrated including redox potential20 and pH 21 the. most widely used is light 11 Thus far the most successful molecular shuttle design is based. upon rotaxanes 22 24 Rotoxanes are supramolecular structures which consist of a central. macrocycle mechanically locked between two end groups termed stations along a linear. thread termed a track Figure 1 224 shows a schematic representation of a rotaxane. molecular shuttle where naphthalimide ni grey and succinamide succ green are two. stations separated by an alkyl chain track In the ground state naphthalimide has a poor. hydrogen bond affinity for the central macrocycle As a result the macrocycle ring is. predominantly 99 bound to the succinamide station However light is used to induce a. significant increase in the hydrogen bond affinity of the macrocycle to the naphthalimide. station Excitation of the naphthalimide station results in intersystem crossing to form a triplet. state The triplet state is then reduced by an external electron donor group 1 4. Diazabicyclo 2 2 2 octane in this case to form a radical anion state of the naphthalimide. station The hydrogen bond affinity of the macrocycle for the radical anion naphthalimide. station then surpasses that of the succinamide station. Figure 1 2 Schematic representation of the shuttling function of a rotaxane molecular. shuttle Excitation of the naphthalimide station ni leads to intersystem crossing to a triplet. state Reduction by an external electron donor 1 4 Diazabicyclo 2 2 2 octane generates a. radical anion state of the ni station The macrocycle affinity is higher for the ni radical. anionic compared to the succinimide station si resulting in shuttling from the si to the ni. station Charge recombination between the radical anion of ni and the radical cation of the. electron donor results in the reversal of this process with the macrocycle returning to the si. station This figure is reproduced from Reference 24. As a result the macrocycle is shuttled along the track from the succinamide station to the. naphthalimide station on a 1 s timescale Charge recombination between the radial anion of. the naphthalimide station and the radical cation of the donor reverses this process with the. macrocycle returning to the succinamide station on a 100 s timescale This is yet another. key example of utilising light as an energy source for controllable motion on a molecular. The concept of driving molecular motion in a selective and controllable manner has been. extended to the design of molecular motors In order to mimic the motor action of biological. motors such as ATP synthase synthetic structures must harness input energy to fuel repetitive. Ultrafast Excited State Reaction Dynamics in Light Driven Unidirectional Rotary Molecular Motors and Fluorescent Protein Chromophores Jamie Conyard School of Chemistry University of East Anglia Norwich UK 2013 A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy at the University of East Anglia

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