FH. Mini-symposium: Spectroscopy with Undergraduates
Friday, 2021-06-25, 10:00 AM
Online Everywhere 2021
SESSION CHAIR: Jacob Stewart (Connecticut College, New London, CT)
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FH01 |
Invited Mini-Symposium Talk |
2 min |
10:00 AM - 10:02 AM |
P4933: UNDERGRADUATE MOLECULAR SPECTROSCOPY APPROACHES IN RESEARCH AND TEACHING AS AN EXPERIENTIAL LEARNING ENTERPRISE AT MISSOURI S&T |
G. S. GRUBBS II, Department of Chemistry, Missouri University of Science and Technology, Rolla, MO, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH01 |
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As most every person at this conference can appreciate, spectroscopy, especially at the undergraduate level, is often considered one of the most difficult subjects to undertake and, due to this mentality, is often avoided at all costs. To overcome this stigma and make the material resonate with undergraduates, it is important to give them avenues by which to actually get involved in the processes of spectroscopy. In this way, the students become invested in some aspect of the subject which is applicable to their own personal interests. At Missouri S&T, this is achieved in multiple ways. In the research lab, students are given tasks that align with their interest, but also achieve a common goal of a spectrometer enhancement or molecular target of interest in microwave spectroscopy. They are given the tools and instruction to succeed as well as the leeway to fail in a project as this is the cornerstone of discovery. When given this freedom, they become leads in a project, guided and mentored by both the graduate students and myself. If a student is interested in teaching, we have had undergraduates create physical chemistry labs and instruct them in order to guide other students through the process of learning, thereby augmenting their own knowledge. For expanded or more general undergraduate spectroscopy outreach, I serve as the physical chemistry lab instructor and the Associate Advisor of our university's Mars Rover Design Team, which always builds and implements an onboard spectrometer for field analyses. The overarching theme of the talk is to get students interested early and keep them involved. The university helps with this by having programs that will get the students involved as young as the high school level. How we have utilized these programs, reached, and kept student interest while also mitigating the costs of such endeavors at Missouri S&T will be discussed.
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FH02 |
Contributed Talk |
1 min |
10:08 AM - 10:09 AM |
P5078: OODLES OF UNDERGRADS UNDERGROUND: CLASSROOM UNDERGRADUATE RESEARCH AT WIND CAVE NATIONAL PARK |
JOSHUA A SEBREE, Department of Chemistry and Biochemistry, University of Northern Iowa, Cedar Falls, IA, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH02 |
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For the past three years, the Department of Chemistry and Biochemistry at the University of Northern Iowa has been leading undergraduate students on spectroscopic expeditions into the depths of Wind Cave National Park in South Dakota. Using some of the newest miniaturized spectrometers, portable XRFs, and Lego Mindstorms Kits, the team has been working with NPS park rangers to look at the cave in a new light while providing unique experiences for the students involved.
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FH03 |
Contributed Talk |
1 min |
10:12 AM - 10:13 AM |
P4791: USING COMPUTATIONAL TOOLS TO ENHANCE LEARNING IN AN UNDERGRADUATE MOLECULAR SPECTROSCOPY COURSE |
M. REZA POOPARI, SHYAM PARSHOTAM, YUNJIE XU, Department of Chemistry, University of Alberta, Edmonton, AB, Canada; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH03 |
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In molecular spectroscopy, our models of the molecular world are built on rigorous spectroscopic experimentation and rich interplay between theory and experiment. To instill such appreciation to undergraduate students, who have little experience in either spectroscopic experiments and theory, is challenging. We have developed a new computational laboratory component to complement the material covered in a senior undergraduate course on molecular spectroscopy. Specifically, we focus on illustrating molecular spectroscopic concepts (some of which can be quite abstract and complicated) taught in class with electronic structure calculations. This talk will describe our implementation and the learning outcome. Two particular examples will be discussed. One is related to the misconception that electron density is the main factor responsible for NMR chemical shifts and how we utilize both experimental data and calculations to help students overcome this common misconception. The other deals with differences in geometries, for example, those obtained using rotational constants directly, isotopic substitution procedures, and electronic structure calculations. This talk will also discuss how the above activities worked in practice and the improvements we plan to implement next time.
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FH04 |
Contributed Talk |
1 min |
10:16 AM - 10:17 AM |
P5599: BIOMOLECULAR STRUCTURE OF TROPINE DETERMINED FROM QUANTUM CHEMISTRY SIMULATIONS OF VIBRATIONAL SPECTROSCOPY |
EMILY LYN YANG, Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT, USA; RYAN P STEELE, Department of Chemistry, University of Utah, Salt Lake City, UT, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH04 |
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r0pt
Figure
For biologically relevant molecules, determining the structure of the compound- and the manner in which it changes upon interaction with other molecules- is a central scientific challenge. However, many biomolecules exhibit multiple low-energy conformers at biologically relevant temperatures. In this work, the vibrational responses of tropine and its protonated analogue are used to explore the structural diversity of these pharmaceutical mimics. Quantum chemistry-based calculations were employed to identify the low-energy conformers and their vibrational signatures, in order to predict and explain these molecules' response to infrared light in experiments. These calculations also allowed for an assessment of the energetic and spectral consequences of protonation on tropine.
During initial attempts to simulate anharmonic behavior, strongly coupled low and high-frequency modes (which are commonly excluded in such calculations) yielded unphysical transition frequencies. A portion of this presentation will be devoted to techniques that allowed for the inclusion of these anharmonic effects without some of the pitfalls that befall traditional anharmonic approaches.
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FH05 |
Contributed Talk |
1 min |
10:20 AM - 10:21 AM |
P5610: AN EXOMOL LINE LIST FOR SO: ROVIBRONIC SPECTRUM OF SULFUR MONOXIDE |
RYAN BRADY, Department of Physics and Astronomy, University College London, London, United Kingdom; GAP-SUE KIM, Dharma College, Dongguk University, Seoul, Korea; WILFRID SOMOGYI, JONATHAN TENNYSON, SERGEI N. YURCHENKO, Department of Physics and Astronomy, University College London, London, United Kingdom; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH05 |
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The work we present here is a diatomic molecule line list study on the molecule sulfur monoxide (SO), suitable for characterising exoplanetary atmospheres up to temperatures of 4000 K. The motivation of this project is to provide comprehensive line list data applicable to modelling high temperature spectra in environments such as e.g. exoplanetary atmospheres, where current spectroscopic databases provide only limited coverage. The new SO line list will be included into the ExoMol database. J. Tennyson et al. J. Quant. Spectrosc. Radiat. Transf., 2020, 255, 107228; www.exomol.com. production of such a line list first includes the creation of a MARVEL T. Furtenbacher, A. G. Császár, J. Tennyson, MARVEL: measured active
rotational-vibrational energy levels, J. Mol. Spectrosc. 245 (2007) 115-125.et of rovibroic energies, calculation of high-level ab initio potential energy curves (PECs), spin-orbit curves (SOCs), electronic-angular momentum curves (EAMCs) and transition moment dipole curves (TDMCs) using MOLPRO
at MRCI level of theory and a solution of coupled ro-vibronic Schrödinger equations using the variational code D UOS. N. Yurchenko, L. Lodi, J. Tennyson, A. V. Stolyarov, Comput. Phys. Commun., 2016, 202, 262 - 275; publicly available at https://github.com/Trovemaster/Duo. The PECs, SOCs and EAMCs are represented by analytical parametrised functional forms and refined by fitting to the MARVEL energies. A rovibronic line list for SO consists of energies, frequencies, Einstein coefficients and a partition function covering all electronic states up to 50 000 cm −1, including X 3Σ −, A 3Π, A′ 3∆, A" 3Σ +, B 3Σ −, C 3Π, a 1∆, b 1Σ + and c 1Σ −. IR/Vis/UV absorption and emission spectra of SO for a set of temperatures are generated using the program ExoCross. S. N. Yurchenko, A. F. Al-Refaie, J. Tennyson, Astron. Astrophys;,
2018, 614, A131; publicly available at https://github.com/Trovemaster/ExoCross.html:<hr /><h3>Footnotes:
J. Tennyson et al. J. Quant. Spectrosc. Radiat. Transf., 2020, 255, 107228; www.exomol.com.A
T. Furtenbacher, A. G. Császár, J. Tennyson, MARVEL: measured active
rotational-vibrational energy levels, J. Mol. Spectrosc. 245 (2007) 115-125.s
S. N. Yurchenko, L. Lodi, J. Tennyson, A. V. Stolyarov, Comput. Phys. Commun., 2016, 202, 262 - 275; publicly available at https://github.com/Trovemaster/Duo..
S. N. Yurchenko, A. F. Al-Refaie, J. Tennyson, Astron. Astrophys;,
2018, 614, A131; publicly available at https://github.com/Trovemaster/ExoCross.
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FH07 |
Contributed Talk |
1 min |
10:28 AM - 10:29 AM |
P5323: COMPUTATIONAL SPECTROSCOPIC SIGNATURES OF PROTEINOGENIC GLUTAMIC ACID AND ITS ISOMERIC SPECIES OF ASTROPHYSICAL IMPORTANCE |
NAMRATA RANI, VIKAS, Department of Chemistry and Centre of Advanced studies in Chemistry, Panjab University, Chandigarh, Chandigarh, India; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH07 |
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The interstellar medium (ISM) is abundant in diverse network of molecules from simple diatomic to interstellar complex organic molecules (COMs). There have been continuous growing attempts to search the molecules of biotic potential such as proteinogenic amino acids. Notably, the amino acids are confirmed in meteoritic composition with considerable enantiomeric excess. Such large sized molecular species in ISM are investigated via their rotational and vibrational spectroscopic traits. Towards this our group performed the computational quantum-mechanical calculations of rotational and vibrational parameters of Glutamic acid and its isomeric species proposed along its stereoinversion pathways in gas phase under conditions akin to the ISM. DFT and MP2 methods are employed in anharmonic calculations utilizing vibrational second order perturbation theory to predict the rotational and vibrational transitions, particularly in millimetre (mm), sub-mm, mid- and far-infrared regions. The varied isomeric species studied, including zwitterionic ammonium ylide, di-carboxylic acid, gem-diol, vicinal-diol and imine can act as a significant aid for the search of Glutamic acid and its isomers in the ISM. Reference: Rani, N.;, Vikas. J. Mol. Spectrosc. 2020, 369, 111271(1-9).html:<hr /><h3>Footnotes:
Reference: Rani, N.;, Vikas. J. Mol. Spectrosc. 2020, 369, 111271(1-9).
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FH08 |
Contributed Talk |
1 min |
10:32 AM - 10:33 AM |
P4843: NARROWING DOWN THE POSSIBLE GEOMETRIES OF A MOLECULE FROM ISOTOPOLOGUE ROTATIONAL CONSTANTS WITH STRUCTURAL FILTERS |
JIEYU YAN, DAVID PATTERSON, Physics, University of California, Santa Barbara, CA, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH08 |
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A computer algorithm is developed to narrow down the list of possible structural geometries of a molecule from the analysis of its isotopologue rotational constants. Based on Kraitchman's equation, the absolute values of the position coordinates of the atoms in a molecule may be obtained from the corresponding isotopologue rotational constants. The algorithm, in attempt to take a step further, narrows down the list of possible combinations of atom positions and bond connections within the molecule. Compared to a previous work by Mayer et al. Mayer, Kevin J., et al. "The Feasibility of Determining the Carbon Framework Geometry of a Molecule from Analysis of the CARBON-13 Isotopologue Rotational Spectra in Natural Abundance." 74th International Symposium on Molecular Spectroscopy. 2019.hich focused on carbon atoms, the algorithm extends the application to more atoms including oxygen, nitrogen, etc. More molecular geometry filters are integrated in the algorithm as well. Five filters involving interatomic distance, bond type, valence, bond angles, and coplanarity based on VSEPR theory are developed. As a result, the algorithm was able to narrow down the number of possible structures for Aspirin, a molecule with 13 non-hydrogen atoms, from 10 10 to 110. However, the exact geometry of molecules could not be determined by the algorithm directly, especially when the molecule is large (usually more than five non-hydrogen atoms). In addition, large errors from Kraitchman's equation near the principle axes of the molecule leads to ambiguous results on those atoms. It leads to the belief that our current understanding may be insufficient to resolve the molecular geometry directly from the isotopologue rotational constants.
Footnotes:
Mayer, Kevin J., et al. "The Feasibility of Determining the Carbon Framework Geometry of a Molecule from Analysis of the CARBON-13 Isotopologue Rotational Spectra in Natural Abundance." 74th International Symposium on Molecular Spectroscopy. 2019.w
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FH09 |
Contributed Talk |
1 min |
10:36 AM - 10:37 AM |
P4853: USE OF STUDENT-SPECIFIC MOLECULES AND THEIR SPECTROSCOPIC PROPERTIES IN PHYSICAL CHEMISTRY COURSES |
DAVID E. WOON, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH09 |
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Spectroscopy is a fundamental component of physical chemistry courses. To encourage students to take more interest in the critical contributions of spectroscopic properties to the subject, I assign different molecules to the students. In the second semester of a two-semester course that covers statistical and classical thermodynamics, the students draw molecules from a hat on the first day of class. They look up spectroscopic properties for their molecules on the web and use the values in various homework, quiz, and exam problems. In a one semester "principles" course, they build a closed-shell molecule from a limited set of atoms. I then provide the students with calculated values of spectroscopic properties, which they use in a term project about their molecules that covers structure, spectra, partition functions, and properties derived from partition functions.
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FH10 |
Contributed Talk |
1 min |
10:40 AM - 10:41 AM |
P4859: THE CHIRPED-PULSE CLUB: MICROWAVE SPECTROSCOPY RESEARCH IN HIGH SCHOOL |
JOSUE CERVANTES, EMILY GERAGHTY, ANISH KANTHAMNENI, ZIWEI LIU, SHAMITHA NANDI, ELIC WEEKS, GARRETT YOUNGBLOOD, GORDON G BROWN, Chemistry, SC Governor's School for Science \& Mathematics, Hartsville, SC, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH10 |
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A new course offering a research experience in microwave spectroscopy to high school students has been developed at the South Carolina Governor's School for Science and Mathematics. Seven students working in small groups completed research projects in microwave spectroscopy during the fall semester of 2020. The students measured the spectra of previously unstudied chemicals, performed relevant ab initio calculations, analyzed the spectra to find the rotational and distortion constants, and prepared presentations for the school's Annual Research Colloquium. Chemicals studied include 2-fluorobenzotrifluoride, trans-2-pentenal, and 2,6-difluorophenol. The spectra were measured on a 8 - 18 GHz chirped-pulse Fourier transform microwave (CP-FTMW) spectrometer. The spectrometer employs an Analog Devices AD-9914 direct digital synthesizer to generate a chirped pulse with a bandwidth of 1 GHz. The chirped pulse is mixed with a tunable carrier frequency and the spectrum is measured in 2 GHz (the output of the mixer includes the lower and upper sidebands) sections. Chemical samples are introduced through a small hole in a spherical mirror in order for the pulsed molecular beam to be coaxial with the microwave pulse. Experimental rotational parameters of the three chemical species will be presented along with a description of the spectrometer.
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FH11 |
Contributed Talk |
1 min |
10:44 AM - 10:45 AM |
P5576: EXPLAINER: EFFECTS OF NUCLEAR QUADRUPOLE COUPLING TENSOR MAGNITUDE, ASYMMETRY, AND ORIENTATION ON THE APPEARANCE OF ROTATIONAL HYPERFINE STRUCTURE |
S. A. COOKE, Natural and Social Science, Purchase College SUNY, Purchase, NY, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH11 |
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r0pt
Figure
Towards easier high resolution spectral assignment for asymmetric molecules bearing nuclei with spins greater than \frac12 a systematic study has been performed examining how different nuclear quadrupole coupling (NQC) tensors cause different hyperfine patterns. The asymmetry of the NQC tensors principal components, the overall magnitudes of the components, and the orientation of the NQC tensor principal axes with respect to the molecular principal axes are considered from the perspective of directly observable rotational transition splittings. Effects of different molecular asymmetry are also considered. Also, while I = \frac32 is the nuclear spin most thoroughly investigated, different nuclear spins are also examined. The SPCAT/SPFIT software has been used to simulate many thousands of spectra with the goal of identifying recognizable patterns which will be presented.
Thoughts concerning the incorporation of this material into the undergraduate curriculum will be presented together with a reflection on the statement " An electrostatic field gradient is a classical quantity and presents no conceptual problem to the undergraduate student in their first year; nuclear quadrupole coupling constants can thus be introduced quite early..." Nuclear Quadrupole Coupling Constants, E. A. C. Lucken, Academic Press Inc. New York, New York, 1969
Footnotes:
Nuclear Quadrupole Coupling Constants, E. A. C. Lucken, Academic Press Inc. New York, New York, 1969.
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FH12 |
Contributed Talk |
1 min |
10:48 AM - 10:49 AM |
P4976: IMPLEMENTING EXTENDED CROSS CORRELATION AS A TOOL FOR SEMI-AUTOMATED MICROWAVE SPECTROSCOPIC ANALYSIS OF WEAKLY BOUND CLUSTER SPECTRA |
HANNAH FINO, REBECCA A. PEEBLES, SEAN A. PEEBLES, Department of Chemistry, Eastern Illinois University, Charleston, IL, USA; CHANNING WEST, BROOKS PATE, Department of Chemistry, The University of Virginia, Charlottesville, VA, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH12 |
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Rapid recording of molecular spectra of complex mixtures has facilitated acquisition of high sensitivity data sets. In studies of weakly bound clusters, these spectra may contain a wide range of cluster sizes and abundances, leading to intensities spanning many orders of magnitude between the strongest and weakest spectra present. The line densities and wide dynamic ranges of these high sensitivity spectra often lead to bottlenecks at the spectroscopic assignment and analysis stages of an experiment. Recent developments in artificial intelligence and machine learning have the potential to lead to fast, automated approaches to the spectroscopic assignment process. Here, we present an implementation of Jacobson, et al’s extended cross correlation (XCC) approach M.P. Jacobson, S.M. Coy, R.W. Field, Extended Cross Correlation: A Technique for Spectroscopic Pattern Recognition, J. Chem. Phys. 107 (1997) 8349–8356.o separating transitions arising from different species. While not leading to fully automated spectroscopic assignment on its own, XCC provides simplified data sets that can be more easily analyzed by visual pattern recognition or combined with other automated approaches. Initial XCC results will be compared with our previous implementation of principal component analysis-based examination of microwave spectra of complex mixtures of fluorinated ethylene/ CO2 clusters. In addition to simplifying raw datasets, these semi-automated analyses may provide insights that help identify the species present in the mixture, as well as helping guide searches for spectra of new species.
Footnotes:
M.P. Jacobson, S.M. Coy, R.W. Field, Extended Cross Correlation: A Technique for Spectroscopic Pattern Recognition, J. Chem. Phys. 107 (1997) 8349–8356.t
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FH13 |
Contributed Talk |
1 min |
10:52 AM - 10:53 AM |
P5011: ENGAGING UNDERGRADUATE STUDENTS IN SPECTROSCOPY RESEARCH VIA DEVELOPMENT AND INCORPORATION OF ADVANCED DATA ANALYSIS TECHNIQUES |
REBECCA A. PEEBLES, SEAN A. PEEBLES, PRASHANSA KANNANGARA, HANNAH FINO, Department of Chemistry, Eastern Illinois University, Charleston, IL, USA; |
IDEALS Archive (Abstract PDF) |
DOI: https://dx.doi.org/10.15278/isms.2021.FH13 |
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The rapidity with which large amounts of spectroscopic data can now be collected is presently driving interest in developing techniques to improve the speed with which spectra can be analyzed. While desirable in a research setting to avoid bottlenecks in the lab, these techniques will also be essential to the commercialization of high resolution spectroscopic methods for analysis of complex mixtures. At the same time, many undergraduate students are intrigued by the concept of data analytics and attracted by the growing job market related to this field. We will present our incorporation of analysis techniques appropriate for large data sets into undergraduate spectroscopy research experiences. Through analysis of high sensitivity microwave spectra of complex mixtures of weakly bound complexes, undergraduate students from a wide range of majors gain skill sets that put them ahead of their peers in areas such as problem solving, basic coding, and computer skills (Excel, DOS, Linux, Python, Mathcad). The majority of spectroscopy undergraduate research students at Eastern Illinois University do not go on to chemistry careers, and these additional skills that they learn provide excellent preparation for a wide range of career choices.
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