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Terahertz Time Domain Spectroscopy of Amino Acids and Sugars

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Terahertz Time Domain Spectroscopy of Amino Acids and Sugars Terahertz Time Domain Spectroscopy of Amino Acids and Sugars Thesis by Matthew Kelley In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy California Institute of Technology Pasadena, California 2013 (Submitted April 23, 2013) ii c 2013 Matthew Kelley All Rights Reserved iii I dedicate this thesis to the Blake Lab, that it may help some poor graduate student find aid while working with THz-TDS or the laser system. iv Acknowledgements I would like to thank my labmates, as for many years they were few and far between. In particular, I will never forget working with Rogier Braakman on the hot electron bolometer, traveling to Hawaii and Australia, playing \pool ball" (a game we invented in Hawaii) watching and discussing the NBA far too much, or arguing endlessly because we were both hard-headed enough not to give in at all when we thought we were right. Daniel Holland has been my labmate for the longest period of time. Dan's many quirks and atypical opinions and practices always left things interesting. His attention to detail contrasts with my natural state, and really opened up a lot of holes in my thought processes and supposed knowledge. Dan constantly introduced me to new scientific experiments and concepts that he had read about. When I was going through tough personal times in 2010, Dan displayed genuine concern and compassion. I am very thankful to Dan for this display. While my labmates proved very helpful in thinking about science, mostly we shared a deep sense of camaraderie due to the academic situation that we were in. Namely, we were all in a lab situation where we were both completely untrained due to lack of senior students and had relatively little supervision. We also underwent a change in the direction of the lab in 2008 when ultrafast lasers were acquired. This is not to demean the intentions of our adviser, Geoff Blake. Geoff always wanted us to learn how to educate ourselves and to be capable of thinking of and executing our own research projects. This often meant giving us the opportunity to fail. He supported whatever interests v we had whether academic or not and often engaged us in discussion about bigger picture issues. Thanks also to Marco Allodi, the \new" student who was to be my replacement well over three years ago. In working with him and teaching him the ways of the lab, I found many holes in my own understanding of things and he helped to further refine the THz-TDS spectrometer. Thanks also to my more recent labmates: Brandon Carroll, Ian Finneran, Brett McGuire, and Sergio Ioppolo. I would also like to thank Laurence Yeung and Kana Takematsu, two of the other experimental physical chemistry students that entered graduate school at the same time that I did. We did problem sets together and remain friends and colleagues today. While academic support has been discussed, this section would be woefully incomplete if I left out the emotional support of my friends and roommates. In my first year, I lived in the Catalina Graduate Apartments with Mike Rubel. Mike was a nth year graduate student who helped me to weather the turmoil of settling into a new place and dealing with the realization that most people at Caltech must learn to accept | that I was not as smart as I though I was and had a lot to learn. Kana, Laurence and I also joined a group of people in weekly potlucks and games. Through the potluck group, I met Eve Stenson, Brian Standley, Jessie Rosenberg, and Neil Halelamien, and we rented a house together for several years, which we dubbed \The Keep." This became the default location for the weekly potlucks. During this time, I spent some time volunteering with the Caltech Y, specifically helping to run our monthly trips to Union Station, a homeless shelter in Pasadena, where we cooked rather complex meals for the residents. Kai Shen, the leader at the time, invited me to join Prufrock, an eating group at Caltech, in which we took turns cooking for each other once a month. I did join and met a variety of students from many disciplines in all years of study. In 2008 we were forced to move out of The Keep due to the real estate crisis of 2008 and I moved into the Prufrock house as a core member. Unfortunately, my stay there did not last long, as we lost the pest control battle to fleas and Caltech Housing vi decided to repurpose the house after presumably getting rid of the problem. I then moved back in with Neil and his brother Marvin in a new house. While I was very angered by the situation at the time, it was a good move for me, as I became very close with Neil and Marvin, and really felt like I had a home for the first time at Caltech. I should also mention the Caltech Floorball Club, of which I have been a member since late 2005. Physical activities have been very important to me at Caltech, but my involvement in most has been short-lived in comparison to Floorball. With Floorball, a game like indoor- hockey but played with a hollow plastic ball, I felt like a real part of a team and a community, along with having the opportunity to release stress through physical activity. A large part of this is due to Andrew and Meredith Beyer, my friends and the leaders of the club for many years. While we have never won a tournament, we have gotten close many times, and our skills have vastly improved. Lastly, I would like to thank Chris Nederveld and Alex Cheng, two of my closest friends, who I met playing online video games, for some of the most fun and carefree times I've ever had. My family, while physically distant during the process of obtaining my Ph D, have had perhaps the most impact on my success to date. Both my mother and father instilled in me the importance of education from a young age. I remember first becoming interested in astronomy | particularly in planets | in the third grade. My dad helped me to find books and pictures from telescopes in books at the library. Later, when I became interested in chemisty, he provided equal assistance in applying for college, scholarships, REU or SURF programs during the summer, and ultimately graduate school. But, perhaps what most enabled my success was the large amount of money put forth. My parents insisted that we go to good schools throughout our education, despite the cost, which was not always easy to bear. One of the biggest decisions in this regard was choice of high school. The school that I wanted to vii go to, and that was academically superior, also cost the most money of the prospects by a large margin. Through financial aid, my own work throughout high school, and my parents' willingness to spend a large portion of their money on education, I was able to attend. There, in AP Chemistry, I was inspired by my teacher, Dr. Claire Baker, to pursue physical chemistry in college. I also wish to thank my family for support during the tough times in my life, before and during graduate school, and, yes Mom, I am finally done now. viii Abstract A time-domain spectrometer for use in the terahertz (THz) spectral range was designed and constructed. Due to there being few existing methods of generating and detecting THz radi- ation, the spectrometer is expected to have vast applications to solid, liquid, and gas phase samples. In particular, knowledge of complex organic chemistry and chemical abundances in the interstellar medium (ISM) can be obtained when compared to astronomical data. The THz spectral region is of particular interest due to reduced line density when compared to the millimeter wave spectrum, the existence of high resolution observatories, and potentially strong transitions resulting from the lowest-lying vibrational modes of large molecules. The heart of the THz time-domain spectrometer (THz-TDS) is the ultrafast laser. Due to the femtosecond duration of ultrafast laser pulses and an energy-time uncertainty relationship, the pulses typically have a several-THz bandwidth. By various means of optical rectification, the optical pulse carrier envelope shape, i.e. intensity-time profile, can be transferred to the phase of the resulting THz pulse. As a consequence, optical pump-THz probe spectroscopy is readily achieved, as was demonstrated in studies of dye-sensistized TiO2, as discussed in chapter 4. Detection of the terahertz radiation is commonly based on electro-optic sampling and provides full phase information. This allows for accurate determination of both the real and imaginary index of refraction, the so-called optical constants, without additional analysis. A suite of amino acids and sugars, all of which have been found in meteorites, were studied in crystalline form embedded in a polyethylene matrix. As the temperature was varied between ix 10 and 310 K, various strong vibrational modes were found to shift in spectral intensity and frequency. Such modes can be attributed to intramolecular, intermolecular, or phonon modes, or to some combination of the three. x Contents Acknowledgements iv Abstract viii 1 Introduction 1 1.1 Terahertz Time Domain Spectroscopy . 8 1.1.1 Ultrafast Lasers . 10 1.1.2 Ultrafast Pulse Principles and Optics . 14 1.1.2.1 The Fourier Transform . 15 1.1.2.2 Dispersion and Chirp . 16 1.1.2.3 Pulse Shaping . 19 1.1.2.4 Nonlinear Effects . 20 1.1.2.5 Phase Matching .
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