16 resultados para Ion removal
em CaltechTHESIS
Resumo:
A novel spectroscopy of trapped ions is proposed which will bring single-ion detection sensitivity to the observation of magnetic resonance spectra. The approaches developed here are aimed at resolving one of the fundamental problems of molecular spectroscopy, the apparent incompatibility in existing techniques between high information content (and therefore good species discrimination) and high sensitivity. Methods for studying both electron spin resonance (ESR) and nuclear magnetic resonance (NMR) are designed. They assume established methods for trapping ions in high magnetic field and observing the trapping frequencies with high resolution (<1 Hz) and sensitivity (single ion) by electrical means. The introduction of a magnetic bottle field gradient couples the spin and spatial motions together and leads to a small spin-dependent force on the ion, which has been exploited by Dehmelt to observe directly the perturbation of the ground-state electron's axial frequency by its spin magnetic moment.
A series of fundamental innovations is described m order to extend magnetic resonance to the higher masses of molecular ions (100 amu = 2x 10^5 electron masses) and smaller magnetic moments (nuclear moments = 10^(-3) of the electron moment). First, it is demonstrated how time-domain trapping frequency observations before and after magnetic resonance can be used to make cooling of the particle to its ground state unnecessary. Second, adiabatic cycling of the magnetic bottle off between detection periods is shown to be practical and to allow high-resolution magnetic resonance to be encoded pointwise as the presence or absence of trapping frequency shifts. Third, methods of inducing spindependent work on the ion orbits with magnetic field gradients and Larmor frequency irradiation are proposed which greatly amplify the attainable shifts in trapping frequency.
The dissertation explores the basic concepts behind ion trapping, adopting a variety of classical, semiclassical, numerical, and quantum mechanical approaches to derive spin-dependent effects, design experimental sequences, and corroborate results from one approach with those from another. The first proposal presented builds on Dehmelt's experiment by combining a "before and after" detection sequence with novel signal processing to reveal ESR spectra. A more powerful technique for ESR is then designed which uses axially synchronized spin transitions to perform spin-dependent work in the presence of a magnetic bottle, which also converts axial amplitude changes into cyclotron frequency shifts. A third use of the magnetic bottle is to selectively trap ions with small initial kinetic energy. A dechirping algorithm corrects for undesired frequency shifts associated with damping by the measurement process.
The most general approach presented is spin-locked internally resonant ion cyclotron excitation, a true continuous Stern-Gerlach effect. A magnetic field gradient modulated at both the Larmor and cyclotron frequencies is devised which leads to cyclotron acceleration proportional to the transverse magnetic moment of a coherent state of the particle and radiation field. A preferred method of using this to observe NMR as an axial frequency shift is described in detail. In the course of this derivation, a new quantum mechanical description of ion cyclotron resonance is presented which is easily combined with spin degrees of freedom to provide a full description of the proposals.
Practical, technical, and experimental issues surrounding the feasibility of the proposals are addressed throughout the dissertation. Numerical ion trajectory simulations and analytical models are used to predict the effectiveness of the new designs as well as their sensitivity and resolution. These checks on the methods proposed provide convincing evidence of their promise in extending the wealth of magnetic resonance information to the study of collisionless ions via single-ion spectroscopy.
Resumo:
This dissertation describes studies of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) using unnatural amino acid mutagenesis to gain high precision insights into the function of these important membrane proteins.
Chapter 2 considers the functional role of highly conserved proline residues within the transmembrane helices of the D2 dopamine GPCR. Through mutagenesis employing unnatural α-hydroxy acids, proline analogs, and N-methyl amino acids, we find that lack of backbone hydrogen bond donor ability is important to proline function. At one proline site we additionally find that a substituent on the proline backbone N is important to receptor function.
In Chapter 3, side chain conformation is probed by mutagenesis of GPCRs and the muscle-type nAChR. Specific side chain rearrangements of highly conserved residues have been proposed to accompany activation of these receptors. These rearrangements were probed using conformationally-biased β-substituted analogs of Trp and Phe and unnatural stereoisomers of Thr and Ile. We also modeled the conformational bias of the unnatural Trp and Phe analogs employed.
Chapters 4 and 5 examine details of ligand binding to nAChRs. Chapter 4 describes a study investigating the importance of hydrogen bonds between ligands and the complementary face of muscle-type and α4β4 nAChRs. A hydrogen bond involving the agonist appears to be important for ligand binding in the muscle-type receptor but not the α4β4 receptor.
Chapter 5 describes a study characterizing the binding of varenicline, an actively prescribed smoking cessation therapeutic, to the α7 nAChR. Additionally, binding interactions to the complementary face of the α7 binding site were examined for a small panel of agonists. We identified side chains important for binding large agonists such as varenicline, but dispensable for binding the small agonist ACh.
Chapter 6 describes efforts to image nAChRs site-specifically modified with a fluorophore by unnatural amino acid mutagenesis. While progress was hampered by high levels of fluorescent background, improvements to sample preparation and alternative strategies for fluorophore incorporation are described.
Chapter 7 describes efforts toward a fluorescence assay for G protein association with a GPCR, with the ultimate goal of probing key protein-protein interactions along the G protein/receptor interface. A wide range of fluorescent protein fusions were generated, expressed in Xenopus oocytes, and evaluated for their ability to associate with each other.
Resumo:
An experimental study was made of the interaction of phosphate rock and aqueous inorganic orthophosphate, calcium, and hydroxyl ions. A model of the reaction was developed by observing electron diffraction patterns in conjunction with concentration changes of chemical components. The model was applied in explaining the performance of batch suspensions of powdered phosphate rock and packed columns of granular phosphate rock. In both cases the reaction consisted initially of a rapid nucleation phase that occurred in a time period of minutes. In the batch system the calcium phosphate nuclei then ripened into larger micro-crystals of hydroxyapatite, which eventually became indistinguishable from the original phosphate rock surface. During column operation the high supersaturation ratio that existed after the rapid nucleation phase resulted in a layer of small nuclei that covered a slowly growing hydroxyapatite crystal.
The column steady-state rate constant was found to increase with increasing temperature, pH, and fluoride concentration, and to decrease with increasing concentrations of magnesium sulfate, ammonium chloride, and bicarbonate ion.
An engineering feasibility study indicated that, based on economic considerations, nucleation of apatite on phosphate rock ore has a potential use as a wastewater phosphate removal treatment process.
Resumo:
Natural waters may be chemically studied as mixed electrolyte solutions. Some important equilibrium properties of natural waters are intimately related to the activity-concentration ratios (i.e., activity coefficients) of the ions in solution. An Ion Interaction Model, which is based on Pitzer's (1973) thermodynamic model, is proposed in this dissertation. The proposed model is capable of describing the activity coefficient of ions in mixed electrolyte solutions. The effects of temperature on the equilibrium conditions of natural waters and on the activity coefficients of the ions in solution, may be predicted by means of the Ion Interaction Model presented in this work.
The bicarbonate ion, HCO3-, is commonly found in natural waters. This anion plays an important role in the chemical and thermodynamic properties of water bodies. Such properties are usually directly related to the activity coefficient of HCO3- in solution. The Ion Interaction Model, as proposed in this dissertation, is used to describe indirectly measured activity coefficients of HCO3- in mixed electrolyte solutions.
Experimental pH measurements of MCl-MHCO3 and MCl-H2CO3 solutions at 25°C (where M = K+, Na+, NH4+, Ca2+ or Mg2+) are used in this dissertation to evaluate indirectly the MHCO3 virial coefficients. Such coefficients permit the prediction of the activity coefficient of HCO3- in mixed electrolyte solutions. The Ion Interaction Model is found to be an accurate method for predicting the activity coefficient of HCO3- within the experimental ionic strengths (0.2 to 3.0 m). The virial coefficients of KHCO3 and NaHCO3 and their respective temperature variations are obtained from similar experimental measurements at 10° and 40°C. The temperature effects on the NH4HCO3, Ca(HCO3)2, and Mg(HCO3)2 virial coefficients are estimated based on these results and the temperature variations of the virial coefficients of 40 other electrolytes.
Finally, the Ion Interaction Model is utilized to solve various problems of water chemistry where bicarbonate is present in solution.
Resumo:
The electrochemical and electrocatalytic behavior of a series of heteropolytungstate anions in which a tungsten atom in the well known Keggin structure has been replaced by an iron atom is described. All of the iron substituted ions exhibit a one electron reversible couple associated with the Fe3+ center and a pair of two electron waves attributed to electron addition and removal from the tungsten oxo framework. The pH and ionic strength effects upon the various electrochemical processes are discussed and interpreted in terms of a competition between protonation and ion pairing of the highly negatively charged ions.
The anions are efficient catalysts for the electroreduction of hydrogen peroxide. A catalytic mechanism involving a formally Fe(IV) intermediate is proposed. Pulse radiolysis experiments were employed to detect the intermediate and evaluate the rate constants for the reactions in which it is formed and decomposed. A chain mechanism for the catalytic decomposition of hydrogen peroxide in which the Fe center shuttles between the +2, +3, and +4 oxidation states is proposed to explain the non-integral stoichiometry observed for the iron substituted polytungstate catalyzed electroreduction of hydrogen peroxide.
The anions are also efficient electrocatalyst for the electrochemical conversion of nitric oxide to ammonia. The catalyzed reduction does not produce hydroxylamine as an intermediate and appears to depend upon the ability of the multiply reduced heteropolytungstates to deliver several electrons to the bound NO group in a concerted step. A valuable feature of the heteropolytungstates is the ease at which the formal potentials of the several redox couples they exhibit may be shifted by changing the identity of the central heteroatom. Exploitation of this feature provided diagnostic information that was decisive in establishing the mechanism of electrocatalytic reduction.
The iron substituted heteropolytungstates are not degraded by repeated cycling between their oxidized and reduced states. They also show superior activity compared to their unsubstituted analogues, indicating that the Fe center acts as a binding site that facilitates inner-sphere electron transfer processes. The basic electrochemistry of several other transition metal substituted Keggin ions is also described.
Resumo:
Part I. Novel composite polyelectrolyte materials were developed that exhibit desirable charge propagation and ion-retention properties. The morphology of electrode coatings cast from these materials was shown to be more important for its electrochemical behavior than its chemical composition.
Part II. The Wilhelmy plate technique for measuring dynamic surface tension was extended to electrified liquid-liquid interphases. The dynamical response of the aqueous NaF-mercury electrified interphase was examined by concomitant measurement of surface tension, current, and applied electrostatic potential. Observations of the surface tension response to linear sweep voltammetry and to step function perturbations in the applied electrostatic potential (e.g., chronotensiometry) provided strong evidence that relaxation processes proceed for time-periods that are at least an order of magnitude longer than the time periods necessary to establish diffusion equilibrium. The dynamical response of the surface tension is analyzed within the context of non-equilibrium thermodynamics and a kinetic model that requires three simultaneous first order processes.
Resumo:
Several different methods have been employed in the study of voltage-gated ion channels. Electrophysiological studies on excitable cells in vertebrates and molluscs have shown that many different voltage-gated potassium (K+) channels and sodium channels may coexist in the same organism. Parallel genetic studies in Drosophila have identified mutations in several genes that alter the properties of specific subsets of physiologically identified ion channels. Chapter 2 describes molecular studies that identify two Drosophila homologs of vertebrate sodium-channel genes. Mutations in one of these Drosophila sodium-channel genes are shown to be responsible for the temperature-dependent paralysis of a behavioural mutant parats. Evolutionary arguments, based on the partial sequences of the two Drosophila genes, suggest that subfamilies of voltage-gated sodium channels in vertebrates remain to be identified.
In Drosophila, diverse voltage-gated K+ channels arise from alternatively spliced mRNAs generated at the Shaker locus. Chapter 3 and the Appendices describe the isolation and characterization of several human K+-channel genes, similar in sequence to Shaker. Each of these human genes has a highly conserved homolog in rodents; thus, this K+-channel gene family probably diversified prior to the mammalian radiation. Functional K+ channels encoded by these genes have been expressed in Xenopus oocytes and their properties have been analyzed by electrophysiological methods. These studies demonstrate that both transient and noninactivating voltage-gated K+ channels may be encoded by mammalian genes closely related to Shaker. In addition, results presented in Appendix 3 clearly demonstrate that independent gene products from two K+-channel genes may efficiently co-assemble into heterooligomeric K+ channels with properties distinct from either homomultimeric channel. This finding suggests yet another molecular mechanism for the generation of K+-channel diversity.
Resumo:
The quality of a thermoelectric material is judged by the size of its temperature de- pendent thermoeletric-figure-of-merit (zT ). Superionic materials, particularly Zn4Sb3 and Cu2Se, are of current interest for the high zT and low thermal conductivity of their disordered, superionic phase. In this work it is reported that the super-ionic materials Ag2Se, Cu2Se and Cu1.97Ag0.03Se show enhanced zT in their ordered, normal ion-conducting phases. The zT of Ag2Se is increased by 30% in its ordered phase as compared to its disordered phase, as measured just below and above its first order phase transition. The zT ’s of Cu2Se and Cu1.97Ag0.03Se both increase by more than 100% over a 30 K temperatures range just below their super-ionic phase transitions. The peak zT of Cu2Se is 0.7 at 406 K and of Cu1.97Ag0.03Se is 1.0 at 400 K. In all three materials these enhancements are due to anomalous increases in their Seebeck coefficients, beyond that predicted by carrier concentration measurements and band structure modeling. As the Seebeck coefficient is the entropy transported per carrier, this suggests that there is an additional quantity of entropy co-transported with charge carriers. Such co-transport has been previously observed via co-transport of vibrational entropy in bipolaron conductors and spin-state entropy in NaxCo2O4. The correlation of the temperature profile of the increases in each material with the nature of their phase transitions indicates that the entropy is associated with the thermodynamcis of ion-ordering. This suggests a new mechanism by which high thermoelectric performance may be understood and engineered.
Resumo:
The disolvated proton, H(OH2)2+ is employed as a chemical reagent in low pressure (˂ 10-5 torr) investigations by ion cyclotron resonance spectroscopy. Since termolecular reactions are absent at low pressure, disolvated protons are not generally observed. However H(OH2)2+ is produced in a sequence of bimolecular reactions in mixtures containing H2O and one of a small number of organohalide precursors. Then a series of hydrated Lewis bases is produced by H3O+ transfer from H(OH2)2+. In Chapter II, the relative stability of hydrated bases containing heteroatoms of both first and second row elements is determined from the preferred direction of H3O+ transfer between BH(OH2)+ complexes. S and P containing bases are shown to bind H3O+ more weakly than O and N bases with comparable proton affinities. A simple model of hydrogen bonding is proposed to account for these observations.
H+ transfer from H(OH2)2+ to several Lewis bases also occurs at low pressure. In Chapter III the relative importance of H3O+ transfer and H+ transfer from H(OH2)2+ to a series of bases is observed to be a function of base strength. Beginning with CH3COOH, the weakest base for which H+ transfer is observed, the importance of H+ transfer increases with increasing proton affinity of the acceptor base. The nature of neutral products formed from H(OH2)2+ by loss of H+ is also considered.
Chapters IV and V deal with thermochemistry of small fluorocarbons determined by photoionization mass spectrometry. The enthalpy of formation of CF2 is considered in Chapter IV. Photoionization of perfluoropropylene, perfluorocyclopropane, and trifluoromethyl benzene yield onsets for ions formed by loss of a CF2 neutral fragment. Earlier determinations of ΔH°f298 (CF2) are reinterpreted using updated thermochemical values and compared with results of this study. The heat of formation of neutral perfluorocyclopropane is also derived. Finally, the energetics of interconversion of perfluoropropylene and perfluorocyclopropane are considered for both the neutrals and their molecular ions.
In Chapter V the heats of formation of CF3+ and CF3I+are derived from photoionization of CF3I. These are considered with respect to ion-molecule reactions observed in CF3I monitored by the techniques of ion cyclotron resonance spectroscopy. Results obtained in previous experiments are also compared.
Resumo:
Acetyltransferases and deacetylases catalyze the addition and removal, respectively, of acetyl groups to the epsilon-amino group of protein lysine residues. This modification can affect the function of a protein through several means, including the recruitment of specific binding partners called acetyl-lysine readers. Acetyltransferases, deacetylases, and acetyl-lysine readers have emerged as crucial regulators of biological processes and prominent targets for the treatment of human disease. This work describes a combination of structural, biochemical, biophysical, cell-biological, and organismal studies undertaken on a set of proteins that cumulatively include all steps of the acetylation process: the acetyltransferase MEC-17, the deacetylase SIRT1, and the acetyl-lysine reader DPF2. Tubulin acetylation by MEC-17 is associated with stable, long-lived microtubule structures. We determined the crystal structure of the catalytic domain of human MEC-17 in complex with the cofactor acetyl-CoA. The structure in combination with an extensive enzymatic analysis of MEC-17 mutants identified residues for cofactor and substrate recognition and activity. A large, evolutionarily conserved hydrophobic surface patch distal to the active site was shown to be necessary for catalysis, suggesting that specificity is achieved by interactions with the alpha-tubulin substrate that extend outside of the modified surface loop. Experiments in C. elegans showed that while MEC-17 is required for touch sensitivity, MEC-17 enzymatic activity is dispensible for this behavior. SIRT1 deacetylates a wide range of substrates, including p53, NF-kappaB, FOXO transcription factors, and PGC-1-alpha, with roles in cellular processes ranging from energy metabolism to cell survival. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an apo form and in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a beta-hairpin structure that complements the beta-sheet of the NAD^+-binding domain, covering an essentially invariant, hydrophobic surface. A comparison of the apo and cofactor bound structures revealed conformational changes throughout catalysis, including a rotation of a smaller subdomain with respect to the larger NAD^+-binding subdomain. A biochemical analysis identified key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain. DPF2 represses myeloid differentiation in acute myelogenous leukemia. Finally, we solved the crystal structure of the tandem PHD domain of human DPF2. We showed that DPF2 preferentially binds H3 tail peptides acetylated at Lys14, and binds H4 tail peptides with no preference for acetylation state. Through a structural and mutational analysis we identify the molecular basis of histone recognition. We propose a model for the role of DPF2 in AML and identify the DPF2 tandem PHD finger domain as a promising novel target for anti-leukemia therapeutics.
Resumo:
Presented in the first part of this thesis is work performed on the ionizing energy beam induced adhesion enhancement of thin (~ 500 Angstrom) Au films on GaAs substrates. The ionizing beam, employed in the present thesis, is the MeV ions (i.e., 16O, 19F, and 35Cl), with energies between 1 and 20 MeV. Using the "Scratch" test for adhesion measurement, and ESCA for chemical analysis of the film-substrate interface, the native oxide layer at the interface is shown to play an important role in the adhesion enhancement by the ionizing radiation. A model is discussed which explains the experimental data on the the dependence of adhesion enhancement on the energy which was deposited into electronic processes at the interface. The ESCA data indicate that the chemical bonds (or compounds), which are responsible for the increase in the thin film adherence, are hydroxides rather than oxides.
In the second part of the thesis we present a research performed on the radiation damage in GaAs crystals produced by MeV ions. Lattice parameter dilatation in the surface layers of the GaAs crystals becomes saturated after a high dose bombardment at room temperature. The strain produced by nuclear collisions is shown to relax partially due to electronic excitation (with a functional dependence on the nuclear and electronic stopping power of bombarding ions). Data on the GaAs and GaP crystals suggest that low temperature recovery stage defects produce major crystal distortion. The x-ray rocking curve technique with a dynamical diffraction theory analysis provides the depth distribution of the strain and damage in the MeV ion bombarded crystals.
Resumo:
The work described in this thesis represents an attempt to summarize to date the information collected on the process of high energy heavy ion induced enhanced adhesion. Briefly, the process involves the irradiation of materials covered by thin (≾3μm) films with high energy (E > 200 keV I nucleon) heavy ion beams (such as Fluorine or Chlorine). Enhanced adhesion has been observed on all material combinations tested, including metal on metal, metal on semiconductor, metal on dielectric and dielectric on dielectric systems. In some cases, the enhancement can be quite large, so that a film that could be wiped off a substrate quite easily before irradiation can withstand determined scrubbing afterwards.
Very little is understood yet about this adhesion mechanism, so what is presented are primarily observations about systems studied, and descriptions of the actual preparation and irradiation of samples used. Some discussion is presented about mechanisms that have been considered but rejected.
Resumo:
I. Nuclear magnetic resonance spectra of appropriately substituted ferrocenylcarbonium ions reveal the α-protons of the substituted ring to be more shielded than β-protons. The observation is discussed in terms of various models proposed for the ferrocenylcarbonium ion and is found to support a model in which the iron is bonded to all six carbona of the substituted ring.
II. Ferrocene catalyzes the photoisomerization of the piperylenes and the photodimerization of isoprene. Our results suggest a mechanism in which a complex of ferrocene and diene is excited to its second singlet state which dissociates to a triplet-state ferrocene molecule and a triplet-state diene molecule. The triplet-state diene, then, proceeds to isomerize or attack ground-state diene to form dimers.
Resumo:
This thesis presents a topology optimization methodology for the systematic design of optimal multifunctional silicon anode structures in lithium-ion batteries. In order to develop next generation high performance lithium-ion batteries, key design challenges relating to the silicon anode structure must be addressed, namely the lithiation-induced mechanical degradation and the low intrinsic electrical conductivity of silicon. As such, this work considers two design objectives of minimum compliance under design dependent volume expansion, and maximum electrical conduction through the structure, both of which are subject to a constraint on material volume. Density-based topology optimization methods are employed in conjunction with regularization techniques, a continuation scheme, and mathematical programming methods. The objectives are first considered individually, during which the iteration history, mesh independence, and influence of prescribed volume fraction and minimum length scale are investigated. The methodology is subsequently extended to a bi-objective formulation to simultaneously address both the compliance and conduction design criteria. A weighting method is used to derive the Pareto fronts, which demonstrate a clear trade-off between the competing design objectives. Furthermore, a systematic parameter study is undertaken to determine the influence of the prescribed volume fraction and minimum length scale on the optimal combined topologies. The developments presented in this work provide a foundation for the informed design and development of silicon anode structures for high performance lithium-ion batteries.
Resumo:
Spreading depression (SD) is a phenomenon observed in several sections of vertebrate central nervous system. It can occur spontaneously or be evoked by a variety of stimuli, and consists of a wave of depression of the normal electrical activity of the nervous tissue which spreads slowly in all directions in the tissue. This wave of depression is accompanied by several concomitants including ion movements. All the concomitants of SD can be explained by an increase in the sodium permeability of the plasma membranes of cellular elements involved in this phenomenon.
In the chicken retina, SD is accompanied by a transparency change which can be detected with the naked eye. The isolated retina is a thin (0.1 mm) membrane in which the extracellular fluid quickly and completely equilibrates with the incubation solutions. This preparation was therefore used to study the ion movements during SD by measuring and comparing the ion contents and the extracellular space (ECS) of retinas incubated in various solutions of which some inhibited SD, whereas others allowed this phenomenon to occur.
The present study has shown that during SD there is a shift of extracellular sodium into the intracellular compartment of the retina, a release of intracellular K and a decrease in the magnitude of ECS. These results are in agreement with previous postulates about SD, although the in vitro experimental condition makes the ion movements appear larger and the loss of ECS smaller than observed in the intact cortical tissue. The movements of Na and K, in opposite directions, are reversible. The development and magnitudes of SD is very little affected by deprivation of the oxygen supply.
It was established that the inward sodium shift is not a consequence of an arrest of the Na-pump. It can be prevented, together with SD by the membrane stabilizers, magnesium and procaine. Spreading depression and the ion movements are incompletely inhibited by tetrodotoxin, which blocks the sodium influx into nerve fibers during the action potential. The replacement of Na in the bathing solution by Li does not prevent SD, which is accompanied by Li accumulation in the intracellular compartment. From these experiments and others it was concluded that the mechanism underlying SD and the ion shifts is an increase in the sodium permeability of cell membranes.