Detection of Atomic Scale Changes in the Free Volume Void Size of Three-Dimensional Colorectal Cancer Cell Culture Using Positron Annihilation Lifetime Spectroscopy

5 p.

Engineering multi-step electron tunneling systems in proteins

Multi-step electron tunneling, or “hopping,” has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.

The protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan “wire.” The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.

Cavity-enhanced spectroscopies for applications of remote sensing, chemical kinetics and detection of radical species

This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O₂ and CO₂ for obtaining laboratory reference data in support of NASA’s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and ¹³C/¹²C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(¹D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado.

Temperature dependence of absorption edge in MOCVD grown GaN

We have studied the temperature dependence of absorption edge of GaN thin films grown on sapphire substrate by metal-organic chemical vapor deposition using optical absorption spectroscopy. A shift in absorption edge of about 55 meV has been observed in temperature range 273-343 K. We have proposed a theoretical model to find the energy gap from absorption coefficient using alpha = alpha(max) + (alpha(min) - alpha(max))/[1 + exp 2(E - E-g + KT)/KT]. Temperature dependence of band gap has also been studied by finding an appropriate theoretical fit to our data using E-g(T) = E-g(273 K) - (8.8 x 10(-4)T(2))/(483 + T) + 0.088 (Varshni empirical formula) and E-g(T) = E-g(273 K)-0.231447/[exp(362/T)-1] + 0.082 relations. It has been found that data can be fitted accurately after adding a factor similar to 0.08 in above equations. Debye temperature (483 K) and Einstein temperature (362 K) in the respective equations are found mutually in good agreement.

Annealing-induced evolution of defects in low-temperature-grown GaAs-related materials

Infrared absorption spectroscopy, optical transient current spectroscopy (OTCS), and photoluminescence (PL) spectroscopy are used to investigate the annealing induced evolution of defects in low-temperature (LT)-grown GaAs-related materials. Two LT samples of bulk GaAs (sample A) and GaAs/AlxGa1-xAs multiple-quantum-well. (MQW) structure (sample B) were grown at 220 and 320 degreesC on (001) GaAs substrates, respectively. A strong defect-related absorption band has been observed in both as-grown samples A and B. It becomes weaker in samples annealed at temperatures above 600 degreesC. In sample A, annealed in the range of 600-800 degreesC, a large negative decay signal of the optical transient current (OTC) is observed in a certain range of temperature, which distorts deep-level spectra measured by OTCS, making it difficult to identify any deep levels. At annealing temperatures of 600 and 700 degreesC, both As-Ga antisite and small As cluster-related deep levels are identified in sample B. It is found that compared to the As cluster, the As-Ga antisite has a larger activation energy and carrier capture rate. At an annealing temperature of 800 degreesC, the large negative decay signal of the OTC is also observed in sample B. It is argued that this negative decay signal of the OTC is related to large arsenic clusters. For sample B, transient PL spectra have also been measured to study the influence of the, defect evolution on optical properties of LT GaAs/AlxGa1-xAs MQW structures. Our results clearly identify a defect evolution from AS(Ga) antisites to arsenic clusters after annealing.

Tuning of conduction intersublevel absorption wavelengths in (In, Ga)As/GaAs quantum-dot nanostructures

We demonstrate that by increasing the amount of (In, Ga)As deposit in a quantum dot layer, the intersublevel absorption wavelength for (In, Ga)As/GaAs quantum-dot infrared photodetectors can be blue-shifted from 15 to 10 mu m while the photoluminescence peak is red-shifted. We directly compare the measured energy spacing between intersublevels obtained from infrared absorption spectroscopy with those obtained from photoluminescence spectroscopy. We find that the intersublevel energy spacing determined from absorption measurements is much larger than that obtained from the photoluminescence measurements. (C) 2000 American Institute of Physics. [S0003-6951(00)04524-1].

The active sites in different TS-1 zeolites for propylene epoxidation studied by ultraviolet resonance Raman and ultraviolet visible absorption spectroscopies

The titanium species in four kinds of titanium-containing MFI zeolites have been studied by ultraviolet (UV)-Raman and ultraviolet visible (UV-Vis) absorption spectroscopies and by the epoxidation of propylene with diluted H2O2 solution (30%). UV-Raman spectroscopy is proved to be a suitable means to estimate qualitatively the framework titanium in TS-l zeolites. Based on the comparison of the relative intensity ratio I-1125/I-380 of UV-Raman spectra, the TS-1(conv.) sample synthesized hydrothermally by the conventional procedure shows the highest amount of framework titanium. UV-Vis spectroscopy reveals that besides minor anatase. titanium species are mainly tetrahydrally coordinated into the framework for TS-l(conv.) or the Ti-ZSM-5 sample prepared by gas-solid reaction between deboronated B-ZSM-5 and TiCl4 vapor at elevated temperatures. For the TS-1(org.) and TS-1(inorg.) samples synthesized hydrothermally using tetrapropylammonium bromide (TPABr) as template and tetrabutylorthotitanite (TBOT) and TiCl3 as titanium source, respectively, the presence of mononuclear and isolated TiOx species which are proposed to bond to the zeolite extraframework is observed. In addition to the framework titanium species, these isolated TiOx species are assumed to be also active for propylene epoxidation.

Determination of the optical band-gap energy of cubic and hexagonal boron nitride using luminescence excitation spectroscopy

Sponsorship: EPSRC, STFC

Surface alloying and mixing at the Mn/Fe(001) interface: Real-time photoelectron spectroscopy and modified embedded atom simulations

Structural and magnetic properties of thin Mn films on the Fe(001) surface have been investigated by a combination of photoelectron spectroscopy and computer simulation in the temperature range 300 Kless than or equal toTless than or equal to750 K. Room-temperature as deposited Mn overlayers are found to be ferromagnetic up to 2.5-monolayer (ML) coverage, with a magnetic moment parallel to that of the iron substrate. The Mn atomic moment decreases with increasing coverage, and thicker samples (4-ML and 4.5-ML coverage) are antiferromagnetic. Photoemission measurements performed while the system temperature is rising at constant rate (dT/dtsimilar to0.5 K/s) detect the first signs of Mn-Fe interdiffusion at T=450 K, and reveal a broad temperature range (610 Kless than or equal toTless than or equal to680 K) in which the interface appears to be stable. Interdiffusion resumes at Tgreater than or equal to680 K. Molecular dynamics and Monte Carlo simulations allow us to attribute the stability plateau at 610 Kless than or equal toTless than or equal to680 K to the formation of a single-layer MnFe surface alloy with a 2x2 unit cell and a checkerboard distribution of Mn and Fe atoms. X-ray-absorption spectroscopy and analysis of the dichroic signal show that the alloy has a ferromagnetic spin structure, collinear with that of the substrate. The magnetic moments of Mn and Fe atoms in the alloy are estimated to be 0.8mu(B) and 1.1mu(B), respectively.

Absolute Absorption Cross-Section Measurement of a Submonolayer film on a silica microresonator

Conventional absorption spectroscopy is not nearly sensitive enough for quantitative overtone measurements on submonolayer coatings. While cavity-enhanced absorption detection methods using microresonators have the potential to provide quantitative absorption cross sections of even weakly absorbing submonolayer films, this potential has not yet been fully realized. To determine the absorption cross section of a submonolayer film of ethylene diamine (EDA) on a silica microsphere resonator, we use phase-shift cavity ringdown spectroscopy simultaneously on near-IR radiation that is Rayleigh backscattered from the microsphere and transmitted through the coupling fiber taper. We then independently determine both the coupling coefficient and the optical loss within the resonator. Together with a coincident measurement of the wavelength frequency shift, an absolute overtone absorption cross section of adsorbed EDA, at submonolayer coverage, was obtained and was compared to the bulk value. The smallest quantifiable absorption cross section is σmin 2.7 × 10−12 cm2. This absorption cross section is comparable to the extinction coefficients of, e.g., single gold nanoparticles or aerosol particles. We therefore propose that the present method is also a viable route to absolute extinction measurements of single particles.

Diagnostic studies of species concentrations in a capacitively coupled RF plasma containing CH4-H2-Ar

Three plasma diagnostic methods, tunable infrared diode laser absorption spectroscopy, optical emission spectroscopy and microwave interferometry have been used to monitor concentrations of transient and stable molecules, CH3, CH4, C2H2, C2H6, and of electrons in capacitively coupled CH4-H-2-Ar radiofrequency (RF) plasmas (f(RF) = 13.56 MHz, p = 100 Pa, phi (total)= 66 sccm) for various discharge power values (P = 10-100 W) and gas mixtures. The degree of dissociation of the methane precursor varied between 3% and 60%. The methyl radical concentration was found to be in the order of 10(12) molecules cm(-3) and the electron concentration in the order of loll cm(-3). The methyl radical concentration and the concentrations of the stable C-2 hydrocarbons, C2H2 and C2H6, produced in the plasma, increased with discharge power. The fragmentation rates of the methane precursor and conversion rates to the measured C-2 hydrocarbons were estimated in dependence on discharge power. Radial distributions of the electron and methyl radical concentrations, and of the gas temperature were measured for the first time simultaneously in the plasma region between the discharge electrodes. The measurements allow us to draw qualitative conclusions on the main chemical processes and the plasma chemical reaction paths.

The masses of the cataclysmic variables AC Cancri and V363 Aurigae

We present time-resolved spectroscopy and photometry of the double-lined eclipsing cataclysmic variables AC Cnc and V363 Aur (=Lanning 10). There is evidence of irradiation on the inner hemisphere of the secondary star in both systems, which we correct for using a model that reproduces the observations remarkably well. We find the radial velocity of the secondary star in AC Cnc to be K-R=176+/-3 km s(-1) and its rotational velocity to be v sin i=135+/-3 km s(-1). From these parameters we obtain masses of M-1=0.76+/-0.03 M-circle dot for the white-dwarf primary and M-2=0.77+/-0.05 M-circle dot for the K2+/-1 V secondary star, giving a mass ratio of q=1.02+/-0.04. We measure the radial and rotational velocities of the G7+/-2V secondary star in V363 Aur to be K-R=168+/-5 km s(-1) and v sin i=143+/-5 km s(-1), respectively. The component masses of V363 Aur are M-1=0.90+/-0.06M(circle dot) and M-2=1.06+/-0.11 M-circle dot giving a mass ratio of q=1.17+/-0.07. The mass ratios for AC Cnc and V363 Aur fall within the theoretical limits for dynamically and thermally stable mass transfer. Both systems are similar to the SW Sex stars, exhibiting single-peaked emission lines with transient absorption features, high-velocity S-wave components and phase-offsets in their radial-velocity curves. The Balmer lines in V363 Aur show a rapid increase in flux around phase 0 followed by a rapid decrease, which we attribute to the eclipse of an optically thick region at the centre of the disc. This model could also account for the behaviour of other SW Sex stars where the Balmer lines show only a shallow eclipse compared to the continuum.

TIME-RESOLVED ABSORPTION, INFRARED, AND RESONANCE RAMAN-SPECTRA OF THE COMPLEXES [RU(X)(R)(CO)(2)(ALPHA-DIIMINE)] (X=HALIDE R=ALKYL) - INFLUENCE OF X ON THE CHARGE-TRANSFER CHARACTER OF THE LOWEST EXCITED-STATE

Nanosecond time-resolved absorption (TA), resonance Raman (TR(3)), and infrared (TRIR) spectra are reported for several complexes [Ru(X)(R)(CO)(2)(alpha-diimine)] (X = Cl, Br, I; R = Me, Et; alpha-diimine = N,N'-diisopropyl-1,4-diaza-1,3-butadiene (iPr-DAB), pyridine-2-carbaldehyde-N-isopropylimine (iPr-PyCa), 2,2'-bipyridine (bpy)). This is the first instance in which the TA, TR(3), and TRIR techniques have been used to probe excited states in the same series of complexes. The TA spectra of the iodide complexes show a transient absorption between 550 and 700 nm, which does not depend on the solvent but shifts to lower energy in the order iPr-DAB > bpy > iPr-PyCa. This band is assigned to an intraligand transition. For the corresponding chloride and bromide complexes this band occurs at higher energy, most probably because of a change of character of the lowest excited state from XLCT to MLCT. The TRIR spectra show an increase in v(CO) (and k(CO)) on promotion to the excited state; however, the shifts Delta v(CO) show a decrease in the order Cl- > Br- > I-. The TR(3) spectra of the excited complexes [Ru(X)(R)(Co)(2)(iPr-DAB)] show v(s)(CN) of the iPr-DAB ligand 50-80 cm(-1) lower in frequency than for the complexes in their ground state. This frequency shift decreases in the order Cl- > Br- > I-, indicating a decrease of CT character of the lowest excited state in this order. However, going from X = Br to I, the effect on Delta v(CO) is much larger than the decrease of Delta v(s)(CN). This different effect on the CO- and CN-stretching frequencies is assigned to a gradual change in character of the lowest excited state from MLCT to XLCT when Cl- is replaced by Br- and I-. This result confirms a similar conclusion derived from previous resonance Raman and emission experiments on these complexes.

TRANSIENT RESONANCE RAMAN AND RAMAN SPECTROELECTROCHEMICAL STUDIES OF CUI COMPLEXES WITH POLYPYRIDYL LIGANDS

Studies by laser flash photolysis, transient Raman spectroscopy, and Raman and UV-vis spectroelectrochemistry are described in which the techniques have been used in parallel to compare the lowest energy charge-transfer excited states of Cu (1) complexes ([Cu(L)2]+ and [ (PPh3)2Cu(L)]+ [L = 2,2'-biquinoline (BIQ) or 6,7-dihydro-5,8-dimethyldibenzo[b,j] [1,10]-phenanthroline (DMCH)) with the species produced by electrochemical reduction in the same group of complexes. Transient resonance Raman spectra for the metal-to-ligand charge-transfer (MLCT) states of [Cu(DMCH)2]+ (1), [Cu(BIQ)2]+ (2), [Cu(DMCH)(PPh3)2]+ (3), and [Cu(BIQ)(PPh3)2]+ (4) are compared with the resonance Raman spectra of the same group of complexes following one-electron electrochemical reduction of the DMCH and BIQ ligands. The UV-vis and resonance Raman evidence suggests that the electrochemical reduction of the [Cu(I)L2]+ species proceeds according to the sequence [LCu(I)L]+ -->e- [LCu0L] -->e- [L.-Cu(I)L.-]-. Several features assignable to modes of the electrochemically generated DMCH.-and BIQ'- radical anions exhibit a close correspondence in both frequency and relative intensity with counterparts in the spectra of the MLCT states of 1 and 2. A notable exception is a band near 1590 cm-1 in the spectra of the electrochemically reduced species which occurs some 15 cm-1 lower in the corresponding spectra of the excited-state species. It is suggested that the shift may reflect the change in oxidation state of the metal center from Cu(I) to Cu(II) which occurs as a result of charge-transfer excitation.

Dynamique de séparation de charges à l'hétérojonction de semi-conducteurs organiques

Une compréhension profonde de la séparation de charge à l’hétérojonction de semi-con- ducteurs organiques est nécessaire pour le développement de diodes photovoltaïques organiques plus efficaces, ce qui serait une grande avancée pour répondre aux besoins mondiaux en énergie durable. L’objectif de cette thèse est de décrire les processus impliqués dans la séparation de charges à hétérojonctions de semi-conducteurs organiques, en prenant en exemple le cas particulier du PCDTBT: PCBM. Nous sondons les excitations d’interface à l’aide de méthodes spectroscopiques résolues en temps couvrant des échelles de temps de 100 femto- secondes à 1 milliseconde. Ces principales méthodes spectroscopiques sont la spectroscopie Raman stimulée femtoseconde, la fluorescence résolue en temps et l’absorption transitoire. Nos résultats montrent clairement que le transfert de charge du PCDTBT au PCBM a lieu avant que l’exciton ne soit relaxé et localisé, un fait expérimental irréconciliable avec la théorie de Marcus semi-classique. La paire de charges qui est créée se divise en deux catégories : les paires de polarons géminales non piégées et les paires profondément piégées. Les premiers se relaxent rapidement vers l’exciton à transfert de charge, qui se recombine radiativement avec une constante de temps de 1– 2 nanoseconde, alors que les seconds se relaxent sur de plus longues échelles de temps via l’effet tunnel. Notre modèle photophysique quantitatif démontre que 2 % de l’excitation créée ne peut jamais se dissocier en porteurs de charge libre, un chiffre qui est en accord avec les rendements élevés rapportés pour ce type de système.