Engaging Undergraduate Students In Spectroscopy Research Via Development And Incorporation Of Advanced Data Analysis Techniques

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

USING CONCENTRATION DEPENDENCE OF MICROWAVE SPECTRA OF 2-COMPONENT MIXTURES TO IDENTIFY SINGLE COMPONENT CLUSTERS - APPLICATION TO (FLUOROETHYLENE)n AND (1,1-DIFLUOROETHYLENE)n

Over the past two years, we have implemented automated analysis of chirped-pulse microwave spectra of two-component mixtures of fluoroethylene (FE) or 1,1-difluoroethylene (DFE) and \chem{CO_2} to facilitate identification of the numerous cluster spectra present in a single scan.\footnote{Rebecca A. Peebles, Prashansa B. Kannangara, Sean A. Peebles, Brooks H. Pate, 73rd International Symposium on Molecular Spectroscopy, Talk TH02, June 19, 2018.} This approach has led to assignment of ten \chem{(FE)_n(CO_2)_m} clusters and one \chem{(DFE)_n(CO_2)_m} cluster, so far. These scans also include spectra of multiple single-component clusters (for instance, \chem{(FE)_n}), which were not apparent in earlier analyses, since “monomer only” peaks were filtered from data sets during analysis. Present efforts utilize intensity variation amongst two-component scans as a way to identify these single-component clusters. Previously unobserved spectra for five clusters involving only FE or only DFE (and in some cases including neon) have now been assigned. Identifying groups of related transitions and assigning their spectra has proven relatively straightforward, but determining compositions and structures of the carriers of these spectra is challenging. Several approaches, including analysis of the concentration dependence of transition intensity and implementation of rapid force-field based structure optimizations, have allowed some progress on determining details of the observed species

Influence of halogen variation on structure and interactions in vinyl halide (H2C=CHX)…CO2 (X = F, Cl, Br) complexes

Chirped-pulse and resonant cavity Fourier-transform microwave spectroscopy have been used to investigate dimers of CO$_2$ with vinyl fluoride (VF), vinyl chloride (VCl) and vinyl bromide (VBr). For all three complexes, CO$_2$ is aligned adjacent to the X--C--H end (X = F, Cl, Br) of the ethylene subunit, with C--X$\cdots$C and C--H$\cdots$O contacts. For VF$\cdots$CO$_2$, a second isomer is also observed, with CO$_2$ roughly parallel to the H--C=C--F side of VFhowever, there is no spectroscopic indication that similar structures are present for VCl$\cdots$CO$_2$ or VBr$\cdots$CO$_2$. For vinyl fluoride$\cdots$CO$_2$, a full structural analysis has previously been published,\footnote {C. L. Christenholz, R. E. Dorris, R. A. Peebles, S. A. Peebles, {\it J. Phys. Chem. A}, {\bf 118}, (2014), 8765-8772.} while for the Cl- and Br-containing species, insufficient data are presently available for complete structure determinations. However, structural information from ab initio calculations, $^{35}$Cl/$^{37}$Cl and $^{79}$Br/$^{81}$Br isotopic substitution, and analysis of chlorine and bromine nuclear quadrupole coupling constants will be presented. In addition, for this series of dimers containing C--H$\cdots$O contacts, further insight into the nature of the weak interactions may be obtained from Quantum Theory of Atoms in Molecules (QTAIM) and other {\it ab initio} analyses that are presently in progress

Assignment of the microwave spectrum of 1,2-difluorobenzene…hcch: lessons learned from analysis of a dense broadband spectrum

Dimers of aromatic molecules with weak proton donors such as acetylene are prototypical systems for investigating weak CH$cdotspi$ interactions. A logical progression from our recent rotational spectroscopic studies of benzene�HCCH and fluorobenzene$cdots$HCCH was to study 1,2-difluorobenzene(1,2-dfbz)$cdots$HCCH, so the effect of increasing the number of electronegative substituents could be investigated. In this talk, structures of benzene, fluorobenzene, and 1,2-difluorobenzene complexed with HCCH will be compared, and the challenges and pitfalls encountered during assignment of the very rich chirped-pulse Fourier-transform microwave (CP-FTMW) spectrum will be discussed. The spectrum of a mixture of 1,2-dfbz and HCCH in a neon carrier was initially recorded using the CP-FTMW spectrometer at the University of Virginia. Transitions matching the patterns and approximate rotational constants predicted for 1,2-dfbz$cdots$HCCH were readily identified; however, efforts to fit the observed frequencies to an asymmetric top Hamiltonian were unsuccessful. A second CP-FTMW scan of only 1,2-dfbz monomer revealed that the transitions initially believed to be 1,2-dfbz$cdots$HCCH were actually present in both scans. Subtraction of lines common to both data sets revealed a previously unidentified pattern of transitions that have now been confirmed by isotopic substitution to belong to 1,2-dfbz$cdots$HCCH. The originally identified transitions are likely 1,2-dfbz$cdots^{20}$Ne, which has a similar mass to the HCCH complex. Ab initio calculations for 1,2-dfbz$cdots$HCCH and 1,2-dfbz$cdots$Ne lead to several possible orientations for each dimer with similar energies and rotational constants, and efforts to improve the computational methods and to reliably identify stationary points on the dimer potential energy surfaces are ongoing

NEW APPROACHES TO DECODING ROTATIONAL SPECTRA: APPLICATIONS TO FLUOROETHYLENE MICROSOLVATION BY CO2

Chirped-pulse Fourier-transform microwave (CP-FTMW) spectrometers such as the instrument at the University of Virginia can acquire spectra with high sensitivity in a short amount of time. This necessitates new approaches to spectroscopic analysis to ensure identification of all species in each recorded spectrum. With an intensity range covering four orders of magnitude after averaging 1 million free induction decays, a recent spectrum of a fluoroethylene (FE)/\chem{CO_2} mixture in the 2 – 8 GHz range has over 11,000 lines with signal-to-noise ratio above $\sim$2.5. These transitions may arise from a combination of monomer, dimer and larger cluster species, including low abundance isotopes and complexes with carrier gas, water or other contaminants. Our current focus is identifying spectra of FE(\chem{CO_2})$_{n}$ clusters, containing progressively larger numbers of \chem{CO_2} molecules. Several methods have been used to facilitate identification of lines for these spectra, which are expected to lose 1-2 orders of magnitude of intensity for each increase in cluster size. These approaches include subtraction of transitions that are observed in the FE-only spectrum from the spectrum of the FE/\chem{CO_2} mixture, visual identification of patterns characteristic of asymmetric molecules, and application of extended cross correlation (XCC) techniques.\footnote{N.P. Jacobson, S.L. Coy, R.W. Field, {\it{J. Chem. Phys.}}, {\bf{107}} (1997) 8349.} In the XCC approach, several spectra with systematically varied conditions (such as pressure or concentration) are compared, and a combination of graphs and computerized algorithms is used to identify transitions that behave similarly under the changing conditions. In addition to applications for fundamental spectroscopic studies, this approach has potential application to identification of the components of complex mixtures

The 21 cm Signature of Cosmic String Wakes

We discuss the signature of a cosmic string wake in 21cm redshift surveys. Since 21cm surveys probe higher redshifts than optical large-scale structure surveys, the signatures of cosmic strings are more manifest in 21cm maps than they are in optical galaxy surveys. We find that, provided the tension of the cosmic string exceeds a critical value (which depends on both the redshift when the string wake is created and the redshift of observation), a cosmic string wake will generate an emission signal with a brightness temperature which approaches a limiting value which at a redshift of $z + 1 = 30$ is close to 400 mK in the limit of large string tension. The signal will have a specific signature in position space: the excess 21cm radiation will be confined to a wedge-shaped region whose tip corresponds to the position of the string, whose planar dimensions are set by the planar dimensions of the string wake, and whose thickness (in redshift direction) depends on the string tension. For wakes created at $z_i + 1 = 10^3$, then at a redshift of $z + 1 = 30$ the critical value of the string tension $\mu$ is $G \mu = 6 \times 10^{-7}$, and it decreases linearly with redshift (for wakes created at the time of equal matter and radiation, the critical value is a factor of two lower at the same redshift). For smaller tensions, cosmic strings lead to an observable absorption signal with the same wedge geometry.Comment: 11 pages, 4 figures; a couple of comments added in the discussion sectio

Microwave, infrared and Raman spectra, r0 structural parameters, ab initio calculations and vibrational assignment of 1-fluoro-1-silacyclopentanea)

The microwave spectrum (6500–18 500 MHz) of 1-fluoro-1-silacyclopentane, c-C4H8SiHF has been recorded and 87 transitions for the 28Si, 29Si, 30Si, and 13C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm−1) of the gas and solid and Raman spectrum (3100-40 cm−1) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much lower energy than the planar conformer. By utilizing the microwaverotational constants for seven isotopomers (28Si, 29Si, 30Si, and four 13C) combined with the structural parameters predicted from the MP2(full)/6–311+G(d,p) calculations, adjusted r0 structural parameters have been obtained for the twist conformer. The heavy atom distances in Å are: r0(SiC2) = 1.875(3); r0(SiC3) = 1.872(3); r0(C2C4) = 1.549(3); r0(C3C5) = 1.547(3); r0(C4C5) = 1.542(3); r0(SiF) = 1.598(3) and the angles in degrees are: ∠CSiC = 96.7(5); ∠SiC2C4 = 103.6(5); ∠SiC3C5 = 102.9(5); ∠C2C4C5 = 108.4(5); ∠C3C5C4 = 108.1(5); ∠F6Si1C2 = 110.7(5); ∠F6Si1C3 = 111.6(5). The heavy atom ring parameters are compared to the corresponding rs parameters. Normal coordinate calculations with scaled force constants from MP2(full)/6–31G(d) calculations were carried out to predict the fundamental vibrational frequencies, infrared intensities, Raman activities, depolarization values, and infrared band contours. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings

The microwave spectrum, ab initio analysis, and structure of the fluorobenzene–hydrogen chloride complex

The fluorobenzene–hydrogen chloride π-hydrogen-bonded complex has been studied by high resolution microwave spectroscopy and ab initio calculations. Rotational spectra of the C6H5F–H35Cl, C6H5F–H37Cl, and C6D5F–H35Cl isotopomers were assigned using pulsed molecular beam techniques in a Fourier-transform microwave spectrometer. The spectra are consistent with a structure of the complex in which the HCl is above the fluorobenzene ring near the ring center, similar to the benzene–HCl prototype dimer. An analysis of the inertial data and the chlorine quadrupole coupling tensor results in two mathematically possible locations for the HCl subunit with respect to the fluorobenzene arising from sign ambiguities in interpreting the spectral constants. One structure has the HCl nearly perpendicular to the aromatic ring; the other has the HCl pointing toward the fluorine end of the ring. Spectral intensities for the μa and μb transitions favor the former configuration. Ab initio calculations (MP2/6-311++G(2df,2pd)+BSSE corrections) indicate that the position of the HCl is driven by electrostatic interactions with the π electrons of the benzene ring. HCl is shifted by 0.16 Å from the center of the ring toward the para-C atom, where the π density is significantly higher. In the equilibrium form, HCl is tilted by δ=14° from perpendicular to the ring with the hydrogen end toward the para-C atom. The H atom can perform an internal rotation or at least a half-circular libration (barriers smaller than 100 cm−1). An average δ value of 0.7° is estimated in reasonable agreement with the derived vibrationally averaged value of 3.8°. The complex binding energy ΔE calculated at the CCSD(T)/6-311++G(2df,2pd)+CP(BSSE) level of theory is 2.8 kcal/mol, suggesting a lower ΔE value for benzene–HCl than previously reported. Fluorobenzene–HCl possesses some charge transfer character; however, just 5.5 melectron are transferred from the benzene ring to HCl. In view of this, π–H bonding in fluorobenzene–HCl is predominantly electrostatic rather than covalent in character contrary to claims made in connection with benzene–HCl

Exploring the mycobacteriophage metaproteome: Phage genomics as an educational platform

Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 "phamilies" of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three - encoding tape-measure proteins, lysins, and minor tail proteins - are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education. © 2006 Hatfull et al