nanotechnology and chiroptical spectroscopy to characterise optically active chiral metamaterials

Glasgow Theses Service http://theses.gla.ac.uk/ theses@gla.ac.uk Abdulrahman, Nadia Abdulkarim (2014) Nanotechnology and chiroptical spectroscopy to characterise optically active chiral metamaterials. PhD thesis. http://theses.gla.ac.uk/5480/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given I Nanotechnology and Chiroptical Spectroscopy to Characterise Optically Active Chiral Metamaterials By Nadia Abdulkarim Abdulrahman MSc. Physical Chemistry Submitted in the fulfilment of the requirements for the Degree of Doctor of Philosophy in the School of Chemistry Collage of Science and Engineering University of Glasgow May 2014 II Abstract Work in this thesis involves manipulating the interaction between light and matter in order to retrieve important information from adsorbed molecules, such as their structure and/or function, and henceforth, to gain insight into highly sensitive detection capabilities for biosensor applications. Such manipulation might be achieved via rationalising the surfaces of optically active metamaterials by taking full advantage of the recent growth in a variety of nanotechnology disciplines. As such, the possibility of characterising biomolecules adsorbed on the surface of chiral and achiral plasmonic metamaterials, referred to as chiral and achiral plasmonic nanostructures, have been investigated. Also, illustration and applications for the so called `Superchiral Field`, which has been generated via circular polarised light (CPL), are presented. Microscopic origin of the chiroptical second harmonic generation (SHG) signal that originates from the surface of the chiral nanostructures has been investigated. Practical visualisation via femtosecond laser beam of regions of intense plasmonic activity, i.e., hot-spot mapping, has been performed. In general, the work described in this thesis involved the use of several linear and non-linear chiroptical techniques namely as extinction (absorption and scattering), CD, ORD and SHG spectroscopy, in addition to scanning imaging namely SEM and AFM microscopy. Given that most biomolecules contain either chiral molecules or adopt chiral structures, the plasmonic nanostructures presented in this work could be used to study a wide range of biological problems, from the structure of biomolecules associated with neurodegenerative illnesses such as Alzheimer’s disease and Parkinson’s disease, to DNA and viruses. As a regard, general classifications for aspects of chirality are presented in order to emphasise the association of the samples used in this chapter with some of these aspects. All samples are fabricated via Electron Beam Lithography (EBL) in JWNC cleanroom/UK; the associated fabrication techniques, the instruments and the experimental methods are described. III Contents Abstract II Contents III Abbreviations used in this thesis VI Publications VIII Acknowledgements X Author`s Declaration XIII 1. Chapter 1: Introduction 1 1.1. Overview 1 1.2. Historical review 13 1.3. References 15 2. Chapter 2: The nanofabrication of plasmonic nanostructures by Electron Beam Lithography 17 2.1. Introduction 17 2.1.1. Electron Beam Lithography 17 2.1.2. Metamaterials 20 2.1.3. Surface plasmon 24 2.1.4. Plasmonic metamaterials 36 2.2. Theory and background 37 2.2.1. Electron beam-substrate surface interferences 37 2.2.2. Electron beam-PMMA resist interferences 40 2.2.3. Resist Development 46 2.2.4. Forms of morphological damages 47 2.3. Instruments 51 2.3.1. VB6 UHR WFE machine 51 2.3.2. Plassys II MEB550S E-beam Evaporator 54 2.3.3. Scanning Electron Microscope (SEM) 57 2.4. Pre-nanofabrication work 68 2.4.1. Pattern Design 68 2.4.2. Substrates preparations 75 2.4.3. Cleaning routine 76 2.5. Nanofabrication parameters 77 2.5.1. PMMA resist 77 2.5.2. Resist spin coating 81 2.5.3. The spot size, the VRU and the Dose parameters 84 2.5.4. Patterns writing 94 2.5.5. Wet etching 95 2.5.6. The Development 96 2.5.7. Metal deposition 99 2.5.8. Lifting off 100 2.6. Samples validation test 105 2.6.1. Influence of the nanopatterns shapes 105 2.6.2. Influence of the nanopatterns chiral orientation 106 2.6.3. Influence of the depth of the metallic layer 107 2.6.4. Pattern reproducibility 109 IV 2.6.5. Influence of the nanofeatures size on CD spectra 111 2.6.6. Compliments necessity 112 2.7. Summary 113 2.8. References 113 3. Chapter 3: Super Chiral Fields to Sense Biomolecules on Gold chiral plasmonic nanostructures via CD spectroscopy and scanning microscopy 117 3.1. Introduction 117 3.1.1. Chirality and biomolecules sensing 117 3.1.2. CD spectroscopy 118 3.2. Theory and background 119 3.2.1. Circular Dichroism (CD) and Optical Rotation (OR) 119 3.2.2. Theoretical aspects of the Superchiral Field 130 3.2.3. Superchiral Field to sense biological molecules 146 3.3. Experimental work 148 3.4. Results and discussions 151 3.4.1. Sensitivity to proteins with α-helical and β- sheet secondary structures 151 3.4.2. Sensitivity to proteins with high order structure level (quaternary structure) 165 3.4.3. Sensitivity to different stages of fibrils growth 168 3.4.4. Adsorption of insulin and a-synuclein on the surface of our nanostructures 178 3.5. Conclusion 180 3.6. References 181 4. Chapter 4:Induced Chirality through electromagnetic field coupling between chiral molecular layer and plasmonic nanostructures 183 4.1. Introduction 183 4.2. Theory and background 185 4.2.1. Theoretical model 185 4.2.2. Mechanism 193 4.2.3. Resonance band considerations 195 4.3. Experimental work 195 4.4. Results 204 4.4.1. Effect of material optical activity on chirality induction 204 4.4.2. Configure extinction spectra for the crosses 207 4.4.3. Configure extinction and CD spectra for FMN on quartz and the crosses substrates 209 4.4.4. Control measurements 210 4.4.5. Configure near-field length scale 212 4.4.6. Configure FMN coverage densities on the crosses substrates 213 4.4.7. Anisotropic factor (g-factor) consideration 214 4.5. Conclusion 217 4.6. References 218 V 5. Chapter 5: The origin of off-resonance non-linear optical activity of Gold chiral nanomaterials 221 5.1. Introduction 222 5.2. Theory and background 224 5.2.1. Linear and non-linear interactions of electromagnetic waves with surfaces 225 5.2.2. Theoretical aspects of the second harmonic generation signal from chiral surfaces 227 5.2.3. The SHG signals from plasmonic surfaces 235 5.3. Experimental work 236 5.3.1. Sample characterisation 238 5.3.2. The optics 239 5.4. Results and discussions 245 5.4.1. The Off-Resonance Configurations 245 5.4.2. Samples reference and SHG errors configurations 247 5.4.3. SHG signal from the gammadion patterns 249 5.4.3.1. Schematic and theoretical treatments to determine the enantiomer sensitivity from the s-out and p-out measurements 251 5.4.3.2. Theoretical treatments to determine electric dipole excitation-induced SHG signal from s-out measurements 260 5.5. Conclusion 262 5.6. References 263 6. Chapter 6: Femtosecond Laser Irradiation for Hot-Spot Mapping on the surface of Chiral Metamaterials 266 6.1 Introduction 266 6.2 Theory and background 269 6.2.1. Hot Spot Imprinting 269 6.2.2. Electromagnetic modelling for hot spot mapping 270 6.3 Experimental work 272 6.4 Results and discussions 273 6.4.1. The damage morphology (or the beam spot track (BST)) 273 6.4.2. Results are in good agreements with theoretical model 282 6.4.3. Hot spot mapping by using linearly polarised laser beam 284 6.4.4. Hot spot mapping by using circularly polarised laser beam 285 6.4.5. Comparison of results to the literatures 287 6.5 Conclusion 288 6.6 References 289 7. Chapter 7: Conclusion and future work 291 8. Appendix A: List of Tables 293 List of Tables in Chapter 2 293 List of Tables in Chapter 3 293 List of Tables in Chapter 5 294 VI 9. Appendix B: List of Figures 295 List of Figures of chapter 1 295 List of Figures of chapter 2 296 List of Figures of chapter 3 304 List of Figures of chapter 4 308 List of Figures of chapter 5 311 List of Figures of chapter 6 313 Abbreviations used in this thesis AAmyloid  peptide AFM Atomic Force Microscope APTS 3-Amino-Propyl-Triethoxy-Silane CARS Coherent Anti- Stokes Raman Scattering CD Circular Dichroism CPL Circularly Polarised Light DNA Deoxyribonucleic acid 2D Two Dimensions 3D Three Dimensions EBL Electron Beam Lithography ECD Electronic Circular Dichroism EPL Elliptically Polarised Light FEG Field Emitter Gun FIB Focused Ion Beam Lithography FMN Flavin Mononucleotide fs femto second FWHM Full-Width Half-Maximum HSQ Hydrogen Silses-Quioxane IPA Iso-Propyl Alcohol IR Infra- Red L Left LSPR Localized Surface Plasmon Resonance MD Molecular Dynamics MIBK Methyl Iso-Butyl Ketone VII n nano Nd:YAG Neodymium Doped Yttrium Aluminum Garnet OA-SHG Optically Active-Second Harmonic Generation OR Optical Rotation ORD Optical Rotary Dispersion PMMA Poly Methyl Meth-Acrylate pp paper page ps picosecond R Right R4 Racemic 4 ROA Raman Optical Activity RSC Resist Spin Coating SDS Sodium dodecyl sulphate SE Secondary Elactrons SEM Scanning Electron Microscopy SERS Surface-Enhanced Raman Scattering SH Second Harmonic SHG Second Harmonic Generation SPPs Surface Plasmon Poalretions SPR Surface Plasmon Resonance UV Ultra-Violet vAC Voltages Alternating Currents vDC Voltages Direct Currents VRU Variable Resolution Unit VCD Vibrational Circular Dichroism VIII Publications 1. Induced Chirality through Electromagnetic Coupling between Chiral Molecular Layers and Plasmonic Nanostructures Abdulrahman N. A., Fan Z., Tonooka T., Kelly S. M., Gadegaard N., Hendry E., Govorov A. O. and Kadodwala M., Nano Lett., 2012, Vol.12, pp (977−983). IX 2. The origin of off-resonance non-linear optical activety of a gold chiral nanomaterial. Nadia A. Abdulrahman, Christopher D.Syme, Calum Jack, Affar Karimuallh, Laurence D.Barron, Nikolaj Gadegaard and Malcolm Kadodwala. The Royal Society of Chemistry, Nanoscale, 2013, Vol.5, pp(12651-12657). [...]... 19] Finally, chiral scaffolds are blocks consisting of chiral and achiral elements, here either the chiral molecules bind to a cluster of the nanoparticles to enhance the optical chirality of the cluster (Figure 6 c) [9, 20], or oppositely, the nanoparticles are binding to helical molecules, such as strands of DNA, to follow its chiral arrangement (Figure 6 d) [9, 21], otherwise, 3D chiral metamaterials. .. left) In principle, the chirality observed in molecules can be attributed to four types of atomic configurations, namely: Chiral centre; Chiral axis; Chiral Helix; and Chiral plane For Chiral centre, Figure 1 illustrates an example of this configuration which is represented by the tetrahedral C atom For Chiral axis, when substituents spatially arranged around a fixed axis with a chiral fashion (i.e the... right handed chirality referred to as d (also written as (+)- [from dextrorotatory Latin dexter: right hand-side]) or left handed chirality referred to as l- (also written as (-)- [from laevorotatory Latin laevus: left hand-side]) In addition, Figure 1 illustrates how the absolute configurations (the spatial orientation) of the chiral centre could be assigned, following Cahn-Ingold-Prelog system, to be... left handed handedness (L) configuration b illustrates how the two twisted ends of the J`s nanostructures could be numbered and then joined up by the black arrows to end up with either right handed handedness (R) or left handed handedness (L) configuration c illustrates how the negative tone areas (the black areas) for the G`s nanostructures could be numbered and then joined up by the red arrows to end... of optically pure molecular compounds, i.e single enantiomer molecular compounds, is essential in the pharmaceutical and drug industries [9] In essence, the characterisation of optically pure molecular compounds means to gain insight into the chiroptical effect associated with chiral compounds Chiral plasmonic nanostructures are potentially useful platforms to sense chiroptical effects As such, chiral. .. setting is arranged for a chiral environment As such, it is required to have the wave vector ̂ , the surface normal ̂, and the light polarization vector ̂ arranged together to exhibit pseudochirality, as shown by 2-docosylamino-5-nitropyridine molecules (Figure 6 a) [9, 17], or further, to exhibit extrinsic chirality which was shown in split ring nanostructures (Figure 6 b) [9, 18], and more examples can... accompanying which was essential to satisfy safety and security policy in the JWNC cleanroom I could not, and will never be able to, find words to thank my God, ALLAH, for his great gift; this is my family Many thanks should go to a patient and supportive mother and father; sister and two brothers, it`s much appreciated Without doubt, great thanks should go to my husband, Dr Karwan Sahibqran, who suffered... interest and this is one of the main reasons for the work described in this thesis In order to investigate the chiroptical properties of chiral molecules, one may transpose the concepts of natural chirality to artificial nanostructured surfaces In principle, the general concepts of chirality (natural and artificial) have been termed in six classes so far, namely as: helical chirality/propellers, helical chirality/spirals,... 240 300 270 Figure 4: SHG spectra for right handed gammadions(R-gammadions (red)) and left handed gammadions (L-gammadions (blue)) as well as for right handed G`s (R-G`s (red)) and left handed G`s (L-G`s (blue)) Clearly, nanostructures with right hand handedness have very comparable spectra (Butterfly like shape) Similarly, nanostructures with left hand handedness have very comparable spectra 7 Chapter... a reporter atom, see Figure 2b Then, following the rules of mass priority system described in Figure 1, we should create an arc from the atom attached to the reporter to the atom of the substituted group, and see (view the arc path from the reporter atom toward the chiral plane) if the arc orientation is clockwise or anticlockwise For cyclophane the orientation of the arc is clockwise and hence, the . Abdulkarim (2014) Nanotechnology and chiroptical spectroscopy to characterise optically active chiral metamaterials. PhD thesis. http://theses.gla.ac.uk/5480/ Copyright and moral rights. adsorbed on the surface of chiral and achiral plasmonic metamaterials, referred to as chiral and achiral plasmonic nanostructures, have been investigated. Also, illustration and applications for. molecule can have right handed chirality referred to as d (also written as (+)- [from dextrorotatory. Latin dexter: right hand-side]) or left handed chirality referred to as l- (also written