Matching Items (11)
Filtering by
- All Subjects: Physical Chemistry
- Creators: Richert, Ranko
- Creators: Levitus, Marcia
Description
The objective of the present investigations is to experimentally determine the fundamental molecular properties of the transient metal containing pieces. The transient molecules have been generated using laser ablation production technique and detected by using laser induced fluorescence technique. Ultra-high resolution spectra of the diatomic molecules, 87SrF, 135&137BaF, YbF, HfF, and IrSi were recorded at a resolution of approximately 30 Mhz. The fine and hyperfine structure of these molecules were determined for the ground and the excited state. The optical Stark splittings of 180HfF and IrSi were recorded and analyzed to determine the permanent electric dipole moments of the ground and the excited state. An effective Hamiltonian operator, including the rotational, centrifugal distortion, spin-orbit, spin-spin, spin-rotation, Λ-doubling, magnetic hyperfine and quadrupole interactions, and Stark effect, was employed to model and analyze the recorded spectra. The electronic spectra of the triatomic molecules, TiO2 and ZrO2, were recorded using pulsed dye laser, LIF, spectrometer at a resolution of 300MHz. These molecules have C2v symmetry. The harmonic frequencies, lifetime measurements were determined. These spectra of ZrO2 and TiO2 were modeled using a normal coordinate analysis and Franck-Condon factor predictions. High resolution field-free and Stark effect spectra of ZrO2 were recorded and for future investigation.
ContributorsLe, Anh Thun (Author) / Steimle, Timothy C (Thesis advisor) / Richert, Ranko (Committee member) / Chizmeshya, Andrew (Committee member) / Arizona State University (Publisher)
Created2013
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
Spider dragline silk is well known for its outstanding mechanical properties - a combination of strength and extensibility that makes it one of the toughest materials known. Two proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2), comprise dragline silk fibers. There has been considerable focus placed on understanding the source of spider silk's unique mechanical properties by investigating the protein composition, molecular structure and dynamics. Chemical compositional heterogeneity of spider silk fiber is critical to understand as it provides important information for the interactions between MaSp1 and MaSp2. Here, the amino acid composition of dragline silk protein was precisely determined using a solution-state nuclear magnetic resonance (NMR) approach on hydrolyzed silk fibers. In a similar fashion, solution-state NMR was applied to probe the "13"C/"15"N incorporation in silk, which is essential to understand for designing particular solid-state NMR methods for silk structural characterization. Solid-state NMR was used to elucidate silk protein molecular dynamics and the supercontraction mechanism. A "2"H-"13"C heteronuclear correlation (HETCOR) solid-state NMR technique was developed to extract site-specific "2"H quadrupole patterns and spin-lattice relaxation rates for understanding backbone and side-chain dynamics. Using this technique, molecular dynamics were determined for a number of repetitive motifs in silk proteins - Ala residing nanocrystalline &beta-sheet; domains, 3"1"-helical regions, and, Gly-Pro-Gly-XX &beta-turn; motifs. The protein backbone and side-chain dynamics of silk fibers in both dry and wet states reveal the impact of water on motifs with different secondary structures. Spider venom is comprised of a diverse range of molecules including salts, small organics, acylpolyamines, peptides and proteins. Neurotoxins are an important family of peptides in spider venom and have been shown to target and modulate various ion channels. The neurotoxins are Cys-rich and share an inhibitor Cys knot (ICK) fold. Here, the molecular structure of one G. rosea tarantula neurotoxin, GsAF2, was determined by solution-state NMR. In addition, the interaction between neurotoxins and model lipid bilayers was probed with solid-state NMR and negative-staining (NS) transmission electron microscopy (TEM). It is shown that the neurotoxins influence lipid bilayer assembly and morphology with the formation of nanodiscs, worm-like micelles and small vesicles.
ContributorsShi, Xiangyan (Author) / Yarger, Jeffery L (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Levitus, Marcia (Committee member) / Marzke, Robert F (Committee member) / Arizona State University (Publisher)
Created2014
Description
Fluorescence spectroscopy is a popular technique that has been particularly useful in probing biological systems, especially with the invention of single molecule fluorescence. For example, Förster resonance energy transfer (FRET) is one tool that has been helpful in probing distances and conformational changes in biomolecules. In this work, important properties necessary in the quantification of FRET were investigated while FRET was also applied to gain insight into the dynamics of biological molecules. In particular, dynamics of damaged DNA was investigated. While damages in DNA are known to affect DNA structure, what remains unclear is how the presence of a lesion, or multiple lesions, affects the flexibility of DNA, especially in relation to damage recognition by repair enzymes. DNA conformational dynamics was probed by combining FRET and fluorescence anisotropy along with biochemical assays. The focus of this work was to investigate the relationship between dynamics and enzymatic repair. In addition, to properly quantify fluorescence and FRET data, photophysical phenomena of fluorophores, such as blinking, needs to be understood. The triplet formation of the single molecule dye TAMRA and the photoisomerization yield of two different modifications of the single molecule cyanine dye Cy3 were examined spectroscopically to aid in accurate data interpretation. The combination of the biophysical and physiochemical studies illustrates how fluorescence spectroscopy can be used to answer biological questions.
ContributorsShepherd Stennett, Elana Maria (Author) / Levitus, Marcia (Thesis advisor) / Ros, Robert (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2015
Description
This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two section, the first one involving the characterization of the Dyad monolayers and conductance measurement in the dark. The Dyads are designed to form charge separated states on illumination. The lifetime of the charged states have been measured efficiently but the single-molecule conductance through the molecules have yet to be characterized. The second part of the project describes the set-up of a novel sample stage which enables the study of molecular conductance under illumination. This part also describes the subsequent study of the molecule under illumination and the observation of a unique charge-separated state. It also contains the verification of the presence of this charge-separated using other characterization techniques like transient absorption spectroscopy. The second project described in the dissertation was studying and comparing the predicted rectifying nature of two molecules, identical in every way except for one stereocenter. This project describes the formation of monolayers of the molecule on gold and then studying and analyzing the current-voltage characteristics of the molecules and looking for rectification. Both the molecules proved to be rectifying, one more than the other as predicted by theoretical calculations.
ContributorsBhattacharyya, Shreya (Author) / Lindsay, Stuart (Thesis advisor) / Moore, Ana (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2011
Description
A driving force for studies of water, alcohols, and amides is the determination of the role of hydrogen bonding. Hydrogen bonds can break and reform, consequently creating supramolecular structures. Understanding the role supramolecular structures play in the dynamics of monohydroxyl alcohols is important to understanding hydrogen bonding in more complex systems such as proteins. Since many monohydroxyl alcohols are good glass formers, dielectric spectroscopy in the supercooled regime is used to gather information about the dynamics of these liquids. Application of high external fields will reversibly alter the polarization responses of the material from the linear response. This results in nonlinear dielectric effects (NDE) such as field induced suppression (saturation) and enhancement of amplitudes (chemical effects) as well as shifts in the time constants toward slower (entropy) and faster (energy absorption) dynamics.
The first part of this thesis describes the nonlinear dielectric experiments on monohydroxyl alcohols, with an emphasis on the time dependence of NDEs. For the first time, time-dependent experiments on monoalcohols were done, the results showed that NDEs occur on the Debye time scale. Furthermore, physical vapor deposition (PVD) is used to modify the supramolecular structure of 4-methyl-3-heptanol. Upon deposition the film cannot form the ring like structures, which are preferred in the bulk material. The as deposited film shows an enhancement of the dielectric peak by a factor of approximately 11 when compared to the bulk material. The conversion from the as deposited material back to the near bulk material was found to occur on the Debye timescale.
The second part of this thesis focuses on the question of what is governing the field induced changes seen in the liquids studied. Here a complete set of high field experiments on highly polar propylene carbonate derivatives were performed. It was demonstrated that these materials exhibit a Debye-like peak and using a combination of Adam-Gibbs and Fröhlich’s definition of entropy, proposed by Johari [G.P. Johari, J. Chem. Phys 138, 154503 (2013)], cannot solely be used to describe a frustration of dynamics. It is important to note that although these material exhibit a Debye like peak, the behavior is much different than monoalcohols.
The first part of this thesis describes the nonlinear dielectric experiments on monohydroxyl alcohols, with an emphasis on the time dependence of NDEs. For the first time, time-dependent experiments on monoalcohols were done, the results showed that NDEs occur on the Debye time scale. Furthermore, physical vapor deposition (PVD) is used to modify the supramolecular structure of 4-methyl-3-heptanol. Upon deposition the film cannot form the ring like structures, which are preferred in the bulk material. The as deposited film shows an enhancement of the dielectric peak by a factor of approximately 11 when compared to the bulk material. The conversion from the as deposited material back to the near bulk material was found to occur on the Debye timescale.
The second part of this thesis focuses on the question of what is governing the field induced changes seen in the liquids studied. Here a complete set of high field experiments on highly polar propylene carbonate derivatives were performed. It was demonstrated that these materials exhibit a Debye-like peak and using a combination of Adam-Gibbs and Fröhlich’s definition of entropy, proposed by Johari [G.P. Johari, J. Chem. Phys 138, 154503 (2013)], cannot solely be used to describe a frustration of dynamics. It is important to note that although these material exhibit a Debye like peak, the behavior is much different than monoalcohols.
ContributorsYoung-Gonzales, Amanda R (Author) / Richert, Ranko (Thesis advisor) / Angell, Charles (Committee member) / Wolf, George (Committee member) / Arizona State University (Publisher)
Created2019
Description
Transient molecules are of great importance having proposed applications in quantum science and technology and tests of fundamental physics. In the present dissertation, the transient molecules studied are SrOH, ThF, ThCl, YbF and YbOH; each having been selected because of their proposed application. Specifically, SrOH is a candidate of constructing a molecular magneto-optical trap (MOT). The simple actinide molecules, ThF and ThCl, were selected as ligand bonding model systems to gain insight into chemical processing of Spent Nuclear Fuel. The lanthanides YbF and YbOH are venues for the determination of electron electric dipole moment (eEDM) and the studies in this dissertation provide the requisite properties for those experiments.
Intense supersonic molecular beams of these transient molecules were generated via laser ablation and spectroscopically characterized using a novel medium-resolution two-dimensional (2D) spectroscopic approach, as well as high-resolution laser induced fluorescence (LIF). The 2D medium resolution approach, which was used in the studies SrOH, ThF, ThCl and YbOH, uses a multiplexing method that simultaneously records dispersed fluorescence and excitation spectra. A significant advantage of 2D-LIF imaging is that all the electronics states can be targeted to determine the electronics states and associated vibrational spacing individually. Consequently, in the 2D spectra of ThF, ThCl and YbOH, several previously unobserved band systems have been detected in one single scan. For the DF spectra of SrOH and YbOH, the determined branching ratios show that the transitions of these molecules are diagonal (i.e. Δv=0), which is essential for the proposed potential for laser cooling. In the high-resolution of YbF, ThF, ThCl and SrOH optical spectra were recorded to an accuracy of ±30 MHz, which represents an unprecedented precision of 1:10+8.
In addition to field free spectra, optical Stark and Zeeman studies were performed to determine the most fundamental magneto-and electro-static properties. Effective Hamiltonian operators were employed to analyze the recorded spectra and determine the spectroscopic parameters. This data set also establishes a contribution toward developing new computational methodologies for treating relativistic effects and electron correlation.
Intense supersonic molecular beams of these transient molecules were generated via laser ablation and spectroscopically characterized using a novel medium-resolution two-dimensional (2D) spectroscopic approach, as well as high-resolution laser induced fluorescence (LIF). The 2D medium resolution approach, which was used in the studies SrOH, ThF, ThCl and YbOH, uses a multiplexing method that simultaneously records dispersed fluorescence and excitation spectra. A significant advantage of 2D-LIF imaging is that all the electronics states can be targeted to determine the electronics states and associated vibrational spacing individually. Consequently, in the 2D spectra of ThF, ThCl and YbOH, several previously unobserved band systems have been detected in one single scan. For the DF spectra of SrOH and YbOH, the determined branching ratios show that the transitions of these molecules are diagonal (i.e. Δv=0), which is essential for the proposed potential for laser cooling. In the high-resolution of YbF, ThF, ThCl and SrOH optical spectra were recorded to an accuracy of ±30 MHz, which represents an unprecedented precision of 1:10+8.
In addition to field free spectra, optical Stark and Zeeman studies were performed to determine the most fundamental magneto-and electro-static properties. Effective Hamiltonian operators were employed to analyze the recorded spectra and determine the spectroscopic parameters. This data set also establishes a contribution toward developing new computational methodologies for treating relativistic effects and electron correlation.
ContributorsNguyen, Duc Trung (Author) / Steimle, Timothy C (Thesis advisor) / Richert, Ranko (Committee member) / Chizmeshya, Andrew V.G. (Committee member) / Arizona State University (Publisher)
Created2019
Description
How water behaves at interfaces is relevant to many scientific and technological applications; however, many subtle phenomena are unknown in aqueous solutions. In this work, interfacial structural transition in hydration shells of a polarizable solute at critical polarizabilities is discovered. The transition is manifested in maximum water response, the reorientation of the water dipoles at the interface, and an increase in the density of dangling OH bonds. This work also addresses the role of polarizability of the active site of proteins in biological catalytic reactions. For proteins, the hydration shell becomes very heterogeneous and involves a relatively large number of water molecules. The molecular dynamics simulations show that the polarizability, along with the atomic charge distribution, needs to be a part of the picture describing how enzymes work. Non Gaussian dynamics in time-resolved linear and nonlinear (correlation) 2D spectra are also analyzed.
Additionally, a theoretical formalism is presented to show that when preferential orientations of water dipoles exist at the interface, electrophoretic charges can be produced without free charge carriers, i.e., neutral solutes can move in a constant electric field due to the divergence of polarization at the interface. Furthermore, the concept of interface susceptibility is introduced. It involves the fluctuations of the surface charge density caused by thermal motion and its correlation over the characteristic correlation length with the fluctuations of the solvent charge density. Solvation free energy and interface dielectric constant are formulated accordingly. Unlike previous approaches, the solvation free energy scales quite well in a broad range of ion sizes, namely in the range of 2-14 A° . Interface dielectric constant is defined such that the boundary conditions in the Laplace equation describing a micro- or mesoscopic interface are satisfied. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value. Molecular dynamics simulation results show that the interface dielectric constant for a TIP3P water model changes from nine to four when the effective solute radius is increased from 5 A° to 18 A° . The small value of the interface dielectric constant of water has potentially dramatic consequences for hydration.
Additionally, a theoretical formalism is presented to show that when preferential orientations of water dipoles exist at the interface, electrophoretic charges can be produced without free charge carriers, i.e., neutral solutes can move in a constant electric field due to the divergence of polarization at the interface. Furthermore, the concept of interface susceptibility is introduced. It involves the fluctuations of the surface charge density caused by thermal motion and its correlation over the characteristic correlation length with the fluctuations of the solvent charge density. Solvation free energy and interface dielectric constant are formulated accordingly. Unlike previous approaches, the solvation free energy scales quite well in a broad range of ion sizes, namely in the range of 2-14 A° . Interface dielectric constant is defined such that the boundary conditions in the Laplace equation describing a micro- or mesoscopic interface are satisfied. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value. Molecular dynamics simulation results show that the interface dielectric constant for a TIP3P water model changes from nine to four when the effective solute radius is increased from 5 A° to 18 A° . The small value of the interface dielectric constant of water has potentially dramatic consequences for hydration.
ContributorsDinpajooh, Mohammadhasan (Author) / Matyushov, Dmitry V (Thesis advisor) / Richert, Ranko (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2016
Description
Fluorescence spectroscopy is a powerful tool for biophysical studies due to its high sensitivity and broad availability. It is possible to detect fluorescence from single molecules allowing researchers to see the behavior of subpopulations whose presence is obscured by “bulk” collection methods. The fluorescent probes used in these experiments are affected by the solution and macromolecular environments they are in. A misunderstanding of a probe’s photophysics can lead researchers to assign observed behavior to biomolecules, when in fact the probe is responsible. On the other hand, a probe’s photophysical behavior is a signature of the environment surrounding it; it can be exploited to learn about the biomolecule(s) under study. A thorough examination of a probe’s photophysics is critical to data interpretation in both cases and is the focus of this work. This dissertation investigates the photophysical behavior of symmetric and asymmetric cyanines in a variety of solution and biomolecular environments. Using fluorescent techniques—such as time-correlated single photon counting (TCSPC) and fluorescence correlation spectroscopy (FCS)—it was found that cyanines are influenced by the local environment. In the first project, the symmetric cyanines are found to be susceptible to paramagnetic species, such as manganese(II), that enhance the intersystem crossing (ISC) rate increasing triplet blinking and accelerating photobleaching. Another project found the increase in fluorescence of Cy3 in the protein induced fluorescence enhancement (PIFE) technique is due to reduced photoisomerization caused by the proximity of protein to Cy3. The third project focused on asymmetric cyanines; their photophysical behavior has not been previously characterized. Dy630 as a free dye behaves like Cy3; it has a short lifetime and can deactivate via photoisomerization. Preliminary experiments on Dy dyes conjugated to DNA show these dyes do not photoisomerize, and do not show PIFE potential. Further research will explore other conjugation strategies, with the goal of optimizing conditions in which Dy630 can be used as the red-absorbing analogue of Cy3 for PIFE applications. In summary, this dissertation focused on photophysical investigations, the understanding of which forms the backbone of rigorous fluorescent studies and is vital to the development of the fluorescence field.
ContributorsCiuba, Monika A (Author) / Levitus, Marcia (Thesis advisor) / Liu, Yan (Committee member) / Vaiana, Sara (Committee member) / Arizona State University (Publisher)
Created2017
Description
The bonding and electrostatic properties of gold containing molecules are highly influenced by relativistic effects. To understand this facet on bonding, a series of simple diatomic AuX (X=F, Cl, O and S) molecules, where upon bond formation the Au atom donates or accepts electrons, was investigated and discussed in this thesis.
First, the optical field-free, Stark, and Zeeman spectroscopic studies have been performed on AuF and AuCl. The simple polar bonds between Au and typical halogens (i.e. F and Cl) can be well characterized by the electronic structure studies and the permanent electric dipole moments, el. The spectroscopic parameters have been precisely determined for the [17.7]1, [17.8]0+ and X1+ states of AuF, and the [17.07]1, [17.20]0+ and X1+ states of AuCl. The el have been determined for ground and excited states of AuF and AuCl. The results from the hyperfine analysis and Stark measurement support the assignments that the [17.7]1 and [17.8]0+ states of AuF are the components of a 3 state. Similarly, the analysis demonstrated the [19.07]1 and [19.20]0+ states are the components of the 3 state of AuCl.
Second, my study focused on AuO and AuS because the bonding between gold and sulfur/oxygen is a key component to numerous established and emerging technologies that have applications as far ranging as medical imaging, catalysis, electronics, and material science. The high-resolution spectra were record and analyzed to obtain the geometric and electronic structural data for the ground and excited states. The electric dipole moment, el, and the magnetic dipole moment, m, has been the precisely measured by applying external static electric and magnetic fields. el andm are used to give insight into the unusual complex bonding in these molecules.
In addition to direct studies on the gold-containing molecules, other studies of related molecules are included here as well. These works contain the pure rotation measurement of PtC, the hyperfine and Stark spectroscopic studies of PtF, and the Stark and Zeeman spectroscopic studies of MgH and MgD.
Finally, a perspective discussion and conclusion will summarize the results of AuF, AuCl, AuO, and AuS from this work (bond lengths, dipole moment, etc.). The highly quantitative information derived from this work is the foundation of a chemical description of matter and essential for kinetic energy manipulation via Stark and Zeeman interactions. This data set also establishes a synergism with computation chemists who are developing new methodologies for treating relativistic effects and electron correlation.
First, the optical field-free, Stark, and Zeeman spectroscopic studies have been performed on AuF and AuCl. The simple polar bonds between Au and typical halogens (i.e. F and Cl) can be well characterized by the electronic structure studies and the permanent electric dipole moments, el. The spectroscopic parameters have been precisely determined for the [17.7]1, [17.8]0+ and X1+ states of AuF, and the [17.07]1, [17.20]0+ and X1+ states of AuCl. The el have been determined for ground and excited states of AuF and AuCl. The results from the hyperfine analysis and Stark measurement support the assignments that the [17.7]1 and [17.8]0+ states of AuF are the components of a 3 state. Similarly, the analysis demonstrated the [19.07]1 and [19.20]0+ states are the components of the 3 state of AuCl.
Second, my study focused on AuO and AuS because the bonding between gold and sulfur/oxygen is a key component to numerous established and emerging technologies that have applications as far ranging as medical imaging, catalysis, electronics, and material science. The high-resolution spectra were record and analyzed to obtain the geometric and electronic structural data for the ground and excited states. The electric dipole moment, el, and the magnetic dipole moment, m, has been the precisely measured by applying external static electric and magnetic fields. el andm are used to give insight into the unusual complex bonding in these molecules.
In addition to direct studies on the gold-containing molecules, other studies of related molecules are included here as well. These works contain the pure rotation measurement of PtC, the hyperfine and Stark spectroscopic studies of PtF, and the Stark and Zeeman spectroscopic studies of MgH and MgD.
Finally, a perspective discussion and conclusion will summarize the results of AuF, AuCl, AuO, and AuS from this work (bond lengths, dipole moment, etc.). The highly quantitative information derived from this work is the foundation of a chemical description of matter and essential for kinetic energy manipulation via Stark and Zeeman interactions. This data set also establishes a synergism with computation chemists who are developing new methodologies for treating relativistic effects and electron correlation.
ContributorsZhang, Ruohan (Author) / Steimle, Timothy C. (Thesis advisor) / Williams, Peter (Committee member) / Richert, Ranko (Committee member) / Arizona State University (Publisher)
Created2017