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 Mutational Analysis Of Thatisin: How Single Point Mutations Impact The Biosynthetic Process Of A Group 16 Graspetide, John F. Boynton Jr

Chemistry and Chemical Biology ETDs

Abstract:

Graspetides are a family of Ribosomally synthesized and Post-translationally modified Peptide (RiPP) natural products named for their ATP Grasp Macrocyclases. We identified several Graspetide Biosynthetic Gene Clusters containing common double glycine cleavage motifs and attempted characterization of the mature Graspetides. One of the resulting peptides, Thatisin, has a topology with two interlocking macrolactones installed by a single ATP Grasp Ligase named ThtC. Here we use single and double point mutations to observe the impact or variation on the installation of these macrocycles. Alanine scan mutagenesis is used to assess leader peptide residues in the precursor peptide ThtA to determine …

A Systematic Approach To The Characterization Of Liquid-Vapor Coexistence In Platinum, Meghan K. Lentz

Physics & Astronomy ETDs

Platinum is a material standard used in high pressure and shock compression experiments at Sandia National Laboratories. During experiments, materials are subjected to a very large range of thermodynamic conditions, during which materials regularly enter the liquid-vapor coexistence region. Despite its status as a standard, the region around the liquid-vapor critical point is poorly understood for platinum, with reported critical temperatures spanning approximately 7000 K. In this dissertation we conduct density functional theory based molecular dynamics (DFTMD) simulations for platinum for a range of temperatures and densities near liquid-vapor coexistence. The phase diagram for platinum is refined near the critical …

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 …

A Computational Method For Detecting Compound Promiscuity In Early-Stage Pharmaceutical Discovery, John Allen Ringer

Computer Science ETDs

Modern drug discovery and chemical biology research relies heavily on analyzing bioassay data. One of the many challenges in bioassay data analysis is identifying false trails, i.e., chemical compounds which initially appear to have desirable activity but are found to be problematic upon further investigation. Badapple (the BioAssay-Data Associative Promiscuity Pattern Learning Engine) was created over ten years ago to help researchers identify promiscuous compounds and thus avoid a common source of these false trails. Through an effort involving software engineering, cheminformatics, and biomedical data science we have developed Badapple 2.0, which incorporates updated assay records and expanded data semantics. …

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 …

Drug Targets Illumination: An Evidence-Based Data Analytics & Informatics Approach To Hypothesis Generation Through Clinical Trials And Genomic Variants, Jeremiah I. Abok

Chemistry and Chemical Biology ETDs

DRUG TARGETS ILLUMINATION: AN EVIDENCE-BASED DATA ANALYTICS & INFORMATICS APPROACH TO HYPOTHESIS GENERATION THROUGH CLINICAL TRIALS AND GENOMIC VARIANTS

Target Illumination Clinical Trial Analytics with Cheminformatics (TICTAC) introduces a scalable data integration pipeline that aggregates multivariate clinical trial evidence to systematically rank disease–target associations. By harmonizing metadata from AACT and employing confidence-scoring techniques, TICTAC facilitates hypothesis-driven target selection for drug discovery, enabling a data-driven approach to therapeutic development. In parallel, a bioinformatics-driven analysis of gnomAD exome mutations in the ZPR1 gene highlights the broader role of genetic variants in disease association. By employing variant effect predictors, protein stability modeling, and …

Excited State Processes In Radical Elaborated Platinum Donor-Acceptor Complexes, Sangita Paudel

Chemistry and Chemical Biology ETDs

Organo-transition metal complexes are being widely studied to understand their photophysical properties for their wide range of applications as efficient emitters in organic light emitting diodes (OLEDs), light emitting electrochemical cells (LEECs), etc. Cyclometalated organo-transition metal complexes such as cyclometalated square planar platinum(II) complexes are becoming suitable candidates for such applications because of their highly efficient luminescence. Understanding the excited properties of such complexes is useful in designing highly efficient and color tunable phosphors with desired excited state lifetimes. We aim to explore the influence of radical substituents on electronic structure, luminescence quantum efficiencies, and excited state lifetimes by synthesizing …

Secondary Electron Yield Of Metals, Alloys, And Metal Oxides From First Principles Based Monte Carlo Simulations, Raul E. Gutierrez

Electrical and Computer Engineering ETDs

Density Functional Theory (DFT) based Monte Carlo (MC) simulations of the Sec-
ondary Electron Yield (SEY) of metals, alloys, and metal oxides are performed to
find material properties that could help reduce or influence the multipactor effect.
In order to accurately model the SEY of materials, knowledge of the frequency- and
momentum-dependent Energy Loss Function (qDepELF) is required. The qDepELF
is difficult to determine from experiment; however, it can be calculated from first
principles. The DFT-MC approach for simulating the secondary electron genera-
tion, propagation, and emission processes is described herein. Material properties,
which are calculated using DFT and used …

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 …

Chemical And Morphological Characterization Of Airborne Particulate Matter At The Jackpile-Paguate Mine, Pueblo Of Laguna, New Mexico: Implications For Potential Metals Exposure, Andreanna C. Roros

Earth and Planetary Sciences ETDs

The inhalation of windblown particulate matter (PM) derived from abandoned uranium mines (AUMs) is a potential environmental health risk to Native American communities that live in proximity to these sites. However, the aeolian transport of metal-bearing PM from AUMs, as a potential exposure pathway, has not been investigated in any detail. In this study, we sampled airborne particulate matter within the Jackpile Mine located on the lands of the Pueblo of Laguna, New Mexico using passive sampling methods to understand the characteristics of dust within the mine site. The objective was to determine the elemental concentrations, mineralogy, and morphology of …

Functional And Structural Analysis Of The Neimann-Pick Disease Type C Pathway To Include Caveolin-1, Anthony Michael Seat

Chemistry and Chemical Biology ETDs

Human disease is often thought of as an all or nothing prospect, either one has the disease or one does not. This does not bear out in clinical or personal experiences, instead demonstrating that disease occurs within a spectrum ranging from presumed unaffected to demonstrably and detrimentally affected.Neimann-Pick disease is one example of this spectrum look into diseased states, with multiple named versions of a phenotypically similar disease. We focus on Neimann-Picktype C (NPC), which is the result of a disruption in the efflux of cholesterol and sphingolipids from the endocytic pathway. NPC demonstrates this concept of a spectrum of …

Molecular Dynamics Insights Into The Structural Behavior And Interactions Of Complex Biological Systems, Shenghan Song

Chemistry and Chemical Biology ETDs

All-atom molecular dynamics (MD) simulations are essential for examining the structural and dynamic aspects of proteins at high resolution, complementing experiments limited by resolution, size, and complexity. Advancements in algorithms and hardware have enhanced the role of computational tools in scientific research, allowing for more accurate simulations of proteins with standard residues. However, simulating real biological systems, which include non-standard residues such as lipid membranes, remains challenging despite the assistance of tools like CHARMM-GUI. My research initially focused on simulating the PICK1 BAR dimer using steered MD simulations to investigate its structure and dynamics. Simulation works expanded to include systems …

Exploring The Complex Landscape Of Proteins: From Intrinsically Disordered Proteins To Peptidomimetics Through Computational Approaches, Tongtong Li

Chemistry and Chemical Biology ETDs

Protein function is closely related to their three-dimensional structures. However, some proteins lack a well-defined structure, so-called intrinsically disordered proteins (IDPs). They prefer to interconvert among different conformations in isolation and undergo a disorder-to-order transition upon binding to a partner. IDPs or proteins with intrinsically disordered regions (IDRs), constituting a large portion of the human proteome, are involved in many cellular activities and are therefore highly relevant to our health. In my dissertation, I used computational methods to systematically study systems including dynamic proteins, disordered proteins in complex with their targets, and synthetic peptidomimetics to reveal the unique physical properties …

Learning, Optimizing, And Simulating Fermions With Quantum Computers, Andrew Zhao

Physics & Astronomy ETDs

Fermions are fundamental particles which obey seemingly bizarre quantum-mechanical principles, yet constitute all the ordinary matter that we inhabit. As such, their study is heavily motivated from both fundamental and practical incentives. In this dissertation, we will explore how the tools of quantum information and computation can assist us on both of these fronts. We primarily do so through the task of partial state learning: tomographic protocols for acquiring a reduced, but sufficient, classical description of a quantum system. Developing fast methods for partial tomography addresses a critical bottleneck in quantum simulation algorithms, which is a particularly pressing issue for …

Investigating The Structural Ensemble And Dynamic Interactions Of Protein Interacting With C-Kinase 1 (Pick1) Using Computational Tools, Amy E. Stevens

Chemistry and Chemical Biology ETDs

Protein Interacting with C Kinase-1 (PICK1) is a scaffolding protein that offers a promising solution to support individuals suffering from substance use disorders. While many efforts have been put towards identifying small-molecule drugs with the potential to target PICK1 and ultimately support individuals suffering from the effects of substance use disorders, all efforts have so far fallen short. The purpose of this work is to use computational tools to assist the design of a small-molecule inhibitor of PICK1 while also advancing the knowledge of its biological functions. This work provides information that is currently missing the field by (1) revealing …

Numerical Solution Of Hybrid Nanofluid And Its Stability Over Permeable Wedge Sheet With Heat Transfer Analysis, Aisha M. Alqahtani, Zeeshan, Waris Khan, Florentin Smarandache, Nidhal Becheikh, Roobaea Alroobaea, Taseer Muhammad

Branch Mathematics and Statistics Faculty and Staff Publications

The inclusion of nanoparticles has the potential to improve the thermal efficiency of the base fluid. The field of nanofluid (NF) dynamics has attracted important attention due to its extensive range of practical uses like fuel cells, solar energy, medication administration, heat transfer, microfabrication, coolant applications, and other related domains. The aim of this study is to scrutinize the impact of Lorentz force, thermal energy, joule heating, heat source and injection parameters, and Brownian and thermoporetic diffusions on the hybrid nanofluid over the moving wedge. The stability inquiry is reported for the existing work in order to confirm the stable …

Godel, Escherian Staircase And Possibility Of Quantum Wormhole With Liquid Crystalline Phase Of Iced-Water - Part I: Theoretical Underpinning, Victor Christianto, T. Daniel Chandra, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

As a senior physicist colleague and our friend, Robert N. Boyd, wrote in a journal (JCFA, Vol. 1,. 2, 2022), Our universe is but one page in a large book [4]. For example, things and Beings can travel between Universes, intentionally or unintentionally. In this short remark, we revisit and offer short remark to Neil’s ideas and trying to connect them with geometrization of musical chords as presented by D. Tymoczko and others, then to Escher staircase and then to Jacob’s ladder which seems to point to possibility to interpret Jacob’s vision as described in the ancient book of Genesis …

Godel, Escherian Staircase And Possibility Of Quantum Wormhole With Liquid Crystalline Phase Of Iced-Water - Part Ii: Experiment Description, Victor Christianto, T. Daniel Chandra, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

The present article was partly inspired by G. Pollack’s book, and also Dadoloff, Saxena & Jensen (2010). As a senior physicist colleague and our friend, Robert N. Boyd, wrote in a journal (JCFA, Vol. 1, No. 2, 2022), for example, things and Beings can travel between Universes, intentionally or unintentionally [4]. In this short remark, we revisit and offer short remark to Neil Boyd’s ideas and trying to connect them with geometry of musical chords as presented by D. Tymoczko and others, then to Escherian staircase and then to Jacob’s ladder which seems to pointto possibility to interpret Jacob’s vision …

Syntheses And Characterization Of Photoactive Ruthenium And Iron Polypyridyl Complexes, Rajani Thapa Magar

Chemistry and Chemical Biology ETDs

Within this dissertation, two distinct classes of metal complexes have been discussed that bear significance in the field of solar energy conversion, photo redox catalysis and memory devices. The first class of the metal complexes is a series of photochromic Ruthenium polypyridyl N-heterocyclic carbene tethered sulfoxide complexes that are reported to undergo unusually slow isomerization from S-bonded to O-bonded and unusually fast thermal reversion from O-bonded to S-bonded configuration. The role of NHC in the excited state dynamics of these complexes have been discussed in detail in Chapter 3.

For the first time in two decades, structural information of the …

Synthesis And Reactivity Of Heteroatom Embedded Cycloalkynes In Spaac, Nickel Catalyzed Alkylarylation Of Alkenes, And Carbofluorination Of Alkynes, Namrata Khanal

Chemistry and Chemical Biology ETDs

Part I covers Chapters 1, 2, and 3

cycloaddition reactions, that is utilized in biorthogonal chemistry. This metal free version The strain promoted azide-alkyne cycloaddition (SPAAC) reaction is one of the popular 1,3-dipolar of click reaction offers advantage over copper catalyzed click reaction. Since it eliminates the use of copper that is toxic to cells, it is considered favorable for biocompatible reaction. Due to the increased reactivity with dipoles without the use of metal catalyst, cycloalkynes, in particular cyclooctynes, have been employed as the biorthogonal reagent in biorthogonal chemical reaction for the study of a biological processes in vivo. The …

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 …

Toward The Yeast Surface Display Of Microviridin B, Jillian Leigh Stafford

Chemistry and Chemical Biology ETDs

Humans have turned to natural products for medicinal therapeutics for millennia. In recent years, the ribosomally synthesized and post-translationally modified peptide (RiPP) class of natural products have garnered a lot of attention due to their ability for heterologous expression, relative ease of mutation, and vast biological activates. Microviridins are a family of RiPPs that contain a tricyclic cage-like structure through the formation of two lactone rings and one lactam ring catalyzed by two ATP-grasp ligase family enzymes. Microviridins are potent inhibitors of serine proteases and mutational studies of a small number of residues indicates the potential of peptide engineering protease …