Physical Sciences and Mathematics Commons^™

Investigating The Effect Of Relative Humidity On Organic New Particle Formation From The Dark Ozonolysis Of Biogenic Volatile Organic Compounds, Austin Callum Flueckiger

Graduate College Dissertations and Theses

Solid or liquid particulate matter suspended in the air, also known as atmospheric aerosols, are a ubiquitous component of Earth’s atmosphere. It is important to understand the chemical and physical processes that lead to the formation of these aerosols as they have an impact on climate health and human health. An important subset of atmospheric aerosols are secondary organic aerosols (SOA) that form from the gas-phase oxidation of volatile organic compounds (VOCs). VOCs can be emitted via biogenic and anthropogenic pathways, however, global estimates place biogenic sources as the major contributor. Although widely studied, some of the fundamental mechanisms that …

Role Of Relative Humidity In New Particle Formation From Ozonlysis Of Atmospheric Volatile Organic Compounds, Christopher Snyder

Graduate College Dissertations and Theses

The impact of relative humidity (RH) on organic new particle formation (NPF) from ozonolysis of biogenic volatile organic compounds (BVOCs) remains an area of active debate. Previous reports provide contradictory results indicating both depression and enhancement of NPF under conditions of moderate RH, while others ignore the potential impact. Only several reports have suggested that the effect may depend on absolute mixing ratio of the precursor volatile organic compound (VOC, ppbv). However, before any experiments could be completed, development of new methods was necessary to overcome the limitation of sampling ultrafine nanoparticles (<50 nm aerodynamic diameter) with aerosol mass spectrometry. This dissertation includes a report on a new Particle Growth Apparatus (PaGA) that artificially grows particles from as small as 17 nm to over 110nm. Considerable effort was made to identify the most suitable growth matrix (squalane) and optimize particle growth for reproducibility and sensitivity.

The PaGA was then utilized in the …

Investigations Of Low-Frequency Vibrations In Crystalline Organic Semiconductors And Their Impact On Material Properties, Peter Alexander Banks

Graduate College Dissertations and Theses

An increasing amount of attention has been dedicated to small-molecule based crystalline organic semiconducting materials, with regular reports of newly-designed molecules that are specifically engineered to produce high-performance organic devices. Commonly, these molecules contain distinct chemical characteristics that are specifically incorporated to inhibit the large-amplitude, low-frequency vibrational motions that occur about intermolecular van der Waals contacts. These molecular motions have been historically considered a primary factor that uniquely limits the semiconducting performance of these materials, as the large displacements induced by these vibrations strongly diminish the electronic coupling between molecules in the lattice. This phenomenon is denoted as electron-phonon coupling, …

Whole Farm Net Zero: Approaches To Quantification Of Climate Regulation Ecosystem Services At The Whole Farm Scale. Vermont Payment For Ecosystem Services Technical Report #7, Christopher Bonasia, Lindsey Ruhl, Benjamin Timothy Dube, Alissa C. White, Heather M. Darby

UVM Extension Faculty Publications

In this report, approaches to the quantification of climate mitigation ecosystem services at the whole farm scale are reviewed and summarized for easy comparison. Eight quantification tools, and three case studies demonstrating possible tool applications, are summarized to fulfill the requirements of the Technical Services Contract—Task 7. Information from a combination of literature review and expert interviews served to document the inputs, outputs, strengths, weaknesses, opportunities, and threats for each quantification tool. This research was conducted in service to the Vermont Soil Health and Payment for Ecosystem Services (PES) Working Group (VT PES working group). It is our hope that …

Computer Aided Design: Targeting The Pac1r For Novel Therapeutics And Investigating Biologically Relevant Materials, Kyle Thomas Mckay

Graduate College Dissertations and Theses

Computer aided drug design, a collection of computational methodologies including structure and ligand based drug design, has emerged as an efficient and accurate way to expedite the drug discovery process. Structure based drug design — methods which rely on the 3-dimensional structural information of biological targets — are of particular interest to chemists. Unfortunately, structural information can be difficult to obtain, and this can limit the usefulness of these methodologies. New methodologies and workflows, which are less reliant on difficult to obtain structural information are needed to fill in the gaps and push the drug development process forward. The first …

Development Of [3,3]-Sigmatropic Rearrangements Of Zwitterionic And Cationic Intermediates Formed By Intramolecular Cyclization Of Tertiary Allylic Amines Tethered To Heterocumulenes, Joseph Pisano

Graduate College Dissertations and Theses

Guanidines are ubiquitous in nature and serve as useful building blocks in biologically active natural products as well as non-nucleophilic bases and organocatalysts. There is thus a need for methods for the synthesis of guanidine compounds as well as isoelectronic groups such as isothioureas. The 1,3-diaza-Claisen rearrangement represents a powerful reaction by which to synthesize highly substituted guanidines.

The scope of the zwitterionic 1,3-diaza-Claisen rearrangement has been further investigated through the introduction of a two-carbon tether. Electron-deficient carbodiimides can be synthesized through desulfurization of isothioureas, which undergo intramolecular cyclization through a tethered tertiary amine bearing an allylic group to afford …

Multiscale Modeling Of Biological Complexes: Strategy And Application, Xiaochuan Zhao

Graduate College Dissertations and Theses

Simulating protein complexes on large time and length scales is often intractable at the atomistic resolution. To address this challenge, we have developed new approaches to integrate coarse-grained (CG), mixed-resolution (referred to as AACG throughout this dissertation), and all-atom (AA) modeling for different stages in a single molecular simulation. First, we developed a top-down multiscale modeling approach — a new approach, which combines CG, AACG, and AA modeling — to simulate peptide self-assembly from monomers. We simulated the initial encounter stage with the CG model, while the further assembly and reorganization stages are simulated with the AACG and AA models. …

Synthesis And Characterization Of Highly Contorted Aromatics And Semiconducting Thioacenes, Adam M. Dyer

Graduate College Dissertations and Theses

Polycyclic aromatic hydrocarbons (PAHs) have shown great promise to produce new organic electronic materials. The networks of delocalized π-electrons present in these conjugated molecules allow for the mobilization of charge carriers. Compared to traditional electronic devices, this new class represents a more sustainable, lower cost, and solution processable alternative. Instability and poor intermolecular interactions are two key challenges preventing widespread adoption of said organic devices. However, the synthetic nature of organic molecules allows for fine tuning of electronic properties, offering a solution to these issues. Introduction of contorted conformations and heteroaromatic rings to PAH systems are discussed within this document …

Vinyl Cations As Cyclopentenone Precursors Via C‒H Insertion Or Alkene Addition Reactions, Magenta Hensinger

Graduate College Dissertations and Theses

We report that Lewis acid mediated reactions of β-hydroxy-α-diazo carbonyls provide facile access to vinyl cation intermediates, which can form mono- and bicyclic cyclopentenone ring systems. Vinyl cations are sp hybridized cations that can be exploited as carbene surrogates or as electrophiles. The methodology reported in this dissertation is important because cyclopentenone rings are common motifs in natural products or can be used as synthetic intermediates.

The first portion of this dissertation will discuss vinyl cations we’ve used as carbene surrogates in metal free C‒H insertion reactions. Treating β-hydroxy-α-diazo carbonyls with a Lewis acid provided vinyl cation intermediates after loss …

Transient Effects In Solution-Processed Organic Thin Films, Jing Wan

Graduate College Dissertations and Theses

Due to the weak van der Waals forces between organic semiconductor molecules, the molecular packing depends sensitively on the processing methods and conditions. Thus, understanding the crystallization mechanisms during solution deposition are essential for fundamental studies and reproducible fabrication of electronic devices.The performance of Organic field effect transistors (OFETs) also depends heavily on extrinsic factors such as contact resistance and interfacial defects, which can produce a different kind of transient effect at the metal-semiconductor contact. We have observed structural transient effects during the crystallization process of two small molecule organic semiconductors made from solution. We report in situ X-ray scattering …

Investigating The Phase Of Green Leaf Volatile Derived Secondary Organic Aerosol Using An Electrical Low Pressure Impactor, Kevin Fischer

Graduate College Dissertations and Theses

Airborne particulate matter consists of small particles suspended in the air and is a ubiquitous component of the Earth’s atmosphere. These particles, known as aerosols, broadly affect both human health and the global climate. Secondary organic aerosol (SOA), a subset of atmospheric aerosol, are produced by the gas phase oxidation of volatile organic compounds (VOCs) originating from anthropogenic and biogenic sources. Of particular interest are a sub class of biogenic VOCs released by stressed plants, green leaf volatiles (GLVs), which are susceptible to oxidation via ozonolysis and form SOA. While important strides have been made in better understanding SOA, many …

Lcms-Based Analysis Explains The Basis Of Oxidative Resistance In Selenium-Containing Thioredoxin Reductase, Daniel Haupt

Graduate College Dissertations and Theses

Selenocysteine (Sec) is referred to as the 21st proteogenic amino acid and is found in place of the redox-sensitive amino acid cysteine (Cys) in a small number of proteins. Sec and Cys carry out similar chemistry and are structural isomers save for a single atom difference; the former contains selenium (Se), while the latter contains sulfur (S) in the identical position. Sec poses a high bioenergetic cost for its synthesis and subsequent incorporation into protein not shared by Cys. Since Sec’s discovery in 1976, scientists have debated why certain proteins express Sec while others express Cys. In recent years, it …

Using Chirality-Assisted Synthesis To Construct Light-Responsive, Freeform Helical Foldamers And Shape-Defined Polymers, Jessica Leigh Bocanegra

Graduate College Dissertations and Theses

Foldamers (i.e. polymers which fold into well-defined shapes) are able to imitate arrangements of proteins, nucleic acids, and polysaccharides. However, previously reported foldamers are limiting in their ability to bind a multitude of guests—mainly due to very rigid conformational skeletal structures. Additionally, these structures commonly rely on π-π stacking and hydrogen bonding to dictate their shapes. We now report a helical foldamer that has (i) the capacity to bind selectively around a myriad of molecules while (ii) still embodying a well-defined, synthetically-controlled shape. We were able to create such structures as single-handed helices with chirality-assisted synthesis (CAS, see: Angew. Chem. …

Investigation Of The Intramolecular 1,3-Diaza-Claisen Rearrangement In The Ring Expansion Reactions Of Vinyl Pyrrolidines And Vinyl Piperidines, Teruki Watanabe

Graduate College Dissertations and Theses

The 1,3-diaza-Claisen rearrangement was discovered and developed in the Madalengoitia group since 2004. The rearrangement is initiated by the desulfurization of the electron deficient thiourea and isothiourea to obtain the highly electrophilic carbodiimide which can be reacted with an allylic tertiary amine to form the zwitterionic intermediate which then undergoes [3,3]-sigmatropic rearrangement. Previous investigation includes multiple examples of successful formation of complex guanidines through intermolecular and intramolecular variants. Providing an easy access to guanidine which is one of the most prevalent functional groups in the biologically relevant system, the rearrangement can be a valuable tool in the organic synthesis.

The …

Bottom-Up Synthesis Of Macromolecules And Their Selective Catalytic Performance At The Nanoscale, Mona Sharafi

Graduate College Dissertations and Theses

Finding sustainable ways to create complex, sequence-defined polymers is

essential for future advances in the fields of medicine, electronics, and energy. Thus,

inspired by how nature builds functional macromolecules, this account aims to discover

catalysts, which will facilitate the accurate replication of synthetic nanoscale structures. In

this regard, the comprehensive sight of the work described within this dissertation is to

resolve the following fundamental questions: i) How to generate large, preorganized

macromolecules which can behave as supramolecular hosts to tune the properties of

molecules present in the vicinity of them? ii) What shapes do sequence-defined

oligomers/polymers adopt in solution under …

Chirality-Assisted Synthesis Of Single-Handed Freeform Helical Ladder Polymers, Kyle Everett Murphy

Graduate College Dissertations and Theses

In nature, shape defines function, and as such scientists have long since attempted to mimic nature in a pursuit to reach a similar level of fidelity. Complex macromolecular structures and shapes have been developed with interesting and unique functionalities—such as the design and synthesis of molecular machines. However, macromolecular structures such as these are difficult to synthesize. My work in the Schneebeli group builds upon this challenge, where I have developed a strategy to precisely control the shape of macromolecules to generate well-defined structures. This was accomplished with stereoisomerically pure triptycene-like derivatives as the building block pieces which have an …

The Development And Expansion Of A Cationic 1,3-Diaza Claisen Rearrangement That Affords Guanidines, Jordan Tocher

Graduate College Dissertations and Theses

Guanidines are found readily in many natural product scaffolds and biological systems. However, the chemical makeup of the guanidines is such that synthesis of guanidine-containing molecules remains challenging. In 2004, the Madalengoitia group first reported a zwitterionic 1,3-diaza Claisen rearrangement that affords complex guanidines. This was later expanded from the initial strained-bridged bicyclic systems to systems that encompassed more linear precursors, positively charged intermediates, and compounds with ring-expansion applications.

Due to the historical precedent that introduction of a positive charge into a rearranging system can benefit the kinetics and thermodynamics of a reaction, experiments were designed in order to probe …

Investigations Of Pnictogen And Boron-Group Compounds Towards The Synthesis Of Group Iii/V Pre-Ceramic Molecules, Brandon James Ackley

Graduate College Dissertations and Theses

Semiconductor ceramics have been the subject of study for many years due to their usefulness in applications ranging from LED devices to computer chips. Despite the ubiquity of semiconductor ceramics in daily life, the synthesis and manufacturing of such devices is tedious, energy intensive, or have a high potential for danger. Manufacturing methods such as deposition require the use of toxic or pyrophoric gases as well as requiring the temperatures often exceeding 1,000 °C. One way to address the issues of toxicity and high thermal barriers can be found in the implementation of pre-ceramic materials; materials which are either molecular …

An Exploration Of Β -Hydroxy- Α -Diazo Carbonyls In Synthesis: Fragmentation, Vinyl Cation Formation And Conjugate Addition Reactions, Jian Fang

Graduate College Dissertations and Theses

β-hydroxy-α-diazo carbonyl compounds have been shown to display diverse reactivity profiles that can lead to a variety of useful products. This specific combination of functional groups can react in several mechanistically distinct ways depending on the presence or absences of other groups within the molecule. For example, -silyloxy-β-hydroxy-α-diazo carbonyls react with Lewis acids via fragmentation reactions to generate tethered aldehyde ynoate or ynone products. A portion of this thesis describes how this methodology was applied toward the synthesis of an important bioactive natural product: aspidospermidine. β-Hydroxy-α-diazo carbonyls are also convenient precursors to vinyl cations. The vinyl cation is generated by …

Sulfur And Selenium In Peptides And Proteins: Part I – Chemoselective Methods For Disulfide Bond Formation, Part Ii – Function Of Selenium In Enzymes., Emma Jean Ste.Marie

Graduate College Dissertations and Theses

Selenocysteine (Sec), the 21st proteogenic amino acid, was first identified in 1976 by Thressa Stadtman. In proteins, Sec replaces the far more common sulfur-containing amino acid cysteine (Cys). A key question since Stadtman’s discovery is: Why does Sec replace Cys? This question is especially relevant since Cys-orthologs of Sec-enzymes catalyze the identical reaction with only slightly reduced efficiency, and incorporation of Sec into a protein is much more complicated and bioenergetically costly compared to Cys. The study of selenoproteins is very difficult because Sec is incorporated into proteins by recoding a UGA stop codon as a sense codon. Production of …

Spectroscopic Investigation Into The Heme Binding And The Heme Degradation By Mycobacterium Tuberculosis Mhud, Biswash Thakuri

Graduate College Dissertations and Theses

MhuD is a heme degrading enzyme found across mycobacteria. In the heme uptake machinery of Mycobacterium Tuberculosis, MhuD is a heme oxygenase (HO) involved in catalyzing the degradation of heme. Canonical HOs, such as human HO, have been shown to degrade heme to non-heme iron, carbon monoxide (CO) and biliverdin. However, MhuD has been demonstrated to degrade heme to non-heme iron and mycobilin without the release of CO. Formation of a novel chromophore by MhuD revealed that it follows a unique heme degradation mechanism compared to that of canonical HOs. Binding of heme to MhuD is the first step in …

Metal Catalyzed Group 14 And 15 Bond Forming Reactions: Heterodehydrocoupling And Hydrophosphination, Michael Cibuzar

Graduate College Dissertations and Theses

Investigation of catalytic main-group bond forming reactions is the basis of this dissertation. Coupling of group 14 and 15 elements by several different methods has been achieved. The influence of Si–N heterodehydrocoupling on the promotion of α-silylene elimination was realized. Efficient Si–N heterodehydrocoupling by a simple, earth abundant lanthanide catalyst was demonstrated. Significant advances in hydrophosphination by commercially available catalysts was achieved by photo-activation of a precious metal catalyst.

Exploration of (N3N)ZrNMe2 (N3N = N(CH2CH2NSiMe3)33–) as a catalyst for the cross-dehydrocoupling or heterodehydrocoupling of silanes and amines suggested silylene reactivity. Further studies of the catalysis and stoichiometric modeling reactions hint …

Spectroscopic Study Of The Formation And Degradation Of Metalated Tetrapyrroles By The Enzymes Cfba, Isdg, And Mhud, Ariel E. Schuelke-Sanchez

Graduate College Dissertations and Theses

Metal tetrapyrroles represent a large class of earth-abundant catalysts but are limited to naturally-occurring combinations. Chelatase enzymes are responsible for the catalyzed metal insertion into a specific tetrapyrrole. CfbA is a class II chelatase from Archaeaglobis

fulgidus that catalyzes the insertion of nickel into sirohydrochlorin to give rise to Coenzyme F430 required for methanogensis. This archaeal chelatase was used to study the substrate scope of divalent metals and tetrapyrroles to probe various metal tetrapyrrole

combinations. A spectroscopic study established that the CfbA is capable of binding to cobalt and nickel, in addition to various tetrapyrroles. Magnetic circular dichroism (MCD) established …

Vo(Dtpa) Complexes Immobilized On Mesoporous Silica: Structural Characterization And Mechanistic Investigation Of Sulfide And Alkene Oxidation Reactions, Jenna R. Taft

Graduate College Dissertations and Theses

It was recently shown that V-doped acid-prepared mesoporous silica (APMS) nanoparticles are active catalysts for the oxidation of the mustard gas analogue 2-chloroethyl ethyl sulfide (CEES) under ambient conditions in the presence of aldehydes, using O2 from air as the oxidation source. However, the vanadium ion leached from the surface when water was present, leading to decreased catalytic activity. Therefore, in this work, the environment around the vanadium is changed, using diethylenetriamine pentaacetic acid (dtpa) as a ligand and anchoring it to the surface of a mesoporous silica nanoparticle, to investigate its effect on vanadium’s ability to perform oxidation reactions. …

Expansion Of The Intramolecular Zwitterionic-1,3-Diaza-Claisen Rearrangement Beyond Bridged-Bicyclic Electron-Deficient Isothioureas To Generate Substituted Cyclic Guanidines, Matthew William Luedtke

Graduate College Dissertations and Theses

Guanidines are ubiquitous in nature and have important applications in biological chemistry and industry, presenting themselves in biomacromolecules and organic materials respectively. The zwitterionic-1,3-diaza-Claisen rearrangement has allowed facile access to a variety of highly-substituted, complex guanidines, which would otherwise require a significant amount of time or resources to synthesize.

Previously, the intramolecular version of the 1,3-diaza-Claisen rearrangement has been used to generate tricyclic guanidines from bridged, bicyclic electron-deficient isothioureas. Extension of this methodology to simpler electron-deficient isothioureas has afforded stable zwitterionic intermediates, which have been isolated via silica gel column chromatography with common organic solvents. Heating the zwitterionic intermediates in …

I. Contorted Polycyclic Aromatic Hydrocarbons: Attempted Synthesis Of [12]Circulene Derivatives Ii. Synthesis And Characterization Of Novel [1]Benzothieno[3,2-B][1]Benzothiophene Derivatives, Jonathan Hollin

Graduate College Dissertations and Theses

There has been increasing interest in the development of organic materials due to their unique structural and electronic properties. Organic compounds have the advantage of being able to be deposited from solution, leading to low-cost, high-area electronics production. Contorted polycyclic aromatic hydrocarbons have been shown to have potential for use in organic field-effect transistors (OFETs) and organic photovoltaic devices (OPVs) due to their supramolecular properties and charge carrier mobilities. Thiophene-based materials have also shown great promise in OFETs due to their high charge carrier mobilities, stability during device operation, solubility in organic solvents, and structural versatility.

[n]Circulenes are a class …

Toward Macromolecular Shape And Size Control: Novel Enantioselective Nitrations And Iterative Exponential Growth Methods For Polymer Synthesis, Joseph Patrick Campbell

Graduate College Dissertations and Theses

Chirality is a key principle in organic chemistry. All chiral compounds are non-superimposable mirror images of each other and therefore lack an improper axis of rotation (Sn). These mirror images often have identical properties in an achiral environment, however when two chiral molecules interact, they produce different shapes and properties. Nature, to this extent takes advantage of this aspect through unique formation of shape defined biological macromolecules that are tailored to carry out various life processes. This level of shape control is only made possible because of natural chiral monomers such as amino acids or glycosides that make up such …

Quantification Of Mouse Cardiac Troponin I And Myosin Binding Protein C Phosphorylation By Liquid Chromatography-Mass Spectrometry (Lc-Ms), Praveena Nukareddy

Graduate College Dissertations and Theses

Heart failure is a major public health issue, with its prevalence estimated to be 6.5 million adults in the USA. Of the hospitalized heart failure (HF) cases, 50% are characterized by preserved ejection function (HFpEF). In HFpEF, the heart pumps a normal proportion of blood that enters it. However, thickening of the ventricular walls inhibits the chamber filling to normal volume. The direct basis of HFpEF is a slowed elongation of the cardiac muscle during the diastolic phase of the cardiac cycle. Elucidation of mechanisms that mediate relaxation of cardiac muscle could help understand the pathogenic mechanisms in HFpEF.

Myocardial …

Fragmentation, Rearrangement, And C-H Insertion: Reactions Of Vinyl Cations Derived From Diazo Carbonyls, Sarah Elizabeth Cleary

Graduate College Dissertations and Theses

Many commercialized medicinal compounds are analogs of chemicals isolated from sources found in nature (also called natural products). However, the natural sources of these chemicals, such as plants, fungi, or insects, only offer small quantities of these bioactive agents. Thus, it is typically desirable to find ways to synthesize these products and their analogs in large quantities using cost-effective methods that also minimize the impact on the environment. It is also important to develop strategies that expedite the process of modifying the natural products, which allows medicinal chemists to determine which functional groups are enhancing or deleterious to the bioactivity. …

Unprecedented Reactivity And Applications Of 1-Aza-2-Azoniaallene Salts, Ramya Srinivasan

Graduate College Dissertations and Theses

1-Aza-2-azoniaallene salts, derived by oxidation of substituted hydrazones, are highly reactive cationic heteroallenes. These species participate in several mechanistically distinct reactions including: (1) intramolecular [3+2] cycloadditions, (2) polar [4 +2] cycloadditions, (3) stereospecific C-H aminations, (4) electrophilic aromatic substitutions, and (5) chloroamination reactions. We have shown that this versatile reactivity is governed by the length of the tether and nature of the π-system.

A novel intramolecular electrophilic aromatic substitution reaction is observed when the tether length separating the 1-aza-2-azoniaallene salt and a pendant aryl ring is three methylene units to generate alkylaryl azo products. Variations in the electronics and sterics …