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Development and Characterization of Fullerene Based Molecular Systems Using Mass Spectrometry and Related Techniques

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Development and Characterization of Fullerene Based Molecular Systems Using Mass Spectrometry and Related Techniques UNIVERSITY OF LIEGE Faculty of Applied Sciences Mass Spectrometry Laboratory Professor E. DE PAUW Development and Characterization of Fullerene Based Molecular Systems using Mass Spectrometry and Related Techniques by Jean-François Greisch Civil Engineer Dissertation submitted to obtain the degree of Doctor of Philosophy in Applied Sciences July 2008 Abstract The investigation and control of the properties of carbon based materials such as fullerenes and nanotubes is a highly dynamic research field. Due to its unique properties, e.g. an almost nano-dimensional size, three-dimensional cage topology, hydrophobicity, rich redox- and photochemistry, large absorption cross section, … C 60 has a high potential as building block for molecular devices and biological applications. It can be functionalized, anchored to a surface and self-assembled into larger supramolecular entities, such as monolayers. Mass spectrometry and related techniques such as ion-molecule reactions, action spectroscopy and ion mobility have been used throughout this work to study fullerene based systems, ranging from hydrides, derivatives, non-covalent complexes and coordinated metal complexes. Simulations predicting structural, electronic and mechanical properties have been combined with the experimental results to assist in their analysis and interpretation. Using ion molecule reactions, the reactivity of gas phase C 60 anions with methanol has been studied. Hydride formation by simple collisions in the gas phase with methanol as well as reversible dehydrogenation by infrared multiphoton activation has been demonstrated. C60 functionalization by 3’-azido-3’-deoxythymidine (AZT) has been performed and the charged product characterized both by collisional activation and action spectroscopy. Deprotonation has been shown to lead to rearrangements of the nucleoside analogue and to a subsequent charge transfer to the fullerene. To prevent unwanted rearrangements and side reactions, encapsulation of C 60 is suggested, the host molecule acting as a steric barrier. C60 complexation by γ-cyclodextrins has been performed and the ions of the complexes characterized both by collisional activation and ion mobility. It has been demonstrated that, compared to deprotonated species, the sodiated C60 :( γ-cyclodextrin) 2 ions were highly compact structures. With only two small polar caps accessible to reagents, sodiated C60 :( γ- cyclodextrin) 2 complexes sterically protect the C 60 core from unwanted side reactions. Finally, explorative work on C60 immobilization on silver colloids using surface enhanced Raman spectroscopy and on the characterization of C60 complexes with iron and manganese porphyrin is presented. i If you hit a wall and find no way out, Look afar, dream larger, you’ll find a way. ii Acknowledgements I would like to express my deepest gratitude to my supervisor Professor Edwin De Pauw for his support and advice, for the latitude allowed to experiment and develop personal approaches and for giving access to wonderful top equipment. His guidance has prepared me well for the challenges that lie ahead. I am ever so grateful to FNRS Director of Research Françoise Remacle for the time spent reading and discussing my work, and for giving me fruitful input. Enlightening discussions with Professor Bernard Leyh are also deeply acknowledged. Furthermore I would like to thank Professor Michael T. Bowers and Dr. Thomas Wyttenbach (University of California Santa-Barbara) for allowing me to perform ion mobility measurements on their equipment. Professor Rainer Weinkauf (Heinrich Heine University Düsseldorf) is also deeply acknowledged for letting me use his equipment for electron detachment measurements and for enlightening discussions. The members of the De Pauw group, both past and present, are also given thanks for their insights on various issues as well as for their friendship. To the “Lab 4” cluster, Gabriel and Dominique, thanks for never letting there be a dull moment! Finally, I wish to express my affectionate thankfulness to my parents for their love, understanding and constant support. iii Publications •- J. F. Greisch, B. Leyh, F. Remacle, E. De Pauw, Reversible C 60 hydrogenation by methanol: a gas phase study. Submitted. J. F. Greisch, B. Leyh, E. De Pauw, Collision induced dissociation of deuterium enriched protonated 2’-deoxyguanosine. European Physical Journal D. (2008) Accepted . J. F. Greisch, S. Kyritsoglou, B. Leyh, E. De Pauw. Mass spectrometric study of the ionized C60 : ( γ-cyclodextrin) 2 inclusion complex by collision induced dissociation. Journal of Mass Spectrometry . 43 , 242 (2008). J. F. Greisch, R. Weinkauf, E. De Pauw, E. S. Kryachko, F. Remacle. Charge distribution in 3'-deoxythymidine-fullerene: Mass spectrometry, laser excitation, and computational studies. Israel Journal of Chemistry . 47 , 25 (2007). J. F. Greisch, E. De Pauw. Mass spectrometric characterization of 3 -imino[60]fulleryl-3 deoxythymidine by collision induced dissociation. Journal of Mass Spectrometry . 42 , 304 (2007). J. F. Greisch, V. Gabelica, F. Remacle, E. De Pauw. Thermometer ions for matrix-enhanced laser desorption/ionization internal energy calibration. Rapid Communications in Mass Spectrometry . 17 , 1847 (2003). iv Table of Contents Chapter 1. General Introduction …………………………………………………… 1 1.1. Molecular Devices and C 60 Based Sensors …………………………… 2 1.2. Thesis Scope …………………………………………………………… 6 Chapter 2. Mass Spectrometry …………………………………………………… 12 2.1. Time-of-Flight (ToF) …………………………………………………… 12 2.2. Linear quadrupole and quadrupole ion trap …………………………… 14 2.2.1 Linear quadrupole (Q) …………………………………… 17 2.2.2 Quadrupole ion trap (QIT) …………………………………… 18 2.2.3 The ion trajectories …………………………………………… 19 2.3 Fourier transform – ion cyclotron resonance (FT-ICR) …………… 23 2.4 Electrospray ionization …………………………………………… 26 2.5 Gas phase techniques related to mass spectrometry …………………… 29 2.5.1 Collisional activation (CA) …………………………………… 29 2.5.2 Infrared multiphoton activation (IRMPA) …………………… 31 2.6 Practical limitations …………………………………………………… 31 Chapter 3. Quantum chemical modelling of molecular properties …………………… 37 3.1 The Born-Oppenheimer approximation …………………………… 37 3.2 The Hartree-Fock method …………………………………………… 38 3.3 Post Hartree-Fock methods …………………………………………… 42 3.4 The semi-empirical MNDO-PM3/PM6 methods …………………… 42 3.5 The Density Functional Theory …………………………………… 43 3.6 Geometry optimization and vibrational modes …………………… 45 3.7 Vibrational spectroscopy …………………………………………… 48 3.7.1 Infrared spectroscopy …………………………………………… 50 3.7.2 Raman spectroscopy …………………………………………… 50 Chapter 4. Ion-molecule reaction studies …………………………………………… 55 4.1. Collision induced dissociation of deuterium enriched protonated 2’- deoxyguanosine …………………………………………………………… 56 4.1.1. Experimental …………………………………………………… 61 4.1.2. Results …………………………………………………………… 64 4.1.2.1. Unlabelled 2’-deoxyguanosine …………………… 64 2 2 2 4.1.2.2. [1’- H]2’-, [2’,2’’- H2]2’-, and [5’,5’’- H2]2’- v deoxyguanosine …………………………………………… 65 4.1.2.3. 2’-deoxyguanosine with partial or total exchange of the labile hydrogen atoms …………………………………………… 65 4.1.3. Discussion …………………………………………………… 69 4.1.3.1. Labelled 2’-deoxyguanosine …………………………… 70 4.1.3.2. 2’-deoxyguanosine with partial or total exchange of the labile hydrogen atoms …………………………………………… 71 4.1.3.3. Kinetic Isotope Effect (KIE) …………………………… 72 4.1.4. Conclusion …………………………………………………… 76 4.2. Gas phase formation of fullerene hydrides by reaction of C 60 anions with methanol at room temperature …………………………………………… 78 4.2.1. Experimental …………………………………………………… 82 4.2.2. Results …………………………………………………………… 85 4.2.3. Discussion …………………………………………………… 89 4.2.4. Conclusion …………………………………………………… 99 Chapter 5. Covalent modification of C 60 …………………………………………… 105 5.1. Synthesis and mass spectrometric characterization of 3’-imino[60]fulleryl- 3’-deoxythymidine …………………………………………………………… 106 5.1.1. Experimental …………………………………………………… 109 5.1.2. Results …………………………………………………………… 111 5.1.3. Discussion …………………………………………………… 118 5.1.4. Conclusion …………………………………………………… 122 5.2. Characterization of 3’-imino[60]fulleryl-3’-deoxythymidine using electron photo-detachment and ab-initio calculations …………………………………… 123 5.2.1. Experimental and modelization …………………………… 125 5.2.2. Results and discussion …………………………………………… 127 5.2.3. Conclusion …………………………………………………… 136 Chapter 6. Non-covalent complexes of C 60 …………………………………………… 142 6.1. Synthesis and mass spectrometric characterization of the C60 :( γ-cyclodextrin) 2 inclusion complex …………………………………… 150 6.1.1. Experimental …………………………………………………… 153 6.1.2. Results …………………………………………………………… 154 6.1.3. Discussion …………………………………………………… 162 6.1.4. Conclusions …………………………………………………… 171 vi 6.2. Cross Section Measurements of the C 60 :( γ-CyD) 2 complex using gas phase ion mobility …………………………………………………………………… 171 6.2.1. Experimental and Theoretical …………………………………… 179 6.2.2. Results …………………………………………………………… 187 6.2.3. Discussion …………………………………………………… 195 6.2.4. Conclusion …………………………………………………… 199 Chapter 7. Interactions of C 60 with transition metals …………………………………… 208 7.1. Surface-enhanced Raman spectroscopy of 3’-imino[60]fulleryl-3’- deoxythymidine …………………………………………………………… 212 7.1.1. Experimental …………………………………………………… 213 7.1.2. Results and Discussion …………………………………… 215 7.1.3. Conclusion …………………………………………………… 218 7.2. Coordination of transition metals with C 60 …………………………… 219 7.2.1. Experimental …………………………………………………… 221 7.2.2. Results and Discussion …………………………………… 222 7.2.3. Conclusion ……………………………………………………
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