Thesis (Ph. D.)--California Institute of Technology, 1972. UM #72-30,822. / Advisor names found in the Acknowledgments pages of the thesis. Title from home page. Viewed 02/09/10. Includes bibliographical references.

Thesis (Ph. D.)--California Institute of Technology, 1979. UM #79-06,210. / Advisor names found in the Acknowledgments pages of the thesis. Title from home page. Viewed 02/10/2010. Includes bibliographical references.

Thesis (Ph. D.)--California Institute of Technology, 1980. UM #80-21,027. / Advisor name found in the Acknowledgments pages of the thesis. Title from home page. Viewed 02/10/2010. Includes bibliographical references.

The vast majority of chemical reactions occurs only in the ground state, however photochemical reactions like chemiluminescence take place in ground and excited states. In almost all chemiluminescence processes oxygen-oxygen bond breakage is involved. But, there is no general reason to explain why these processes occur via an oxygen-oxygen cleavage. These types of phenomena are usually highly exothermic. Computational chemistry has risen as a powerful tool to characterize and analyze chemical phenomena. Quantum mechanics are utilized to explain chemical observations. Applying these equations, one can compute the chemical properties of any system in any state. In the present study, three chemiluminescence reactions derived from luminol are modeled; nitrogen based, oxygen based and dianion nitrogen based models. The key factor of oxygen-oxygen bond rupture is discussed and rationalized. The electronic potential energy surfaces of the three compounds are computed at complete active space self-consistent field theory. Peroxide compounds compared to the dinitrogenated  compounds show a lower activation energy and they are more exothermic. This study allows us to rationalize why luminol needs to be presented in a basic medium and oxidized in order to produce chemiluminescence.

An accurate description of the exchange-correlation energy is central to density functional theory (DFT). In this thesis a series of exchange-correlation functionals are developed using new approaches based on exchange-correlation potentials and enhancement factors. The functionals are assessed for a wide range of molecular properties. Chapter 1 describes Hartree Fock theory, introducing the key concepts of exchange and correlation. Chapter 2 describes the fundamental ideas of DFT and the implementation of Kohn-Sham theory. Chapter 3 describes a new approach for determining exchange-correlation functionals solely from ab initio potentials. A series of functionals are developed and assessed. Chapter 4 investigates the performance of one of these functionals, which provides particularly high quality structural predictions. A challenging benchmark of sulfur-containing compounds and a new benchmark of diatomic molecules are considered. Results are assessed in terms of the enhancement factor. In Chapter 5, the enhancement factor is used to develop new functionals that satisfy several exact physical conditions. The potential energy curve of the Helium dimer is investigated, since this is known to be sensitive to the enhancement factor. In Chapter 6 a series of hybrid functionals are determined. Particular attention is paid to their performance for chemical reactions and the relationship of these results to self-interaction errors. Chapter 7 investigates a new definition of the exchange-correlation charge (hole), which is directly related to the exchange-correlation potential. The first such calculations on molecular systems are presented. Concluding remarks are presented in Chapter 8.

This thesis aims to rationally design nanoparticles and promote their applications in biomedical imaging and photovoltaic cells. Quantum dots (QDs) are promising fluorescent probes for biomedical imaging. We have fabricated two types of MSA capped QDs: CdTe/ZnSe core/shell QDs synthesized via an aqueous method and CdTe QDs via a hydrothermal method. They present high quantum yields (QYs), narrow emission band widths, high photo- and pH-stability, and low cytotoxicity. QD-IgG probes were produced and applied for labeling breast cancer marker HER2 proteins on MCF-7 cells. For the purpose of single molecule tracking using QDs as fluorescent probes, we use small affibodies instead of antibodies to produce QD-affibody probes. Smaller QD-target protein complexes are obtained using a direct immunofluorescence approach. These QD-affibody probes are developed to study the dynamic motion of single HER2 proteins on A431 cell membranes. Fluorescence blinking in single QDs is harmful for dynamic tracking due to information loss. We have experimentally studied the blinking phenomenon and the mechanism behind. We have discovered an emission bunching effect that two nearby QDs tend to emit light synchronously. The long-range Coulomb potential induced by the negative charge on the QD surface is found to be the major cause for the single QD blinking and the emission bunching in QD pairs. We have studied the in vitro cytotoxicity of CdTe QDs to human umbilical vein endothelial cells (HUVECs). The QDs treatment increases the intracellular reactive oxygen species (ROS) level and disrupts the mitochondrial membrane potential. The protein expression levels indicate that the mitochondria apoptosis is the main cause of HUVCEs apoptosis induced by CdTe QDs. Gold nanorods (GNRs) are scattering probes due to their tunable surface plasmon resonance (SPR) enhanced scattering spectrum. In order to control the yield and morphology of GNRs, we have systematically studied the effects of composition and concentration in the growth solution on the quality of the GNRs produced via a seed-mediated method. The aspect ratios of GNRs were found to be linearly depended on the concentration ratio of silver ions and CTAB. The high quality GNRs obtained were adsorbed to COS-7 cell membranes for dark field imaging. We have rationally designed two types of QDs by wave function engineering so as to improve the efficiency of QD-sensitized solar cells. A reversed type-I CdS/CdSe QD confines excitons in the shell region, whereas a type-II ZnSe/CdS QD separates electrons in the shell and holes in the core. Their absorbed photon-to-current efficiencies (APCE) are as high as 40% and 60% respectively. In conclusion, rationally designed nanoparticles are proven a high potential for applications as probes in biomedical labeling, imaging and molecule tracking, and as sensitizers for photovoltaic cells. / QC 20110511

The study of surface adsorption and reaction is not only interesting from a scientific point of view, but also important in many application fields such as energy, environment, catalysis, corrosion, electronic device, and sensor. Theoretical calculations are essential in these studies. In this thesis, first principles studies for the structure and reaction of some important single molecules on the surface are presented. Dehydrogenation of single trans-2-butene molecule on a Pd(110) surface is the first example. The adsorption configurations of both reactant and produce are assigned and the whole dehydrogenation pathway is revealed. Our calculations show that the reactant, i.e. trans-2-butene molecule, undergoes a rotation before dehydrogenation occurs, which is an important detail that cannot be observed directly in scanning tunneling microscopy (STM) experiments. The dissociation and rotation processes of single oxygen molecule on a Pt(111) surface have been a subject of extensive studies in the past. A new intermediate state with a peculiar configuration is identified. The puzzled adsorption site is well explained. The calculated energy barriers agree well with experimental results for both dissociation and rotation processes. Another aspect addressed in this thesis is the mechanism of molecular electronic switches induced by molecular structural changes. By carefully examining the tautomerization process of a naphthalocyanine molecule, an intermediate state is located on the potential surface of the tautomerization. Our calculations indicate that the experimentally observed switching involves four-states, rather than the two-state as proposed by the experimentalists. In a joint experimental and theoretical study the dehydrogenation, tautomerization, and mechanical switching processes of a single melamine molecule on a Cu(100) surface have been comprehensively examined. A new dual-functional molecular device with integrated rectifying and switching functions is made for the first time. In collaborating with another experimental group, we have simulated the switching process of a single 1,1,2,3,4,5-hexaphenylsilole molecule on a Cu(111) surface. The role of the orientation of the molecule is carefully examined and a new switching mechanism is proposed. Switching processes are strongly associated with the inelastic electron tunneling. We have proposed a statistical model that allows explaining the non-integer exponent in the power-law relationship between the switching rate and tunneling current. In this model, the importance of the randomness in inelastic electron excitations and the lifetime of the immediate state are emphasized. It has shown that the inelastic electron tunneling is a collection of various n-electron processes with different statistical weight. / QC 20110524

QC 20110520

α-helical membrane proteins constitute 20-30% of all proteins in a cell and are involved in many essential cellular functions. The structure is only known for a few hundred of them, which makes structural models important. The most common structural model of a membrane protein is the topology which is a two-dimensional representation of the structure. This thesis is focused on three different aspects of membrane protein structure: improving structural predictions of membrane proteins, improving the level of detail of structural models and the concept of dual topology. It is possible to improve topology models of membrane proteins by including experimental information in computer predictions. This was first performed in Escherichia coli and, by using homology, it was possible to extend the results to 225 prokaryotic organisms. The improved models covered ~80% of the membrane proteins in E. coli and ~30% of other prokaryotic organisms. However, the traditional topology concept is sometimes too simple for complex membrane protein structures, which create a need for more detailed structural models. We created two new machine learning methods, one that predicts more structural features of membrane proteins and one that predicts the distance to the membrane centre for the amino acids. These methods improve the level of detail of the structural models. The final topic of this thesis is dual topology and membrane protein evolution. We have studied a class of membrane proteins that are suggested to insert either way into the membrane, i.e. have a dual topology. These protein families might explain the frequent occurrence of internal symmetry in membrane protein structures.

The current thesis deals with one important branch of the physics of ultrafast processes, namely modeling of femtosecond nuclear dynamics. We suggest a new type of time resolved spectroscopy, the phase sensitive infrared-x-ray pump probe spectroscopy, which combines rich opportunities of IR laser techniques in quantum control of molecular systems with the site selectivity of x-rays. We have developed and applied a dynamical theory of x-ray pump-probe spectroscopy to study different molecular systems. Special attention is paid to design of the wave packets of desirable shape and spectral composition. Such a quantum control of the nuclear wave packet enables the study of molecular properties in regions that are unavailable by standard x-ray spectroscopies. The IR - x-ray pump probe spectroscopy is nicely suited to perform mapping of wave packet trajectories, to study revival phenomena, femtosecond chemical dynamics, and proton transfer, to mention a few examples. Our simulations show that the phase of the infrared pulse strongly influences the trajectory of the nuclear wave packet, and hence, the x-ray spectrum. Such a dependence is caused by the transfer of the phase of the IR field to the wave packet through the interference of the one (x-ray) and two-photon (IR + x-ray) excitation channels. The time resolved x-ray spectra are sensitive to the shape, duration and delay time between the pulses. The phase of the IR pulse influences the molecular dynamics also when the Rabi period becomes comparable with the period of vibrations, breaking down the rotating wave approximation. We predict a phase memory effect which is a promising technique in studies of chemical dynamics on different time scales. It is shown that the final state interaction with the pump affects the probe spectrum when the pump and probe pulses overlap. In a further step, we explore the electronic recoil effect in x-ray photoelectron spectroscopy, which has recently attracted attention of experimentalists due to its sensitivity to intramolecular interaction. We show that an IR field enhances the manifestation of the recoil effect through the formation of extensive vibrational wave packets. The theory of x-ray Raman scattering from molecules with strong spin-orbit coupling accompanied by electron-hole interaction is developed and applied to simulations of resonant x-ray Raman scattering of the HCl molecule. Special attention is paid to the theoretical methodologies to reduce the computational cost of our wave packet codes. / QC 20100825