Dissertations / Theses on the topic 'Chemistry, Analytical. Chemistry, Physical'

Energy generation via organic photovoltaic (OPV) cells provide many advantages over alternative processes including flexibility and price. However, more efficient OPVs are required in order to be competitive for applications. One way to enhance efficiency is through manipulation of exciton mechanisms within the OPV, for example by inserting a thin film of bathocuproine (BCP) and gold nanoparticles between the C₆₀/Al and ZnPc/ITO interfaces, respectively. We find that BCP increases efficiencies by 330% due to gains of open circuit voltage (V_oc) by 160% and short circuit current (J_sc) by 130%. However, these gains are complicated by the anomalous photovoltaic effect and an internal chemical potential. Exploration in the tuning of metallic nanoparticle deposition on ITO was done through four techniques. Drop casting Ag nanoparticle solution showed arduous control on deposited morphology. Spin-coating deposited very low densities of nanoparticles. Drop casting and spin-coating methods showed arduous control on Ag nanoparticle morphology due to clustering and low deposition density, respectively. Sputtered gold on glass was initially created to aid the adherence of Ag nanoparticles but instead showed a quick way to deposit aggregated gold nanoparticles. Electrodeposition of gold nanoparticles (AuNP) proved a quick method to tune nanoparticle morphology on ITO substrates. Control of deposition parameters affected AuNP size and distribution. AFM images of electrodeposited AuNPs showed sizes ranging from 39 to 58 nm. UV-Vis spectroscopy showed the presence of localized plasmon resonance through absorption peaks ranging from 503 to 614 nm. A linear correlation between electrodeposited AuNP size and peak absorbance was seen with a slope of 3.26 wavelength(nm)/diameter(nm).

Electrospray ionization (ESI) is a premier method for volatilizing and ionizing biological analytes for mass spectrometry. In conventional mass spectrometry (MS), the spectrum of mass-to-charge ratio (m/z) for an ensemble of ions is measured. ESI produces a distribution of charges for each ionized species, and the mass of each species is determined by assigning a charge state to each peak in the m/z spectrum. These peaks are difficult to resolve for species above the 100-kDa range because of peak broadening and shifting due to salt adducts, incomplete desolvation, and intrinsic heterogeneity. Without resolved charge states, the mass cannot be determined. Charge detection mass spectrometry (CDMS) offers a solution to this problem.

In CDMS, both the m/z and the charge are measured simultaneously for individual ions. Multiplying those measurements for each ion yields the mass. Thus, there is no need for charge state resolution in an m/z spectrum. CDMS can therefore be used to measure the masses of extremely heavy and heterogeneous analytes far beyond the capabilities of conventional MS. This comes at the cost of efficiency, since single ions are measured serially, and resolution, since the charge measurement historically has been imprecise in CDMS.

Here we report a nearly perfect charge measurement in CDMS by analyzing each ion for 3 s in an electrostatic ion trap and implementing a novel analysis method. Then we discuss spontaneous mass and charge losses of trapped ions. Finally, we discuss multiple applications of CDMS to bacteriophage P22. P22 capsids assemble into T = 7 ‘procapsids’ with the assistance of a distribution of scaffolding proteins; we report the typical width of that distribution. Next we report our observation of mass loss in P22 procapsids over the course of weeks due to precipitation of scaffolding proteins. Then we discuss how the charge on electrosprayed P22 capsids allows us to distinguish morphologies of P22 capsids. Finally, we report an accurate mass measurement of the infectious P22 phage, a >50 MDa particle containing nucleic acid and nine kinds of protein.

A novel concept to provide position-sensitivity to a microchannel plate (MCP) is described. While several designs exist to make MCPs position sensitive, all these designs are based upon collection of the electrons. In contrast, this approach utilizes an induced signal as the electron cloud emanates from an MCP and passes a wire plane. We demonstrate the validity of the concept by constructing a device that provides single electron detection with 98 μm position resolution (FWHM) over an area of 50 mm × 50 mm. The characteristics of the detector are described through both bench-top tests and simulation. After characterization of the detector, the sense wire detector was utilized for slow-neutron radiography. Furthermore, we utilized our knowledge of position-sensitive techniques to realize a beam-imaging MCP detector useful for radioactive beam facilities.

We have studied the pyrolysis of aromatic combustion intermediates using an array of detection techniques. The molecules investigated include cyclic aromatic molecules with hydrocarbon substituents (ethylbenzene, n-propylbenzene, isopropylbenzene, and styrene), oxygen-containing substituents (anisole and phenol), resonance stabilized radicals (benzyl radical and tropyl radical) and phenyl radical. At the exit of a resistively heated micro-reactor (1 mm inner diameter, 3 cm long), the pyrolysis fragments are detected using photoionization mass spectrometry (PIMS), matrix isolation vibrational spectroscopy, microwave spectroscopy, tunable VUV synchrotron-based PIMS, and tabletop VUV PIMS with photoelectron photoion coincidence spectroscopy (PEPICO). This array of detection methods allows for the identification of all possible fragments including metastables, radicals, and atoms. The findings allow for detailed mechanistic information regarding which pathways are active at different pyrolysis temperatures and can also be used to help identify products and individual isomers that are formed during the gas-phase thermal decomposition of aromatic systems. By providing direct experimental pyrolysis data, models for fuel decomposition and soot formation can be improved to help understand current combustion systems and eventually aid in the design of superior fuel sources in the near future.

The objective in this thesis is to study the structure of peptides using molecular spectroscopy. Molecular spectroscopy, both vibrational and electronic, can be used as a sensitive tool to study molecular structure. Since it is an inherently low resolution method, theoretical calculations are essential for a complete understanding of vibrational and electronic spectra. The first part of this thesis contains quantum chemical calculations of the molecular spectra of several small peptide systems with different secondary structures. Optical trapping is a method that allows for the manipulation of sub-micron scale objects using tightly focused laser light. Raman spectroscopy, which is sensitive to molecular vibrations also requires intense laser light. Combined with optical tweezing, Raman spectroscopy can prove to be a very powerful tool to study small sample volumes and probe single living cells. In the second part of this thesis, I detail the construction an such an instrument, an optical trapping Raman spectrometer (OTRS). Our OTRS can measure Raman spectra from sub micron systems while at the same time quantifying the mechanical forces that are acting upon them. Thus the OTRS can give insight into the relationship between mechanical forces acting upon cells and their molecular structure.

We studied the interactions of glyoxylic acid, pyruvic acid and oxalic acid with ammonium and corresponding sodium salts in aqueous solutions simulating a dark and radical free atmospheric aqueous aerosol condition. Cleavage of a carbon-carbon bond in pyruvic acid and glyoxylic acid leading to the decarboxylation was observed in the presence of ammo¬nium salts but was not observed from oxalic acid. At the beginning of the reaction, the decarboxylation appeared to proceeding slower compare to the later stage of reaction. The empirical rate constants for decarboxylation in the reaction solutions were estimated using a 'quasi-steady state' model: (i) glyoxylic acid and ammonium sulfate was 3.3 (± 0.7)×10^-8 M^-1 s^-1; (ii) glyoxylic acid and ammonium nitrate was 1.4 (± 0.3)×10^-8 M^-1 s^-1; (ii) glyoxylic acid and ammonium chloride was 1.9 (± 0.2)×10 ^-8 M^-1 s^-1; and (iii) pyruvic acid and ammonium sulfate was 15.8 (± 0.4)×10^-8 M ^-1 s^-1. Negligible CO₂ was observed in the experiments with the corresponding sodium salts indicating the ammonium ion or ammonia is facilitating the carbon-carbon bond cleavage leading to carboxyl fragmentation of the &agr;-oxo carboxylic acids. It was observed that pyruvic acid undergoes decarboxylation at least four times faster than that of glyoxylic acid under similar reaction conditions. This indicates that the structure of the acid plays an important role in the decarboxylation. In the case of pyruvic acid, the reaction is likely faster because of the inhibited hydration of the carbonyl moiety due to the inductive effect of the adjacent methyl group. A tentative set of reaction mechanisms is proposed involving nucleophilic attack by ammonia on the carbonyl carbon leading to fragmentation of the carbon-carbon bond between the carbonyl and carboxyl carbons. Similar carbon-carbon bond cleavage is anticipated for &agr;-dicarbonyl compounds, which are structurally similar to the &agr;-oxo carboxylic acids. In the absence of photolysis and under limited availability of OH radicals, the decay of pyruvic acid can be dominated by the reaction with ammonium sulfate and can be an order of magnitude higher than the loss via reaction with the OH radical. Under similar conditions the reactions with ammonium salts are likely be a major sink for &agr;-oxo carboxylic acids in the atmospheric aqueous phase.

Cytochrome P450s (P450s) are a superfamily of enzymes that catalyze oxidation of unactivated hydrocarbons. However, the means by which P450s control (1) regioselectivity of their activity and (2) specificity in their molecular recognition remain largely elusive. Toward investigation of the role of dynamics in the regioselectivity of the archetypal cytochrome P450cam (P450cam), two-dimensional infrared spectroscopy has been applied with heme-bound carbon monoxide (CO) as an infrared probe of the active site. The data support a model for P450cam regioselectivity in which binding of different substrates to P450cam variably stabilizes the active site into two distinct states, each associated with different dynamics linked to different levels of regioselectivity. To investigate the role of conformational heterogeneity in P450cam substrate specificity, infrared spectoscopy was combined with the site-specific incorporation of nitrile probes at distinct P450cam microenvironments. This approach enabled differentiation of changes experienced at each of those environments when d-camphor and/or CO binds to the active site. Finally, the impact of conformational heterogeneity on the affinity of substrate molecular recognition by wild-type and mutant P450cam was evaluated using both CO and nitrile probes. This study suggests that the nature of the conformations populated in the unbound states influences the affinity for different substrates. Collectively, these studies provide new insight into the roles of conformational heterogeneity and dynamics in P450cam activity. Furthermore, these studies help to lay the foundation for efforts toward understanding the roles of conformational heterogeneity and dynamics in the function of human P450s, for which unraveling the mechanisms involved in Phase I metabolism is a topic of great pharmacological concern.

The generation of attosecond-duration (1 as = 10^–18 s) coherent light through the process of high-order harmonic generation has opened the perspective for probing fundamental processes, such as photoionization, on the natural timescale of electron dynamics in matter. One probing technique is the attosecond streaking method, in which the momentum of the photoelectron is measured as a function of the time delay between the ionizing, attosecond extreme ultraviolet (XUV) pulse, and a weak, femtosecond near-infrared (NIR) pulse which streaks the momentum of the photoelectron, known as a streaking trace. The observed trace contains time information about the photoionization process in the form of a time offset to the vector potential of the streaking field, known as the streaking time delay. Theoretical simulations show that for one-photon ionization this time delay is accumulated by the photoelectron in the continuum when propagating away from the parent ion, whereas for resonant two-photon ionization there exists an additional absorption delay which depends on the properties of the XUV pulse. In this thesis, we use both analytical techniques and numerical simulations to study the contributions of the total time delay observed in streaking, and further explore applications of the streaking time delay to gain insights into the electron dynamics. We first derive an analytical formula for the streaking time delay in one-photon ionization. The predictions based on the model formula, which can be performed within seconds of computation time, are in good agreement with those of computationally extensive numerical simulations.

We demonstrate that the analytical formula not only allows deeper insight into the nature of the time delay, but also offers the opportunity to effectively analyze other theoretical interpretations and potential effects, such as the effect of a chirp in the ionizing attosecond pulse on the time delay measurement. We then apply time-dependent perturbation theory to derive an analytical formula for the absorption delay in resonant two-photon ionization. We use the analytical formula to demonstrate how the absorption delay can be controlled further by the attosecond pulse duration and central frequency in case of an isolated resonance. Furthermore, we show how multiple resonances within the bandwidth of the ionizing pulses as well as the streaking field influence the absorption delay in model systems as well as simple atoms and molecules. We conclude by exploring the option to apply isolated elliptically polarized attosecond pulses to obtain sub-attosecond temporal information via the observation of photoelectron angular distributions as a function of the ellipticity of the pulse.

The use of spectrofluorometers to examine nanomaterials is quite popular using either fluorescence or synchronous measurements. However, understanding how a material’s optical properties can influence spectral acquisition are of great importance to accurately characterize nanomaterials. This dissertation presents a series of computational and experimental studies aimed at enhancing the quantitative understanding of nanoparticle interactions with matter and photons. This allows for more reliable spectrofluorometer based acquisition of nanoparticle containing solutions.

Chapter I presents a background overview of the works described in this dissertation. Correction of the gold nanoparticle (AuNP) inner filter effect (IFE) on fluorophore fluorescence using PEGylated AuNPs as an external reference method is demonstrated in Chapter II. The AuNP IFE is corrected to quantify tryptophan fluorescence for surface adsorbed proteins. We demonstrate that protein adsorption onto AuNPs will only induce ~ 20% tryptophan fluorescence reduction instead of the commonly assumed 100% reduction.

Using water Raman intensities to determine the effective path lengths of a spectrofluorometer for correction of fluorophore fluorescence is discussed in Chapter III. Using Ni(NO3)2 and K2Cr2O7 as Raman IFE references, the excitation and emission path lengths are found to exhibit chromophore and fluorophore independence, however path lengths are spectrofluorometer dependent.

Finally, ratiometric resonance synchronous spectroscopy (R2S2) is discussed in Chapter IV. Using a combination of UV-vis and R2S2 spectroscopy, the optical cross sections of a wide range of nanomaterials were determined. Also on-resonance fluorescence in solution is demonstrated for the first time. The nanoparticles discussed range from photon absorbers, scatterers, simultaneous photon absorbers and scatterers, all the way to simultaneous photon absorbers, scatterers, and emitters.

Over recent years, Ion Mobility–Mass Spectrometry (IMS–MS) measurements have become a widely used tool in a number of disciplines of scientific relevance, including, in particular, the structural characterization of mass-selected biomolecules such as proteins, peptides, or lipids, brought into the gas-phase using a variety of ionization methods. In these structural studies, the measured electrical mobilities are customarily interpreted in terms of a collision cross-section, based on the classic kinetic theory of ion mobility. For ideal ions interacting as smooth, rigid-elastic hard-spheres with also-spherical gas molecules, this collision cross-section (CCS) is identical to the true, geometric cross section. On the other hand, for real ions with non-perfectly spherical geometries and atomically-rough surfaces, subject to long-range interactions with the gas molecules, the expression for the CCS can become fairly intricate.

This complexity has frequently led to the use of helium as the drift gas of choice for structural studies, given its small size and mass, its low polarizability (minimizing long-range interactions), and its sphericity and lack of internal degrees of freedom, all of which contribute to reduce departures between measured and true cross-sections. Recently, however, a growing interest has arisen for using moderately-polarizable gases such as air, nitrogen, or carbon dioxide (among others) in these structural studies, due to a number of advantages they present over helium, including their higher breakdown voltages (allowing for higher instrument resolutions) and better pumping characteristics. This shift has, nevertheless, remained objectionable in the eye of those seeking to infer accurate structural information from ion mobility measurements and, accordingly, there is a critical need to study whether or not measurements carried out in such gases may be corrected for the finite size of the gas molecules and their long-range interactions with the ions, in order to provide cross-sections truly representative of ion geometry. A first step to address this matter is undertaken here for the special case of nearly-spherical, nanometer-sized ions.

In order to attain this goal, we have performed careful and accurate IMS–MS measurements of hundreds of electrospray-generated nanodrops of the ionic liquid (IL) 1-ethyl-3-methylimidazolium tetrafluoroborate (EMI-BF ₄), in a variety of drift gases (air, CO₂, and argon), covering a wide range of temperatures (20-100 °C, for both air and CO₂), and considering nanodrops of both positive and negative polarity (the latter in room-temperature air only). Thanks to the combined measurement of the mass and mobility of these nanodrops, we are able to simultaneously determine a mobility-based collision cross-section and a mass-based diameter (taking into account the finite compressibility of the IL matter) for each of them, which then allows us to establish a comparison between the two.

Over the entire range of experimental conditions investigated, our measurements show that the electrical mobilities of these nearly-spherical, multiply-charged IL nanodrops are accurately described by an adapted version of the well-known Stokes—Millikan (SM) law for the mobility of spherical ions, with the nanodrop diameter augmented by an effective gas-molecule collision diameter, and including a correction factor to account for the effect of ion—induced dipole (polarization) interactions, which result in the mobility decreasing linearly with the ratio between the polarization and thermal energies of the ion–neutral system at contact. The availability of this empirically-validated relation enables us, in turn, to determine true, geometric cross-sections for globular ions from IMS—MS measurements performed in gases other than helium, including molecular or atomic gases with moderate polarizabilities. In addition, the observed dependence of the experimentally-determined values for the effective gas-molecule collision diameter and the parameters involved in the polarization correction on drift-gas nature, temperature, and nanodrop polarity, is further evaluated in the light of the results of numerical calculations of the electrical mobilities, in the free-molecule regime, of spherical ions subject to different types of scattering with the gas molecules and interacting with the latter under an ion–induced dipole potential. Among the number of findings derived from this analysis, a particularly notable one is that nanodrop–neutral scattering seems to be of a diffuse (cf. elastic and specular) character in all the scenarios investigated, including the case of the monatomic argon, which therefore suggests that the atomic-level surface roughness of our nanodrops and/or the proximity between their internal degrees of freedom, rather than the sphericity (or lack of it) and the absence (or presence) of internal degrees of freedom in the gas molecules, are what chiefly determine the nature of the scattering process.

The development of better energy conversion and storage devices, such as fuel cells and batteries, is crucial for reduction of our global carbon footprint and improving the quality of the air we breathe. However, both of these technologies face important challenges. The development of lower cost and better electrode materials, which are more durable and allow more control over the electrochemical reactions occurring at the electrode/electrolyte interface, is perhaps most important for meeting these challenges. Hence, full characterization of the electrochemical processes that occur at the electrodes is vital for intelligent design of more energy efficient electrodes.

X-ray absorption spectroscopy (XAS) is a short-range order, element specific technique that can be utilized to probe the processes occurring at operating electrode surfaces, as well for studying the amorphous materials and nano-particles making up the electrodes. It has been increasingly used in recent years to study fuel cell catalysts through application of the Δ&mgr; XANES technique, in combination with the more traditional X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) techniques. The Δ&mgr; XANES data analysis technique, previously developed and applied to heterogeneous catalysts and fuel cell electrocatalysts by the GWU group, was extended in this work to provide for the first time space resolved adsorbate coverages on both electrodes of a direct methanol fuel cell. Even more importantly, the Δ&mgr; technique was applied for the first time to battery relevant materials, where bulk properties such as the oxidation state and local geometry of a cathode are followed.