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Conformational and UV photochemistry studies of amino acids in matrix-isolation FTIR spectroscopy Toh, Shin Yi 2016

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Conformational and UV Photochemistry Studies of Amino Acids inMatrix-Isolation FTIR SpectroscopybyShin Yi TohB.Sc. Chemistry, The University of British Columbia, 2012A THESIS SUBMITTED IN PARTIAL FULFILLMENTOF THE REQUIREMENTS FOR THE DEGREE OFMaster of ScienceinTHE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES(Chemistry)The University of British Columbia(Vancouver)July 2016c© Shin Yi Toh, 2016AbstractThe existence of amino acids in interstellar space has been a hot topic among researchers in astronomicalscience because of the biological molecules relevance to the origin of life. One of the most popular toolsemployed for the study of amino acids in relation to interstellar chemistry is matrix-isolation spectroscopy,as the cold and isolated environment provided by the matrix crystal mimics various astrophysical media suchas interstellar ice. In the presented work, we reported the conformational and UV photochemistry studiesof b -alanine and a-alanine via matrix-isolation Fourier transform infrared (MI-FTIR) spectroscopy in solidparahydrogen. This is the first time b -alanine and a-alanine have been registered in parahydrogen matrices,and the crystal has proven to be a more beneficial host over argon matrices for conformational analysis andin-situ UV irradiation experiment. Our claim on the superiority of solid parahydrogen is supported by thedetection of high energy amino acids conformers in solid parahydrogen, which are unobserved in noble gasmatrices. These conformers are conformer III for b -alanine, and conformer VI and V for a-alanine. Asfor UV irradiation experiment in solid parahydrogen, we obtained predominantly conformational changefor b -alanine. However, a-alanine underwent complete photodestruction to give CO2 and other unknownphotoproducts we are still attempting to identify. Finally, we observed the possibility of b -alanine zwitterionformation in parahydrogen matrices, and are currently in the process of performing high accuracy quantumcalculations on several b -alanine zwitterion conformers to assist us in spectral assignment.iiPrefaceAll the work presented henceforth was conducted under the supervision of Dr.Takamasa Momose in theChemistry Department of University of British Columbia, Point Grey campus.The parahydrogen converter used in this project was designed and built in the year 2008 by Dr.Momoseand his associates Dr.Brian A. Tom, Mr.Siddharta Bhasker, and Dr.Benjamin J. McCall from Universityof Illinois, and Dr.Yuki Miyamoto from University of British Columbia. The figures of the converter inChapter 3. Figures 3.1 and 3.2 are used with the permission from Tom et al. [1] on the groups detailedpublication of the converter design. The cryogenic sample chamber, the Knudsen cell, and the housing fordeuterium lamp used in this project were designed and built by our lab technician, Mr.Pavle Djuricanin. TheFTIR spectrometer used in the project is from the company Bruker Cooperation, and was assembled andcalibrated by Dr.Momose and Mr.Djuricanin in the year 2011.Ms.Angel Ying-Tung Wong and I were the lead investigators for the projects located in Chapter 5.Sections 5.1 and 5.2. where we designed the experiments, collected the data, performed the major analysisand quantum computations, and composed the manuscripts, with equal responsibilities. Ms.Ellen Chua hasassisted us in some of the computational works for the projects. A version of Chapter 5. Section 5.1 hasbeen published [2], and the preliminary analysis of the project was included in Ms.Wong’s bachelor’s thesis[3]. A journal manuscript of the result from Chapter 5. Section 5.2 has also been written for publication inthe near future [4].The projects presented in Chapter 5. Sections 5.3 and 5.4 were my original works. I was responsiblefor the major areas of experimental design, data collection, spectra analysis, quantum calculations, andmanuscript composition. Mr.Brandon Moore has assisted me in some computation and analysis works forthese projects.The project described in Chapter 7. Section 7.2 was a collaboration work with Dr.Shang-Chen Huangfrom National Chiao Tung University. The liquid He cooled cryogenic sample chamber were designedand built by Dr.Momose, and was modified by Mr.Djuricanin. Dr.Huang and I has input some set-upsmodification and reconstruction ideas, and were responsible for the experimental design, data collection,spectra analysis, quantum calculations, and manuscript composition, with equal contributions. Ms.JanetLeung has assisted us in some computation and analysis works for this project.iiiTable of ContentsAbstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iiPreface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iiiTable of Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ivList of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viiList of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viiiList of Abbreviations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiAcknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32.1 Matrix-Isolation Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32.1.1 Fourier Transform Infrared (FTIR) Spectroscopy . . . . . . . . . . . . . . . . . . . 52.1.2 Solid Parahydrogen as Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62.2 Conformational Isomerism Studies of Amino Acid with Matrix-Isolation Spectroscopy . . . 92.2.1 b -alanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102.2.2 a-alanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112.2.3 Amino Acids Zwitterions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153.1 Experimental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153.1.1 Making Enriched Parahydrogen Gas . . . . . . . . . . . . . . . . . . . . . . . . . . 153.1.2 Preparing Argon Matrix Gas . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173.1.3 Sublimation of Amino Acid with a Knudsen Cell . . . . . . . . . . . . . . . . . . . 173.1.4 Deposition of Amino Acid in Solid Parahydrogen . . . . . . . . . . . . . . . . . . . 193.1.5 Deposition of Amino Acid in Argon Matrices . . . . . . . . . . . . . . . . . . . . . 203.1.6 In-Situ UV-irradiation of Amino Acid within the Solid Matrices . . . . . . . . . . . 20iv3.1.7 FTIR Measurement Parameters and Detection System Set-ups . . . . . . . . . . . . 223.2 Computational . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233.2.1 Quantum Calculation with WebMO . . . . . . . . . . . . . . . . . . . . . . . . . . 234 Theory and Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244.1 Relative Energy and Relative Gibbs Free Energy . . . . . . . . . . . . . . . . . . . . . . . . 244.1.1 Calculation of the Relative Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . 244.1.2 Calculation of the Relative Gibbs Free Energy . . . . . . . . . . . . . . . . . . . . . 254.2 Boltzmann Distribution Law . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295.1 Conformational Analysis of b -alanine in Solid Parahydrogen and Argon Matrices . . . . . . 295.1.1 Experimental and Computational Details for b -alanine Conformational Study . . . . 295.1.2 Solid Parahydrogen Matrix-Isolated Spectra of b -alanine . . . . . . . . . . . . . . . 315.1.3 Comparison between Conformational Composition of b -alanine in a ParahydrogenMatrix and in an Argon Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385.1.4 Sublimation Temperature Dependence of b -alanine Conformational Population inSolid Parahydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405.2 Conformational Analysis of a-alanine in Solid Parahydrogen and Argon Matrices . . . . . . 405.2.1 Experimental and Computational Details for a-alanine Conformational Study . . . . 415.2.2 Conformers of a-alanine Isolated in Solid Parahydrogen and Argon Matrices . . . . 425.2.3 Populations of a-alanine Conformers in Solid Parahydrogen and in Solid Argon atVarious Sublimation Temperatures . . . . . . . . . . . . . . . . . . . . . . . . . . . 525.2.4 UV-irradiation of a-alanine in Solid Parahydrogen and in Solid Argon . . . . . . . . 535.3 UV Photolysis of Deuterated a-alanine in Solid Parahydrogen . . . . . . . . . . . . . . . . 565.3.1 Experimental and Computational Details for Deuterated a-alanine UV Photochem-istry Study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565.3.2 Spectra Comparison between a-alanine and Deuterated a-alanine . . . . . . . . . . 575.3.3 Assignment Attempt on the UV Photoproducts of Deuterated a-alanine . . . . . . . 605.4 Study of Amino Acid Zwitterions in Solid Parahydrogen . . . . . . . . . . . . . . . . . . . 625.4.1 Experimental Details for b -alanine Zwitterion Study . . . . . . . . . . . . . . . . . 625.4.2 Spectra Result of b -alanine Zwitterion in Solid Parahydrogen . . . . . . . . . . . . 626 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677.1 Conformational, UV Photochemistry, and Zwitterion Studies of Other Amino Acids . . . . . 677.2 Investigation on The Vibrational Dephasing of Molecules in Solid Parahydrogen, and TheAnnealing Effect in Parahydrogen and Argon Matrices . . . . . . . . . . . . . . . . . . . . 677.3 Chirality Studies of Amino Acid in Matrix-Isolation System . . . . . . . . . . . . . . . . . 70vBibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71A Supplementary Material: Conformational Analysis of b -alanine in Solid Parahydrogen andArgon Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80B Supplementary Material: Conformational Analysis of a-alanine in Solid Parahydrogen andArgon Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88C Supplementary Material: UV Photolysis of Deuterated a-alanine in Solid Parahydrogen . . . 99D Supplementary Material: Study of Amino Acid Zwitterions in Solid Parahydrogen . . . . . . 108viList of TablesTable 5.1 Relative Energies and Relative Gibbs Free Energies of b -alanine Conformers . . . . . . . 31Table 5.2 Spectral Assignment of b -alanine in Parahydrogen and Argon Matrices . . . . . . . . . 32Table 5.3 Relative Energies and Relative Gibbs Free Energies of a-alanine Conformers . . . . . . 42Table 5.4 Spectral Assignment of a-alanine in Parahydrogen and Argon Matrices . . . . . . . . . 44Table 5.5 Conformational Population of a-alanine in Solid Parahydrogen vs in Solid Argon inRelation to Various Sublimation Temperature . . . . . . . . . . . . . . . . . . . . . . . . 53Table 5.6 Percent Decrease of a-alanine Population in Solid Parahydrogen vs in Solid Argon uponUV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Table 5.7 Relative Energies and Relative Gibbs Free Energies of Deuterated a-alanine Conformers 58Table 5.8 Spectral Assignment of Deuterated a-alanine in Parahydrogen in Relation to Non-deuterateda-alanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59Table A.1 Theoretical Wavenumbers and Intensities of b -alanine Conformers . . . . . . . . . . . . 81Table B.1 Theoretical Wavenumbers and Intensities of a-alanine Conformers . . . . . . . . . . . . 89Table C.1 Theoretical Wavenumbers and Intensities of Deuterated a-alanine Conformers . . . . . . 100Table C.2 Photoproduct peaks from Deuterated a-alanine in Solid Parahydrogen upon 3 hrs of UV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103Table C.3 Theoretical Wavenumbers and Intensities of Deuterated a-alanine Photoproduct Candidates103viiList of FiguresFigure 2.1 Bruker FTIR Spectrometer Illustration . . . . . . . . . . . . . . . . . . . . . . . . . . . 6Figure 2.2 Structure of b -alanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10Figure 2.3 Structure of a-alanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12Figure 2.4 Structure of b -alanine and a-alanine Zwitterions . . . . . . . . . . . . . . . . . . . . . 13Figure 3.1 Schematic of the Parahydrogen Converter with an Expanded View on the Rector Coil . . 16Figure 3.2 Schematic of the Parahydrogen Converter with Trace of H2 Gas Flow . . . . . . . . . . 16Figure 3.3 Schematic of the Knudsen Cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18Figure 3.4 Picture of the Cryogenic Sample Chamber . . . . . . . . . . . . . . . . . . . . . . . . . 19Figure 3.5 Pictures of the Deuterium Lamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Figure 3.6 Schematic of the Cryogenic Sample Chamber with the Path of UV-radiation Shown . . . 21Figure 3.7 Schematic of the Cryogenic Sample Chamber with the Path of IR Light Shown . . . . . 22Figure 5.1 Structures of the Eleven Lowest Energy b -alanine Conformers . . . . . . . . . . . . . . 30Figure 5.2 FTIR Spectra of b -alanine in Solid Parahydrogen . . . . . . . . . . . . . . . . . . . . . 37Figure 5.3 FTIR Spectra Comparison of b -alanine in Solid Parahydrogen vs in Solid Argon . . . . . 39Figure 5.4 Structures of the Eight Lowest Energy L-a-alanine Conformers . . . . . . . . . . . . . 41Figure 5.5 FTIR Spectra of a-alanine in Solid Parahydrogen and Solid Argon Taken in the Regionof n(OH) and n(C=O) Vibrational Modes . . . . . . . . . . . . . . . . . . . . . . . . . 50Figure 5.6 FTIR Spectra of a-alanine in Solid Parahydrogen and Solid Argon Taken in the Regionof n(C-O) and w(NH2) Vibrational Modes . . . . . . . . . . . . . . . . . . . . . . . . . 51Figure 5.7 FTIR Spectra Comparison of a-alanine in Solid Parahydrogen vs in Solid Argon inRelation to Various Sublimation Temperature . . . . . . . . . . . . . . . . . . . . . . . 54Figure 5.8 FTIR Spectra Comparison of a-alanine in Solid Parahydrogen vs in Solid Argon uponUV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Figure 5.9 Structure of Deuterated a-alanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56Figure 5.10 Structures of the Twelve Lowest Energy Deuterated a-alanine Conformers . . . . . . . 57Figure 5.11 FTIR Spectra Comparison of Deuterated a-alanine vs Non-Deuterated a-alanine inSolid Parahydrogen at Deposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58Figure 5.12 FTIR Spectra Comparison of Deuterated a-alanine vs Non-Deuterated a-alanine inSolid Parahydrogen upon UV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . 61viiiFigure 5.13 FTIR Spectra Comparison of Water-doped b -alanine vs Neutral b -alanine in Solid Parahy-drogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63Figure 5.14 FTIR Spectra Comparison of Water-doped b -alanine vs Neutral b -alanine in Solid Parahy-drogen: Focus on Zwitterion Bands . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64Figure 7.1 Structure of Serine, Aspartic Acid, and Glutamic Acid . . . . . . . . . . . . . . . . . . 67Figure 7.2 FTIR Spectra of a-alanine in Solid Parahydrogen Deposited at 2.2 K and Annealed to4.2 K . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68Figure 7.3 FTIR Spectra of a-alanine in Solid Argon Deposited at 2.2 K and Annealed to 4.2 K . . 69Figure 7.4 FTIR Spectra of a-alanine in Solid Argon Deposited at 18 K and Annealed to 35 K . . . 69Figure A.1 FTIR Spectra of b -alanine in Solid Parahydrogen at Deposition (750 - 2000 cm−1 region) 80Figure A.2 FTIR Spectra of b -alanine in Solid Parahydrogen at Deposition (2000 - 3700 cm−1 region) 84Figure A.3 FTIR Spectra of b -alanine in Solid Parahydrogen upon UV-irradiation (750 - 2000 cm−1region) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84Figure A.4 FTIR Spectra of b -alanine in Solid Parahydrogen upon UV-irradiation (2000 - 3700cm−1 region) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85Figure A.5 FTIR Spectra of b -alanine in Solid Argon at Deposition (750 - 2000 cm−1 region) . . . . 85Figure A.6 FTIR Spectra of b -alanine in Solid Argon at Deposition (2000 - 3700 cm−1 region) . . . 86Figure A.7 FTIR Spectra of b -alanine in Solid Argon upon UV-irradiation (750 - 2000 cm−1 region) 86Figure A.8 FTIR Spectra of b -alanine in Solid Argon upon UV-irradiation (2000 - 3700 cm−1 region) 87Figure B.1 Full FTIR Spectra of a-alanine (420 K Sublimation) in Solid Parahydrogen at Deposition 88Figure B.2 Full FTIR Spectra of a-alanine (420 K Sublimation) in Solid Argon at Deposition . . . . 91Figure B.3 Full FTIR Spectra of a-alanine (420 K Sublimation) in Solid Argon after Annealing . . . 91Figure B.4 Full FTIR Spectra of a-alanine (410 K Sublimation) in Solid Parahydrogen at Deposition 92Figure B.5 Full FTIR Spectra of a-alanine (410 K Sublimation) in Solid Argon at Deposition . . . . 92Figure B.6 Full FTIR Spectra of a-alanine (430 K Sublimation) in Solid Parahydrogen at Deposition 93Figure B.7 Full FTIR Spectra of a-alanine (430 K Sublimation) in Solid Argon at Deposition . . . . 93Figure B.8 Full FTIR Spectra of a-alanine in Solid Parahydrogen at Deposition and before UV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94Figure B.9 Full FTIR Spectra of a-alanine in Solid Parahydrogen after 1 hr of UV-irradiation . . . . 94Figure B.10 Full FTIR Spectra of a-alanine in Solid Parahydrogen after 2 hrs of UV-irradiation . . . 95Figure B.11 Full FTIR Spectra of a-alanine in Solid Parahydrogen after 3 hrs of UV-irradiation . . . 95Figure B.12 Full FTIR Spectra of a-alanine in Solid Parahydrogen after 4 hrs of UV-irradiation . . . 96Figure B.13 Full FTIR Spectra of a-alanine in Solid Argon at Deposition and before UV-irradiation . 96Figure B.14 Full FTIR Spectra of a-alanine in Solid Argon after 1 hr of UV-irradiation . . . . . . . . 97Figure B.15 Full FTIR Spectra of a-alanine in Solid Argon after 2 hrs of UV-irradiation . . . . . . . 97Figure B.16 Full FTIR Spectra of a-alanine in Solid Argon after 3 hrs of UV-irradiation . . . . . . . 98Figure B.17 Full FTIR Spectra of a-alanine in Solid Argon after 4 hrs of UV-irradiation . . . . . . . 98ixFigure C.1 Full FTIR Spectra of Deuterated a-alanine in Solid Parahydrogen at Deposition andbefore UV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106Figure C.2 Full FTIR Spectra of Deuterated a-alanine in Solid Parahydrogen after 3 hrs of UV-irradiation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107Figure C.3 Difference FTIR Spectra of Deuterated a-alanine in Solid Parahydrogen (3 hrs of UV-irradiation – Deposition) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107Figure D.1 Full FTIR Spectra of b -alanine in Solid Parahydrogen without Water Dosage . . . . . . 108Figure D.2 Full FTIR Spectra of b -alanine in Solid Parahydrogen with 100 ppm Water Dopant . . . 109Figure D.3 Full FTIR Spectra of b -alanine in Solid Parahydrogen with 500 ppm Water Dopant . . . 109xList of AbbreviationsB3LPY/6-31++G** Becke 3-Parameter (Density Functional Theory) with 6-31G Split Valance Basis Setplus Diffuse Functions plus PolarizationB3LYP/6-311++G** Becke 3-Parameter (Density Functional Theory) with 6-311G Triple Split ValanceBasis Set plus Diffuse Functions plus PolarizationB3LYP/aug− cc−pVDZ Becke 3-Parameter (Density Functional Theory) with an AugmentedDouble-Zeta Basis SetB3LYP/aug− cc−pVTZ Becke 3-Parameter (Density Functional Theory) with an Augmented Triple-ZetaBasis SetBaF2 Barium Fluorideccm Cubic Centimetre per MinuteCCSD(T)/aug− cc−pVTZ Coupled Cluster Calculation with Single and Double Subtitutions fromHartree-Fock plus Triple Excitations Non-Iteratively plus an Augmented Triple-Zeta Basis SetCFI Canadian Foundation for InnovationCRUCS Center for Research on Ultra-Cold SystemsDC Direct CurrentDCN Deuterated Hydrogen CyanideESR Electron Spin Resonancefcc Face-Centered CubicFTIR Fourier Transform InfraredH-bond Hydrogen-BondH2C=NH MethylimineH3C-CH2-NH2 EthylaminexiHCN Hydrogen Cyanidehcp Hexagonal-Closed PackedHe-Ne Helium-NeonHF/4-31G Hartree-Fock Theory with a 4-31G Split-Valence Basis SetHF/6-31G* Hartree-Fock Theory with a 6-31G Split-Valence Basis Set plus PolarizationHF/6-31+G* Hartree-Fock Theory with a 6-31G Split-Valence Basis Set plus Diffuse Functions plusPolarizationHWHM Half Width at Half MaximumI Nuclear Spin Angular MomentumIR InfraredJ Rotational Quantum NumberKBr Potassium BromideLA-MB-FTMW Laser-Ablation Molecular-Beam Fourier Transform MicrowaveMCD Magnetic Circular DichorismMCT Mercury Cadmium TellurideMgF2 Magnesium FluorideMI Matrix-IsolationMI-IR Matrix-Isolation InfraredMI-FTIR Matrix-Isolation Fourier Transform InfraredMIR Mid-InfraredMP2/6-31+G* Møller-Plesset Perturbation Theory with 6-31G Split Valance Basis Set plus DiffuseFunctions plus PolarizationMP2/6-311++G** Møller-Plesset Perturbation Theory with 6-311G Triple Split Valance Basis Set plusDiffuse Functions plus PolarizationMP2/aug− cc−pV5Z Møller-Plesset Perturbation Theory with an Augmented Quintuple-Zeta Basis SetMP2/aug− cc−pVDZ Møller-Plesset Perturbation Theory with an Augmented Double-Zeta Basis SetMP3/aug− cc−pVQZ Møller-Plesset Perturbation Theory at the Third Order with an AugmentedQuadruple-zeta Basis SetxiiNBS National Bureau of StandardsNIR Near-InfraredNIST National Institute of Standard and TechnologyOFHC Oxygen Free High ConductivityPES Potential Energy Surfaceppm Parts per MillionpH2 ParahydrogenRHF/6-31G* Restricted Hartree-Fock Theory with a 6-31G Split-Valence Basis Set plus PolarizationSLM Standard Liter per MinuteUV UltravioletVEEL Vibrational and Electronic Energy Levelvs VersusZPE Zero-Point EnergyxiiiAcknowledgementsI would like to thank everyone who has helped me over the past couple years on my work here at UBC.Thank you to Dr.Takamasa Momose for taking me on as a student and for providing me with constantsupport and guidance throughout my work here. Special thanks to my partner in experiment, Ms.AngelYing-Tung Wong, for being the most remarkable researcher I have ever work with, and our lab technician,Mr.Pavle Djuricanin for designing, building, and maintaining most of the machines used for this project.Thank you to Dr.Jun Miyazaki, Dr.Watheq Al-Basheer, and Dr.Shang-Chen Huang for their expertise adviceand mentorship on the field of my work. Thank you to my students, Ms.Ellen Chua, Mr.Brandon Moore,and Ms.Janet Leung for assisting me in the analysis and computational works for this project. Thank you toMr.Tony Mittertreiner and Mr.Milan Coschizza for their technical support on the FTIR spectrometer. Thankyou to all my fellow colleagues in the Momose Group, especially Mr.Thomas Prescott, Dr.Eric Miller,Dr.Yang Liu, Dr.Manish Vashihta, Dr.Omid Nourbakhsh, Dr.Mario Michan, and Dr.Polly Yu, with whom Ihave the honoured to worked alongside during my academic years in the laboratory. And lastly, thank youto my parents, who have supported me throughout my years of education, both morally and financially.This research was supported by an NSERC Discovery Grant and funds from CFI to the Centre for Re-search on Ultra Cold Systems (CRUCS) at UBC.xivChapter 1IntroductionAmino acids have been subjected to multiple fundamental studies due to their importance in basic anatomy,and their relevance to the origin of life. Amino acids are the building blocks of biological molecules,prompting the investigation of their physical and chemical properties essential for the understanding oftheir functions in biological system. In addition, the existence of amino acids in interstellar space has beendiscussed for many years, but it is still under intense debate. The search for glycine, the simplest aminoacid, in interstellar space is a good example of the controversies encountered by this field of exploration.In 2003, Kuan et al. [5] claimed to observe 27 glycine lines in 19 different millimeter-wave bands fromthree astronomical sources, Sgr B2(N-LMH), Orion KL, and W51 e1/e2. The discovery, however, was laterdisconfirmed by Snyder et al. [6] in 2004 with their rigorous but unsuccessful attempt on verifying Kuanet al. reported glycine assignments, and by Cunningham et al. [7] in 2007 with their fruitless search forinterstellar glycine in the Sgr B2(N-LMH) and Orion KL using the Mopra Telescope.The origin and formation of interstellar amino acids are particularly hot topics of scientific investigations.Several extraterrestrial amino acids have been found in various type of carbonaceous chondrite meteorites[8–12], with over eighty distinct amino acids have been identified in Murchison meteorite alone [13]. How-ever, the amino acids exact location of origin and the mechanism of synthesis are yet to be discovered. Someresearchers have suggested the formation of these organic compounds through Strecker-type synthesis onthe meteorite parent body, in which involved the reaction of hydrogen cyanide, ammonia, and aldehyde inthe aqueous astrophysical media [14, 15]; while others argued that interstellar amino acids are the productsof interstellar ion-molecule reactions [16, 17].Another focus of investigations on interstellar amino acids involve the stability of these organic com-pounds in extraterrestrial environments, specifically their photostability against UV radiation. The effect ofUV radiation on amino acids is one of the keys for their search in interstellar space. Amino acids mightundergo chemical degradation, racemization [18], or conformational change [19] when being exposed to UVrays. Several research groups have demonstrated that gas phase amino acids might be highly susceptible toUV photodestruction, and would most likely not survive in the space medium in which strong UV radiationexists [20, 21]. However, the possibility of observing interstellar amino acids in their full forms should notbe ruled out completely. Thus, it is especially essential to check the conformational behavior and racemiza-tion properties of amino acids upon UV-irradiation, and also identify the photoproducts resulting from the1photodecomposition of amino acids.Matrix-isolation (MI) spectroscopy technique has been widely used for extraterrestrial prebiotic moleculesstudies due to its ability to stimulate conditions close to that of an extraterrestrial environment, such as ininterstellar gas or on interstellar grains [20]. This high resolution spectroscopy technique allows for theobservation of higher energy conformer molecules and intermediary photoproducts due to its capability ofsustaining reactive molecules in the ice crystal [22]. Matrix-isolation method has also provided a simplerplatform for researchers to conduct photochemistry experiments, by allowing in-situ irradiation of isolatedsample trapped within the matrix cage [22].For the work presented in this thesis, my collaborators and I explored the conformational properties andUV photochemical behaviours of two simple amino acids, namely b -alanine and a-alanine, by employingmatrix-isolation Fourier transform infrared (MI-FTIR) spectroscopy using parahydrogen as our matrix. Wecompared our findings in solid parahydrogen to those of argon matrices. We also attempted to produce andinvestigate these amino acids in their zwitterion forms using matrix-isolation method. The observed spectraand associated analysis were discussed in relation to interstellar chemistry.2Chapter 2Background2.1 Matrix-Isolation SpectroscopyMatrix-isolation method involves the trapping of active molecules in solid matrix with inert properties [23].The technique is achieved by rapid condensation of the mixed guest sample - host matrix gas onto a surfaceof cryogenic temperature [22]. Under this extremely cold temperature, the non-reactive matrix environmentwill inhibit diffusion of the molecules, keeping individual analyte encaged within the isolated pockets of thecrystalline matrix, and preventing intermolecular interaction between the active molecules [23].The incorporation of matrix-isolation method with infrared spectroscopy was first thought out by GeorgeC. Pimentel and his two colleagues, Eric Whittle and David A. Dows, in the early 1950’s [23]. They the-orized that inert solids, made out of rare gases and nitrogen, are transparent over a wide range of spectralregion from the far infrared to the vacuum UV, allowing the direct infrared detection of the trapped moleculewithin the matrix. The group tested the application of matrix-isolation infrared (MI-IR) spectroscopy on un-stable molecules, such as free radicals and reaction intermediates, and succeed in producing infrared spectraof the reactive samples with good quality [23]. The low temperature environment of the matrix evidentlyprohibits intramolecular reactions of the molecule with an appreciable amount of activation energies [22].And with the absent of quantum diffusion, intermolecular interactions are minimized due to the isolation ofanalyte as mention above. With the lack of both intra- and intermolecular reactions, the lifetime of unsta-ble molecules are lengthened, thus making the physical and chemical studies of the reactive species easilyaccessible through matrix-isolation spectroscopy techniques [22].Soon after the development of MI-IR spectroscopy, Marilyn E. Jacox and Dolphus E. (Dick) Milliganexpanded the study of free radicals in cold inert matrix at the Mellon Institute, and then under the SurfaceChemistry Section at the National Bureau of Standards (NBS) [24]. From their researches, Jacox and Mil-ligan realized the occurrence of limited atomic diffusion within the matrix media, which aids in stabilizingthe encaged free radicals by migration of the lighter atoms through the matrix to react with other trappedspecies [25]. They also worked intensively on the photochemistry of free radicals in matrix environment,using lamps of vacuum UV-region as their irradiation sources [24]. Despite the early death her associateMilligan, Jacox, considered now as a pioneer in infrared spectroscopy, continued with their researches in3matrix-isolation. She extended the application of MI-IR spectroscopy to molecular ions [24, 26], and uti-lized the method to compile vibrational and electronic energy-level data of neutral and ionic polyatomictransient molecules under the VEEL project with the National Institute of Standard and Technology (NIST)[24, 27–29].One of criticism received by researchers in matrix-isolation field is that the trapped species are nottruly isolated or free due to some perturbation by the medium [30]. The interaction energy between the inertmatrix host and the active guest molecule is minimal but non-zero, and will affect the structure and dynamicsof the encaged molecule resulting in spectral shift [30, 31]. However, Jacox had addressed this drawbackof matrix-isolation by comparing spectra of gas-phase spectroscopy to that of inert, rigid matrix, and foundthat the infrared absorption of the trapped active molecules in solid argon and neon appeared within 1 % ofthe corresponding gas-phase band centers [24, 31]. With this generalization, MI-IR spectroscopy has provedto be a step-up in gas-phase spectroscopy, allowing for the qualitative and quantitative spectral observationsof gaseous sample with high accuracy.Aside from its application on reactive species, matrix-isolation technique is also widely used in spec-troscopy studies of stable molecules [22, 30]. Molecules trapped within inert matrices could be detectedwith a higher resolution as compared to other condensed phases and the vapour phase [22]. The lack ofintermolecular interactions due to sample isolations in solid matrices results in a great sharpening of soluteabsorptions, giving spectra signals of smaller bandwidths than those obtained in the liquid and solid phases;whereas the absence of rotation within the matrix cages (with the exception of very small molecules) causesthe bands to be much narrower as contrasted to gas phase absorptions. The low temperature itself is alsocontributing to the reduction in bandwidths, producing a more defined spectra than those taken at roomtemperature [22]. With the advantage of producing sharper signals, matrix spectral can be used to resolvenear-degenerate bands, which overlap completely even in the gas phase or in dilute solution [22]. As matrix-isolation spectroscopy allows for more accurate vibrational assignments of near-degenerate fundamentals,the application is especially popular in conformational isomerism studies, where difference of vibrationalfrequencies between two or more conformers could be minuscule [22].Matrix-isolation method is now used in various fields of spectroscopy, like vibrational, electronic (ab-sorption and emission), MCD, ESR, and Mossbauer spectroscopy, just to name a few [22]. The techniqueis most widely coupled with infrared and Raman spectroscopy due to its ability of providing vibrationalspectral with more detailed features than those taken in the liquid, solid, and gas phases, as mentioned above[22]. As for the matrix host, rare gases such as argon and neon are the predominant choices due to theirchemical inertness and physical simplicity, as compared to molecular matrix like nitrogen [32, 33]. How-ever, all combinations of spectroscopic tools and matrix materials have their own strengths and weaknesses,depending on the nature of the experiments. For our conformational isomerism studies of simple aminoacids, we employed parahydrogen as our matrix host, and combined the matrix isolation application withFTIR spectroscopy. We believed that this combination, known as solid parahydrogen MI-FTIR spectroscopy,would give us vibrational spectra of the highest achievable resolution, allowing us to proceed with spectralassignments with the greatest confidence.42.1.1 Fourier Transform Infrared (FTIR) SpectroscopyThe design of the optical pathway has produced a pattern known as an interferogram. This wave-like signalcontains frequency information that would make up a time-domain infrared spectrum. However, spectro-scopists prefer spectra of frequency-domain, which is easier to read and interpret than its time-domaincounterpart. Thus, the creation of a mathematical operation called a Fourier transform, that can extractindividual absorption frequencies from the interferogram and translate the obtained information from anintensity versus time plot to an intensity versus wavenumber (or wavelength) spectrum [34].Fourier transform infrared (FTIR) spectrometer is based on the Michelson interferometer. The spec-trometer is equipped with a beam splitter that splits the incoming IR beam into two beams of equal powerintensity, and directs the separated beams to a movable and a fixed mirror, respectively. The movable mirroroscillates at a constant speed with a known position at all instant, giving consistently spaced periodic beamsof varied path lengths upon each beam reflection. The two split beams are then being reflected back tothe beam splitter, recombined as a beam of interference pattern, and sent through the sample towards thedetector [35]. This dual mirror design allows for precise signal sampling and signal averaging, resulting inan overall more improved signal than that obtained by dispersive spectrometers [35].A way to further improve the signal sampling and averaging aspects of a FTIR instrument is to incor-porate two or three interferometers, rather than just one, into the spectrometer. For a triple interferometersystem arrangement, the instrument contains a laser-fringe reference system and a white-light system, ontop of an IR system that carries the analytical information to produce the final interferogram [35]. The laser-fringe reference system consists of a He-Ne laser, and the system function is to provide sampling-intervalinformation to the spectrometer. With a static cosine output wave from the laser feedback, the system giveshighly reproducible and regularly spaced sampling interval. The laser signal is also used to control themotor-drive of the movable mirror, keeping the speed of oscillation to be at a constant level [35]. Thewhite-light system is equipped with a tungsten source, and the purpose of the system is to trigger the start ofdata sampling for each sweep at a highly reproducible point. The system is arranged in a way that its zeroretardation appears as a strong maximum at a position prior to that for analytical signal, indicating it as thestarting point of a measurement sweep [35].The instrument (Bruker, IFS 125HR) we employed for our experiment is a single beam FTIR spectrom-eter with a double interferometer system. Our FTIR spectrometer applies a He-Ne laser system to providereference signal for acquiring data, and a IR source system to give the ultimate interferogram and to es-tablish zero retardation [36]. The maximum in the IR interferogram could be considered as an excellentreference point, because it is the only point at which all wavelengths interfere constructively [35]. Figure2.1 illustrated the design and optical pathway of our FTIR spectrometer.FTIR spectrometer poses multiple advantages over dispersive infrared instruments, making it a prefer-able tool for infrared region analysis. The first advantage imposed by FTIR spectrometer is the throughputadvantage. With fewer optical elements and no narrow width slits to attenuate the radiation beam, the radi-ant power reaching the detector in a FTIR instrument is much greater, thus producing better signal-to-noiseratio than that of dispersive instruments by more than an order of magnitude [35]. FTIR instrument pro-vides extremely high resolving power and wavenumber reproducibility, revealing previously unsuspected5IR SourceFolding Mirror Fixed MirrorReferenceLaserMoving MirrorBeamSplitterFolding Mirror Focus MirrorCollimating MirrorFocus Mirror DetectorSampleDetectorFigure 2.1: Set-ups and optical pathways of a Bruker FTIR spectrometer. The instrument consists oftwo interferometer systems, which are the IR system and the laser-fringe reference system. Thered arrows indicate the path of the IR beam; whereas the green arrows indicate the path of theHe-Ne laser beam.fine structures on many spectra bands, and allowing for the determination of molecular signals with higheraccuracy and precision [35]. As all the elements of the source reach the detector simultaneously in an FTIRspectrometer, the instrument possesses multiplex advantage, indicating a faster data collection time as com-pared to dispersive spectrometers [35]. Finally, FTIR spectrometer tends to be free from problem of strayradiation, as each IR frequency is chopped at a different frequency before being sent through for detection[35].2.1.2 Solid Parahydrogen as MatricesAs previously mentioned, noble gases are most commonly used as matrix host for matrix-isolation spec-troscopy due to their chemical inertness [32, 33]. However, rare gas matrices pose some disadvantages thatmake them not as practical to be applied in high resolution spectroscopy. One of these disadvantages is theobservation of undesirable spectral broadening as a result of homogeneous and inhomogeneous interactionsin the matrices [32, 33, 37, 38]. Homogenous line broadening arises from the weak but considerable per-turbation of the isolated guest molecules on the surrounding matrix host atoms, due to the close physicalproximity of the two in the rigid noble gas solid [22]; on the other hand, inhomogeneous line broadening isa consequence of the mixed hexagonal-closed packed (hcp) and face-centered cubic (fcc) caging structuresof such matrices, in which the ratio of hcp to fcc structures can varies with the concentration of dopant andthe procedure of deposition [22]. The matrix-guest interaction also manifests another major matrix effect,namely multiple trapping sites effect [22, 39]. Molecules occupy into a matrix cage through substitution pro-6cess via the removal of one or more matrix atoms, and more than often the amount of removed atoms variesamong different substitution sites within the same matrix [22]. Even though the different trapping sites onlydiffer slightly from each other, this effect still leads to the observation of multiple bands which could pointto the same vibrational behaviour, thus further complicates the process of spectral analysis [22, 39]. Interms of photochemistry investigations in matrix environments, rare gas matrices inherently hard and rigidcage effect inhibits effective in-situ photolysis on the trapped species. This drawback often leads to theutilization of photoirradiation or photoexcitation techniques prior to the sample deposition step, which mostlikely causes complication to the system to be studied [32]. The limitation imposed by noble gas matriceson matrix-isolation spectroscopy, however, can be overcome by employing parahydrogen matrices.Normal hydrogen consists of ortho- and parahydrogen in a ratio of three to one at room temperature[32, 40]. The two classes of molecular hydrogens arise from the symmetric and antisymmetric nuclearspin state of diatomic hydrogen, with orthohydrogen associates with spin angular momentum of one (I= 1) and rotational states of odd quantum number (J = odd), and parahydrogen is characterized by spinangular momentum of zero (I = 0) and rotational states of even quantum number (J = even) [32]. As thesmallest mass molecule, hydrogen possesses a large rotational constant, giving an exceptionally big energygap between the first excited and the ground rotational states for both ortho- and parahydrogen. Therefore,at cryogenic temperature as in solid matrix, ortho- and parahydrogen exist exclusively in their rotationalground states, which is J = 1 and J = 0, respectively [32]. With the spherical nature of its rotational groundstate, parahydrogen has a permanent multipole moment of zero, making it behaves electrostatically as anoble gas atom [32]. On the other hand, orthohydrogen has a permanent quadrupole moment of the lowestmultipole moment as a result of its rotational ground state anisotropic nature in charge distribution [32, 40].From a spectroscopic point of view, the presence of orthohydrogen is unwanted, as the inhomogeneityof internal electrostatic field implied by orthohydrogen would lead to undesirable spectral line broadening[32, 37]. Fortunately, the transitions between odd and even rotational states are forbidden, making it possibleto prepare and keep sample of highly pure parahydrogen for high resolution matrix-isolation spectroscopy[40]. Moreover, the concentration of thermal equilibrate orthohydrogen appears to decrease with decreasingtemperature, with approximately 75 % at room temperature, 0.4 % at the boiling point of liquid helium(20.28 K at 1 atm), and down to 0.0045 % at the triple point of hydrogen (13.8 K). Thus, the purity ofparahydrogen can be hyped up to more than 99.995 % by using an ortho-parahydrogen converter operatingat a temperature of 13.8 K and lower [32]. However, the conversion of ortho- to parahydrogen is slow byitself. Therefore, magnetic catalysts are often used to apply magnetic perturbation on the cooled hydrogensample and speed up the interconversion rate between the two nuclear spin angular momenta [32].In 1989, Okumura, Chan, and Oka discovered the linewidth of J = 6← 0 transition is as narrow as 0.003cm−1 HWHM in 99.8 % pure solid parahydrogen [41], which is much smaller than the Doppler-broadenedand Dicke-narrowed spectral lines of gaseous hydrogen by one order of magnitude [38]. Their discoverytook the field of spectroscopy by surprise as such large DJ rotational transitions are highly forbidden in gasphase, better yet with such high resolution observation [38]. Following the work of Okumura et al., theexploration on spectral linewidth of solid parahydrogen was extended into impurities doped parahydrogenexperiments, and the sharpest spectral lines observed thus far are from the rotation-vibration transitions of7deuterated hydrogen in parahydrogen matrices, with linewidth as narrow as 2 MHz (= 0.0000667 cm−1)HWHM [42]. The breakthrough achievement of Okumura and his colleagues has thus revolutionized theutilization of solid parahydrogen in high resolution matrix-isolation spectroscopy, as the technique allowsfor the study of intermolecular and crystal-field interactions with exceptional clarity and precision, indicatingthe solid to be a superb medium over other gas matrix alternatives [38].What makes solid parahydrogen so remarkable is its categorization as a quantum crystal [32, 38, 40].Parahydrogen molecules are assembled by van der Waals forces into a crystal of purely hcp structure be-longing to the D3h point group. The nearest neighbour distance, i.e., lattice constant, of the crystal structureis 3.783 A˚, with a large zero-point lattice vibrational amplitude of approximate 18 % of the lattice constant.Such large zero-point motion causes quantum effect to dominate over classical lattice dynamic [40]. Asquantum solid of exceptionally large intermolecular distance as compared to the atomic distance of othernoble gas crystals (e.g., Ne = 3.16 A˚, Ar = 3.76 A˚), solid parahydrogen supplies more free space to the guestmolecules which in terms causes weaker guest-host interaction, resulting in sharper spectral lines than thoseof rare gas matrices [37]. The pure hcp structure of solid parahydrogen offers a homogeneous environmentfor the trapped sample, eliminating inhomogeneous line broadening effect which arise from the mixed hcpand fcc structural arrangement in rare and other molecular gas matrices [37]. Parahydrogen matrix is alsofree from multiple trapping sites effect due to its quantum properties. The large zero-point lattice vibra-tion amplitude of parahydrogen allows for self-reparation of defected crystal around the trapped analyte,providing the same trapping site features spanning across the whole matrix [37].In addition, the spacious and less-perturbative parahydrogen matrix allows the encaged molecules tohave almost free vibrational and rotational quantum states, opens up to the possibility of trapping and sta-bilizing higher energy states molecules [32, 38]. The energy density of solid parahydrogen is relativelydispersed for a molecular solid due to its exceedingly large rotational constant of 60.853 cm−1, fundamentalvibrational frequency of 4401.2 cm−1, first excited electronic energy of 91700 cm−1, and Debye temperatureof 100 K (' 70 cm−1), as compared to the parameters of other molecules [40]. These features further pro-long the lifetime of excited molecules encaged in solid parahydrogen by bringing down the reactive species’relaxation process to an extraordinarily slow rate [32].Lastly, the spacious characteristic of solid parahydrogen has featured the matrix as a soft medium oppos-ing the hard and rigid non-quantum solids such as rare gases [32]. The large lattice constant and amplitudezero-point lattice vibration experienced in parahydrogen crystal also results in a higher than usual valuefor compressibility cT (defined as cT = − 1n (dV=dP)T ) of approximately 50×10−10 Pa−1 at temperaturebelow 5 K [40]. Moreover, highly pure parahydrogen crystal appears to have exceptionally large thermalconductivity value, with approximately 50 Wm−1K−1 for a sample of 0.2 % orthohydrogen at liquid heliumtemperature [40]. The soft and compressible features of parahydrogen matrix has thus make it the mostsuitable medium for in-situ photochemistry studies, as the photoproduct fragments can be separated easilyvia diffusion, and the separated fragments are quickly froze out by the high thermal conductivity nature ofthe quantum solid [32].82.2 Conformational Isomerism Studies of Amino Acid withMatrix-Isolation SpectroscopySpectral bands of molecular conformers often differ by only a few wavenumbers. Therefore, a spectroscopytechnique of high resolution is required to perform qualitative and quantitative conformational analysis ona molecule. Matrix isolation infrared (MI-IR) spectroscopy is one of the most powerful tools for conforma-tional isomerism studies [22]. The cryogenic and inert matrix environment rapidly cools the sample mixedwith the matrix gases upon contact with the cold window, preventing equilibration of the conformationalmixture with energy barrier higher than 3 6 kJ·mol−1, thus preserving the gas phase equilibrium composi-tion of the sample that is present prior to deposition [43, 44]. As mentioned previously (see Section 2.1),MI-IR spectroscopy is capable of producing high resolution spectra with exceptionally sharp bands, resolv-ing the typically overlap spectra signals of two and more conformers when taken in gas, liquid, or solidphase [22]. However, despite the high resolution provided by MI-IR spectroscopy, conformational spectrastill suffer from superposition of bands, appearing as unresolved low intensity signals and shouldering peaks.Nonetheless, these congested bands can be distinguished by altering the conformational ratio of the trappedmolecule with techniques such as matrix annealing [19, 43, 45, 46], in-situ photoirradiation [2, 19, 47–51],and sample deposition temperature variation [4, 52–54].Numerous conformational studies in noble gas matrices have shown to be effective. Nevertheless, raregases are not the best host materials for conformational isomerism analysis with MI-IR spectroscopy becauseof the varies matrix effect drawbacks imposed by the non-quantum solids, as highlighted in the previousSection 2.1.2 . Moreover, different matrices have been shown to have different capabilities in capturingthe gas phase conformational equilibrium population of a system [2, 4, 53, 55, 56]. In a set of xenon,krypton, and argon matrices, the ability of each type of matrix to maintain the gas phase population wasfound to increase with decreasing atomic radii and mass [56]. In fact, our group has observed a completedepletion of some high energy conformers in argon matrices as a result of collisional relaxation imposed bythe bulky argon gas atoms to the relatively unstable molecular conformers [2, 4] (see Sections 5.1 and 5.2).Subsequently, the use of inert gases as matrix materials could lead to a loss of conformational information,as the produced results might deviate from the actual gas phase conformational equilibria of a molecule.Solid parahydrogen might come out as a better contender against rare gas matrices for conformationalisomerism studies with MI-IR spectroscopy. Because of the quantum nature of solid parahydrogen, thevibrational spectra provided by solid parahydrogen MI-IR spectroscopy appear to be less complex thanthose by noble gas matrices, free from multiple trapping sites and spectral line broadening effects (seeSection 2.1.2). In addition, parahydrogen matrix is expected to be more prominent in stabilizing higherenergy states due to its small molecular size and light mass. In a conformational study of acetylacetonein solid parahydrogen, a higher abundance of keto/enol ratio was observed in solid parahydrogen than inrare gas matrices, in which the keto-form is the less stable state between the enol and keto tautomers of thesample [55].Even though solid parahydrogen seems like a more suitable medium, most, if not all, of the confor-mational composition studies of amino acids with MI-IR spectroscopy were achieved using classical noblegas matrices. With the outstanding advantages provided by parahydrogen matrices, we have implored the9worth to reinvestigate the conformational stability of amino acids using solid parahydrogen MI-IR spec-troscopy, and we started our case study with two of the simplest amino acids, namely b - and a-alanine. Wealso attempted to extend our investigation on the zwitterion forms of simple amino acids. The followingsubsections highlighted some previous computational and experimental works done on the conformationalisomerism studies of b -alanine, a-alanine, and amino acids zwitterions, plus summarized the relation ofthese samples to interstellar space.2.2.1 b -alanineb -alanine (Figure 2.2) is the only naturally occurring b -amino acid, and it is an organic compound of par-ticular importance in interstellar space. b -alanine was found in various classes of carbonaceous meteorites[8, 9, 14], and is the most abundant type of amino acid in the CI chondrites [8, 14]. It was also demonstratedthat synthesis of gas-phase alanine can be achieved via ion-molecule reactions with smaller molecules foundin interstellar medium, in which b -alanine was formed preferentially over a-alanine [16]. Such discoveryhas implied that the b -alanine found in the CI chondrites could be product of pure interstellar reactions,which in terms gives us an insight to the origin of life in space.NH2 OHOFigure 2.2: Structure of b -alanine.b -alanine has been subjected to multiple conformational investigations, both computationally and ex-perimentally. The conformational study of b -alanine began with Ramek, who performed computationalcalculation on the conformers of b -alanine at the HF/4-31G level of theory and found twenty stable con-formers [57]. The list of twenty were reduced down to nineteen after McGlone and Godfrey recalculated thestable b -alanine conformers deduced by Ramek with a slightly higher level of theory at HF/6-31G*. Fur-thermore, McGlone and Godfrey have experimentally observed two gaseous b -alanine species of gaucheconformations using free-expansion jet spectrometry, and identified them as conformer I and conformer V[58]. A decade after their study, Sanz et al. refined McGlone’s and Godfrey’s theoretical calculations on thenineteen conformers using MP2/6-311++G** level of theory, and confirmed their observation of conformerI and V using Fourier transform microwave spectroscopy coupled with pulsed supersonic jet and laser ab-lation. Sanz et al. have also identified two additional b -alanine conformers through their experimentalprocedures, namely conformer II and III [59].The first conformational investigation of b -alanine with MI-IR spectroscopy was reported by Rosadoand his colleagues in 1997 [60]. The group utilized argon gas as their matrix host, and compared theresulting MI-IR spectra to calculated values at RHF/6-31G* level of theory, FTIR spectra from KBr pelletmethod, and Raman spectra using a 514.5 nm argon laser with 220 mW power as excitation source. Even10though only one conformer was confidently assigned by Rosado et al., the group suggested the presenceof multiple different conformers within solid argon, attributed by the observation of several well structuredspectra bands at the same vibrational frequency region [60]. Since then, a number of follow-up studieshave been performed with the attempt to identify the conformational forms of b -alanine trapped in inertmatrices. Most recently are the research performed by Dobrowolski and his group in 2008 [61], and twostudies done by Stepanian and his company in 2012 [19] and 2016 [62]. Dobrowolski et al. isolated b -alanine in argon matrices, and determined the presence of at least three conformers, which were conformerI, II and IV following Ramek’s nomenclatures. They accomplished the spectral assignments by matchingthe experimental vibrational numbers and intensities to that of high accuracy theoretical calculations atB3LYP/aug− cc−pVDZ level of theory. Their results also further indicated the possible presence of otherhigher energy b -alanine conformers in matrix environment [61]. Stepanian et al. expanded the search ofhigh energy b -alanine conformers in solid argon by coupling MI-FTIR spectroscopy with matrix annealingand in-situ UV-irradiation techniques, with the intend to resolve the overlapping spectra bands of b -alanine.They also performed an extensive potential energy surface (PES) scan at MP2/aug− cc−pVDZ level oftheory and found twenty stable conformational states of b -alanine. Through these exhaustive computationaland experimental works, Stepanian et al. were able to identify and assign five b -alanine conformers in argonmatrices, namely conformer I, II, IV, V, and VII [19]. The group then provided additional confirmation ontheir observation of conformer V, a highly unstable b -alanine conformer, in solid argon by performing thesame experiment on the deuterated analog of b -alanine (b -alanine-d3) [19, 62].2.2.2 a-alaninea-alanine (Figure 2.3) is the smallest amino acids with a chiral carbon atom. The search of chiral aminoacids, and other chiral biological molecules, in interstellar space has been intensive due to their relevanceto the origin of homochirality of life [63]. Many mechanisms have been proposed on the formation ofchiral homogeneity organic molecules in the prebiotic Earth since the discovery of homochirality effect inthe 19th century [64]. However, due to the complications and the limitations imposed by the formationmechanisms, most of the proposed processes seemed highly improbable to be carried out terrestrially on thechaotic environment of the prebiotic Earth. To overcome these difficulties, Bonner has suggested that theproduction of chiral biomolecules on Earth to be an extraterrestrial origin [64], and his concrete view wassupported by the discovery of an enantiomeric excess of L-amino acids in the Murchison meteorite [65, 66].a-alanine has been the subject of many theoretical conformational studies. One of the first compu-tational study of a-alanine was performed by Gronert and O’Hair who derived ten stable conformationalstates of the amino acid using HF/6-31G*, HF/6-31+G*, and MP2/6-31+G* levels of theory [67]. Aroundthe same period of time, another group led by Scha¨fer was conducting a similar computational investigationon a-alanine but with larger basis sets of 6-31G** and 6-311G**, and was able to identify three additionalconformers [68]. The most detailed theoretical analysis of a-alanine was carried out by Csa´sza´r [69]. Heemployed various levels and basis sets for his computational calculations, and obtained the same thirteen sta-ble conformers of a-alanine as located by Scha¨fer and his co-workers. These thirteen a-alanine conformerswere conformer I, IIA, IIB, IIIA, IIIB, IVA, IVB, VA, VB, VI, VII, VIIIA, and VIIIB according to Csa´sza´r’s11H3CNH2OHOFigure 2.3: Structure of a-alanine.nomenclatures, in which the notation “A” and “B” represent the L- and D- enantiomer pairs, respectively[69]. Recently, Balabin performed an ab initio analysis of a-alanine with the highest level of computationparameters thus far, using CCSD(T)/aug− cc−pVTZ, MP3/aug− cc−pVQZ, and MP2/aug− cc−pV5Z cal-culations at B3LYP/aug− cc−pVTZ geometries. Contrary to his predecessors, Balabin was only able to de-rive twelve stable a-alanine configurations, with conformer IIIB (from Csa´sza´r’s list as stated above) beingundetected through Balabin’s highly accurate calculations [70].a-alanine has also been the interest of multiple experimental conformational studies, being analyzedwith methods ranging from gas-phase electron diffraction [71, 72] to various spectroscopic techniques[45, 47, 60, 73–80]. The following accounts highlight a few selected experimental conformational char-acterizations of gas phase a-alanine performed since the early 90’s until recent years. In 1991, Iijima andBeagley performed a gas phase electron diffraction study on a-alanine and observed only one conformerof the neutral species [71]. Two years later in 1993, a millimeter-wave spectroscopy of a-alanine was re-ported by Godfrey et al., in which the group was able to identify the two most stable forms of a-alanineconformations, namely conformer I and IIA (according to Csa´sza´r’s nomenclatures), in the 54.2 - 65.4 GHzregion by using a Stark-modulated free-expansion jet spectrometer [73]. Godfrey’s and his co-workers’observation was later confirmed by Blanco et al. in 2004 with laser-ablation molecular-beam Fourier trans-form microwave (LA-MB-FTMW) spectroscopy in the 6 - 18 GHz region [75], and by Hirata et al. in 2008with millimeter-wave spectroscopy in 80 - 99 GHz and 160 - 180 GHz regions by applying a continuousmolecular beam [76]. More recently in 2010, Balabin carried out a jet-cooled Raman spectroscopy study ona-alanine and detected two additional conformers, conformer IIB and IIIA, together with the two previouslyidentified conformer I and IIA [78].MI-IR spectroscopy is another popular spectroscopy technique used for conformational studies of a-alanine [45, 47, 60, 80]. Together with its isomer b -alanine (see Section 2.2.1), the first MI-IR spectroscopyof a-alanine was executed by Rosado et al. in 1997 with only one conformer, conformer I, found by thegroup [60]. In the subsequent year, Stepanian et al. performed a similar argon MI-IR analysis on a-alanineand reported the observation of two conformers, conformer I and IIA, in their matrix. They characterizedtheir spectra using B3LYP/aug− cc−pVDZ and MP2/aug− cc−pVDZ geometry and frequency theoreticalcalculations [45]. The presence of conformer IIIA in argon environment was identified by Lambie et al.12in 2002, along with the previously observed conformer I and IIA. The group combined high resolutionMI-FTIR spectroscopy with highly accurate theoretical calculations at B3LYP/6-311++G** level of theoryto accomplish their spectral assignments [80]. Nevertheless, conformer IIIA was undetected in the mostrecent MI-FTIR experiment by Bazso´ et al., where a-alanine was isolated in argon, krypton and nitrogencrystals [47]. The group utilized near-infrared (NIR) laser irradiation to distinguish the overlapping con-formers’ bands and induce conformational change of a-alanine. They also performed quantum calculationsat B3LPY/6-31++G** and MP2/6-311++G** level of theories on selected conformer candidates to aidthem in spectral analysis. Both conformer I and IIA were found to be present in the prior-irradiated ma-trices. Interestingly, Bazso´ et al. observed the production of the short lived conformer VI at the expenseof conformer I upon short NIR laser irradiation. Conformer VI was absent in the as-deposited matrices,indicating it as a product purely by photoirradiation. They also detected the slow conversion of conformer Ito conformer IIA after a prolonged irradiation process [47].2.2.3 Amino Acids ZwitterionsAmino acids exist predominantly in their zwitterionic forms in the aqueous and crystalline media, but inneutral forms in gas phase. Zwitterion is the result of solvent effect on an amino acid, where a proton fromthe acidic group is transferred to the amino group of the molecule (Figure 2.4). Water is considered to be themain culprit in inducing zwitterion formation. In fact, only a small amount of water molecules is required todrive the ionic transformation of amino acid. Xu et al. reported in their hydration studies that the lower limitof five water molecules were required to transform glycine into its zwitterion, while only four each wereneeded for phenylalanine and tryptophan [81]. In terms of interstellar chemistry, water is one of the mostabundant species present in astronomical media, especially in astrophysical ices. Thus, it is highly possiblethat amino acids in extraterrestrial frozen particles interact with the trapped water molecules, resulting inthe production of zwitterions in interstellar space [82].OONH3CH3+-OO NH3+-(a) (b)Figure 2.4: Structure of (a) b -alanine and (b) a-alanine zwitterions.Many computational [83–90] and experimental[81, 82, 91–95] studies have been performed on variousamino acids in their zwitterionic forms to investigate the structural properties and chemical stabilities ofthe ionic molecules. However, only a few of these investigations were carried out with MI-IR spectroscopytechnique [82, 92, 94]. In 2004, Ramaekers et al. reported an argon MI-FTIR spectroscopy study of neutral13and zwitterion glycine·H2O complexes. The aim of their research was to investigate the H-bond interactionbetween glycine and water in matrix environment, and they registered the observation of zwitterionic H-bondcomplexes at a higher stoichiometry complexes glycine·(H2O)n with n larger than 3. The experiment hasalso provided the first IR evidence of zwitterion formation in cryogenic isolated condition [94]. Ramaekers’sand his colleagues’ observation was supported by Espinoza et al., where the group performed a similarhydration of glycine experiment in argon crystal. Although Espinoza et al. did not purposely producezwitterion in their study, the group observed clear geometrical alterations as the first, and then the second,water molecule was introduced to the bare glycine. They have also pinpointed the mode of H-bondingas glycine interacted with the surrounding water [92]. Recently, Rodri´guez-Lazcano et al. recorded theIR spectra of pure a-alanine crystal grown in cryogenic temperature of 25 K, and slowly warmed to 200K. The group also co-deposited a-alanine with H2O, CO2 or CH4 onto the cold substrate to create icemixtures of different polarity analogous to astrophysical ices. From their experiment, Rodri´guez-Lazcano etal. observed neutral/zwitterion ratio of 60 % for pure alanine and H2O mixtures, and 90 % for the non-polarmatrices of CO2 and CH4 crystals, as deposited at 25 K. The ratio was shown to drop as the temperature ofthe crystals rose, leaving only the ionic species at 200 K. The rate of neutral to zwitterion conversion alsoappeared to be environment-dependent, with sample in non-polar matrices acquired a slower conversion ratethan those in pure sample crystals and polar matrices [82].14Chapter 3Method3.1 Experimental3.1.1 Making Enriched Parahydrogen GasNormal hydrogen gas of 99.99 % purity (Praxair Canada Inc.) was converted into parahydrogen gas of99.9955 % purity using a parahydrogen converter. This specific device was designed and built by mysupervisor, Dr.Takamasa Momose, and his associates from University of Illinois and University of BritishColumbia during the year of 2008 [1]. The system is an improvement to the converter developed by Tam andFajardo in the year of 1999, which used a closed-cycle He cryostat, thus liquid He instead of the conventionalliquid N2 or liquid H2 as cryogen [96].Briefly on the parahydrogen converter design, the converter consists of a commercial closed-cycle Hecryostat (APD Cryogenics Inc., Daikin Cryotec He Compressor Unit U104CW) modified to mount an ortho-para reactor coil onto its cold head (Figure 3.1). The coil is a solid piece of oxygen free high conductivity(OFHC) copper around which a 6.35 mm diameter copper tubing has been wound and permanently attachedto it. The copper tubing was filled with 3.3 grams of a 30 × 50 mesh hydrous ferric oxide catalyst (Sigma-Aldrich, catalyst grade), which is the main component for conversion of orthohydrogen to parahydrogen.The copper tubing loops around the OFHC core 14 times in an upward helical fashion, providing approx-imately 1.3 m of conversion path length. The last segment of the tubing passes through the center of thecore, thus ensuring that the final portion of the conversion process happened at the coldest temperature ofthe assembly. Two 1.59 mm austenitic stainless steel tubings are bended and arranged transverse to thelength of the cryostat with their ends connected to the head and tail of the reaction coil (Figure 3.2), pro-viding hydrogen gas with an incoming and outgoing routes to and from the coiled conversion section. Theentry and exit ports of the cryostat chamber are each connected to a flow counter (Kojima Instruments Inc.,Kofloc mass flow meter 3720, Gas H2, range 10 SLM) in order to read the incoming and outgoing controlledflow rates of hydrogen gas. Two separate silicon diode temperature sensors (Cryogenic Control System,Inc., Temperature Sensor S900-BB) and controller systems (Cryogenic Control System, Inc., TemperatureController Cryo.CON 34) are attached to each ends of the reactor coil to act as temperature monitors and15control devices for the apparatus. The whole instrumentation is operated under high vacuum, and the sys-tem is evacuated by a roughing oil pump (Alcaltel Pascal 2021 SD) backed-up with a diffusion oil pump(Diavaclimited Diffusion Pump DPF6Z) to get the pressure down to ≤10−4 torr range.Figure 3.1: Diagram of the parahydrogen converter with a close-up of the reactor coil in which ismounted on the cold head of the closed-cycle cryostat refrigerator and is filled with hydrousferric oxide catalyst. The image is used with the permission of Tom et al. [1].Figure 3.2: Diagram of parahydrogen converter with (right) and without (left) the vacuum shroud. Thetraces of hydrogen gas flowing into and out of the reaction coil section (red trace) is shown in theschematic with the shroud removed. The image is used with the permission of Tom et al. [1].On the procedure, we first set the temperature controllers to 13 K from the coldest chamber temperatureof 7 K. It typically took only 5 min for the system to reach 13 K, but we added another 30 min to our heatingtime to ensure thermal equilibrium across the entire coil. As previously mentioned, the temperature of 13K is close to the triple point of hydrogen at 13.8 K in which corresponds thermodynamically to 99.9955 %16of parahydrogen (see Section 2.1.2). Note that as it took 5 hrs for the cryogenic chamber to be cooled fromroom temperature to the coldest point of 7 K, we always kept our cryostat on and running, and only shut itdown on a monthly basis for maintenances purposes.Once the chamber temperature was stabilized at 13 K, we slowly flowed hydrogen gas into the converterwith a flow rate of 0.8 SLM. Hydrogen gas underwent a phase change to liquid upon entering the coldcoil section, and we waited 30 min for the entire coil to be filled with liquid hydrogen. After the wholecoil was filled, we let gas flowed through and out of the converter for at least 10 min (which equates toalmost a standard litre) with a flow rate of 0.4 SLM to (a) ensure that any residue gas from the previousexperiment will be purged out of the system, and (b) clean the stainless steel gas lines involved in routingthe gas from the converter to the storage cylinders with pure parahydrogen gas. This gas was then evacuatedusing the roughing oil pump. Note that a reasonably slow flow rate was applied to give sufficient time forthe conversion of ortho- to parahydrogen via magnetic perturbation by the catalyst. However, if the flow ratewas too slow, we might encounter an issue with the backing pressure, which might cause a back flow of gasfrom the exit port of the converter back into the coil system. For our system, we found that the flow rate of0.4 SLM seemed to supply ample of time for the conversion process in the converter, and yet gave enoughpressure to push the gas moving forward.After an appropriate amount of purging was completed, we allowed the freshly produced parahydrogengas to flow into the 1 L storage tank, and the vessel was being filled up to 700 - 900 torr. Parahydrogenwas known to undergo back conversion when being exposed to stainless steel surface or impurities suchas paramagnetic O2 molecule [1]. To minimize this back conversion occurrence, we used a teflon-linedstainless steel gas cylinder (D01-3A1800 Whitey P-5EK086-304L-HDF4-1000CC), with a stainless steelquarter turn plug valve (Swagelock S-43S4) sealed to its opening end, as our storage vessel. The backconversion rate of parahydrogen in this storage system was calculated by Tom et al. to be 1.7 % per week,and was most likely due to the exposure of the gas to a small stainless steel area at the end cap of thecylinder [1]. We also never stored our parahydrogen gas for more than 24 hrs, and made a new badge forevery experimental run to ensure that the sample used as matrix gas was in its purest and cleanest availableform.3.1.2 Preparing Argon Matrix Gas99.99 % purity argon gas (Praxair Canada Inc.) was employed with no further modifications. Prior todeposition procedure, we flowed and stored the required amount of argon gas (700 - 900 torr), into another1 L teflon-lined stainless steel gas cylinder equipped with a stainless steel metering valve (Swagelock SS-DSS4) at its opening end. The gas was flowed from the gas cylinder source through a leak-free nylon tubing(Freelin-Wade: A Coil Hose Co.) followed by the stainless steel gas lines routing to the storage vessel.3.1.3 Sublimation of Amino Acid with a Knudsen CellMost samples used for matrix-isolation spectroscopy experiment are high vapour pressure solvents, and theyare introduced into the matrices simply by pre-mixing the matrix gas with an appropriate amount of vapoursample. However, this method of doping is inapplicable on our powdered amino acid stocks. Amino acids17exist only as neutral forms in the gas phase. Whereas in the condense phases, amino acids exist mainly aszwitterions (see Section 2.2.3). To dope neutral amino acid into the matrices, we need a mechanism thatallow us to sublime the solid sample into gas, and a Knudsen effusion cell is the most efficient device to doso.We used an built in-house Knudsen cell (Figure 3.3) to sublimate our amino acid sample directly intothe matrix chamber. Our design is that of a simple resistance-heated Knudsen cell. The copper cell body is42 mm long and 8 mm wide, with its threaded cap connected to an 18 mm long and 1.6 mm wide coppernozzle, giving an orifice of 1 mm in diameter. The cell is heated with a ceramic heater (Thorlabs, HT15WCartridge Heater) attached to the rear end of the cell. A DC power supply (Takasago, LTD. Japan, GP0110-1Regulated DC Power Supply) is used to regulate the heating power of the heater, and the temperature of thecell is monitored by a temperature sensor (Thorlabs, TH10K NTC Thermistor) situated behind the samplecompartment of the cell. This set-up allows us to carefully control and maintain the temperature of the cellwithin an accuracy of ±1 K.Figure 3.3: Diagram of the inner compartment (left) and outer shell (right) of our built in-house Knud-sen cell which was employed to sublimate the amino acid samples.As we were exploring the relation of amino acids’ conformational populations with varying sublimationtemperatures, we needed to employ a range of sublimation temperatures onto our samples. These temper-atures must be high enough to ensure an ample amount of gaseous sample is produced for deposition, yetnot too high to cause thermal decomposition of amino acids. To find these appropriate, but narrow, range ofsublimation temperatures, we did a deposition test run in solid parahydrogen for each amino acid samplesused in our project. The procedure for sample deposition was described in the following section (see Section3.1.4). On these test runs, we started the deposition with the lowest predicted sublimation temperature. Wethen took a quick measurement on the sample crystal after 15 min of deposition at a specific temperature,and increased the Knudsen cell temperature by 10 K increment after each measurements. We continued withthis process until we saw signs of fragmentations from amino acid, which were indicated by the present ofadditional peaks aside from the expected molecular signals in our spectrum. From the spectra taken, wecould then deduce the minimum sublimation temperature from the first sight of amino acid signals, and themaximum sublimation temperature from the first indication of sample decomposition. Note that some frag-mented products could be reactive, and they could interact with the molecular amino acids and the matrixenvironment, giving us undesired results.183.1.4 Deposition of Amino Acid in Solid ParahydrogenOur cryogenic chamber (Figure 3.4) is a 22 cm wide doubly shielded chamber, with a 1 cm thick and 20cm inner diameter wide stainless steel outer shield, and a 1 cm thick and 14 cm inner diameter wide copperinner shield. A 10 cm wide copper cold plate is sitting on top of the cold head of a closed-cycle Gifford-McMahon refrigerator (Sumitomo Heavy Industries, Ltd., Helium Compressor Unit CKW-21A, CryocoolerSRDK-205) situated in the center of the chamber. The refrigerator can cool the cold plate down to 3.6 K,and the cold substrate to 4 K. The cold substrate is a BaF2 wedged window (Pier Optics Co., Ltd., 25 mmin diameter, 2 mm in mean thickness) held by a 4 cm by 4 cm copper window holder mounted onto thecold plate. Two separate silicon diode temperature sensors (Cryogenic Control System, Inc., TemperatureSensor S900-BB) are attached each to the cold plate and the cold substrate, with a temperature controller(Cryogenic Control System, Inc., Temperature Controller Cryo.CON 34) coupled with the sensor on coldplate, to allow for careful monitoring of the chamber temperature. The matrix gas is introduced into thechamber through a 1.59 mm stainless steel inlet tubing with its tip positioned 3.5 cm away from the coldsubstrate at a 45◦ angle. A gas flow controller (Stec Inc., Mass Flow Controller SEC-4400M0-MK3, GasH2, Flow Rate 500 ccm) is installed on the stainless steel tubing outside the chamber to allow for controlledflow rate of matrix gas onto the cold substrate. The tip of the Knudsen cell is placed 2.5 cm away fromthe cold substrate at another 45◦ angle, making a 90◦ angle with the matrix gas feed-in tube. The chamberis kept under high vacuum by a turbo pump (Pfeiffer Vaccum D-35614 Assiar, HiCube 80 Eco), giving apressure of 3×10−6 torr at room temperature, and 3×10−8 torr at cryogenic temperature of 4 K.Figure 3.4: Picture of the cryogenic chamber used for sample deposition with the covers removed. Thechamber is a doubly shielded chamber, with the a BaF2 window positioned in the middle of thecenter copper cold plate. The line at the top left corner of the image, situated at a 45◦ angle to thecold window, is the stainless steel matrix gas feed-in tube; whereas the object at the bottom leftcorner of the image, situated at another 45◦ angle to the cold window, is the Knudsen cell usedfor amino acid sample sublimation.Deposition was done at the coldest window temperature of 4 K. The crystal sample was grown directlyon the cold substrate by simultaneously sending parahydrogen gas and the sublimated amino acid sampleinto the chamber, thus allowing gaseous amino acid to mix into the matrix gas before being deposited onto19the cold surface. To achieve this procedure, we heated the Knudsen cell up to the targeted sublimationtemperature for the first 5 - 10 min, and stabilized the cell temperature within ±1 K range. We then flowedparahydrogen into the chamber with a low flow rate of 4 - 5 ccm.Ideally, the cold substrate temperature should remain at 4 K before, during, and after deposition. How-ever, due to the introduction of hot matrix gas and thermal irradiation from the Knudsen cell, we noticed thatour cold substrate temperature increased a little during deposition. The annealing temperature for parahy-drogen is at 5 K, and deposition at the annealing temperature or higher will cause the formation of theopaque and hard amorphous crystal, instead of the soft and clear quantum crystal. To avoid the formationof amorphous crystal, we kept the cold substrate temperature at 4±0.3 K, and never exciding 4.5 K, byensuring that the flow rate of parahydrogen into the chamber and the heating power implemented on theKnudsen cell remain low throughout the whole deposition process. Note that the window temperature afterdeposition was typically around 4.15±0.02 K.The specificity of deposition procedure, such as the range of sublimation temperatures used and theduration of deposition, for each amino acid experiment was briefed in the Result portion under the individualsamples’ subsections (see Sections 5.1.1, 5.2.1, 5.3.1, and 5.4.1).3.1.5 Deposition of Amino Acid in Argon MatricesThe procedure of depositing amino acid in argon matrices was similar to that of solid parahydrogen, asidefor a few discrepancies. Instead of depositing at the coldest substrate temperature of 4 K, we grew ourargon crystal sample on an 18 K window. After deposition, we also performed annealing on the solidargon to reduce the site slitting effects often associated with rare gas matrices. Annealing was done byslowing heating the argon crystal up to the annealing temperature of 35 - 40 K, stabilizing the matrix at theannealing temperature for 10 - 15 min, then slowly reducing the window temperature back down to 4 K totake measurement. We repeated these steps until no more site shifting was observed from the spectra.3.1.6 In-Situ UV-irradiation of Amino Acid within the Solid MatricesWe used a modified deuterium lamp (Hamamatsu Photonics K.K., L2D2 Lamp L7295, Power 30 W, SpectralDistribution 160 - 400 nm), housed in a custom made lamp housing and controlled by its associated powersupply (Hamamatsu Photonics K.K., Deuterium Lamp Power Supply C1518), as our UV-irradiation source(Figure 3.5). The light was sent in through a MgF2 window (Thorlabs, WG61050, 25.4 mm in diameter,5 mm thickness) installed at the side portal of the chamber, and hit the BaF2 cold window from the back(Figure 3.6). Note that the matrix sample was grown on the front of the cold window. Thus, UV photonswere transmitted through the cold window to reach the sample molecule. BaF2 window has a transmissionrange of 200 nm - 12 mm, making it a suitable cold substrate for this irradiation set-ups.We typically irradiated the deposited sample for a total of 3 - 4 hrs, and recorded a spectrum at eachhour of irradiation. All UV-irradiation were done at 4 K. The specificity of UV-irradiation procedure foreach amino acid experiment was briefed in the Result portion under the individual samples’ subsections(see Sections 5.1.1, 5.2.1, and 5.3.1).20Figure 3.5: Pictures of the deuterium lamp enclosed within its housing used for the in-situ UV-irradiation experiments.Figure 3.6: Diagram of cryogenic sample chamber with the portal of UV-irradiation from the deu-terium lamp through the back MgF2 window to the back-side of the BaF2 cold window.21Figure 3.7: Diagram of the cryogenic sample chamber with the path of IR light from the FTIR spec-trometer travelling through the three BaF2 cold windows (with the middle window holds thesample crystal), and to the MCT detector by being deflected in the transfer optic chamber with aparabolic mirror.3.1.7 FTIR Measurement Parameters and Detection System Set-upsWe used a FTIR spectrometer (Bruker, IFS 125HR), equipped with a KBr beam splitter, MIR globar lightsource, and a liquid nitrogen cooled MCT detector (InfraRed Associates. Inc., D316/2M), to attain all theoptical measurements for our experiments. The instrumentation was maintained under low pressure of0.05 hPa with a mechanic pump (Adixen OMF 40S). As the sample chamber was situated outside thespectrometer, the IR beam was sent into the cryogenic chamber by deflecting the light at an angle of 90◦ viaa parabolic mirror. The beam passed through two separated BaF2 windows (Pier Optics Co., Ltd., 25 mmin diameter, 2 mm in mean thickness) upon entering and exiting the chamber, and hit the sample substratesituated at the middle of the chamber from the back. The beam was then travelled to another parabolic mirrorcontained within an built in-house transfer optic chamber (11 cm × 11 cm), and being deflected at another90◦ angle into the MCT detector (Figure 3.7). The transfer optic chamber was kept under low pressure witha small mechanical pump (Oerlikon Leybold Vacuum, DIVAC0.8LT).All spectra were registered at 4 K in the range of 700 - 4800 cm−1, with either 0.2 cm−1 or 0.05 cm−1resolution, and a total of 1000 number of measurements. The specific measurement parameters for eachamino acid experiment was briefed in the Result portion under the individual samples’ subsections (seeSections 5.1.1, 5.2.1, 5.3.1, and 5.4.1).223.2 Computational3.2.1 Quantum Calculation with WebMOWe performed quantum calculations at B3LYP/aug− cc−pVTZ level of theory on the most stable conform-ers of our amino acid samples using WebMO [97]. The corresponding relative energies, relative Gibbs freeenergies, and theoretical vibrational wavenumbers and intensities were then derived from the calculationsin order to interpret our experimental spectra. To ensure a calculated result with the highest obtainableaccuracy, tight optimization was applied on each geometry used.The amino acids’ conformers chosen for quantum calculations must be local minimum conformers forthe derived vibrational wavenumbers to be real. We explored published theoretical materials to determinethe most appropriate conformational structures of amino acids to be used for calculations. Details on eachamino acid configuration used for theoretical calculation was mentioned in the Result portion under theindividual samples’ subsections (see Sections 5.1.1, 5.2.1, and 5.3.1).23Chapter 4Theory and Calculations4.1 Relative Energy and Relative Gibbs Free EnergyA way to determine the stability of a molecular conformer is to check the conformer’s relative energies andrelative Gibbs free energies. From thermodynamic perspective, conformers with the lowest relative energyand relative Gibbs free energy are often attributed to the most stable configurations of the molecule [98].This relation is thus applied by spectroscopists to predict the probability of detecting specific conformerconfigurations in their experimental spectra in particular in IR spectra.The acquired information for the calculation of relative energies and the relative Gibbs free energies ofa molecule can be extracted from the sample output of quantum computing programmes such as Gaussianor WebMO [99]. The following subsections highlight the calculation steps to determine the relative energiesand relative Gibbs free energies associated with our amino acids investigations, with WebMO being thequantum computing program utilized for our studies.4.1.1 Calculation of the Relative EnergyThe calculation of the relative energy of a specific conformer is fairly straightforward. It must be notedthat WebMO uses the lowest possible energy state (i.e., the zero-point energy (ZPE))of a system, instead ofthe minimum of the classical potential well, to determine many of the calculated thermodynamic quantities[99]. These computed quantities include the total electronic energy, Etot , which is the energy of the moleculerelative to the separated nuclei and electron [100]. Therefore, to obtained the real total energy of a moleculein its specific conformational state, E j, we must correct the total electronic energy of the conformer, Etot( j)listed in the sample output of WebMO to the conformer’s ZPE byE j = Etot( j)+ZPE: (4.1)The relative energy of the conformer, DE j, can then be computed by weighing E j to the real total energyof the lowest energy conformer, E1 (assuming Conformer I to be the conformational configuration with thelowest energy), as shown withDE j = E j−E1: (4.2)244.1.2 Calculation of the Relative Gibbs Free EnergyGibbs free energy, G, correlates with the temperature of the system through the relationG≡ H−T S (4.3)in which H is the expression for enthalpy, S is the expression for entropy, and T represent the temperatureof the system [98]. For our amino acids studies, T would be the sublimation temperature of an amino acidsample for a particular deposition procedure.The WebMO program carries out its thermodynamic computations by assuming an ideal gas at atmo-spheric pressure (1 atm) and room temperature (298.15 K) [97, 99]. This assumption does not align withour real experiment system of varying sublimation temperatures, which are in the range of 380 - 430 Kdepending on the sample employed. Therefore, to calculate the Gibbs free energies at a specific amino acidsublimation temperature, GT , we must start our calculation from the very core of thermochemistry, i.e., themolecular partition functions.The first factors to be determined for GT calculation are the thermal correction to the internal thermalenergy, Ecorr, and the entropy, Scorr, of a molecular system. Ecorr and Scorr are given as the sum over allfour components of contributions, which are the translational (trans), rotational (rot), and vibrational (vib)degrees of freedom, plus the electronically excited states (el) [99]. The relations of Ecorr and Scorr to thefour contributional components are represented byEcorr = Etrans +Erot +Evib +Eel (4.4)andScorr = Strans +Srot +Svib +Sel (4.5)respectively. Note that the internal thermal energy contribution from partition function, Eq, is given byEq = NkBT 2(d ln(q)dT)V (4.6)where kB is the Boltzmann constant; whereas the entropy contribution, Sq is given bySq = R(ln(q)+T (dqdT)V ) (4.7)where R is the gas constant [101].The electronic partition function, qel , of a molecule is defined asqel = w0e−e0=kBT +w1e−e1=kBT +w2e−e2=kBT + ::: (4.8)in which w is the degeneracy of the the energy level and en is the energy of the nth level [101]. In WebMO,an assumption is made on the energies of the first and higher electronic excitation states to be much greaterthan kBT, thus making these states inaccessible at any temperature [99]. Additionally, the energy of the25ground electronic state is set to be the ZPE of the system, equating e0 to zero [99]. These assumptions havesimplify qel toqel = w0; (4.9)and simplify the entropy due to electronic motion, Sel toSel = R(ln(qel)+0) = R(ln(w0)) (4.10)which equates to zero (Sel = 0). Furthermore, as there are no temperature dependent terms in the assumedelectronic partition function (Equation 4.9), the contribution to the internal thermal energy due to electronicmotion, Eel is also equates to zero (Eel = 0).The translation partition function, qtrans, of a molecule is defined asqtrans = (2pmkBTh2)3=2V = (2pmkBTh2)3=2kBTP(4.11)in which m is the mass of the molecule and h is the Planck constant [101]. Translational entropy, Strans isthusStrans = R(ln(qtransk)+T32T) = R(lnqtrans +1+3=2) (4.12)in which k is the factor originating from Stirling’s approximation, and the contribution to the internal thermalenergy due to translation, Etrans isEtrans =32RT: (4.13)The rotational partition function, qrot , of a non-linear polyatomic molecule is defined asqrot =p1=2sr(T 3=2(Qr;xQr;yQr;z)1=2) (4.14)in which sr is the rotational symmetry number and Qr is the rotational temperature of the molecule inrelation to the molecular axis [101]. The values of sr and Qr are provided in the WebMO output [97, 99],allowing us to quickly calculate the rotational entropy, Srot , and the contribution to internal thermal energydue to rotation, Erot , through the equationsSrot = R(lnqrot +32) (4.15)andErot =32RT; (4.16)respectively.The vibrational partition function, qvib;K , of a specific vibrational mode is defined asqvib;K =e−Qv;K=2T1− e−Qv;K=T (4.17)26where Qv;K is the vibration temperature given by Qv;K = hnK=kB. The overall vibrational partition functionof a molecule, qvib, is thusqvib =PKe−Qv;K=2T1− e−Qv;K=T (4.18)[101]. In WebMo, the vibrational temperatures of all the calculated vibrations are listed in the output [97,99], allowing us to calculate the vibrational entropy, Svib, and the contribution to internal thermal energy dueto vibration, Evib, through the equationsSvib = RSK(Qv;K=Te−Qv;K=T −1 − ln(1− e−Qv;K=T )) (4.19)andEvib = RSKQv;K(12+1e−Qv;K=T −1): (4.20)From the obtained Ecorr and Scorr, we can determine the thermal correction to the enthalpy, Hcorr, andthe Gibbs free energy, Gcorr, of the molecular system through the equationsHcorr = Ecorr + kBT (4.21)andGcorr = Hcorr−T Scorr: (4.22)GT can then be obtained by correcting the total electronic energy, Etot , to Gcorr throughGT = E0 +Gcorr: (4.23)Finally, the relative Gibbs free energy of a specific molecular conformer at a fixed sublimation temperature,DGT ( j) can be calculated by weighing the Gibbs free energies of the conformer at the indicated sublimationtemperature, GT ( j) to the Gibbs free energy of the lowest energy conformer at the same sublimation temper-ature, GT (1) (again, assuming Conformer I to be the conformational configuration with the lowest energy),as shown withDGT ( j) = GT ( j)−GT (1): (4.24)For our experiment, the relative Gibbs free energy, DGT ( j), would be a more accurate interpretation ofthe amino acids’ conformational stability than the relative energy, DE j. DE j only considers the electroniccomponent of the molecule, in which is independent from the temperature of the system [101]. However, forour experiments of varying sublimation temperatures, the temperature-dependent components in a molecu-lar system are the keys to determine the stability of a molecular conformer at a specific system temperatureas the partition functions between different systems change due to the difference in temperature. The vibra-tional degree of freedom is the largest contribution to a temperature-dependent molecular system [100] asdescribed in Equations 4.17-4.20; whereas the rotational and translational degrees of freedom input a littleof their contributions to the system as explained in Equations 4.14-4.16 for rotation and Equations 4.11-4.13for translation. DGT ( j) is derived with the consideration on vibrational, rotational, and translational con-27tributions, meaning it is a component with a relation to the temperature of a specific system, thus a betterrepresentation of the energy of our conformational molecules.4.2 Boltzmann Distribution LawThe distribution of conformers within a system of constant temperature is given by the Boltzmann distribu-tion lawN jNtot=e−e j=kBTåi e−ei=kBT(4.25)where N j is the number of molecules corresponding to conformer “j”, Ntot is the sum of all the conformer’smolecules, e is the energy of conformer state, kB is the Boltzmann constant, and T is the temperature of thesystem [98]. For our amino acid studies, we employed T to be the sublimation temperature of the aminoacids for a particular deposition procedure, and e to be the calculated Gibbs free energy of the sampleat specific sublimation temperature, DGT , as highlighted above (see Section 4.1.2). From the Boltzmanndistribution law, we can deduce that lower energy conformers would be more predominantly exist in thesystem as compared to higher energy conformers. We can also acquire a trend of increasing population inthe higher energy conformers with the increase in the system temperature. Indeed, we have applied theseconclusions to our experimental analysis on the relation of sublimation temperature to the population ofgaseous amino acids (see Section 5.2.3).28Chapter 5Results and Discussions5.1 Conformational Analysis of b -alanine in Solid Parahydrogen andArgon MatricesWe investigated the conformational stability of b -alanine in solid parahydrogen using FTIR spectroscopy,and compared the results to those in argon matrices. We also explored the behaviour of b -alanine conformersin an UV environment by performing in-situ photoirradiation.We had published our results in the Journal of Molecular Spectroscopy on January 2015 [2]. The fol-lowing subsections are mostly copies from our original paper, with minor editions and rearrangements toaccommodate the format and coherency of this thesis.5.1.1 Experimental and Computational Details for b -alanine Conformational StudyThis section highlights the experimental and computational specificities applied in our b -alanine conforma-tional study. The general set-ups and procedure have been described previously (see Chapter 3).Similar to the general deposition procedures, the matrix gas was deposited onto the cold BaF2 windowsimultaneously with b -alanine sublimation, with deposition being performed at 4 K for solid parahydrogenmatrix experiments, and 18 K for argon matrix experiments. The gas flow rate was 5 ccm for parahydrogen.However, a much lower gas flow rate of 0.1 ccm was applied for argon. A typical deposition duration was1.5 hrs for parahydrogen and 2 hrs for argon.From the deposition test run, we observed that the b -alanine sample (Sigma Aldrich, 99 % purity, usedas received) started to sublimate at around 360 K and decompose above 400 K with our Knudsen cell. Inthis study, b -alanine was sublimed at 390±1 K for both solid parahydrogen and argon experiments. Samplewas also introduced into the matrix at 340 K, below the reported sublimation temperature of b -alanine, inorder to identify spectral peaks due to impurities in the samples. The flow of gaseous b -alanine was simplyregulated by the temperature of the Knudsen cell. The concentration of b -alanine in the matrix was unknownfor all experiments, but in general the concentration of sample in solid parahydrogen was ten times less thanthat in argon matrices due to the differences in gas flow rate and deposition time. Spectral lineshapes weremonitored to ensure no clustering compounds were formed.29Figure 5.1: Structures of the eleven lowest energy b -alanine conformers using Ramek’s nomencla-tures. All conformers, except for VII, belong to the C1 point group. Conformer VII belongs tothe Cs point group.For in-situ photoirradiation, the deposited samples were irradiated for 4 hrs straight, using a modifieddeuterium lamp. The results acquired were mainly employed to aid with spectral assignment, as b -alaninewere shown to undergo conformational conversion upon UV-irradiation over an extended period of time.The optical measurements were obtained using a FTIR spectrometer, with all spectra recorded at 0.2cm−1 resolution and 1000 number of measurements. The obtained spectral bands were fitted with a Lorentzianfunction in order to obtain the corresponding band heights, widths and areas.Quantum calculations were performed at the B3LYP/aug− cc−pVTZ level of theory. The structures ofthe b -alanine conformers obtained by Stepanian et al. [19] were used as initial geometries for geometryoptimizations of the eleven lowest energy conformers (Figure 5.1). Vibrational wavenumbers and IR ab-sorption intensities were calculated analytically after tight optimization of each geometry. All calculated30vibrational wavenumbers were found to be real, which indicates that the eleven conformers were all localminimum conformers. In this paper, all b -alanine conformers are denoted using Ramek’s nomenclatures[57].5.1.2 Solid Parahydrogen Matrix-Isolated Spectra of b -alanineIn this section, we present the results regarding the conformational composition and the UV-irradiationbehaviour of b -alanine in a solid parahydrogen matrix. The conformers of b -alanine were identified bycomparisons between the experimental spectrum obtained (Figures A.1 and A.2 of Appendix) and the the-oretical wavenumbers and intensities of the eleven lowest energy conformers (Table A.1 of Appendix).The ZPE corrected relative energies and the relative Gibbs free energies of the eleven conformers (Table5.1) were also taken into consideration in the course of the assignments. The experimental and the theo-retical wavenumbers and intensities of all observed b -alanine bands are listed in Table 5.2. Upon in-situUV-irradiation, peak intensities were observed to change with different behaviours (Figures A.3 and A.4 ofAppendix). Overlapping peaks contained within various wide bands were resolved after the UV-irradiation.Peaks which increased and decreased in intensity upon irradiation are shown by “+” and “-”, respectively,in Table 5.2.Table 5.1: ZPE-corrected relative energies, DE, and relative Gibbs free energies at 390 K, DG390K , ofthe eleven lowest energy b -alanine conformers calculated by B3LYP/aug− cc−pVTZ.We expect conformer I to occur predominantly in the matrix as it is the lowest energy conformer. Thestability of this conformer can be attributed to its intramolecular N-H—O bond. A comparison betweenexperimental and theoretical spectra confirmed that some of the most intense experimental bands correspondto conformer I. These bands were observed to decrease in intensity upon UV-irradiation. Bands that alsodecreased in intensity but could not be assigned to conformer I were deduced to originate from conformers IIand VII. Bands that increased in intensity upon irradiation agreed with the theoretical spectra of conformersIII and IV.A more detailed analysis is described below. The presence of certain conformers is explained based onthe FTIR spectra in the spectral regions of the NH2 wagging modes (w(NH2)), the C-O stretching/OH bend-ing modes (n(C-O)/d (OH)), the C=O stretching modes (n(C=O)), and the OH stretching modes (n(OH)),respectively. These are some of the most intense peaks in the derived spectra of b -alanine conformers. Theassignment of other regions of the spectra can be found in Table 5.2.Region of the w(NH2) Vibrational Mode (770 - 840 cm−1)In this spectral region, five peaks were clearly resolved consisting of different UV-irradiation behaviours(Figure 5.2). This indicates that some or all peaks are due to different b -alanine conformers. According to31Table 5.2: Experimental wavenumbers (n , cm−1), peak heights (h, arbitrary unit) and spectrallinewidths (w, cm−1) of b -alanine sublimed at 390 K trapped in solid parahydrogen and argonmatrices. The corresponding theoretical wavenumbers (n , cm−1) and intensities (I, km·mol−1)were calculated by B3LYP/aug− cc−pVTZ.323334a Scaling factors: 0.955 for vibrational modes with wavenumbers greater than 2000 cm−1,0.985 for all other vibrational modes. b “+” indicates that the corresponding peak intensity in-creased upon UV-irradiation, while “-” indicates those which decreased. c asy - asymmetric, bend- bending, rock - rocking, scissor - scissoring, str - stretching, s - symmetric, tor - torsion, twist- twisting, wag - wagging. d UV-irradiation indicated overlapping of multiple peaks. e Assign-ment applicable to solid parahydrogen matrix isolation spectra only. f Assignment applicable tosolid argon matrix isolation spectra only. Note experimental bands in the region of approximately1520 cm−1 to 1700 cm−1 are not listed in the table. These assignments were difficult due to theinterference of water absorption.the theoretical calculation, a peak due to conformer I is expected to be observed at a high wavenumber inthis region with a strong intensity, as it has a theoretically predicted wavenumber of 836.0 cm−1 and it isthe most stable conformer of b -alanine. Two intense peaks were observed in the high wavenumber regionat 819.9 cm−1 and 822.7 cm−1. If we assign the peak at 822.7 cm−1 to conformer I, the peak at 819.9cm−1 can be assigned to conformer II since (1) the theoretically calculated wavenumber (820.1 cm−1) isslightly lower than that of conformer I, (2) the predicted intensity is larger than that of the correspondingpeak of conformer I, and (3) conformer II is the third lowest energy conformer among the eleven conformers(Table 5.1), therefore a large abundance is expected. The assignment of the peaks due to conformers I andII also suggests that the difference between the theoretical and the experimental wavenumbers in this regionis expected to be within 15 cm−1. Referring to the calculated wavenumbers, intensities and the stability ofconformers, the band at 797.9 cm−1 was attributed to conformer VII. Bands corresponding to conformersI, II and VII were all observed to decrease in intensity upon UV-irradiation (Figure 5.2b). The differencespectrum shows that the peaks occurring at 809.6 cm−1 and 781.8 cm−1 increased in intensity upon UV-irradiation, and were resolved into multiple sharp peaks. These bands were attributed to conformers III andIV based on similar assignment criteria as described above. Besides peaks corresponding to conformers I,II, III, IV and VII, unassigned bands with minor intensities, such as the peak at 803.4 cm−1, are still presentin this region. These bands could not be allocated consistently to any theoretically predicted peaks.35Region of the n(C-O)/d (OH) Vibrational Modes (1090 - 1160 cm−1)The presence of conformers I, II, III, IV and VII deduced by the spectral analysis in the w(NH2) region wasalso confirmed in the n(C-O)/d (OH) region (Figure 5.2). Two peaks at 1113.8 cm−1 and 1153.0 cm−1 in then(C-O)/d (OH) region reduced in intensity upon UV-irradiation. The spectral analysis in the w(NH2) regionrevealed that conformers I, II and VII were observed to have the same behaviour upon UV-irradiation. Fromthe theoretical wavenumbers, the peak at 1153.0 cm−1 can be assigned to conformer VII, whose theoreticalwavenumber is 1128.4 cm−1. The calculation showed comparable intensities between the n(C-O)/d (OH)and the w(NH2) modes, which also supports the assignment. The band located at 1113.8 cm−1 was ascribedto both conformers I and II, whose theoretical wavenumbers are 1108.9 cm−1 and 1107.9 cm−1, respectively.Due to the proximity of the calculated wavenumbers, these peaks are expected to overlap completely. Peaksat 1101.3 cm−1 and 1119.3 cm−1 showed an increase in intensity upon UV-irradiation. Referring to thetheoretical values, these peaks were assigned to conformers III and IV, respectively.Region of the n(C=O) Vibrational Mode (1725 - 1790 cm−1)The most intense band (at 1771.1 cm−1) and the second most intense band (at 1734.3 cm−1) in this regionshowed a decrease in intensity upon UV-irradiation, and therefore these were attributed to conformers I andII, respectively. Their theoretical wavenumbers are 1770.9 cm−1 and 1752.7 cm−1, respectively, which arein good agreement with the observed wavenumbers. The n(C=O) modes of conformers IV and III, whosetheoretical wavenumbers are 1776.9 cm−1 and 1782.0 cm−1, respectively, were identified at 1762.3 cm−1and 1781.2 cm−1, respectively. These bands showed an increase in intensity upon UV-irradiation. The bandoriginating from the n(C=O) mode of conformer VII, predicted at 1777.4 cm−1, was unobserved as it ismost likely masked by the presence of other peaks.Region of the n(OH) Vibrational Mode (3560 - 3580 cm−1)The spectral region of the n(OH) vibrational mode showed only one feature, which results from the overlapof multiple peaks. Upon UV-irradiation, the peaks at 3567.8 cm−1 and 3569.3 cm−1 deceased in intensity,while the peak at 3571.5 cm−1 was resolved into two components which increased in intensity. Based onthe calculated wavenumbers and these UV-irradiation behaviours, the peak at 3567.8 cm−1 was assigned toconformers II and VII, and the peak at 3569.3 cm−1 was attributed to conformer I, and the two resolvedbands were assigned to conformers IV and III, respectively.Other Spectral RegionsFrom the regions of w(NH2), n(C-O)/d (OH), n(C=O) and n(OH) vibrational modes, we were able to de-duce the presence of five conformers, conformers I, II, III, IV, and VII, in solid parahydrogen, and obtaintheir corresponding UV-irradiation behaviour. The bands in the remaining regions were then assigned ac-cording to these results, and also the theoretical wavenumbers and intensities. The majority of the bands inthe recorded spectra originated from conformer I due to its large abundance in the matrix. Out of its twenty-four theoretical bands in the region of 700 cm−1 - 4800 cm−1, all but three were identified experimentally.36Figure 5.2: FTIR spectra of b -alanine sublimed at 390 K and isolated in a parahydrogen matrix (T =4 K) taken from regions of n(OH), n(C=O), n(C-O)/d (OH), and w(NH2). Panel (a) shows thespectrum recorded immediately after deposition. Panel (b) is the difference spectrum obtainedby subtracting the deposition spectrum from the spectrum observed after 4 hrs of UV-irradiation.Panel (c) shows the theoretically predicted vibrational wavenumbers assuming a Boltzmann dis-tribution at 390 K. The theoretical wavenumbers are corrected by a factor of 0.955 for vibrationalmodes which are derived to be above 2000 cm−1, and 0.985 for all other vibrational modes. Theconformational assignment is given at each peak by Ramek’s nomenclatures.37Conformer II is the second most stable conformer out of the five found in our matrix. This conformer isstabilized by an intramolecular N-H—O bond as is the case in conformer I. Due to the structural similaritybetween conformers I and II, many of the corresponding vibrational bands are expected to overlap. Conse-quently, only twelve vibrational bands were assigned to conformer II. The structure of conformer IV differsconsiderably from that of conformers I and II. As a result, the corresponding bands were more resolved, andtwelve vibrational bands were attributed to conformer IV despite its instability as compared to conformerII. Since conformers VII and III are unstable compared to the other detected conformers, only six and eightbands, respectively, with intensities predicted to be large were identified.Upon UV-irradiation, bands corresponding to conformers I, II, and VII were found to reduce in intensity,while bands from conformers III and IV increased in intensity. Since conformers I and II are the most stableamong these five conformers, UV excitation by 200 nm - 250 nm radiation induces conformational changesin b -alanine to less stable structures via electronically excited states.Conformer III is stabilized by an n - p* interaction by the delocalization of electron density from thenon-bonding orbital of the nitrogen to the anti-bonding orbital of the carbonyl group [59], but its free energyis 6.8 kJ·mol−1 higher than the lowest conformer I. Its population is about a few percent at the sublimationtemperature of 390 K. Conformer III has been detected by Sanz et al. [59] by the laser ablation techniqueusing microwave spectroscopy, but no vibrational spectroscopy has been reported. This is the first time thepresence of conformer III in a matrix environment has been confirmed.5.1.3 Comparison between Conformational Composition of b -alanine in a ParahydrogenMatrix and in an Argon MatrixThe conformational composition of b -alanine was also investigated in an argon matrix (Figures A.5, A.6,A.7 and A.8 of Appendix). Spectral assignment was performed similarly to our analysis of the spectra insolid parahydrogen. As a result, four b -alanine conformers, conformers I, II, IV and VII, were identifiedand assigned in an argon matrix (Table 5.2). Twelve, seven, nine and six vibrational modes were assignedexperimentally for conformers I, II, IV and VII, respectively.The vibrational wavenumbers of the peaks detected in a parahydrogen matrix and in an argon matrixwere observed to differ by less than 9 cm−1. It was found that the spectral linewidth of b -alanine in solidargon was slightly narrower than that in solid parahydrogen. Spectral linewidths of rotationally resolvedvibrational transitions in solid parahydrogen were reported to be much narrower than those in rare gasmatrices due to a long rotational decoherence time in solid parahydrogen [32, 37, 102–104]. In the case ofb -alanine, rotational motion is completely quenched even in solid parahydrogen. The broader linewidth insolid parahydrogen indicates that the vibrational decoherence time is much shorter in solid parahydrogenthan in solid argon. Because of the narrower linewidth, the argon spectra were used to resolve some of theoverlapping bands detected in the parahydrogen spectra, in particular, the bands corresponding to the n(C-O)/d (OH) of conformers I and II. Contrary to expectations, the slightly broader linewidth in parahydrogencrystals is less desirable for matrix isolation spectroscopy of amino acids.The effect of UV-irradiation in an argon matrix is similar to that in a parahydrogen matrix - conformers I,II and VII decreased in intensity, and conformer IV increased in intensity (Figure 5.3). However, the change38Figure 5.3: FTIR spectra of b -alanine sublimed at 390 K taken from regions of n(OH), n(C=O), n(C-O)/d (OH), and w(NH2) in solid parahydrogen (blue trace) and in solid argon(black trace). Eachpanel consists of (a) a spectrum taken immediately after deposition, and (b) a difference spectrumobtained by subtracting the deposition spectrum from the spectrum observed after 4 hrs of UV-irradiation. The assignments of conformers are given in each argon spectrum. “*” mark the bandsof conformer III, which were observed in the solid parahydrogen spectrum but not in the argonspectrum. The band marked by “↓” in the w(NH2) region is assigned to another vibrational modeassociated with conformer IV.39in intensity upon irradiation was less pronounced in solid argon. The intensity of conformer I decreasedby 14 % in parahydrogen matrices after 4 hrs UV-irradiation, while it decreased by 10 % in argon matricesunder the same irradiation condition. The larger conformational change found in parahydrogen matrices isdue to the softer environment provided by these matrices as compared to the rare gas matrices. The softnessof the parahydrogen matrix environment is a result of the quantum nature of solid hydrogen (see Section2.1.2). As a consequence, in-situ photoirradiation results in more conformational changes in parahydrogenmatrices than in argon matrices.Conformer V was unobserved in both solid parahydrogen and argon matrices in our experiments, asopposed to what was previously reported. Stepanian et al. [19] reported that the n(OH) stretching modeof conformer V was observed at 2982.8 cm−1 in an argon matrix. We did not observe any peaks in thisspectral region in an argon matrix or in a parahydrogen matrix. Furthermore, none of the observed bands inthe regions of w(NH2), n(C-O)/d (OH), and n(C=O) agree with the theoretical wavenumbers and intensitiesof the corresponding modes of conformer V. Thus, the presence of conformer V is unsupported by ourexperimental results. Indeed, the free energy of conformer V is relatively high at 390 K, although its ZPE-corrected energy is low (see Table 5.1).5.1.4 Sublimation Temperature Dependence of b -alanine Conformational Population inSolid ParahydrogenWe attempted to investigate the correlation between sublimation temperature and conformational populationratio of gas phase b -alanine in solid parahydrogen, by introducing our sample into the matrices at differentsublimation temperatures of 390 K and 380 K. All b -alanine conformers which were observed at 390 K werealso detected at 380 K. We then tried to obtain the relative abundance of each conformer at deposition byextracting the experimental peak areas and weighing them by the theoretical intensities. However, we foundthis task quite impossible to accomplish due to the presence of unresolved overlapping peaks involvingmultiple conformers. As we could not accurately calculate the population of each conformer from our data,we aborted this study for b -alanine, and reinvestigated it on another amino acid, namely a-alanine.5.2 Conformational Analysis of a-alanine in Solid Parahydrogen andArgon MatricesSimilar to b -alanine experiment, we investigated the conformational stability of a-alanine in solid parahy-drogen using FTIR spectroscopy, and compared the results to those in argon matrices. We mainly analyzedthe correlation between sublimation temperature and conformational population ratio of gaseous a-alaninein both matrices. We also explored the effect of UV-irradiation on a-alanine by performing in-situ photoir-radiation.We have prepared a manuscript on our result for publication in the near future [4]. The following sub-sections are mostly copies from our written draft, with minor editions and rearrangements to accommodatethe format and coherency of this thesis.40Figure 5.4: Structures of the eight lowest energy a-alanine conformers using Csa´sza´r’s nomenclaturesand Baladin’s geometric configurations. All conformers presented are in the L-form of a-alanineenantiomer. Therefore, we omitted the “A” and “B” labels which accompanied the L- and D-enantiomers, respectively, in Csa´sza´r’s notations.5.2.1 Experimental and Computational Details for a-alanine Conformational StudyThis section highlights the experimental and computational specificities applied in our a-alanine conforma-tional study. The general set-ups and procedure have been described previously (see Chapter 3).The a-alanine gas and the matrix gas were simultaneously deposited directly onto a BaF2 cold windowfor 30 min at a gas flow rate of 5 ccm, for both solid parahydrogen and argon matrix experiments. a-alaninegas was obtained by subliming the a-alanine sample (L-a-alanine, Sigma Aldrich, ≥99.5 % purity, usedas received) using a built-in house copper Knudsen cell. The sample was sublimed at a temperature of420±1 K in order to identify the conformers present in the matrices and to investigate the effects of in-situ UV-irradiation, and also at temperatures of 410±1 K and 430±1 K in order to study the relationshipbetween conformational population and sublimation temperature. Thermal decomposition of a-alanine was41monitored for all experiments, and no degradation products were observed. The molar ratio of matrix gas toa-alanine was unknown for all experiments. However, formation of clusters was monitored by examiningthe spectral line shapes.For the in-situ UV-irradiation experiments, a modified deuterium lamp was employed, and the depositedsamples were irradiated for 4 hrs in total, with a spectrum recorded at each hour of irradiation.The optical measurements were obtained using a FTIR spectrometer, with all spectra recorded at 0.2cm−1 resolution and 1000 number of measurements. The obtained spectral bands were fitted with a Gaussianand/or Lorentzian function in order to obtain the corresponding band heights, widths and areas.The structures of the eight stable L-a-alanine configurations found by Balabin [70] was employed asa foundation for geometry optimization at the B3LYP/aug− cc−pVTZ level of theory (Figure 5.4). All a-alanine conformers in this study are denoted using Csa´sza´r’s nomenclatures [69]. The corresponding ZPE-corrected relative energies, the relative Gibbs free energies, and the theoretical vibrational wavenumbersand intensities were derived in order to interpret our experimental FTIR spectra. Tight optimization of eachgeometry was first performed, and the vibrational wavenumbers were then calculated analytically. The eightconformers were found to be local minimum conformers as all of the derived vibrational wavenumbers werecalculated to be real.5.2.2 Conformers of a-alanine Isolated in Solid Parahydrogen and Argon MatricesThe conformational compositions of a-alanine in our parahydrogen matrix and in our argon matrix wereidentified by comparing the spectra obtained immediately after deposition (Figures B.1 and B.1 of Appendix,respectively) with the calculated wavenumbers and intensities (Table B.1 of Appendix) of the eight lowestenergy conformers, while taking into consideration the corresponding ZPE-corrected relative energies andthe relative Gibbs free energies (Table 5.3). In order to identify peaks which result from site splitting inan argon matrix environment, we also performed annealing experiments and compared the correspondingspectrum (Figure B.3 of Appendix) with the spectrum recorded immediately after deposition in an argonmatrix.Table 5.3: ZPE-corrected relative energies, DE, and relative Gibbs free energies at 420 K, DG420K , ofthe eight lowest energy a-alanine conformers calculated by B3LYP/aug− cc−pVTZ.We expect conformer I to be the most abundant in our matrices as it is the lowest energy conformer.We also anticipate the presence of conformer II, the third lowest energy configuration, as its occurrence in amatrix environment has been reported previously [45, 47, 80]. A comparison between the theoretical spectraand the experimental spectra reveals that the most predominant bands in our spectra indeed correspond toconformer I and II. Other unassigned bands still remain in our spectra after the allocation of the conformerI and conformer II bands. In the solid parahydrogen spectra, these bands were concluded to arise fromconformer IV and V; while in the argon spectra, no additional conformers were identified. In order to illus-42trate the presence of these conformers in our matrices, a more detailed analysis of the spectra is describedbelow. The discussion will focus on four regions of the spectra: the region of the OH stretching modes(n(OH)), the C=O stretching modes (n(C=O)), the C-O stretching modes (n(C-O)), and the NH2 waggingmodes (w(NH2)), respectively, as these regions consist of the strongest theoretical vibrational motions. Thespectral assignments of the remaining bands observed in our recorded spectra can be found in Table 5.4.Region of the n(OH) Vibrational Mode (3560 - 3580 cm−1)In this region of the spectra, a peak associated with conformer I is derived to be observed at 3565.4 cm−1(Figure 5.5a). This band is also predicted to be strong as conformer I is derived as the most stable configu-ration by the ZPE-corrected relative energies and the relative Gibbs free energies, hence it can be expectedto occur with the greatest abundance in our matrices. In the solid parahydrogen spectrum (Figure 5.5b)a strong peak is detected at 3565.3 cm−1, and thus was attributed to conformer I. In the argon spectrum(Figure 5.5c), a predominant band was observed at 3564.4 cm−1. However, it was concluded to result fromsite splitting rather than conformational effects as it decreased drastically upon annealing (Figure 5.5d). Asa result, the conformer I peak was attributed to the band at 3574.5 cm−1 instead. As compared to conformerI, conformer II consists of an intramolecular OH—N hydrogen bond which is absent in conformer I (Figure5.4). Consequently, the n(OH) band of conformer II was predicted to be downshifted with respect to theconformer I band. Such a band was observed at 3210.0 cm−1 in the solid parahydrogen spectrum and at3196.0 cm−1 in the argon spectrum. Peaks corresponding to conformers IV and V were also identified inthis region of the solid parahydrogen spectrum. According to the derived spectra, the bands of conformersIV and V should occur at a higher wavenumber than conformer I; moreover, conformers IV and V are cal-culated to be relatively unstable, thus they should be low in abundances and the corresponding bands shouldbe weak in intensities. Two bands at 3577.5 cm−1 and at 3579.3 cm−1 were observed to fit these criteria inour solid parahydrogen spectrum and they were attributed to conformer IV and V, respectively. These bandswere unobserved in the spectrum obtained in crystalline argon. Other unassigned bands were still present inthis region of the solid parahydrogen spectrum after the allocation of bands corresponding to conformers I,II, IV and V, and the argon spectra after the identification of the bands corresponding to conformers I andII. We were unable to identify these bands as the corresponding wavenumbers and intensities disagree withwhat is predicted theoretically by our derived spectra and the calculated stability of the conformers.Region of the n(C=O) Vibrational Mode (1770 - 1805 cm−1)From the n(OH) region of the spectrum, there is evidence supporting the occurrence of four a-alanineconformers (conformer I, II, III and IV) in a parahydrogen matrix, and two conformers (conformer I andII) in an argon matrix. These conclusions are reached once again in this region of the spectra, thus furtherconfirming our initial analysis. Based on the calculated spectra (Figure 5.5a), a peak corresponding toconformer I should be found at 1775.9 cm−1 with an intensity that is greater than the conformer I peakobserved in the n(OH) region. Furthermore, a weaker band due to conformer II can be anticipated to occurat a higher wavenumber than the conformer I band since conformer II is less stable than conformer I andthus should be less abundant in our matrices, and the corresponding band has a calculated wavenumber of43Table 5.4: Experimental wavenumbers (n , cm−1), peak heights (h, arbitrary unit) and spectrallinewidths (w, cm−1) of a-alanine sublimed at 420 K and trapped in solid parahydrogen and argonmatrices. The corresponding theoretical wavenumbers (n , cm−1) and intensities (I, km·mol−1)were calculated by B3LYP/aug− cc−pVTZ. The brackets indicate bands due to site splitting.44454647a asy - asymmetric, bend - bending, rock - rocking, scissor - scissoring, str - stretching, s -symmetric, twist - twisting, wag - wagging, Ca - a carbon, Cb - b carbon. b Vibrational modeswith wavenumbers above 2000 cm−1 are scaled by a factor of 0.955, and all other vibrationalmodes are scaled by a factor of 0.985.1804.0 cm−1. In the solid parahydrogen spectrum (Figure 5.5b), a strong band is observed at 1773.1 cm−1and a weaker band is observed at 1790.5 cm−1. These bands were assigned to conformer I and conformerII, respectively. A band associated with conformer IV was also detected in this region of the spectrumas a small shouldering band located at 1783.1 cm−1. This assignment agrees well with the theoreticalspectra as the band was derived to occur at 1781.4 cm−1. The band corresponding to conformer V wasunobserved in this region and was concluded to be masked by the conformer IV band since the conformerV band was calculated to occur at 1785.7 cm−1, which is in close proximity of the conformer IV band. Arelatively intense band at 1776.8 cm−1 remains unassigned after the allocation of the bands correspondingto conformers I, II, IV and V in this region of the spectrum. The identity of this band cannot be deducedbased on the theoretical calculations employed as the position and relative intensity of this band does notagree with any of the bands in the predicted spectra. In the argon spectrum (Figure 5.5c), multiple bandswere found in this region, and the amount of bands observed in this region of the spectrum greatly exceedsthe amount of conformers which are expected to be present in the matrix. Upon annealing (Figure 5.5d),the number of bands detected reduced significantly, indicating that most of these bands are a result of sitesplitting. Using similar methods employed for the assignment of the solid parahydrogen spectrum, the bandassociated with conformer I was located at 1775.8 cm−1, while the band corresponding to conformer II wasfound at 1793.3 cm−1. In the region where the conformer IV band in the solid parahydrogen spectrum waslocated, a small band at 1779.2 cm−1 is found in the argon spectrum. Nevertheless, this band cannot beattributed to conformer IV or V. According to the theoretical spectra, the n(C=O) and the n(C-O) modes ofthese two conformers are derived to occur with similar intensities. Hence, if the n(C=O) mode is detected,then the n(C-O) mode should also be detected. In the n(C-O) region of the argon spectrum, only one bandat 1122.7 cm−1 that is not associated with other conformers was detected in the range of the calculatedwavenumber of the n(C-O) vibrational motion of conformer IV and V (Figure 5.6c). However, the originof this band was concluded to differ from the band observed at 1779.2 cm−1 as the band at 1779.2 cm−1vanished upon annealing (Figure 5.5d), while the band at 1122.7 cm−1 remained (Figure 5.6d). Thus, the48band at 1779.2 cm−1 cannot be assigned to either conformer IV and/or V as the corresponding n(C-O) bandis undetected, and there is a lack of evidence for the presence of conformer IV and V in this region of theargon spectrum.Region of the n(C-O) Vibrational Mode (1000 - 1400 cm−1)The most apparent band in this region of the solid parahydrogen spectrum at 1112.2 cm−1 (Figure 5.6b) wasassigned to the n(C-O) vibrational mode of conformer I. In the argon spectrum (Figure 5.6c), this conformerI band is located at 1112.1 cm−1, with a shouldering band at 1110.0 cm−1 as a result of site splitting. Asper our theoretical calculations, there is an absence of peaks which correspond to the n(C-O) vibrationalmotion of conformer II in our experimental spectra. Moreover, bands associated with conformer IV andV are predicted to be slightly redshifted with respect to that of conformer I at 1119.1 and 1117.7 cm−1,respectively (Figure 5.6a). Two small bands shouldering that of conformer I is observed at 1123.5 cm−1and 1127.6 cm−1 in our solid parahydrogen spectrum, and these bands were concluded to originate fromconformer V and IV, respectively. In the solid argon spectrum, small shouldering bands at 1118.8 cm−1 and1122.7 cm−1 are also observed at the higher wavenumber side of the conformer I band. The peak at 1118.8cm−1 was attributed to another vibrational mode of conformer II (n(CN)) which is derived to occur in thisregion. The band at 1122.7 cm−1 cannot be assigned to conformer IV or V. As discussed in the sectionconcerning the n(C=O) region of the spectra, the n(C-O) bands and the n(C=O) bands of conformers IVor V were calculated to occur with comparable intensities. Consequently, if the n(C-O) band is observed,the n(C=O) band is also expected to be detected and vice-versa. However, this was unobserved in our solidargon spectrum. Furthermore, if the band at 1122.7 cm−1 was allocated to conformer IV or V, the intensityof the peak would indicate that other vibrational modes of conformer IV or V should also be detected inthe n(OH) and the w(NH2) regions of the spectra. Yet, these bands were unobserved in an argon matrixenvironment. As a result, the band at 1122.7 cm−1 was not attributed to either conformer IV or conformerV, and the origin of this peak cannot be deduced based on the theoretical spectra.Region of the w(NH2) Vibrational Mode (800 - 880 cm−1)In this region of the spectra, a strong peak associated with conformer I is calculated to occur in a higherwavenumber range at 870.5 cm−1 (Figure 5.6a). This band was allocated at 855.7 cm−1 in a solid parahy-drogen environment (Figure 5.6b), and at 853.3 cm−1 in a solid argon environment (Figure 5.6c). At alower wavenumber region of the conformer I peak, two smaller peaks with similar intensities are observedin both the solid parahydrogen and the solid argon spectrum, which are at 806.4 cm−1 and 828.4 cm−1 inthe parahydrogen spectrum, and at 805.5 cm−1 and 827.2 cm−1 in the argon spectrum. These were assignedto conformer II as two bands associated with this conformer were derived to occur with comparable inten-sities and blue-shifted from the conformer I band. Additional bands at 803.9 cm−1 and at 815.6 cm−1 wereobserved in this region of our solid parahydrogen spectrum but not in our solid argon spectrum. A compari-son between the theoretical spectra and the solid parahydrogen spectra reveals that the band at 803.9 cm−1belongs to conformer IV and the band at 815.6 cm−1 belongs to conformer V. Consequently, the absent ofthese bands in the argon spectrum suggests a lack of conformer IV and V in our argon matrix.49Figure 5.5: The n(OH) and n(C=O) regions of the vibrational spectra of a-alanine sublimedat 420 K. Panel (a) is the theoretical spectra of the observed conformers derived byB3LYP/aug− cc−pVTZ. The theoretical wavenumbers are corrected by a factor of 0.955 forthe n(OH) region and 0.985 for the n(C=O) region, and the relative intensities are scaled withrespect to the Boltzmann distribution at 420 K assuming that only conformers I, II, IV and V arepresent. Panel (b) shows the FTIR spectra of a-alanine isolated in a parahydrogen matrix (Tdep= 4 K) obtained immediately after deposition. Panel (c) is the argon matrix isolation FTIR spec-tra (Tdep = 18 K) recorded immediately after deposition, while panel (d) is the correspondingspectra registered after annealing (10 mins, 40 K). The “*” and ”↓” donates the conformer IVand V bands, respectively, which are present in the parahydrogen spectra, but absent in the argonspectra.50Figure 5.6: The n(C-O) and w(NH2) regions of the vibrational spectra of a-alanine sublimedat 420 K. Panel (a) is the theoretical spectra of the observed conformers derived byB3LYP/aug− cc−pVTZ. The theoretical wavenumbers are corrected by a factor of 0.985 forboth n(C-O) and w(NH2) regions, and the relative intensities are scaled with respect to the Boltz-mann distribution at 420 K assuming that only conformers I, II, IV and V are present. Panel (b)shows the FTIR spectra of a-alanine isolated in a parahydrogen matrix (Tdep = 4 K) obtainedimmediately after deposition. Panel (c) is the argon matrix isolation FTIR spectra (Tdep = 18 K)recorded immediately after deposition, while panel (d) is the corresponding spectra registeredafter annealing (10 mins, 40 K). The “*” and ”↓” donates the conformer IV and V bands, respec-tively, which are present in the parahydrogen spectra, but absent in the argon spectra. The bandmarked by “×” corresponds to the n(CN) mode of conformer II present in the n(C-O) region ofthe argon spectrum.51From our solid parahydrogen matrix isolation spectra, we were able to observe and identify the presenceof four gas phase a-alanine conformers, conformer I, II, IV and V. Conformer I is stabilized by a cis COOHstructure [69] and two N-H—O=C hydrogen bonds. It is the lowest energy conformer, and as a result,has the greatest abundance in our matrix and is responsible for some of the most intense bands. Out of thetwenty-four bands calculated to occur in the region of our recorded spectra, all but two were observed exper-imentally. Conformer II is the third lowest energy conformation and the only trans COOH structure which isdetected in our solid parahydrogen matrix. A total of twenty-one bands (out of twenty-five) associated withthis conformation were identified in our spectrum. Similar to conformer I, conformer IV is also stabilizedby a NH—O=C interaction; however, conformer IV consists of only one hydrogen bond. As a result, it is thefourth most stable conformation, and only fourteen bands were assigned. The highest energy conformationthat is detected in our solid parahydrogen matrix is conformer V. Due to its low abundance in the matrix, thecorresponding bands were weak in intensity and only seven bands were identified experimentally.As compared to solid parahydrogen, the argon spectra were more complex due to site splitting, conse-quently, spectral analysis was more difficult. Furthermore, the argon matrix also consists of less gaseousa-alanine conformers - only conformer I and II were detected, with twenty-two bands attributed to eachconformer, respectively. The absence of conformer IV and V in crystalline argon can be attributed to thelarge mass of argon and a low energy barrier between conformational states. Subsequently, the collision be-tween argon atoms and a-alanine molecules results in a conversion from higher energy states (IV and V) tolower energy states (I and II). On the other hand, parahydrogen atoms are lighter in mass and thus providesa softer collision between the matrix atoms and a-alanine molecules. As a result, the solid parahydrogenmatrix was able to preserve a more complete set of gas phase a-alanine conformers.Contrary to literature [80], we were unable to find evidence to support the presence of conformer III ina solid parahydrogen or a solid argon environment. The most predominant band that was observed for thisconformer was reported to occur at 838 cm−1. However, we did not detect this band in the w(NH2) regionof solid parahydrogen and solid argon spectra, or any of the bands which corresponds to the n(OH), n(C-O)or n(C=O) vibrational modes of conformer III. The absence of this conformer is most like due to low energybarrier heights, which results in fast relaxation to lower energy states. This explanation is supported by aprevious conformational study of a-alanine performed by Balabin using jet-cooled Raman spectroscopy,where conformer III was observed to result in lower energy conformers (I or II) via collision as indicated bythe decrease in intensity of the conformer III bands as nozzle-laser distance was increased [78].5.2.3 Populations of a-alanine Conformers in Solid Parahydrogen and in Solid Argon atVarious Sublimation TemperaturesThe effects of sublimation temperature on the population of a-alanine conformers in a crystalline parahy-drogen environment was compared with that of a solid argon environment. Three different sublimationtemperatures, 410 K, 420 K, and 430 K, were employed and the corresponding spectra can be found infigures B.4, B.5,B.1, B.2, B.6 and B.7 of Appendix, respectively. The conformational population at eachtemperature (Table 5.5) were extracted from the experimental areas of peaks that are derived to be predom-inant.52Table 5.5: Experimental (Exp., %) and theoretical relative populations (Boltzmann, %) of the gaseousa-alanine conformers detected in parahydrogen matrices (Para-H2) and argon matrices (Ar) atsublimation temperatures of 410 K, 420 K, and 430 K.a Experimental relative populations of conformer I, II, IV, and V were derived from the bandcorresponding to the n(C=O), n(C-O), d (NH2) and w(NH2), respectively. b Conformer IV and Vwere undetected in argon matrices.In both matrices, the same set of conformers were observed in the spectra obtained at sublimation tem-peratures of 410 K and 430 K as compared to the spectra recorded using a sublimation temperature of 420K. In contrast with the results obtained in crystalline argon, the population of each conformer taken fromthe solid parahydrogen spectra is in better agreement with the corresponding Boltzmann distribution (Table5.5). This is attributed to the superior ability of solid parahydrogen to preserve a more complete set ofconformers. Furthermore, in the solid parahydrogen spectra, a sublimation temperature induced excitationbetween conformational states as predicted by the Boltzmann distribution was detected - the lowest energyconfiguration, conformer I, decreased in abundance while the higher energy configurations, conformer IIand V, increased in abundance as the sublimation temperature was raised (Figure 5.7). The population ofconformer IV was approximately constant as a function of sublimation temperature, which suggests that theenergy barrier of this conformer is comparatively larger. On the other hand, a lack of any excitation wasobserved in the argon spectrum (Figure 5.7). The population of conformers in an argon matrix remainedrelatively fixed as the sublimation temperature was varied. A change of less than 1 % was observed for eachconformer, which is too small to be concluded as a result of the variation in sublimation temperature. Thislack of excitation is once again due to the large mass of argon atoms, which facilitates collisional relaxation.Subsequently, any higher energy states which were obtained due to an increase of sublimation temperatureswere lost in an argon matrix.5.2.4 UV-irradiation of a-alanine in Solid Parahydrogen and in Solid ArgonThe effects of in-situ UV-irradiation on a-alanine were investigated in crystalline parahydrogen and crys-talline argon. The sample was irradiated for 4 hours in total, and a spectrum was taken at each hour ofirradiation. For the spectra obtained in solid parahydrogen, please see Figures B.8 - B.12 of Appendix, andfor the spectra recorded in solid argon, please see Figures B.13 - B.17 of Appendix. For both matrices,in-situ UV-irradiation resulted in photodissociation of a-alanine, as indicated by a decrease in all conform-ers and an increase in CO2, instead of excitation to higher energy configurations. Thus, the same sets ofconformers were observed after irradiation as compared to immediately after deposition. Furthermore, ir-radiation was more influential in solid parahydrogen. In the parahydrogen matrix, conformer I bands were53Figure 5.7: Regions of the FTIR spectra of a-alanine prepared using different sublimation tempera-tures (410 K, 420 K, and 430 K) that were employed for conformational population calculations(Table 5.5). Panels (a) - (c) give the spectra obtained in parahydrogen matrices, while panels(d) and (e) consist of the spectra recorded in argon matrices. The intensities of the bands in thespectra acquired at sublimation temperatures of 410 K and 430 K are weighted by the sampleconcentration at 420 K.54found to decrease at a faster rate as compared to the corresponding bands in the argon matrix (Table 5.6 andFigure 5.8). Upon 4 hour of irradiation, a 35.3 % decrease was observed for conformer I in a solid parahy-drogen environment, while an 8.3 % decrease was found in a solid argon environment. The more prominenteffects observed in the parahydrogen matrix is due to the quantum nature of hydrogen crystals, which al-lows the corresponding matrices to provide a softer environment for the analytes as compared to noble gasmatrices (see Section 2.1.2). Consequently, the effects of in-situ photoirradiation are more pronounced insolid parahydrogen than in solid argon.Table 5.6: The percent decrease (%) in the intensity of conformer I observed in parahydrogen andargon matrices upon 1 hr, 2 hrs, 3 hrs, and 4 hrs of UV-irradiation as compared to depositionintensity.Figure 5.8: FTIR spectra of the n(C=O) band of a-alanine conformer I recorded in solid parahydrogenmatrices and argon matrices immediately after deposition, and after 1 hr, 2 hrs, 3 hrs, and 4 hrsof in-situ UV-irradiation.Upon prolonged UV-irradiation, we also noticed the formations of weak photoproducts band in ourspectra. Therefore, we decided to expand our investigation on the UV photolysis of a-alanine with thedeuterated analogue of the amino acid (see Section 5.3).555.3 UV Photolysis of Deuterated a-alanine in Solid ParahydrogenAs mentioned in the Introduction (Chapter 1), the effect of UV radiation on amino acids is one of the keysfor their search in interstellar space, where strong UV radiation exist. In our experiment, we have inves-tigated the UV photochemistry of both b - and a-alanine encaged in parahydrogen and argon matrices. Insolid parahydrogen, b -alanine mainly exhibited conformational change upon UV-irradiation with minimalphotodissociation outcomes; a-alanine, on the other hand, experienced photodecomposition almost com-pletely. Aside from the decay of a-alanine sample and the production of CO2, we observed the formationof several new, but weak, photoproducts bands in our parahydrogen spectra upon prolonged UV-irradiation.In order to better assess these photoproducts peaks, we have reinvestigated the photolysis of a-alanine inparahydrogen matrices by using the deuterated form of a-alanine (Figure 5.9). We also hope to clarify therole played by the parahydrogen environment on the UV photochemistry of a-alanine by employing thedeuterated a-alanine sample in our experiment.NH2OHOD3CDFigure 5.9: Structure of deuterated a-alanine: DL-Alanine2,3,3,3-d.5.3.1 Experimental and Computational Details for Deuterated a-alanine UVPhotochemistry StudyThe experimental procedures for this study were similar to that of a-alanine conformational study as de-scribed previously (see Section 5.2.1), with some slight variations. Parahydrogen gas was predominantlyused as the matrix material for this experiment. We acquired longer deposition durations of 2.5 hrs for thedeuterated a-alanine sample (DL-Alanine-2,3,3,3-d4, Sigma Aldrich, 98 atom % D isotopic purity, usedas received), with a gas flow rate of 5 ccm. The sublimation temperature of deuterated a-alanine was 380K, and the mixed amino acid and matrix gas sample was grown directly onto the 4 K BaF2 cold window.The sample matrix was subjected to in-situ UV-irradiation with a modified deuterium lamp, and a total of 3hrs of irradiation was applied to the deposited sample. In terms of spectra measurements, all FTIR spectracollected in this experiment were recorded at 0.05 cm−1 resolution and 1000 number of measurements, withthe aim of obtaining stronger photoproducts signals induced by the increase in signal-to-noise ratio.On the computation aspect, we performed calculations at B3LYP/aug− cc−pVTZ level of theory on thetwelve stable a-alanine conformers, as denoted by Csa´sza´r’s nomenclatures [69] and Balabin’s geometric56configurations [78], in their deuterated forms (Figure 5.10, and Table C.1 of Appendix). We have alsoapplied the same theoretical calculation parameters on seventeen photoproduct candidates we predicted toresult from the UV photolysis of deuterated a-alanine (Table C.3 of Appendix).Figure 5.10: Structures of the twelve lowest energy deuterated a-alanine conformers using byCsa´sza´r’s nomenclatures and Balabin’s geometric configurations. The labels “A” and “B” de-noted the L- and D- enantiomers, respectively.5.3.2 Spectra Comparison between a-alanine and Deuterated a-alanineBefore we proceed with analyzing the UV photoproducts, we did a quick spectra comparison between a-alanine and deuterated a-alanine. As the corresponding ZPE-corrected relative energies and the relativeGibbs free energies of the calculated deuterated a-alanine conformers (Table 5.7) are close in values tothose of a-alanine (Table 5.3), we could assume that the same four conformers observed in the a-alanineexperiment should also be obtained in the deuterated a-alanine experiment. Due to the present of deuterationon the carbon backbone (Ca ) and the extension carbon (Cb ), the deuterated a-alanine spectra experienced anoverall downshift in wavenumbers as compared to the a-alanine spectra (Figure 5.11), by 15 - 30 cm−1 formost regions and up to 700 - 800 cm−1 for the CH3 symmetric and asymmetric stretch regions. The only tworegions that seemed to be unaffected by the deuteration effect were the n(OH) and n(C=O) regions, whichremained relatively at the same wavenumber positions as that in a-alanine spectra. The deuterated a-alanine57spectra also featured two strong bands which were previously unobserved or weak in the a-alanine spectra.These two bands were the peaks at 1144.9 cm−1 and 920.7 cm−1, which were attributed to conformer Iwith the CaH bending and NH2 twisting vibrational modes. The peak at 1144.9 cm−1 also had vibrationalcontribution from the OH bending mode. Table 5.8 summarized the spectral assignments of deuterated a-alanine as deposited in parahydrogen matrices, in the approximate regions of n(OH), n(C3H), n(C=O), n(C-O), and w(NH2). The identities of deuterated a-alanine spectral signals were determined by comparing theresulting spectra to the assignment conclusions from the a-alanine conformational experiment (see Table 5.4for the complete assignments of a-alanine) and to the computed vibrational frequencies values of deuterateda-alanine at B3LYP/aug− cc−pVTZ level of theory.Table 5.7: ZPE-corrected relative energies, DE, and relative Gibbs free energies at 380 K, DG380K , ofthe twelve lowest energy deuterated a-alanine conformers calculated by B3LYP/aug− cc−pVTZ.Figure 5.11: FTIR spectra of deuterated a-alanine (black trace) and non-deuterated a-alanine (redtrace, scaled to match deuterated a-alanine signal intensities) in the regions of w(NH2), n(C-O), n(C=O), and n(OH) in solid parahydrogen taken immediately after deposition.58Table 5.8: Experiment wavenumbers (n , cm−1) and peak height (h, arbitrary unit) of Deuterated a-alanine sublimed at 380 K trapped in solid parahydrogen in comparison with the experiment valuesof non-deuterated a-alanine as presented in Section 5.2. The corresponding theoretical wavenum-bers (n , cm−1) and intensities (I, km·mol−1) were calculated by B3LYP/aug− cc−pVTZ.a Scaling factor: 0.955 for vibrational modes with wavenumbers greater than 2000 cm−1,0.985 for all other vibrational modes. b The difference between the wavenumber of deuterateda-alanine and non-deuterated a-alanine at the same vibrational mode. “+” denotes a blue-shifton the peak position of a-alanine to the deuterated a-alanine, and “-” denotes a red-shift. c asy -asymmetric, bend - bending, rock - rocking, str - stretching, s - symmetric, twist - twisting, wag -wagging. d Assignment applicable to deuterated a-alanine spectra only.595.3.3 Assignment Attempt on the UV Photoproducts of Deuterated a-alanineFigure 5.12 highlighted the spectra results of deuterated a-alanine after 3 hrs of in-situ UV-irradiation inparahydrogen matrix. For the full spectra obtained for this investigation, please see Figures C.1 - C.3 ofAppendix. From the spectra results, we observed the dominant production of CO2 (at 2345 cm−1) withthe expense of the amino acid molecules upon prolonged UV-irradiation. We also noticed the formation ofseveral new, but often small, bands across our spectra after the UV-irradiation (see Table C.2). We deducedthat these bands must be resulting from photodecarboxylation of the acid group from the deuterated a-alanine, which gave CO2 and another major photoproduct with the amine group latched on it. We came outwith seventeen possible photoproducts for this photolysis reaction (Table C.3 of Appendix).One plausible outcome of amino acids UV photolysis is the production of hydrogen cyanide (HCN). In2001, Ehrenfreund et al. reported the formation of HCN along with CO2 from their photolysis studies ofseveral amino acids, including a-alanine, in argon matrix [20]. The group stated that HCN was formedthrough rapid decay of R-CH2-NH2 (in which “R” is the specific amino acids side chain) into the interme-diate methylimine (H2C=NH), which then decompose to yield HCN. Their argument was supported by thedetection of HCN predominant peak at 3300 cm−1 and two smaller peaks at 2100 cm−1 and 711 cm−1 in theirspectra. The group also observed several weak peaks consistent with the wavenumbers of the intermediateH2C=NH throughout their spectra [20]. Contrary to the findings of Ehrenfreund et al., we were unable to findevidence to support the production of HCN, or its deuterated analogue DCN, after UV photolysis of deuter-ated a-alanine in solid parahydrogen environment. The predominant peak at 3300 cm−1 for HCN and 2600cm−1 for DCN were undetected in our spectra. We also did not observe several theoretically intense signalsof H3C-CH2-NH2, H2C=NH, and their deuterated analogoues in our spectra, impliying these intermediarymolecules must have underwent a secondary or tertiary photochemical reaction to produce photoproductsthat is other than HCN. However, as to what the final photoproducts might be is still unknown to us, andwe are still in the process of concisely assessing the identities of the obtained photoproducts bands with thephotoproduct candidates we calculated.Another puzzle we encountered in our attempt to identify the photoproducts of deuterated a-alanine insolid parahydrogen was the observation of several photoproduct bands not associated with the amine groupwithin our spectra. Two of these bands were located at 1845 cm−1 and 3612 cm−1. Interestingly, thesephotoproduct bands were also present in the non-deuterated a-alanine spectra, and displayed a decayingfeature upon leaving the irradiated sample matrix overnight in the dark. After further investigation, we hadtentatively assigned these photoproduct bands to be from HOCO radical. HOCO radical is particularly im-portant in atmospheric chemistry for the production of CO2, through the reaction OH + CO *) HOCO·*)H + CO2 [105]. This unstable molecule was previously obtained in solid parahydrogen as a photoproductof formic acid (HCOOH) via photolysis with an 192 nm ArF excimer laser [106]. This was the first ob-servation and determination of HOCO radical as a reaction intermediate for the production of CO2 throughphotodecarboxylation of an amino acid using UV radiation source.60Figure 5.12: FTIR spectra of deuterated a-alanine in solid parahydrogen in the regions of n(OH),n(C=O), n(C-O), and w(NH2) taken immediately after deposition (blue trace) and after 3 hrsof UV-irradiation (black trace). The FTIR spectra of CO2 signal before and after UV irradiationis also shown. Each panel consists of (a) absorbance spectra of sample as deposited and afterphotolysis, and (b) a difference spectrum (the spectrum measured immediately after depositionsubtracted from the spectrum recorded after 3 hrs of UV irradiation).615.4 Study of Amino Acid Zwitterions in Solid ParahydrogenWe attempted to grow b -alanine zwitterions in parahydrogen matrices by doping the gas mixture with waterprior to deposition. This method was previously applied by Ramaekers et al. on glycine in solid argon, andthe group reported the requirement of at least three water molecules per glycine to transform the amino acidinto its zwitterionic form [94]. The water-doped b -alanine spectra were compared to the spectrum of neutralb -alanine for spectral analysis purposes.5.4.1 Experimental Details for b -alanine Zwitterion StudyThe experimental procedures for this study were similar to that of neutral b -alanine (see Section 5.1.1), withthe addition of one preparatory step. Water-doped parahydrogen was prepare prior to deposition by mixingthe appropriate amount of water vapour into the parahydrogen gas storage vessels. Twice distilled water wasused and the concentrations of water employed for our study were 100 ppm and 500 ppm. We then depositedthe gaseous b -alanine sample (sublimated at 390 K) and H2O/pH2 mixture gas simultaneously onto the 4 KBaF2 cold window at a flow rate of 5 ccm for 1.5 hrs. No UV-irradiation experiment was performed for thisstudy. All the FTIR spectra for this experiment were registered at 0.2 cm−1 resolution with 1000 number ofmeasurements.5.4.2 Spectra Result of b -alanine Zwitterion in Solid ParahydrogenFigure 5.13 shows the spectra of b -alanine with 100 ppm and 500 ppm water-dopant in comparison withthe spectra of neutral b -alanine. For the full spectra obtained for this investigation, please see Figures D.1 -D.3 of Appendix. All five conformers observed in the neutral b -alanine spectra were attained in the water-doped b -alanine spectra as well, with the same wavenumber position and comparable intensity. Moreover,both 100 ppm and 500 ppm water-doped b -alanine spectra displayed the presence of additional bands, mostof which increased in intensity with the increased concentration of water-dopant. These bands most likelyarose from the H-bondings of water to the amine and acidic group of the isolated amino acid within thematrix environment.However, we also observed several bands in the spectra which did not follow the typical increasingtrend with increasing water concentration. These bands were the peaks at 1406.4 cm−1, 1505.6 cm−1,1578.6 cm−1, and 2651.2 cm−1, which appeared with higher intensities in the 100 ppm water-doped b -alanine spectra than in the 500 ppm water-doped spectra (Figure 5.14). We suspected these bands to bethe spectral signals of b -alanine zwitterions formed via H2O-assisted proton transfer in the amino acid.The bands at 1406.4 cm−1, 1505.6 cm−1, and 1578.6 cm−1 were aligned with the NH+3 bending (d (NH+3 ))mode of an amino acid zwitterion; whereas the band at 2651.2 cm−1 can be attributed to the zwitterionvibrational mode of NH+3 stretching (n(NH+3 )) [94]. Note that the formation of zwitterions in noble gasmatrices required annealing processes to drive the proton transfer mechanism [60]. As zwitterions wereevident in the as-deposited parahydrogen matrix sample, we deduced that the proton transfer process toform zwitterions in solid parahydrogen is of tunnelling nature, promoted by the soft and quantum aspectsof parahydrogen matrix. The decreased signals in the 500 ppm water-doped b -alanine spectra could arose62Figure 5.13: FTIR spectra of b -alanine in solid parahydrogen in the regions of n(OH), n(C=O), n(C-O), and w(NH2) taken immediately after deposition. For each panel, the bottom black tracedenotes the sample without water dosage, the middle blue trace denotes the sample with 100ppm of water dopant, and the top red trace denotes the sample with 500 ppm of water dopant.from one of the two factors: (a) the number of water to stabilized zwitterions in an isolated enviroment (suchas matrices) is so crucial that addition of water above the threshold point might destabilize the zwitterionform instead, making the neutral form more preferable; or, (b) at a certain concentration of water, the dopedsolvent has somehow acted as a strong base and stripped away a proton from the NH+3 branch of zwitterion,destructed the geometry of the ionic molecule. Anyhow, we could not pinpoint the true causes of thisreceding features with our current experimental data, and further investigations are underway to find thesource of this observed phenomenon.Lastly , we noticed some intense bands at 3500 cm−1, 3520 cm−1, and 3579 cm−1 in the 500 ppmwater-doped sample spectra which were not consistent with the assignment of b -alanine zwitterions orH-bonding of water with b -alanine. We suspected these bands to be the absorption of b -alanine dimers insolid parahydrogen. The most stable amino acid dimer was reported to be in a stacked structure where theamino acids monomers were positioned one on top of another, with a point of contact between the acidic63Figure 5.14: FTIR spectra of b -alanine in solid parahydrogen taken immediately after deposition andfocused on 1300 - 1600 cm−1 and 2500 - 3000 cm−1 regions. For each panel, the bottom blacktrace denotes the sample without water dosage, the middle blue trace denotes the sample with100 ppm of water dopant, and the top red trace denotes the sample with 500 ppm of waterdopant. The “*” denotes the bands that show in the 100 ppm water-doped b -alanine spectra, butdecrease in the 500 ppm water-doped b -alanine.and amino groups of the monomers via weak H-bonding interactions [107]. The most characteristic peaksof a stacked structure amino acid dimer were at the n(OH) region, which matched well with the three strongbands of 3500 cm−1, 3520 cm−1, and 3579 cm−1 observed in our spectral. We deduced that b -alaninedimers in our parahydrogen matrices were formed by the clustering of b -alanine zwitterions, as those peaksonly appeared in the water-doped b -alanine spectra, and not on the neutral b -alanine spectra.Tentative assignments of the new bands due to H-bonding interactions and possible zwitterion formationare needed, but the quantum calculations involved in determining the theoretical wavenumber and intensitiesfor peak identifications can be extensive. Currently, we are attempting to perform high accuracy theoreticalcalculations of all predicted b -alanine neutral and zwitterion conformers, in association with the hydrationeffect from the water molecules, to aid us in completing the spectral assignments of this experiment in thenear future.64Chapter 6ConclusionFor the presented work, we have reported the conformational and UV photochemistry studies of two of thesimplest amino acids, b - and a-alanine, using MI-FTIR spectroscopy. Parahydrogen matrices were mainlyemployed for our study, and we compared the results obtained in solid parahydrogen to those obtained inargon matrices. Due to the soft quantum nature of solid parahydrogen, the matrix possesses several ad-vantages over argon matrix in conformational studies of amino acids. Noble gas matrices like solid argonoften suffer from site splitting effects; solid parahydrogen, however, is free from such effects, allowing us toobtain cleaner spectra which correspond to simpler conformational analysis process. We have also trappedhighly unstable amino acids conformers within parahydrogen matrices, which are previously unobservedin noble gas matrices. Furthermore, solid parahydrogen is better than noble gas at sustaining the confor-mational population of amino acids as present in their sublimating temperature, giving us a more accurateinterpretation of the conformers distribution in the gas phase. As on UV photolysis investigation, we ob-served more efficient in-situ UV irradiation outcomes for samples encaged in the parahydrogen matricesas compared to argon matrices. These aspects have thus highlighted the strength of using parahydrogenmatrices for spectroscopic investigation of molecules with large conformational flexibility.FTIR spectra of b -alanine isolated in solid parahydrogen were registered for the first time. Together withtheoretical spectra of eleven stable b -alanine conformers obtained at the B3LYP/aug− cc−pVTZ level oftheory and in-situ UV-irradiation, the spectral characterization of five conformers, conformer I, II, III, IV,and VII, was accomplished. In contrast, only four conformers, conformer I, II, VI, and VII, were observerin solid argon, with highly unstable conformer III being undetected in the rare gas matrices. In-situ UV-irradiation resulted in conformational change of b -alanine, with a decrease in band intensities for conformerI, II, and VII and an increase for conformer III and VI.FTIR spectra of a-alanine isolated in solid parahydrogen were registered for the first time. A comparisonbetween the theoretical spectra of eight stable a-alanine conformers calculated at the B3LYP/aug− cc−pVTZlevel of theory and the recorded FTIR spectra shows that four conformers, conformer I, II, IV, and V arepresent in the parahydrogen matrices. In contrast, only two conformers, conformer I and II were detectedin the argon matrices, and the higher energy conformers, conformer IV and V, were unobserved. Upon pro-longed UV-irradiation, a-alanine underwent total phototdestruction to yield CO2 and several photoproducts.We expanded our investigation on UV photolysis of a-alanine to the deuterated analogue of the amino acid,65in the hope to simplify our analysis on the photoproducts’ bands. However, the full identification of thesephotoproducts are still incomplete and we are in the process of matching the photoproducts’ signals to theseventeen possible product candidates we predicted. We did observed an interesting outcome, which wasthe formation of HOCO radical as a reaction intermediate to produce CO2 via photodecarboxylation of botha-alanine and deuterated a-alanine with UV radiation source.Lastly, we have detected evidence for the possible production of b -alanine zwitterion in as-depositedsolid parahydrogen. We tried to accomplish the formation of zwitterions by doping the appropriate amountof water into our matrix system, leading to the H2O-assisted proton transfer in the amino acid. Asidefrom the bands which arose from the H-bondings of water to the b -alanine sample, we have observedseveral new vibrational bands that can be attributed to amino acid zwitterions. We also observed severalbands in the n(OH) region which suggest the formation of b -alanine dimers coinciding with the growth ofzwitterions in solid parahydrogen. We are currently attempting to identify these new bands by utilizing highaccuracy computational method, with consideration of H-bonding contributions from water molecules, onall predicted b -alanine neutral and zwitterion conformers, and then comparing the theoretical values to ourexperimental spectral signals.66Chapter 7Future Work7.1 Conformational, UV Photochemistry, and Zwitterion Studies of OtherAmino AcidsSolid parahydrogen has proven to be a superior matrix for the spectroscopic studies of neutral or ionicsample with high conformational flexibility. In-situ UV-irradiation in parahydrogen matrix has also shownto be more effective than in argon matrix. Proceeding our success in conformational analysis of b - anda-alanine in solid parahydrogen, we hope to extend our investigation to other simple amino acids, and thecandidates for our next studies are serine, aspartic acid and glutamic acid (Figure 7.1). These amino acidscontain an a-amino group (-NH2), an a-carboxylic acid group (-COOH), and a side chain with anothercarboxylic acid latched to its end. With the present of two acidic end points on the molecules, we predictedthat the formation of zwitterions would be more accessible through these amino acids. We would also liketo perturb the zwitterions formed in solid parahydrogen with UV-irradiation and study the photochemistryreaction of amino acids zwitterions in cold isolated environment.OHO (a) (b)NH2HO OHONH2HOOOHNH2HOO O (c)Figure 7.1: Structure of (a) serine, (b) aspartic acid, and (c) glutamic acid.7.2 Investigation on The Vibrational Dephasing of Molecules in SolidParahydrogen, and The Annealing Effect in Parahydrogen and ArgonMatricesSharper spectral signal is expected to be produced with solid parahydrogen FTIR spectroscopy as comparedto rare gases (see Section 2.1.2). However, for our amino acids experiments, the spectral linewidth in67parahydrogen matrices appeared to be slightly broader than in argon matrices. This observation indicatedthe occurrence of fast vibrational dephasing of molecules with large flexibility in parahydrogen crystal (seeSection 5.1.3). Due to the broader linewidth, conformers bands of close proximity tended to overlap inparahydrogen matrices, making this features unfavourable for the spectral identification.A way to check on vibrational dephasing effect is to perform MI-FTIR spectroscopy at a lower tempera-ture than 4 K. We have recently partaken in this investigation using a liquid helium cryostat chamber, wherethe temperature of the cold window could be brought down to as low as 2.2 K. The lower temperature limitat 2.2 K also allowed us to investigate the annealing effect of parahydrogen matrix on the trapped aminoacids. We used a-alanine (sublimated at 425 K) as the principle sample for this investigation and comparedthe spectra taken in solid parahydrogen to those in argon matrices.Figure 7.2 shows the spectral result of a-alanine deposited at 2.2 K in solid parahydrogen and underwentmultiple annealing process to 4.2 K. After the first annealing process, we observed the upward shift ofwavenumber in the solid parahydrogen spectra. If this observation was caused by the vibrational dephasingof trapped a-alanine, we expect the peak shifting process to be reproducible and reversible with varyingtemperature. However, the wavenumber position remained relatively constant upon the second and thirdannealing process, indicating the shift in wavenumber observed during the first annealing process was just aresult of matrix annealing effect. On another note, the spectral linewidth in 2.2 K parahydrogen matrices didnot improve much from the linewidth as deposited at 4 K, being still generally broader than the linewidth inargon matrices.Figure 7.2: FTIR spectra of a-alanine in solid parahydrogen deposited at 2.2 K and subjected to mul-tiple annealing processes to 4.2 K. Minimal to no spectral change was observed upon the 2nd and3rd annealing processes. The signal shown is the n(C-O) band of conformer I.As for the spectral of a-alanine deposited in solid argon at 2.2 K (Figure 7.3), we did not detect anyspectral change, even during the first annealing process to 4.2 K. We deduced that the annealing temperature68range might be too low and narrow for the crystalline argon environment. Thus, we repeated the annealingexperiment of a-alanine in argon matrices in our closed-cycle refrigerator cryostat chamber, depositing oursample at 18 K and annealing the argon crystal up to a temperature of 35 K (Figure 7.4). Interestingly, weobserved a reversible spectral shift after the first annealing process, where the wavenumber experienced ablue-shift upon heating the matrix up to 35 K, and a red-shift upon cooling it down to 4 K.Figure 7.3: FTIR spectra of a-alanine in solid argon deposited at 2.2 K and annealed to 4.2 K. Minimalto no spectral change was observed even on the 1st annealing process. The signal shown is then(C-O) band of conformer I.Figure 7.4: FTIR spectra of a-alanine in solid argon deposited at 18 K and subjected to multiple an-nealing processes to 35 K. The sample was cooled to 4 K before taking the deposition spectrum.The spectral bands exhibited a blue-shift with the increase in matrix temperature, and a red-shiftwith the decrease. The signal shown is the n(C=O) band of conformer I.697.3 Chirality Studies of Amino Acid in Matrix-Isolation SystemAnother interesting project to be consider for the spectroscopy of amino acid in matrix environment is theinvestigation of the molecules’ chiral nature. As mention previously (see Section 2.2.2), homochirality isbelieved to be a pre-requisite for the origin of life. Therefore, the investigation of homochirality in biologicalmolecules, including amino acids, is of a topic of high interest.Monomeric enantiomers are known to exhibit the same vibrational behaviours, deeming them indistin-guishable under IR spectroscopy. A way to get around this problem is to make dimer clusters of enantiopureor racemic composition, then measure and compare the molecule-to-molecule interactions between homo-and heterochiral dimers. This proposal has proven to be successful through the conduction of several IRspectroscopies of various gaseous chiral molecules with supersonic expansions techniques [108]. Therefore,we would like to apply similar principle and procedure in a matrix-isolation system, and hope to expand thestudy of chiral molecules in the matrix-isolation field.70Bibliography[1] Brian A. Tom, Siddhartha Bhasker, Yuki Miyamoto, Takamasa Momose, and Benjamin J. McCall.Producing and quantifying enriched para-h2. Review of Scientific Instruments, 80(1):016108, 2009.ISSN 00346748. doi:10.1063/1.3072881. → pages iii, 15, 16, 17[2] Angel Ying-Tung Wong, Shin Yi Toh, Pavle Djuricanin, and Takamasa Momose. Conformationalcomposition and population analysis of -alanine isolated in solid parahydrogen. Journal ofMolecular Spectroscopy, 310:23–31, April 2015. ISSN 00222852. doi:10.1016/j.jms.2015.01.002.→ pages iii, 9, 29[3] Angel Ying-Tung Wong. Matrix-Isolation FT-IR Spectroscopy of Amino Acids, April 2014. →pages iii[4] Angel Ying-Tung Wong, Shin Yi Toh, Pavle Djuricanin, and Takamasa Momose. ConformationalAnalysis of Gaseous -alanine: A Solid Parahydrogen and Argon Matrix Isolation FT-IR Study.Manuscript in preparation. 2016. → pages iii, 9, 40[5] Yi-Jehng Kuan, Steven B. Charnley, Hui-Chun Huang, Wei-Ling Tseng, and Zbigniew Kisiel.Interstellar glycine. The Astrophysical Journal, 593(2):848, 2003. → pages 1[6] Lewis E. Snyder, Francis J. Lovas, J. M. Hollis, D. N. Friedel, P. R. Jewell, A. Remijan, V. V.Ilyushin, E. A. Alekseev, and S. F. Dyubko. A rigorous attempt to verify interstellar glycine. TheAstrophysical Journal, 619(2):914, 2005. → pages 1[7] M. R. Cunningham, P. A. Jones, P. D. Godfrey, D. M. Cragg, I. Bains, M. G. Burton, P. Calisse,N. H. M. Crighton, S. J. Curran, T. M. Davis, J. T. Dempsey, B. Fulton, M. G. Hidas, T. Hill,L. Kedziora-Chudczer, V. Minier, M. B. Pracy, C. Purcell, J. Shobbrook, and T. Travouillon. Asearch for propylene oxide and glycine in Sagittarius B2 (LMH) and Orion. Monthly Notices of theRoyal Astronomical Society, 376(3):1201–1210, April 2007. ISSN 0035-8711, 1365-2966.doi:10.1111/j.1365-2966.2007.11504.x. → pages 1[8] Oliver Botta, Zita Martins, and Pascale Ehrenfreund. Amino acids in Antarctic CM1 meteorites andtheir relationship to other carbonaceous chondrites. Meteoritics & Planetary Science, 42(1):81–92,2007. → pages 1, 10[9] James G. Lawless. Amino acids in the Murchison meteorite. Geochimica et Cosmochimica Acta, 37(9):2207–2212, 1973. → pages 10[10] Daniel P. Glavin, Jason P. Dworkin, Andrew Aubrey, Oliver Botta, James H. Doty, Zita Martins, andJeffrey L. Bada. Amino acid analyses of Antarctic CM2 meteorites using liquidchromatography-time of flight-mass spectrometry. Meteoritics & Planetary Science, 41(6):889–902,2006. → pages71[11] Mark A. Sephton. Organic compounds in carbonaceous meteorites. Natural Product Reports, 19(3):292–311, May 2002. ISSN 02650568, 14604752. doi:10.1039/b103775g. → pages[12] Oliver Botta and Jeffrey L. Bada. Extraterrestrial Organic Compounds in Meteorites. Surveys inGeophysics, 23(5):411–467, September 2002. ISSN 0169-3298, 1573-0956.doi:10.1023/A:1020139302770. → pages 1[13] S. Pizzarello, R. V. Krishnamurthy, S. Epstein, and J. R. Cronin. Isotopic analyses of amino acidsfrom the Murchison meteorite. Geochimica et Cosmochimica Acta, 55(3):905–910, March 1991.ISSN 0016-7037. doi:10.1016/0016-7037(91)90350-E. → pages 1[14] Pascale Ehrenfreund, Daniel P. Glavin, Oliver Botta, George Cooper, and Jeffrey L. Bada.Extraterrestrial amino acids in Orgueil and Ivuna: Tracing the parent body of CI type carbonaceouschondrites. Proceedings of the National Academy of Sciences, 98(5):2138–2141, 2001. → pages 1,10[15] E. T. Peltzer, J. L. Bada, G. Schlesinger, and S. L. Miller. The chemical conditions on the parentbody of the Murchison meteorite: some conclusions based on amino, hydroxy and dicarboxylicacids. Advances in space research: the official journal of the Committee on Space Research(COSPAR), 4(12):69–74, 1984. ISSN 0273-1177. → pages 1[16] Voislav Blagojevic, Simon Petrie, and Diethard K. Bohme. Gas-phase syntheses for interstellarcarboxylic and amino acids. Monthly Notices of the Royal Astronomical Society, 339(1):L7–L11,2003. → pages 1, 10[17] Antonio Largo, Pilar Redondo, and Carmen Barrientos. Theoretical study of possible ion-moleculereactions leading to precursors of glycine in the interstellar medium. International Journal ofQuantum Chemistry, 98(4):355–360, 2004. ISSN 0020-7608, 1097-461X. doi:10.1002/qua.20070.→ pages 1[18] Bernard Barbier, Annie Chabin, Didier Chaput, and Andre´ Brack. Photochemical processing ofamino acids in Earth orbit. Planetary and Space Science, 46(4):391–398, April 1998. ISSN0032-0633. doi:10.1016/S0032-0633(97)00150-5. → pages 1[19] Stepan G. Stepanian, Alexander Yu. Ivanov, Daryna A. Smyrnova, and Ludwik Adamowicz.UV-induced isomerization of -alanine isolated in argon matrices. Journal of Molecular Structure,1025:6–19, October 2012. ISSN 00222860. doi:10.1016/j.molstruc.2012.04.093. → pages 1, 9, 11,30, 40[20] P. Ehrenfreund, M. P. Bernstein, J. P. Dworkin, S. A. Sandford, and L. J. Allamandola. Thephotostability of amino acids in space. The Astrophysical Journal Letters, 550(1):L95, 2001. →pages 1, 2, 60[21] Paul V. Johnson, Robert Hodyss, Victoria F. Chernow, Dawn M. Lipscomb, and Jay D. Goguen.Ultraviolet photolysis of amino acids on the surface of icy Solar System bodies. Icarus, 221(2):800–805, November 2012. ISSN 00191035. doi:10.1016/j.icarus.2012.09.005. → pages 1[22] A. J. Barnes, W. J. Orville-Thomas, A. Mu¨ller, and R. Gaufre`s, editors. Matrix IsolationSpectroscopy, volume 76. Springer Netherlands, Dordrecht, 1981. ISBN 978-94-009-8542-1978-94-009-8540-7. → pages 2, 3, 4, 6, 7, 972[23] Eric Whittle, David A. Dows, and George C. Pimentel. Matrix Isolation Method for theExperimental Study of Unstable Species. The Journal of Chemical Physics, 22(11):1943–1943,November 1954. ISSN 0021-9606, 1089-7690. doi:10.1063/1.1739957. → pages 3[24] Marilyn E. Jacox. On Walking in the Footprints of Giants *. Annual Review of Physical Chemistry,61(1):1–18, March 2010. ISSN 0066-426X, 1545-1593.doi:10.1146/annurev.physchem.012809.103439. → pages 3, 4[25] Dolphus E. Milligan and Marilyn E. Jacox. Infrared Spectroscopic Evidence for the Species HO2.The Journal of Chemical Physics, 38(11):2627, 1963. ISSN 00219606. doi:10.1063/1.1733562. →pages 3[26] Marilyn E. Jacox. The spectroscopy of molecular reaction intermediates trapped in the solid raregases. Chemical Society Reviews, 31(2):108–115, March 2002. ISSN 03060012, 14604744.doi:10.1039/b102907j. → pages 4[27] Marilyn E. Jacox. Vibrational and electronic energy levels of polyatomic transient molecules:Supplement 1. Journal of Physical and Chemical Reference Data, 19(6):1387–1546, November1990. ISSN 0047-2689, 1529-7845. doi:10.1063/1.555848. → pages 4[28] Marilyn E. Jacox. Vibrational and Electronic Energy Levels of Polyatomic Transient Molecules.Supplement A. Journal of Physical and Chemical Reference Data, 27(2):115–393, March 1998.ISSN 0047-2689, 1529-7845. doi:10.1063/1.556017. → pages[29] Marilyn E. Jacox. Vibrational and Electronic Energy Levels of Polyatomic Transient Molecules.Supplement B. Journal of Physical and Chemical Reference Data, 32(1):1–441, March 2003. ISSN0047-2689, 1529-7845. doi:10.1063/1.1497629. → pages 4[30] V. E. Bondybey and V. A. Apkarian. Preface. Chemical Physics, 189(2):137–138, December 1994.ISSN 0301-0104. doi:10.1016/0301-0104(94)89003-X. → pages 4[31] Ingeborg Iping Petterson. Marilyn Jacox, a Pioneer in Infrared Spectroscopy. Spectroscopy, 29(6):40–44, June 2014. ISSN 08876703. → pages 4[32] Takamasa Momose and Tadamasa Shida. Matrix-Isolation Spectroscopy Using Solid Parahydrogenas the Matrix: Application to High-Resolution Spectroscopy, Photochemistry, and Cryochemistry.Bulletin of the Chemical Society of Japan, 71(1):1–15, 1998. ISSN 0009-2673.doi:10.1246/bcsj.71.1. → pages 4, 6, 7, 8, 38[33] Takamasa Momose, Hiroyuki Katsuki, Hiromichi Hoshina, Norihito Sogoshi, TomonariWakabayashi, and Tadamasa Shida. High-resolution laser spectroscopy of methane clusters trappedin solid parahydrogen. The Journal of Chemical Physics, 107(19):7717–7720, November 1997.ISSN 0021-9606, 1089-7690. doi:10.1063/1.475086. → pages 4, 6[34] Donald L. Pavia, Gary M. Lampman, George S. Kriz, and James A. Vyvyan. Introduction toSpectroscopy. Cengage Learning, 4th edition edition, March 2009. → pages 5[35] Douglas A. Skoog, F. James Holler, and Stanley R. Crouch. Principles of Instrumental Analysis.Thomson Brooks/Cole, 6th edition edition, 2007. ISBN 978-0-495-01201-6. → pages 5, 6[36] User’s Manual for IFS 125HR. Bruker Optik GmbH, 1st edition edition, April 2006. ISBN I26013.→ pages 573[37] Takamasa Momose, Hiromichi Hoshina, Mizuho Fushitani, and Hiroyuki Katsuki. High-resolutionspectroscopy and the analysis of ro-vibrational transitions of molecules in solid parahydrogen.Vibrational Spectroscopy, 34(1):95–108, January 2004. ISSN 09242031.doi:10.1016/j.vibspec.2003.06.001. → pages 6, 7, 8, 38[38] Takeshi Oka. High-resolution spectroscopy of solid hydrogen. Annual Review of PhysicalChemistry, 44(1):299–333, 1993. → pages 6, 7, 8[39] Justinas Ceponkus, Wutharath Chin, Miche`le Chevalier, Michel Broquier, Andre´ Limongi, andClaudine Cre´pin. Infrared study of glycolaldehyde isolated in parahydrogen matrix. The Journal ofChemical Physics, 133(9):094502, 2010. ISSN 00219606. doi:10.1063/1.3474994. → pages 6, 7[40] Isaac F. Silvera. The solid molecular hydrogens in the condensed phase: Fundamentals and staticproperties. Reviews of Modern Physics, 52(2):393–452, April 1980.doi:10.1103/RevModPhys.52.393. → pages 7, 8[41] Mitchio Okumura, Man-Chor Chan, and Takeshi Oka. High-Resolution Infrared Spectroscopy ofSolid Hydrogen: The Tetrahexacontapole-Induced J= 6 Transitions. Physical review letters, 62(1):32, 1989. → pages 7[42] D. P. Weliky, T. J. Byers, K. E. Kerr, T. Momose, R. M. Dickson, and T. Oka. High-resolution laserspectroscopy of theQ v (0) transitions in solid parahydrogen. Applied Physics B, 59(3):265–281,1994. → pages 8[43] Peter Klaeboe and Claus J. Nielsen. Recent advances in infrared matrix isolation spectroscopy.Invited lecture. Analyst, 117(3):335–341, 1992. → pages 9[44] Peter Klaeboe. Conformational studies by vibrational spectroscopy: a review of various methods.Vibrational Spectroscopy, 1(9):3–17, 1995. ISSN 0924-2031. → pages 9[45] S.G Stepanian, I. D. Reva, E. D. Radchenko, and L Adamowicz. Conformational Behavior of-Alanine. Matrix-Isolation Infrared and Theoretical DFT and ab Initio Study. Journal of PhysicalChemistry A, 102(24), 1998. ISSN 1089-5639. doi:10.1021/jp973479z. → pages 9, 12, 42[46] Igor D. Reva, Alexander M. Plokhotnichenko, Stepan G. Stepanian, Alexander Yu. Ivanov,Eugeni D. Radchenko, Galina G. Sheina, and Yuri P. Blagoi. The rotamerization of conformers ofglycine isolated in inert gas matrices. An infrared spectroscopic study. Chemical Physics Letters,232:141–148, January 1995. ISSN 0009-2614. doi:10.1016/0009-2614(95)90630-B. → pages 9[47] Ga´bor Bazso´, Eszter E. Najbauer, Ga´bor Magyarfalvi, and Gyo¨rgy Tarczay. Near-Infrared LaserInduced Conformational Change of Alanine in Low-Temperature Matrixes and the TunnelingLifetime of Its Conformer VI. The Journal of Physical Chemistry A, 117(9):1952–1962, March2013. ISSN 1089-5639, 1520-5215. doi:10.1021/jp400196b. → pages 9, 12, 13, 42[48] A. Yu. Ivanov, A. M. Plokhotnichenko, V. Izvekov, G. G. Sheina, and Yu. P. Blagoi. FTIRinvestigation of the effect of matrices (Kr, Ar, Ne) on the UV-induced isomerization of themonomeric links of biopolymers. Journal of Molecular Structure, 408409:459–462, June 1997.ISSN 0022-2860. doi:10.1016/S0022-2860(96)09554-3. → pages[49] A. Yu Ivanov, G. Sheina, and Yu P. Blagoi. FTIR spectroscopic study of the UV-inducedrotamerization of glycine in the low temperature matrices (Kr, Ar, Ne). Spectrochimica Acta Part A:Molecular and Biomolecular Spectroscopy, 55(1):219–228, 1999. → pages74[50] Eszter E. Najbauer, Ga´bor Bazs, Sa´ndor Go´bi, Ga´bor Magyarfalvi, and Gy0¨rgy Tarczay. Exploringthe Conformational Space of Cysteine by Matrix Isolation Spectroscopy Combined withNear-Infrared Laser Induced Conformational Change. The Journal of Physical Chemistry B, 118(8):2093–2103, February 2014. ISSN 1520-6106, 1520-5207. doi:10.1021/jp412550q. → pages[51] Eszter E. Najbauer, Ga´bor Bazso´, Rui Apo´stolo, Rui Fausto, Malgorzata Biczysko, VincenzoBarone, and Gyo¨rgy Tarczay. Identification of Serine Conformers by Matrix-Isolation IRSpectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2d CorrelationAnalysis, and Quantum Mechanical Anharmonic Computations. The Journal of Physical ChemistryB, 119(33):10496–10510, August 2015. ISSN 1520-6106, 1520-5207.doi:10.1021/acs.jpcb.5b05768. → pages 9[52] C. E. Blom, R. P. Mller, and Hs H. Gu¨nthard. S-trans and S-cis acrolein: trapping from thermalmolecular beams and uv-induced isomerization in argon matrices. Chemical Physics Letters, 73(3):483–486, 1980. → pages 9[53] Ana Borba, Andrea Go´mez-Zavaglia, Leszek Lapinski, and R. Fausto. Rotational isomers of lacticacid: first experimental observation of higher energy forms. Phys. Chem. Chem. Phys., 6(9):2101–2108, 2004. ISSN 1463-9076, 1463-9084. doi:10.1039/B316642B. → pages 9[54] P. Huber-Wa¨lchli and Hs H. Gu¨nthard. Trapping of unstable conformations from thermal molecularbeams in argon matrices: 1, 2-difluoroethane and 1, 3-butadiene, ir spectra and conformer equilibria.Spectrochimica Acta Part A: Molecular Spectroscopy, 37(5):285–304, 1981. → pages 9[55] Rolando R. Lozada-Garcia, Justinas Ceponkus, Wutharath Chin, Miche`le Chevalier, and ClaudineCre´pin. Acetylacetone in hydrogen solids: IR signatures of the enol and keto tautomers and UVinduced tautomerization. Chemical Physics Letters, 504(4-6):142–147, March 2011. ISSN00092614. doi:10.1016/j.cplett.2011.01.055. → pages 9[56] I.D Reva, S.G Stepanian, L Adamowicz, and R Fausto. Missing conformers. Comparative study ofconformational cooling in cyanoacetic acid and methyl cyanoacetate isolated in low temperatureinert gas matrixes. Chemical Physics Letters, 374(5-6):631–638, June 2003. ISSN 00092614.doi:10.1016/S0009-2614(03)00782-6. → pages 9[57] Michael Ramek. Ab initio SCF investigation of -alanine. Journal of Molecular Structure:THEOCHEM, 208(34):301–355, September 1990. ISSN 0166-1280.doi:10.1016/0166-1280(90)80014-F. → pages 10, 31[58] Shane J. McGlone and Peter D. Godfrey. Rotational Spectrum of a Neurohormone:. beta.-Alanine.Journal of the American Chemical Society, 117(3):1043–1048, 1995. → pages 10[59] M. Eugenia Sanz, Alberto Lesarri, M. Isabel Pen˜a, Vanesa Vaquero, Vanessa Cortijo, Juan C. Lo´pez,and Jose´ L. Alonso. The Shape of -Alanine. Journal of the American Chemical Society, 128(11):3812–3817, March 2006. ISSN 0002-7863, 1520-5126. doi:10.1021/ja058194b. → pages 10, 38[60] Ma´rio Tu´lio S. Rosado, Maria Leonor RS Duarte, and Rui Fausto. Vibrational spectra (FT-IR,Raman and MI-IR) of -and -alanine. Journal of Molecular Structure, 410:343–348, June 1997. →pages 10, 11, 12, 62[61] Jan Cz. Dobrowolski, Michal H. Jamro´z, Robert Kolos, Joanna E. Rode, and Joanna Sadlej. IRLow-Temperature Matrix and ab Initio Study on -Alanine Conformers. ChemPhysChem, 9(14):2042–2051, October 2008. ISSN 14394235, 14397641. doi:10.1002/cphc.200800383. → pages 1175[62] Stepan G. Stepanian, Alexander Yu Ivanov, and Ludwik Adamowicz. FTIR spectra andconformational structure of deutero--alanine isolated in argon matrices. Journal of MolecularSpectroscopy, 320:13–24, February 2016. ISSN 00222852. doi:10.1016/j.jms.2015.12.010. →pages 11[63] J. Bailey, A. Chrysostomou, J. H. Hough, T. M. Gledhill, A. McCall, S. Clark, F. Me´nard, andM. Tamura. Circular polarization in star-formation regions: implications for biomolecularhomochirality. Science (New York, N.Y.), 281(5377):672–674, July 1998. ISSN 0036-8075. →pages 11[64] William A. Bonner. Terrestrial and extraterrestrial sources of molecular homochirality. Origins ofLife and Evolution of the Biosphere, 21(5-6):407–420, 1991. → pages 11[65] John R. Cronin and Sandra Pizzarello. Enantiomeric Excesses in Meteoritic Amino Acids. Science,275(5302):951–955, February 1997. ISSN 0036-8075, 1095-9203.doi:10.1126/science.275.5302.951. → pages 11[66] M. H. Engel and S. A. Macko. Isotopic evidence for extraterrestrial non- racemic amino acids in theMurchison meteorite. Nature, 389(6648):265–268, September 1997. ISSN 0028-0836.doi:10.1038/38460. → pages 11[67] Scott Gronert and Richard AJ O’Hair. Ab initio studies of amino acid conformations. 1. Theconformers of alanine, serine, and cysteine. Journal of the American Chemical Society, 117(7):2071–2081, 1995. → pages 11[68] M. Cao, S. Q. Newton, J. Pranata, and L. Scha¨fer. AB INITIO CONFORMATIONAL ANALYSISOF ALANINE. Journal of molecular structure. Theochem, 332(3):251–267, 1995. ISSN0166-1280. → pages 11[69] Attila G. Csa´sza´r. Conformers of gaseous -alanine. The Journal of Physical Chemistry, 100(9):3541–3551, 1996. → pages 11, 12, 42, 52, 56[70] Roman M. Balabin. Conformational equilibrium in alanine: Focal-point analysis and ab initio limit.Computational and Theoretical Chemistry, 965(1):15–21, April 2011. ISSN 2210271X.doi:10.1016/j.comptc.2011.01.008. → pages 12, 42[71] Kinya Iijima and Brian Beagley. An electron diffraction study of gaseous -alanine, NH 2chch 3co2h. Journal of Molecular Structure, 248:133–142, August 1991. ISSN 0022-2860.doi:10.1016/0022-2860(91)85008-Q. → pages 12[72] K Iijima and M Nakano. Reinvestigation of molecular structure and conformation of gaseousl-alanine by joint analysis using electron diffraction data and rotational constants. Journal ofMolecular Structure, 485486:255–260, August 1999. ISSN 0022-2860.doi:10.1016/S0022-2860(99)00047-2. → pages 12[73] P. D. Godfrey, S. Firth, L. D. Hatherley, R. D. Brown, and A. P. Pierlot. Millimeter-wavespectroscopy of biomolecules: alanine. Journal of the American Chemical Society, 115(21):9687–9691, October 1993. ISSN 0002-7863. doi:10.1021/ja00074a039. → pages 12[74] Peter D. Godfrey, Ronald D. Brown, and Fiona M. Rodgers. Spectroscopy and Quantum ChemicalTheory Applied to Problems in Molecular StructureThe missing conformers of glycine and alanine:relaxation in seeded supersonic jets. Journal of Molecular Structure, 376(1):65–81, February 1996.ISSN 0022-2860. doi:10.1016/0022-2860(95)09065-7. → pages76[75] Susana Blanco, Alberto Lesarri, Juan C. Lo´pez, and Jose´ L. Alonso. The Gas-Phase Structure ofAlanine. Journal of the American Chemical Society, 126(37):11675–11683, September 2004. ISSN0002-7863, 1520-5126. doi:10.1021/ja048317c. → pages 12[76] Y. Hirata, S. Kubota, S. Watanabe, T. Momose, and K. Kawaguchi. Millimeter-wave spectroscopy of-alanine. Journal of Molecular Spectroscopy, 251(1-2):314–318, September 2008. ISSN 00222852.doi:10.1016/j.jms.2008.03.022. → pages 12[77] Rolf Linder, Kai Seefeld, Andreas Vavra, and Karl Kleinermanns. Gas phase infrared spectra ofnonaromatic amino acids. Chemical Physics Letters, 453(1-3):1–6, February 2008. ISSN 00092614.doi:10.1016/j.cplett.2007.12.069. → pages[78] Roman M. Balabin. The identification of the two missing conformers of gas-phase alanine: ajet-cooled Raman spectroscopy study. Physical Chemistry Chemical Physics, 12(23):5980, 2010.ISSN 1463-9076, 1463-9084. doi:10.1039/b924029b. → pages 12, 52, 57[79] H. Farrokhpour, F. Fathi, and A. Naves De Brito. Theoretical and Experimental Study of ValencePhotoelectron Spectrum of <span style=”font-variant:small-caps;”>d</span> , <spanstyle=”font-variant:small-caps;”>l</span> -Alanine Amino Acid. The Journal of PhysicalChemistry A, 116(26):7004–7015, July 2012. ISSN 1089-5639, 1520-5215. doi:10.1021/jp3023716.→ pages[80] Bert Lambie, Riet Ramaekers, and Guido Maes. On the contribution of intramolecular H-bondingentropy to the conformational stability of alanine conformations. Spectrochimica Acta Part A:Molecular and Biomolecular Spectroscopy, 59(6):1387–1397, 2003. → pages 12, 13, 42, 52[81] Shoujun Xu, J. Michael Nilles, and Kit H. Bowen. Zwitterion formation in hydrated amino acid,dipole bound anions: How many water molecules are required? The Journal of Chemical Physics,119(20):10696, 2003. ISSN 00219606. doi:10.1063/1.1620501. → pages 13[82] Yamilet Rodri´guez-Lazcano, Bele´n Mate´, Oscar Ga´lvez, Vi´ctor J. Herrero, Isabel Tanarro, andRafael Escribano. Solid L--alanine: Spectroscopic properties and theoretical calculations. Journal ofQuantitative Spectroscopy and Radiative Transfer, 113(11):1266–1275, 2012. → pages 13, 14[83] Christine M. Aikens and Mark S. Gordon. Incremental Solvation of Nonionized and ZwitterionicGlycine. Journal of the American Chemical Society, 128(39):12835–12850, October 2006. ISSN0002-7863, 1520-5126. doi:10.1021/ja062842p. → pages 13[84] Yanbo Ding and Karsten Krogh-Jespersen. The glycine zwitterion does not exist in the gas phase:results from a detailed ab initio electronic structure study. Chemical Physics Letters, 199(34):261–266, November 1992. ISSN 0009-2614. doi:10.1016/0009-2614(92)80116-S. → pages[85] Antonio Ferna´ndez-Ramos, Zorka Smedarchina, Willem Siebrand, and Marek Z. Zgierski. Adirect-dynamics study of the zwitterion-to-neutral interconversion of glycine in aqueous solution.The Journal of Chemical Physics, 113(21):9714, 2000. ISSN 00219606. doi:10.1063/1.1322084. →pages[86] Animesh K. Ojha and Snehasis Bhunia. Different proton transfer channels for the transformation ofzwitterionic alanine(H2o) n=2-4 to nonzwitterionic alanine(H2o) n=2-4: a density functional theorystudy. Journal of Molecular Modeling, 20(3), March 2014. ISSN 1610-2940, 0948-5023.doi:10.1007/s00894-014-2124-9. → pages77[87] P. Selvarengan and P. Kolandaivel. Potential energy surface study on glycine, alanine and theirzwitterionic forms. Journal of Molecular Structure: THEOCHEM, 671(1-3):77–86, February 2004.ISSN 01661280. doi:10.1016/j.theochem.2003.10.021. → pages[88] Emadeddin Tajkhorshid, K. J. Jalkanen, and Sa´ndor Suhai. Structure and vibrational spectra of thezwitterion L-alanine in the presence of explicit water molecules: a density functional analysis. TheJournal of Physical Chemistry B, 102(30):5899–5913, 1998. → pages[89] Francisco R. Tortonda, Juan-Luis Pascual-Ahuir, Estanislao Silla, In˜aki Tun˜o´n, and Francisco J.Rami´rez. Aminoacid zwitterions in solution: Geometric, energetic, and vibrational analysis usingdensity functional theory-continuum model calculations. The Journal of Chemical Physics, 109(2):592, 1998. ISSN 00219606. doi:10.1063/1.476596. → pages[90] Basak Turan and Cenk Selcuki. Conformational analysis of glutamic acid: a density functionalapproach using implicit continuum solvent model. Journal of Molecular Modeling, 20(9),September 2014. ISSN 1610-2940, 0948-5023. doi:10.1007/s00894-014-2396-0. → pages 13[91] Martine N. Blom, Isabelle Compagnon, Nick C. Polfer, Gert von Helden, Gerard Meijer, Sa´ndorSuhai, Be´la Paizs, and Jos Oomens. Stepwise Solvation of an Amino Acid: The Appearance ofZwitterionic Structures . The Journal of Physical Chemistry A, 111(31):7309–7316, August 2007.ISSN 1089-5639, 1520-5215. doi:10.1021/jp070211r. → pages 13[92] Clifton Espinoza, Jan Szczepanski, Martin Vala, and Nick C. Polfer. Glycine and Its HydratedComplexes: A Matrix Isolation Infrared Study. The Journal of Physical Chemistry A, 114(18):5919–5927, May 2010. ISSN 1089-5639, 1520-5215. doi:10.1021/jp1014115. → pages 13, 14[93] A Pawlukojc´, J Leciejewicz, J Tomkinson, and S.F Parker. Neutron spectroscopic study of hydrogenbonding dynamics in l-serine. Spectrochimica Acta Part A: Molecular and BiomolecularSpectroscopy, 58(13):2897–2904, November 2002. ISSN 13861425.doi:10.1016/S1386-1425(02)00086-0. → pages[94] Riet Ramaekers, Joanna Pajak, Bert Lambie, and Guido Maes. Neutral and zwitterionicglycine.H[sub 2]O complexes: A theoretical and matrix-isolation Fourier transform infrared study.The Journal of Chemical Physics, 120(9):4182, 2004. ISSN 00219606. doi:10.1063/1.1643735. →pages 13, 14, 62[95] Thomas Wyttenbach, Matthias Witt, and Michael T. Bowers. On the Stability of Amino AcidZwitterions in the Gas Phase: The Influence of Derivatization, Proton Affinity, and Alkali IonAddition. Journal of the American Chemical Society, 122(14):3458–3464, April 2000. ISSN0002-7863, 1520-5126. doi:10.1021/ja992546v. → pages 13[96] Simon Tam and Mario E. Fajardo. Ortho/para hydrogen converter for rapid deposition matrixisolation spectroscopy. Review of Scientific Instruments, 70(4):1926, 1999. ISSN 00346748.doi:10.1063/1.1149734. → pages 15[97] Jordan R. Schmidt and William F. Polik. WebMO, 2014. URLhttp://abacus.chem.ubc.ca/webmo/cgi-bin/jobmgr.cgi. → pages 23, 25, 26, 27[98] Ira Levine. Physical Chemistry. McGraw-Hill Education, Boston, 6 edition edition, May 2008.ISBN 978-0-07-253862-5. → pages 24, 25, 28[99] Joseph W. Ochterski. Thermochemistry in gaussian. Gaussian Inc, Pittsburgh, PA, pages 1–17,2000. → pages 24, 25, 26, 2778[100] Hendrik Zipse. Thermochemistry. URLhttp://www.cup.uni-muenchen.de/ch/compchem/vib/thermo1.html. → pages 24, 27[101] Donald A. McQuarrie and John D. Simon. Molecular Thermodynamics. University Science Books,Sausalito, California, 1 edition edition, 1999. ISBN 978-1-891389-05-4. → pages 25, 26, 27[102] Hiroyuki Katsuki and Takamasa Momose. Observation of rovibrational dephasing of molecules inparahydrogen crystals by frequency domain spectroscopy. Physical review letters, 84(15):3286,2000. → pages 38[103] Takamasa Momose, Masaaki Miki, Tomonari Wakabayashi, Tadamasa Shida, Man-Chor Chan,Steven S. Lee, and Takeshi Oka. Infrared spectroscopic study of rovibrational states of methanetrapped in parahydrogen crystal. The Journal of Chemical Physics, 107(19):7707–7716, November1997. ISSN 0021-9606, 1089-7690. doi:10.1063/1.475085. → pages[104] Takamasa Momose. Rovibrational states of a tetrahedral molecule in a hexagonal close-packedcrystal. The Journal of Chemical Physics, 107(19):7695–7706, November 1997. ISSN 0021-9606,1089-7690. doi:10.1063/1.475084. → pages 38[105] Joseph S. Francisco, James T. Muckerman, and Hua-Gen Yu. Hoco radical chemistry. Accounts ofChemical Research, 43(12):1519–1526, 2010. doi:10.1021/ar100087v. PMID: 20929216. → pages60[106] Leif O. Paulson, Fredrick M. Mutunga, Shelby E. Follett, and David T. Anderson. Reactions ofatomic hydrogen with formic acid and carbon monoxide in solid parahydrogen i: Anomalous effectof temperature. The Journal of Physical Chemistry A, 118(36):7640–7652, 2014.doi:10.1021/jp502470j. PMID: 25112906. → pages 60[107] Jana Chocholous˘ova´, Jaroslav Vacek, Friedrich Huisken, Olav Werhahn, and Pavel Hobza. Stackedstructure of the glycine dimer is more stable than the cyclic planar geometry with two oho hydrogenbonds: Concerted action of empirical, high-level nonempirical ab initio, and experimental studies.The Journal of Physical Chemistry A, 106(47):11540–11549, 2002. ISSN 1089-5639, 1520-5215.doi:10.1021/jp025925a. → pages 64[108] Anne Zehnacker and MartinA. Suhm. Chirality Recognition between Neutral Molecules in the GasPhase. Angewandte Chemie International Edition, 47(37):6970–6992, September 2008. ISSN14337851, 15213773. doi:10.1002/anie.200800957. → pages 7079Appendix ASupplementary Material: ConformationalAnalysis of b -alanine in Solid Parahydrogenand Argon MatricesThe following presents raw data from the b -alanine conformational studies discussed in Section 5.1. Theseinclude full FTIR spectra taken for each procedure, and tables of theoretically calculated wavenumbers andassociated intensities tabulated for each b -alanine conformer candidate.Figure A.1: The 750 - 2000 cm−1 region of the FTIR spectrum of b -alanine sublimed at a temperatureof 390 K and trapped into a parahydrogen matrix observed immediately after deposition.80Table A.1: Theoretical wavenumbers (cm−1) and intensities (km·mol−1) of the eleven b -alanine con-formers (Conformer I to XI) calculated at the B3LYP/aug− cc−pVTZ level of theory in the regionof 700 - 4800 cm−1.81Table A.1 Continued82Table A.1 Continueda A scaling factor of 0.955 was employed for vibrational modes with wavenumbers greaterthan 2000 cm−1, and a scaling factor of 0.985 was employed for all other vibrational modes.83Figure A.2: The 2000 - 3700 cm−1 region of the FTIR spectrum of b -alanine sublimed at a temperatureof 390 K and trapped into a parahydrogen matrix observed immediately after deposition.Figure A.3: The 750 - 2000 cm−1 region of the FTIR spectrum of b -alanine in solid parahydrogenrecorded after 4 hrs of UV-irradiation of the sample shown in Figures A.1 and A.284Figure A.4: The 2000 - 3700 cm−1 region of the FTIR spectrum of b -alanine in solid parahydrogenrecorded after 4 hrs of UV-irradiation of the sample shown in Figures A.1 and A.2Figure A.5: The 750 - 2000 cm−1 region of the FTIR spectrum of b -alanine sublimed at a temperatureof 390 K and trapped into an argon matrix observed immediately after deposition.85Figure A.6: The 2000 - 3700 cm−1 region of the FTIR spectrum of b -alanine sublimed at a temperatureof 390 K and trapped into an argon matrix observed immediately after deposition.Figure A.7: The 750 - 2000 cm−1 region of the FTIR spectrum of b -alanine in solid argon recordedafter 4 hrs of UV-irradiation of the sample shown in Figures A.5 and A.686Figure A.8: The 2000 - 3700 cm−1 region of the FTIR spectrum of b -alanine in solid argon recordedafter 4 hrs of UV-irradiation of the sample shown in Figures A.5 and A.687Appendix BSupplementary Material: ConformationalAnalysis of a-alanine in Solid Parahydrogenand Argon MatricesThe following presents raw data from the a-alanine conformational studies discussed in Section 5.2. Theseinclude full FTIR spectra taken for each procedure, and tables of theoretically calculated wavenumbers andassociated intensities tabulated for each a-alanine conformer candidate.Figure B.1: The solid parahydrogen matrix isolation FTIR spectrum of a-alanine (Tsub = 420 K, depo-sition time = 30 min, flow rate = 5 ccm, Tdep = 4 K) measured immediately after deposition.88Table B.1: Theoretical wavenumbers (cm−1) and intensities (km·mol−1) of the eight a-alanine con-formers (Conformer I to VIII) calculated at the B3LYP/aug− cc−pVTZ level of theory in theregion of 700 - 4800 cm−1.89Table B.1 Continueda A scaling factor of 0.955 was employed for vibrational modes with wavenumbers greaterthan 2000 cm−1, and a scaling factor of 0.985 was employed for all other vibrational modes.90Figure B.2: The solid argon matrix isolation FTIR spectrum of a-alanine (Tsub = 420 K, depositiontime = 30 min, flow rate = 5 ccm, Tdep = 18 K) measured immediately after deposition.Figure B.3: FTIR spectrum of a-alanine isolated in an argon matrix (Tsub = 420 K, deposition time =30 min, flow rate = 5 ccm, Tdep = 18 K) recorded immediately after annealing (10 min, 40 K).91Figure B.4: FTIR spectrum of a-alanine sublimed at a temperature of 410 K and isolated in a parahy-drogen matrix (deposition time = 30 min, flow rate = 5 ccm, Tdep = 4 K).Figure B.5: FTIR spectrum of a-alanine sublimed at a temperature of 410 K and isolated in an argonmatrix (deposition time = 30 min, flow rate = 5 ccm, Tdep = 18 K).92Figure B.6: FTIR spectrum of a-alanine sublimed at a temperature of 430 K and isolated in a parahy-drogen matrix (deposition time = 30 min, flow rate = 5 ccm, Tdep = 4 K).Figure B.7: FTIR spectrum of a-alanine sublimed at a temperature of 430 K and isolated in an argonmatrix (deposition time = 30 min, flow rate = 5 ccm, Tdep = 18 K).93Figure B.8: FTIR spectrum of a-alanine trapped in a parahydrogen matrix recorded immediately afterdeposition and before UV-irradiation (deposition time = 30 min, flow rate = 5 ccm, Tsub = 420K, Tdep = 4 K).Figure B.9: Solid parahydrogen matrix isolation spectrum of a-alanine measured after 1 hr of UV-irradiation (deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 4 K).94Figure B.10: Solid parahydrogen matrix isolation spectrum of a-alanine measured after 2 hrs of UV-irradiation (deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 4 K).Figure B.11: Solid parahydrogen matrix isolation spectrum of a-alanine measured after 3 hrs of UV-irradiation (deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 4 K).95Figure B.12: Solid parahydrogen matrix isolation spectrum of a-alanine measured after 4 hrs of UV-irradiation (deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 4 K).Figure B.13: FTIR spectrum of a-alanine trapped in an argon matrix recorded immediately after de-position and before UV-irradiation (deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K,Tdep = 18 K).96Figure B.14: Solid argon matrix isolation spectrum of a-alanine measured after 1 hr of UV-irradiation(deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 18 K).Figure B.15: Solid argon matrix isolation spectrum of a-alanine measured after 2 hrs of UV-irradiation(deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 18 K).97Figure B.16: Solid argon matrix isolation spectrum of a-alanine measured after 3 hrs of UV-irradiation(deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 18 K).Figure B.17: Solid argon matrix isolation spectrum of a-alanine measured after 4 hrs of UV-irradiation(deposition time = 30 min, flow rate = 5 ccm, Tsub = 420 K, Tdep = 18 K).98Appendix CSupplementary Material: UV Photolysis ofDeuterated a-alanine in SolidParahydrogenThe following presents raw data from the deuterated a-alanine UV photolysis studies discussed in Sec-tion 5.3. These include full FTIR spectra taken for each procedure, and tables of theoretically calculatedwavenumbers and associated intensities tabulated for each deuterated a-alanine conformer candidate andalso for each photoproduct candidate.99Table C.1: Theoretical wavenumbers (cm−1) and intensities (km·mol−1) of the twelve deuterated a-alanine conformers (Conformer I to VIII: considering both L- and D- form with labels “A” and“B”, respectively) calculated at the B3LYP/aug− cc−pVTZ level of theory in the region of 700 -4800 cm−1.100Table C.1 Continued101Table C.1 Continueda A scaling factor of 0.955 was employed for vibrational modes with wavenumbers greaterthan 2000 cm−1, and a scaling factor of 0.985 was employed for all other vibrational modes.102Table C.2: Experimental wavenumbers (cm−1) and intensities (arbitrary unit) of all the photoproductsobserved in the solid parahydrogen spectra upon subjecting deuterated a-alanine to 3 hrs of UV-irradiation.Table C.3: Theoretical wavenumbers (cm−1) and intensities (km·mol−1) of the seventeen predictedphotoproducts of deuterated a-alanine plus CO2 calculated at the B3LYP/aug− cc−pVTZ levelof theory in the region of 700 - 4800 cm−1.103Table C.3 ContinuedTable C.3 Continued104Table C.3 Continued105Table C.3 Continueda A scaling factor of 0.955 was employed for vibrational modes with wavenumbers greater than 2000cm−1, and a scaling factor of 0.985 was employed for all other vibrational modes.Figure C.1: FTIR spectra of deuterated a-alanine trapped in a solid parahydrogen matrix recordedimmediately after deposition and before UV-irradiation (deposition time = 2.5 hrs, flow rate = 5ccm, Tsub = 380 K, Tdep = 4 K).106Figure C.2: Solid parahydrogen matrix isolation spectrum of deuterated a-alanine acquired after 3 hrsof UV-irradiation (deposition time = 2.5 hrs, flow rate = 5 ccm, Tsub = 380 K, Tdep = 4 K).Figure C.3: Difference spectrum of deuterated a-alanine obtained by subtracting the spectrum ac-quired immediately after deposition (Figure C.1) from the UV-irradiation spectrum after 3 hrs ofirradiation (Figure C.2).107Appendix DSupplementary Material: Study of AminoAcid Zwitterions in Solid ParahydrogenThe following presents raw data from the b -alanine zwitterion studies discussed in Section 5.4. Theseinclude full FTIR spectra taken for each procedure.Figure D.1: FTIR spectrum of b -alanine trapped in a solid parahydrogen matrix without water dosagerecorded immediately after deposition (deposition time = 1.5 hrs, flow rate = 5 ccm, Tsub = 390K, Tdep = 4 K).108Figure D.2: FTIR spectrum of b -alanine trapped in a solid parahydrogen matrix with 100 ppm waterdopant recorded immediately after deposition (deposition time = 1.5 hrs, flow rate = 5 ccm, Tsub= 390 K, Tdep = 4 K).Figure D.3: FTIR spectrum of b -alanine trapped in a solid parahydrogen matrix with 500 ppm waterdopant recorded immediately after deposition (deposition time = 1.5 hrs, flow rate = 5 ccm, Tsub= 390 K, Tdep = 4 K).109

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