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PRUNING INTERSTELLAR SPACE

Permanent Link: http://ncf.sobek.ufl.edu/NCFE004841/00001

Material Information

Title: PRUNING INTERSTELLAR SPACE ROTATIONAL SPECTROSCOPY OF SMALL ORGANIC MOLECULES
Physical Description: Book
Language: English
Creator: Phillips, Maria
Publisher: New College of Florida
Place of Publication: Sarasota, Fla.
Creation Date: 2013
Publication Date: 2013

Subjects

Subjects / Keywords: Rotational Spectroscopy
ISM
Interstellar Space
Genre: bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

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Abstract: The rotational spectra of 2-methoxyethanol, 2-ethoxyethanol, and n-propylamine were recorded from 8.7 – 26.5 GHz using a waveguide, chirped-pulse Fourier transform microwave spectrometer at 253 K using a recently designed flow-through chiller system. These molecules were chosen for study because of recent developments in the field of astrochemistry. An automated spectral fitting program, the triples fitter, assisted in assigning the spectra of both 2-methoxyethanol and 2-ethoxyethanol. The triples fitter was recently developed and some guidelines for its use are discussed. The ground state and four vibrationally excited states were fit in the spectrum of 2-methoxyethanol and the ground state was fit in 2-ethoxyethanol. The spectrum of n-propylamine could not be assigned due to a dense data set containing the spectra of five conformers present in roughly equal abundance.
Statement of Responsibility: by Maria Phillips
Thesis: Thesis (B.A.) -- New College of Florida, 2013
Electronic Access: RESTRICTED TO NCF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE
Bibliography: Includes bibliographical references.
Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The New College of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Local: Faculty Sponsor: Shipman, Steven

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Source Institution: New College of Florida
Holding Location: New College of Florida
Rights Management: Applicable rights reserved.
Classification: local - S.T. 2013 P5
System ID: NCFE004841:00001

Permanent Link: http://ncf.sobek.ufl.edu/NCFE004841/00001

Material Information

Title: PRUNING INTERSTELLAR SPACE ROTATIONAL SPECTROSCOPY OF SMALL ORGANIC MOLECULES
Physical Description: Book
Language: English
Creator: Phillips, Maria
Publisher: New College of Florida
Place of Publication: Sarasota, Fla.
Creation Date: 2013
Publication Date: 2013

Subjects

Subjects / Keywords: Rotational Spectroscopy
ISM
Interstellar Space
Genre: bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract: The rotational spectra of 2-methoxyethanol, 2-ethoxyethanol, and n-propylamine were recorded from 8.7 – 26.5 GHz using a waveguide, chirped-pulse Fourier transform microwave spectrometer at 253 K using a recently designed flow-through chiller system. These molecules were chosen for study because of recent developments in the field of astrochemistry. An automated spectral fitting program, the triples fitter, assisted in assigning the spectra of both 2-methoxyethanol and 2-ethoxyethanol. The triples fitter was recently developed and some guidelines for its use are discussed. The ground state and four vibrationally excited states were fit in the spectrum of 2-methoxyethanol and the ground state was fit in 2-ethoxyethanol. The spectrum of n-propylamine could not be assigned due to a dense data set containing the spectra of five conformers present in roughly equal abundance.
Statement of Responsibility: by Maria Phillips
Thesis: Thesis (B.A.) -- New College of Florida, 2013
Electronic Access: RESTRICTED TO NCF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE
Bibliography: Includes bibliographical references.
Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The New College of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Local: Faculty Sponsor: Shipman, Steven

Record Information

Source Institution: New College of Florida
Holding Location: New College of Florida
Rights Management: Applicable rights reserved.
Classification: local - S.T. 2013 P5
System ID: NCFE004841:00001


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PRUNING INTERSTELLAR SPACE: ROTATIONAL SPECTROSCOPY OF SMALL ORGANIC MOLECULES BY MARIA PHILLIPS A Thesis Submitted to the Division of Natural Science New College of Florida in partial fulfillment of the requirements for the degree Bachelor of Arts Under the sponsorship of Dr. Steven Shipman Sarasota, Florida May, 2013

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ii Acknowledgments There are too many wonderful people in my life to acknowledge everyone here. I am so very lucky to have so many incredible friends in my life; thank you all for always being there. I would not be here today with out the never ending support from my family. I would like to thank my P ing me how to start at the beginnin g of every problem. Thank you M ama for showing my how easy it is to work hard and for always being there to talk about anything Becca, thank you enough for teaching me patience and for showing me unconditional love. Rachel Weisman, I am always so awed by the fact that some how we were made roommates and from the very beginning best friends and soul mates You are my boulder. made it through some of those early morning natsci classes and these last four years without you. bump s along the way I am so happy I can call you one of my best friends. Ch ristian Metzger thanks for always being there to gossip and for being there through this whole thesis process. Late nights in lab were always bearable with you there. Austin Mooney, you really are the best. You made my worst thesis days so much better a Christopher Mulholland and Ashlyn King, I am so grateful to have you two as role models through out my New College career and always. Thank you to my lab mates, Ben Rooks and Bri Gordon, for goi ng through this whole crazy thesis thing with me. To my little ducks, Zachary Decker, Anne Emig, Michael Davis, and Sam Weldon, I hope you all stick with rotational spectroscopy and have a wonderful New College experience. Ian Finneran, I will never be ab le to thank you enough for the pressure robot or for the triples fitter. Those things alone made my thesis experience so much easier. I semester with out them feeding me. here and for always being enthusiastic about science. I will be forever in debt to you f enough for s upporting me and believing in me through out my New College career. I really do not know where I would be academically with out your support and motivation. Thank you again.

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iii Table of Contents

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iv Table of Figures

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v Table of Tables

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vi

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vii PRUNING INTERSTELLAR SPACE: ROTATIONAL SPECTROSCOPY OF SMALL ORGANIC MOLECULES Maria Phillips New College of Florida, 2013 ABSTRACT The rotational spectra of 2 methoxyethanol, 2 ethoxyethanol, and n propylamine were recorded from 8.7 26.5 GHz using a waveguide, chirped pulse Fourier transform microwave spectrometer at 253 K using a recently designed flow through chiller system. These molecules were chosen for study because of recent developments in the field of astrochemistry. An automated spectral fitting program, the triples fitter, assisted in assigning the spectra of both 2 methoxyethanol and 2 ethoxyethanol. The triples fitter was recently developed and some guidelines for its use are discussed. The ground state and four vibrationally excited states were fit in the spectrum of 2 methoxyethanol and the ground state was fit in 2 ethoxyethanol. The spectrum of n propylamine could not be assigned due t o a dense data set containing the spectra of five conformers present in roughly equal abundance. Dr. Steven Shipman Division of Natural Sciences

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1 1 Introduction Rotational transitions of molecules occur in the microwave region of th e electromagnetic spectrum; when properly analyzed these transitions can be used to both determine molecular structure and to to identify molecules in complex mixtures. In order to study a molecule with rotational spectr oscopy, it must have an electr ic dipole moment. Generally, more rigid molecules with fewer conformers have simpler spectra, which makes them easier to analyze. Because of this, many small molec ules have already been completely analyzed leaving larger, more complicated molec ules next in line for study. At room temperature, there is usually sufficient energy in the system for the molecules to become vibrationally excited or to occupy multiple conformational states. E ach vibrationally excited state a n d conformer of the molec ule has a different shape, and so they each have diffe rent rotational constants This leads each state to have a unique spectrum, all of which are combined in the observed spectrum. The observed spectrum is therefore very dense and difficult to analyze This is a particularly sever e problem for larger, less rigid, molecules with multiple conformers This effect is illustrated in Figure 1.1. An important application of rotational spectroscopy lies in astroche mistry. In order to c orrectly identify molecules, radio astronomers need to have laboratory data because the experimental data they collect contains rotational transitions from many different molecules. A strochemists have been using radio telescopes to identify molecules in t he interstellar medium since 19 40 when the first m olecule, the CH radical was detected [1] Since the n, r adio astronomers

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2 Figure 1.1 Simulated spectra showing how different conformers of one molecule makes each spectrum unique combine in a single observed spectrum. It is impossible to tell which transition originates from which conformer spectrum in the combined spectrum.

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3 have identified many small organic molecules, such as methanol[2], methyl formate[3], and methylamine[4]. Small organ ic molecules, or weeds, such as these are so abundant in the ISM that their signals obscure the molecules radio astronomers are interested in, amino acids for example, or flowers. The field of a strochemistry has been growing rapidly and there are many new radio telescope arrays that have become recently operation al or are currently in production. ALMA, the Atacama Large Millimeter/Submillimeter Array, located in Atacama, Chile is currently in production and will be the largest radio telescope array to date. ALMA when completed, will be made up of 50 antennas of 12 m These antennas can be placed in various configurations with sizes ranging from 150 m to 16 km, covering a collecting area of up to 5650 m 2 The main array can cover a frequ ency range from 30 950 GHz Depending on the number of dishes used and their spatial configurations, a wide variety of different measurements can be made, ranging from broad survey scans of single point sources to mapping out the spatial distribution of particular molecules across a large fraction of the sky. The various configurations that the array can be placed i n affects the data collected ; the closer together the arr ay is, the lower the resolution of the data but the more area of the sky covere d and the largest array configuration has the highest spatial resolution and can be used to make chemical maps There will also be a compact array, the Atacama Compact Array (ACA) with 12 antennas of 7 m diameters that will have the same receivers the large array has, as well as three extra recei vers. There will also be 4 single dishes with 12 m diameters for calibrations as well as single dish observations[5]. With these improvem ents along with new radio telescope arrays curre ntly in production, such as the Ver y Large Array in New Mexico [6] larger molecules than previously seen should be

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4 identifiable in the ISM. The molecules studied in this thesis, 2 methoxyethanol, 2 ethoxyet hanol, and n propylamine, were chosen because they are all slightly larger and more complicated than molecu les already detected in the ISM but have not yet been detected themselves. Because the radio telescopes are improving and researchers are becoming more interested in larger molecules, improved techniques for handling complicated spectra are needed. A n automated spect ral fitting program called the triples f itter is currently in development Ian Finneran was integral in developing this software to i ts current state. The triples fitter is a brute force spectral fitting program that assigns every possible peak in the expe rimental spectrum to a set of transitions, performs a fit on e ach combination, and then compar es to the full spectrum. The triples f itter was extremely useful in fitting 2 methoxyethanol; it found the rotational constants for the ground state as well as four vibrationally excited states from a single initial guess The ground state of 2 ethoxyethanol was also assigned using starting rotational constants determined by the triples fitter. As t he triples fitter i s still in the testing phase, practical suggestions for its use are included in the experimental section and future development directions are discussed in the conclusion. In a ddition to discussing the triples fitter, this thesis also describes the design and operation of a flow through chiller, a nother recent development to the lab The flow through chiller cools the waveguide, where the molecules are held while data is being c ollected This simplifies the observed spectrum because there is less energy in a colder system, meaning that there are fewer populated rotational states, vibrationally excite d states and conformers that contribute to the observed spectrum.

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5 The theory behind rotational spectroscopy is dense and will not be discussed in this thesis because there are a lready many sources that thoroughly cover it well. Ian Finneran basic rotational spectroscopy theory and also contains a very good list o f sources. A brief overview of the theory is given below The rotation of molecules is not continuo us, but quantized. The rotations are determined by the moment s of inertia of the molecule and its angular momentum, J The moment s of inertia I, are ba sed on the mass distribution of the molecule and have three components along the three vectors of principal axis system (PAS), a, b, and c. The PAS has its origin at the center of mass of the molecule Further, the axes are labeled such that I a I b I c Rotational spectroscopists convert these components into the A, B, and C rotational constants : w here X = A, B, or C Molecules are classified by symmetry into five groups: linear ( I a = 0, I b = I c ), spherical (I a = I b = I c ), oblate (I a = I b < I c ), prolate (I a < I b = I c ), and asymmetric (I a < I b < I c ). All of the molecules discussed in this thesis are asymmetric which makes the analysis difficult. Three quantum numbers must be used to determine the rotational energy levels of a molecule, J, K a and K c J is the angular momentum quantum number K a is the projection of the angular momentum along the a axis (only exact if the molecule was prolate ) and K c is the projection of the angu lar momentum along the c axis (only exact if the molecule was oblate) In rotational spectroscopy, the peaks in a spectrum represent the transition from one rotational energy level to a

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6 different rotational energy level. This transition is denoted J K a K c a c where the single primes refer t othe higher energy state and the double primes refer to the lower energy state Only certain transitions are allowed for certain molecules and these are determined by the dipole components along each axis. These are designated as a type transitions b type tr ansitions and c type transitions are defined by a c a a c b a c c This thesis is divided into 6 chapters. The second chapter describes the chirped pulse microwave spectrometer, the recently developed flow through chiller system, and the triples fitter and gives some guidelines for its use. Chapters 3 5 examine the rotational spectr a of 2 methoxyethanol, 2 ethoxyethanol, and n propy lamine, respectively. Chapter 6 concludes this thesis with a n overall summary of the results of the molecules studied, as well as future work for their analysis and for the lab.

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7 2 Experiment al There are many different techniques that are used when collecting and analyzing rotational spectra. Microwave circuits produce the pulse that excites the molecules and collects the data, a chiller system was recently developed in order to cool the mol ecules, and an automated spectral fitting program is currently in development to speed up the analysis process. These will be discussed in more detail in this chapter. The Microwave Circuit A chirped pulse Fourier tr ansform microwave spectrometer wa s used to collect the rotational spectra of small molecules from 8.7 26.5 GHz. In this instrument t he full bandwidth is broken into three separate bands; detailed descriptions of the circuits used for the two lower bands, 8.7 13.5 GHz and 13.5 18.3 GH z, can be ] theses and a complete description of the newest band, 18 26.5 GHz, can be found in Bri ] thesis. In the spectrometer, a chirped pulse (linear frequency sweep) is generated by an arbitr a ry waveform generator and is then shifted to one of the three frequency ranges using mixers, a phase locked dielectric resonator oscillator, and filters. The pulse is then amplified, after which it enters the waveguide and interacts with a molecular sampl e. At this point, the pulse transiently aligns the molecules, which then begin rotating in phase with the electric field provided by the pulse. Once the pulse comes to an end, the molecules continue rotating together and emit their own, small, electric f ield. As time continues, the molecules fall out of phase due to collisions between the

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8 molecules and collisions with the walls of the waveguide. This results in a free induction decay, or a FID. This FID is amplified and collected by the oscilloscope in the time domain and is then Fourier transformed into a spectrum in the frequency domain. The circuit schematic can be found in Figure 2.1. Figure 2.1 General Circuit Diagram. Box 1 shows the front end of the circuit where t he pulse in generated at the Arbitrary Waveform Generator mixed up to the correct frequency, and amplified. Box 2 is where the pulse interacts with the molecules in the waveguide and Box 3 depicts the back end, where the spectrum is collected at the oscilloscope. Flow Through Wave guide Chiller A goal in the Shipman lab is to speed up the analysis of rotational spectroscopy. One way to do that is to simplify the observed spectrum In a microwave spectrum, t he number of populated states, also known as the partition function, depen ds on a variety of conditions, one of which is the temperature of the molecules. If the partition function is large, there are a large number of populated excited states, each of which has a different rotational spectrum. This makes the full data set mor e complicated to analyze since each spectrum is

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9 overlaid; for a fixed number of molecules, this also reduces the intensity of each spectrum since there are fewer molecules in each state. Lowering the temperature leads to a lower partition function which l eads to fewer populated excited states This both simplifies the spectrum and makes it stronger As a simple spectrum is easier to analyze than a complicated one, lowering the temperature therefore makes the fitting process much simpler. With that in mi nd, we have built a flow through chiller system that brings the sample temperature down to approximately 25 o C. The schematic for the flow through chiller is in Figure 2.2 In the past, the coiled waveguide was held in a 10 gallon fish tank that was filled with ice and water to cool the waveguide to 0 o C during data collection. During the summer of 2012, a design was made for a flow through waveguide chiller and the lab received money from the CAA for supplies to build it. The design for the chille r was based on cooling systems for brewing beer. Home brewers must cool their beer quickly to prevent bacteria from growing before the yeast is added [10 ] Placing copper coils either around or in the pot the beer is brewing in and then running cold water through the coils cools the beer quickly. Usin g this method as a guide for our chiller, inch ID copper tubing was purchased to coil around the inside and outside of the waveguide. Before the copper tubing was coiled around the wavegu ide, thermal pads were placed so that there would be even conduction over the whole waveguide. The copper tubing was coiled around the inside and o utside of the waveguide so the maximum surface area of the waveguide was covered by tubing for consistent cooling. For the ins ide of the waveguide, the tubing was first shaped with a soup pot with an outer diameter close to the inner diameter o f the waveguide so that the copper coils were close to the desired shape. For the

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10 outside of the waveguide, the copper tubing was simply coiled around the waveguide itself by hand. The inner and outer copper coils were held to the waveguide with aluminum zip ties. In the coiling process, sections of tubing had to be soldered together using a propane torch, flux, and solder. Figure 2.2 Flow through chiller schematic. The fluid flows in a loop through both chillers and can cool the waveguide to temperatures as low as 25 o C. Once the waveguide was covered in the coils, they were covered with thermally conductive paste to provide a more even temperature transfer and to prevent heat leaks. Next, the inside and outside of the waveguide and coils were covered in expanding insulation foam to insulate the waveguide. The copper coils were then connected to a PolyScience Refrigerated Circulat ing Bath ( AD15R 40 A11B ) containing PolyScience polycool liquid (060330 ) with a temperature range of 50 o C to 218 o C. Although the liquid can be used at very high temperatures, the O rings that seal the waveguide can only withstand temperatures up to 50 o C for an extended period of time before the waveguide begins leaking. These high temperatures are used when doing a bake out to clear the waveguide so data on a new molecule can be taken. With just one circulating bath connected to the inner and outer c oils, the waveguide temperature only reached about 13 o C; a second circulating bath was then purchased and the base tempera ture now reaches approximately 25 o C.

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11 Triples Fitter Once the spectrum is collected, the next step is to analyze the data, also referred to as fi t t ing the spectrum. In order to fit the spectrum, the lines must be assigned to specific rotational transitions, after which a set of rotational constants are adjusted to minimize the difference between the observed and predicted spectrum. This can be done with various software packages. While the software has greatly decreased the amount of time it takes to fit the data, it can still take week s or months to fully analyze a spectrum. The fitting process is difficult for a number of different reasons. One reason it is difficult is while ab initio calculatio ns are fairly accurate, the predicted rotational constants are usually off by about 1 3% and this difference can cause the predict ed spectrum to be su bstantially different from the experimental spectrum making it difficult to correctly assign transitions especially when the spectrum is dense (Figure 2.3 ) Another difficulty comes from the number of peaks present in a spectrum collected close to room temperature Because our spectrometer operates at or near roo m temperature each spectrum usually contains contributions from multiple vibration al modes and conformers. E ach of these species has its own individual spectrum w ith different rotational const ants leading to a very dense observed spectrum Because of these reasons the fitt ing process is the bottleneck in the lab W e are trying to accelerate this process so that we can increase the number of molecules we can study each year The t riples fi tter is an automated spectr al fitting program that has been developed to assist with the fitting process. The current version was written by Ian Finneran and is based on a script from the Pate lab at the University of

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12 Virginia. This software is fully des below [8] The t riples fitter uses rotational and distortion constants from ab init i o calculations or previous work as inputs to predict a spectrum. F rom this that have been predicted to be particularly intense, and the displayed list is made up of all possible combinations of the top 10 20 peaks. Using selection rules, a set of triples is chosen that best fits the molec ule in question. F or example if the molecule has a strong a type dipole and a medium b type dipole, a triple containing two a type transitions and one b type transition should be chosen Once the triple is picked a search window is selected and a l ist of 10 20 sorting transitions are chosen as well. The search window determines the frequency range used when assigning transitions to the experimental peaks. Sorting transitions are the transitions that are used to score each fit. The program works by t aking the experimental peak list and fitting every combination of three peaks within the search window to the three transitions in the triple and determines rotational constants for each fit. These rotational constants are used to predict a new spectrum, which is scored by comparing the sorting transitions to the experimental peaks. This is extremely helpful because while the rotational cons tants still need to be improved they are much closer to the final constants than the ab intio values. U sing the t r iples fitter can reduce the time spent fitting by weeks. The triples fitter has been of great use in fitting the spectra in this thesis. Some useful guidelines for using the software have been found while experimenting with it. Before se lecting a triple, a list of the peaks found in the

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13 Figure 2.3. Comparison of ab initio rotational constants versus final rotational constants for 2 ethoxyethanol. The positive scale is experimental data and t he nega tive scale is simulated sp ectra. T he dark blue spectrum is simulated using the final rotational constants and the light blue spectrum is simulated using the ab initio rotational constants. Asterisks indicate matching transitions (i.e. the light blue cluster predicted to to be near 21.5 GHz actually corresponds to the experimental cluster near 21.75 GHz instead).

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14 experimental spectrum must be created. The proper intensity threshold must be determined to give the triples fitter enough experimental peaks to use when fit ting the predicted transitions If rotation al and distortion constants from previous papers are availab le, the peak list should be made by setting the threshold to three times the noise level. It has been found that it is better to have more peaks in the peak in the peak list means there i s a better chance of finding accurate rotational constants since this progra m relies on brute force fitting The peak list may need to be adjusted a few times before the right cut off is determined. Once the peak list is made but before the triple and check peaks are chosen, it is useful to predic t the spectrum. F irst simulate the spectrum up to about J = 50 or higher to see which type of transitions are expected to be most abundant a nd again at a lower J, around J = 10 20, in order to choose the most intense peaks for the triples and check transitions. Using transitions of lower J generally leads to better results, since the distortions are less import ant and so inaccurate values will not greatly harm the prediction However, these peaks are usually less intense than higher J transitions near 250 K, so some sort of trade off is inevitable. Once it has been determined which transitions are dominant in the observed spectrum, the same types of transitions for the triple should be chosen. When choosing a triple, the three transitions should be ideally kept in the experimental d ata where there are not many peaks. Another important factor for a successful triples fitter job is the search window. If a short test job will be used to see if reasonable transitions have been chosen and if the peak list has a reasonable cut off, the nu mber of triples to fit

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15 should be kept at or below one million. Typical jobs will usually have at least two or more million triples to fit. On a two core machine, this will take anywhere from 4 to 24+ hours. The triples fitter has only been tested on sin gle computers, but the lab is working on modifying the triples fitter so that it can run on a cluster like Amazon EC2, which will greatly reduce the run time All of the recent developments discussed in this chapter have been performed to accel erate the analysis of rotational spectr a The chiller system was designed to simplify the observed spectrum and the triples fitter was developed to shorten the amount of time it takes to fully analyze the observed rotational spectrum. Both of these advances were used to study the spectra of 2 methoxyethanol (Chapter 3), 2 ethoxyethanol (Chapter 4), and n propylamine (Chapter 5).

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16 3 : 2 Methoxyethanol With recent developments to the Atacama Large Millimeter Array (ALMA)[1 1 ], organic mol ecules with more than three heavy atoms should be detectable in the interstellar medium (ISM). This should be true since ALMA collects data with high spatially resolved molecular information as well as uses broadband spectral acquisition instead of the li ne by line approach that older ground based radio telescope arrays used in the past. Using a list of molecules that have been previously detected in the ISM[12 ], 2 methoxyethanol (MEO), shown in Figure 3 .1, was chosen for study by using known ISM formatio n reactions and predicting that MEO could form via a similar process to how methoxymethanol forms 2 Methoxyethanol has a methyl rotor that can undergo internal rotation, along with three other large amplitude motions along the CO CC, OC CO and CC OH bonds In 1999 Gil conducted ab initio calculations on MEO and found four stable conformers[ 1 3]. Those conformers were tgg g, and ttt about the dihedral bonds stated previously. El ab initio calculations on twelve conform ers of MEO in 2006 and the lowest energy 1 4]. The four lowest energy co nformers can be seen in Figure 3 .1. Conformer labeling schemes are different in the different papers, but here we adopt the scheme used by Gil. The lowest energy conformer is the trans gauche ( ) conformer. In this species, the dipole moment is strongest along the a axis but is significant along the b axis as well; there is almost no dipole moment along the c axis. The dipole moments for all four c onformers can be seen in Table 3 .1.

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17 The microwave spectrum of 2 methoxyethanol was first collected by Buckley and Brochu in 1971[ 1 5]. They recorded the spectrum at 40 o C with a 100 kHz Stark modulated spectrometer from 8 26.5 GHz. In their spectrum, 38 lines with transitions up to J = 4 were recorded and fit to the ground state. They observed the spectra of three excited vibrational states and assigned 47 transition s up to J = 9. Figure 3 .1 The four l owest energy conformers of 2 methoxyethanol The first letter denotes the conformation around the CO CC bond, the second letter about the OC CO bond and the third about the CC OH bond. Relative energies of the conformers are provided (B3LYP/6 311++G(d,p)) Buckley and Brochu also deuterated the hydroxyl group and fit 8 lines of this species in the ground state up to J = 3. From these results, they determined that the predominant confor mer was 1 1 Using present notation. Buckley and Brochu referred to this as gauche gauche gauche.

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18 examined the 2 methoxyethanol spectrum. The spectrum was collected using a Hewlett Packard 8040A computer controlled Stark modulated spectrometer at 25 o C[ 1 6]. Table 3 .1. Calculated and observed dipole moments of four conformers of MEO. Conformers l A l (Debye) l B l (Debye) l C l (Debye) Relative E a) (cm 1 ) tgg' 2.243 1.2336 0.0897 0.0 0 Observed [ 1 5 ] 2.03 1.15 0.25 -ttt 0.0559 0.3833 0.0046 858.34 ttg 1.3268 1.2364 1.2465 898.00 0.7455 0.4167 1.9814 1319.85 a) Calculated using B3LYP/6 311++G(d,p), not zero point corrected Caminati et al. were able to resolve the A E splitting due to internal rotation of the methyl rotor for J = 0 for the ground and several excited states. They assigned transitions up to J = 70 for the ground state and analyzed multiple excited states in detail. A semirigid model was used to fit the A states and a flexible model treatment was used in order to reproduce the splittings found in the excited states that were determined to be due to the methyl rotor ground state cons tants and can be seen in Table 3 .2 along with calculated and experimental rotational constant s from the present work. Although 2 methoxyethanol has been previously examined its spectrum was last analyzed over 20 years ago. Because Stark modulated spectrometers are not very sensitive, we expect to see many more transitions using a chirped pulse spectrometer. Further, with more advanced spectral fitting packages than were available in 1986, we should be able to obtain a more precise fit of both the ground and excited state spectra. Refined constants with fits extending to h igh J values will be neede d in order to be able to easily search for this compound in the ISM.

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19 Table 3 .2 Past, calculated, triples fitter, and current g round state rotational constants for MEO GS Buckley [15] Caminati [16] Calculated B3LYP/6 311++g( d,p) Triples Fitter Current A (MHz) 12982.35 12982.398(5) 12954 103 12982.0 12982.413(82) B (MHz) 2742.48 2742.502(2) 2718 1054 2742.505 2742.5065(171) C (MHz) 2468.10 2468.1039(4) 2445 1545 2468.107 2468.1081(158) J (kHz) -1.396(4) 1 4 386 1.396 1.4255(232) JK (kHz) -12.27(5) 12 057 12.27 11.939(305) K (kHz) -93.37(6) 94 545 93.37 93.06(35) J (kHz) -0.2859(7) 0. 29118 0.2859 0.28485(161) K (kHz) -3.90(8) 4 3814 3.90 4.13(48) H J (Hz) -0.00144(9) --0.00157(55 ) H KJ (Hz) -0.226(7) --0.2 17(59 ) Lines Fit 38 122 --257 Fit RMS (MHz) -0.07 --0.0 72 Highest J 9 70 --78

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20 Before the rotational spectrum was collected, ab initio calculations were performed on 2 metho xyethanol using Gaussian09 at the B3LYP/6 311++G(d,p) level of theory Optimizations were performed on the four lowest energy con formers of 2 methoxyethanol found by Gil and El Hefnawy. In agreement with their results, we found that t he trans gauche gauche conformer was the most stable of the four (relative energies for each c onformer can be found in Table 3 .1) I n order to obtain starting rotational constants for the excited states of each conformer t he v ibrational modes and vibration rotation coup ling constants were calculated. The c onstants for the conformer are shown in Table 3 .3 ; constants for the three higher energy conformers can be found in Appendix A Table 3 .3 Calculated vibrational energies with their descriptions and vibration rotation coupling constants of MEO Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) C (MHz) 93 119.16 7.39 5.82 O C Torsion 137 113.43 10.21 7.54 C C Torsion 223 13.04 3.28 3.02 Methyl Torsion 277 11.02 2.51 1.04 In plane wag 366 78.94 8.04 6.32 Symmetric in plane wag 423 66.43 20.31 12.13 Hydroxyl Wag 545 33.14 8.04 5.89 Twist After the geometry optimization of each conformer was complete, a potential energy scan was performed for each species about the methyl rotor dihedral angle, consisting of 36 total points with 1 point every 10 o The potential energy scan was then fit to a V 3 potential for the conformer ( Figure 3 2). From this fit (V 3 ~ 780 cm 1 ), it was determined that the chirped pulse instrument will not be

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21 able to resolve the A E splitting. However, these splittings may be resolvable in the first excited state of the methyl torsional mode. Figure 3 .2 B3LYP/6 311++G(d,p) dihedral scan abou t the methyl group. Black squares are calculated data points and the red line is the V 3 potential energy fit. The spectrum of 2 methoxyethanol was recorded in three separate frequency ranges (8.7 13.5, 13.5 18.3, and 18.0 26.5 GHz) at 253 K with a 4 FID at a pressure of 5 mTorr. The spectrum in each band was averaged for 1 million shots, and the full spectrum can be seen in Figure 3 .3. An expanded view of t he spectrum is shown in Figure 3 .4, which shows the spectrum, its accompan ying blank, and a line at the 3:1 signal to noise level.

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22 Figure 3 .3 Full s pectrum of MEO from 8.7 The spectrum was averaged for 1 million shots. The 8.7 18 .3 GHz frequency range has been scaled by a factor of 4 for clarity

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23 Figure 3 .4 Expanded view of the s pectrum of MEO with the blank spectrum in red and the 3: 1 signal to noise line in blue, at roughly 13 intensity units. In the full spectru m, there are 1974 peaks abo ve the 3:1 signal to noise ratio

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24 state rotation and distortion consta nts, the triples fitter was able to simultaneously find the rotational constants of the ground and four vibrationally excited states of MEO in 30 minutes with the spectrum shown in Figure 3.3 By comparison to and the ab init io vibration rotation constants the excited states can be assigned to the first and second vibrationally excited state s of the O C torsion (93 and 186 cm 1 ), the first vibrationally excited state of the C C torsion (137 cm 1 ), and the first vibrationally excited state of a combination of the two torsions (230 cm 1 order to compare how well the triples f itter is actually performing as second triples fitter run was performed using the ab inito rotational constants and distortions as a starting point Under these circumstances the triples fitter was as starting parameters. However, doing so required that the search wind ow be increased to 800 MHz, which increased the number of triples to evaluate from 102,600 to 1,043,100. This required ~10 times as much time ( 4.5 hours) to find all five states. Starting from triples fi tter results e ach of these states was then refined with SPFIT and SPCAT. The current fits of the ground state, the first and second vibrationall y excited states of the O C torsion the first vibrationally excited state of the C C torsion and the first vibrationall y excited state of the two torsions to get her, can be found in Tables 3 .2, 3 .4, 3 .5, 3 .6, and 3 .7 respectively, calculated constants, and past constants.

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2 5 Table 3 .4 Past, calculated, triples fitter, and current assignment s of t he first vibrationally excited state of the O C torsion Buckley [15] v sk1 = 1 Caminati [16] v sk1 = 1 Calculated B3LYP/6 311++g(d,p) a Triples Fitter Current v sk1 = 1 A (MHz) 12868.55 12868.533(8) 12863.236 12870.0 12868.526(82) B (MHz) 2750.43 2750.477(2) 2749.895 2750.443 2750.443(171) C (MHz) 2473.78 2473.7850(5) 2473.927 2473.782 2473.7820(171) J (kHz) -1.498(3) 1 4 386 1.396 1.4935(215) JK (kHz) -12.46(4) 12 057 12.27 12.48(38) K (kHz) -87.29(5) 94 545 93.37 87.42(53) J (kHz) -0.3058(9) 0. 29118 0.2859 0.3056(59) K (kHz) -3.25(9) 4 3814 3.90 3.30(63) Lines Fit 18 74 --142 Fit RMS (MHz) -0.08 --0.075 Highest J 9 49 --69 a Calculated distortion constan ts from ground state calculation

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26 Table 3 .5 Past, calculated, triples fitter, and current assignments of t he second vibrationally excited state of the O C torsion Buckley [15] v sk1 = 2 Caminati [16] v sk1 = 2 Calculated B3LYP/6 311++g(d,p) a Triples Fitter Current v sk1 = 2 A (MHz) 12757.95 12757.83(1) 12744.076 12756.95 12757.791(86) B (MHz) 2759.12 2759.159(3) 2757.285 2759.146 2759.1535(179) C (MHz) 2479.76 2479.773(3) 2479.747 2479.768 2479.7663(191) J (kHz) -1.586(3) 1 4 386 1.396 1.5770(290) JK (kHz) -13.02(5) 12 057 12.27 13.10(44) K (kHz) -82.60(6) 94 545 93.37 82.65(55) J (kHz) -0.331(2) 0. 29118 0.2859 0.3312(56) K (kHz) -2.57(12) 4 3814 3.90 2.60(89) Lines Fit 13 79 --123 Fit RMS (MHz) -0.10 --0.087 Highest J 9 47 --79 a Calculated distortion constants from ground state calculation

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27 Table 3 .6 Past, calculated, triples fitter, and current assignments of t he first vibrationally excited state of the C C torsion Buckley [15] v sk2 = 1 Caminati [16] v sk2 = 1 Calculated B3LYP/6 311++g(d,p) a Triples Fitter Current v sk2 = 1 A (MHz) 13101.80 13101.62(1) 13095.86 13099.0 1310 1.368(113) B (MHz) 2731.09 2731.118(2) 2732.29 2731.11 2731.1284(247) C (MHz) 2459.87 2459.860(2) 2460.57 2459.87 2459.8579(267) J (kHz) -1.372(3) 1 4 386 1.396 1.418(90) JK (kHz) -12.60(4) 12 057 12.27 12.32(142) K (kHz) -105.3(8) 94 545 93.37 83.00(191) J (kHz) -0.2718(8) 0. 29118 0.2859 0.2744(143) K (kHz) -4.75(9) 4 3814 3.90 5.93(249) Lines Fit 24 58 --81 Fit RMS (MHz) -0.07 --0.079 Highest J 9 46 --57 a Calculated distortion constants from ground state calculation

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28 Table 3 .7 Past, calculated, triples fitter, and current assignments of t he c ombination band of v = 1 in the O C torsion and v = 1 in the C C torsion. Caminati [ 16] v combination = 1 Calculated B3LYP/6 311++g(d,p) a Triples Fitter Current v combination = 1 A (MHz) 12965.22(2) 12976.66 12965.0 12965.253(102) B (MHz) 2738.238(2) 2760.11 2738.242 2738.2374(201) C (MHz) 2465.5303(6) 2466.387 2465.527 2465.5310(208) J (kHz) 1.460(8) 1 4 386 1.396 1.466(36) JK (kHz) 13.38(9) 12 057 12.27 13.38(65) K (kHz) 97(18) 94 545 93.37 99.76(90) J (kHz) 0.293(1) 0. 29118 0.2859 0.2915(113) K (kHz) 3.4(2) 4 3814 3.90 3.43(166) Lines Fit 35 --82 Fit RMS (MHz) 0.08 --0.078 Highest J 50 --70 a Calculated distortion constants from ground state calculation

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29 Overall, 257 lines were assigned to the ground state of MEO. While Caminati was able to assign A E splitting in the ground state, we were not able to assign any split lines to the ground state or any other state because the frequency resolution of the chirped pulse instrument from a 4 FID is not sufficient to resolve the split tings. 142 lines were fit for v = 1 of the C O torsion and 123 lines were assigned for v = 2 of this state. The first excited state of the C C torsion has 81 lines assigned and the combination of both torsions ( v C O = 1, v C C = 1) has 82 lines assigned. The spectra of the ground and four vibrationally excite d states can be seen in Figure 3 .5 on the negative scale. The highest J assigned for all the states is J = 79. The RMS (root mean squared) fit residual for all of the fits is either the same or sm twice as many lines assigned, but the uncertainty of the various rotational constants in the current fits is significantly larger than what Caminati reported. This should not be possible, as more assignments and a re duced fit RMS should solely from the data in the paper in order to understand the discrepancy in the uncertainties. Currently, Christian Metzger, another thesis student in the Shipman lab, has synthesized the methyl 13 C isotop omer of MEO and has assigned its ground and second vibrational ly excited state of the O C torsion as of this writing [17] In the future for the normal species the other four vibrationally excited sta tes of conformer that Caminati found should be searched for, and if present, assigned in our spectra. For the excited state of the methyl torsion, this would include assigning both A and E states to find an experimental V 3 barrier. After that, the next step would be to search for the next lowest energy MEO conformer, ttt Figure 3 .6 shows the residual lines in the MEO spectra after the ground and

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30 vibrationally excited states have been fit. Any new spectra would need to be assigned from these remaining lines. Another objective for MEO would be to collect its spectrum with the new spectrometer that will be built in the Shipman lab this summer. The new spectrometer will cover the range of 110 170 GHz and will have a real time digi tizer. The larger bandwidth will help to further refine the fit, which will make the constants even more precise providing additional aid to the radio astronomers who might search for MEO in the ISM. The real time digitizer will also be able to increase the speed of data collection by at least a factor of 60. This me ans that many more averages could be collected in a short period of time, result ing in higher quality spectra with less noise, more excited states, and more conformers present.

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31 Figure 3.5. Observed spectrum of MEO from 8.7 18.3 GHz with simulated ground state and vibrationally excited state fits on the negative scale.

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32 Figure 3 .6. Full observed spectrum of MEO from 8.7 26.5 GHz on the bottom and t he 1,289 lines left unassigned after the ground state, first and vibrationall y excited states of the O C torsion the first vibrationally exc ited state of the C C torsion and the first vibrationally excited state of the com bination of the O C and C C torsions have been assigned and removed from the full observed spectrum

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33 4 : 2 Ethoxyethanol 2 Ethoxyethanol (EEO) Figure 4 .1, was chosen for study in the same way and for the same reasons as 2 methoxyethanol and differs from it by an extra methylene grou p attached to the ether oxygen. EEO has eight stab le conformers in the gas phase[18 ], but only the four lowest energy conformers have been examined in this thesis. The conformers result from changes in the dihedral angles along the HO CC, OC CO, CC OC, a nd CO CC bonds. The lowest energy conformer is the The other three low energy conformers are the and conformers; all four can be seen in F igure 4 .1. The strongest dipole component in the g conformer is along the a axis and there is also a fairly strong dipole along the b axis as well. Dipole moments and relative energies for these conformers can be found in T able 4 .1. The microwave spectrum of 2 ethoxyethanol has not been previously collec ted. As far as can be determined, the only prior studies that have been performed on EEO were ab initio calculations[1 8] and FT IR measurements[14 ] in 2002 and 2005. Both Tafazzoli and El Hefnawy were able to determine the most stable conformers of EEO a nd their total dipole moments. Before collecting the rotational spectrum of 2 ethoxyethanol, ab initio calculations were performed in order to confirm the results of the calculations done by Tafazzoli and El eters for fitting. Optimizations were performed on the conformers using the B3LYP functional and the 6 311++G(d,p) basis set. Once the geometry optimization was complete, a potential energy scan was performed

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34 Figure 4 .1. Lowest energy conformers of 2 e thoxyethanol The first letter denotes the conformation about the HO CC bond, the second letter about the OC CO bond, the third letter about the CC OC, and the fourth letter about the CO CC bond. The relative energies at the B3LYP/6 311++G(d,p) level of theory as shown. Table 4 .1: Calculated dipole moments of four lowest energy conformers of EEO Conformers l A l (Debye) l B l (Debye) l C l (Debye) Relative E a) (cm 1 ) gg'tt 2.0333 1.5781 0.0833 0.00 2.4963 0.9174 0.3012 443.65 2.2218 1.3471 0.5677 530.54 1.8171 1.4113 1.3171 633.10 a)The B3LYP/6 311++G(d,p) level of theory, not zero point corrected. about the methyl rotor dihedral angle consisting of 36 total points (1 point per 10 o ) and was then fit to a V 3 potential ( Figure 4 .2). The barrier height of ~79 0 cm 1 was too high for us to observe splittings due to methyl group internal rotation at our resolution; this makes analyzing the spectrum of EEO significantly simpler. Vibration rotation coupling constants and vibrational frequencies were

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35 calculated for the four lowest energy conformers and the resu lts for the conformer are shown in Table 4 .2. The results for the other three conformers can be found in Appendix B. Table 4 .2: Calculated vibrational energies and vibration rotation coupling constants of EEO Figure 4 .2: B3LYP/6 311++G(d,p) dihedral scan about the methyl group of the conformer of EEO. Black squares are calculated data points and the red line is the V 3 potential energy fit Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 76 1.89 1.34 1.20 In Plane Ethyl Torsion 82 12.99 1.26 1.14 Out of Plane Ethyl Torsion 147 28.67 3.96 3.24 Hydroxyl Stretch Out of Plane Twist 209 7.48 1.50 0.92 In Plane Stretch 255 1.05 1.95 1.61 M ethyl Torsion

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36 The spectrum of 2 ethoxyethanol was recorded in three separate frequency ranges (8.7 13.5, 13.5 18.3, and 18.0 26.5 GHz) at 253 K with a 4 FID at a pressure of 7 mTorr. The spectrum in each band was averaged for 1 million shots, and the full spectrum can be seen in Figure 4 .3. An expanded view of the spectrum is shown in Figure 4 .4 with its accompanying blank and a horizontal line at the 3:1 signal to noise level. Table 4 .3 Calculated and current rotational and distortion constants of the ground state of g EEO GS Calculated Triples Fitter Current A (MHz) 8761.148 8701.3 8795.637(49) B (MHz) 1612.882 1631.52 1630.9787(91) C (MHz) 1457.318 1472.37 1473.4453(93) J (kHz) 0.5174 0.5174 0.4839(171) JK (kHz) 4.700 4.700 4.512(225) K (kHz) 459.77 459.77 433.1(43) J (kHz) 0.114 0.114 0.11 4 K (kHz) 3.314 3.314 2.70(52) Lines Fit --268 Fit RMS (MHz) --0.0969 Highest J --98

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37 Figur e 4 .3 O bserved spectrum of EEO from 8.7 26.5 GHz collected a temperature of 253 K, at a pressure of 7 mTorr, with 1 million averages of a 4

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38 Figure 4 .4 An expanded view of the EEO spectrum with the blank shown in red and the 3: 1 signal to noise line in blue, at roughly 13 intensity units. In the full spectrum, there are 3,109 peaks above the 3:1 signal to noise ratio.

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39 The spectrum of EEO was fit with some difficulty. After many triples fitter runs failed, the spectrum was simulated in JB95, a graphical interface for fitting spectra Using JB95, rotational constants with a reasonable visual match to the observed spectrum were estimated and used as starting parameters ( with ab initio dis tortion constants) for a fin al triples fitter run. This run used a search window of 600 MHz with 6 ,954,472 triples to be fit This took roughly 36 hours on a two core comp uter. Starting from the best match, 268 transitions were assigned to the ground vibrational state of EEO up to J = 98 (Figure 4 .5). Ab initio constants, final triples fitter consta nts, and current c onstants can be found in Table 4 .3. These constants are in good agreement with the calculated constants and provide support for the idea that this is the most stable conformer. The next step fo r analyzing the spectrum of EEO is to search for vibrationally ex cited states using the vibration rotation coupling constants calculated previously. In examining the spectrum while fitting the ground state, patterns consistent vibrationally excited states were obs erved and should be assigned An additional objective for EEO would be to collect its spectrum with the new 110 170 GHz spectrometer that is being built in the Shipman lab this summer. This new spectrometer will also have a real time digitizer. While the current fit is fairly refin ed, assigning the spectrum in the higher frequency range will further refine the fit, possibly extending to J = 15 0 and allowing us to determine the sextic distortion constants.

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40 Figure 4 .5 Observed spectrum of EEO on the positive scale with the best fit ground state simulated spectrum on the negative scale from 8.7 26.5 GHz.

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41 5 : n Propylamine n Propylamine (PA) was chosen for study in the same way that MEO and EEO were chosen; a methyl group was added to ethylamine, seeing as ethylamine has b een studied pr eviously in the lab and found in the ISM[1 9 ]. Coincidentally, Bri Gordon, another thesis student in the Shipman lab, is studying n propanethiol, which is the same as n propylamine except with a thiol group in place of the amine group. P A Figure 5 .1, has five conformers th at are present in the gas phase: trans trans ( Tt ), trans gauche ( Tg ), gauche trans ( Gt ), and two gauche gauche conforme rs ( Gg and )[2 0 ]. The conformers are labeled according to the position of the amine group ( T = t rans, G = gauche ) to the methyl group and the relative position of the amine rotor ( ). The most stable conformer, Tt has the strongest dipole moment along the b axis, followed by the a axis, with no dipole moment along the c axis. The dipole moments vary for each conformer and can be found in Table 5 .1 along with the relative energies of each conformer. Table 5 .1 Cal culated dipole moments and relative energies of five lowest conformers of PA Conformers l A l (Debye) l B l (Debye) l C l (Debye) Relative E a) (cm 1 ) Tt 0.9877 1.0748 0.0002 0.00 Tg 0.0215 0.7035 1.0752 35.73 Gg 0.8251 1.0259 0.234 143.62 Gt 1.2879 0.0815 0.6189 152.17 0.1065 0.083 1.2517 179.85 a)Basis set and Method B3LYP/6 311+G(d,p) not zero point corrected

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42 Figure 5 .1. Five lowest energy conformers of PA The first letter denotes the position of the amine group to the methyl group and the second letter the position of the amine group. The energies are the calculated relative energies. The rotational spectrum of propylamine has not been previously recorded, but Durig performed extensive theoretical and experimental Raman and IR work on PA in 2011[2]. Durig and co workers performed many ab initio calculations with varying methods and basis sets; they also collected temperatu re dependent Raman and far infrared spectra on solid, liquid, and gaseous forms of PA They determined tha t the five conformers ( Figure 5 .1) are present in almost equal amounts While Tt is most st able, it only has a degeneracy of one. Higher

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43 energy species, with gauche conformations have a degenera cy of two or four which compensates for their unfavorable Bolztmann factors. A b initio calculations were carried out results Optimizations were perform ed on all five conformers at the B3LYP/ 6 311+G(d,p) level of theory Potential energy scans of the methyl group rotation ( 36 steps per 10 o ) were calculated to determine the barrier height to internal rotation of this group These scans were then fit to a V 3 potential to determine whether or not A E splittings were going to be observed. The A E splittings will not be observed since the lowest barrier heig ht of all five conformers is 89 0 cm 1 The potential energy scan for the Tt conformer is shown in Figure 5 .2 and the potential energy scans for the other conformers can be found in Appendix C. Vibration rotation coupl ing constants were calculated for all five conformers (Tables 5 .2, 5.3, 5.4, 5.5, 5 .6) in order to determine calc ulated rotational constants for excited states of PA Figure 5 .2 B3LYP/6 311++G(d,p) p otential energy scan about the methyl group of Tt PA. Black squares are the data points and the red line is the V 3 fit.

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44 Table 5 .2: The calculated vibrational energies and vibration rotation coupling constants of Tt PA Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 130 418.38 0.113 5.66 CH 2 NH 2 Wag 228 164.74 1.66 0.89 Methyl Torsion 266 542.76 2.72 2.89 NH 2 CH 3 Scissor 275 4.14 0.28 1.07 Amine Torsion 443 38.12 2.69 4.45 NCC Bend Table 5 .3: The calculated vibrational energies and vibration rotation coupling constants of Tg PA Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 125 418.21 0.60 6.92 CH 2 NH 2 Wag 227 165.01 3.57 1.77 Methyl Torsion 250 169.00 3.40 2.94 NH 2 CH 3 Symmetric Wag 285 342.10 1.70 3.39 NH 2 Wag 453 40.03 2.91 4.65 NCC Bend Table 5 .4: The calculated vibrational energies and vibration rotation coupling constants of Gt PA Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 134 56.70 13.28 4.87 CH 3 CH 2 Wag 227 2.20 7.21 6.25 Methyl Torsion 264 95.89 27.44 13.26 Amine Torsion 329 61.85 10.46 0.36 CH 2 CH 2 Twist 459 59.67 12.92 6.85 CH 2 CH 2 Rock

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45 Table 5 .5: The calculated vibrational energies and vibration rotation coupling constants of Gg PA Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 143 31.95 5.19 3.53 CH 3 CH 2 Torsion 221 21.43 8.59 5.48 Methyl Torsion 233 56.81 4.32 7.99 Amine Torsion 319 40.71 4.34 5.22 CH 2 CH 2 Twist 474 57.83 14.90 8.50 CH 2 CH 2 Rock Table 5 .6: The calculated vibrational energies and vibration rotation coupling constants of PA Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 142 68.41 20.68 6.02 NH 2 CH 3 Scissor 221 32.06 0.19 0.82 Methyl Torsion 254 104.79 40.55 17.49 Amine Rock 332 58.24 7.73 2.65 CH 2 CH 2 Twist 465 65.76 15.54 8.54 CH 2 CH 2 Rock The spectrum of PA was recorded in three separate frequency ranges (8.7 13.5, 13.5 18.3, and 18.0 26.5 GHz) at 253 K with a 4 FID. The spectrum in each band was averaged for 1 million shots at 9 mTorr and the full spectrum can be seen in Figure 5 .3. The analysis of this spectrum was attempted multiple times both by hand and with the triples fitter, but the spectrum was too complicated to be analyzed in a reasonable amount of time The spectrum is complicated for multiple reasons the most important of which is that five conformers are present in roughly equal abundance Th is can be seen in Figure 5 .4. This makes fitting the spectrum complicated because it is difficult to tell whether a line in the experimental data Further, 14 N has a

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46 Figure 5.3. Observed spectrum of PA from 8.7 26.5 GHz collected at a temperature of 253 K, and a pressure of 9 mTorr with a FID 18.3 frequency range has been scaled by a factor of 3 for clarity.

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47 F igure 5.4 S imulated spectra 26.5 GHz

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48 nuclear spin of 1; this leads to hyperfine splitting that further increases the line density. Hyperfine split ting arises when there is quadru pole coupling in the mo lecule. A molecu le has a quadru pole when the nuclear spin quant um number, I, is greater than R otational en ergy level splitting occurs due to the coupling of nuclear and rotational angular momenta. For J < I, 2J + 1 splittings occur and for J > 1, 2I + 1 splittings oc cur. In addition to complicating the spectrum, this adds another selection rule to consider where F = J + I Due to the hyperfine splitting, the current triples fitter was not able to find plausible rotational constants for any of the conformers of PA. A modified version of the software to handle hyperfine effects was written, but due to the extreme line density (4 147 peaks in the peak list), even small search windows lead to extremely la rge numbers of triples. There has not been su fficient time to carry out systematic searches, but this would be a promising candid ate if the cluster computing version of the triples fitter is developed. The next step for assigning the spectrum of PA would be to perform double resonance measurement s In rotational spectroscopy, transitions are connected to other transitions by sh ared energy levels ; double resonance measurements are performed by pumping a transition and seeing which other peaks are connected to that transition. A double resonance measurement uses two pulses instead of just a single chirped pulse. T he chirped pulse is first and establishes a rotational coherence The molecules then interact with a second pulse tuned to the frequency of an intense peak in the spectrum. This second

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49 pulse partially destroys the coherence of any transitions connected to the first leading to destructive interference. This leads to a strong decrease in the intensity of the affected transitio ns in the spectrum (Figure 5.5 ) This i ntensity change allows us to easily determine which transitions are connected to the pumped peak. This information makes assigning the spectrum much simpler because once the connected transitions are determined, the y can be assigned w ith great certainty. Once a few peaks have been assigned in this manner approximate rotational constants can be found that are usually close to true rotational constants From this initial fit the rest of the experimental spectrum can be fit easily. Multiple double resonance measurements make this process even more accurate. For PA double resonance measurements should be performed on all of the most intense peaks in this frequency rang e. The transitions that should be connected for each conformer can be found in Tabl es 5 .7, 5.8, and 5 .9. The Gt, and conformers of PA have no connected transitions from 18 26.5 GHz. Once one conformer is assigned, fitting the residual lines in the spectrum will be much easier as the assigned lines can be rem oved from the observed spectrum, reducing the overall line density to hopefully manageable levels.

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50 Figure 5.5. Double resonance measurements of iodobenzene. The bottom spectra were collected with a single chirped (no double resonance pulses) pulse was centered at 15608.6 MHz and the marked peak at 142 second pulse was centered at 14211.8 MHz and the marked peak at 15608.6 MHz is the only transition modulated. These modulations afte r the second pulses demonstrate that the two peaks are connecte d by a transition. [8]

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51 Table 5 .7 Connected transitions for double resonance measurements in 18 26.5 GHz for Tt PA Connected Transitions Predicted Frequencies (MHz) 2 1 1 2 0 2 3 1 2 2 1 1 21638.05 21579.30 2 1 1 2 0 2 3 0 3 2 0 2 21638.05 21265.85 Table 5 .8 Connected transitions for double resonance measurements in 18 26.5 GHz for Tg PA Connected Transitions Predicted Frequencies (MHz) 5 1 4 5 0 5 6 0 6 5 1 5 23539.34 22871.33 5 1 4 5 0 5 5 1 5 5 0 5 23539.34 20018.97 4 1 3 4 0 4 4 1 4 4 0 4 22923.11 20575.85 3 1 2 3 0 3 3 1 3 3 0 3 22438.61 21029.93 2 1 1 2 0 2 2 1 2 2 0 2 22080.29 21375.53 1 1 0 1 0 1 1 1 1 1 0 1 21842.99 21608.99 Table 5 .9 Connected transitions for double resonance measurements in 18 26.5 GHz for Gg PA Connected Transitions Predicted Frequencies (MHz) 7 1 6 7 0 7 7 2 5 7 1 6 21677.19 23808.15 8 2 6 8 1 7 8 1 7 8 0 8 23909.42 25835.10 6 2 4 6 1 5 6 1 5 6 0 6 24183.00 18197.54 4 2 2 4 1 3 4 2 3 4 1 3 25803.53 25290.99

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52 6 : Conclusion The rotational spectra of 2 methoxyethanol (MEO), 2 ethoxyethanol (EEO), and n propylamine (PA) were recorded from 8.7 26.5 GHz at 253 K. In MEO, a total of 685 transitions were assigned to the ground state and four vibrationally excited states. This was done using starting parameters from Caminati et al [15] ground state was fit with 268 transitions assign ed. The triples fitter greatly reduced the amount of time spent assigning the spectra of both MEO and EEO. Fitting the spectrum of PA was attempted, both with and without the triples fitter. The spectrum could not be assigned due to five conformers pre sent in roughly equal abundance, which makes the spectrum extremely difficult to assign. Another difficulty was that the nitrogen atom in PA contributes hyperfine splitting to the spectrum, further increasing the line density. The triples fitter was rece ntly modified to account for hyperfine splitting but initial tests on PA were unfortunately not successful. To assist in assigning the spectrum in the future, double resonance measurements should be performed on the most intense lines in the spectrum of P A. Connected transitions in the 18 26.5 GHz band have been identified for this purpo se and can be found in Chapter 5 of this thesis. The triples fitter was very h elpful in assigning the spectra of MEO and EEO While it has not been successful in assigning PA, many triples fitter runs have been performed for this thesis and in doing those runs a few guidelines have been developed; these can be found in Chapter 2. In the future, the improved triples fitter wit h hyperfine capabilities should be tested on molecules with assigned spectra that contain hyperfine splitting, such as allyl chloride (studied in January 2010) or iodobenzene[1]. The triples fitter should also be tested on other previously assigned molecu les in order to further refine the guidelines in Chapter 2 for future users. This should be done with starting

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53 parameters from ab initio calculations because many molecules have not been previously studied and ab initio constants are not always precise en ough to start a successful manual fit. Currently, Seth Hear ld is working on improving the triples fitter so that it can be run on a cluster. This will improve the speed of the triples fitter and will also allow the user to implement a larger search windo w with a larger number of triples to be fit. This will also allow the starting parameters to be less precise since, in theory, every peak in the observed spectrum could be fit to every trans ition with a sufficiently large cluster. A flow through chiller s ystem was designed and developed by Christian Metzger, Benjamin Rooks and myself during the summer of 2012. This simplifies the spectra by removing energy from the system so that fewer vibrationally excited states and conformers are populated. While this chiller system is a great improvement over the previous ice water bath cooling system, additional improvements can be made. A simple improvement would be to better insulate the tubing to reduce the number of heat leaks. A more com plicated but still easi ly implemented improvement would be to install a valve between the two chillers, which would allow us to more precisely regulate their relative liquid levels and let us leave the system unattended for longer periods of time. A time consuming task that wou ld improve the ch iller system would be to determine precisely which settings on the chillers produced the lowest temperature on the waveguide. This would be incredibly time consuming because lower set point temperatures also change the fluid viscosity, wh ich may require different optimal pumping speeds (higher pump speeds force the liquid through the system faster, but also generate more waste heat). Since our system is not perfectly insulated, it is worth doing these tests so that the chiller system work s to its highest potential. The future of the Shipman lab is bright. In the next six months, a new spectrometer with a bandwidth of 110 170 GHz will be built. This additional spectral

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54 coverage will help with assigning spectra in the future because man y intense transitions occur in that frequency range shown in Figure 6. 1; Figure 6.2 shows an expanded view of the spectrum at 165.6 166.4 GHz The larger bandwidth will also make the final rotational and distortion constants more precise because data c an be combined from both the current frequency range and the new frequency range. This will be incredibly helpful for the radio astronomers because the more exact and complete the laboratory data is, the more confident they can be in identifying molecules in the ISM. Another major improvement that will come along with the new spectrometer is a real time digitizer. This digitizer will increase the data collection speed by at least a factor of 60. With this speed, there are many new things that can be don e with rotational spectroscopy. For instance, it should be possible to collect the rotational spectrum of unstable molecules that are produced via photolysis These unstable molecules could be reaction intermediates or free radicals that are likely to be found in the ISM but are not stable under terrestrial conditions. The real time digitizer will also expand and improve on our use of double resonance measurements. Since data collection will be so rapid, it will be possible to perform double resonance m easurements on essentially every peak in the spectrum in only a few hours This added information would make it much easier to assign spectra.

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55 Figure 6.1 Simulated EEO data from 110 170 GHz. For reference, a J = 20 transition at 17.7 GHz has an in tensity of 0.0546 on this scale; the signal levels in this region are roughly 550x higher than in the 13.5 18.3 GHz region.

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56 Figure 6.2 Expanded view of simulated data EEO data from 165.6 166.4 GHz showing several b type Q branch transitions

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57 References [1] 1940, 52 187 192 [2 ] Lees, R. M.; of molecules o f astrophysical interest: III. M et Journal of Physical and Chemical Reference D ata 1973 2 205. [3 ]Takano, S.; Sakai, Y.; Kakimoto, S.; Sasaki, M; Kobayashi, K. Detection of Methyl Formate in the Second Torsionally Excited State (v t Publications of the Astronomical Society of Japan 2012 64, 9 [4 ] Kaifu, N.; Morimoto, M.; Nagane, K.; Akabane K.; Iguchi, T.; Takagi, K. Astrophysical Journal, 1974 191, L135. [5] Atacama Large Millimeter/Submillimeter Array: In Search of Our Cosmic Origins http://www.almao bservatory.org/ (accessed April 26 th 2013) [6] National Radio Astronomy Observatory The Expanded Very Large Array Project: A Radio Telescope to Resolve Cosmic Evolution http://www.aoc.nrao.edu/evla/ (accesse d April 29 th 2013) [7 substituted Benzenes at Senior Thesis at New College of Florida 2010 [8 Senior Thesis at New College of Florida 2011 [9 Waveguide Chirped Pulse Fourier Transform Microwave Spectra of Small Alkylthiols Senior Thesis at New College of Florida 2013 [10 ] BeerSmith Home Brewing Blog. Chilling Your Brew: Building an Immersion Chill er. http://beersmith.com/blog/2008/11/20/chilling your brew building an immersion chiller/ (accessed Feb. 26 th 2013)

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58 [ 1 1] Weaver, S. W.; Bowman, J.; Dun can, M.; Lis, D.; Pearson, J.; Shipman, S.; 2012 [ 1 2] Personal Communication with Dr. Susanna Widicus Weaver, Emory University [ 1 3] Gil, F.; Teixeira methoxyethanol conformers: an ab initio DFT study using the SCI Journal of Molecular Structure 1999 482 483 621 625 [ 1 4] El Moment and Conformation of C n H 2n+1 O(CH 2 CH 2 O) m H Investigated by the Measurements of Permittivity and FT IR Spectra in Heptane Solutions and by Ab Initio Calculations The Chemical Society of Japan 2006 79, 845 856 [ 1 Spectrum, Dipole Moment, and Intramolecular Hydrogen Bond of 2 Canadian Journal of Chemistry 1972 50, 1149 1156 [ 1 Analysis of the Methyl Group A E doubline as Obtained from the Microwave Spectrum, in Several Torsionally Excited States of 2 Chemical Physics 1986 110, 67 82 [17] Rotational Spectroscopy of trans Isopropylamine and 2 (methoxy 13 C) ethanol Senior Thesis at New College of Florida 2013 [1 8 Ethoxyethanol in Continuum Configurational B iased Procedure: C onformational A nalysis and A ssociation in A queous and N on A queous M edia Theoretical Chemistry Accounts 2002 107, 162 172

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59 [1 9 ] Apponi, A J.; Sun, M.; Halfen, D. T.; Ziurys, L. M. of Anti Ethylamine ( CH 3 CH 2 NH 2 ) From 10 to 270 GHz: A Laboratory Study and Astronomical Search in Sgr B2(N) The Astrophysical Jornal, 2008 673, 1240 1248 [2 0 ] Durig, J.; Darkhalil, I.; Klaassen, J.; Herrebout, W.; Dom, J.; Veken, B. propylamine from temperature dependent Raman and far infrared spectra of xenon solutions and ab initio Journal of Raman Spectroscopy 2012 43, 1329 13336

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60 Appendix A This a ppendix contains calculated vibration rotation coupling constants and potential energy scans for the higher energy conformers of MEO Table A.1 Calculated vibrational energies and vibration rotation coupling constants of ttt MEO Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) C (MHz) 96 555.02 2.52 4.88 CH 2 CH 2 In Plane Wag 104 46.58 2.16 1.97 CH 2 CH 2 Out of Plane Wag 191 53.03 6.28 3.28 Hydroxyl Torsion 201 483.50 2.47 0.15 In Plane CH 3 OH Stretch 227 16.33 3.02 1.57 Methyl Torsion 430 45.03 1.90 2.41 COC Stretch Table A.2. Calculated vibrational energies and vibration rotation coupling constants of ttg MEO Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) C (MHz) 100 447.37 1.21 3.70 CH 2 CH 2 Wag 116 158.91 1.57 2.06 CH 2 O Wag 196 543.73 2.68 0.0013 In P lane CH 3 OH S t retch 228 8.69 2.89 1.46 Methyl Torsion 301 51.42 1.44 0.91 Hydroxyl Torsion 423 42.06 1.95 2.32 COC S tretch

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61 Table A.3. Calculated vibrational energies and vibration rotation coupling constants of MEO Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) C (MHz) 86 22.23 13.55 0.11 CH 3 O Torsion 147 21.47 8.66 5.44 Symmetric CH 3 OH Stretch 201 10.41 31.96 9.37 Methyl Torsion 271 26.40 14.28 3.53 Hydroxyl Torsion 330 12.47 6.01 2.96 CH 2 CH 2 Symmetric Stretch 391 1.79 11.05 4.29 COC Bend 521 9.41 16.11 7.16 CH 2 CH 2 Anti symmetric Stretch Figure A.1. B3LYP/6 311++G(d,p) dihedral scan about the methyl group of ttt Black squares are calculated data points and the red line is the V 3 potential energy fit.

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62 Figure A.2. B3LYP/6 311++G(d,p ) dihedral scan about the methyl group of ttg Black squares are calculated data points and the red line is the V 3 potential energy fit. Figure A.3. B3LYP/6 311++G(d,p) dihedral scan about the methyl group of Black squares are calculated data points and the red line is the V 3 potential energy fit.

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63 Appendix B This appendix contains calculated vibration rotation coupling constants and potential energy scans for the higher energy conformers of EEO. Table B.1. Calculated vibrational energies and vibration rotation coupling constants of EEO Table B.2. Calculated vibrational energies and vibration rotation coupling constants of EEO Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 46 147.83 0.41 3.59 CH 3 CH 2 Rock 96 125.67 0.25 1.65 CH 2 CH 2 OH Stretch 156 47.57 5.87 4.05 CH 3 CH 2 Torsion 220 19.63 1.57 1.31 Methyl Torsion 280 14.56 0.22 0.46 OHCH 2 Rock Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 41 1.85 4.21 2.10 CH 3 CH 2 Symmetric Stretch 100 16.55 1.65 2.31 CH 3 CH 2 Asymmetric Stretch 154 57.65 11.03 10.32 CH 2 OH Stretch 222 7.39 1.08 1.23 Methyl Asymmetrical Stretch 290 39.65 2.92 1.68 CH 2 CH 2 Asymmetrical Stretch

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64 Table B.3 Calculated vibrational energies and vibration rotation coupling constants of EEO Figure B.1. B3LYP/6 311++G(d,p ) dihedral scan about the methyl group of of EEO. Black squares are calculated data points and the red line is the V 3 potential energy fit. Energy (cm 1 ) Vibration Rotation Coupling Constants Descriptions A (MHz) B (MHz) B (MHz) 65 0.70 2.14 1.09 CH 3 CH 2 Torsion 73 24.05 3.21 0.41 COC Bend 149 121.41 21.74 16.93 CH 2 OH Torsion 243 20.29 3.84 1.39 Methyl Torsion 268 43.29 3.19 0.83 COC Stretch

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65 Figure B.2. B3LYP/6 311++G(d,p) dihedral scan about the methyl group of of EEO. Black squares are calculated data points and the red line is the V 3 potential energy fit. Figure B.3. B3LYP/6 311++G(d,p) dihedral scan about the methyl group of of EEO. Black squares are calculated data points and the red line is the V 3 potential energy fit.

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66 Appendix C This appendix contains calculated potential energy scans for the higher energy conformers of PA. Figure C.1. B3LYP/6 311++G(d,p) p otential energy scan about the methyl group of T g PA. Black squares are the data points and the red line is the V 3 fit. Figure C.1 B3LYP/6 311++G(d,p) p otential energy scan about the methyl group of Gg PA. Black squares are the data points and the red line is the V 3 fit.

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67 Figure C.3. B3LYP/6 311++ G(d,p) p otential energy scan about the methyl group of Gt PA. Black squares are the data points and the red line is the V 3 fit. Figure C.4. B3LYP/6 311++G(d,p) p otential energy scan about the methyl group of PA. Black squares are the data points a nd the red line is the V 3 fit.


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