Supernovae (SNe) are energetic explosions that signal the end of a star's life. These events and the supernova remnants (SNRs) they leave behind play a central role in stellar feedback by adding energy and momentum and metals to the interstellar medium (ISM). Emission associated with these feedback processes, especially atomic and molecular line emission as well as thermal and nonthermal continuum emission is known to be enhanced in regions of high density, such as dense circumstellar matter (CSM) around SNe and molecular clouds (MCs). In this thesis, I begin with a brief overview of the physics of SN shocks in Chapter 1, focusing on a foundation for studying pan-chromatic signatures of interactions between SNe and dense environments. In Chapter 2, I examine an unusual SN with signatures of CSM interaction in the form of narrow lines of hydrogen (Type IIn) and thermal continuum emission. This SN appears to belong to a class of Type Ia SNe that shares spectroscopic features with Type IIn SNe. I discuss the difficulties of decomposing spectra in a regime where interaction occurs between SN ejecta and CSM, potentially confusing the underlying SN type. This is followed by a discussion of rebrightening that occurred at late-time in 𝐵 and 𝑉 band photometry of this SN, possibly associated with clumpy or dense CSM at large distances from the progenitor. In Chapter 3, I examine synchrotron emission from Cassiopeia A, observed in the 𝐾ₛ band over multiple epochs. The synchrotron emission is generally diffuse over the remnant, but there is one location in the southwest portion of the remnant where it appears to be enhanced and entrained as knots of emission in the SNR ejecta. I evaluate whether the 𝐾ₛ band knots are dominated by synchrotron emission by comparing them to other infrared and radio imaging that is known to be dominated by synchrotron emission. Concluding that they are likely synchrotron-emitting knots, I measure the magnetic field strength and electron density required for their evolution over the ~ 10 yr baseline they were observed and find 𝐵 ≈ 1.3-5.8 mG and 𝑛ₑ≈ 1,000-15,000 cm⁻³. The magnetic field strengths appear enhanced beyond values required by the adiabatic strong shock limit, arguing in favor of other forms of magnetic field amplification in the shock. In Chapter 4, I again discuss Cassiopeia A and interaction between the remnant and nearby MCs as seen at mid-infrared and millimeter wavelengths. I report detection of a SNR-MC interaction and analyze its signatures in broadened molecular lines. I extend this analysis in Chapter 5 to a large survey for SNR-MC interactions in the ¹²CO 𝐽=2-1 line. Although broadened ¹²CO 𝐽=2-1 line emission should be detectable toward virtually all SNR-MC interactions, I find relatively few examples; therefore, the number of interactions is low. This result favors mechanisms other than supernova feedback as the basic trigger for star formation. In addition, I find no significant association between TeV gamma-ray sources and MC interactions, contrary to predictions that SNR-MC interfaces are the primary venues for cosmic ray acceleration. I end this dissertation in Chapter 6 with a brief summary of my results and two extensions of this work: examining the late-time radio light curves of CSM-interacting SNe for signatures of radio synchrotron emission and dense or clumpy CSM at large distances from the progenitor and re-observing SNR-MC interactions in ¹²CO 𝐽=3-2 in order to verify the presence of shock-heated molecular gas and perform a census on the densities and temperatures of post-shock molecular gas.

Small-molecule libraries with enhanced structural diversity are of value in drug discovery campaigns where novel biologically active hits are desired. As such, multicomponent reactions (MCRs) have proven fruitful to enhance the molecular diversity of chemical collections and expedite forward progression of the drug discovery chain. Bicalutamide (Casodex), an anticancer drug, and Telaprevir (Incivek), an antiviral, are two examples of marketed drugs that can be synthesized using an MCR. The research topic of this dissertation involves the design, discovery, and development of novel MCRs and new combinations of MCRs with post-condensation modifications to generate over twenty-five new drug-like scaffolds in an operationally friendly, atom-economical, time- and cost-effective fashion. The developed chemical methodologies possess inherent 'iterative efficiency','high exploratory power', and 'bond forming efficiency' that allow them to quickly explore chemical space and navigate the 'hypothesis-synthesis-screening' loop that is key for a medicinal chemistry project. The prepared molecules were submitted to the Community for Open Antimicrobial Drug Discovery (CO-ADD) for antimicrobial screening against pathogens that are known to cause drug-resistance infections.

Ultra-violet and visible light induced processes in small organic molecules play very important roles in many fields, e.g., environmental sciences, biology, material development, chemistry, astrophysics and many others. Thus it is of great importance to better understand the mechanisms behind these processes. To achieve this, a bottom-up approach is most effective, where the photo-induced dynamics occurring in the simplest organic molecule (ethylene) are used as a starting point. Simple substituents and functional groups are added in a controlled manner to ethylene, and changes in the dynamics are investigated as a function of these modifications. In this manner, the dynamics occurring in more complex systems can be explored from a known base. In this thesis, the excited state dynamics of small organic molecules are studied by a combination of time-resolved photoelectron spectroscopy and various computational methods in order to determine the basic rules necessary to help understand and predict the dynamics of photo-induced processes. The dynamics occurring in ethylene involve a double bond torsion on the ππ* excited state, followed by the decay to the ground state coupled with pyramidalization and hydrogen migration. Several different routes of chemical modification are used as the basis to probe these dynamics as the molecular complexity is increased. (i) When ethylene is modified by the addition of an alkoxyl group (-OCnH2n+1), a new bond cleavage reaction is observed on the πσ* state. When modified by a cyano (-CN) group, a significant change in the carbon atom involved in pyramidalization is observed. (ii) When ethylene used to build up small cyclic polyenes, it is observed that the motifs of the ethylene dynamics persist, expressed as ring puckering and ring opening. (iii) In small heteroaromatic systems, i.e., an aromatic ring containing an ethylene-like sub-structure and one or two non-carbon atoms, the type of heteroatom (N: pyrrole, pyrazole O: furan) gives rise to different bond cleavage and ring puckering channels. Furthermore, adding an aldehyde group (-C=O) onto furan, as a way to lengthen the delocalised ring electron system, opens up additional reaction channels via a nπ* state. The results presented here are used to build up a more complete picture of the dynamics that occur in small molecular systems after they are excited by a visible or UV photon, and are used as a basis to motivate further investigations. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 5: Manuscript. Paper 6: Manuscript.</p>

The problem of the quadrupole interaction occurring in a vibrating-rotating C₃v symmetric top molecule has been studied in detail. The quadrupole interaction has been treated as another perturbation term to a general frequency expression accounting for the vibrating-rotating interaction of the molecule so that a complete frequency formula is obtained for both interactions, and from which hyperfine spectral components are predicted and measured. The hyperfine transitions in the ground, and v₈=1 and v₈=2 excited vibrational states of the ¹³C isotopes of methyl cyanide have been investigated in the frequency range 17-72 GHz, primarily in the low J transitions (0≤J≤3). The study of the ground state of isotope i3CH3i3CN, and the v₈=1, v₈=2 excited vibrational states for all the isotopes have been conducted here for the first time. A substantial perturbation has been discovered and discussed at the ΔJ=3→4 transitions within the Kl=1 sets in the v₈=1 mode for isotopes ¹³CH₃CN and CH₃¹³CN. A total of 716 hyperfine transitions have been assigned from measurements, only 7 of which have been measured previously. A total of 84 molecular constants have been reported; 70 of these constants are derived for the first time from microwave data.

The energy states of C₃ᵥ symmetric top polyatomic molecules were studied. Both classical and quantum mechanical methods have been used to introduce the energy states of polyatomic molecules. Also, it is shown that the vibration-rotation spectra of polyatomic molecules in the ground and excited vibrational states can be predicted by group theory. A comprehensive model for predicting rotational frequency components in various v₁₀ vibrational levels of propyne was developed by using perturbation theory and those results were compared with other formulas for C₃ᵥ symmetric top molecules. The v₁₀=1,2,3 and ground rotational spectra of propyne in the frequency range 17-70 GHz have been reassigned by using the derived comprehensive model. The v₁₀=3 and v₁₀=4 rotational spectra of propyne have been investigated in the 70 GHz, and 17 to 52 GHz regions, respectively, and these spectral components assigned using the comprehensive model. Molecular constants for these vibrationally excited states have been determined from more than 100 observed rotational transitions. From these experimentally observed components and a model based upon first principles for C₃ᵥ symmetry molecules, rotational constants have been expressed in a form which enables one to predict rotational components for vibrational levels for propyne up to v₁₀=5. This comprehensive model also appears to be useful in predicting rotational components in more highly excited vibrational levels but data were not available for comparison with the theory. Several techniques of assignment of rotational spectra for each excited vibrational state are discussed. To get good agreement between theory and experiment, an additional term 0.762(J+1) needed to be added to Kℓ=1 states in v₁₀=3. No satisfactory theoretical explanation of this term has been found. Experimentally measured frequencies for rotational components for J→(J+1)=+1 (0≤J≤3) in each vibration v₁₀=n (0≤n≤4) are presented and compared with those calculated using the results of basic perturbation theory. The v₉=2 rotational spectrum of the propyne molecule was introduced in Appendix A to compare the rotational spectra of the same molecule in different vibrational levels v₉ and v₁₀.

The problem of a vibrating-rotating polyatomic molecule is treated, with emphasis given to the case of molecules with C_3v symmetry. It is shown that several of the gross features of the rotational spectra of polyatomic molecules in excited vibrational states can be predicted by group theoretical considerations. Expressions for the rotational transition frequencies of molecules of C_3v symmetry in the ground vibrational state, singly excited degenerate vibrational states, and doubly excited degenerate vibrational states are given. The derivation of these expressions by fourth order perturbation theory as given by Amat, Nielsen, and Tarrago is discussed. The ground and V_10=1 rotational spectra of propyne have been investigated in the 17 to 70 GHz, and 17 to 53 GHz regions, respectively, and compared with predictions based on higher frequency measurements. The V_9=1 and V_10=2 rotational spectra of propyne have been investigated and assigned for the first time. A perturbation of the V_9=1 rotational spectra for K=-l has been discovered and discussed.

(1). An improved method for synthesizing bicyclo (2,2,1) hepta-2,5-diene-7-spiro-1'-cyclopentane (5) has been developed. Thermal reaction of compound (5) with neat iron pentacarbonyl under nitrogen atmosphere affords the corresponding cage dimer (6). Some aspects of the syntheses, spectra, and chemistry of compound (5) and (6) are discussed. (2). A structure isomer of decamethyldodecahedrane (C₃₀H₄₀), molecule (11), is expected to be synthesized via thermal reaction of iron carbonyl complexes with compound (10). An intermediate in this synthesis, 2,2- tetramethylene-1,4-dibromobutane (9) was efficiently synthesized starting from cyclopentanone. Some aspects of the syntheses, spectra, and chemistry of compound (1) to (9) will be discussed.

Immunoassays have traditionally been employed for the determination of plasma concentration-time profiles for pharmacokinetic studies of therapeutic proteins and peptides. These ligand binding assays have high sensitivity but require significant time for antibody generation (1 to 2 years) for assay development. Despite high sensitivity, these assays suffer from cross-reactivity that can lead to inaccurate results. As an alternative to immunoassays, this dissertation was focused on the development and validation of assays that can be used for quantitative analysis of peptides or proteins in plasma using liquid chromatography tandem mass spectrometry (LC-MS/MS). Two approaches were considered for measurement of proteins and peptides fortified in plasma. The first approach involved employing signature peptides as quantitative surrogates of a target protein. This approach is a multistep process that includes: computer simulated (in silico) peptide predictions, protein purification, proteolytic digestion, peptide purification, and ultimately mass spectrometry. Signature peptides were determined through in silico peptide predictions and iterative tuning processes to represent Amevive® (Alefacept), a therapeutic for psoriasis, for quantification in human plasma. Horse heart myoglobin was chosen as a protein analogue internal standard to compensate for errors associated with matrix effects and to track recovery throughout the entire sample pretreatment process. Samples were prepared for analysis by selective precipitation of the target proteins with optimized pH and heat conditions followed by enzymatic digestion, dilution, and filtration. Combining selective precipitation and protein analogue internal standard lead to a method validated according to current FDA guidelines and achieved a linear range (250-10,000 ng/mL) suitable for monitoring the therapeutic levels of Alefacept (500 -6000 ng/mL) without the use of antibodies. A second approach exploited the mass spectrometric behavior of intact polypeptides. A polypeptide can exist in multiple charge states separated by mass to charge ratio (m/z). Herein, the charge state distribution and the formation of product ions to form selected reaction monitoring (SRM) transitions for intact polypeptide quantitative analysis was evaluated in plasma. Oxyntomodulin, a 37 amino acid anorectic peptide (4449 Da), was employed as a model for analysis in rat plasma. The +7 charge state form of OXM was used to form an SRM for quantitative analysis. Two-dimensional reversed phase ion pair chromatography, a modified solid phase extraction, and a multiply charged SRM of oxyntomodulin enabled a lower limit of quantification of 1 ng/mL. Following development of the LC-MS/MS method, a validation of this approach was performed according to FDA guidelines. Finally, to show further utility of LC-MS/MS, the validated oxyntomodulin method was used in a pharmacokinetic study with sprague-dawley rats. Rats were dosed with oxyntomodulin through intravenous or intratracheal instillation routes of administration. Plasma concentration-time profiles were determined. Using these profiles, noncompartmental parameters were determined for each dose and routes of administration.

Alpha7 Neuronal nicotinic acetylcholine receptors (nAChRs) are involved in essential physiological functions and play a role in disorders such as Alzheimer’s disease. MD-354 (3-chlorophenylguanidine; 21), the first small–molecule negative allosteric modulator (NAM) at alpha7 nAChRs, served as a lead in developing structure–activity relationships for NAMs at a7 nAChRs. MD-354 (21) also binds at 5-HT3 receptors. Analogs of MD-354 with structural features detrimental to 5-HT3 receptor affinity were evaluated in patch-clamp recordings and an aniline N-methyl analog resulted in a more potent and selective NAM than MD-354. A new N-methyl series of compounds was synthesized in which the 3-position was replaced with different substituents considering their electronic, lipophilic, and steric nature. Comparative studies were initiated to investigate whether or not the MD-354 series and the N-methyl series bind in the same manner; 3D models of the extracellular domain of human alpha7 nAChRs were developed, allosteric sites identified, and docking studies conducted.

Gas phase studies of organometallic systems have provided deep insight into reaction mechanisms and reaction intermediates. In this thesis, several metal/ligand systems were examined in an effort to form metal carbenes in the gas phase. With cobalt and iron porphyrins, the carbene undergoes metal-ligand insertion. With copper bis-oxazolines, metal carbenes tend to undergo metal-ligand insertion and a Wolff rearrangement. To avoid insertions, we turned to a rigid ligand, 1, 10-phenanthroline. Under ESI conditions, a copper (I) complex with phenanthroline can be formed. When treated with diazoacetate esters, the dominant product results from addition with loss of nitrogen followed by loss of CO. This appears to be the result of a Wolff rearrangement of the metal carbene to give a metal ketene complex that spontaneously loses CO. There is no evidence of any stable metal carbenes in this reaction system. Trimethylsilyldiazomethane was also used as a carbene precursor, and its reaction with the copper phenanthroline complex gives addition with loss of nitrogen; but the product exhibits no carbene reactivity with alkenes. Here computational modeling suggests that the metal carbene undergoes a 1, 2 methyl migration, giving an exceptionally stable sila-alkene complex with the copper. As an alternative path to a metal carbene, we have used ESI to form a complex between the copper (I) phenanthroline and betaine (N, N, N-trimethylglycine). Under CID, this complex wills decarboxylates to give a copper ylide complex. Further CID leads to loss of trimethylamine and the formation of a complex between methylene and the copper phenanthroline. Depending on the CID conditions, two isobaric products are formed. One exhibits no carbene reactivity and the other readily gives carbene behavior with alkenes. The former is likely a metal-ligand insertion product, and the latter is the true metal carbene species. We explored the reactions of the carbene with electron-rich alkenes, such as ethyl vinyl ether and 3, 4-dihydro-2H-pyran, and electron-deficient alkenes, such as trichloroethylene.