Physical Chemistry Commons^™

Information Theory Analysis Of Water Vapor Stable Isotopes From The Sail Campaign, Matthew John Rybecky

Earth and Planetary Sciences ETDs

Understanding the processes that control water vapor isotopic composition in mountain environ- ments is essential for interpreting isotope records and predicting water resource responses to cli- mate change. This thesis applies information theory to continuous, high-resolution water vapor stable isotope measurements from the Surface Atmosphere Integrated Field Laboratory (SAIL) campaign in the East River watershed of Colorado’s Upper Gunnison Basin, spanning the winter- to-spring transition of 2022–2023. The analysis employs Shannon entropy, mutual information, transfer entropy, and joint transfer en- tropy (JTE) to quantify how environmental variables, including surface meteorology, radiation, tur- bulent fluxes, and ERA5 reanalysis products, transfer information …

Elucidation Of Spin-Hamiltonian Parameters Via Spectroscopy, Magnetization, And Computation, Joshua C. Mengell

Chemistry and Chemical Biology ETDs

Molecular Quantum Information Science (QIS) is fundamentally concerned with using spin-systems as quantum bits (qubits) or as sensors. Prerequisite to using molecular systems for QIS applications, it must be understood how one can design molecules with bespoke magnetic characteristics. Herein we study various paramagnetic molecular compounds, describing their complex magnetic characteristics using a spin-Hamiltonian formalism. We utilize various (sometimes novel) methods for determining these spin-Hamiltonian parameters. Many of these molecules possess magnetic characteristics, which make them attractive as qubits or for sensing applications. These characteristics include higher total spin-states (qudits—S_T>1/2), forbidden interstate electronic transitions, systems of spatially distant …

Exploring The Nature And Role Of Local Cation Ordering In Disordered Rock Salt Cathodes For Li- And Na-Ion Batteries, You Wang

Chemistry and Chemical Biology ETDs

Cation-disordered rock-salt (DRX) cathodes provide a highly tunable platform for next-generation Li- and Na-ion batteries, but their electrochemical behavior is strongly influenced by local structural features hidden in average crystal structures. This dissertation systematically investigates local cation ordering in Li- and Na-based DRX cathodes to understand its effects on Li+/Na+ transport, redox activity, structural evolution, and electrochemical performance. In Li-based systems, Raman spectroscopy and electrochemical analysis reveal that local layered cation ordering in Mn- and Fe-based DRX cathodes is closely correlated with electrochemical behavior. Over-stoichiometric Li-based DRX oxyfluorides further demonstrate that excess Li can regulate local cation ordering, improve Li+ …

Nanoscale Structure And Spontaneous Self-Assembly Of Hydrothermal Organic Products, Glorianne P. Dorce

Chemistry and Chemical Biology ETDs

Carbon nanomaterials derived from citric acid and urea exhibit behaviors that challenge conventional structure–property models based on static bulk descriptions. This study examines how precursor pairing and reaction duration, post‑synthetic thermal history, and time‑dependent aging govern nanoscale organization and optical response. Through controlled synthesis and processing, distinct nanostructures with tunable structural and spectroscopic profiles are generated.

A multiscale framework integrating nano‑FTIR, atomic force microscopy, and thermal analysis reveals chemical heterogeneity and continuous structural reorganization across length scales. By correlating local chemical environments with optical behavior, we show that fluorescence efficiency and photostability depend on specific nanoscale architectures rather than average …

Computational Design Of Peptides And Proteins Through Machine Learning Approaches, Emily J. Hendrix

Chemistry and Chemical Biology ETDs

Advancements in machine learning have emerged as a pivotal tool in computational biochemistry, offering new advancements to address challenges in protein structure and function. However, current machine-learning approaches offer limited insight in understanding protein dynamics. The purpose of this work is to combine traditional physics-based computational tools, such as molecular dynamics and coarse-grained simulations, with recently developed AI-driven computational tools to bridge gaps and advance the understanding of proteins in both structural and dynamic aspects. I investigated several approaches such as (i) traditional physics-based methods to study protein conformation and ensembles; (ii) identifying a peptide inhibitor for the PICK1 PDZ …

A Study Of Machine Learning Techniques In Solving Biochemical And Chemical Problems, Kenneth Micheal Plackowski

Chemistry and Chemical Biology ETDs

Data-driven approaches to solving problems in biology and chemistry require utilization of reliable techniques and machine learning algorithms are the modern reliable approach. This work presents three problems that involve use of supervised learning techniques when classification is the goal and unsupervised learning techniques when global data representation is the goal.

In the first problem, we demonstrate the use of unsupervised clustering techniques, self-organizing maps and K-means, to ascertain analyte detection capabilities of carbon nitride dots. In the second problem, we add scalability features to a functional group classification model applied to infrared data and evaluate its ability to inform …

The Delocalized Toolbox: Tuning Strain, Energetic And Optoelectronic Properties Of Aryl Heterocyclic Scaffolds For Application-Driven Endeavors, Michael Josef Holzmann

Chemistry and Chemical Biology ETDs

This is a three-part dissertation. Part 1 is composed of chapters 1-3 which revolves around the optimization of cyclononyne reactivity towards 1,3 dipolar cycloadditions. Specifically, the synthesis and reactivity of sulfate, sulfamate and sulfamide-bearing cyclononynes will be discussed. Chapters 4-5 comprise Part 2 which addresses optimization of ruthenium olefin metathesis towards reversible activation and inhibition. The mechanism of reversible inhibition mediated by a hexaarylbiimidazole photo-inhibitor will be elucidated. Part 3 consists of chapters 6-8 which describes structure-functional relationship studies on carbon dots and harnessing that insight for sensing applications. Data relating to assays performed with explosive analytes will be analyzed …

Theoretical And Spectroscopic Insights Into Molybdenum- And Tungsten-Sulfur Bonding, Jesse Lepluart

Chemistry and Chemical Biology ETDs

Molybdenum and tungsten chemistry in biology is dominated by bonding interactions with sulfur and the other chalcogens. The highly-conserved structures of these enzymes’ active sites suggest an early evolution in the history of life, with molybdenum and/or tungsten enzymes likely expressed by the last universal common ancestor. Despite their active site similarities, molybdenum and tungsten enzymes catalyze a diverse array of reactions via equally diverse mechanisms. A deep understanding of the electronic structures of these enzyme active sites and their catalytic intermediates is key to understanding this remarkable chemistry.

The work presented here aims to deepen the understanding of molybdenum …

Photophysical Properties Of Synthetic Oligomeric Phenylene Ethynylene, Hugh F. Fritz Jr.

Chemistry and Chemical Biology ETDs

Oligomeric Phenylene Ethynylenes (OPEs) are a class of synthetically prepared compounds with the basic structure of phenylene rings connected by triple-bonded carbon atoms, also known as an ethyne link. This structure can be modified by incorporating functional groups onto one or more of the phenylene rings. The addition of functional groups, such as sulfoxide or imidazole, may alter the photophysical properties in detectable ways. The photophysical techniques used in this report include fluorescence, spectroscopy in the ultraviolet and visible light range (UVVIS), and photon-based excitation using a photo chamber.

One attractive function of OPEs is their antimicrobial property. Previously published …

Methods Of Magneto-Optical Spectroscopy And Analysis For Porphyrins And Polymer Thin-Films, Emigdio E. Turner

Chemistry and Chemical Biology ETDs

This dissertation describes the construction of two high precision magneto-polarimeters for performing Faraday rotation and Magnetic Circular Dichroism (MCD) measurements of polymer thin-films. There is a focus in materials science on the development of thin-film magneto-optically active materials. These materials could allow for the construction of a thin-film optical diode, an important device for next-generation photonic technology. Upon completion of the Faraday rotation spectrometer, two publications were generated from Faraday rotation measurements of novel polymer thin-film materials.

With growing interest by materials scientists in magneto-optically active transition-metal containing materials, an MCD spectrometer was constructed to study these materials. This spectrometer …

Mechanisim Of Plasmon-Driven Photochemical Reactions, Hamed Kookhaee

Chemistry and Chemical Biology ETDs

Understanding a photocatalytic reaction condition that selectively leads to a desired product on metal surfaces is a longstanding research problem in heterogeneous catalysis. Here, using plasmon enhanced N-demethylation of methylene blue (MB) as model reaction, we show that high degree of product selectivity can be achieved by switching the mechanism from charge transfer to adsorbate electronic excitation and vice versa using surface ligands. In the presence of cetyl trimethyl ammonium bromide (CTAB) surface ligand on gold nanoparticles, MB is selectively transformed to thionine at 633 nm excitation wavelength that overlaps with the electronic transition of the adsorbate. At resonant excitation …

Synthesis, Characterization And Spectroscopic Studies Of Novel Donor-Acceptor Complexes, Shiyue Gao

Chemistry and Chemical Biology ETDs

Square-planar compounds of the (dichalcogenolene)Pt(diimine) series are possess unique photophysical properties that include long-lived excited state lifetimes, which result in their being potential candidates for numerous applications. These applications include solar energy conversion, photocatalysis, nonlinear optics, and photoluminescent probes of biological systems. The most interesting feature of the (dichalcogenolene)Pt(diimine) series of molecules is the bpydichalcogenolene ligand-to-ligand charge transfer (LL’CT) band. To better understand their photoluminescent decay mechanism, and understand their excited dark state properties, we have synthesized and characterized new compounds that include (Thp-bpy)Pt(CAT), (Thp2-bpy)Pt(CAT), (Thp-bpy)Pt(bdt), and (Thp2-bpy)Pt(bdt). Through interpretation of electronic absorption, resonance Raman, XAS, photoluminesce spectroscopy, in addition …

Theoretical Studies Of Molecule-Surface Interactions And Dynamics, Yingqi Wang

Chemistry and Chemical Biology ETDs

Gas-surface scattering involves the conversion of energy in different forms in the impinging molecule, possible bond breaking and forming, and the energy transfer across gas-solid interface. Possible energy dissipation channels include adiabatic energy transfer to the motion of surface phonons and non-adiabatic interactions with surface electron-hole pairs. A complete understanding of the interplay of energy dissipation and physical/chemical changes in the molecule is vital for many important applications such as materials fabrication and heterogenous catalysis.

Gas-surface encounters may occur where non-adiabatic effects are negligible. Two such systems were investigated, both with ample experimental data. One is concerned with the scattering …

Computational, Synthetic And Spectroscopic Studies On Donor Acceptor Transition Metal Complexes, Ranjana Dangi

Chemistry and Chemical Biology ETDs

Fundamental advances in our ability to design and construct electronic components at the nanoscale will require new design paradigms. One proposed nanoscale electronic component is the molecular rectifier. Molecular and molecule-based electronic components are advantageous due to their ease of synthetic manipulation, and the fact that the size dimensions of molecules are inherently at the nanoscale (0.5 - 3nm). Our group has shown how the Donor-Bridge-Acceptor biradical approach can be used to derive key structure-property relationships that allow insight into the choice of bridge fragments for molecular rectification by using constitutional isomers of the donor-bridge-acceptor biradical (NN-Th-Py-SQ) (S=1/2 ortho-semiquinonate, …

Approaches In Molecular Engineering To Optimize The Desired Properties Of Photoactive Molecules, Douglas Joseph Breen

Chemistry and Chemical Biology ETDs

Within this dissertation, photochemical systems that bear significance to next-generation photonic materials and devices are explored. Notable advances in the design, synthesis, and characterization of three distinct groups of photoactive molecules are achieved through molecular design and spectroscopic analysis. First, novel ruthenium sulfoxide complexes bearing substituted phosphine ligands are found to provide extraordinary control over photoisomerization quantum yields. A comparison of these complexes reveals ground-state characteristics that are instrumental in this reactivity, while a novel spectroscopic technique provides rare structural evidence for an O-bonded metastable isomer. Ruthenium complexes bearing chelating carbene-sulfoxide ligands rapidly thermally revert from the O-bonded metastable isomer …

The Profound Photophysical Effects Of Organic Chromophore Connectivity And Coupling, David J. Walwark Jr

Nanoscience and Microsystems ETDs

Through-bond and through-space interactions between chromophores are shown to have wide-ranging effects on photophysical outcomes upon light absorption in organic molecules. In collapsed poly(3-hexylthiophene), through-space coupling creates hybrid chromophores that act as energy sinks for nearby excitons and favorable sites for molecular oxygen to dock. Upon excitation with visible light the highly-coupled chromophores react with the docked oxygen and subsequently do not quench nearby excitons as efficiently. In tetramer arrays of perylene diimide chromophores the central moiety through-bond connectivity is synthesized in two variants which exhibit vastly different single-molecule blinking behavior and theoretically-predicted electronic transition character. In the more-connected tetramer …

A Compendium Of Inorganic Photochemistry: Synthetic And Spectroscopic Discoveries, Sebastian B. Vittardi

Chemistry and Chemical Biology ETDs

This dissertation reports and examines contributions made in the advancement of inorganic photochemistry. Empirically driven assessments are allotted to the interplay between ligand sets, excited states, and photochemistry observed in metal complexes. A methodical spectroscopic examination is provided for oligothiophene-sensitized lanthanides. Their excited state dynamics were elucidated by femtosecond pump-probe spectroscopy and used to develop a model explaining their wavelength-dependent dual functionality. Iron (II) cyanide and isocyanides are evaluated to identify the efficacy of strong-field ligands in promoting charge-transfer excited states. Fundamentals of ligand field theory helped conceptualize the synthetically tunable parameters and effects transposed to their absorption dynamics. Transition …

Pt-Containing Conjugated Polymers And Small Molecules For Bhj Photovoltaic Devices, Yunjeong Kwon

Chemistry and Chemical Biology ETDs

The current state of organic photovoltaic (OPV) devices involve series of small molecular or polymeric systems that can absorb light from the solar spectrum in concert with another material that acts as an acceptor material. Together these materials serve to generate and split bound excitation species then transport the separate charges to their respected electrode. Several limitations have restricted the widescale use of these materials. Since these devices have their genesis in organic materials the OPV devices inherit short exitonic lifetimes, narrow absorption window and a lack of precise control over the morphology. To overcome these limitations, additional molecular engineering …

Petrology And Geochemistry Of Evolved Achondrites: Planetesimal Mantles And Crusts, Zoltan Vaci

Earth and Planetary Sciences ETDs

Melting and differentiation are fundamental to early solar system evolution on planetary bodies that accreted enough material to heat up radioactively or through impacts and breach their solidi. Partially and fully melted material is present in the meteorite record in the form of primitive achondrites and achondrites, which are fragments of planetesimals that underwent heating events in the first few million years of solar system history. Although the vast majority of this material is mafic or ultramafic, new evolved samples, recovered in the last few decades, are pushing the petrologic and geochemical boundaries of planetesimal melting, differentiation, and crust formation. …

Studies Of The Rectification Behavior Of The Pdt Ligand And The Active Site Of Msrp, Laura J. Ingersol

Chemistry and Chemical Biology ETDs

Molybdenum (Mo) is an essential element that plays an important role in global nitrogen, carbon, and sulfur cycles with a critical role in human metabolism and ecological balance. It becomes catalytically active when complexed with the pyranopterin dithiolene ligand (PDT), forming the nearly ubiquitous molybdenum cofactor (Moco). The complex biosynthetic pathway of Moco, its presence in all three domains of life, and its role as a constituent cofactor in the last universal common ancestor (LUCA) all point toward the importance of the PDT in the development of life on Earth. Molybdoenzymes catalyze the two-electron oxidation or reduction of substrates that …

Synthesis And Characterization Of Regioregular Cross-Conjugated Poly(Thienylene Vinylene)S, Yousef M. Katba Bader

Chemistry and Chemical Biology ETDs

Poly(thienylene vinylene)s (PTVs) is special a class of conjugated polymers (CPs) that show remarkable optoelectronic properties and promising applications. The main reason that hinders their application, is the lack of synthetic methodologies for preparing new derivatives with various functionality. Developing new PTVs with improved structures based on structure-property relationships increases the potential of utilizing this type of polymers in advanced applications. Most available preparation methods lead to regio-random PTVs (ra-PTVs) structures due to the different placement of the sidechain in the polymer backbone, which results in reduced crystallinity. In this study, we developed a novel strategy that produces a series …

Understanding The Role Of Atom Trapping In The Evolution Of Hydrocarbon Transformation Catalyst Morphology, Griffin Alexander Canning

Chemistry and Chemical Biology ETDs

Converting alkanes to other, more chemically and economically valuable molecules requires catalysts that can survive elevated temperatures and highly reducing environments. These environments can cause many metal-nanoparticle based catalysts to sinter rapidly, causing a loss of activity. They must also tolerate the coke formation, as well, since coke can restrict access to active sites by gas phase molecules, thus lowering catalytic activity. While there are routes to improve both the sinter and coke resistance of catalysts, an alternative strategy is to develop a protocol for regenerating the activity of the catalyst in question when coke formation or sintering becomes problematic. …

Radial Basis Densities And The Density Functional-Based Atom-In-Molecule: Designing Charge-Transfer Potentials, Godwin Amo-Kwao

Nanoscience and Microsystems ETDs

Classical potentials that are capable of describing charge transfer and charge polarization in complex systems are of central importance for classical atomistic simulation of biomolecules and materials. Current potentials—regardless of the system—do not generalize well, and, with the exception of highly-specialized empirical potentials tuned for specific systems, cannot describe chemical bond formation and breaking. The charge-transfer embedded atom method (CT-EAM), a formal, DFT-based extension to the original EAM for metals, has been developed to address these issues by modeling charge distortion and charge transfer in interacting systems using pseudoatom building blocks instead of the electron densities of isolated atoms. CT-EAM …

Design And Applications Of Charge-Separated Metal-Organic Frameworks, Sheela Thapa

Chemistry and Chemical Biology ETDs

Ionic tetrapodal ligands with colinear coordinating arms are very effective for designing hybrid porous materials with unusual structure and properties. The novelty of this research work lies in the utilization of a unique borate ligand that leads to charge-separated MOF structure with tailor designed properties. Borate ligands being tetrahedral afford 3D materials and the negative charge of borate anion can compensate the positive charge of metal ion in the framework. The borate ligands designed in this research consists of quaternary ammonium cation and anionic borate with four pyridine arms. These ligands upon coordination with Cu(I), Cu(II), Ag(I) and Co(II) metal …

Self-Assembly, Integration, Characterizations And Applications Of Plasmonic And Excitonic Nanomaterials, Bijesh Kafle

Chemistry and Chemical Biology ETDs

Plasmon on metal nanoparticles can efficiently confine, amplify light at the nanoscale. This property is beneficial for different applications such as harvesting energy of the broad solar spectrum, highly sensitive spectroscopy, photocatalysis, and many other optoelectronic applications. For plasmonic applications, it is necessary to understand the fundamental physical properties of the individual, coupled plasmonic nanomaterials, and their interaction with the surrounding environment, which is not fully understood yet. In this dissertation, the chemical and optical interaction in plasmonic interfaces has been investigated. Plasmon-enhanced photochemistry of p-aminothiophenol as a model molecule is investigated using highly sensitive surface-enhanced Raman spectroscopy (SERS). The …

Triplet Population Dynamics And Excited State Relaxation In Chalcogenophene Polymers, Benjamin D. Datko

Chemistry and Chemical Biology ETDs

The conventional understanding of intersystem crossing in multichromophoric conju- gated polymers is usually depicted via a pure electronic model, neglecting contributions of vibrations or conformational order. Obtaining accurate structure-function correlations on spin-conversion processes involving photogenerated singlet excitons to triplet excitons and the excited state dynamics requires sensitivity to the subtle conformational ordering within conjugated polymers. This dissertation seeks to understand the kinetics of multi-exciton singlet-triplet interactions and the excited state relaxation of chalcogen containing (S, Se) conjugated polymers. Utilizing single molecule modulation spectroscopy allows determi- nation of triplet formation of individual conjugated polymer chains and aggregates. This technique resolves triplet-induced …

Electron Model Based On Helmholtz’S Electron Vortex Theory & Kolmogorov’S Theory Of Turbulence, Florentin Smarandache, Victor Christianto, Robert Neil Boyd

Branch Mathematics and Statistics Faculty and Staff Publications

In this paper, we explore a new electron model based on Helmholtz’s electron vortex and Kolmogorov theory of turbulence. We also discuss a new model of origination of charge and matter.

Development Of Functional Chemical Probes For The Study Of Viscosity, Fe(Ii), And Ferroptosis And Photo-Triggered Drug Delivery, Yongyi Wei

Chemistry and Chemical Biology ETDs

Small molecule probes are useful tools for the study of biology. In particular, the dye derived fluorescence probes enable to spatiotemporally monitor the events of analytes of interest. The noninvasive feature is particularly attractive for the biological studies in live cells. The challenge is to develop chemical probes capable of detection of the analyte of interest with high specificity.

Toward this end, my Ph. D. study centers on the development of novel chemical probes for the study and understanding of the alternation of important cellar contents and substances and their functions and relationship between normal and disease states. In the …

Synthesis, Characterization And Application Of Structurally Diverse Poly(Chalcogenylene Vinylene)S, Zhen Zhang

Chemistry and Chemical Biology ETDs

Conjugated polymers have found widespread applications in flexible and printable electronic devices, among which poly(thienylene vinylene) (PTV) displays outstanding optoelectronic properties and promising applications. However, further studies of its structure-property-function relationship have been greatly impeded mainly due to the synthetic difficulty of generating new structures beyond its rudimentary form.

To further investigate this class of material, I have developed a facile methodology for the preparation of structurally diverse poly(chalcogenylene vinylene)s (PCVs) through a combination of acyclic diene metathesis (ADMET) polymerization and post-polymerization modification techniques. Specifically, a series of halogenated and cross-conjugated PCVs have been designed and synthesized, followed by complete …

Detection Of Salen-Type Tracers For Subterranean Fluid Flow Monitoring Using Surface-Enhanced Raman Spectroscopy, Jenny C. Sanchez

Chemistry and Chemical Biology ETDs

A series of hydrocarbon and aqueous soluble salen-type ligands have been synthesized and characterized by electronic and vibrational spectroscopy. Aqueous soluble salen-type ligands were complexed to a metal and investigated as potential underground fluid flow tracers using Surface-Enhanced Raman Spectroscopy (SERS) as the analytical technique. Vibrational spectra obtained from SERS was shown to have enhanced the spectral signal for these complexes in low concentrations though did not show significant differences between the free ligands and their metal complexes. This research has shown that, with some structural modifications, salen-type ligands can be effective candidates as subterranean fluid flow tracers when SERS …