High-resolution infrared absorption spectra have been analyzed for two bicyclo[111]pentane isotopologues, C₅H₈ (-d₀) and C₅H₇D (-d₁), where in the latter the D-atom replaces a hydrogen on the C₃ symmetry axis such that the molecular symmetry is reduced from D₃ₕ to C₃ᵥ. Two (a"₂) parallel bands, v₁₇ and v₁₈, of bicyclopentane-d₀...
This paper is a continuation of earlier work in which the high resolution infrared spectrum of [1.1.1]propellane was measured and its k and l structure resolved for the first time. Here we present results from an analysis of more than 16,000 transitions involving three fundamental bands v₁₀ (E' - A'₁),...
The photoelectron spectra of a series of halogenated
molecules have been investigated in the gas phase. Both
core-ionization energies and Auger kinetic energies were
measured to probe the nature of the interaction that holds
a core electron to the molecule.
It was found that satellite structure (shake) could be
used...
Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes 2 the conversion of cysteine (Cys) to cysteine sulfinic acid (CSA) by an unclarified mechanism. 3 One structural study revealed a Cys-persulfenate (or Cys-persulfenic acid) formed in the active 4 site, but quantum mechanical calculations have been used...
Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes 2 the conversion of cysteine (Cys) to cysteine sulfinic acid (CSA) by an unclarified mechanism. 3 One structural study revealed a Cys-persulfenate (or Cys-persulfenic acid) formed in the active 4 site, but quantum mechanical calculations have been used...
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, Corvallis, OR 97331 8
b
Department ofMolecular Medicine, 618 Tower Rd, Cornell University, Ithaca, NY
Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes 2 the conversion of cysteine (Cys) to cysteine sulfinic acid (CSA) by an unclarified mechanism. 3 One structural study revealed a Cys-persulfenate (or Cys-persulfenic acid) formed in the active 4 site, but quantum mechanical calculations have been used...
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is weaker than that of the Cys93 Sγ, consistent with the iron having 5
decreased occupancy. We
A variety of laser spectroscopic methods are employed in this
thesis research for studies of CF₃NO, an interesting model
photodissociative system, and for investigation of low energy rotations
and vibrations of small molecules and low molecular weight clusters in
free jet expansions.
Nonradiative energy decay for electronically excited CF₃NO is...
A high-spectral resolution laser-excited molecular fluorescence
system was developed that utilizes a pulsed supersonic expansion to
simplify the fluorescence excitation spectra of large, gas-phase
aromatic molecules diluted in an excess of a monatomic gas. A
microcomputer was used to control and synchronize the instrumental
components, which included a Chromatix CMX-4...
A new experimental apparatus was built at Oregon State University to perform high resolution stimulated Raman spectroscopy in a pulsed molecular jet at state densities of the order of 10¹¹ cm⁻³. The technique uses a stimulated Raman step to first populate a vibrational/rotational level and then a resonantly enhanced multiphoton...
The capabilities of the Tektronix Model J2C/7J20 Rapid Scanning
Spectrometer for the determination of molecular species resulting from
Otto cycle combustion were experimentally investigated after a literature
search of the subject area. Combustion of hydrogen-air, carbon monoxideair,
and gasoline-air mixtures in the combustion chamber of a Cooperative
Fuel Research engine...
Two nonlinear optical experiments are presented in which the third-order electronic susceptibility of molecules is used to generate Raman signals. The first one uses a single 532 nm beam from a Nd:YAG laser to produce Stimulated Raman Scattering in benzene and deuterated benzene. With a simple experimental set-up, stimulated emission...
RNA silencing is an evolutionarily conserved system that
functions as an antiviral mechanism in higher plants and
insects. To counteract RNA silencing, viruses express
silencing suppressors that interfere with both siRNA- and
microRNA-guided silencing pathways. We used comparative
in vitro and in vivo approaches to analyse the molecular
mechanism of...
The temporal and spatial characteristics of a laser microprobe plume were investigated using the spectroscopic methods of emission, absorption and fluorescence. The plume was produced by rapid vaporization of a small quantity (1 μg) of a solid sample using a focussed pulsed dye laser (110 MW/cm²). For absorption and fluorescence...
A new x-ray source capable of operating at up to 80
watts has been designed and developed, and put to use with
the Oregon State University Cylindrical Electrostatic
Analyzer. The new source produces over four times the
photoelectron intensity of its predecessor, from gaseous
samples, and accommodates a wider selection...
There is increasing evidence that aging is affected by biological (circadian) clocks – the internal mechanisms that coordinate daily changes in gene expression, physiological functions and behavior with external day/night cycles. Recent data suggest that disruption of the mammalian circadian clock results in accelerated aging and increased age‐related pathologies such...
Background: Considering the pharmacokinetic and pharmacodynamic aspects of different medications, it is plausible that the age of a smoker could affect the half-life of these drugs. The aim of this study was to compare the effectiveness of smoking cessation drugs (nicotine replacement therapy, bupropion, and varenicline) used either in isolation...
The interaction of lecithin-cholesterol acyltransferase (LCAT) with apolipoprotein A-I (apoA-I) plays a critical role in highdensity lipoprotein (HDL) maturation.Wepreviously identified a highly solvent-exposed apoA-I loop domain (Leu¹⁵⁹–Leu¹⁷⁰) in nascent HDL, the so-called “solar flare” (SF) region, and proposed that it serves as an LCAT docking site (Wu, Z., Wagner, M....
Cadmium is a common impurity in phosphatic fertilizers and may contribute to soil Cd accumulation. Changes in total and bioavailable Cd burdens to agricultural soils and the potential for plant Cd accumulation resulting from fertilizer input was investigated. Three year field studies were conducted using three dose levels of cadmium-rich,...
Plasma sources with multiple electrodes have been developed and
characterized in this research for atomic emission spectroscopy.
Multi-electrode plasma sources use electrodes to shape the plasma in
order to continuously entrain a sample stream in the center of hot
plasma, in a manner similar to an inductively coupled plasma (ICP)...
A method by which barrier heights in potential functions
hindering internal rotation in organic molecules can be obtained solely
from thermal data for the solid phase is studied. The observed
heat capacities are analyzed in terms of contributions from the lattice
vibrations, the intramolecular vibrations, the expansion of the lattice,...
The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream
analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming
more prevalent in the agricultural and environmental sciences and many...
We report vibrational information of both the first electronically excited state and the ground
cationic state of jet-cooled triphenylene via the techniques of resonantly enhanced multiphoton
ionization (REMPI) and zero kinetic energy (ZEKE) photoelectron spectroscopy. The first excited
electronic state S₁ of the neutral molecule is of A₁' symmetry and...
The history of entomopathogenic nematology is briefly reviewed. Topic selections include early descriptions of members
of Steinernema and Heterorhabditis, how only morphology was originally used to distinguish between the species; descriptions of the
symbiotic bacteria and elucidating their role in the nematode- insect complex, including antibiotic properties, phase variants, and...
Spreadsheet created to provide Horticulture Department faculty at Oregon State University with cost comparison information for the journals in which they most often published in 2003-2005. Includes journal titles, cost, impact factor (2004), and publisher information.
This thesis reports on an investigation of the growth, by
Molecular Beam Epitaxy, of III,III-V ternary compound semiconductors.
Strained and unstrained growth was studied via the deposition of InGaAs
on GaAs and InP substrates. Lattice matched InGaAs on InP was grown,
and an in situ method was developed to find...
Time-resolved fluorescence spectroscopy was used to monitor the effects of
varying ionic strength on nucleosome core particle structure. Two main methods were
used in these studies. First, the fluorescence anisotropy decay of bound ethidium was
measured and was shown to reflect the rotational tumbling of the core particle through
solution,...
Ultrafast spectroscopy can exploit the structure-function relationship of chemical- and biological-based systems. More specifically, femtosecond stimulated Raman spectroscopy (FSRS) provides ground- and excited-state vibrational information with simultaneously high spectral (spatial) and temporal resolutions. The electronic counterpart, femtosecond transient absorption (fs-TA), complements FSRS data analysis as part of a comprehensive approach...
A nonflame method for atomic absorption spectroscopy is
described. A helical tungsten filament from a commercially available
6-V, 4-A light bulb, heated to :incandescence in an argon atmosphere
is used to atomize 2-μl aqueous samples for metals analyses. Studies
of two hollow cathode lamp tungsten filament orientations, a
modulated light...
The variable length, six-electrode plasma source for atomic
emission spectroscopy described here is operated from three
compact, simple, and inexpensive direct current power supplies. The
vertical arcs formed between the three electrode pairs completely
entrain the sample and are typically operated at 40 V and 20 A.
Three concentric quartz...
The down‐regulation of dominant oncogenes, including C‐MYC, in tumor cells often leads to the induction of
senescence via mechanisms that are not completely identified. In the current study, we demonstrate that MYC‐depleted
melanoma cells undergo extensive DNA damage that is caused by the underexpression of thymidylate synthase (TS) and
ribonucleotide...
In this dissertation, my research work on excited state dynamics of small organic molecules in solutions is presented. Using femtosecond stimulated Raman spectroscopy (FSRS) as the main experimental tool, the excited state hydrogen-bonding dynamics (ESHBD) of Coumarin 102, a common laser dye molecule, in ethanol solution is examined with <150...
Includes general information about journal costs and costs of commercial versus society publications. Spreadsheet represents the journals in which faculty in the Chemistry Department most often publish and includes journal title, cost, impact factor, publisher, and information about whether the journal is published by a scholarly society or a for-profit...
Deoxyribonucleoside triphosphate pools in mammalian mitochondria are highly
asymmetric, and this asymmetry probably contributes toward the elevated
mutation rate for the mitochondrial genome as compared with the nuclear
genome. To understand this asymmetry, we must identify pathways for synthesis
and accumulation of dNTPs within mitochondria. We have identified
ribonucleotide reductase...
The CARS apparatus at OSU was modified to permit studies in the 0-500 cm⁻¹ spectral region. The new low frequency capabilities were then used to study molecular clusters formed in free expansion jets of carbon dioxide. A strong cluster band was observed at 73 cm⁻¹, with a weaker shoulder at...
Intrinsically disordered protein (IDP) duplexes composed of two IDP chains cross-linked by bivalent partner proteins form scaffolds for assembly of multiprotein complexes. The N-terminal domain of dynein intermediate chain (N-IC) is one such IDP that forms a bivalent scaffold with multiple dynein light chains including LC8, a hub protein that...
The high resolution stimulated Raman spectrometer at OSU was
modified to improve its sensitivity and to extend its range of
applications to low Raman shifts and to the spectroscopy of solids and
liquids. As part of the characterization of the spectrometer, optical
Stark effects on rotational and vibrational transitions of...
Hub proteins bind a large number of partners to facilitate structural changes and downstream protein interactions. LC8, a highly conserved protein homodimer, is a unique hub that regulates the activity of proteins in a wide range of cellular processes by binding to intrinsically disordered regions. With many of these systems,...
The spectrophone method for the study of vibrational relaxation
has been claimed to possess a distinct advantage over the more commonly
used ultrasonic techniques in that it permits the relaxation of
the various infrared-active vibrational modes in a polyatomic molecule
to be studied separately. A discussion of the rate equations...
Elevated hepatic expression of fatty acid elongase-5 (Elovl5) induces
FoxO1 phosphorylation, lowers FoxO1 nuclear content and suppresses expression of
genes involved in gluconeogenesis. In this report we define the molecular and metabolic
basis of Elovl5 control of FoxO1 phosphorylation. Adenoviral-mediated (Ad-Elovl5)
induction of hepatic Elovl5 in diet induced obese-glucose intolerant...
The techniques of coherent anti-Stokes Raman spectroscopy (CARS)
and inverse Raman spectroscopy (IRS) are used to examine carbon dioxide
aggregation in a supersonic jet expansion. To promote the formation of
small clusters, a BMW injector valve is modified to permit its use as a
pulsed nozzle at very cold temperatures....
In this dissertation, I present electronic spectra of a few polycyclic aromatic hydrocarbons (PAHs): tetracene, pentacene, pyrene, benzo[g,h,i]perylene and benzo[a]pyrene using resonantly enhanced multiphoton ionization (REMPI) and zero kinetic energy (ZEKE) photoelectron spectroscopy. The work of tetracene and pentacene also combine a laser desorption source with a ZEKE spectrometer, demonstrating...
A state-of-the-art radiation detection system for simultaneous spectroscopy
of beta-particles and gamma-rays has been developed. The system utilizes a triplelayer
phoswich detector and a customized Digital Pulse Processor (DPP) built in
our laboratory. The DPP board was designed to digitally capture the analog signal
pulses and, following several digital preprocessing...
Due to its importance, the phenomenon of hydrogen
bonding has been the subject of much research over the
years. Among the different techniques used to study
hydrogen bonded systems, vibrational spectroscopy is
perhaps the most sensitive because of the striking
changes induced in molecular spectra by the formation of
hydrogen...
This dissertation presents nonlinear terahertz (THz) properties of carbon nanomaterials investigated by time-resolved high-field THz spectroscopy. In order to determine THz characteristics of nanomaterials, we performed THz power spectrum measurement, THz raster imaging, THz time-domain spectroscopy (THz-TDS) and time-resolved pump-probe experiment on two different types of single layer graphene and...
Theoretical studies and experimental results are presented for the rotational motion of molecule's in crystalline solids. The group theory is solved for molecules of any symmetry matrix isolated at a site in a crystal field of any symmetry. As the potential terrier to rotation of the molecule relative to the...
Molecular dynamics (MD) simulations are used to study, in detail, the transfer of thermal (vibrational) energy between objects with discrete vibrational spectra to those with a semi-continuum of spectra. The transfer of energy is stochastic and strongly dependent on the instantaneous separation between the bodies. The insight from the MD...
The satellite structure ("shake-up") present in the X-ray
photoelectron spectra of several planar molecules containing
double bonds has been investigated in the gas phase.
This set consists of three five-membered heterocyclic
molecules, ethylene and two of its fluorinated analogs, and
benzene with three of its fluorinated analogs. In addition,
core...
Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy and AIDS related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin resistant strains of Mycobacterium tuberculosis. As part of our effort to...
Aqueous film-forming foams (AFFFs) are significant sources of per- and polyfluoroalkyl substances (PFAS) in the environment. Current analytical methods that provide quantitative measures of individual PFAS in AFFFs, such as liquid chromatography – tandem mass spectrometry (LC-MS/MS), are often complicated, time-consuming, and expensive. Methods for total fluorine analysis, though quantitative,...
Paclitaxel is a very important anticancer drug commonly called Taxol®.
We know from previous work (Hoffman, et al., 1998) that Taxol exists in filbert, Corylus avellana L. material. Quantification of Taxol in filbert plant material is painstaking and hitherto was accomplished by rapidly processing single batches in a complicated procedure...
Mutation of repetitive DNA by repeat-induced point mutation (RIP) is a process that occurs in many filamentous fungi of the Ascomycota during the sexual cycle. Concurrently, direct DNA repeats are often deleted by homologous recombination at high frequency during the sexual cycle. Thus, the processes of RIP and deletion compete...
In order to observe laser phase noise, this noise must be converted to
amplitude noise, which can be achieved using either an interferometer or an
absorption resonance in an atomic/molecular vapor or gas. When phase noise is
converted to amplitude noise, it is manifested as a heterodyne signal in the...
The development and applications of a 0.2 cm⁻¹ resolution
Nd-YAG laser powered coherent anti-Stokes Raman
spectroscopy, CARS, spectrometer for gas phase studies is
chronicled in this thesis. Applications including CARS
lineshape analysis, resonant CARS, and CARS of transient
species and excited state molecules is reported.
The intensity of the signal...
The photoelectron spectra of a series of ketone
compounds have been investigated in the gas phase. Core
ionization energies were measured to probe the effects of
molecular size and connectivity number on core ionization
energies.
It was found that core ionization energies roughly
decrease with increasing connectivity number as expected....
In this dissertation, I describe spectroscopic studies of jet-cooled polycyclic aromatic hydrocarbons (PAH) and one nitrogen substituted PAH (PANH) using pulsed field zero kinetic energy (ZEKE) photoelectron spectroscopy and resonantly enhanced multiphoton ionization (REMPI) spectroscopy. Recently, there has been a demand for far-infrared (FIR) spectral information of astrophysically relevant molecules...
Stacked sheets of polyethylene terephthalate andpolystyrene provide a means
for recovering projectiles travelling at hypervelocities. The transparency of these
multiple diaphragms is utilized so that light generated from hypervelocity impacts
can be studied.
A method for gathering visible as well as ultraviolet light from less
transparent polymer foams has been...
This thesis will cover work that I have completed relating to the field of terahertz (THz) science. My work has consisted of generating tunable, narrowband THz pulses in a table-top optical setup and using both narrow- and broadband THz pulses to study various material systems. Broadband THz pulses were used...
Spreadsheet represents the journals in which faculty in the Botany and Plant Pathology Department most often published from 1999-2004. Includes journal title, cost, impact factor, publisher, information about whether the journal is published by a non-profit or commercial publisher, average number of pages over a 5 year period, and cost...
The two sulfur isotopomers of sulfur trioxide, ³²S¹⁶O₃ and ³⁴S¹⁶O₃, have been studied via high resolution infrared and Coherent anti-Stokes Raman (CARS) spectroscopy. The v₁ symmetric SO stretching Q-branches observed by the latter are quite different, being especially complex for ³²S¹⁶O₃ Understanding this band structure required analysis of infrared-active hot...
BiCuOSe and SnS are layered, moderate band gap (ε[subscript G] ≈ 1 eV) semiconductors that exhibit intrinsic p type conductivity. Doping of BiCuOSe with Ca results in a slight expansion of the lattice and an increase of the hole concentration from 10¹⁸ cm⁻³ to greater than 10²⁰ cm⁻³. The large...
Temporal variations in individual spectrum lines
emitted by a microwave discharge in pure helium are
investigated: The discharge is produced in a quartz tube
located inside of a section of waveguide which carries
pulsed 3 centimeter microwaves. The helium used is purified by a three-fold process consisting of treatment with...
Ambient-pressure X-ray photoelectron spectroscopy has been used to study the initial stages of dry thermal oxidation of Si₀.₆₀Ge₀.₄₀(001) grown epitaxially on Si(001). Chemical state resolved AP-XPS was performed at temperatures up to 300 ˚C and O₂ pressures up to 1 mbar. Comparisons were made to Si(001) and Ge(001). The Si...
When trace quantities of an alkali element are added to a flame,
its optical and electrical properties change significantly. Addition of
alkali seed to both premixed and diffusion flames has been used in the
development of two new techniques, one for flame temperature measurement
and the other for enhanced mixing....
The core-electron ionization potentials for mono- and
di(trifluoromethyl)benzene, for chlorofluoromethanes and for
chlorine have been measured in order to give information on
the electron distribution in these molecules and to investigate
differences between the inductive effect of fluorine
and that of CF3. For trifluoromethylbenzene the measured
ionization potentials in eV...
A procedure for evaluating the precision of atomic absorption
measurements is presented and applied to 21 elements under varying
instrumental conditions. The experimental relative standard deviations
(RSD's) in absorbance obtained from repetitive measurements made
with a high resolution voltmeter and on-line computer, are compared
to those predicted by a recently...
There are six types of Cl. botulinum (Types A, B, C, D, E,
and F). The differentiation between these types is based upon the
antigenic structure of the toxin. Many strains of these various types
have been isolated. In addition, a number of nontoxigenic "type Elike"
strains have come to...
Techniques have been developed for measuring the
temperature, stable species concentrations, and atomic
radical concentrations during a transient combustion
event. They combine the features of direct sampling with
two spectroscopic techniques to produce relatively simple
diagnostic techniques to obtain time-resolved
measurements. In this study, a transient event was
provided by...
In this dissertation, I present electronic spectroscopy of a few biologically relevant species and their complexes with solvent molecules in the gas phase using a variety of techniques, including resonantly enhanced multiphoton ionization (REMPI), laser induced fluorescence (LIF), and zero kinetic energy (ZEKE) photoelectron spectroscopy. My work on several methylated...
In this thesis, I present a new method we developed to study low frequency (< 700 cm⁻¹) vibrational dynamics: Time-resolved third-harmonic generation (TRTHG) spectroscopy. Among a variety of vibrational spectroscopy techniques, TRTHG differentiates itself with robustness, versatility, and simplicity. In TRTHG experiment, that involves only two ultrashort laser pulses, the...
The physical properties of hydrochloric acid and deuterium chloride were derived through the use of the harmonic oscillator and rigid rotor quantum mechanical models. By first obtaining angular momentum quantum values for HCl and DCl through Fourier Transform Infrared Spectroscopy, these two systems could be summed and processed with additional...
Our oceans surround us, and we depend upon them for food, transportation, and recreation. They affect us daily as they shape our climate and rattle our world with unexpected events. Current headlines indicate that they are in flux and perhaps in trouble. Coral reefs are dying due to rising ocean...
DNA reassociations, measured by optical and double label
membrane filter techniques, were used to assess genetic relationships
among Aeromonas and enterobacteria. Aeromonads from human
sources, food, fresh water, fish, and pet turtles were examined. The
base compositions of three A. salmonicida isolates were 58% G+C
while the base compositions of...
Applications of several methods of coherent nonlinear Raman Spectroscopy have been made in this thesis research. The theory and potential of one of these, Photoacoustic Raman Spectroscopy (PARS), is discussed in chapter two. Experimental results are presented which illustrate the sensitivity of this method and establish sampling conditions for maximum...
Mapping out multidimensional potential energy surfaces has been a goal of
physical chemistry for decades in the quest to both predict and control chemical
reactivity. Recently a new spectroscopic approach called Femtosecond Stimulated Raman
Spectroscopy or FSRS was introduced that can structurally interrogate multiple
dimensions of a reactive potential energy...
The development of a least squares model for the
determination of compliance constants from various combinations
of vibration frequency, mean square amplitudes
of vibration and centrifugal distortion data is discussed.
The resultant model is applied to frequency and mean square
amplitude data for NO₂ and N₂O₄ and to frequency and...
Experiments were performed to assess regulatory factors governing maize
embryo maturation and vivipary. Both visual and molecular markers of embryo
development were used to examine the roles of the hormones abscisic acid (ABA)
and gibberellins (GAs), as well as water stress in governing transit from early
embryogeny to maturation-phase development....
A more quantitative understanding of peptide entrapment and elution from otherwise protein-repellent polyethylene oxide (PEO) brush layers will provide direction for development of new strategies for drug storage and delivery. Here we describe criteria for peptide integration and structural change within the PEO brush, and discuss the reversibility of peptide...