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Photoelectron Spectroscopy of Nitrogen Containing Molecules of Biological and Industrial Interest

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Photoelectron Spectroscopy of Nitrogen Containing Molecules of Biological and Industrial Interest ABCDEFF ABBCDEEFD EBB BADAEE EADEDBDEB EBBBEFEEDFEE ABB EFBFFEFEBBFEB BBEFEBBF ABBEFE BEFBF"#EFB BBBFEBBF ABBEFE C$DEE FFEBBFFE#EE#EEFE%EBB C$EF#C$EFFEBBF&'BFB&EF#FE (EF#C$EFFEBBF)F#E#*EEBFE+EF )EFEEFBFEBBF%##AE FEBBFF-E#&ED FEBBF"#EFB FEBBFFEFEBBFEB B !"" Photoelectron Spectroscopy of Nitrogen Containing Molecules of Biological and Industrial Interest Rui Montenegro Val-do-Rio Pinto December 2011 Photoelectron Spectroscopy of Nitrogen Containing Molecules of Biological and Industrial Interest Copyright c 2011 by Rui Montenegro Pinto, FCT/UNL and UNL. All rights reserved. Faculdade de Ciˆencias e Tecnologia and Universidade Nova de Lisboa have the perpetual right and with no geographic limitation, to archive and publish this dissertation using printed or digital copies, or by other known, or yet to be invented, method, and to divulge it through scientific repositories, and to admit its copy and distribution to educational or research proposes, not commercial, if the merit is attributed and recognized to the author and editor. The above copyright notice applies only to Chapters 1, 2, 3, 7 and 12. The remaining chapters are reproduced with permission from the original editors and subject to their own copyright restrictions. Acknowledgements The work presented herein would not be possible without the scientific supervision and patient guidance of Prof. Maria Lourdes Costa and Prof. Ant´onio Dias, to whom a word of sincere acknowledgement is given. My potential offspring as a scientific researcher is mainly due to them. The friendship and confidence demonstrated towards me throughout this years are on the basis of my own trust and achievements, and our successful operation as a team. Thank you both! To Prof. Jos´ePaulo dos Santos a very respectful thank you, for the first insights into quantum physics during my undergraduate years, to the support and help provided during the course of this thesis. The computational resources made available for the group were indispensable for completing this work. Prof. John Dyke and Dr. Grant Copeland are also acknowledged for the indispens- able support in the work performed in collaboration with the historical PES group, in the School of Chemistry of the University of Southampton. Their contribution was priceless and deeply appreciated. The University of Southampton is of course also acknowledged for the hosting conditions and research facilities. A special thanks to Dr. Marcello Coreno, Dr. Monica de Simone and Dr. Barbara Michela Giuliano, without whom the work performed at Elettra (in Trieste, Italy) would not be possible. Thank you for sharing the opportunity of making science in a totally different environment, in a large-scale open-lab, boiling from intense scientific activity. Thanks to the technical staff at Elettra, for providing good light conditions. A very special thanks to Prof. Maria Teresa Barros, Prof. Christopher Maycock and Dr. Paula Rodrigues, from Requimte-ITQB, FCT-UNL, for synthesizing the azido compounds, with renowned efficiency and improved ability. The work on the azides also benefited from the expertise and analysis of Prof. Maria Teresa Fernandez, Prof. Maria Filomena Duarte and Dr. Filipa Martins, from CQB, FC-UL. To Prof. Teresa Fernandez a special thanks for enlightening me with some important concepts behind mass spectrometry and radical formation. The majority of the work was performed at the Photoionisation Laboratory in the Department of Physics of FCT-UNL, therefore a great deal of respect and acknowl- edgement is due to this institution and all academic staff lecturing there, with special emphasis to the head of the department, Prof. Adelaide de Jesus. A special thanks to the people who indirectly contributed in various forms to this thesis, by occasionally clarifying my many questions: Prof. Augusto Moutinho, Prof. Orlando Teodoro, Prof. Ant´onio Paiva, Dr. Andr´eWemans, Dr. Cl´audia Quaresma, Juscelino Ferreira and Jo˜aoFaustino. To the masterful Mr. Jos´eCarlos Mesquita and the skilful Mr. Eduardo Jobling a very big thanks, for all the technical help provided, regarding the construction of electronic circuits and the machining of scientific equipment. To all the students who worked in the lab with me, specially Jo˜aoFranco and Carolina Matias. To all my colleagues and working comrades – Mauro Guerra, Diana Guimar˜aes, Pedro Amaro, and Susana Gomes, Diogo Almeida, Gon¸calo Martins, and Rodrigo Antunes – who struggle(d) to make a living out of making science, I express a very joyful thanks. You represent the second-order perturbation effect in a charge-transfer process, arising from the vibronic coupling of a ππ∗ transition, mediated by the “bofi˜ao” elementary particle in a ubiquitously spread Pb compound, deposited on a PCL matrix, a problem only treatable with the modified BEB approach in a two-photon transition framework; without you, things would not be as interesting or as funny as they were. Sincere thanks! To all my friends and family. To both my grandparents with whom I had the luck to grow and absorb history and inspiration. A warm embrace to my mother, for showing me how to put one’s heart in place of one’s head, at all the right times. A big hug to my father who, by example, taught me how to be curious and rationale in approaching and resolving life’s problems, and for his immense support. A special thanks to the shark princess for all the love and moments shared. Finally, I would also like to express my gratitude to Funda¸c˜aopara a Ciˆencia e Tecnologia (FCT) for the doctoral grant SFRH/BD/40308/2007 that allowed me to continue with my education. iv Abstract The work presented herein is based on the gas-phase spectroscopic characterization of several molecules of high nitrogen content which are relevant to organic synthesis, industry and fundamental research on molecular physics. It is mainly an experimental enterprise on selected organic azides and tetrazoles, with heavy support on theoretical results from readily available computational methods. Part of the work relies on the design and construction of scientific apparatus, which substantially improve the existing equipment and extend the limits of the experiment. The electronic structure and gas-phase thermal decomposition of methyl 2-azidopro- pionate (M2AP, N3CH3CHCO2CH3), benzyl azide (BA, C6H5CH2N3), 2-, 3- and 4- methyl benzyl azide (2-, 3- and 4-MBA, CH3C6H4CH2N3), 5-aminotetrazole (5ATZ, NH2CN4H), and 5-methyltetrazole (5MTZ, CH3CN4H) are investigated through photo- electron spectroscopy, using either He(I) (21.22 eV) or synchrotron radiation in the X- ray range. Relevant information obtained from mass spectrometry and matrix-isolation infrared spectroscopy is used to complement characterization of the samples. Regarding each molecules’ thermal decomposition, pathways are proposed which account for the observed end products. Conformational analysis is performed, and the special case of annular tautomerism is addressed in the tetrazole compounds. High-temperature pyrolysis work is performed in collaboration with the University of Southampton, and XPS analysis using synchrotron radiation is performed at Elettra, the multidisciplinary synchrotron light laboratory in Trieste, Italy. Experimental findings are rationalized using different computational methods, based on post-Hartree-Fock approaches: many-body perturbation theory (MPn), configura- tion interaction (CI) and Green’s function methods (OVGF, P3), as well as density functional theory (DFT), are used extensively to obtain optimized molecular geome- tries, ionization energies, orbital contours, relative energies, vibrational frequencies, and to assess possible pathways for thermal or electron impact fragmentation. Com- posite methods (Gn and CBS) are used to estimate to kcal mol−1 accuracy the energy balance between reactants, transition structures and products in the overall decompo- sition process of the specified molecules. Keywords: azides; tetrazoles; molecular physics; electronic structure; UVPES; XPS. vi Resumo O trabalho apresentado no ˆambito desta tese incide sobre a caracteriza¸c˜aoespec- trosc´opica de diferentes mol´eculas com grande quantidade de azoto, relevantes na s´ıntese qu´ımica de compostos orgˆanicos, na ind´ustria e em investiga¸c˜aofundamental na ´area da f´ısica molecular. Baseia-se, fundamentalmente, numa abordagem experimental `acar- acteriza¸c˜aode algumas azidas orgˆanicas e tetraz´ois, com vasto recurso a m´etodos com- putacionais. Parte do trabalho consiste no dimensionamento e constru¸c˜aode equipa- mento cient´ıfico que melhora substancialmente o equipamento existente e amplia os limites da experiˆencia. A estrutura electr´onica e a decomposi¸c˜aot´ermica em fase gasosa do metil 2-azido- propionato (M2AP, N3CH3CHCO2CH3), benzil azida (BA, C6H5CH2N3), 2-, 3- e 4-metil benzil azida (2-, 3- and 4-MBA, CH3C6H4CH2N3), 5-aminotetrazol (5ATZ, NH2CN4H) e 5-metiltetrazol (5MTZ, CH3CN4H), s˜aoinvestigados atrav´es da espec- troscopia de fotoelectr˜oes, recorrendo a radia¸c˜aoHe(I) (21.22 eV) ou de sincrotr˜ao na gama dos raios-X. As t´ecnicas de espectrometria de massa e de espectroscopia de infravermelhos em matriz-isolada s˜aoutilizadas como t´ecnicas complementares `acar- acteriza¸c˜aodos compostos. Relativamente `adecomposi¸c˜aot´ermica de cada mol´ecula, s˜aoapresentados trajec- tos de decomposi¸c˜aoque explicam a forma¸c˜aodos produtos detectados. E´ realizada a an´alise conformacional dos compostos, com especial enfˆase para o tautomerismo anular exibido pelos compostos tetraz´olicos. O processo de pir´olise a alta-temperatura
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