Development and Application of Embedding Methods for the Simulation of Large Chemical Systems

The high computational cost of correlated wavefunction theory (WFT) calculations has motivated the development of numerous methods to partition the description of large chemical systems into smaller subsystem calculations. For example, WFT-in-DFT embedding methods facilitate the partitioning of a system into two subsystems: a subsystem A that is treated using an accurate WFT method, and a subsystem B that is treated using a more efficient Kohn-Sham density functional theory (KS-DFT) method. Representation of the interactions between subsystems is non-trivial, and often requires the use of approximate kinetic energy functionals or computationally challenging optimized effective potential calculations; however, it has recently been shown that these challenges can be eliminated through the use of a projection operator. This dissertation describes the development and application of embedding methods that enable accurate and efficient calculation of the properties of large chemical systems.

Chapter 1 introduces a method for efficiently performing projection-based WFT-in-DFT embedding calculations on large systems. This is accomplished by using a truncated basis set representation of the subsystem A wavefunction. We show that naive truncation of the basis set associated with subsystem A can lead to large numerical artifacts, and present an approach for systematically controlling these artifacts.

Chapter 2 describes the application of the projection-based embedding method to investigate the oxidative stability of lithium-ion batteries. We study the oxidation potentials of mixtures of ethylene carbonate (EC) and dimethyl carbonate (DMC) by using the projection-based embedding method to calculate the vertical ionization energy (IE) of individual molecules at the CCSD(T) level of theory, while explicitly accounting for the solvent using DFT. Interestingly, we reveal that large contributions to the solvation properties of DMC originate from quadrupolar interactions, resulting in a much larger solvent reorganization energy than that predicted using simple dielectric continuum models. Demonstration that the solvation properties of EC and DMC are governed by fundamentally different intermolecular interactions provides insight into key aspects of lithium-ion batteries, with relevance to electrolyte decomposition processes, solid-electrolyte interphase formation, and the local solvation environment of lithium cations.

Molecular mechanisms of interleukin-2 gene inducibility: developmental control and combinatorial action of transcription factors

Interleukin-2 is one of the lymphokines secreted by T helper type 1 cells upon activation mediated by T-cell receptor (TCR) and accessory molecules. The ability to express IL-2 is correlated with T-lineage commitment and is regulated during T cell development and differentiation. Understanding the molecular mechanism of how IL-2 gene inducibility is controlled at each transition and each differentiation process of T-cell development is to understand one aspect of T-cell development. In the present study, we first attempted to elucidate the molecular basis for the developmental changes of IL-2 gene inducibility. We showed that IL-2 gene inducibility is acquired early in immature CD4- CD8-TCR- thymocytes prior to TCR gene rearrangement. Similar to mature T cells, a complete set of transcription factors can be induced at this early stage to activate IL-2 gene expression. The progression of these cells to cortical CD4^+CD8^+TCR^(1o) cells is accompanied by the loss of IL-2 gene inducibility. We demonstrated that DNA binding activities of two transcription factors AP-1 and NF-AT are reduced in cells at this stage. Further, the loss of factor binding, especially AP-1, is attributable to the reduced ability to activate expression of three potential components of AP-1 and NF-AT, including c-Fos, FosB, and Fra-2. We next examined the interaction of transcription factors and the IL-2 promoter in vivo by using the EL4 T cell line and two non-T cell lines. We showed an all-or-none phenomenon regarding the factor-DNA interaction, i.e., in activated T cells, the IL-2 promoter is occupied by sequence-specific transcription factors when all the transcription factors are available; in resting T cells or non-T cells, no specific protein-DNA interaction is observed when only a subset of factors are present in the nuclei. Purposefully reducing a particular set of factor binding activities in stimulated T cells using pharmacological agents cyclosporin A or forskolin also abolished all interactions. The results suggest that a combinatorial and coordinated protein-DNA interaction is required for IL-2 gene activation. The thymocyte experiments clearly illustrated that multiple transcription factors are regulated during intrathymic T-cell development, and this regulation in tum controls the inducibility of the lineage-specific IL-2 gene. The in vivo study of protein-DNA interaction stressed the combinatorial action of transcription factors to stably occupy the IL-2 promoter and to initiate its transcription, and provided a molecular mechanism for changes in IL-2 gene inducibility in T cells undergoing integration of multiple environmental signals.

The intramolecular Buchner reaction of α-diazo-β-ketonitriles : development and application to the total synthesis of (+)-Salvileucalin B

Since its discovery in 1896, the Buchner reaction has fascinated chemists for more than a century. The highly reactive nature of the carbene intermediates allows for facile dearomatization of stable aromatic rings, and provides access to a diverse array of cyclopropane and seven-membered ring architectures. The power inherent in this transformation has been exploited in the context of a natural product total synthesis and methodology studies.

The total synthesis work details efforts employed in the enantioselective total synthesis of (+)-salvileucalin B. The fully-substituted cyclopropane within the core of the molecule arises from an unprecedented intramolecular Buchner reaction involving a highly functionalized arene and an α-diazo-β-ketonitrile. An unusual retro-Claisen rearrangement of a complex late-stage intermediate was discovered on route to the natural product.

The unique reactivity of α-diazo-β-ketonitriles toward arene cyclopropanation was then investigated in a broader methodological study. This specific di-substituted diazo moiety possesses hitherto unreported selectivity in intramolecular Buchner reactions. This technology was enables the preparation of highly functionalized norcaradienes and cyclopropanes, which themselves undergo various ring opening transformations to afford complex polycyclic structures.

Finally, an enantioselective variant of the intramolecular Buchner reaction is described. Various chiral copper and dirhodium catalysts afforded moderate stereoinduction in the cyclization event.

Part I. A study of the velocity structure of the earth by the use of core phases. Part II. The 1971 San Fernando earthquake series focal mechanisms and tectonics

The initial objective of Part I was to determine the nature of upper mantle discontinuities, the average velocities through the mantle, and differences between mantle structure under continents and oceans by the use of P'dP', the seismic core phase P'P' (PKPPKP) that reflects at depth d in the mantle. In order to accomplish this, it was found necessary to also investigate core phases themselves and their inferences on core structure. P'dP' at both single stations and at the LASA array in Montana indicates that the following zones are candidates for discontinuities with varying degrees of confidence: 800-950 km, weak; 630-670 km, strongest; 500-600 km, strong but interpretation in doubt; 350-415 km, fair; 280-300 km, strong, varying in depth; 100-200 km, strong, varying in depth, may be the bottom of the low-velocity zone. It is estimated that a single station cannot easily discriminate between asymmetric P'P' and P'dP' for lead times of about 30 sec from the main P'P' phase, but the LASA array reduces this uncertainty range to less than 10 sec. The problems of scatter of P'P' main-phase times, mainly due to asymmetric P'P', incorrect identification of the branch, and lack of the proper velocity structure at the velocity point, are avoided and the analysis shows that one-way travel of P waves through oceanic mantle is delayed by 0.65 to 0.95 sec relative to United States mid-continental mantle.

A new P-wave velocity core model is constructed from observed times, dt/dΔ's, and relative amplitudes of P'; the observed times of SKS, SKKS, and PKiKP; and a new mantle-velocity determination by Jordan and Anderson. The new core model is smooth except for a discontinuity at the inner-core boundary determined to be at a radius of 1215 km. Short-period amplitude data do not require the inner core Q to be significantly lower than that of the outer core. Several lines of evidence show that most, if not all, of the arrivals preceding the DF branch of P' at distances shorter than 143° are due to scattering as proposed by Haddon and not due to spherically symmetric discontinuities just above the inner core as previously believed. Calculation of the travel-time distribution of scattered phases and comparison with published data show that the strongest scattering takes place at or near the core-mantle boundary close to the seismic station.

In Part II, the largest events in the San Fernando earthquake series, initiated by the main shock at 14 00 41.8 GMT on February 9, 1971, were chosen for analysis from the first three months of activity, 87 events in all. The initial rupture location coincides with the lower, northernmost edge of the main north-dipping thrust fault and the aftershock distribution. The best focal mechanism fit to the main shock P-wave first motions constrains the fault plane parameters to: strike, N 67° (± 6°) W; dip, 52° (± 3°) NE; rake, 72° (67°-95°) left lateral. Focal mechanisms of the aftershocks clearly outline a downstep of the western edge of the main thrust fault surface along a northeast-trending flexure. Faulting on this downstep is left-lateral strike-slip and dominates the strain release of the aftershock series, which indicates that the downstep limited the main event rupture on the west. The main thrust fault surface dips at about 35° to the northeast at shallow depths and probably steepens to 50° below a depth of 8 km. This steep dip at depth is a characteristic of other thrust faults in the Transverse Ranges and indicates the presence at depth of laterally-varying vertical forces that are probably due to buckling or overriding that causes some upward redirection of a dominant north-south horizontal compression. Two sets of events exhibit normal dip-slip motion with shallow hypocenters and correlate with areas of ground subsidence deduced from gravity data. Several lines of evidence indicate that a horizontal compressional stress in a north or north-northwest direction was added to the stresses in the aftershock area 12 days after the main shock. After this change, events were contained in bursts along the downstep and sequencing within the bursts provides evidence for an earthquake-triggering phenomenon that propagates with speeds of 5 to 15 km/day. Seismicity before the San Fernando series and the mapped structure of the area suggest that the downstep of the main fault surface is not a localized discontinuity but is part of a zone of weakness extending from Point Dume, near Malibu, to Palmdale on the San Andreas fault. This zone is interpreted as a decoupling boundary between crustal blocks that permits them to deform separately in the prevalent crustal-shortening mode of the Transverse Ranges region.

Part I. Efforts directed towards the total synthesis of shionone. Part II. Conversion of estrone to androst-4-EN-3-ONE: a new method for activating the C-9 and C-10 positions of estrogenic steroids for substitution

Part I: An approach to the total synthesis of the triterpene shionone is described, which proceeds through the tetracyclic ketone i. The shionone side chain has been attached to this key intermediate in 5 steps, affording the olefin 2 in 29% yield. A method for the stereo-specific introduction of the angular methyl group at C-5 of shionone has been developed on a model system. The attempted utilization of this method to convert olefin 2 into shionone is described.

Part II: A method has been developed for activating the C-9 and C-10 positions of estrogenic steroids for substitution. Estrone has been converted to 4β,5β-epoxy-10β-hydroxyestr-3-one; cleavage of this epoxyketone using an Eschenmoser procedure, and subsequent modification of the product afforded 4-seco-9-estren-3,5-dione 3-ethylene acetal. This versatile intermediate, suitable for substitution at the 9 and/or 10 position, was converted to androst-4-ene-3-one by known procedures.

Part I. Energy straggling of ^4He below 2.0 MeV in Al, Ni, Au and Pt. Part II. Studies of the Ti-W metallization system on Si

Part I.

In recent years, backscattering spectrometry has become an important tool for the analysis of thin films. An inherent limitation, though, is the loss of depth resolution due to energy straggling of the beam. To investigate this, energy straggling of ⁴He has been measured in thin films of Ni, Al, Au and Pt. Straggling is roughly proportional to square root of thickness, appears to have a slight energy dependence and generally decreases with decreasing atomic number of the adsorber. The results are compared with predictions of theory and with previous measurements. While Ni measurements are in fair agreement with Bohr's theory, Al measurements are 30% above and Au measurements are 40% below predicted values. The Au and Pt measurements give straggling values which are close to one another.

Part II.

MeV backscattering spectrometry and X-ray diffraction are used to investigate the behavior of sputter-deposited Ti-W mixed films on Si substrates. During vacuum anneals at temperatures near 700°C for several hours, the metallization layer reacts with the substrate. Backscattering analysis shows that the resulting compound layer is uniform in composition and contains Ti, Wand Si. The Ti:W ratio in the compound corresponds to that of the deposited metal film. X-ray analyses with Reed and Guinier cameras reveal the presence of the ternary Ti_xW_(1-x)Si₂ compound. Its composition is unaffected by oxygen contamination during annealing, but the reaction rate is affected. The rate measured on samples with about 15% oxygen contamination after annealing is linear, of the order of 0.5 Å per second at 725°C, and depends on the crystallographic orientation of the substrate and the dc bias during sputter-deposition of the Ti-W film.

Au layers of about 1000 Å thickness were deposited onto unreacted Ti-W films on Si. When annealed at 400°C these samples underwent a color change,and SEM micrographs of the samples showed that an intricate pattern of fissures which were typically 3µm wide had evolved. Analysis by electron microprobe revealed that Au had segregated preferentially into the fissures. This result suggests that Ti-W is not a barrier to Au-Si intermixing at 400°C.

I. Foehn winds of southern California. II. Foehn wind cyclo-genesis. III. Weather conditions associated with the Akron disaster. IV. The Los Angeles storm of December 30, 1933 to January 1, 1934

I. Foehn winds of southern California.
An investigation of the hot, dry and dust laden winds occurring in the late fall and early winter in the Los Angeles Basin and attributed in the past to the influences of the desert regions to the north revealed that these currents were of a foehn nature. Their properties were found to be entirely due to dynamical heating produced in the descent from the high level areas in the interior to the lower Los Angeles Basin. Any dust associated with the phenomenon was found to be acquired from the Los Angeles area rather than transported from the desert. It was found that the frequency of occurrence of a mild type foehn of this nature during this season was sufficient to warrant its classification as a winter monsoon. This results from the topography of the Los Angeles region which allows an easy entrance to the air from the interior by virtue of the low level mountain passes north of the area. This monsoon provides the mild winter climate of southern California since temperatures associated with the foehn currents are far higher than those experienced when maritime air from the adjacent Pacific Ocean occupies the region.

II. Foehn wind cyclo-genesis.
Intense anticyclones frequently build up over the high level regions of the Great Basin and Columbia Plateau which lie between the Sierra Nevada and Cascade Mountains to the west and the Rocky Mountains to the east. The outflow from these anticyclones produce extensive foehns east of the Rockies in the comparatively low level areas of the middle west and the Canadian provinces of Alberta and Saskatchewan. Normally at this season of the year very cold polar continental air masses are present over this territory and with the occurrence of these foehns marked discontinuity surfaces arise between the warm foehn current, which is obliged to slide over a colder mass, and the Pc air to the east. Cyclones are easily produced from this phenomenon and take the form of unstable waves which propagate along the discontinuity surface between the two dissimilar masses. A continual series of such cyclones was found to occur as long as the Great Basin anticyclone is maintained with undiminished intensity.

III. Weather conditions associated with the Akron disaster.
This situation illustrates the speedy development and propagation of young disturbances in the eastern United States during the spring of the year under the influence of the conditionally unstable tropical maritime air masses which characterise the region. It also furnishes an excellent example of the superiority of air mass and frontal methods of weather prediction for aircraft operation over the older methods based upon pressure distribution.

IV. The Los Angeles storm of December 30, 1933 to January 1, 1934.
This discussion points out some of the fundamental interactions occurring between air masses of the North Pacific Ocean in connection with Pacific Coast storms and the value of topographic and aerological considerations in predicting them. Estimates of rainfall intensity and duration from analyses of this type may be made and would prove very valuable in the Los Angeles area in connection with flood control problems.

Magnetic behavior of basic iron(III) compounds. I. Magnetic behavior of the basic iron sulphates and basic iron chromate. II. Magnetic behavior of delta ferric oxide hydroxide

I. The thermomagnetic behavior and infrared spectroscopic features of KFe₃(SO₄)₂(OH)₆ (jarosite), (H₃O)Fe₃(SO₄)₂ (OH)₆ (hydronium jarosite), KFe₃(CrO₄)₂ (OH)₆, Fe(OH)SO₄ (basic iron sulfate), and Fe(OH)CrO₄ (basic iron chromate) are reported. Fe(OH)CrO₄ and KFe₃(CrO₄)₂ (OH)₆ are shown to be weak ferro magnets with Curie temperatures of 73 and 71 °K, respectively. This unusual magnetic behavior is rationalized in terms of the ionic spin configurations of the phases. Exchange coupling through chromate bridging groups is shown to be weak.

II. The magnetic behavior and the influence of preparative history on the magnetic behavior of δFeO(OH) is reported. δFeO(OH) is shown to be a fine-particulate, uniaxial, magnetic species. Magnetization data for this species are shown to be consistent with the existence of magnetically inactive layers surrounding magnetic particles.