Strong atom-light interactions along nanostructures: Transition from free-space to nanophotonic interfaces

An exciting frontier in quantum information science is the integration of otherwise "simple'' quantum elements into complex quantum networks. The laboratory realization of even small quantum networks enables the exploration of physical systems that have not heretofore existed in the natural world. Within this context, there is active research to achieve nanoscale quantum optical circuits, for which atoms are trapped near nano-scopic dielectric structures and "wired'' together by photons propagating through the circuit elements. Single atoms and atomic ensembles endow quantum functionality for otherwise linear optical circuits and thereby enable the capability of building quantum networks component by component. Toward these goals, we have experimentally investigated three different systems, from conventional to rather exotic systems : free-space atomic ensembles, optical nano fibers, and photonics crystal waveguides. First, we demonstrate measurement-induced quadripartite entanglement among four quantum memories. Next, following the landmark realization of a nanofiber trap, we demonstrate the implementation of a state-insensitive, compensated nanofiber trap. Finally, we reach more exotic systems based on photonics crystal devices. Beyond conventional topologies of resonators and waveguides, new opportunities emerge from the powerful capabilities of dispersion and modal engineering in photonic crystal waveguides. We have implemented an integrated optical circuit with a photonics crystal waveguide capable of both trapping and interfacing atoms with guided photons, and have observed the collective effect, superradiance, mediated by the guided photons. These advances provide an important capability for engineered light-matter interactions, enabling explorations of novel quantum transport and quantum many-body phenomena.

Directed evolution of terpene synthases for non-natural substrates

Terpenes represent about half of known natural products, with terpene synthases catalyzing reactions to increase the complexity of substrates and generate cyclizations of the linear diphosphate substrates, therefore forming rings and stereocenters. With their diverse functionality, terpene synthases may be highly evolvable, with the ability to accept a wide range of non-natural compounds and with high product selectivity. Our hypothesis is that directed evolution of terpene synthases can be used to increase selectivity of the synthase on a specific substrate. In the first part of the work presented herein, three natural terpene synthases, Cop2, BcBOT2, and SSCG_02150, were tested for activity against the natural substrate and a non-natural substrate, called Surrogate 1, and the relative activities on both the natural and non-natural substrates were compared. In the second part of this work, a terpene synthase variant of BcBOT2 that has been evolved for thermostability, was used for directed evolution for increased activity and selectivity on the non-natural substrate referred to as Surrogate 2. Mutations for this evolution were introduced using random mutagenesis, with error prone polymerase chain reactions, and using site-specific saturation mutagenesis, in which an NNK library is designed with a specific active site amino acid targeted for mutation. The mutant enzymes were then screened and selected for enhancement of the desired functionality. Two neutral mutants, 19B7 W367F and 19B7 W118Q, were found to maintain activity on Surrogate 2, as measured by the screen.

Measurement of the band bending and surface dipole at chemically functionalized Si(111)/vacuum interfaces

The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH₃ groups, respectively. The surface termination influenced the band bending, with the Si 2p_3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH₃ (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH₃ surfaces exposed to Br₂(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br₂(g)-exposed Si(111)-CH₃ was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.

New strategies for the total synthesis of aza-propellane natural products

The propellane alkaloids comprise a large class of natural products that possess varying degrees of structural complexity and biological activity. The earliest of these to be isolated was acutumine, a chlorinated alkaloid that has been shown to exhibit selective T-cell cytotoxicity and antiamnesic properties. Alternatively, the hasubanan family of natural products has garnered considerable attention from the synthetic community in part due to its structural similarities to morphine. While these alkaloids have been the subject of numerous synthetic studies over the last forty years, very few enantioselective total syntheses have been reported to date.

As part of a research program directed towards the synthesis of various alkaloid natural products, we have developed a unified strategy for the preparation of the hasubanan and acutumine alkaloids. Specifically, a highly diastereoselective 1,2-addition of organometallic reagents to benzoquinone-derived tert-butanesulfinimines was established, which provides access to enantioenriched 4-aminocyclohexadienone products. This methodology enabled the enantioselective construction of functionalized dihydroindolones, which were found to undergo intramolecular Friedel-Crafts conjugate additions to furnish the propellane cores of several hasubanan alkaloids. As a result of these studies, the first enantioselective total syntheses of 8-demethoxyrunanine and cepharatines A, C, and D were accomplished in 9-11 steps from commercially available starting materials.

More recent efforts have focused on applying the sulfinimine methodology to the synthesis of a more structurally complex propellane alkaloid, acutumine. Extensive studies have determined that a properly functionalized dihydroindolone undergoes a photochemical [2+2] cycloaddition followed by a lactone fragmentation/Dieckmann cyclization to establish the carbocyclic framework of the natural product. The preparation of more appropriately oxidized propellane intermediates is currently under investigation, and is anticipated to facilitate our synthetic endeavors toward acutumine.

Investigations of charge-carrier dynamics at semiconductor/liquid interfaces

Theoretical and experimental investigations of charge-carrier dynamics at semiconductor/liquid interfaces, specifically with respect to interfacial electron transfer and surface recombination, are presented.

Fermi's golden rule has been used to formulate rate expressions for charge transfer of delocalized carriers in a nondegenerately doped semiconducting electrode to localized, outer-sphere redox acceptors in an electrolyte phase. The treatment allows comparison between charge-transfer kinetic data at metallic, semimetallic, and semiconducting electrodes in terms of parameters such as the electronic coupling to the electrode, the attenuation of coupling with distance into the electrolyte, and the reorganization energy of the charge-transfer event. Within this framework, rate constant values expected at representative semiconducting electrodes have been determined from experimental data for charge transfer at metallic electrodes. The maximum rate constant (i.e., at optimal exoergicity) for outer-sphere processes at semiconducting electrodes is computed to be in the range 10^-17-10^-16 cm⁴ s^-1, which is in excellent agreement with prior theoretical models and experimental results for charge-transfer kinetics at semiconductor/liquid interfaces.

Double-layer corrections have been evaluated for semiconductor electrodes in both depletion and accumulation conditions. In conjuction with the Gouy-Chapman-Stern model, a finite difference approach has been used to calculate potential drops at a representative solid/liquid interface. Under all conditions that were simulated, the correction to the driving force used to evaluate the interfacial rate constant was determined to be less than 2% of the uncorrected interfacial rate constant.

Photoconductivity decay lifetimes have been obtained for Si(111) in contact with solutions of CH₃OH or tetrahydrofuran containing one-electron oxidants. Silicon surfaces in contact with electrolyte solutions having Nernstian redox potentials > 0 V vs. SCE exhibited low effective surface recombination velocities regardless of the different surface chemistries. The formation of an inversion layer, and not a reduced density of electrical trap sites on the surface, is shown to be responsible for the long charge-carrier lifetimes observed for these systems. In addition, a method for preparing an air-stable, low surface recombination velocity Si surface through a two-step, chlorination/alkylation reaction is described.

A unified strategy to ent-kauranoid natural products : total syntheses of (–)-maoecrystal Z, (–)-trichorabdal A, and (–)-longikaurin E

The diterpenoid constituents of the Isodon plants have attracted reasearchers interested in both their chemical structures and biological properties for more than a half-century. In recent years, the isolations of new members displaying previously unprecedented ring systems and highly selective biological properties have piqued interest from the synthetic community in this class of natural products.

Reported herein is the first total synthesis of such a recently isolated diterpenoid, (–)-maoecrystal Z. The principal transformations implemented in this synthesis include two highly diastereoselective radical cyclization reactions: a Sm^(II)-mediated reductive cascade cyclization, which forms two rings and establishes four new stereocenters in a single step, and a Ti^(III)-mediated reductive epoxide-acrylate coupling that yields a functionalized spirolactone product, which forms a core bicycle of maoecrystal Z.

The preparation of two additional ent-kauranoid natural products, (–)-trichorabdal A and (–)-longikaurin E, is also described from a derivative of this key spirolactone. These syntheses are additionally enabled by the palladium-mediated oxidative cyclization reaction of a silyl ketene acetal precursor that is used to install the bridgehead all-carbon quaternary stereocenter and bicyclo[3.2.1]octane present in each natural product. These studies have established a synthetic relationship among three architecturally distinct ent-kaurane diterpenoids and have forged a path for the preparation of interesting unnatural ent-kauranoid structural analogs for more thorough biological study.

The development of an asymmetric palladium-catalyzed conjugate addition and its application toward the total syntheses of taiwaniaquinoid natural products

The asymmetric synthesis of quaternary stereocenters remains a challenging problem in organic synthesis. Past work from the Stoltz laboratory has resulted in methodology to install quaternary stereocenters α- or γ- to carbonyl compounds. Thus, the asymmetric synthesis of β-quaternary stereocenters was a desirable objective, and was accomplished by engineering the palladium-catalyzed addition of arylmetal organometallic reagents to α,β-unsaturated conjugate acceptors.

Herein, we described the rational design of a palladium-catalyzed conjugate addition reactions utilizing a catalyst derived from palladium(II) trifluoroacetate and pyridinooxazole ligands. This reaction is highly tolerant of protic solvents and oxygen atmosphere, making it a practical and operationally simple reaction. The mild conditions facilitate a remarkably high functional group tolerance, including carbonyls, halogens, and fluorinated functional groups. Furthermore, the reaction catalyzed conjugate additions with high enantioselectivity with conjugate acceptors of 5-, 6-, and 7-membered ring sizes. Extension of the methodology toward the asymmetric synthesis of flavanone products is presented, as well.

A computational and experimental investigation into the reaction mechanism provided a stereochemical model for enantioinduction, whereby the α-methylene protons adjacent the enone carbonyl clashes with the tert-butyl groups of the chiral ligand. Additionally, it was found that the addition of water and ammonium hexafluorophosphate significantly increases the reaction rate without sacrificing enantioselectivity. The synergistic effects of these additives allowed for the reaction to proceed at a lower temperature, and thus facilitated expansion of the substrate scope to sensitive functional groups such as protic amides and aryl bromides. Investigations into a scale-up synthesis of the chiral ligand (S)-tert-butylPyOx are also presented. This three-step synthetic route allowed for synthesis of the target compound of greater than 10 g scale.

Finally, the application of the newly developed conjugate addition reaction toward the synthesis of the taiwaniaquinoid class of terpenoid natural products is discussed. The conjugate addition reaction formed the key benzylic quaternary stereocenter in high enantioselectivity, joining together the majority of the carbons in the taiwaniaquinoid scaffold. Efforts toward the synthesis of the B-ring are presented.

Applications of a Concise and General Strategy for the Syntheses of Transtaganolide and Basiliolide Natural Products

Herein are described the total syntheses of all members of the transtaganolide and basiliolide natural product family. Utilitzation of an Ireland–Claisen rearrangement/Diels–Alder cycloaddition cascade (ICR/DA) allowed for rapid assembly of the transtaganolide and basiliolide oxabicyclo[2.2.2]octane core. This methodology is general and was applicable to all members of the natural product family.

A brief introduction outlines all the synthetic progress previously disclosed by Lee, Dudley, and Johansson. This also includes the initial syntheses of transtaganolides C and D, as well as basiliolide B and epi-basiliolide B accomplished by Stoltz in 2011. Lastly, we discuss our racemic synthesis of basililide C and epi-basiliolide C, which utilized an ICR/DA cascade to constuct the oxabicyclo[2.2.2]octane core and formal [5+2] annulation to form the ketene-acetal containing 7-membered C-ring.

Next, we describe a strategy for an asymmetric ICR/DA cascade, by incorporation of a chiral silane directing group. This allowed for enantioselective construction of the C8 all-carbon quaternary center formed in the Ireland–Claisen rearrangement. Furthermore, a single hydride reduction and subsequent translactonization of a C4 methylester bearing oxabicyclo[2.2.2]octane core demonstrated a viable strategy for the desired skeletal rearrangement to obtain pentacyclic transtaganolides A and B. Application of the asymmetric strategy culminated in the total syntheses of (–)-transtaganolide A, (+)-transtaganolide B, (+)-transtaganolide C, and (–)-transtaganolide D. Comparison of the optical rotation data of the synthetically derived transtaganolides to that from the isolated counterparts has overarching biosynthetic implications which are discussed.

Lastly, improvement to the formal [5+2] annulation strategy is described. Negishi cross-coupling of methoxyethynyl zinc chloride using a palladium Xantphos catalyst is optimized for iodo-cyclohexene. Application of this technology to an iodo-pyrone geranyl ester allowed for formation and isolation of the eneyne product. Hydration of the enenye product forms natural metabolite basiliopyrone. Furthermore, the eneyne product can undergo an ICR/DA cascade and form transtaganolides C and D in a single step from an achiral monocyclic precursor.

Effect of Microstructural Interfaces on the Mechanical Response of Crystalline Metallic Materials

Advances in nano-scale mechanical testing have brought about progress in the understanding of physical phenomena in materials and a measure of control in the fabrication of novel materials. In contrast to bulk materials that display size-invariant mechanical properties, sub-micron metallic samples show a critical dependence on sample size. The strength of nano-scale single crystalline metals is well-described by a power-law function, σαD^-n, where D is a critical sample size and n is a experimentally-fit positive exponent. This relationship is attributed to source-driven plasticity and demonstrates a strengthening as the decreasing sample size begins to limit the size and number of dislocation sources. A full understanding of this size-dependence is complicated by the presence of microstructural features such as interfaces that can compete with the dominant dislocation-based deformation mechanisms. In this thesis, the effects of microstructural features such as grain boundaries and anisotropic crystallinity on nano-scale metals are investigated through uniaxial compression testing. We find that nano-sized Cu covered by a hard coating displays a Bauschinger effect and the emergence of this behavior can be explained through a simple dislocation-based analytic model. Al nano-pillars containing a single vertically-oriented coincident site lattice grain boundary are found to show similar deformation to single-crystalline nano-pillars with slip traces passing through the grain boundary. With increasing tilt angle of the grain boundary from the pillar axis, we observe a transition from dislocation-dominated deformation to grain boundary sliding. Crystallites are observed to shear along the grain boundary and molecular dynamics simulations reveal a mechanism of atomic migration that accommodates boundary sliding. We conclude with an analysis of the effects of inherent crystal anisotropy and alloying on the mechanical behavior of the Mg alloy, AZ31. Through comparison to pure Mg, we show that the size effect dominates the strength of samples below 10 μm, that differences in the size effect between hexagonal slip systems is due to the inherent crystal anisotropy, suggesting that the fundamental mechanism of the size effect in these slip systems is the same.

Expanding the Toolkit for Synthetic Biology: Frameworks for Native-like Non-natural Gene Circuits

Synthetic biology combines biological parts from different sources in order to engineer non-native, functional systems. While there is a lot of potential for synthetic biology to revolutionize processes, such as the production of pharmaceuticals, engineering synthetic systems has been challenging. It is oftentimes necessary to explore a large design space to balance the levels of interacting components in the circuit. There are also times where it is desirable to incorporate enzymes that have non-biological functions into a synthetic circuit. Tuning the levels of different components, however, is often restricted to a fixed operating point, and this makes synthetic systems sensitive to changes in the environment. Natural systems are able to respond dynamically to a changing environment by obtaining information relevant to the function of the circuit. This work addresses these problems by establishing frameworks and mechanisms that allow synthetic circuits to communicate with the environment, maintain fixed ratios between components, and potentially add new parts that are outside the realm of current biological function. These frameworks provide a way for synthetic circuits to behave more like natural circuits by enabling a dynamic response, and provide a systematic and rational way to search design space to an experimentally tractable size where likely solutions exist. We hope that the contributions described below will aid in allowing synthetic biology to realize its potential.

Enantioselective Total Synthesis of Diketopiperazinecontaining Natural Products: (–)-Lansai B, (+)-Nocardioazines A and B, and (–)-Acetylapoaranotin

Diketopiperazine (DKP) motif is found in a wide range of biologically active natural products. This work details our efforts toward two classes of DKP-containing natural products.

Class one features the pyrroloindoline structure, derived from tryptophans. Our group developed a highly enantioselective (3 + 2) formal cycloaddition between indoles and acrylates to provide pyrroloindoline products possessing three stereocenters. Utilizing this methodology, we accomplished asymmetric total synthesis of three natural products: (–)-lansai B, (+)-nocardioazines A and B. Total synthesis of (–)-lansai B was realized in six steps, and featured an amino acid dimerization strategy. The total synthesis of (+)-nocardioazine B was also successfully completed in ten steps. Challenges were met in approaching (+)-nocardioazine A, where a seemingly easy last-step epoxidization did not prove successful. After re-examining our synthetic strategy, an early-stage epoxidation strategy was pursued, which eventually yielded a nine-step total synthesis of (+)-nocardioazine A.

Class two is the epidithiodiketopiperazine (ETP) natural products, which possesses an additional episulfide bridge in the DKP core. With the goal of accessing ETPs with different peripheral structures for structure-activity relationship studies, a highly divergent route was successfully developed, which was showcased in the formal synthesis of (–)-emethallicin E and (–)-haematocin, and the first asymmetric synthesis of (–)-acetylapoaranotin.

Longitudinal dispersion in laboratory and natural streams

This study concerns the longitudinal dispersion of fluid particles which are initially distributed uninformly over one cross section of a uniform, steady, turbulent open channel flow. The primary focus is on developing a method to predict the rate of dispersion in a natural stream.

Taylor's method of determining a dispersion coefficient, previously applied to flow in pipes and two-dimensional open channels, is extended to a class of three-dimensional flows which have large width-to-depth ratios, and in which the velocity varies continuously with lateral cross-sectional position. Most natural streams are included. The dispersion coefficient for a natural stream may be predicted from measurements of the channel cross-sectional geometry, the cross-sectional distribution of velocity, and the overall channel shear velocity. Tracer experiments are not required.

Large values of the dimensionless dispersion coefficient D/rU* are explained by lateral variations in downstream velocity. In effect, the characteristic length of the cross section is shown to be proportional to the width, rather than the hydraulic radius. The dimensionless dispersion coefficient depends approximately on the square of the width to depth ratio.

A numerical program is given which is capable of generating the entire dispersion pattern downstream from an instantaneous point or plane source of pollutant. The program is verified by the theory for two-dimensional flow, and gives results in good agreement with laboratory and field experiments.

Both laboratory and field experiments are described. Twenty-one laboratory experiments were conducted: thirteen in two-dimensional flows, over both smooth and roughened bottoms; and eight in three-dimensional flows, formed by adding extreme side roughness to produce lateral velocity variations. Four field experiments were conducted in the Green-Duwamish River, Washington.

Both laboratory and flume experiments prove that in three-dimensional flow the dominant mechanism for dispersion is lateral velocity variation. For instance, in one laboratory experiment the dimensionless dispersion coefficient D/rU* (where r is the hydraulic radius and U* the shear velocity) was increased by a factory of ten by roughening the channel banks. In three-dimensional laboratory flow, D/rU* varied from 190 to 640, a typical range for natural streams. For each experiment, the measured dispersion coefficient agreed with that predicted by the extension of Taylor's analysis within a maximum error of 15%. For the Green-Duwamish River, the average experimentally measured dispersion coefficient was within 5% of the prediction.

Stability of Electrode-Electrolyte Interfaces during Charging in Lithium Batteries

In this thesis we study the growth of a Li electrode-electrolyte interface in the presence of an elastic prestress. In particular, we focus our interest on Li-air batteries with a solid electrolyte, LIPON, which is a new type of secondary or rechargeable battery. Theoretical studies and experimental evidence show that during the process of charging the battery the replated lithium adds unevenly to the electrode surface. This phenomenon eventually leads to dendrite formation as the battery is charged and discharged numerous times. In order to suppress or alleviate this deleterious effect of dendrite growth, we put forth a study based on a linear stability analysis. Taking into account all the mechanisms of mass transport and interfacial kinetics, we model the evolution of the interface. We find that, in the absence of stress, the stability of a planar interface depends on interfacial diffusion properties and interfacial energy. Specifically, if Herring-Mullins capillarity-driven interfacial diffusion is accounted for, interfaces are unstable against all perturbations of wavenumber larger than a critical value. We find that the effect of an elastic prestress is always to stabilize planar interfacial growth by increasing the critical wavenumber for instability. A parametric study results in quantifying the extent of the prestress stabilization in a manner that can potentially be used in the design of Li-air batteries. Moreover, employing the theory of finite differences we numerically solve the equation that describes the evolution of the surface profile and present visualization results of the surface evolution by time. Lastly, numerical simulations performed in a commercial finite element software validate the theoretical formulation of the interfacial elastic energy change with respect to the planar interface.