Search results

Title: Petroleum Analysis by Atmospheric Pressure Photoionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.
Creator: Purcell, Jeremiah Michael, Marshall, Alan, Salters, Vincent, Cooper, William, Logan, Timothy, Rodgers, Ryan, Hendrickson, Christopher, Department of Chemistry and Biochemistry,...
Show morePurcell, Jeremiah Michael, Marshall, Alan, Salters, Vincent, Cooper, William, Logan, Timothy, Rodgers, Ryan, Hendrickson, Christopher, Department of Chemistry and Biochemistry, Florida State University
Show less
Abstract/Description: Petroleum and petroleum products are an integral part of today's society. Although petroleum is projected to be the dominant energy source for the next fifty years, the depletion of light sweet crude oil reserves has led to the refinement of heavier feedstocks. Heavier petroleum feedstocks contain higher weight percent sulfur-, nitrogen- and oxygen-containing species. Not only is the combustion of these species harmful to the environment, they can also poison catalytic and hydrotreatment...
Show morePetroleum and petroleum products are an integral part of today's society. Although petroleum is projected to be the dominant energy source for the next fifty years, the depletion of light sweet crude oil reserves has led to the refinement of heavier feedstocks. Heavier petroleum feedstocks contain higher weight percent sulfur-, nitrogen- and oxygen-containing species. Not only is the combustion of these species harmful to the environment, they can also poison catalytic and hydrotreatment refining equipment. The United States Environmental Protection agency has limited allowable heteroatom weight percents in petroleum products. Moreover, sulfur is the third most abundant element in petroleum and has been regulated to parts-per-million levels and further reduction slated for the year 2010. To meet the more stringent environmental regulations, refineries are facing major challenges. Mass spectrometry has proven to be a valuable tool for the molecular speciation of petroleum. Notably, electrospray ionization Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry has proven invaluable for the speciation of the polar compounds in crude oil. This analysis has added to the understanding of specific refinery problems, e.g., solid deposition and flocculation. However, hydrocarbons and non-polar sulfur species are not accessible by ESI mass spectrometry. Atmospheric Pressure PhotoIonization (APPI) can produce ions from non-polar (and polar) species. Chapter 1 is a brief discussion of basic ICR principles, APPI pathways, instrumentation and data analysis. In Chapter 2, I describe an APPI source coupled to the in house built 9.4 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer at the National High Magnetic Field Laboratory (NHMFL) in Tallahassee, Florida. This chapter highlights the complexity of crude oil analysis with an APPI source. The possibility of forming two ion types (protonated compounds and radical molecular ions) from one compound complicates an already complex spectrum. Model compound spectra demonstrate the necessity of ultra-high resolution mass spectrometry to resolve common mass doublets (3.4 mDa, the mass difference between C3 vs. SH4; 4.5 mDa, the mass difference between 12CH and 13C) found in petroleum spectra. Also, this report establishes the highest number of resolved (and assigned elemental formulas) spectral peaks (>12,000 peaks in a single mass spectrum and up to 63 peaks of the same nominal mass) in one mass spectrum.12,000 peaks in a single mass spectrum and up to 63 peaks of the same nominal mass) in one mass spectrum. Although APPI is considered to be a soft ionization technique, the analyte is nebulized and heated before ion formation. On the other hand, ESI is a well established soft ionization process. Therefore, in Chapter 3, I compare ESI and APPI data from the same crude oil and also pyridinic and pyrrolic nitrogen model compounds. The chapter defines instrument parameters which can cause fragmentation (loss of H2) and parameters which do not. ESI and APPI crude oil spectra yield the same elemental species, providing evidence that APPI can produce an ion population without fragmentation. A dopant (proton donor) is advantageous for APPI mass spectrometry because proton transfer reactions are enhanced. For simple mixture analysis, the proton donor is predominantly the dopant. However, for complex mixture analysis (crude oil), the solution matrix can contain species which could also participate in proton transfer reactions. In Chapter 4, I investigate the proton transfer reaction for a Canadian bitumen petroleum in deuterated toluene (C7D8). Nitrogen class compounds are also analyzed in deuterated toluene. The dopant percent contribution to the even-electron ions (protonated and deuterated compounds) of the petroleum is ~5 %. The nitrogen model compounds exhibited a similar trend. Petrochemical analysis commonly employs the saturates-aromatic-resins-asphaltenes (SARA) separation method. In Chapter 5, the sulfur containing compounds of a Middle East crude oil are speciated. The crude oil is additionally fractionated by the SARA method and its fractions are analyzed by APPI FT-ICR mass spectrometry. Molecular species from the whole crude oil and its fractions are compared to ascertain differences and similarities between sulfur species in the fractions. Non-polar sulfur species are not efficiently ionized by ESI. However, derivatization chemistry can methylate polycyclic aromatic sulfur species and form cations in solution with subsequent analysis by ESI mass spectrometry. In Chapter 6, the derivatized and non-derivatized samples of a petroleum vacuum bottom residue (the highest boiling point fraction of petroleum and hence, the most complex heteroatom content) are analyzed by ESI and APPI. Significant differences in the double bond equivalent values (DBE, value equal to the number of rings plus double bonds in the molecular structure calculated from the elemental formula) between the ESI and APPI analyzed sulfur species are identified. Furthermore, this report provides data that probes APPI ionization efficiency. Chapter 7 is a synopsis of the APPI technology applied to petroleum analysis. The chapter also includes a real world application of APPI FT-ICR mass spectrometry. The Institute of Petroleum at France (IFP) is interested in the development of new hydroconversion processes to upgrade vacuum bottom residue to more useful petroleum products. A substantial fraction of vacuum bottom residue is the asphaltenes; the most heteroatom rich fraction in petroleum. The chapter presents molecular speciation from intermediate stages of a hydroconversion process; a first step in hydroconversion catalytic technology improvement. A Ph.D. thesis may also include research outside the scope of the primary dissertation research to achieve a broader understanding of the sciences. Appendix A describes the ongoing construction and adaptation of an ion cluster source to an existing FT-ICR mass spectrometer. The primary investigator is Professor Harry Kroto, Nobel prize laureate for the discovery of fullerenes. Fullerenes are closed cage molecules consisting of 12 pentagonal and several hexagonal rings. Fullerenes with 60 carbon atoms or larger follow the isolated pentagon rule (IPR). Smaller fullerenes ( In appendix B, the reaction products of C60 and hydrogen at high temperature and pressure are resolved and identified. The product species formed at elevated temperature and hydrogen pressure are characterized by APPI FT-ICR mass spectrometry. Only the APPI analysis (and Field Desorption, FD) were accomplished at Florida State University and the first report (of three published reports) is presented.
Show less
Date Issued: 2007
Identifier: FSU_migr_etd-0477
Format: Thesis

Title: Excited States and Electrical Properties of Fe (III) and V (IV) Clusters.
Creator: Zipse, David, Dalal, Naresh, Molnár, Stephan von, Goldsby, Kenneth, Steinbock, Oliver, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: This dissertation describes the characterization of the magnetic and electrical properties of a unique class of transition metal complexes known as single-molecule magnets (SMMs). The experimental work of this dissertation is focused on the SMMs [(C6H15N3)6Fe8O2(OH)12]Br7(H2O)Br •8H2O (Fe8Br8), K6[V15As6O42(H2O)] • 8H2O (V15), as well as the analogous cluster compounds [NH(C2H5)3]4[V84.5+V44+As8O40(H2O)]•H2O (V12) and [(C6H15N3)4Fe4O(OH)5]I7 • 2.5 H2O (Fe4). SMMs are transition metal cluster...
Show moreThis dissertation describes the characterization of the magnetic and electrical properties of a unique class of transition metal complexes known as single-molecule magnets (SMMs). The experimental work of this dissertation is focused on the SMMs [(C6H15N3)6Fe8O2(OH)12]Br7(H2O)Br •8H2O (Fe8Br8), K6[V15As6O42(H2O)] • 8H2O (V15), as well as the analogous cluster compounds [NH(C2H5)3]4[V84.5+V44+As8O40(H2O)]•H2O (V12) and [(C6H15N3)4Fe4O(OH)5]I7 • 2.5 H2O (Fe4). SMMs are transition metal cluster complexes that exhibit single-molecule hysteresis and quantum tunneling of the magnetization (QTM). Fe8Br8 is one of the best characterized SMMs with its ground state spin S = 10, while V15 exhibits SMM behavior with a spin of S = ½. The foci of our investigations were the single-spin model in Fe8Br8, the basic electrical properties of V15 and V12, and the synthesis and characterization of the analogous cluster compound Fe4. Chapter 2 describes the characterization (magnetic parameters and energetic location) of the S = 9 excited state in Fe8Br8 by high field electron paramagnetic resonance, while Chapter 3 focuses on the measurement of the unpaired electron density distribution in Fe8Br8 as determined by 81Br solid state NMR. Both of these chapters bring into question the validity of the currently accepted single-spin model for Fe8Br8. Chapter 4 details the dielectric relaxation properties of V15 as determined by an ac impedance method. The semiconductive behavior of both V15 and V12 is described in Chapter 5, along with its comparison to optical absorption measurements, while the synthesis and magnetic characterization of the new cluster compound Fe4 is described in Chapter 6. The summary and main conclusions are presented in Chapter 7. The results presented herein should make a significant contribution to the fundamental understanding of the mechanism of quantum tunneling in Fe8Br8 and the basic electrical properties of SMMs for their potential use in future applications.
Show less
Date Issued: 2004
Identifier: FSU_migr_etd-0481
Format: Thesis

Title: Computational Analysis of the U2 Snrna-Intron Duplex.
Creator: Xu, Darui, Greenbaum, Nancy L., Li, Hong, Alabugin, Igor, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Pairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine, whose 2' OH initiates the nucleophilic attack at the pre-mRNA 5' splice site during the first step of splicing. The structure of the spliceosomal branch site solved by Newby and Greenbaum showed that a highly conserved pseudouridine...
Show morePairing of a consensus sequence of the precursor (pre)-mRNA intron with a short region of the U2 small nuclear (sn)RNA during assembly of the eukaryotic spliceosome results in formation of a complementary helix of seven base pairs with a single unpaired adenosine, whose 2' OH initiates the nucleophilic attack at the pre-mRNA 5' splice site during the first step of splicing. The structure of the spliceosomal branch site solved by Newby and Greenbaum showed that a highly conserved pseudouridine residue in U2 snRNA induces a dramatically altered structure compared with that of its unmodified counterpart. In this study, both modified and unmodified U2 snRNA-intron duplexes were analyzed using computer simulations including preliminary molecular dynamics (MD) simulations, electrostatic potential, surface area, and solvation free energy calculations. The preliminary MD simulations produce stable trajectories of the RNA duplexes in solution. The surface electrostatic potentials were calculated using finite difference Poisson-Boltzmann algorithm and a hybrid boundary element and finite difference Poisson-Boltzmann approach. Results show a region of exceptionally negative potential near the 2' OH of the branch site adenosine. The two RNA duplexes have similar solvent accessible surface areas, whereas the surface accessible area of the 2' OH of the branch site adenosine of the modified RNA duplex is considerably smaller than that of the unmodified RNA duplex. The solvation free energy calculation indicates that the unmodified RNA duplex is favored over the modified RNA duplex.
Show less
Date Issued: 2003
Identifier: FSU_migr_etd-0414
Format: Thesis

Title: Molecular Characterization of Tea Catechin Treated Human Prostate Cancer Cell Lines.
Creator: Suh, Yewseok, Sang, Qing-Xiang Amy, III, Thomas C.S. Keller, Schlenoff, Joseph B., Li, Hong, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Prostate cancer is the most prevalent cancer diagnosed among men in the United States. The major green tea polyphenol epigallocatechin-3 gallate (EGCG) has been shown to exert remarkable preventive effects against various types of cancer including prostate cancer. Recent human clinical study proved that EGCG can prevent progression of high grade prostatic intraepithelial neoplasia (PIN) to prostate cancer. Cellular studies show that EGCG exhibits antiproliferative and apoptotic effects in...
Show moreProstate cancer is the most prevalent cancer diagnosed among men in the United States. The major green tea polyphenol epigallocatechin-3 gallate (EGCG) has been shown to exert remarkable preventive effects against various types of cancer including prostate cancer. Recent human clinical study proved that EGCG can prevent progression of high grade prostatic intraepithelial neoplasia (PIN) to prostate cancer. Cellular studies show that EGCG exhibits antiproliferative and apoptotic effects in androgen-responsive LNCaP and androgen-unresponsive DU145, PC3 prostate cancer cell lines. Previously, we have established a new type of prostate cancer line, androgen repressed carcinoma of prostate (ARCaP). ARCaP cells are highly invasive and metastatic and this cell line showed unique response to androgen since the hormone repressed the proliferation. In this study, we show that androgen-repressed ARCaP prostate cancer cell line, which represents more advanced and aggressive type of prostate cancer, is resistant to EGCG treatment. In Western blot analyses, EGCG treated ARCaP cell line showed increase in phosphorylation of NF-κB and decrease in activation of p38 MAPK and Bax/Bcl-2 ratio. The levels of p21/CIP1/WAF1, cyclin-dependent kinases (CDKs) 2, 4, 6, activated forms of Akt and c-Jun NH2-terminal protein kinase (JNK) remain unchanged in EGCG treated ARCaP cells whereas decrease in active Akt, active JNK, and CDKs 2, 4, 6, and increased level of p21/CIP1/WAF1 were observed in LNCaP cells upon EGCG treatment. Moreover, EGCG treatment confers stronger adherence to types I, II, IV collagen extracellular matrix proteins on ARCaP cells. On the contrary, LNCaP cells lost the adhesion significantly to all extracellular matrix proteins tested, including collagens, fibronectin, laminin, vitronectin, and tenascin. Most importantly, ARCaP cells formed more colonies on soft agar in our anchorage-independent assay when treated with EGCG whereas the colony forming ability of LNCaP cells was totally abolished under the same condition. This study suggests that the use of tea catechin EGCG as anticancer agent may not be effective for treating patients with androgen repressed subtype of prostate cancer. This is the first study of apoptosis in ARCaP cell line. The GeneChip microarray analysis revealed several genes that were differentially expressed when treated with EGCG. Among those, matrix metalloproteinases (MMPs) 1 and 3 were significantly up regulated in LNCaP cells upon EGCG treatment. Both RNA transcription and protein secretion/activation of these MMPs were observed by GeneChip assay, reverse transcription-polymerase chain reaction (RT-PCR) and by enzyme linked immunosorbent assay (ELISA) which can detect proMMP1 and total MMP3 in cell culture media. This feature is very unique in that (1) the MMPs are generally known to be involved in tumor invasion and metastasis not the cell death, and (2) the other EGCG sensitive prostate cancer cell lines, DU145 and PC3, did not display such characteristics. EGCG did not affect the expression of these MMPs in ARCaP cells also. Using GeneChip analysis, we found several genes whose expressions were oppositely regulated in LNCaP and ARCaP cells upon EGCG treatment. These include early growth response -1 (EGR1), growth arrest and DNA damage inducible gene 45 (GADD45). The expression level of EGR1 and GADD45 were decreased in ARCaP cells but the level was increased in LNCaP cells after EGCG treatment. These results suggest that the proapoptotic EGR1 and GADD45 may play a role in EGCG induced apoptosis in LNCaP cells and thus may explain, at least in part, the resistance of ARCaP cells against such apoptotic stimuli. The role of these proteins in EGCG induced apoptosis is not known. The decreased level of topoisomerase II in EGCG treated LNCaP cells is also exciting. Topoisomerases are necessary in DNA replication and thus for survival of the organism. Since only LNCaP cells, but not ARCaP cells, displayed reduced expression of topoisomerase II during EGCG induced apoptosis and since ARCaP cells underwent apoptosis when treated with topoisomerase inhibitor etoposide, the function of this enzyme might be involved in life or death decision of ARCaP and LNCaP cells. Elucidating the molecular effects of these proteins and the mechanisms of how these proteins function in ARCaP and LNCaP cell lines would help understanding the prostate cancer and may help with future design of cancer chemopreventive and chemotherapeutic agents.
Show less
Date Issued: 2006
Identifier: FSU_migr_etd-0402
Format: Thesis

Title: Characterization and Applications of Ph-Responsive Polyelectrolyte Complex and Multilayers.
Creator: Sui, Zhijie, Schlenoff, Joseph B., Alamo, Rufina G, Dorsey, John G., Rill, Randy L., Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Polyelectrolyte complexes (PECs) have received a growing interest since the early sixties. PECs have been used for large-scale industrial applications and have demonstrated enormous potentials in various fields such as coatings, binders and flocculants. Using the Layer-by-layer deposition technique, an ultrathin polyelectrolyte multilayer coating was first built in 1990 and soon both theoretical and practical interest in these coatings were growing exponentially. In the first part of this...
Show morePolyelectrolyte complexes (PECs) have received a growing interest since the early sixties. PECs have been used for large-scale industrial applications and have demonstrated enormous potentials in various fields such as coatings, binders and flocculants. Using the Layer-by-layer deposition technique, an ultrathin polyelectrolyte multilayer coating was first built in 1990 and soon both theoretical and practical interest in these coatings were growing exponentially. In the first part of this dissertation, studies were focused on the fundamental properties of polyelectrolyte multilayer and complex systems, such as the effect of molecular weight of polyelectrolytes and the effect of ionic strength on the multilayer buildup and the thermodynamics of the polyelectrolyte complexation. In the second part, a series of pH-tunable polyelectrolyte complexes and pH-responsive multilayers were designed and studied. Random copolymers composed of pH-independent "strongly" charged parts and pH-dependent "weakly" charged parts were introduced for making pH-tunable polyelectrolyte complex and pH-responsive multilayers. A systematic study of the pH induced change of multilayer configuration, including film decomposition, phase separation and surface charge rearrangement, was conducted. It was found, by varying the mole percent of the weakly charged segments in the multilayers, the outcome of external pH changes on the multilayers varied from total film decomposition, to forming microporous surface, and finally to yielding a surface-charge-tunable multilayer, which meant the ability of controlling the surface charge polarity and density via pH. The outcome was essentially due to the combination of two types of charge interaction, charge extrusion and charge expulsion. It was also demonstrated that, with the use of the pH-responsive polyelectrolyte multilayer coatings to modify the substrate surface, the adsorption and release of biomaterials, such as proteins, could be controlled by varying the surface charge property via simple pH switch. Potential applications of this finding were proposed in the dissertation.
Show less
Date Issued: 2004
Identifier: FSU_migr_etd-0401
Format: Thesis

Title: Organic Synthesis and Methodology Related to the Malaria Drug Artemisinin.
Creator: Engel, Douglas Aaron, Dudley, Gregory B., Keller, Thomas, Krafft, Marie, Zhu, Lei, Strouse, Geoffery, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Malaria is a global epidemic, resulting in the deaths of nearly one million people every year. Part 1 of this dissertation will focus on the history of Malaria and ways to combat this devastating disease. Artemisinin has emerged as the drug of choice for treatment of malaria due to its effectiveness against all strains of the malaria parasite. Access to artemisinin through isolation, bio-engineering, and chemical synthesis will be described. Our attempts to access the artemisinin family of...
Show moreMalaria is a global epidemic, resulting in the deaths of nearly one million people every year. Part 1 of this dissertation will focus on the history of Malaria and ways to combat this devastating disease. Artemisinin has emerged as the drug of choice for treatment of malaria due to its effectiveness against all strains of the malaria parasite. Access to artemisinin through isolation, bio-engineering, and chemical synthesis will be described. Our attempts to access the artemisinin family of anti-malarials through the total synthesis of dihydro-epi-deoxyarteannuin B and dihydroartemisinic acid will be discussed fully. Key features of the syntheses will include alkylation of menthone derivatives using Noyori's zincate enolate method and nucleophilic addition to a hindered ketone using either organocerium or acetylide nucleophiles. In addition, two alternative olefin metathesis approaches are described for the final cyclization. Problems associated with the olefination of a key intermediate in our efforts toward dihydroartemisinic acid led us to develop a two-step olefination of ketones and aldehydes. Part II will discuss this olefination strategy which consists of acetylide addition to generate a propargyl alcohol followed by a Meyer-Schuster rearrangement to the corresponding α,β-enone. A complete history of the Meyer-Schuster rearrangement will be presented, highlighting the short comings of the method prior to our work. A complete overview of our research pertaining to the Meyer-Schuster reaction will be given. Key topics will include development of a Au(III)-catalyzed rearrangement of propargyl ethynyl ethers into α,β-unsaturated esters and its use in the olefination of hindered ketones, efforts to control the (E/Z)-selectivity of the Meyer-Schuster rearrangement, and the search for more affordable catalysts.
Show less
Date Issued: 2009
Identifier: FSU_migr_etd-0563
Format: Thesis

Title: Compositional Analysis of Complex Organic Mixtures by Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.
Creator: Wu, Zhigang, Marshall, Alan G., Landing, William M., Cooper, William T., Cross, Timothy A., Rodgers, Ryan P., Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has ultrahigh mass resolving power (m/Dm50% >300,000) and high mass accuracy (300,000) and high mass accuracy (ppm), which enables separation and identification of elemental compositions of complicated mixture. Electrospray ionization (ESI) provides selective ionization of polar heteroatomic compounds without chromatographic isolation. In addition, Kendrick mass plot is introduced in petrochemical analysis for an easy and...
Show moreFourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) has ultrahigh mass resolving power (m/Dm50% >300,000) and high mass accuracy (300,000) and high mass accuracy (ppm), which enables separation and identification of elemental compositions of complicated mixture. Electrospray ionization (ESI) provides selective ionization of polar heteroatomic compounds without chromatographic isolation. In addition, Kendrick mass plot is introduced in petrochemical analysis for an easy and fast data reduction. We first applied ESI FT-ICR mass spectrometry to the analysis of petrochemical samples like coal extracts and crude oils then extended this work into other complex mixtures, such as vegetable oils, hydrotreated fuels and military explosives. Detailed elemental compositions can be used as "fingerprint" to characterize each mixture sample. Three-dimensional van Krevelen diagram can be applied to characterize different fossil fuels. We demonstrate the great potential of ESI-FT-ICR MS in analysis of complex organic mixtures.
Show less
Date Issued: 2004
Identifier: FSU_migr_etd-0710
Format: Thesis

Title: Activation Profiles and Regulatory Cascades of the Human Kallikrein-Related Peptidases.
Creator: Yoon, Hyesook, Blaber, Michael, Tang, Hengli, Miller, Brian, Steinbock, Oliver, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: This work describes the activation profiles and regulatory cascades of the human kallikrein-related peptidases. The human kallikrein (KLK)-related peptidases are the largest family of serine peptidases, comprising 15 members (KLK1–15) and with the majority (KLK4–15) being identified only within the last decade. Members of this family are associated with important diseased states (including cancer, inflammation, and neurodegeneration) and have been utilized or proposed as clinically important...
Show moreThis work describes the activation profiles and regulatory cascades of the human kallikrein-related peptidases. The human kallikrein (KLK)-related peptidases are the largest family of serine peptidases, comprising 15 members (KLK1–15) and with the majority (KLK4–15) being identified only within the last decade. Members of this family are associated with important diseased states (including cancer, inflammation, and neurodegeneration) and have been utilized or proposed as clinically important biomarkers or therapeutic targets of interest. All human KLKs are synthesized as prepro-forms that are proteolytically processed to secreted pro-forms via the removal of an amino-terminal secretion signal peptide. The secreted inactive pro-KLKs are then activated extracellularly to mature peptidases by specific proteolytic release of their amino-terminal propeptide. Although a key step in the regulation of KLK function, details regarding the activation of the human pro-KLKs are unknown, to a significant extent, but have been postulated to involve "activation cascades" with other KLKs and endopeptidases. To characterize more completely the KLK activation cascades, an individual KLK propeptides fused to the amino terminus of a soluble carrier protein have been expressed from Escherichia coli. The ability of 14 different mature KLKs to process the 15 different pro-KLK peptide sequences has been determined. Various autolytic and cross activation relationships identified using this system have subsequently been characterized using recombinant pro-KLK proteins. The results demonstrate the potential for extensive KLK activation cascades and, when combined with available data for the tissue-specific expression of the KLK family, permit the construction of specific regulatory cascades. One such tissue-specific cascade is proposed for the central nervous system. Much recent work has been devoted to elucidating the potential for activation cascades between members of the KLK family, with physiologically relevant KLK regulatory cascades now described in skin desquamation and semen liquefaction. Despite this expanding knowledge of KLK regulation, details regarding the potential for functional intersection of KLKs with other regulatory proteases are essentially unknown. To elucidate such interaction potential, the ability of proteases associated with thromostasis to hydrolyze the pro-peptide sequences of the KLK family have been characterized, using the previously described (chapter 2) pro-KLK fusion protein system. A subset of positive hydrolysis results were subsequently quantified with proteolytic assays using intact recombinant pro-KLK proteins. The results show that proteases of the thrombostasis family can efficiently activate specific pro-KLKs, uncovering for the first time the potential for important regulatory interactions between these two major protease families. Proteases of the thrombostasis system are activated under conditions of injury, inflammation, and tissue remodeling, such as occurs in various disease states, including cancer. Activation of KLKs by thrombostasis proteases is therefore relevant for KLK activity in such diseases states.
Show less
Date Issued: 2008
Identifier: FSU_migr_etd-0712
Format: Thesis

Title: Autonomous and Guided Motion of Active Components at Interfaces.
Creator: Dhar, Prajnaparamita, Fischer, Thomas, Wiedenh¨over, Ingo, Steinbock, Oliver, Miller, Brian, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Nature presents active components in the form of proteins and molecular motors that are involved in locomotion and inter compartmental transport. Inspired by nature, this dissertation focuses on presenting experimental means to understand the motion of active components at interfaces. Active components are defined as components that either autonomously move or start to move in a viscous fluctuating environment. We investigate mechanisms by which energy may be converted into directed motion in...
Show moreNature presents active components in the form of proteins and molecular motors that are involved in locomotion and inter compartmental transport. Inspired by nature, this dissertation focuses on presenting experimental means to understand the motion of active components at interfaces. Active components are defined as components that either autonomously move or start to move in a viscous fluctuating environment. We investigate mechanisms by which energy may be converted into directed motion in case of synthetic nanomotors. Strategies for achieving guided motion along predetermined paths by overcoming fluctuations are explored. In addition we attempt to use dissipation in these systems to achieve guided motion at interfaces. Thus, this dissertation lays some of the foundations necessary for an understanding and smart design of synthetic motors.
Show less
Date Issued: 2008
Identifier: FSU_migr_etd-0746
Format: Thesis

Title: Deconvolution of Mobile Phase Contributions to Band Broadening in Reversed-Phase Liquid Chromatography.
Creator: Simmons, Carolyn Rebecca, Dorsey, John G., Locke, Bruce, Marshall, Alan G., Stiegman, Albert E., Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: High Performance Liquid Chromatography (HPLC) is the most widely used technique for the separation and identification of components in complex liquid samples. From groundwater to biological fluids, HPLC dependably provides efficient separations. Reversed-phase liquid chromatography (RPLC) has for the last several decades been the most popular mode of LC. The nonpolar stationary phase and adjustable polarity mobile phase of RPLC provide for simple optimization schemes and the ability to...
Show moreHigh Performance Liquid Chromatography (HPLC) is the most widely used technique for the separation and identification of components in complex liquid samples. From groundwater to biological fluids, HPLC dependably provides efficient separations. Reversed-phase liquid chromatography (RPLC) has for the last several decades been the most popular mode of LC. The nonpolar stationary phase and adjustable polarity mobile phase of RPLC provide for simple optimization schemes and the ability to separate both ionic and neutral compounds. In addition, the use of small stationary phase support particles and high pressure capabilities allows RPLC to provide the fast, efficient separations required by industrial users. More than a century has passed since the advent of liquid chromatography and since that time great advances have been made in the field. Regardless, there still remain unanswered questions to many fundamental problems associated with HPLC. One particular area of interest is band broadening. A sample band is injected onto the head of the column as a narrow pulse. Due to band broadening, the solute bands that elute are no longer narrow pulses, but rather Gaussian shaped peaks. The variance of the peaks essentially determines the peak capacity of the separation. HPLC users demand high throughput separations in a minimal amount of time, which becomes quite difficult when band broadening is excessive. What are the kinetic processes that cause the solute bands to disperse, and what can we do to prevent this detrimental occurrence? The work described in the following chapters attempts to answer these questions. Band broadening occurs due to molecular diffusion of the solutes, multiple paths available to the solutes through the packed bed, resistance to mass transfer of the solutes when partitioning into the stationary phase, and resistance to mass transfer through the mobile phase. It has been a topic of much debate as to whether the variance due to each process is independent of the others or if the effects should be coupled. The broadening taking place in the mobile phase is the topic of the following chapters. The columns in RPLC are typically packed with porous stationary phase support particles. Pressure-driven flow does not provide for convective velocity within the particle pores. As a result, the mobile phase becomes trapped and stagnant. There are conflicting views in the literature as to the magnitude of the broadening taking place in the stagnant mobile phase. It has been suggested that this source of broadening is insignificant and that the only way to reduce dispersion in the mobile phase is to redesign the interstitial region in a more ordered fashion. However, it is very unlikely that the two billion dollar a year HPLC industry will drastically change the existing internal architecture of the column without substantial experimental evidence. It was the purpose of this work to provide a quantitative assessment of how much of the broadening taking place in the mobile phase can be attributed to dispersion in the stagnant pore volume versus the interstitial regions. As a first attempt, the void volume measured by nonretained solutes was monitored over the flow rate range 0.1 to 3.0 mL/min. If the stagnant mobile phase caused a significant resistance to mass transfer, it was predicted that the measured volume would increase as the flow rate decreased. In other words, the solutes would have more time at the lower flow rates to diffuse through the stagnant mobile phase and thus measure a higher volume. The results of the study did not support this theory. The measured void volume remained constant over the flow rate range. Our next attempt to assess the stagnant mobile phase contribution to dispersion was to chromatographically isolate it from the broadening in the interstitial space. Low concentrations of ionic solutes experience electrostatic exclusion from the stationary phase pores in unbuffered mobile phases. NaNO3 was used as the probe solute for this study, because it is unretained on the reversed-phase surface. A high concentration of NaNO3 experienced dispersion as a result of both interstitial and stagnant mobile phase broadening. However, a low concentration did not sample the pore regions and was only affected by the interstitial dispersion. Using these solutes it was determined that the broadening taking place in the stagnant mobile phase was a significant source of dispersion, contributing 30-40% of the total mobile phase dispersion. These experiments were repeated on a nonporous reversed-phase column. Unfortunately, due to complications with the data analysis software, the instrument, and the column capacity this portion of the study did not further our understanding of mobile phase broadening. The final chapter of this work describes a study to determine which of the four most popular efficiency equations provides the best model for chromatographic plate height data. For more than fifty years, separations scientists have attempted to derive an equation to mathematically model band broadening contributions. Three of the most popular equations derived from theory are the equations of van Deemter, Giddings, and Horvath and Lin. The empirical Knox equation was also included in this study. Plate height data for benzene, toluene, ethylbenzene, propylbenzene, and butylbenzene were collected for four mobile phase compositions. The efficiency equations were fit to the data, and all four equations gave comparable fits. The Horvath and Lin equation consistently performed as well as or better than the others, while the Knox equation typically provided the worst fit to the data. An unexpected dependence of fit quality on retention factor k' was observed. The plate height data for solutes with k' values of approximately 3 provided the best fits to the four equations.
Show less
Date Issued: 2005
Identifier: FSU_migr_etd-0330
Format: Thesis

Title: Alternative Electrophiles in the Morita−Baylis−Hillman Reaction.
Creator: Seibert, Kimberly A., Krafft, Marie E., Cronin, J. Joseph, Holton, Robert A., Dudley, Gregory B., Goldsby, Kenneth, Department of Chemistry and Biochemistry, Florida State...
Show moreSeibert, Kimberly A., Krafft, Marie E., Cronin, J. Joseph, Holton, Robert A., Dudley, Gregory B., Goldsby, Kenneth, Department of Chemistry and Biochemistry, Florida State University
Show less
Abstract/Description: Discovering new carbon-carbon bond forming reactions is not only fundamental for the construction of organic molecular frameworks but is vital for the advancement of synthetic organic chemistry. The Morita–Baylis–Hillman reaction (MBH), dating back to both German and Japanese patents, is an organocatalytic three component reaction involving the coupling of the α-position of activated alkenes with carbon electrophiles under the catalytic influence of a nucleophilic species, providing a simple...
Show moreDiscovering new carbon-carbon bond forming reactions is not only fundamental for the construction of organic molecular frameworks but is vital for the advancement of synthetic organic chemistry. The Morita–Baylis–Hillman reaction (MBH), dating back to both German and Japanese patents, is an organocatalytic three component reaction involving the coupling of the α-position of activated alkenes with carbon electrophiles under the catalytic influence of a nucleophilic species, providing a simple and convenient method for the synthesis of densely functionalized molecules. The reaction mechanism is believed to proceed through a Michael type addition-elimination sequence in which the nucleophilic catalyst undergoes a reversible Michael-type nucleophilic addition to an activated alkene to form a zwitterionic enolate. Nucleophilic addition of this zwitterionic enolate to a carbonyl electrophile in an aldol fashion generated a second zwitterionic intermediate. Subsequent proton migration and release of the catalyst furnished the desired product. Although the Morita-Baylis-Hillman reaction was discovered in the late 1960's, it was not until the early 1980's when researchers began to study this reaction more thoroughly. Since then, the intermolecular Morita-Baylis-Hillman reaction has seen an exponential growth in terms of all three essential components and now encompasses a wide variety of activated alkenes, electrophiles and nucleophilic catalysts. However there has been significantly less research into the intramolecular Morita-Baylis-Hillman reaction. This, coupled with the fact that simple allylic electrophiles or unactivated alkyl halides have not been used as the electrophilic partner in this intriguing reaction, has influenced my research, which is aimed at extending the scope of the intramolecular Morita-Baylis-Hillman reaction with particular interest to using new electrophiles. Recently Krafft and Haxell reported a Morita-Baylis-Hillman reaction using allylic chlorides as the electrophilic partner. It occurred to us that a natural extension of this work was to explore the feasibility of the related cycloalkylation chemistry using sp3-hybridized electrophiles. We have successfully developed a novel, entirely organomediated, one-pot convenient method for the synthesis of cyclic enones through the use of an alternative electrophile in the Morita-Baylis-Hillman reaction. The method tolerates both alkyl- and aryl-enones with and without various substitution patterns on the tether to generate five- and six-membered rings in excellent yields. We have further expanded the method to proceed using only catalytic amounts of the tributylphosphine nucleophile with little to no reduction in yields. We have extended this reaction to include thioesters as viable activated alkenes providing the cyclized MBH adducts in good to excellent yields. We have further shown the thioester substrates to form the desired products when a catalytic amount of PBu3 is employed. Additionally, we have isolated for the first time a Morita-Baylis-Hillman intermediate exhibiting an unprecedented trans-geometry of the positively charged phosphorous and negatively charged oxygen. Our results suggested the interaction of the oxygen and phosphorous, which has been long understood to provide stabilization for the intermediate, is not a requirement for a successful MBH alkylation providing new insight into the Morita-Baylis-Hillman mechanism.
Show less
Date Issued: 2007
Identifier: FSU_migr_etd-0281
Format: Thesis

Title: Preparing Packed Capillaries for Use in Capillary Electrochromatography: Studies of Mobility, Dispersion, and Reproducibility.
Creator: Piraino, Stephanie M., Dorsey, John G., Dorsey, Jodee, Vickers, Thomas, Stiegman, Albert, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Packing capillaries for use in Capillary Electrochromatography (CEC) is described in detail. Qualitative observations regarding the general packing procedure are elucidated. Because forming frits to retain the stationary phase is one of the greatest challenges regarding the fabrication of packed capillaries, the performance of several types of frits including sintered frits, photopolymerized frits, and frits made by sol- gel technologies is evaluated. The frits are formed in open capillaries,...
Show morePacking capillaries for use in Capillary Electrochromatography (CEC) is described in detail. Qualitative observations regarding the general packing procedure are elucidated. Because forming frits to retain the stationary phase is one of the greatest challenges regarding the fabrication of packed capillaries, the performance of several types of frits including sintered frits, photopolymerized frits, and frits made by sol- gel technologies is evaluated. The frits are formed in open capillaries, and the electroosmotic mobilities are calculated and compared to those obtained in an open capillary. Run-to-run, day-to-day, and column- to-column reproducibilities are evaluated. In all cases, the run-to-run reproducibility varied by less than 4%. The greatest mobility was through the capillaries with the sol- gel frits (1.29 x 10-3 cm2/V·s) which also exhibited the best day-to-day reproducibility. The capillaries with the photopolymerized frits had the best column-tocolumn reproducibility yet the slowest mobility (1.00 x 10-3 cm2/V·s). The second central moment of benzene as a solute is calculated and plotted as a function of time to estimate the differences in peak dispersion among the various frits studied. Although the mobilities through the capillaries with the sintered frits were the most irreproducible, these frits are associated with the least amount of band broadening. As the sintered frits are the most common type of frit used for CEC, modifications to the equipment used to sinter the frits were made in an effort to make more reproducible and reliable sintered frits. The revisions made to the frit heater include the use of a transformer to vary the voltage, a nichrome ribbon to generate smaller frits, and a thermocouple to estimate the temperature while heating the capillary. The band broadening of an uncharged solute was measured as a function of sintering times and temperatures to calculate the amount of heat used to sinter the frits. It was determined that more homogeneous frits were made as more heat was applied to sinter the frit, resulting in less dispersion.
Show less
Date Issued: 2003
Identifier: FSU_migr_etd-0674
Format: Thesis

Title: The 3D Solution Structure of the C Terminal Domain of Diphtheria Toxin Repressor: in the Free and Bound Forms.
Creator: Wylie, George P., Logan, Timothy M., Fajer, Piotr G., Blaber, Michael, Dalal, Naresh, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Diphtheria toxin repressor protein (DtxR) is a 226 amino acid protein that regulates the genes for iron uptake in Corynebacterium diphtheria and also regulates the Diphtheria toxin production. The known functions of this protein include binding divalent metals, dimerazation, and DNA binding. All these functions are accounted for by the N terminal domain of the protein. The C terminal domain was not well defined in early crystal structures but by 2000 both crystallography and NMR agreed that...
Show moreDiphtheria toxin repressor protein (DtxR) is a 226 amino acid protein that regulates the genes for iron uptake in Corynebacterium diphtheria and also regulates the Diphtheria toxin production. The known functions of this protein include binding divalent metals, dimerazation, and DNA binding. All these functions are accounted for by the N terminal domain of the protein. The C terminal domain was not well defined in early crystal structures but by 2000 both crystallography and NMR agreed that the C terminal domain has an SH3 like fold. This has led us to investigate the possible role of the C terminal domain as a "switch" for the activation of DtxR. We propose that the C terminal domain binds to the linker between the N and C terminal domains of this protein and stabilizes the monomeric form of DtxR. Once this region is released by the C terminal domain the N terminal domain most have some sort of "folding event" then metal is bound and dimerazation can take place. To investigate the mechanism of binding to this linker region by the C terminal domain two protein constructs were made one from residues D144-L226 and the other from D110-L226. The first construct would be the Free form and the second would be the bound form thus given us insight into the mechanism of binding. Here the 3D solution structures of these two domains and a comparison is presented.
Show less
Date Issued: 2003
Identifier: FSU_migr_etd-0689
Format: Thesis

Title: Use of Inorganic Quantum Dot-Cationic Liposome Hybrids for the Delivery and Expression of Calcium-Sequestering Parvalbumin into Mammalian Cell Cultures.
Creator: Ellis, Charles Christian, Strouse, Geoffrey, Logan, Timothy, Li, Hong, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Left Ventricular Diastolic Dysfunction is one of the main causes of Heart Failure. It is caused by a defect in the relaxation of cardiac muscle usually as the result of failure of the heart cells to remove cytoplasmic Ca2+ following muscle contraction. This defect is corrected by the presence of Ca2+ sequestering Parvalbumin Major Isoform I (Parvalbumin), a naturally occurring soluble protein in skeletal muscle, which then binds free Ca2+, resulting in increased rates of diastolic relaxation....
Show moreLeft Ventricular Diastolic Dysfunction is one of the main causes of Heart Failure. It is caused by a defect in the relaxation of cardiac muscle usually as the result of failure of the heart cells to remove cytoplasmic Ca2+ following muscle contraction. This defect is corrected by the presence of Ca2+ sequestering Parvalbumin Major Isoform I (Parvalbumin), a naturally occurring soluble protein in skeletal muscle, which then binds free Ca2+, resulting in increased rates of diastolic relaxation. Since Parvalbumin does not naturally occur in cardiac tissue, ectopic expression through gene therapy provides a vehicle to deliver the gene needed to express this therapeutic protein. This has been accomplished by others using viral vectors but due to the problems associated with viral delivery, non-viral delivery methods are becoming more popular. Cationic Liposomes are a commonly used non-viral method of gene delivery and due to their physical and chemical properties inorganic nano-particles are attracting much interest in the field as well. It is the aim of this research to investigate whether cationic liposomes containing organic-phase fluorescent CdSe/ZnS quantum dots can be used as an efficient method of gene delivery into mammalian cells with built-in optical tracers. Organic-phase CdSe/ZnS was synthesized, purified and encapsulated into liposomes using various ratios of 1,2 – dioleoyl – 3 – trimethylammonium – propane (DOTAP), 1,2 – dioleoyl – sn – glycero – 3 – phosphoethanolamine (DOPE), Cholesterol and 3β – [N – (N', N' – dimethylaminoethan) – carbamoyl] cholesterol (DC-Chol) and used to deliver circular plasmid DNA coding for a Parvalbumin-mCherry fusion protein into Chinese Hamster Ovary (CHO) cells. We are able to show that using this system of cationic liposome-quantum dot hybrids we are able to deliver and express the target gene.
Show less
Date Issued: 2010
Identifier: FSU_migr_etd-0571
Format: Thesis

Title: New Strategies for Proteomics and Peptidomics Using Polymer Liquid Crystals for Electrophoresis.
Creator: Al-Sayah, Mohammad Ahmed, Rill, Randolph L., Winkle, David H. Van, Dorsey, John G., Schlenoff, Joseph B., Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Different gel matrices were explored to extend the use of two dimensional (2D) gel electrophoresis for peptide analysis. Excellent separations of peptides labeled with the fluorescent dye Cascade Yellow were achieved in one dimension on two gel media: traditional polyacrylamide and reversible liquid crystalline gels of Pluronic F127. Separations on both media depended primarily on size to charge ratio, excepting a few peptides strongly retained by Pluronic F127. A unique 2D gel...
Show moreDifferent gel matrices were explored to extend the use of two dimensional (2D) gel electrophoresis for peptide analysis. Excellent separations of peptides labeled with the fluorescent dye Cascade Yellow were achieved in one dimension on two gel media: traditional polyacrylamide and reversible liquid crystalline gels of Pluronic F127. Separations on both media depended primarily on size to charge ratio, excepting a few peptides strongly retained by Pluronic F127. A unique 2D gel electrophoresis system for peptide separation coupled with MALDI-TOF mass spectrometry for identification was developed. Cascade Yellow succinimidyl ester, an amine-reactive dye, labels the amino-terminus of peptides and the å-amino group of lysines at pH 7-9. Occasional labeling of tyrosine residues was also observed. Specific amino-terminal labeling was achieved at alkaline pH (pH >10) due to the base-lability of the å-amino and the tyrosine adducts. The 2D system utilized 15% polyacrylamide with the basic (pH 8.3) Laemmli buffer system (without SDS) in the first dimension. Pluronic F127 (24%) was used in the second dimension with acidic Tris-ClCH2COOH buffer (pH 3.0). The second dimension in Pluronic F127 was done horizontally with a thin overlayer of buffer to provide direct access to the separated peptides. Due to its semi-fluid nature, Pluronic F127 provided a good interface between the two dimensions so that the peptides migrated smoothly from the first dimension to the second. The peak capacity of the 2D mini-gel system (8x10 cm) was approximately 500. Larger gels are expected to yield a peak capacity of about 2000, competitive with many 2D HPLC methods. MALDI-TOF MS was used to identify peptides in spots directly sipped from gels. Peptide samples with concentrations > 0.5 ìg/ml were directly spotted on MALDI targets and identified without further purification. Small polymer chains contaminating Pluronic F127 started to interfere with the detection of peptides at concentrations 10) due to the base-lability of the å-amino and the tyrosine adducts. The 2D system utilized 15% polyacrylamide with the basic (pH 8.3) Laemmli buffer system (without SDS) in the first dimension. Pluronic F127 (24%) was used in the second dimension with acidic Tris-ClCH2COOH buffer (pH 3.0). The second dimension in Pluronic F127 was done horizontally with a thin overlayer of buffer to provide direct access to the separated peptides. Due to its semi-fluid nature, Pluronic F127 provided a good interface between the two dimensions so that the peptides migrated smoothly from the first dimension to the second. The peak capacity of the 2D mini-gel system (8x10 cm) was approximately 500. Larger gels are expected to yield a peak capacity of about 2000, competitive with many 2D HPLC methods. MALDI-TOF MS was used to identify peptides in spots directly sipped from gels. Peptide samples with concentrations > 0.5 ìg/ml were directly spotted on MALDI targets and identified without further purification. Small polymer chains contaminating Pluronic F127 started to interfere with the detection of peptides at concentrations 0.5 ìg/ml were directly spotted on MALDI targets and identified without further purification. Small polymer chains contaminating Pluronic F127 started to interfere with the detection of peptides at concentrations
Show less
Date Issued: 2004
Identifier: FSU_migr_etd-0025
Format: Thesis

Title: Synthesis and Physical Characterization of Biocompatible Hydrogels.
Creator: Campbell, Tedric Dewayne, Steinbock, Oliver, Trombley, Paul Q., Fulton, Robert L., Stiegman, Albert E., Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Polymers are a group of materials composed of molecules which have long sequences of atoms linked to each other by covalent bonds. They have existed in natural forms since life began; however, in 1910 Leo Baekeland produced bakelite, a phenolformaldehyde resin, which became the first commercialized fully-synthetic polymer. Nevertheless, it took another decade for scientists to truly accept the unusual properties of polymers as well as the forces that accompany them. The attractive forces...
Show morePolymers are a group of materials composed of molecules which have long sequences of atoms linked to each other by covalent bonds. They have existed in natural forms since life began; however, in 1910 Leo Baekeland produced bakelite, a phenolformaldehyde resin, which became the first commercialized fully-synthetic polymer. Nevertheless, it took another decade for scientists to truly accept the unusual properties of polymers as well as the forces that accompany them. The attractive forces between polymer chains play a large part in determining the polymer's properties. Because polymer chains are so long, these inter-chain forces are amplified far beyond the attractions between conventional molecules. In addition, the more entangled and elongated the chains are, the more amorphous is the polymer. Polymer chain length can be attributed to the monomer content within its structure. If the monomer is able to polymerize with a crosslinking agent, then this new macromolecule can be referred to as a gel. The gel is a semi-rigid mass of a lyophilic sol in which all the dispersion medium has penetrated into the sol particles. A particular class of gels, hydrogels, are hydrophilic polymer networks, which can take up large volumes of water and swell while retaining their shape. These materials are usually formed by radical polymerization of hydrophilic monomers and cross-linkers that dissolve in aqueous medium. The cross-linker can be a bifunctional monomer forming a network during polymerization. Depending on the particular chemical structure, these swollen networks display different properties due to external stimulation. The goal of this dissertation is the preparation of poly [N-(2-hydroxypropyl) methacrylamide] (PHPMA) hydrogels in which the typically random polymer network is altered to arrays of parallel channels. One particular application is to use the PHPMA hydrogels as templates for nerve cells. Ideally, the diameter of these channels should match the archetypal diameter of neuronal cell bodies or axons in order to provide a maximal internal surface area. With that aim in mind, we devised and optimized an experimental technique in which a modified HPMA-pregel solution is polymerized and cross-linked in the presence of an externally applied electric field. In addition, the effects of the porogen, polyethylene glycol, on the efficacy of channel formation, swelling dynamics, and the mechanical and structural characteristics of the resulting material are investigated. In conjunction with the aforementioned goal, we also functionalized the PHPMA hydrogels by incorporating Poly-L-Lysine into the polymer matrix. Poly-L-Lysine, a highly positively charged amino acid chain, is commonly used as a coating agent to promote cell adhesion in culture. Poly-L-Lysine will be used as a subbing solution in the biocompatible scaffolds that will serve as a host for mammalian olfactory bulb neurons. The research outlined above represents the major focus of this dissertation. The long-term goal was to enhance prosthetics in the area of biomedical engineering. Moreover, the dissertation is complemented by the description of two minor projects that (a) describe the creation of a mesoporous silica monolith containing oriented macroporous channels and (b) document light-scattering measurements of Belousov-Zhabotinsky(BZ) solutions in sodium bis (2-ethylhexyl) sulfosuccinate(AOT) water-in-oil microemulsions. The latter data should be helpful for understanding non-equilibrium Turing patterns in BZ-AOT systems.
Show less
Date Issued: 2007
Identifier: FSU_migr_etd-0068
Format: Thesis

Title: Exploration of Poly(Ethylene Glycol) Oligomers as Ion Exchange Media for Porous and Layered Oxides.
Creator: Canfield, Gina Marie, Latturner, Susan E., Locke, Bruce R., Stiegman, Albert E., Dalal, Naresh, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Zeolite structures consist of a negatively charged, porous, aluminosilicate framework with the ability to ion exchange its charge balancing cations. However, problems associated with traditional methods of aqueous ion exchange can adversely affect the behavior and the industrial quality of these zeolites. In this work, an alternative to traditional ion exchange media was explored. Poly ethylene glycol (PEG) oligomers are known to dissolve and transport cations; therefore it was theorized that...
Show moreZeolite structures consist of a negatively charged, porous, aluminosilicate framework with the ability to ion exchange its charge balancing cations. However, problems associated with traditional methods of aqueous ion exchange can adversely affect the behavior and the industrial quality of these zeolites. In this work, an alternative to traditional ion exchange media was explored. Poly ethylene glycol (PEG) oligomers are known to dissolve and transport cations; therefore it was theorized that these solvents could be used to mobilize and exchange ions into zeolite structures. The theory was first tested with the ion exchange of Li+ for Na+ into hydrated and dehydrated sodalite using a series of PEG oligomers with different chain lengths and end groups. The outstanding results from this phase of work, with over 90% Li ion exchange, prompted its continuation with the exchange of catalytically active transition metal ions (Mn2+, Fe2+, and Co2+) into hydrated and dehydrated Zeolite X. Use of these oligomer solvents helped maintain the zeolite structure and allowed for a maximum of 91% ion exchange under hydrated conditions. Although more extensive oligomer incorporation under dehydrated conditions allowed for only 6% exchange, the catalytic activity of these samples was vastly improved over traditionally exchanged samples. The maximum turnover frequency of dehydrated Mn oligomer exchanged samples toward decomposition of NO was 2.37 x 10-2 s-1, whereas that of hydrated Mn aqueous exchanged samples was 9.67 x 10-4 s-1. Parallel ion exchange experiments involving luminescent rare earth metals (Nd3+ and Er3+) gave similar positive results. In addition, data from Raman spectroscopy indicated that while the aqueous exchange method promoted rare earth framework substitution, the oligomer solvents maintained exchange into the zeolite cages. The optimal conditions provided by the oligomer exchange method allowed for improved luminescence of the RE ions. Given its success, this method has been extended to the ion exchange of layered oxides, such as perovskites and cobaltates. Although this work has just begun, promising initial data indicate the possibility of continuing this work far into the future.
Show less
Date Issued: 2009
Identifier: FSU_migr_etd-0096
Format: Thesis

Title: 5-Endo-Dig Cyclization of a Carbon-Centered Radical and Utility of Cyclopentene Bromosulfone Product.
Creator: Abrams, Jason Nathaniel, Alabugin, Igor, Landing, William, Dudley, Gregory, Miller, Brian, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: The Baldwin rules provide a robust guideline for predicting the favorability of ring closure of reactive intermediates based upon stereoelectronic considerations. Our group was intrigued by the lack of examples of 5-endo-dig cyclizations with carbon-centered radicals, particularly because these reactions were suggested to be favorable according to the Baldwin rules and to our previous computational investigations using density functional analysis. We therefore set out to fill the gap in the...
Show moreThe Baldwin rules provide a robust guideline for predicting the favorability of ring closure of reactive intermediates based upon stereoelectronic considerations. Our group was intrigued by the lack of examples of 5-endo-dig cyclizations with carbon-centered radicals, particularly because these reactions were suggested to be favorable according to the Baldwin rules and to our previous computational investigations using density functional analysis. We therefore set out to fill the gap in the arsenal of radical C-C bond forming processes by using computational data to design a new radical process. The first part of this thesis describes our studies aimed at the discovery of the first efficient 5-endo-dig cyclization of a carbon-centered radical. This is followed by experimental design and synthesis of substrates and finally reaction conditions which yield products through this novel mode of cyclization. The second part of this thesis explores the synthetic utility of the cyclized cyclopentene bromosulfone products. First, background information for the preparation and utility of vinyl sulfones is provided. This is followed by our results for derivatization of the bromide functional group of our cyclopentene bromosulfone products. Proper design of substrates and reaction conditions has allowed the 5-endo-dig radical cyclizations to finally become an experimental reality after more than forty years since the original prediction. The cyclized products which are enriched with functionality have been transformed into a variety of other products, emphasizing the importance of this discovery.
Show less
Date Issued: 2009
Identifier: FSU_migr_etd-0105
Format: Thesis

Title: Characterization of Subcritical Water as a Chromatographic Mobile Phase in Reversed-Phase Liquid Chromatography.
Creator: Allmon, Steven D., Dorsey, John G., Sathe, Shridhar, Striegel, André M., Roper, Michael G., Steinbock, Oliver, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Liquid chromatography, particularly reversed-phase liquid chromatography (RPLC), is a ubiquitous analytical method throughout various industries. It has proven vital to the regulatory framework of agencies worldwide to ensure product quality and safety. With traditional RPLC, organic modifiers (e.g. acetonitrile, methanol, tetrahydrofuran) are generally used in conjunction with water to form a mobile phase with sufficient eluotropic strength to elute analytes of interest from the...
Show moreLiquid chromatography, particularly reversed-phase liquid chromatography (RPLC), is a ubiquitous analytical method throughout various industries. It has proven vital to the regulatory framework of agencies worldwide to ensure product quality and safety. With traditional RPLC, organic modifiers (e.g. acetonitrile, methanol, tetrahydrofuran) are generally used in conjunction with water to form a mobile phase with sufficient eluotropic strength to elute analytes of interest from the chromatographic stationary phase to the detector employed for the liquid chromatography system. The organic modifiers used are costly as the analyst must pay not only to procure them but also to safely dispose of them. Additionally, the organic modifiers are usually toxic and flammable. The use of 100% water as a chromatographic mobile phase would present an attractive alternative, however, ambient water is far too polar in most instances to be of much use as a mobile phase for RPLC. Subcritical water, considered in the present work to be water at a temperature greater than 100°C with sufficient pressure applied to keep it within the liquid state (but still below the supercritical point), has been proposed as an alternative to traditional organic modifiers due to the apparent similarities in polarity between subcritical water and traditional organic modifiers. The present work explores the differences between RPLC using subcritical water and traditional organic modifiers. Thermodynamic data presented indicates that there are differences in the analyte retention process between the two systems. Retention in subcritical water is characterized by large, favorable enthalpy of transfer values and unfavorable entropic constributions to retention. Traditional RPLC shows favorable (to a lesser degree) enthalpic contributions to retention with negligible or not as unfavorable entropic contributions to retention. From the thermodynamic data, as well as subsequent linear solvation energy relationship analysis, the differences are attributed primarily to a large disruption in the hydrogen bonding network in water at elevated temperature, as well as the lack of sorbed organic modifier in the stationary phase (increasing dispersive interactions of the analyte with the stationary phase) when using 100% subcritical water as a mobile phase. Selectivity for a shape-constrained analytes is also shown to decrease when using subcritical water mobile phases, likely due to a decrease in conformational ordering of the stationary phase at elevated temperatures. Reduced ordering of the stationary phase coupled with an unfavorable entropy change upon retention also strongly suggests that a significant amount of disordering occurs in the pure water mobile phase at elevated temperatures. Later studies were aimed at estimating the retention factor in pure water, k'w, using a high temperature to low temperature extrapolation. Analysis of the results of this study revealed such an extrapolation is not comparable to the more traditional organic modifier fraction extrapolation to 100% water due to an underestimation of the hydrogen bond donating ability of the subcritical water system during the extrapolation. Finally, subcritical water as an extractions solvent with subsequent analyte focusing is explored. It is shown that it is feasible to re-focus a chromatographic peak using the unique properties of subcritical water with very modest instrumentation. Additionally, differences in effective selectivity were demonstrated resulting from on-column migration of the focused peak. Potential applications of this technique are also discussed.
Show less
Date Issued: 2010
Identifier: FSU_migr_etd-0176
Format: Thesis

Title: The Active Site Cysteine of Arginine Kinase: Structural and Functional Analysis of Partially Active Mutants.
Creator: Gattis, James L., Chapman, Michael, Ellington, W. Ross, Blaber, Michael, Cross, Timothy, Marshall, Alan, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Arginine kinase buffers cellular ATP levels by catalyzing reversible phosphoryl transfer between ATP and arginine. A conserved cysteine has long been thought important in catalysis. Here, cysteine 271 of horseshoe crab arginine kinase has been mutated to serine, alanine, asparagine, or aspartate. Catalytic turnover rates were 0.02-1.0% of wild type, but the activity of uncharged mutations could be partially rescued with chloride. Steady state binding constants were slightly increased, more so...
Show moreArginine kinase buffers cellular ATP levels by catalyzing reversible phosphoryl transfer between ATP and arginine. A conserved cysteine has long been thought important in catalysis. Here, cysteine 271 of horseshoe crab arginine kinase has been mutated to serine, alanine, asparagine, or aspartate. Catalytic turnover rates were 0.02-1.0% of wild type, but the activity of uncharged mutations could be partially rescued with chloride. Steady state binding constants were slightly increased, more so for phospho-L-arginine than ADP. Substrate binding synergy observed in many phosphagen kinases was reduced or eliminated in mutant enzymes. The crystallographic structure of the alanine mutant at 2.3Å resolution, determined as a transition state analog complex with arginine, nitrate, and MgADP, was nearly identical to wild-type. Enzyme–substrate interactions are maintained as in wild-type, and substrates remain at least roughly aligned for in-line phosphoryl transfer. Homology models with serine, asparagine, or aspartate replacing the active site cysteine similarly show only minor structural changes. Most striking, however, is the presence in the C271A mutant crystallographic structure of a chloride ion within 3.5Å of the non-reactive Nη substrate nitrogen, approximating the position of the sulfur in the wild-type's cysteine. Together the results contradict prevailing speculation that the cysteine mediates a substrate-induced conformational change, confirm that it is the thiolate form that is relevant to catalysis, and suggest that one of its roles is to help enhance the catalytic rate through electrostatic stabilization of the transition state.
Show less
Date Issued: 2004
Identifier: FSU_migr_etd-0137
Format: Thesis

Title: Reaction Discovery Using Neopentylene-Tethered Coupling Partners: Methodology and Applications of Dienyne Cycloisomerizations.
Creator: Kramer, Nicholas J. James, Dudley, Gregory B., Frederich, James H., Fadool, James M., Alabugin, Igor V., Shatruk, Mykhailo, Florida State University, College of Arts and...
Show moreKramer, Nicholas J. James, Dudley, Gregory B., Frederich, James H., Fadool, James M., Alabugin, Igor V., Shatruk, Mykhailo, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Within the past few decades, metal-catalysis has emerged as a key facet in synthetic organic chemistry, perpetuating a continuous need for the development of methods within this sect of chemistry. In tandem, cycloisomerization reactions of tethered enynes have garnered considerable interest as emphasis on annulation strategies to access polycyclic systems becomes necessary for the generation of important bioactive structures. Driven by both methodological and total synthesis applications,...
Show moreWithin the past few decades, metal-catalysis has emerged as a key facet in synthetic organic chemistry, perpetuating a continuous need for the development of methods within this sect of chemistry. In tandem, cycloisomerization reactions of tethered enynes have garnered considerable interest as emphasis on annulation strategies to access polycyclic systems becomes necessary for the generation of important bioactive structures. Driven by both methodological and total synthesis applications, metal-catalyzed cycloisomerizations remain at the forefront of interest for effective atom-economic reactions. We have identified a strategic gap in the methodology of 1,6-enyne cycloisomerizations bearing heteroatom, methylene, and malonate tethers. Herein will be described a method for the [4 + 2] formal Diels-Alder cycloisomerization of neopentylene-tethered dienynes, closing the gap previously mentioned and highlighting a valuable reactivity profile of this new tether. Also demonstrated is significant progress in the Diels-Alder cyclization of electron-deficient dienynes, for which the literature has shown to be relatively unexplored, presumably due to the apparent poor reactivity of these substrates. Further investigation into isolation of the [4 + 2] Diels-Alder products as well as elaboration on the previously published fragmentation/olefination methodology is included in this manuscript. Using these effective annulation strategies developed in our lab, we have sought to gain access to sesquiterpene natural products of particular interest bearing the gem-dimethylcyclopentane, an extension of the indane core. These methods have been employed in a six-step total synthesis of Alcyopterosin A and in the efforts toward the synthesis of Fomajorin D.
Show less
Date Issued: 2017
Identifier: FSU_FALL2017_Kramer_fsu_0071E_14204
Format: Thesis

Title: Understanding Magnetic Exchange Behavior in Core@Shell Nanoparticles.
Creator: Carnevale, David J. (David John), Shatruk, Mykhailo, Strouse, Geoffrey F., Xiong, Peng, Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department...
Show moreCarnevale, David J. (David John), Shatruk, Mykhailo, Strouse, Geoffrey F., Xiong, Peng, Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: As green technology advances, the need for cheaper, stronger permanent magnets becomes more and more vital everyday. Electric motors, like those used in wind turbines and electric cars, rely heavily on Dy doped Nd2Fe14B in order to achieve the required efficiencies to be successful, however both Nd and Dy are expensive rare-earth elements that the field is trying to move away from relying on. In order to approach this issue, many are trying to combine these powerful permanent magnets with...
Show moreAs green technology advances, the need for cheaper, stronger permanent magnets becomes more and more vital everyday. Electric motors, like those used in wind turbines and electric cars, rely heavily on Dy doped Nd2Fe14B in order to achieve the required efficiencies to be successful, however both Nd and Dy are expensive rare-earth elements that the field is trying to move away from relying on. In order to approach this issue, many are trying to combine these powerful permanent magnets with cheaper and more abundant soft magnetic materials in order to create exchange-spring magnets. While exchange coupling behavior has been studied for several decades now, there are major issues with controlling the uniformity in the generated materials leading to a limited understanding of the properties of these assemblies. In order to address both of these issues at the same time, we devised an approach to create a hard magnetic nanoparticle of fcc-FePt, which was then shelled with the soft magnet Co. In order to gain the desired control of the final core@shell particles, a mix and round bottom and microwave heating was utilized, the synthetic details of which are laid out in Chapter 2. Chapter 3 lays out the results from applying a layer-by-layer shell of Co onto a constant 5 nm FePt particle. From this shelling, the transition from hard-exchange to exchange-spring to decoupling of the core@shell system can be observed. The limit of these regions were found to be very small, with the hard-exchange regime only being in the case of shell sizes smaller than 1.4 nm and decoupling occurring in the materials with >2nm of Co shelled on. This limited range is due to cobalt’s short range coupling, which can not support strong coupling beyond 3-4 layers of Co.
Show less
Date Issued: 2017
Identifier: FSU_FALL2017_Carnevale_fsu_0071E_14044
Format: Thesis

Title: Quantum Chemical Methods and Algorithms for Ground and Excited Electronic States.
Creator: Nascimento, Daniel R. (Daniel Ricardo), DePrince, A. Eugene (Albert Eugene), Shanbhag, Sachin, Dalal, Naresh S., Steinbock, Oliver, Florida State University, College of Arts and...
Show moreNascimento, Daniel R. (Daniel Ricardo), DePrince, A. Eugene (Albert Eugene), Shanbhag, Sachin, Dalal, Naresh S., Steinbock, Oliver, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: In this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute high-accuracy ground and excited electronic states. Chapters 1 and 2 should be seen as introductory Chapters, where the mathematical foundations of modern electronic structure theory necessary to understand this work are laid down. Chapters 3 and 4 covers the development of methods and algorithms relevant to ground state computations. We propose a semi-definite...
Show moreIn this dissertation, we address some of the needs faced in the development of modern ab initio quantum chemical methods to compute high-accuracy ground and excited electronic states. Chapters 1 and 2 should be seen as introductory Chapters, where the mathematical foundations of modern electronic structure theory necessary to understand this work are laid down. Chapters 3 and 4 covers the development of methods and algorithms relevant to ground state computations. We propose a semi-definite-based algorithm to compute ground-state Hartree-Fock energies and wave functions, that can be easily extended to Kohn-Sham density functional theory. We also propose a parametrized coupled-pair functional to compute accurate non-covalent molecular interaction energies. Chapters 3 through 7 cover methods relevant to excited state computations. We propose an explicitly time-dependent coupled-cluster framework rooted on the equation-of-motion formalism to compute linear absorption spectra of molecular systems. The method is further expanded by recasting a linear absorption line shape function in terms of Pad ́e approximants. The expanded method is shown to be an efficient tool for the simulation of near-edge X-ray absorption fine structure. Finally, we propose a time-dependent Hartree-Fock method within the framework of cavity quantum-electrodynamics that allows us to simulate the interaction of molecular systems with quantized radiation fields, such as those found on plasmonic nanoparticles and nano cavities.
Show less
Date Issued: 2017
Identifier: FSU_FALL2017_Nascimento_fsu_0071E_14251
Format: Thesis

Title: Tuning the Emission and Quantum Yield of Gold and Silver Nanoclusters through Ligand Design and Doping.
Creator: Mishra, Dinesh, Mattoussi, Hedi, Xiong, Peng, Alabugin, Igor V., Shatruk, Mykhailo, Strouse, Geoffrey F., Florida State University, College of Arts and Sciences, Department of...
Show moreMishra, Dinesh, Mattoussi, Hedi, Xiong, Peng, Alabugin, Igor V., Shatruk, Mykhailo, Strouse, Geoffrey F., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Nanoparticles have been extensively studied in the past few decades due to the possibilities they offer in applications ranging from medicine to energy generation. A new class of ultra-small noble metal nanoparticles consisting of tens to hundreds of atoms, commonly known as clusters or nanoclusters, have drawn interest of the research community recently due to their unique optical, electronic and structural properties. Over the past few years, advances have been made in the synthesis of...
Show moreNanoparticles have been extensively studied in the past few decades due to the possibilities they offer in applications ranging from medicine to energy generation. A new class of ultra-small noble metal nanoparticles consisting of tens to hundreds of atoms, commonly known as clusters or nanoclusters, have drawn interest of the research community recently due to their unique optical, electronic and structural properties. Over the past few years, advances have been made in the synthesis of atomically precise noble metal clusters (for example, silver and gold) with distinct optical properties. Their ultra-small size distinguishes them from conventional plasmonic nanoparticles and the properties are very sensitive to the slight variation in the compositon of the cluster, i.e. the number of the metal atoms and/or the nature of the ligands. These clusters are interesting because of their potential applications in field such as sensing, imaging, catalysis, clean energy, photonics, etc. as well as they provide fundamental insight into the evolution of the optical and electronic properties of these clusters. In this project, we explored the strategies to synthesize luminescent metallic clusters of gold and silver and to promote their solubility and stability in aqueous and biological medium. We focused particularly on the thiolate protected clusters due to the higher affinity of gold and silver to sulfur. Lipoic acid (Thioctic acid) is a bio-molecule with a cyclic disulfide ring, which also acts as a chelating ligand. Due to the higher binding affinity of the cyclic disulfide ring to nanocrystal surface, lipoic acid and chemically modified lipoic acid molecules have been widely reported for the synthesis and functionalization of inorganic nanocrystals. Here, we describe the use of bidentate lipoic acid ligands in the one phase growth of luminescent gold and silver nanoclusters. In addition, we have synthesized a new set of monothiol ligands containing PEG and zwitterion for the functionalization of fluorescent clusters. Chapter 1 introduces the fundamental properties of metallic clusters and the origin of these properties from electronic and structural point of view. The optical properties of ultra-small nanocrystals (<2 nm) in comparison to the plasmonic particles is described. In addition, the variation of optical and structural properties from one metal to another as well as one ligand to another is also compared. Chapter 2 describes the synthesis of ultra-small size gold clusters with different optical emission (ranging from blue to red) using photo-activated LA-PEG ligands. The influence of various factors on the growth of the clusters is also studied. Optical properties of the clusters were studied by UV-visible absorption, PL emission and excitation and time resolved fluorescence spectroscopy. XPS and DOSY NMR were used to characterize the oxidation states and sizes of these clusters. The photo-chemical transformation of LA-PEG ligands to thiols and the effect of various experimental parameters such as solvent, oxygen, ligand functional group and effect of acid are described in chapter 3. Thiol yield percentage was quantified using ellman assay. Chapter 4 describes the one phase aqueous synthesis of Ag29 clusters capped with bidentate dihydrolipoic acid (DHLA). We also describe the drastic enhancement of the PL intensity upon gold doping of the Ag29 clusters. Optical properties along with the size characterization by electrospray ionization mass spectrometry is also described. We further describe the growth of these clusters using DHLA-PEG molecules. Chapter 5 describes the synthesis of highly fluorescent Au25-xAgx clusters stabilized with two types of ligands (triphenylphosphine and thiols). We designed a set of monothiolate ligands appended with PEG and zwitterionic moieties. This approach allows to prepare water soluble and stable metallic clusters with enhanced photoluminescence and well defined optical properties. Chapter 6 is the overall summary of our findings and prospects and outlook.
Show less
Date Issued: 2017
Identifier: FSU_FALL2017_Mishra_fsu_0071E_14122
Format: Thesis

Title: The Evaluation of Industrial Methods of Size-Exclusion Chromatography (SEC) of Difficult-to-Dissolve Polymers.
Creator: McNeel, Kelsey, Chemistry
Abstract/Description: In experiments presented here, well-characterized polystyrene and poly(methyl methacrylate) standards were analyzed using size-exclusion chromatography and an approach in which the mobile phase differed from the solvent in which the polymer was dissolved. Solvent combinations included a mobile phase in which the polymer was insoluble and a mobile phase that was immiscible with the solvent. It is important to determine the accuracy of molar mass averages and distributions obtained from such...
Show moreIn experiments presented here, well-characterized polystyrene and poly(methyl methacrylate) standards were analyzed using size-exclusion chromatography and an approach in which the mobile phase differed from the solvent in which the polymer was dissolved. Solvent combinations included a mobile phase in which the polymer was insoluble and a mobile phase that was immiscible with the solvent. It is important to determine the accuracy of molar mass averages and distributions obtained from such experiments because the averages and distributions are frequently used in industry to give information about physical properties of the analyte. It is often expensive and time consuming to determine the ideal solvent in which to analyze a polymer, and even more so to purge the system of the previous solvent and condition it with the new one. To circumnavigate these problems, polymers are sometimes dissolved in a known solvent and injected into an instrument containing a chemically different mobile phase, a mobile phase that is already in the instrument. We found that performing experiments using this industrial approach needs to be done with caution. The molar mass averages and distributions can be determined accurately when the mobile phase is a solvent for the polymer and miscible with the solvent, but other cases were less conclusive. Using a mobile phase that is not a solvent for the polymer appears to yield accurate results for low molar mass polymers (<20,000 g/mol) but, in some solvent combinations, yields exclusively solvent peaks. It is likely that the larger polymers precipitate when the miscible solvent and mobile phase mix and the polymers are adsorbed onto the column. Experiment set 5, in which the mobile phase was a solvent for the polymer but was immiscible with the solvent in which the polymer was dissolved, yielded no peaks in these experiments. It is hypothesized that this lack of peaks is a result of enthalpic interactions between the stationary phase, sample solution, and mobile phase. It appears that the elution of the polymer may not be driven by entropic interactions, as is the case in a size-exclusion mechanism, resulting in the co-elution of the polymer and the solvent.
Show less
Date Issued: 2011
Identifier: FSU_migr_uhm-0026
Format: Thesis

Title: Physical Models and Classroom Demonstrations based on Applying the Hydraulic Analogy to Chemical Equilibrium, Thermodynamics, and Kinetics.
Creator: Lev-Ran, Dana, Department of Chemistry and Biochemistry
Abstract/Description: The hydraulic analogy for electrical circuits is a well-known, if limited, model for understanding potential and current. The work described in this thesis extends this analogy to chemical reactions by constructing apparatuses that model chemical equilibrium and the dynamics of forming kinetic and thermodynamic products in a chemical reaction. The apparatuses were designed so that they could be constructed from readily available and affordable materials by middle or high school students under...
Show moreThe hydraulic analogy for electrical circuits is a well-known, if limited, model for understanding potential and current. The work described in this thesis extends this analogy to chemical reactions by constructing apparatuses that model chemical equilibrium and the dynamics of forming kinetic and thermodynamic products in a chemical reaction. The apparatuses were designed so that they could be constructed from readily available and affordable materials by middle or high school students under the supervision of a shop or science teacher. The resulting hydrodynamic models were evaluated qualitatively and quantitatively with respect to the well-established theories of chemical equilibria, kinetics, and thermodynamics. The effectiveness and utility of the hydrodynamic models to illustrate chemical behavior, as well as their limitations, are discussed.
Show less
Date Issued: 2014
Identifier: FSU_migr_uhm-0417
Format: Thesis

Title: The Orthogonal Space Tempering Scheme and Its Application to Complex Biomolecular Processes.
Creator: Harris, William T. (William Thomas), Yang, Wei, Rikvold, Per Arne, Knappenberger, Kenneth L., Steinbock, Oliver, Florida State University, College of Arts and Sciences,...
Show moreHarris, William T. (William Thomas), Yang, Wei, Rikvold, Per Arne, Knappenberger, Kenneth L., Steinbock, Oliver, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Molecular dynamics (MD) simulations have advanced greatly in the recent decades, but are not without their limitations. This work first details the pitfalls of MD simulations, then presents the details of a new, robust method, orthogonal space tempering (OST) which can achieve accurate and efficient sampling in MD simulations as well as accurate recovery of desired thermodynamic quantities. This method is then applied to understanding the mechanistic details and free energy of passive...
Show moreMolecular dynamics (MD) simulations have advanced greatly in the recent decades, but are not without their limitations. This work first details the pitfalls of MD simulations, then presents the details of a new, robust method, orthogonal space tempering (OST) which can achieve accurate and efficient sampling in MD simulations as well as accurate recovery of desired thermodynamic quantities. This method is then applied to understanding the mechanistic details and free energy of passive transmembrane permeation of small molecules through a lipid bilayer, as well as bulky and charged species. Furthermore, the method is applied to the study of the conformational and dynamical properties of a very important human neuropeptide Y homologue, avian pancreatic peptide.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Harris_fsu_0071E_12913
Format: Thesis

Title: Surface Charge Density in Polyelectrolyte Multilayers and Its Role in Cell Behavior.
Creator: Arias Ramos, Carlos J, Schlenoff, Joseph B., Keller, Thomas C. S., Marshall, Alan G. (Alan George), Mattoussi, Hedi, Florida State University, College of Arts and Sciences,...
Show moreArias Ramos, Carlos J, Schlenoff, Joseph B., Keller, Thomas C. S., Marshall, Alan G. (Alan George), Mattoussi, Hedi, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: The role of charge density in polyelectrolyte multilayer coatings used in 2-D cell culture was investigated in this dissertation. First it is important to comprehend that cells do not attach directly to surfaces, they attach to proteins adhered to surfaces. Surface charge density in polyelectrolyte films affects not only protein coverage, but also interferes with protein exchange (Vroman effect), highly charge surfaces favor irreversible absorption of non-adhesive proteins like albumin, which...
Show moreThe role of charge density in polyelectrolyte multilayer coatings used in 2-D cell culture was investigated in this dissertation. First it is important to comprehend that cells do not attach directly to surfaces, they attach to proteins adhered to surfaces. Surface charge density in polyelectrolyte films affects not only protein coverage, but also interferes with protein exchange (Vroman effect), highly charge surfaces favor irreversible absorption of non-adhesive proteins like albumin, which directly affects cell behavior on these ultrathin films.
Show less
Date Issued: 2016
Identifier: FSU_2016SP_AriasRamos_fsu_0071E_13111
Format: Thesis

Title: Synthesis of Oxide and Spinel Nanocrystals for Use in Solid State Lighting.
Creator: Foley, Megan Elizabeth, Strouse, Geoffrey F., Landing, William M., Stiegman, Albert E., Dudley, Gregory B., Florida State University, College of Arts and Sciences, Department of...
Show moreFoley, Megan Elizabeth, Strouse, Geoffrey F., Landing, William M., Stiegman, Albert E., Dudley, Gregory B., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: In this dissertation, microwave chemistry is employed to synthesize a variety of different crystalline nanoparticles (NPs). This introduction will describe the structures, properties and applications of the NPs studied within the dissertation, with a main focus being on ligand sensitization for the goal of enhanced luminescence. The use of metal acetylacetonate complexes to make Europium (III) doped Ytrrium (Y₂O₃) NPs is explored, where the acetylacetonate acts both as a source of oxygen for...
Show moreIn this dissertation, microwave chemistry is employed to synthesize a variety of different crystalline nanoparticles (NPs). This introduction will describe the structures, properties and applications of the NPs studied within the dissertation, with a main focus being on ligand sensitization for the goal of enhanced luminescence. The use of metal acetylacetonate complexes to make Europium (III) doped Ytrrium (Y₂O₃) NPs is explored, where the acetylacetonate acts both as a source of oxygen for the synthesis of Y₂O₃, as well as an organic chromophore acting as an "antenna" for the absorption of light and subsequent excitation transfer to the incorporated Europium (III) (Chapter 2). Other host materials are investigated by method of metal acetylacetonate decomposition to synthesize a variety of different nanospinels, having the general formula AB₂X₄, with sulfide variants made by decomposition of diethyldithiocarbamate, (Chapter 3). The antenna ligand thenoyltrifluoroacetone (tta), which is known to undergo a Dexter energy transfer (DET) mechanism to efficiently sensitize Europium (III) emission, is used to determine the distance of energy transfer in Europium (III) doped nanospinels by passivating the surface of the nanospinel with a tta (Chapter 4). A variety of ligands are explored in order to optimize the sensitization efficiency in relation to the difference in energy between the singlet and triplet levels of the ligands versus the ⁵D₀ and ⁵D₄ energy levels of Europium (III) and Terbium (III) respectively (Chapter 5).
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Foley_fsu_0071E_12919
Format: Thesis

Title: Microwave Gas-Solid Reactivity in Industrially Relevant Systems.
Creator: Ferrari, Anthony, Stiegman, Albert E., , Vincent J. M., Dudley, Gregory B., Latturner, Susan, Dorsey, John G., Florida State University, College of Arts and Sciences, Department...
Show moreFerrari, Anthony, Stiegman, Albert E., , Vincent J. M., Dudley, Gregory B., Latturner, Susan, Dorsey, John G., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Abstract Gas-Solid reactivity was extensively studied throughout the early 20th century and the kinetics of these systems have become well established and well understood. Recently, microwave active materials (conductive or magnetic materials that absorb microwave irradiation) have been shown to produce increased reactivity in a significantly different way when compared to conventional heating. Any of these materials can be used to improve reactivity in industrially relevant gas-solid systems...
Show moreAbstract Gas-Solid reactivity was extensively studied throughout the early 20th century and the kinetics of these systems have become well established and well understood. Recently, microwave active materials (conductive or magnetic materials that absorb microwave irradiation) have been shown to produce increased reactivity in a significantly different way when compared to conventional heating. Any of these materials can be used to improve reactivity in industrially relevant gas-solid systems. Many of these rate enhancements can be measured by using reaction kinetics, and these kinetic rates can be compared to the previously studied, well established, thermal measurements. By understanding the difference between microwaves and conventional heating we may better predict which systems would be ideal candidates for increased reactivity. Specifically the reaction between steam and carbon has been measured extensively in the past and could be ideal to benefit from microwave irradiation. C + H2O → H2 + CO. At 131 kJ/mol this endothermic reaction uses carbon as its microwave active material. This solid can be any form of carbon (activated carbon, graphite, coal etc.) and it selectively heats in a microwave reactor. This reaction was shown to have a large difference in apparent activation energies and kinetic rates when compared to the thermal rates and energies. By using an Arrhenius plot, the apparent microwave equilibrium constants were calculated at various wattages and shown to be lower when matched against comparable temperature ranges of the conventional thermal reactions. The enthalpy and entropy of the systems were then calculated to give an effective thermodynamic value to describe the energy differences. Not only was the reaction more efficient in the microwave, but the microwave composition of the product gases included less CO2, which would be produced from a water gas shift side reaction. These findings, of a system that produces less side products at lower temperatures, are evidence that microwave gas-solid reactions could provide unique chemistry that should be applied to more industrially relevant systems. Probing the mechanisms of these results was done by using a nitrous oxide and carbon system to observe the compositional difference in reactivity. 2C + 2NO2 → N2 + 2CO2. The interfacial polarization of the carbon is understood to be the method of heating in a microwave reactor. Electron hole pairs are created as the charges separate and become trapped at grain boundaries across the surface of the material. These electron hole pairs create an active site on the surface that helps facilitate reactivity and sometimes leads to different compositional makeup of product gases. Probing this mechanism was important to help describe which systems would be good candidates to study in further research endeavors.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Ferrari_fsu_0071E_12936
Format: Thesis

Title: Magnetic Behavior of Heavy Elements and Heterobimetallic Systems.
Creator: Diefenbach, Kariem T., Albrecht-Schmitt, Thomas E., Chiorescu, Irinel, Dalal, Naresh S., Schlenoff, Joseph B., Steinbock, Oliver, Florida State University, College of Arts and...
Show moreDiefenbach, Kariem T., Albrecht-Schmitt, Thomas E., Chiorescu, Irinel, Dalal, Naresh S., Schlenoff, Joseph B., Steinbock, Oliver, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: The focus of this dissertation is the study of the magnetic properties of several novel lanthanide and actinide metal complexes, of particular concentration is the use of SQUID magnetochemistry coupled with electron paramagnetic resonance (EPR). Through these techniques, a deeper understanding of the magnetic behavior of the f elements and their structure-property relationships are realized. The novel neptunium selenite compounds presented in Chapter 3 are simple systems in which to probe the...
Show moreThe focus of this dissertation is the study of the magnetic properties of several novel lanthanide and actinide metal complexes, of particular concentration is the use of SQUID magnetochemistry coupled with electron paramagnetic resonance (EPR). Through these techniques, a deeper understanding of the magnetic behavior of the f elements and their structure-property relationships are realized. The novel neptunium selenite compounds presented in Chapter 3 are simple systems in which to probe the magnetic susceptibilities of transuranic compounds and a soft ferromagnetic material with strong temperature independent paramagnetic effects was synthesized. Chapter 4 also concerns neptunium but in this case a comparison between neptunium iodates, which are expected to be nonmagnetic, assuming a formal oxidation state of +5 which yields a singlet ground (S = 1) assuming spin only contributions. The compounds actually display ferromagnetic ordering at approximately 12 K. Of even further interest is the frequency dependence of the magnetic susceptibility which should not be evident in a magnetically ordered system thus signifying the material have spin glass properties or exhibit magnetic frustrations. The focus of Chapter 5 is the correlations between structure and magnetic properties that are correlated in a large family of heterobimetallic compounds containing lanthanides and copper. The tuning of the magnetic properties can be controlled by careful substitution of lanthanide ions. Of particular interest is the magnetic information revealed via electron paramagnetic resonance which may go unnoticed by bulk magnetization techniques. These measurements clarified the magnetic description of the compounds. Chapter 6 highlights several other compounds that were found to be magnetically interesting. Particularly interesting is a uranium ion in the +4 oxidation state that exhibits spin frustration. Furthermore, a large family of lanthanide-transition metal ions with tellurium and sulfate anions, where both the lanthanides and transition metal ions are able to be substituted yielded a large diversity of magnetic properties. Finally, a compound was synthesized that exhibited two crystallographically unique copper atoms which are distinguishable via high field electron paramagnetic resonance and order antiferromagnetically.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Diefenbach_fsu_0071E_12835
Format: Thesis

Title: Redefining the Actinide Series.
Creator: Cary, Samantha K. (Samantha Kim), Albrecht-Schmitt, Thomas E., Berg, Bernd A., Dorsey, John G., Stiegman, Albert E., Dalal, Naresh S., Florida State University, College of Arts...
Show moreCary, Samantha K. (Samantha Kim), Albrecht-Schmitt, Thomas E., Berg, Bernd A., Dorsey, John G., Stiegman, Albert E., Dalal, Naresh S., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: This dissertation focuses on probing the fundamental chemistry of the actinide series, specifically the structure and bonding in complexes of transuranium elements. The actinides consist of the elements from actinium to lawrencium in the periodic table, best known for uranium and plutonium, which were used to develop nuclear weapons and power. Today, nuclear power is used to generate over 17% of the electricity across the world.[1, 2] Although an effective means of generating electricity, the...
Show moreThis dissertation focuses on probing the fundamental chemistry of the actinide series, specifically the structure and bonding in complexes of transuranium elements. The actinides consist of the elements from actinium to lawrencium in the periodic table, best known for uranium and plutonium, which were used to develop nuclear weapons and power. Today, nuclear power is used to generate over 17% of the electricity across the world.[1, 2] Although an effective means of generating electricity, the waste generated from nuclear reactors is a major issue with relatively little progress being made to reduce the amount and radiotoxicity of the waste. Overall, this problem stems from the chemical complexity and highly radioactive nature of the actinides. Because of this the actinides are understudied, particularly beyond uranium, and as a result much of the fundamental chemistry is poorly understood. The goal of this work is to prepare coordination complexes that can be used as probes for elucidating changes in structure and bonding across the actinide series. Over the past couple decades, neutral nitrogen donating ligands have shown to have a greater affinity towards the actinides over the lanthanides.[1] The work discussed in this dissertation has focused on using nitrogen-containing carboxylates to explore periodic trends through the lanthanide and actinide series. The first step of this project was to explore structure and bonding differences between the lanthanide (4f) and actinide (5f) series. The early lanthanides, such as Ce and Nd are often used as surrogates for the actinides because they possess f orbitals and are relatively similar in size to that of their actinide analogs.[3] Depending on the coordinating ligand, the structure and bonding between the 4fs and 5fs can either mimic each other or diverge greatly. In some cases the structure of the actinides and lanthanides are very similar, but the electronic properties are vastly different. In chapters 3 and 4, unique structures and electronic properties of Pu and Ce complexes are explored. The second portion of this research was to investigate the differences in structure and bonding between of the transplutonium actinides, americium through californium (Am-Cf). Traditionally these later actinides were believed to mimic the lanthanides in both their structure and bonding characteristics, but as we explore the actinides more we find this might not be true. Our approach used a pyridine dicarboxylate derivative to make an isomorphous series of both the trivalent actinides and lanthanides. It was found that the late actinides, starting at Cf, have different electronic properties that are not paralleled by any of the lanthanides or early actinides. Much to our surprise, it seems that Cf represents a second transition in the actinide series, which is discussed in chapters 5 through 7. Overall, this dissertation focuses on exploring the structure and bonding of the f elements through solid-state chemistry utilizing a variety of characterization techniques.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Cary_fsu_0071E_12680
Format: Thesis

Title: Molecular-Scale Multicoordinating Ligands for Coating Luminescent QDs and Gold Nanoparticles.
Creator: Zhan, Naiqian, Mattoussi, Hedi, Tang, Hengli, Dudley, Gregory B., Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department of Chemistry and...
Show moreZhan, Naiqian, Mattoussi, Hedi, Tang, Hengli, Dudley, Gregory B., Schlenoff, Joseph B., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Colloidal semiconductor quantum dots (QDs) are inorganic nanocrystals that possess several unique photophysical properties, including tunable narrow emission and remarkable photo- and chemical stability. They have large surface areas, and thus can be decorated with large numbers and a variety of molecular vectors. These properties combined offer a potentially superior alternative to traditional organic fluorophore for advanced applications in bio-imaging and bio-sensing. Herein, our effort...
Show moreColloidal semiconductor quantum dots (QDs) are inorganic nanocrystals that possess several unique photophysical properties, including tunable narrow emission and remarkable photo- and chemical stability. They have large surface areas, and thus can be decorated with large numbers and a variety of molecular vectors. These properties combined offer a potentially superior alternative to traditional organic fluorophore for advanced applications in bio-imaging and bio-sensing. Herein, our effort has centered on developing a series of metal coordinating ligands with controllable structures to modify the QD surfaces and construct biocompatible nanocrystals. The ligand architecture accounts for several factors: (i) variable coordination number, (ii) nature of the hydrophilic moiety, polyethylene glycol (PEG) or zwitterion, and (iii) versatility of end-reactive groups including amine, azide, carboxylic acid and aldehyde. The ligand design is combined with a newly developed photoligation strategy to promote the dispersion of luminescent QDs in buffer media. The dissertation is organized in six chapters: In chapter 1, we provide a brief introduction of the basic photophysical properties of QDs and the synthesis history for growing high quality semiconductor nanocrystals. We also present some of the most effective methods reported to date to prepare aqueous QD dispersions, discuss the effective chemical coupling strategies for conjugating biomolecules, and review the recent literatures that have used QD-bioconjugates for imaging and sensing purposes. In Chapter 2, we describe a novel photoligation strategy to promote the transfer of luminescent QDs from hydrophobic to hydrophilic media using lipic acid (LA)-based ligands. We also discusse the experimental conditions, mechanismfor in-situ ligand exchange and the generosity of the method towards the diverse functionality while maintaining the optical properties of the nanocrystals. In chapter 3, we present the design and synthesis of three sets of compact zwitterionic ligands comprising either one or two lipoic acid (LA) groups chemically linked to a zwitterion moiety. These ligands are then combined with the photoligation strategy to promote the phase transfer of QDs to buffer media. The high compactness and the stability of the nanocrystals over a broad range of conditions have been discussed.This chapter also highlights the conjugation of mCherry to the QD surface via metal-histidine coordination, as a proof-of-concept, to develop FRET-based sensors. In chapter 4, we detail a versatile strategy to prepare a series of poly (ethylene glycol) containing multicoordinating ligands optimized for the surface-functionalization of luminescent QDs and gold nanoparticles (AuNPs) alike. Our chemical design relies on the modification of chiral L-aspartic acid precursor, and the advantages of using aminoacid combined with lipoic acid and reactive PEG moieties have been discussed. Nonetheless, the two sets of ligands: bis(LA)-PEG-FN and LA-(PEG-FN)₂ described here are compatible with photoligation strategy to yield hydrophilic, colloidally stable and reactive nanoparticles (QDs and AuNPs). In chapter 5, we discuss the preparation of hydrophilic QDs with intact azide (-N3) and aldehyde (-CHO) bio-orthorgonal functionalities on their surfaces. Strain promoted click chemistry and hydrazine ligation will be discussed to illustrate the orthogonality of two reactive groups, azide and aldehyde. Additionally, we demonstrate an optical method to extract the number of reactive -CHO groups per QD and finally estimate the total number of ligands bound to each QD for a few distinct size nanocrystals.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Zhan_fsu_0071E_12929
Format: Thesis

Title: Magnetic Intermetallics Grown from the Rare Earth/Transition Metal Fluxes.
Creator: Zhou, Sixuan, Latturner, Susan, Locke, Bruce R., Shatruk, Mykhailo, Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of Chemistry and...
Show moreZhou, Sixuan, Latturner, Susan, Locke, Bruce R., Shatruk, Mykhailo, Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Abstract Metal eutectic fluxes are useful for exploratory synthesis of rare earth intermetallics. In this work, the use of rare earth/transition metal eutectics such as: Nd/Co, Pr/Co, Ce/Co, Nd/Ni and Sm/Ni have yielded many structually and magnetically complex phases, which also help us to to gain better understanding of reactivity trends of various elements in the flux. The intermetallic compounds R₂Co₂SiC (R = Pr, Nd) were prepared from the reaction of silicon and carbon in either Pr/Co or...
Show moreAbstract Metal eutectic fluxes are useful for exploratory synthesis of rare earth intermetallics. In this work, the use of rare earth/transition metal eutectics such as: Nd/Co, Pr/Co, Ce/Co, Nd/Ni and Sm/Ni have yielded many structually and magnetically complex phases, which also help us to to gain better understanding of reactivity trends of various elements in the flux. The intermetallic compounds R₂Co₂SiC (R = Pr, Nd) were prepared from the reaction of silicon and carbon in either Pr/Co or Nd/Co eutectic flux. These phases crystallize with a new structure type in orthorhombic space group Immm, with unit cell parameters a = 3.978(4) Å, b = 6.094(5) Å, c = 8.903(8) Å (Z = 2; R₁ = 0.0302) for Nd₂Co₂SiC. Silicon, cobalt, and carbon atoms are connected with each other to build up two-dimensional flat sheets which are separated by puckered layers of rare-earth cations. Magnetic susceptibility measurements indicate that the rare earth cations in both analogs order ferromagnetically at low temperature (TC = 10 K for both). Single crystal neutron diffraction data for Nd₂Co₂SiC indicates this ordering occurs in two steps. Crystals of two new germanide intermetallic compounds were grown from Nd/Co or Pr/Co eutectic flux. The crystal structure of Nd₈Co[subscript 4-x]Al[subscript x]Ge₂C₃ (Pbcm, a=8.00Å, b=11.71Å,c=15.07Å; Z=4, R₁=0.0261) features germanium centered neodymium clusters Ge@Nd₉ capped with Co and C atoms which form infinite zigzag chains. Magnetic susceptibility measurements indicate the Nd ions order at 50K. Magnetic anisotropy studies show the Nd[superscript 3+] magnetic moments tend to align ferrimagnetically along the c axis. The phase RE₆Co₅Ge[subscript 1+x]Al[subscript 3-x] (RE=Pr, Nd) crystallizes with the Nd₆Co₅Ge[subscript 2.2] structure type in hexagonal space group P-6m2 (a = 9.203(2)Å, c = 4.202(1) Å, R1 = 0.0109 for Pr₆Co₅Ge[subscript 1.80]Al[subscript 2.20]; and a = 9.170(3) Å, c = 4.195(1) Å, R1 = 0.0129 for Nd₆Co₅Ge[subscript 1.74]Al[subscript 2.26]), featuring chains of face-sharing Ge@RE₉ clusters intersecting hexagonal cobalt nets linked by aluminum atoms. Magnetic susceptibility measurements indicate that both phases exhibit ferromagnetic ordering of the cobalt layers with TC in the range of 130-140K, and the rare earth ions order at low temperature (30-40K). The magnetic measurements on oriented crystals of Nd₆Co₅Ge[subscript 1.74]Al[subscript 2.26] show a strong preference of the Co moments to order along the c-axis. A cerium cobalt borocarbide compound, Ce₁₀Co[subscript 2.75]B[subscript 11.5]C₁₀(triclinic, P-1, a = 8.5131(5)Å, b = 8.5144(5)Å, c = 13.5709(7)Å, ɑ = 100.870(1)°, β = 93.677(1)°, ɣ = 90.041(1)°, Z = 2, R₁ = 0.0293) was grown as large crystals from reactions of boron and carbon in cerium/cobalt eutectic melts. The structure of the cerium-rich product features Co₄ squares capped by borocarbide chains. Magnetic studies show a ferromagnetic transition at 10 K and also indicate fluctuating cerium valence.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Zhou_fsu_0071E_12884
Format: Thesis

Title: Frequency Modulated Fluorescence Detection for Multiplexing on Microfluidic Devices.
Creator: Schrell, Adrian Mark, Roper, Michael Gabriel, Locke, Bruce R., Dorsey, John G., Stagg, Scott, Florida State University, College of Arts and Sciences, Department of Chemistry and...
Show moreSchrell, Adrian Mark, Roper, Michael Gabriel, Locke, Bruce R., Dorsey, John G., Stagg, Scott, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: The work in this dissertation presents a method for multiplexing fluorescence measurements in both polymerase chain reaction (PCR) and anisotropy. For PCR, two dual color infrared mediation assays were demonstrated on a microfluidic device. Infrared mediated PCR on a microchip allowed a 40 cycle assay, which would require 1 hour on a traditional instrument to be reduced to 35 min due to the decrease volume and increased heating and cooling efficiency. A plasmid, PU19, was amplified in the...
Show moreThe work in this dissertation presents a method for multiplexing fluorescence measurements in both polymerase chain reaction (PCR) and anisotropy. For PCR, two dual color infrared mediation assays were demonstrated on a microfluidic device. Infrared mediated PCR on a microchip allowed a 40 cycle assay, which would require 1 hour on a traditional instrument to be reduced to 35 min due to the decrease volume and increased heating and cooling efficiency. A plasmid, PU19, was amplified in the presence of a DNA intercalating dye, EvaGreen™, and a passive reference dye, ROX, with an efficiency of 96%. The ROX signal was used to correct for inter-run and inter-chip variations in excitation volume. A melt curve was taken simultaneously with amplification and showed a single peak at 82 °C corresponding to the known melt temperature of the plasmid. Frequency modulation was used to isolate the fluorescence signals for the EvaGreen™ and the ROX from the large background present due to the tungsten lamp providing infrared light for the heating of the microfluidic device as well as demonstrate the first multi-color infrared quantitative PCR on a microfluidic device. Frequency modulation was used to demonstrate a multi-analyte anisotropy method inflow on a microfluidic device. An anisotropy immunoassay was developed for the simultaneous detection of insulin and glucagon at physiologically relevant levels. Frequency modulation was used to reduce the number of optics required for multi-fluorophore anisotropy measurements as well as increase the signal to noise in the measurement by 20 fold. The increased signal to noise ratio resulting in an improvement in the limit of detection from 10 nM to 50 pM. The anisotropy immunoassay assay was expanded to an online format used to measure the secretion of insulin by islets of Langerhans which were housed on the microfluidic device. The microfluidic system was able to stimulate islet with 3mM and 20 mM glucose and measure the resulting secretions. The temporal resolution of the system was less than 5 minutes and the highly automated fashion in which the online assay function should make it amenable to further islet studies as well as other biological systems.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Schrell_fsu_0071E_12933
Format: Thesis

Title: Application of Flow-Based Methods to Inorganic Materials Synthesis.
Creator: Miller, Levi Zane, Shatruk, Mykhailo, McQuade, D. Tyler (David Tyler), Alamo, Ruﬁna G., Stiegman, Albert E., Strouse, Geoffrey F., Roper, Michael Gabriel, Florida State...
Show moreMiller, Levi Zane, Shatruk, Mykhailo, McQuade, D. Tyler (David Tyler), Alamo, Ruﬁna G., Stiegman, Albert E., Strouse, Geoffrey F., Roper, Michael Gabriel, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Controlling particularly reactive substances to achieve desired outcomes is a constant challenge in materials chemistry. Reactants and products consisting of main group and transition metal elements often exhibit extreme sensitivity to their environments. Therefore, it is desirable to develop new methods of synthesis and handling of the starting materials and resulting products in order to extend the chemical space available within this domain of science. Reactivity must be defined within the...
Show moreControlling particularly reactive substances to achieve desired outcomes is a constant challenge in materials chemistry. Reactants and products consisting of main group and transition metal elements often exhibit extreme sensitivity to their environments. Therefore, it is desirable to develop new methods of synthesis and handling of the starting materials and resulting products in order to extend the chemical space available within this domain of science. Reactivity must be defined within the context of this dissertation. Herein, 'reactive' is exceptional sensitivity to air and moisture leading to degredation of reactants or desired products. Reactivity may also correspond to the explosive or pyrophoric nature of reactants and products inevitably preventing their isolation and handling under ambient conditions. Several observations which are pertinent to the fundamental understanding of the reactivity of various metalorganic, orgnaometallic, and main group complexes are chronicled within this dissertation. A comparison is provided for two methods (batch and flow) that are typically used to perform and control reactions. Due to the prevalence flow chemistry within my work, emphasis will be placed upon flow-based methods. In chapter 1, a short primer on fluid dynamics relevant to materials chemistry will be provided to compare and contrast batch versus flow chemistry. Examples of flow chemistry applied to organic reactions are given, followed by examples of inorganic chemistry in flow which is much less developed. Finally, the overarching goals of this work are as follows: 1) Present the basics of fluid dynamics to provide a basis for the flow chemical approaches within this work. 2) Provide a discussion of current flow-based methods applied to organic and inorganic synthesis. 3) To detail and study the application of flow chemistry techniques to the synthesis of new and existing metal organic, organometallic, and main group compounds and materials. In chapter 2, a simplified droplet generator is introduced and utilized to yield hollow silica capsules from a liquid–liquid interfacial polymerization reaction. Further use of this simple droplet generator is examined for preparation of SiO2-TiO2 hybrid capsules along with a cartridge-based method to modify the capsule surface with additional TiO2. In chapter 3, our growing interest in reactive materals led to the discovery that alkali metal oxides can be trapped and crystallized using diethlyzinc. From this observation, a family of complexes were isolated and characterized. Chapter 3 will also incoporate flow-based synthesis of organozinc complexes. First, the continuous preparation of organozinc halides is established and then coupled directly to Negishi reactions for the production of desirable building blocks for active pharmaceutical ingredients. Second, a catridge-based method for the utilzation of pyrophoric solid reagent Na2(HZnEt2)2 is presented leading to a series of novel organozincates. In chapter 4, the traditional methods used to synthesize alkali metal polyphosphides are discussed. Our discovery of solution-phase methods which allow facile access to homoatomic polyanions of phosphorus which do not involve harsh reducing alkali metals or the white allotrope of the element is detailed. We then demonstrate a high-throughput continuous-flow approach for rapid generation of gram quantities of these soluble polyphosphide anions.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Miller_fsu_0071E_12886
Format: Thesis

Title: Size and Morphology Variation in Multiferroic MOFs: A Magnetic, Dielectric and Spectroscopic Study.
Creator: Abhyankar, Nandita, Dalal, Naresh S., Chiorescu, Irinel, Strouse, Geoffrey F., Zhu, Lei, Knappenberger, Kenneth L., Florida State University, College of Arts and Sciences,...
Show moreAbhyankar, Nandita, Dalal, Naresh S., Chiorescu, Irinel, Strouse, Geoffrey F., Zhu, Lei, Knappenberger, Kenneth L., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: This dissertation is organized in two parts. The first part summarizes work in a newly developed synthetic route to perovskite-like MOFs, offering control over particle size and morphology. The second part of the dissertation cover spectroscopic work done to elucidate the nature of the ferroelectric transition in this family of metal-organic frameworks.
Date Issued: 2015
Identifier: FSU_2015fall_Abhyankar_fsu_0071E_12924
Format: Thesis

Title: Isolation of Marine Siderophores by Immobilized Metal Affinity Chromatography.
Creator: Farst, Carley, Landing, William M., Cooper, William T., Salters, Vincent J. M., Marshall, Alan G., Stiegman, Albert E., Florida State University, College of Arts and Sciences,...
Show moreFarst, Carley, Landing, William M., Cooper, William T., Salters, Vincent J. M., Marshall, Alan G., Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: This dissertation details the isolation of marine siderophores by Immobilized Metal Affinity Chromatography (IMAC). Siderophores are biologically produced, low molecular weight (400 Da-1000Da), strong iron-binding ligands. These compounds are thought to form strong complexes with [greater than]95% of the dissolved Fe(III) in the oceans and therefore play extremely important roles in the biological uptake and biogeochemical cycling of Fe in the oceans. The challenges with isolating these...
Show moreThis dissertation details the isolation of marine siderophores by Immobilized Metal Affinity Chromatography (IMAC). Siderophores are biologically produced, low molecular weight (400 Da-1000Da), strong iron-binding ligands. These compounds are thought to form strong complexes with [greater than]95% of the dissolved Fe(III) in the oceans and therefore play extremely important roles in the biological uptake and biogeochemical cycling of Fe in the oceans. The challenges with isolating these ligands from seawater is they are present in very low concentrations (nM) in a matrix with a very high ionic strength (~0.7M). The most important considerations for isolating siderophores are selectivity, concentrating, and desalting. In this work, we studied the use of Immobilized Metal Affinity Chromatography (IMAC) followed by Solid-Phase Extraction (SPE) to isolate and concentrate marine siderophores from natural seawater samples. The theory behind the IMAC extraction technique is that organic compounds that form complexes with particular metal cations can be isolated and/or separated via their attraction to a cation chelating resin that has been pre-loaded with the metal cation of interest. To recover the organic compounds from the IMAC resin, elution conditions are chosen based on the analyte of interest and involves either ligand competition or stripping the column of the metal at low pH. In the case of Fe-IMAC, the best method to use was a competing ligand, in this case ethylenediaminetetraacetic acid (EDTA), since acid elution would generate an eluate with a very high ([greater than]50mM) total dissolved Fe(III) concentration that would interfere with subsequent processing and analysis. By using a high EDTA concentration (50mM) the column could be eluted effectively. The Fe-binding ligands in the EDTA eluate were further concentrated via extraction on a silica C-18 resin column (SPE) which will concentrate free ligands and ligand metal complexes that are sufficiently hydrophobic. This "purifies" the IMAC eluate by extracting the analytes of interest from the EDTA eluent. After rinsing with water, the organic compounds were eluted from the SPE column with HPLC-grade methanol, thereby converting the sample matrix to methanol which is easy to dry down for further concentration and is easy to analyze using electrospray ionization mass spectrometry (ESI-MS). Method development and method validation measurements were performed using (+)Electrospray Ionization(ESI) Time of Flight Mass Spectrometry (MS) and (+)ESI-Quattro MS. Open ocean samples were analyzed using (+)ESI Fourier Transform Ion Cyclotron MS. In addition to the internal standard (desferrioxamine B), we found evidence for the presence of three known siderophores (ferrioxamine A1/A2, agrobactin, and ferrioxamine X1) in a seawater sample from the central North Atlantic Ocean.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Farst_fsu_0071E_12828
Format: Thesis

Title: Structural Elucidation in Biomolecules by Nanometal Surface Energy Transfer Contact Points.
Creator: Armstrong, Rachel Elizabeth, Strouse, Geoffrey F., Fajer, Peter G., Knappenberger, Kenneth L., Stiegman, Albert E., Lenhert, Steven, Florida State University, College of Arts...
Show moreArmstrong, Rachel Elizabeth, Strouse, Geoffrey F., Fajer, Peter G., Knappenberger, Kenneth L., Stiegman, Albert E., Lenhert, Steven, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Optical technology in biophysics has seen significant growth with development of high resolution techniques, like single-molecule FRET, to investigate biological structures under native conditions. Additionally, with the rise in gold nanoparticle use in drug delivery, bioassays, and intracellular tracking, Nanometal surface energy transfer (NSET) applications have also improved since its limited beginnings on 2nm gold nanoparticles. This dissertation aims to further exploit the surface...
Show moreOptical technology in biophysics has seen significant growth with development of high resolution techniques, like single-molecule FRET, to investigate biological structures under native conditions. Additionally, with the rise in gold nanoparticle use in drug delivery, bioassays, and intracellular tracking, Nanometal surface energy transfer (NSET) applications have also improved since its limited beginnings on 2nm gold nanoparticles. This dissertation aims to further exploit the surface plasmon – organic dye coupling properties by investigating a series of nucleic acid secondary structures with modified gold nanoparticles and fluorophores as structural contact points. Chapter 1 and Chapter 2 introduce the importance of tracking nucleic acid structures by describing their essential roles in biology as well as state-of-the-art techniques to monitor various conformers. In Chapter 3, gold nanoparticle-based aptamer sensors are investigated and manipulated to detect a multi-magnitude range of target concentrations. It is observed that the aptamer's degree of exposure to the target predictably decreases the limit of detection in optical aptasensors. In sequential Chapters 4-6, a variety of G-quadruplex structures are investigated for their structural characteristics as well as their more global, cooperative relationships. The gold nanoparticle acts as a distant-dependent quencher for these surface-appended, dynamic nucleic acid sequences, in which the intensity of a DNA-functionalized dye distinguishes the specific G- quadruplex structure. In Chapter 7, NSET is pushed to further limits, by adding a distant- dependent contact point to the gold nanoparticle surface in the form of a FRET pair, to build a theorem for an NSET-FRET hybrid system for optical triangulation. The observed quenching of the donor lifetime in the presence of additional decay pathways confirms the efficacy of the NSET-FRET hybrid system and lays the groundwork for a mathematically predictable distance dependence model.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Armstrong_fsu_0071E_12883
Format: Thesis

Title: Tandem Processes Involving an Alkynogenic Fragmentation and Applications in Sesquiterpene Syntheses.
Creator: Hoang, Tung T. (Tung Thanh), Dudley, Gregory B., Levitan, Don R., Alabugin, Igor V., Miller, Brian G., Florida State University, College of Arts and Sciences, Department of...
Show moreHoang, Tung T. (Tung Thanh), Dudley, Gregory B., Levitan, Don R., Alabugin, Igor V., Miller, Brian G., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: This dissertation focuses on the development of novel chemical reactions for enhancing the efficiency of synthesis. In particular, we disclose the development of a tandem fragmentation-olefination reaction for the synthesis of 1,6-enynes and its applications to the syntheses of several natural products. The first chapter reviews fragmentation methodologies for the preparation of alkynes, with insights and discussion in historical aspects, mechanisms, stereoelectronics, and tactics. The second...
Show moreThis dissertation focuses on the development of novel chemical reactions for enhancing the efficiency of synthesis. In particular, we disclose the development of a tandem fragmentation-olefination reaction for the synthesis of 1,6-enynes and its applications to the syntheses of several natural products. The first chapter reviews fragmentation methodologies for the preparation of alkynes, with insights and discussion in historical aspects, mechanisms, stereoelectronics, and tactics. The second chapter starts with a brief background on values of 1,6-enynes leading to various cyclic and polycyclic structures, currently available methods for the preparation of 1,6-enynes, and challenges these methods are facing, especially in preparing neopentyl tethered 1,6-enynes. Then we describe our development of the tandem fragmentation-olefination reaction, which took advantage of tandem process to overcome intermediate instability, providing the final products more efficiently. In chapter 3, this method was applied in the syntheses of several natural products, either to showcase the efficiency of the methodology or to supply material with potential bioactivities. In case of alcyopterosin A, the synthesis was shortened by half when compared with previous approaches. We also have established a divergent approach to both illudalic acid and illudinine. The approach relies on two key transformations: a tandem fragmentation-Knoevenagel condensation and an inversed electron demand intramolecular dehydrogenative Diels-Alder reaction.
Show less
Date Issued: 2015
Identifier: FSU_2015fall_Hoang_fsu_0071E_12945
Format: Thesis

Title: Assessment of the Utility of Chemical Pretreatments for Estimating Carbon and Phosphorus Sequestration in Soils by 13C and 31P NMR Spectrscopy.
Creator: El-Rifai, Hasan M., Cooper, William T., Landing, William M., Dorsey, John G., Schlenoff, Joseph B., Safron, Sanford A., Department of Chemistry and Biochemistry, Florida State...
Show moreEl-Rifai, Hasan M., Cooper, William T., Landing, William M., Dorsey, John G., Schlenoff, Joseph B., Safron, Sanford A., Department of Chemistry and Biochemistry, Florida State University
Show less
Abstract/Description: Sandy soils are a major forest resource in the southeastern U.S and intensive forest management is escalating; yet the effect of forest management on soil organic carbon (SOC) is not well documented. It is unclear to what degree root and aboveground litter inputs add to SOC; and if the relative importance of an input source changes with forest management. All these questions add to the ongoing discussion on the role of the soil in SOC storage and sequestration, as well as the impact of forest...
Show moreSandy soils are a major forest resource in the southeastern U.S and intensive forest management is escalating; yet the effect of forest management on soil organic carbon (SOC) is not well documented. It is unclear to what degree root and aboveground litter inputs add to SOC; and if the relative importance of an input source changes with forest management. All these questions add to the ongoing discussion on the role of the soil in SOC storage and sequestration, as well as the impact of forest management. Investigating the questions described above will allow us to better understand SOC sequestration and protection. In the first part of this work we have characterized labile and recalcitrant SOC pools from upland and wetland forests by acid hydrolysis (6 M HCl, 1 M HCl) and hot-water extraction. 13C nuclear magnetic resonance (NMR) spectroscopy was used to quantify the effect of acid hydrolysis and hot-water extraction on recalcitrant and labile carbon pools. Burial of phosphorus associated with organic matter has been reported as a major mechanistic sink for phosphorus in wetlands. Wetland soils tend to accumulate organic matter due to the production of detrital (plant) material from wetland biota and the suppressed rates of decomposition. Soil accretion rates for constructed wetlands are on the order of millimeters per year, although accretion rates in productive natural systems such as the Everglades have been reported as high as one centimeter per year or more. Current design of constructed wetlands for phosphorus removal is based upon this soil accretion. The rate of phosphorus accretion through this process is used to calculate the area needed to meet designed effluent criteria. However, although much of the phosphorus added to wetlands is retained within the system, this can serve as a phosphorus source to the water column for long periods of time, even after external loads are reduced. Wetlands are often used as `buffer zones' between agricultural areas and adjacent water bodies. The long-term effectiveness of these wetlands to retain and store phosphorus in stable forms depends upon interacting biogeochemical processes in water, detrital layers, and soil. Recognizing that detrital tissue and soil organic matter are the dominant components of wetlands, the breakdown of these materials and the release of nutrients have direct bearing on water quality and productivity of the ecosystem. Relationships developed between processes and physical and chemical properties of detrital plant tissue and soil organic matter can be incorporated into predictive models for extrapolation of results to other sites. The second phase of the research summarized in this dissertation addresses this important issue, and has several unique themes. First, the organic phosphorus forms in a range of wetland ecosystems and their relationships with soil physical and chemical properties have never been studied. We have addressed these issues here by employing state-of-the-art NMR techniques to provide insight into the forms of inorganic and organic phosphorus and organic carbon in recently accreted and native Everglades soils. Second, rarely have linkages been developed between organic carbon and organic phosphorus forms as they relate to their stability under a range of environmental perturbations, but this is of key importance for understanding the biogeochemistry of organic phosphorus in the environment. This research therefore provided information on the composition and stability of soil organic phosphorus and carbon in wetlands, again using primarily NMR techniques. Liquid chromatography and high resolution time-of-flight mass spectrometry were also used to validate the NMR studies.
Show less
Date Issued: 2007
Identifier: FSU_migr_etd-0579
Format: Thesis

Title: The Intrinsic Dynamics of Arginine Kinase.
Creator: Davulcu, Omar, Chapman, Michael S., Logan, Timothy M., Ellington, W. Ross, Dorsey, John G., Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Arginine kinase reversibly catalyzes phosphoryl transfer between ATP and arginine, thus providing a mechanism for buffering ATP levels in cells with high or variable energy requirements. X-ray crystal structures of a substrate-free and transition state analog form of arginine kinase suggest large conformational changes upon substrate binding. Steady state enzyme kinetics show that arginine kinase follows a random, bimolecular bimolecular kinetic mechanism with a turnover rate of ~135 sec¬¬-1....
Show moreArginine kinase reversibly catalyzes phosphoryl transfer between ATP and arginine, thus providing a mechanism for buffering ATP levels in cells with high or variable energy requirements. X-ray crystal structures of a substrate-free and transition state analog form of arginine kinase suggest large conformational changes upon substrate binding. Steady state enzyme kinetics show that arginine kinase follows a random, bimolecular bimolecular kinetic mechanism with a turnover rate of ~135 sec¬¬-1. While the crystal structures have provided a wealth of information about the conformational changes of arginine kinase, they provide little to no data on dynamics. Crystal structures provide static snapshots at endpoints of rather complex equilibria. The link between enzyme dynamics and function is increasingly apparent but still remains relatively unexplored. Recently developed NMR techniques which probe dynamics on the micro- to millisecond timescale have provided insight into connection between dynamics and catalysis in a number of systems. The work presented in this dissertation is an NMR-based investigation into the dynamics or arginine kinase. Expression and purification of arginine kinase enriched with 15N, 13C, and 2H, a requirement for the NMR experiments, was achieved. Another prerequisite, resonance assignment, was accomplished using a standard suite of triple resonance NMR experiments and urea-induced unfolding and refolding to allow for back-exchange of amide deuterons in the core with solvent protons. Backbone amide resonances were assigned for 329 of 344 assignable residues. At the time, arginine kinase was one of the five largest monomeric units to be assigned. Using 15N transverse relaxation dispersion experiments, the dynamics of substrate-free arginine kinase were probed. These experiments implicate a number of residues, which cluster in four regions of the enzyme, in slow micro- to millisecond timescale dynamics. Most interesting is the loop spanning residues I182-G209, which the crystal structures show undergoes a large conformational change to interact with substrate nucleotide. The rate of exchange for this loop was found to be approximately 800 sec-1, on the same order as turnover, indicating that the motion associated with this loop may be a rate-limiting step upon catalysis. Furthermore, the changes associated with binding of substrates have been probed by substrate titrations in conjunction with 2D [15N, 1H]-TROSY spectroscopy. These experiments, which segregate the conformational changes seen in the crystal structures into those induced by binding of individual substrates, show that phosphagen and nucleotide binding elicits relatively independent changes in the N-terminal and C-terminal domains, respectively. The loop spanning residues I182-C201, however, appears to be affected by both substrates. Interestingly, this is the same loop relaxation dispersion experiments implicate in slow dynamics. As a bimolecular enzyme representative of a large enzyme class, the transferases, the amenability of arginine kinase to both x-ray crystallography and NMR make it a unique model system for understanding the connections between dynamics and function. The work described here outlines the potentially rate limiting intrinsic dynamics of arginine kinase and changes induced by substrate binding. These results highlight the importance of dynamics and reflect the growing view that enzymes have evolved both structure and dynamics simultaneously.
Show less
Date Issued: 2008
Identifier: FSU_migr_etd-0800
Format: Thesis

Title: Molecular Characterization of Marine and Terrestrial Dissolved Organic Matter Using Ultrahigh Resolution Mass Spectrometry.
Creator: D'Andrilli, Juliana, III, William T. Cooper, Chanton, Jeffrey P., Fulton, Robert L., Dalal, Naresh, Department of Chemistry and Biochemistry, Florida State University
Abstract/Description: Various analytical techniques have been employed to probe the chemical identity and characteristics of complex Dissolved Organic Matter (DOM) mixtures. With continuing advances in readily available highly developed mass spectrometers, the amount of information generated for analysis is steadily rising. Currently, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) at high magnetic field (> 9 Tesla), is the only advanced analytical technique capable of ultrahigh resolution...
Show moreVarious analytical techniques have been employed to probe the chemical identity and characteristics of complex Dissolved Organic Matter (DOM) mixtures. With continuing advances in readily available highly developed mass spectrometers, the amount of information generated for analysis is steadily rising. Currently, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) at high magnetic field (> 9 Tesla), is the only advanced analytical technique capable of ultrahigh resolution and mass accuracy that can distinguish upwards of 10,000 spectral peaks. This technique facilitates the identification of thousands of unambiguous molecular formulae for complex DOM. The most commonly used ionization method, Electrospray Ionization (ESI), has proven to be an excellent source for DOM ionization prior to MS analysis. ESI coupled to FT-ICR-MS provides an ideal combination necessary for investigating and characterizing DOM from unique natural environments. 9 Tesla), is the only advanced analytical technique capable of ultrahigh resolution and mass accuracy that can distinguish upwards of 10,000 spectral peaks. This technique facilitates the identification of thousands of unambiguous molecular formulae for complex DOM. The most commonly used ionization method, Electrospray Ionization (ESI), has proven to be an excellent source for DOM ionization prior to MS analysis. ESI coupled to FT-ICR-MS provides an ideal combination necessary for investigating and characterizing DOM from unique natural environments. DOM represents the largest reservoir of organic carbon stored in the oceans. Its source has been proposed to originate from marine primary and bacterial production, with limited land-derived contributors. Marine DOM is a complex mixture of biomolecules that either exist naturally or have been transformed from living and decaying organisms in the ocean. Previous research has identified only a small portion of deep sea DOM, due to the complexity of the mixture and lack of advanced techniques available; however, ultrahigh resolution mass spectrometry has succeeded for DOM characterization where other techniques have failed. In Chapter 3, we compare ultrahigh resolution mass spectra of marine DOM isolated from two sites in the Weddell Sea (Antarctica) using ESI and Atmospheric Pressure Photoionization (APPI). These spectra, obtained on a 9.4 Tesla FT-ICR-MS, indicate the two ionization techniques are complementary. Ions produced by APPI extend to higher carbon undersaturation compared to ESI, indicated by higher double-bond equivalence minus oxygen (DBE-O) values, while ions in the ESI spectra are more oxygenated. Moreover, many sulfur-containing compounds were efficiently ionized by ESI but not detected by APPI. These results show that the differences in mass spectra obtained by ESI and APPI FT-ICR-MS are significant and that both are necessary to obtain a complete description of the molecular composition of marine DOM. Peatlands are extraordinary carbon reservoirs due to their sequestration and emission of greenhouse gases. Chapter 4 depicts the importance of investigating the molecular characterization of terrestrial DOM from the Glacial Lake Agassiz Peatlands (GLAP) of northern Minnesota, to reveal the potentially pivotal role it plays in global carbon cycling. ESI-FT-ICR-MS was used to identify the qualitative differences between DOM in fen and bog porewaters of the Red Lake II system in the GLAP. Approximately 80% of molecular composition observed in surface porewater was maintained throughout the bog profile (0.17 to 2.50m). The qualitative stability of the molecular composition of DOM was accompanied by a quantitative increase in Dissolved Organic Carbon (DOC) with depth. The composition of DOM in the fen was significantly different at depth with slightly varying DOC levels. Using Aromaticity Index (AI) values we identified condensed aromatic phenol-type compounds in the porewaters of both peatlands. Surface bog and deep fen DOM had surprising similar molecular compositions. We suggest that enzymatic degradation via phenol oxidase and slower hydrologic transport down the bog vertical profile are responsible for the observed variations in DOM composition. In Chapter 5, molecular composition and optical properties were correlated for two samples of DOM from different peat formations in the GLAP. Fen and bog DOM were analyzed using 9.4 T FT-ICR-MS to determine the aromatic content as a function of depth. UV/Vis absorbance and Excitation Emission Matrix Fluorescence Spectroscopy (EEMS) were used to identify changes in the optical properties associated with the chromophoric fractions of DOM (CDOM). Higher specific UV absorbance (SUVA) at 254 nm indicated more abundant aromatic content for surface bog and deep fen DOM. EEMS results were also found to be in agreement with the absorption spectra and molecular characterization as determined by FT-ICR-MS. The strong correlations we have observed suggest that optical spectroscopy techniques represent an effective surrogate approach to characterizing DOM provided some detailed molecular information is available for calibrating the observed correlations. Finally, comparative analysis of sample preparatory methods for ESI-FT-ICR-MS is presented for terrestrial DOM in Chapter 6. Freeze drying and solid phase extraction using a modified styrene divinyl benzene polymer sorbent (Varian PPL) were considered. Molecular composition was determined using a 9.4Tesla ESI-FT-ICR-MS for Red Lake II fen and bog DOM of the GLAP. 78% of the DOM composition was found to be common to both freeze dried and SPE Bog 0.17m. The unique SPE Bog 0.17m molecular formulas were characterized by higher aromaticity index values and higher DBE-O values which correspond to more aromatic and condensed structures. Similar results were observed for Fen 2.50m DOM. Mass spectral comparisons of SPE DOM and salt water treated SPE DOM produced 93% and 94% common molecular formulas for Fen 2.50m and Bog 0.17m respectively. No outstanding signature originating from the SPE cartridge or by saltwater contributions was identified. The results emphasize the ability of SPE to elute a more representative and effectively prepared DOM sample for high resolution ESI-FT-ICR-MS.
Show less
Date Issued: 2009
Identifier: FSU_migr_etd-0861
Format: Thesis

Title: Low Dimensional Electron Correlated Materials.
Creator: Pak, Chongin, Shatruk, Mykhailo, Hellstrom, Eric, Albrecht-Schmitt, Thomas E., Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of...
Show morePak, Chongin, Shatruk, Mykhailo, Hellstrom, Eric, Albrecht-Schmitt, Thomas E., Stiegman, Albert E., Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: This PhD thesis is devoted to investigation of inorganic materials with low-dimensional structures. Such materials attract significant fundamental and applied interest due to the potential to achieve highly anisotropic properties, which can be controlled by various external stimuli. After brief introduction to this research area in Chapter 1 and description of experimental and theoretical methods in Chapter 2, we describe the study of ternary manganese selenides, Na2Mn2Se3 and Na2Mn3Se4, in...
Show moreThis PhD thesis is devoted to investigation of inorganic materials with low-dimensional structures. Such materials attract significant fundamental and applied interest due to the potential to achieve highly anisotropic properties, which can be controlled by various external stimuli. After brief introduction to this research area in Chapter 1 and description of experimental and theoretical methods in Chapter 2, we describe the study of ternary manganese selenides, Na2Mn2Se3 and Na2Mn3Se4, in Chapter 3. The relationship between the layered crystal structure of these materials and their magnetic behavior is discussed based on the arrangement of magnetic sites in each layer, and results of quantum chemical calculation on Na2Mn2Se3 and Na2Mn3Se4 indicate both compounds are semiconductors. Na2Mn2Se3 does not exhibit magnetic ordering down to 1.8 K, but strong antiferromagnetic correlations were confirmed by field-dependent magnetization measurements. Neutron diffraction study on powder and single crystal samples also did not reveal clear signatures of magnetic ordering. The strong magnetic frustration was confirmed by calculating the frustration factor. A new antiferromagnetic compound, Na2Mn3Se4, was also discovered. It exhibits antiferromagnetic transition at 27 K. Additional magnetic transition is observed at 50 K in single crystal and powder neutron diffraction studies. The magnetic structure of this material shows a complex combination of ferromagnetic and antiferromagnetic interactions that alternate along the crystallographic a-axis. Strong magnetic frustration due to triangulated spin arrangement is confirmed. Synthesis, crystal structure, and magnetic properties of layered materials ACeSe2 (A = Li, Na) are described in Chapter 4. The unconventional magnetism of these compounds is due to the arrangement of magnetic sites on the regular triangular lattice, which causes strong magnetic frustration. A detailed investigation of magnetic properties reveals no magnetic ordering down to 1.8 K. The Weiss constant, determined from fitting experimental data to the Curie-Weiss law, is –71 K, suggesting a very large magnetic frustration factor for this system. The relationship between the structural and magnetic properties of the geometrically frustrated magnetic system is discussed. The extension of studies of layered structures to potentially two-dimensional magnetic materials, Fe3GeTe2 and Bi2MnSe4, is described in Chapter 5. These crystal structures contain stacks of 2D magnetic sheets interacting through weak interlayer van der Waals forces. Chemical vapor transport method is employed to grow high-quality single crystals. The structural and magnetic properties of these materials, including magnetocrystalline anisotropy of bulk samples, were confirmed by temperature dependent magnetic susceptibility measurement. The potential to modify magnetic behavior for few-layer materials, down to the monolayer limit obtained by mechanical or liquid phase exfoliation methods, is yet to be investigated. Chapter 6 describes the study of one-dimensional structures that contain tubular or ribbon-shaped polyphosphide fragments. Thin nano-ribbons were obtained by mechanical and liquid-phase exfoliation of bulk KP15, due to the weak van der Waals interactions between the polyphosphide tubes. Optical bandgap slightly increases as the thickness of nano-ribbons decreases which is an indication of bandgap tunability in the material. Nevertheless, the results of Raman spectroscopy, high resolution transmission electron microscopy, and selected area electron diffraction studies suggest the decreased stability of the samples that contain thinner nanoribbons (<20 nm).
Show less
Date Issued: 2018
Identifier: 2018_Su_Pak_fsu_0071E_14679
Format: Thesis

Title: Crystal Structure Prediction via Deep Learning.
Creator: Ryan, Kevin, Shatruk, Mykhailo, Barbu, Adrian G., DePrince, A. Eugene, Latturner, Susan, Florida State University, College of Arts and Sciences, Department of Chemistry and...
Show moreRyan, Kevin, Shatruk, Mykhailo, Barbu, Adrian G., DePrince, A. Eugene, Latturner, Susan, Florida State University, College of Arts and Sciences, Department of Chemistry and Biochemistry
Show less
Abstract/Description: Vast information on existing crystal structures, which is available through the large open-access and commercialized repositories of crystallographic data, provides an excellent starting point for the implementation of deep learning techniques to the discovery of hidden relationships that might be contained in such large datasets. The machine learning algorithm can be thought of as a fitting procedure for a complicated heuristic model using a large amount of data.1-2 This model is later...
Show moreVast information on existing crystal structures, which is available through the large open-access and commercialized repositories of crystallographic data, provides an excellent starting point for the implementation of deep learning techniques to the discovery of hidden relationships that might be contained in such large datasets. The machine learning algorithm can be thought of as a fitting procedure for a complicated heuristic model using a large amount of data.1-2 This model is later tested to estimate its ability to generalize to unknown crystal structures in a holdout set, i.e. its predictive ability. Herein, we describe a neural network model trained to predict the likelihood of chemical elements adopting different topologies of atomic sites in known crystal structures. The neural network is shown examples of topologies from known crystal structures and trained to predict the element that adopted that topology. We apply the trained model to predict possible compositions of unknown compounds that might be pursued by a synthetic chemist. We demonstrate that the deep neural network is capable of automatically “discovering” relevant descriptors from high-dimensional “raw representations” of the crystallographic data. Since the input data contain purely geometrical and topological information, any chemical knowledge residing within the neural network output must have been learned during training, and thus was “discovered”. The neural network’s learned representation of local topology shows evidence of known geometric and chemical trends not explicitly provided to the network during training.
Show less
Date Issued: 2018
Identifier: 2018_Su_Ryan_fsu_0071E_14685
Format: Thesis

Title: Isolating and Crystallizing the Permuted HD Domain of CRISPR.
Creator: Hubert, Joshua, Li, Hong, Ramia, Nancy, Department of Chemistry and Biochemistry
Abstract/Description: CRISPR-cas systems have been found to confer RNA guided immunity in prokaryotes comparable to the eukaryotic RNA interference. These Clustered Regularly Interspaced Short Palindromic Repeats, as their name entails, are repeated sequences varying from 25 to 45 nucleotides in length separated by variable spacers. The CRISPR system has been found in many different bacteria and Archaea. Associated with the CRISPR locus are cas genes, which are thought to encode for nucleases, helicases, and...
Show moreCRISPR-cas systems have been found to confer RNA guided immunity in prokaryotes comparable to the eukaryotic RNA interference. These Clustered Regularly Interspaced Short Palindromic Repeats, as their name entails, are repeated sequences varying from 25 to 45 nucleotides in length separated by variable spacers. The CRISPR system has been found in many different bacteria and Archaea. Associated with the CRISPR locus are cas genes, which are thought to encode for nucleases, helicases, and polymerases involved in the CRISPR defense mechanism. The mechanism involved with the defense occurs when the CRISPR locus is transcribed into a long RNA that will be processed into short sequences used as a guide to target and cleave the invader genome sequences through base pairing. Together, the CRISPR-cas systems are able to protect the bacteria or archaea from invading DNA or RNA. Cas 10 is the signature protein of type III CRISPR systems and is characterized by a permuted Histidine-Aspartic acid (HD) domain predicted to possess a nuclease activity. The presence of the permuted HD and the presence of a nucleotidyl cylcase-like have guided the belief that the permuted HD domain may be the activity site. After several attempts, it was found that the HD domain protein from both PF1129 and TTHB147 is insoluble in water and is consistently lost in the pellet during centrifugation. However, there is still a small concentration of the domain collected in the elution, showing that some of the HD domain can be purified to the last step. The max concentration collected of the permuted HD domain from the TTHB147 was found to be 2.45 mg/mL.
Show less
Date Issued: 2014
Identifier: FSU_migr_uhm-0317
Format: Thesis

Title: Design and Synthesis of a Chiral, Amino Acid Derived, Six-Membered N-Heterocyclic Carbene Copper(I) Complex.
Creator: Fleming, Jeffrey, Department of Chemistry and Biochemistry
Abstract/Description: A catalyst is any species that increases the reaction rate of a chemical reaction by decreasing activation energy without being consumed. Catalysts are used in organic synthesis to increase reaction rates and to enable the synthesis of optically pure products. Asymmetric catalysis is crucial to the synthesis of pharmaceutical intermediates and novel catalysts are needed to synthesize the intermediates of future medicines. The study of N-heterocyclic carbene (NHC) metal complexes is a growing...
Show moreA catalyst is any species that increases the reaction rate of a chemical reaction by decreasing activation energy without being consumed. Catalysts are used in organic synthesis to increase reaction rates and to enable the synthesis of optically pure products. Asymmetric catalysis is crucial to the synthesis of pharmaceutical intermediates and novel catalysts are needed to synthesize the intermediates of future medicines. The study of N-heterocyclic carbene (NHC) metal complexes is a growing field that has provided many selective catalysts. NHC ligands with tunable properties enable rapid development of new synthetic methods. Building off previous work in the McQuade research group, a novel six-membered NHC copper(I) catalyst has been designed using a modular approach to tunable NHCs. Interchangeable amino acid-based starting materials provide a readily accessible source of chirality to control the steric and electronic environment surrounding the metal atom bound to the NHC. The synthesis of several complexes enables relative catalytic ability to be tested and provides increased insight into catalyst design.
Show less
Date Issued: 2014
Identifier: FSU_migr_uhm-0306
Format: Thesis

Title: Novel Carbon Nanotube Structures and Microcellular Foams.
Creator: Amrhein, Christina, Department of Biological Science
Abstract/Description: Structural foams reinforced with carbon nanotubes could prove to be beneficial in numerous industrial applications. High internal phase emulsion foams are emerging as new and important forms of microcellular foams. Microcellular foams, foams with a pores size of 0.1-10 μm, have numerous advantages, such as high impact strength. The dispersal of carbon nanofibers, as wall pore reinforcements, within microcellular foams promises to enhance the foams' mechanical properties. This research has...
Show moreStructural foams reinforced with carbon nanotubes could prove to be beneficial in numerous industrial applications. High internal phase emulsion foams are emerging as new and important forms of microcellular foams. Microcellular foams, foams with a pores size of 0.1-10 μm, have numerous advantages, such as high impact strength. The dispersal of carbon nanofibers, as wall pore reinforcements, within microcellular foams promises to enhance the foams' mechanical properties. This research has developed a novel method for creating such foam.
Show less
Date Issued: 2014
Identifier: FSU_migr_uhm-0290
Format: Thesis

Title: Capillary Electrophoresis Separation of Formaldehyde Cross-Linked Aptamer-Protein Complexes.
Creator: Duren, Joseph, Biochemistry
Abstract/Description: An Immunoglobulin-E (IgE) DNA aptamer was covalently bound to IgE using a formaldehyde cross-linking method. The resulting complex was then separated from free aptamer by capillary electrophoresis (CE). The bound-to-free peak area ratios were preserved as a result of the cross-linking, which acted as a "freeze-frame" of the reaction in equilibrium. Elevated temperature occurring during CE separations can cause dissociation of non-covalently bound molecules and their targets, decreasing the...
Show moreAn Immunoglobulin-E (IgE) DNA aptamer was covalently bound to IgE using a formaldehyde cross-linking method. The resulting complex was then separated from free aptamer by capillary electrophoresis (CE). The bound-to-free peak area ratios were preserved as a result of the cross-linking, which acted as a "freeze-frame" of the reaction in equilibrium. Elevated temperature occurring during CE separations can cause dissociation of non-covalently bound molecules and their targets, decreasing the usefulness of the information obtained. Due to the formaldehyde cross-linking performed, the bound-to-free ratio was preserved over that of the uncross-linked control, which showed a decreased bound-to-free ratio upon heating. Additional trials were run on bovine serum albumin (BSA), anti-BSA, glucagon, and anti-glucagon using the formaldehyde cross-linking method. The results for this section were not conclusive due to difficulties in the separation and mechanistic issues with formaldehyde cross-linking. With the use of formaldehyde cross-linking, complexes that easily dissociate, under stringent separation conditions, can be covalently linked to prevent dissociation and allow for more sensitive analyses to be performed. Keywords:
Show less
Date Issued: 2011
Identifier: FSU_migr_uhm-0012
Format: Thesis

Title: Medium Effects on the Photoisomerization of Trans, Trans-1, 4-Diphenyl-1, 3-Butadiene.
Creator: Redwood, Christopher, Chemistry
Abstract/Description: Photoisomerization of trans,trans-1,4-diphenyl-1,3-butadiene (tt-DPB) has been rigorously studied with the assumption that torsion about the excited state is the sole radiationless decay pathway in competition with fluorescence12, 13, 14. This assumption is questioned and tested as it disregards the many channels for photochemical radiationless deactivation of the excited state, which have been rigorously studied33. Irradiation of tt-DPB in acetonitrile, cyclohexane, decane, ethanol,...
Show morePhotoisomerization of trans,trans-1,4-diphenyl-1,3-butadiene (tt-DPB) has been rigorously studied with the assumption that torsion about the excited state is the sole radiationless decay pathway in competition with fluorescence12, 13, 14. This assumption is questioned and tested as it disregards the many channels for photochemical radiationless deactivation of the excited state, which have been rigorously studied33. Irradiation of tt-DPB in acetonitrile, cyclohexane, decane, ethanol, isopropyl alcohol, methanol, and methylcyclohexane was performed and monitored by UV-Vis spectroscopy. Notably, it is found that trans to cis photoisomerization is occurs faster than alcohol photoaddition from the excited state of tt-DPB. Additionally, methods for automatic baseline correction of degassed samples are discussed.
Show less
Date Issued: 2011
Identifier: FSU_migr_uhm-0035
Format: Thesis

Theses and Dissertations (336)	+ -
Undergraduate Honors Theses (11)	+ -

Biochemistry (149)	+ -
Biophysics (45)	+ -
Molecular biology (44)	+ -
Materials science (17)	+ -
Polymers (12)	+ -

Chemistry, Organic (11)	+ -
Chemistry, Inorganic (10)	+ -
Chemistry, Physical and theoretical (7)	+ -
Chemistry, Analytic (3)	+ -
Nanoscience (3)	+ -
Physics (3)	+ -
Chemical engineering (2)	+ -
Engineering (2)	+ -
Nuclear chemistry (2)	+ -
Aerospace engineering (1)	+ -
Bioinformatics (1)	+ -
Biology (1)	+ -
Biotechnology (1)	+ -
Ecology (1)	+ -
Geology (1)	+ -
Materials (1)	+ -
Mathematics (1)	+ -
Mechanical engineering (1)	+ -
Nanotechnology (1)	+ -
Optics (1)	+ -
Philosophy (1)	+ -
Physical sciences (1)	+ -
Plasma (Ionized gases) (1)	+ -
Science (1)	+ -

text (347)	+ -
doctoral thesis (45)	+ -
master thesis (2)	+ -

Florida State University (336)	+ -
Department of Chemistry and Biochemistry (330)	+ -
College of Arts and Sciences (86)	+ -
Stiegman, Albert E. (55)	+ -
Steinbock, Oliver (54)	+ -

Search In

Pages

Pages

Sort Results By:

Narrow results by:

Collection

Topical Subject

Genre

Type of Resource

Language

Creator

Owner