Chemistry Dissertations and Theseshttps://hdl.handle.net/1808/139442024-03-29T14:43:00Z2024-03-29T14:43:00ZExperimental and Theoretical Study of Resonance Raman Spectroscopy in Ground and Excited Electronic StatesBarclay, Matthewhttps://hdl.handle.net/1808/315002021-03-05T16:53:01Z2019-12-31T00:00:00ZExperimental and Theoretical Study of Resonance Raman Spectroscopy in Ground and Excited Electronic States
Barclay, Matthew
Spectroscopy is a powerful tool for the identification, study, and selective control of molecular processes. Raman scattering is particularly useful in observing the vibrational properties of molecules, and identifying compounds based on structure. While the experimental measurements provide structural information on the vibrational transitions, the detailed interpretation of Raman spectra for complex molecules requires assignment of the observed Raman bands to specific vibrational motions. As a result, experimental spectra are often compared with calculated vibrational frequencies and Raman intensities. Therefore, it is necessary that the simulated spectra correctly reproduce the experimental Raman spectra. Although simulations of Raman spectra generally have good agreement with experiment, additional work is required to understand the effects of intramolecular electronic and nuclear structure on the Raman intensities of molecules with extended π conjugation. Conjugated thiophene derivatives have a variety of interesting optical and electronic properties, which makes them ideal targets for studies of charge-transport processes. Additionally, the delocalized π electron distribution gives these compounds relatively large scattering cross-sections, making them excellent model compounds for Raman spectroscopic studies. In particular, time-resolved techniques are able to measure transient Raman spectra in electronically excited states, allowing for the direct observation of structural dynamics following optical excitation, which is instrumental in understanding the charge separation processes in these molecules. Due to small excited-state population, transient Raman measurements typically rely on electronic resonance enhancement, which increases the Raman transition intensities for specific vibrational modes by up to several orders of magnitude. This mode-specific enhancement occurs for vibrations with large displacements along the potential energy surfaces of the higher-lying electronic states, therefore, detailed information can be obtained about the structure of higher-lying states based on which vibrations have enhanced Raman scattering intensity. Although resonance-enhanced excited-state Raman measurements are often used to increase signal, the role of the resonant electronic transition has been largely overlooked. By combining experimental measurements and theoretical simulations of excited-state Raman spectra, it is possible to gain a more comprehensive understanding of the structure of the higher-lying electronic states. In this dissertation, we measured resonance-enhanced Raman spectra in excited singlet and triplet electronic states for a set of conjugated thiophene derivatives, and compared the experiments with calculated Raman intensities for the excited states. Using relatively inexpensive computational methods, we were able to assign the experimental Raman bands to specific vibrational motions by considering the resonance enhancement condition in detail. Additionally, it was found that the experimental resonance Raman intensities can be qualitatively reproduced by calculations of the energy gradient of the higher-lying electronic state along vibrational displacements, particularly for vibrations that have relatively large resonance enhancements. We also investigated the effect of inter-ring torsion on the Raman intensities of aryl-substituted benzene and thiophene compounds in the ground state, for which density functional theory calculations tend to overestimate the delocalization of the π electron distribution between aryl rings. In addition to providing a benchmark for the accuracy of theoretical methods, the combination of experimental and simulated Raman spectra provided more detailed insight into the electronic and structural properties of the conjugated thiophene molecules than could be obtained by either approach alone. Finally, we studied the excited-state dynamics of 2,5-diphenylthiophene (DPT) following photoexcitation. We found that, by examining the potential energy gradients of higher-lying electronic states, it was possible to characterize vibrational coherences observed in the excited-state absorption spectrum, ultimately providing a more complete interpretation of the excited-state dynamics of this model compound.
2019-12-31T00:00:00ZAnion Relay Cyclopropanation and Aryl Vinyl Cyclopropane Cope RearrangementsAllegre, Kevin Michaelhttps://hdl.handle.net/1808/313722024-01-16T16:44:30Z2019-08-31T00:00:00ZAnion Relay Cyclopropanation and Aryl Vinyl Cyclopropane Cope Rearrangements
Allegre, Kevin Michael
Anion Relay Chemistry is a powerful tool for the rapid development of molecular complexity in an operationally simple manner. Much of the work in this field has been pioneered and developed by the Smith group, whose work has primarily focused on silicon and phosphorus Brook rearrangements to effect anion relay. Presented herein is the development of a retro-Claisen condensation protocol to effect anion relay in the synthesis of vinyl cyclopropanes, and subsequent aromatic Cope rearrangement of those vinyl cyclopropanes. This protocol provides a supplementary method of anion relay utilizing readily accessible nucleophiles, which obviates the need for synthesis of alkyl silanes or phosphines as starting materials. Chapter 1 is a review of anion relay chemistry, which focuses on through-space anion relay over 3 or more bonds. It covers both new developments and applications to total synthesis of through-space anion relay more than three bonds since the field was last reviewed by Smith in 2008. Chapter 2 begins with an overview of retro-Claisen activation of allylic alcohols and its application to decarboxylative and deacylative allylation reactions (DcA and DaA). This synopsis is followed by an overview of a novel anion relay cyclopropanation accomplished through a retro-Claisen activation of a nascent allylic alcohol following an initial Tsuji-Trost allylation between a carbon nucleophile and a vinyl epoxide. This reaction constitutes the latest example of retro-Claisen activation of allylic alcohols presented by our group, and a novel application of anion relay chemistry. Of note is that the anion relay is accomplished without a Brook rearrangement, obviating the necessity to synthesize alkyl silanes or phosphonates. Furthermore, it is an example of [1,6]-anion relay, examples of which are much less common than [1,2]-and [1,4]-anion relay. In chapter 3, aromatic vinyl cyclopropane Cope rearrangements are reviewed. This review is followed by a description of the aromatic Cope rearrangement of the vinyl cyclopropanes made using the methodologies outlined in Chapter 2. While divinyl cyclopropane Cope rearrangements are common and facile at room temperature, aryl vinyl cyclopropane Cope rearrangements are much less common, tend to require forcing conditions such as high temperatures and usually further require rigorously stereodefined starting materials to take advantage of the cyclopropane strain release to drive dearomatization. The reaction described in this document features a dynamic equilibrium of aryl vinyl cyclopropane diastereomers prior to Cope rearrangement, allowing the difficult Cope rearrangement to be accomplished even without stereodefined starting materials.
2019-08-31T00:00:00ZMolecular Simulation of the Passive Permeation of Small Peptides across Lipid BilayersLee, Brent Lawrencehttps://hdl.handle.net/1808/313592021-03-05T16:53:01Z2019-08-31T00:00:00ZMolecular Simulation of the Passive Permeation of Small Peptides across Lipid Bilayers
Lee, Brent Lawrence
The passive permeation of small peptides across lipid bilayers was studied by using molecular dynamics simulations and umbrella sampling. The knowledge gained in this work furthers our understanding of permeation across cell membranes and provides insight into the intelligent design of future pharmaceutical compounds. The passive permeation of the three resonant amino acids – phenylalanine, tyrosine, and tryptophan – in blocked form was studied in a bilayer consisting of 50 DOPC lipid molecules. The potential of mean force displays a free energy minimum at the interface, followed by an energy barrier at the center of the bilayer. Translational diffusion constants are surprisingly flat; however, the reorientation of the entire molecule and the amino acid sidechains indicates a significant rotational barrier. A conformational and clustering analysis of phi, psi, chi-1, and chi-2 angles demonstrates that each amino acid adopts different conformations based upon its bilayer depth. Radial distribution functions, coordination numbers, and the number of solvating water molecules were also examined. The phenylalanine dipeptide was then studied as it permeates lipid bilayers consisting of either 50 DOPC, 50 POPC, or 40 POPC lipid molecules. DOPC lipid molecules are more disordered than POPC lipids. In DOPC, the potential of mean force is therefore broader and more rotational conformations were sampled. All other analyses confirmed our prior, general observations and were surprisingly insensitive to either lipid type or system size. Position dependent diffusion constants were then calculated for the permeation of the phenylalanine dipeptide using the Fluctuation-Dissipation theorem, Green-Kubo expressions, Einstein relations, the Hummer Displacement method, and a numerical approximation to the Smoluchowski equation. We found the numerical approximation method to be the most reliable, although the Fluctuation-Dissipation theorem also yields acceptable results when unconstrained simulations were conducted. Finally, the prior analyses were applied to the permeation of wh5, one of the smallest peptides capable of forming an alpha helix. For most of the permeation process, the alpha helix remains intact and only begins to unravel at select distances in the aqueous region and at the center of the lipid bilayer. The presence of the lipid bilayer influences the tertiary structure of wh5.
2019-08-31T00:00:00ZGenetic and Chemical Intervention of the BfrB:Bfd Interaction Dysregulate Iron Homeostasis in Pseudomonas aeruginosa and Affect its Broader MetabolismPunchi Hewage, Achala Niwanthi Dharmasirihttps://hdl.handle.net/1808/312492024-01-16T16:44:29Z2020-05-31T00:00:00ZGenetic and Chemical Intervention of the BfrB:Bfd Interaction Dysregulate Iron Homeostasis in Pseudomonas aeruginosa and Affect its Broader Metabolism
Punchi Hewage, Achala Niwanthi Dharmasiri
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that is accountable for multiple types of infections, including pneumonia, wound, burn, and urinary tract infections. P. aeruginosa is an emerging threat in the hospital environments and preferentially found in comorbid illnesses. Current treatments for the P. aeruginosa infections recommend the use of combination therapy, a β-lactam with an aminoglycoside or a fluoroquinolone. Also, resistance to such procedures is rapidly emerging. Moreover, P. aeruginosa has been given critical priority for anti-infective development in the 2017 World Health Organization (WHO) report on prioritizing pathogens to guide the discovery of new antibiotics. Iron metabolism in bacteria has gained much more attention as a potential target for antibiotic development. Regulation of iron homeostasis is crucial for cells to have enough iron for growth while avoiding iron-induced toxicity. Iron homeostasis involves iron uptake, storage, and mobilization. Two iron storage molecules co-exist in P. aeruginosa, FtnA, and BfrB. Previous in-vitro studies established the importance of the bacterioferritin associated ferredoxin (Bfd) in iron mobilization from BfrB. The X-ray crystallographic structure and biochemical characterization of the BfrB:Bfd complex identified the hot spot residues of the interaction. The residues E81, E85, and L68 in BfrB, and M1, Y2, and L5 in Bfd majorly contribute to the binding energy. Mutating E81 and L68 to alanine completely inhibited iron mobilization from BfrB. The insights gathered from these in-vitro studies were used in this work to interrogate the importance of the BfrB:Bfd interaction in P. aeruginosa cells. In this work, P. aeruginosa, wild type (PAO1), Δbfd, bfrB(E81A/L68A), and ΔbfrB cells were used to study the significances of the BfrB:Bfd interaction in P. aeruginosa cells. A Native-PAGE method was optimized to image iron in BfrB in P. aeruginosa lysates. This advanced technique allowed us to identify BfrB as the main iron storage protein of P. aeruginosa. The same method was used to image iron storage in BfrB and its subsequent mobilization in P. aeruginosa cells (wild type, Δbfd, and bfrB(E81A/L68A)). The intact BfrB:Bfd interaction capable wild type cells showed maximum accumulation of iron during the early stationary phase, and iron mobilization from BfrB during the late stationary phase. In contrast, the Δbfd and bfrB(E81A/L68A) mutants demonstrated irreversible accumulation of iron in BfrB. Due to the irreversible flux of iron into BfrB, the Δbfd and bfrB(E81A/L68A) mutants developed low cytosolic free iron levels and a high total iron to free iron ratio. The consequences of the genetic blockade of the BfrB:Bfd interaction was further investigated by comparing the expression proteomes of the wild type and Δbfd mutant cells. The iron homeostasis dysregulation affected the iron-dependent and independent metabolic processes in the Δbfd mutant cells. Proteins involved in the TCA cycle, amino acid biosynthesis, oxidative stress regulation, and respiratory chain were under-represented in the Δbfd mutant cells. On the other hand, proteins involved in the iron acquisition systems (pyoverdine, pyochelin, Heme iron acquisition), sulfur assimilation, quorum sensing were over-represented in the Δbfd mutant cells. These findings show that iron homeostasis dysregulation can affect the broader metabolism of P. aeruginosa cells. The chemical intervention of the BfrB:Bfd interaction in P.aeruginosa cells was carried out with small molecule inhibitors, analogs of 4-aminoisoindoline-1,3-dione. These analogs acted on their target, BfrB in P. aeruginosa cells. Moreover, the analogs elicited a concentration-dependent growth retardation, and a pyoverdine hyper-production as a result of cytosolic iron deprivation. Analog-treated cells experienced an irreversible accumulation of iron in BfrB and high total iron content in the treated cells. Hence, the developed 4-aminoisoindoline-1,3-dione derivatives were potent to dysregulate iron homeostasis in P. aeruginosa cells. The BfrB:Bfd inhibitors also potentiated the activity of fluoroquinolones in P. aeruginosa (PA01), and in two cystic fibrosis isolates, MR3B and MR60. The growth impairment of the cystic fibrosis and urinary tract clinical isolates of P. aeruginosa, and Acinetobacter baumannii (AB5075) demonstrate the potential widespread application of the developed 4-aminoisoindoline-1,3-dione derivatives in blocking the BfrB:Bfd interaction. These findings strongly support the suitability of inhibiting the BfrB:Bfd interaction as a novel target in anti-infective development.
2020-05-31T00:00:00Z