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Towards Ab Initio Simulations of High-Temperature Superconductivity
Get PDFHigh-temperature superconductors have been discovered for more than three decades. Nonetheless, the theoretical understanding of their microscopic properties remains unclear with substantial difficulties in linking the observed phenomena to material composition and structures. This thesis aims to establish a theoretical hierarchy (from lattice models to realistic materials) for faithful simulations of high temperature superconductivity.
We start with the lattice models of superconductors by using quantum embedding theory, whose self-consistency allows magnetic and superconducting phases to emerge. We extended the density matrix embedding theory (DMET) with improved self-consistency algorithms and determined the ground-state phase diagrams for both one-band [Chap. 3] the three-band Hubbard models [Chap. 4]. In particular, in the three-band model, we explored the atomic-scale nature of the antiferromagnetic and superconducting orders for different model parametrizations, and highlighted the role of the oxygen degrees of freedom beyond the one-band picture.
To go beyond the models, we therefore extended the original theory [DMET and dynamical mean-field theory (DMFT)] to ab initio realistic solids [Chap. 5]. The methods, namely the full-cell quantum embedding, are distinct from other embedding schemes in three aspects: (i) all local orbitals in a unit cell are included in the embedding problem whereas the bath orbitals are truncated according the atomic valence characters; (ii) The embedding Hamiltonian is of full quartic fermionic form rather simplified Hubbard like Hamiltonians; (iii) Many-body quantum chemistry solvers such as coupled cluster (CC) are used to generate embedding density matrix and Green’s functions. As demonstrated across a variety of semiconducting and insulating materials, the full-cell quantum embedding provides accurate energy, equation of state, spin-spin correlation functions and excited-state band structures.
We then applied our ab initio quantum embedding methods to the parent state of a series of cuprate superconductors [Chap. 6]. We uncovered microscopic trends in the electron correlations and revealed the link between the material composition and magnetic energy scales via a many-body picture of excitation processes involving the buffer layers. We found the competition between the in-plane superexchange and the CuO₂-buffer layer excitations, which explains the magnetic coupling difference among a series of superconducting materials.
Finally, we investigated the doped cuprates, where the superconducting orders enter into the phase diagram [Chap. 7]. We generalized our ab initio framework to allow the particle-number symmetry breaking states such that the superconducting orders can spontaneously emerge during the self-consistency. We showed that the d-wave superconducting magnitude increases with the pressure applied to crystals and the trend connects to the superexchange coupling J . Furthermore, we also studied the layer effect on superconductivity. Unlike the pressure effect, the layer effect between different compounds is affected by more factors - both magnetic coupling J and charge distribution matters. The work provides a promising route to study the material-specific physics in high-temperature superconductivity.
The aforementioned applications also relied on (i) the development and adaptation of many-body solvers, including the CC singles and doubles (CCSD) with Newton-Krylov method for better numerical convergence, and active-space quantum chemistry techniques with large-scale density matrix renormalization group. (ii) projection-based orbital localizations for metallic systems, frozen core techniques and symmetry adaptations. These contents are discussed in Chap. 2 and Appendices, including their efficient implementation and parallelization.
In the concluding remarks [Chap. 8], we summarized the current status and limitations of the high-temperature superconductivity studies. In addition, we proposed several possible directions to address the challenges in electronic correlation and atomic modelling of other exotic phases from an ab initio perspective.</p
Electronic Structure and Reactivity of Metal Complexes
Get PDFTransition metals are at the core of addressing global energy needs. Functioning as catalysts, these systems have long demonstrated competency to promote thermodynamically challenging reactions, lowering energetic barriers and facilitating desired transformations with applied light or potential. Employing infrared, visible, ultraviolet, and x-ray spectroscopy, chemists are afforded insight into the electronic structures of transition metal complexes, investigating ligand field strengths and metal-ligand interactions. Addition of time-resolved techniques affords resolution of dynamic processes in molecular species, such as electron transfer pathways.
Chapter 1 reviews the electronic structure and reactivity of homoleptic tungsten(0) arylisocyanides W(CNAr)₆ to provide the foundation for much of this work.
In Chapter 2, application of W(CNAr)₆ species for one- and two-photon photoredox catalysis are explored. The two-photon absorption cross-sections of W(CNAr)₆ are remarkably large (δ₈₁₀ = 180–1900 GM) and enable these photocatalysts to operate under excitation from visible or near infrared light. Photoredox activity is evaluated via base-promoted homolytic aromatic substitution (BHAS) reaction of thermodynamically challenging substrates. In Chapter 3, solvent perturbations enhance visible light-activated BHAS catalysis from W(CNAr)₆. Increased solvent dielectric (benzene to 1,2-difluorobenzene) and solvated electrolyte combine to increase *W(CNAr)₆ quenching rates up to one order of magnitude with greater cage-escape yields.
In Chapter 4, the electronic structure of linear gold(I) arylisocyanide complexes ([Au(CNDipp-R)₂]⁺; CNDipp = 2,6-diisopropylphenylisocyanide) are assigned using insights from UV-visible spectroscopy and time-dependent density functional theory (TD-DFT) calculations. In Chapter 5, the electronic structure of Fe(II) and Co(II) quaterpyridine photo-/electro-catalysts for CO₂ reduction are evaluated using UV-visible-NIR, ¹H NMR, Mössbauer, and infrared spectra. Assignment of the absorption transitions are supported by TD-DFT calculations.</p
Insertion of Olefins into Nickel Alkyl Complexes: Mechanistic Studies and Polymerization Catalysis
Get PDFPolyolefins account for over half of global plastic production. The incorporation of polar functionalities can provide value-added polyolefins with desirable material properties and potential degradability. To achieve this, coordination copolymerization of ethylene and fundamental polar comonomers by transition-metal catalysts is the most direct, economical, and environmentally friendly method. Though it has been pursued for decades, the catalyst performance (e.g. activity, thermal stability) is still far below practical thresholds. The major issue is the "polar monomer problem": coordination of the polar group in the comonomer to the metal center competes with vinyl coordination, a prerequisite for the monomer enchainment (chain propagation).
This thesis describes mechanism-driven developments of industrially applicable molecular catalysts toward addressing the "polar monomer problem", with a focus on nickel catalysts for ethylene/acrylate copolymerization.</p
Development of Oxidation and Transition Metal-Mediated Reactions and Application to Natural Product Synthesis
Get PDFExpedient access to complex molecules via chemical synthesis is important for assessing their biological activity and medicinal properties. In one approach, convergent joining of fragments of similar size and complexity is followed by minimal scaffold tailoring steps to rapidly access natural products. This strategy hinges on the ability to (1) tailor peripheral oxidation, ideally via creative redox transformations, and (2) forge strategic bonds within a complex scaffold through C–C bond formation. We disclose efforts to address these aims by developing broadly useful chemical tools and applying them to the preparation of bioactive natural products.
Toward the first aim, we investigated unusual oxidative reactivity mediated by selenium dioxide. To address the second aim, we developed nickel-catalyzed reductive cross-coupling reactions to study: catalyst-controlled enantioselectivity in the preparation of medicinally relevant small molecules, substrate-controlled stereoselectivity, and selectivity for ring formation. The latter studies enabled the exploration of transition metal-mediated cyclization as a convergent annulation strategy toward the rearranged isoryanodane diterpene (+)-cassiabudanol A, as well as the formal synthesis of the macrocyclic cytotoxin (–)-cylindrocyclophane F.</p
The Emerging Mechanochemistry of Naphthopyran
Get PDFAsserting remote control over reactivity is a pervasive goal in modern chemistry. Several external stimuli can supply energy to facilitate productive chemical transformations. In recent years, that list has grown to include mechanical force. In the growing field of polymer mechanochemistry, privileged, mechanically sensitive molecules called mechanophores undergo desirable chemical reactions under force. Force is transduced to mechanophores through covalently attached polymer chains. Among many applications, mechanophores that react to produce colored species can be used for visual stress and damage detection in plastics. Naphthopyran is a highly modular molecular switch that can undergo ring-opening reaction to generates intensely colored merocyanine dyes. The studies described in this dissertation have thoroughly established the versatility and complexity of naphthopyran-based mechanochromic mechanophores.
In Chapter 1, the history of naphthopyran molecular switches is summarized with particular emphasis on the exhaustive and generalizable merocyanine structure-property relationships established for photochromic naphthopyrans. Naphthopyran mechanochemistry is reviewed and contextualized among other mechanochromic mechanophores. Mechanochromic structure-function relationships are highlighted, as well as a series of studies using the naphthopyran platform for illustration of the unusual reaction pathways accessible under force, and studies demonstrating that multimodal naphthopyrans are an ideal platform for multicolor mechanochromism.
As discussed extensively in Chapter 1, merocyanines are typically susceptible to thermal recyclization. However, Chapter 2 describes a scissile naphthopyran mechanophore that undergoes an unusual secondary mechanochemical ester cleavage after the ring-opening reaction. By revealing a β-hydroxy ketone group with a stable intramolecular hydrogen bonding interaction, mechanical force uniquely generates persistent merocyanine species.
The irreversible reaction sequence described in Chapter 2 enables determination of mechanochemical reaction kinetics under solution-phase ultrasound-mediated mechanical force. However, common methods for determining reaction rate constants under these conditions are time-intensive and convoluted by the competitive side reaction of nonspecific polymer backbone scission. In Chapter 3, through model studies on the highly efficient scissile naphthopyran and a comparatively inefficient coumarin dimer mechanophore, we validate a time-efficient and accurate initial rates method for determination of selective mechanophore reaction kinetics under ultrasonication.
The ability to colorimetrically report on the magnitude of applied stress is a grand challenge in the field of mechanochromism. Chapter 4 describes the first single mechanophore capable of such behavior. Mechanical force induces unexpectedly simultaneous ring-opening reactions from a bis-naphthopyran mechanophore, biasing a dynamic equilibrium between two distinct merocyanine states to effect gradient force-dependent multicolor mechanochromism.
In further studies seeking multicolor mechanochromic systems, it was discovered that mechanical force facilitates the first reported dual-ring-opening reaction of naphthodipyran. Chapter 5 describes the mechanochemical generation of an unusual dimerocyanine species with near-IR absorption that is not formed photochemically.</p
Computational Imaging for Phase Retrieval and Biomedical Applications
Get PDFIn conventional imaging, optimizing hardware is prioritized to enhance image quality directly. Digital signal processing is viewed as supplementary. Computational imaging intentionally distorts images through modulation schemes in illumination or sensing. Then its reconstruction algorithms extract desired object information from raw data afterwards. Co-designing hardware and algorithms reduces demands on hardware and achieves the same or even better image quality. Algorithm design is at the heart of computational imaging, with model-based inverse problem or data-driven deep learning methods as approaches. This thesis presents research work from both perspectives, with a primary focus on the phase retrieval issue in computational microscopy and the application of deep learning techniques to address biomedical imaging challenges.
The first half of the thesis begins with Fourier ptychography, which was employed to overcome chromatic aberration problems in multispectral imaging. Then, we proposed a novel computational coherent imaging modality based on Kramers-Kronig relations, aiming to replace Fourier ptychography as a non-iterative method. While this approach showed promise, it lacks certain essential characteristics of the original Fourier ptychography. To address this limitation, we introduced two additional algorithms to form a whole package scheme. Through comprehensive evaluation, we demonstrated that the combined scheme outperforms Fourier ptychography in achieving high-resolution, large field-of-view, aberration-free coherent imaging.
The second half of the thesis shifts focus to deep-learning-based methods. In one project, we optimized the scanning strategy and image processing pipeline of an epifluorescence microscope to address focus issues. Additionally, we leveraged deep-learning-based object detection models to automate cell analysis tasks. In another project, we predicted the polarity status of mouse embryos from bright field images using adapted deep learning models. These findings highlight the capability of computational imaging to automate labor-intensive processes, and even outperform humans in challenging tasks.</p
Mechanics of River Erosion and its Effects on Floodplain Biogeochemistry
Get PDFRivers transport water, sediment, and nutrients across Earth’s surface. They shape landscapes, eroding mountain ranges and building floodplains, simultaneously providing important resources and posing a hazard to nearby communities. Here, I present field work, flume experiments, numerical models, and laboratory analyses addressing three main themes: permafrost river and floodplain dynamics, river meandering without plants, and rates of bedrock incision. Arctic rivers migrate rapidly across their floodplains and their migration rates are predicted to increase as permafrost thaws due to climate change. However, no mechanistic model is capable of predicting permafrost riverbank annual erosion rates. To address this knowledge gap, I developed a calibrated numerical model for permafrost riverbank erosion. A previously published theory assumes that permafrost erosion rates are limited by pore-ice thaw, but underestimates thaw rates due to bank roughness increasing heat transfer from the river to its banks (Chapter 3). Results indicate that thaw-limited erosion is orders of magnitude higher than observed erosion rates, and permafrost riverbank erosion must instead be limited by sediment entrainment and the collapse of overhanging blocks to match observed rates (Chapter 2). Based on experimental results, I developed a 1D numerical model that includes roughness-dependent permafrost thaw and sediment entrainment and tracks how heat transfer within the riverbank can form a thawed layer (Chapter 4). Results indicate that permafrost riverbank erosion rates respond to changes in river discharge due to climate change, which affect both bank thaw and entrainment rates, and are only sensitive to changes in water temperature via thawed layer failure. As a case study, I conducted fieldwork along the Koyukuk River in Alaska, which is located in discontinuous permafrost. I found that changes in riverbank erosion rates may more rapidly erase permafrost from floodplains (Chapter 7) and change the spatial patterns of floodplain methane emissions (Chapter 5). While riverbank erosion releases eroded organic carbon to be oxidized as greenhouse gases or transported downstream, a portion of this carbon is re-deposited in the floodplain, modulating the effects of river migration on regional carbon cycling (Chapter 6). To understand the effects of vegetation on river migration rates and fluvial stratigraphy, I conducted long-term monitoring of the unvegetated, ephemeral Amargosa River in Death Valley, California (Chapter 8). This study found that the Amargosa is actively meandering at very slow rates and frequently avulses, producing muddy stratigraphy with isolated sand bodies that is thought to be unique to vegetated meandering rivers. Sediment transport has also been proposed as a primary control on bedrock river incision rates, where saltating grains gradually abrade the channel bed over geologic timescales. However, uncertainty about long-term sediment supply and the frequency of floods that cause significant bedrock incision has prevented using saltation-abrasion to model landscape evolution. Using a global data compilation, I calculated a best-fit sediment supply-normalized flood intermittency parameter so that the saltation-abrasion model can be broadly applied (Chapter 9). Together, these studies advance understanding of how riverine sedimentary transport governs permafrost riverbank erosion, Arctic floodplain biogeochemistry, stratigraphic deposits of unvegetated rivers, and bedrock incision rates.</p
Tetranuclear CaMn₃O₄ and Mn₄O₄ Complexes as Spectroscopic Models of the Oxygen Evolving Complex of Photosystem II
No full textThis thesis describes a series of studies focused on tetranuclear model complexes of the Oxygen Evolving Complex (OEC) of Photosystem II (PSII). The OEC is a unique CaMn4O4 metallocofactor responsible for biological water oxidation, producing the dioxygen in the atmosphere required for aerobic life. Advances in spectroscopic and structural studies have deepened our understanding of the mechanism and S-state intermediates of the OEC, but details regarding the (1) role of Ca2+, (2) location of substrate waters, (3) (electronic) structures of the S-states, and (4) precise mechanism of the O−O bond formation remain debated. It is proposed that synthetic model complexes, due to tunability in aspects such as metal composition, oxidation state, geometry, and ligand environment, can provide important structure-function and structure-property relationships applicable to the OEC. However, due to synthetic challenges, series of complexes suitable for such comparisons remain rare in the literature.
In Chapter 1, a brief introduction to the OEC and recent advances in the characterization of the S-state intermediates is discussed. Relationships between synthetic model complexes and how they influence mechanistic proposals for the biological system are highlighted. While it is clear spin state and cluster geometry are strongly correlated, it is important to also consider the effects of smaller, systematic changes in structure and ligand environment on the spectroscopic properties of multimetallic model complexes.
Chapter 2 presents a magnetometry and spectroscopic study of a series of related CaMnIV3O4 complexes varying in the symmetry of the cluster core, ligand environment, and protonation state of the bridging oxo groups. These complexes serve as models of the CaMnIV3 cuboidal subsite, where cluster spin state has been previously proposed to be indicative of cluster geometry. Results from our study show that intact CaMnIV3O4 cubane structures can possess spin states of S = 3/2, 5/2, and 9/2, with spin state changes attributed to minor distortions within the cluster core and, importantly, from protonation state of bridging oxo moieties. Thus, interpretation of and structural assignments based on the assumption of a S = 9/2 CaMnIV3O4 subsite must be done cautiously.
Chapter 3 presents a series of MnIIIMnIV3 cuboidal complexes as spectroscopic models of the S2 state of the OEC. Though not in the same geometric arrangement of Mn ions as in the OEC, these model complexes bear remarkably similar EPR spectroscopic features to the low-spin multiline signal of the S2 state. Importantly, differences within this series of essentially isostructural complexes emphasize how the electronic structures of tetranuclear Mn complexes are highly sensitive to changes in ligand environment. Specifically, the energy gap between the ground S = 1/2 spin state and higher spin excited states can be tuned based on ligand electronics, resulting in complexes where both high-spin and low-spin features can be observed by EPR spectroscopy.
In Chapter 4, we expand upon our previous series of MnIIIMnIV3 model complexes utilizing a new synthetic approach to access complexes varying in Mn coordination numbers of five and six. Importantly, both proposed structures of the S2 state contain a five-coordinate MnIII poised for binding an additional aquo or hydroxide ligand in the S2 to S3 transition. Results from this study demonstrate that Mn coordination number can significantly affect the spin state and observed spectroscopy of tetramanganese-oxo clusters. The complex featuring a five coordinate MnIII possesses a ground spin state of SG = 5/2 and reactivity with water generates a MnIIIMnIV3O4 complex with all pseudo-octahedral Mn centers displaying a S = 1/2 ground state.
Chapter 5 details ligand design strategies in accessing higher oxidation state clusters beyond MnIIIMnIV3. The S3-state is the last observable intermediate prior to O−O bond formation and assigned as S = 3. Previous studies from our group demonstrated the first synthetic example corroborating this spin state, concurrent with a change from antiferromagnetic coupling within the cluster core to overall ferromagnetic coupling upon oxidation to the MnIV4 oxidation state. Synthetic challenges remain in accessing related, isolable clusters. Utilizing aspects of ligand charge and basicity of a disiloxide ligand, a room temperature stable MnIV4O4 cluster was isolated and studied via magnetometry and EPR spectroscopy. Results provide a second example of a MnIV4 cluster assigned as S = 3.
While unfinished, Appendix 1 presents spectroscopic studies of model MnIIIMnIV3 complexes putatively bound to biologically relevant substrates such as water, hydroxide, methanol, and ammonia. Such chemical alterations and the spectroscopic effects arising from them have been widely studied in the biological system, providing information on the electronic structure of the OEC as well as, importantly, ruling out potential substrate water binding sites. As reactivity with small molecules typically requires an open-coordination site, such studies have been rare in the literature due to the difficulty in accessing lower-coordinate Mn sites within multimetallic Mn clusters. Thus, the ongoing characterization of these reaction products are proposed to be invaluable as benchmarking tools for future mechanistic work.</p
The Orbits of Young Extrasolar Planets as Formation Probes
Get PDFIn this thesis, I have translated a few flavors of exoplanet timeseries measurements into constraints on exoplanet orbital parameters, and used these to make inferences about planet formation. I begin by introducing the two main observational techniques I used to perform these analyses: optical interferometry and stellar radial velocity monitoring. I then discuss some of the big open questions of exoplanet formation, particularly the mechanism for forming giant planets close to and far from their stars, where core accretion is thought to be too inefficient to form giant planet cores in time for them to accrete atmospheres.
High cadence radial velocity monitoring enables advances in our understanding of stellar activity, the fundamental stumbling block in the path to discovering and characterizing planets like the Earth. In my second thesis chapter, I present an argument that previously published RV-derived activity models of the PMS star V1298~Tau suffer from overfitting, casting doubt on published mass estimates of the young planets in the system which necessitated rapid contraction after formation, in tension with formation theory. I walk through several potential explanations for this overfitting, pointing out that the star has a strong differential rotation signal which is not included in published model fits, and encourage broader use of cross validation techniques in stellar activity model evaluation.
Optical interferometry, particularly using the VLTI/GRAVITY instrument, enables astrometry measurements that are orders of magnitude more precise than contemporary coronographic instruments, which translates to precise orbital parameters. In my third thesis chapter, I present and analyze two new VLTI/GRAVITY astrometric measurements of a young, widely separated planet and use them to make a preliminary argument that the planet's eccentricity is low or moderate. This sets an upper limit on the time (relative to disk dispersal) that the planet attained its current wide separation, and downweights the possibility of scattering after disk dispersal.
In the next two chapters, I showcase my contributions to two widely used open-source orbit-fitting software toolkits: orbitize! and radvel. I highlight two major new features of orbitize! that are available in the main code base as of the release of version 2: jointly fitting radial velocity measurements and jointly fitting absolute astrometry measurements. In the radvel chapter, I motivate and describe an updated Gaussian Process regression model for stellar activity modeling that reduces the potential for overfitting.</p
The Elastic, Electronic, and Structural Properties of Hydrous, Sulfur-Bearing Minerals in Planetary Environments: from the Surface to Deep Interiors
Get PDFIn this thesis, a comprehensive investigation of the hydrous iron endmember sulfate szomolnokite (FeSO₄·H₂O) has been conducted using a suite of complementary techniques to measure its structural, elastic, electronic, and vibrational properties under extreme conditions. Through X-ray diffraction (XRD), nuclear resonant inelastic X-ray scattering (NRIXS), synchrotron Mössbauer spectroscopy (SMS), and synchrotron Fourier transform infrared spectroscopy (FTIR) in the diamond anvil cell, the material properties of szomolnokite have been characterized under high pressures and low temperatures relevant to hydrous, sulfur-rich planetary environments. XRD measurements presented in this work have revealed two structural phase transitions occurring at pressures between 5.0 and 6.6 GPa and between 12.7 and 16.8 GPa, with the latter phase stable up to 80 GPa. The elastic parameters of each phase have been determined by fitting third-order Birch-Murnaghan equations of state. I compare our results with elastic parameters of other relevant sulfate
phases, highlighting the importance of reporting and comparing these parameters at the pressures where the phases are stable. Using NRIXS and SMS, the lattice vibrational response and the effects on the iron electronic environments during the structural transitions are examined. The NRIXS and SMS data reveal distinct features and pressure-dependent behaviors that characterize alterations in both iron-site specific and bulk lattice properties associated with the phase transitions, including lattice softening and decreased iron-coordination environment symmetry. Utilizing both the NRIXS and XRD results, I discuss how the presence of sulfates in the ice-rich crusts of planetary bodies could affect tidal loading observations. Synchrotron FTIR measurements demonstrate that structurally bound H₂O is retained within the unit cell during the structural transitions and upon subsequent decompression, confirming the retention of water up to 23 GPa and temperatures as low as 20 K and indicating the reversibility of both structural transitions. Supported by our quantum mechanics molecular dynamics simulations, the existence of two vibrationally unique water sites in szomolnokite’s crystal structure is proposed to explain the experimentally observed H2O-related features. I develop a spectral diagnostic for observing the high pressure structural transformations at ambient and low temperatures. The measured partial phonon density of states, predicted vibrational density of states, and measured FTIR spectrum are compared. Drawing from the insights gained, we emphasize the advantages of employing complementary experimental and computational techniques and discuss future research directions that can further enhance our knowledge of hydrous, sulfur-rich planetary environments