Chemistry Commons^™

From Biophysics To Cellular Function: Neural Telcs-Membrane-Anions Capacitor Transmembrane Potential, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Based on the transmembrane-electrostatically localized protons/cations charges (TELCs) theory, neural transmembrane potential including both resting and action potential is now well elucidated as the voltage contributed by the TELCs-membrane-anions capacitor biophysics in a neuron. Accordingly, neural transmembrane potential has an inverse relationship with TELCs surface density, which may represent a substantial progress in bettering the fundamental understanding of neuroscience. In this article, I will present a review on the latest development of the TELCs neural transmembrane potential theory and address Silverstein’s interesting arguments regarding the TELCs model that may constitute a complementary development to both the Hodgkin-Huxley classic cable theory …

Metathesis Or Isomerization: Counteranion Directed Reactivity Of Grubbs I, Paul D. Miller, Joe B. Calkins, Craig A. Bayse, Trandon A. Bender

Chemistry & Biochemistry Faculty Publications

Catalytic isomerization of alkenes has garnered interest for many years, but there are remaining challenges when it comes to thermodynamic selectivity and uncontrolled isomerization. Nonbiased substrates, be it sterically or thermodynamically, remain challenging for many catalysts, with a few examples available in the more modern literature. Herein, we present the controlled isomerization of linear alkenes with a cocatalytic mixture of commercially available catalyst and reagents: Grubbs I, tris(pentafluorophenyl)borane, and triethylsilane. DFT calculations indicate that an observed alkylidyne hydride intermediate is in rapid equilibrium with an alkylidene that binds the alkene substrate. This combination results in a pi-acidic metal and a …

Stack Bonding In Pentacene And Its Derivatives, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Understanding the nature of π-stacking interactions is important to molecular recognition, self-assembly, and organic semiconductors. The stack bonding order (SBO) model of π-stacking has shown that the conformations of dimers occur when the combinations of monomer MOs are overall stack bonding in character. DFT calculations show that minima found on the potential energy surface for the π-stacked dimers of pentacene and perfluoropentacene occur when the dimer MOs are constructed from combinations of monomer MOs with an allowed SBO. An ex-amination of the MOs of π-stacked dimers extracted from X-ray structures of alkynyl derivatives like TIPS-pentacene pack at one or more …

Molecular Characterization Of Humic And Fulvic Acids On Watterlogged And Well-Drained Amazonian Podzols, Amanda M. Tadini, Aleksandar I. Goranov, Stéphane Mounier, Débora M.B.P. Milori, Célia R. Montes, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

The Amazon rainforest is the largest tropical rainforest in the world. Amazonian Podzol soils, characteristic of this region, are known to store substantial amounts of organic carbon in both their surface and deep horizons. Despite decades of research, the molecular-level composition of these soils remains uncharacterized. This study addresses this knowledge gap by employing ultrahigh resolution mass spectrometry, namely, Fourier transform–ion cyclotron resonance–mass spectrometry (FT-ICR-MS), to determine the molecular composition of humic acid (HA) and fulvic acid (FA) fractions from two Amazonian Podzol profiles of varying levels of groundwater exposure (waterlogged vs well-drained). In the waterlogged soil compounds containing nitrogen, …

Protonic Capacitor Cell Energetics: Transmembrane-Electrostatically Localized Protons/Cations, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

The transmembrane-electrostatically localized protons/cations charges (TELPs/TELCs) theory can serve as a theoretical framework to better explain cell electrophysiology and elucidate bioenergetic systems including both delocalized and localized protonic coupling. According to the TELCs model, the excess positive charges of TELCs at one side of the membrane are balanced by the excess negative charges of transmembrane-electrostatically localized hydroxides anions (TELAs) at the other side of the membrane. Through the TELCs-membrane-TELAs capacitor model, the energetics of oxidative phosphorylation have recently been better elucidated in mitochondria and alkalophilic bacteria, leading to the identification of a novel Type-B energetic process. Both the TELCs model …

Deciphering The Chemistry Of Condensed Aromatic "Black" Carbon And Nitrogen In Amazonian Anthrosols, João Vitor Dos Santos, Aleksandar I. Goranov, Laís G. Fregolente, Marcia C. Bisinoti, Zhenhuan Sun, Klaus Schmidt-Rohr, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

Amazonian anthrosols are renowned for their high fertility and dark color, properties primarily attributed to the abundance of condensed aromatic carbon (ConAC) in the soil organic matter. ConAC, commonly referred to as black carbon, play a key role in the stability and nutrient retention of these soils. However, the processes governing the formation of ConAC and its transformation into oxygenated derivatives remain poorly understood. In this study, we used multiple analytical platforms to investigate the chemistry of ConAC-rich humic acids (HA) extracted from Terra Mulata de Indio, a type of Amazonian anthrosol. The results reveal that ConAC are predominantly …

Formation Of Pyramidal Palladium Enhanced By B(C₆F₅)₃ Additive Enabling Selective Alkene Monoisomerization, Paul D. Miller, Trandon A. Bender

Chemistry & Biochemistry Faculty Publications

The addition of a strong Lewis acid, tris(pentafluorophenyl)borane, facilitates the reduction of Pd(cod)Cl₂ with Et₃SiH to form palladium nanoparticles in organic solvents. It was found that these palladium nanoparticles are capable of selective monoisomerization of linear alkenes. This heterogeneous palladium catalyst is tolerant of a wide variety of functional groups, confirmed by substrate and robustness screenings. It is also possible to utilize poly(methylhydro)siloxane, an industrial waste byproduct, as the reductant to enable similar isomerization chemistry.

Experimental Demonstration And Study Of Transmembrane-Electrostatically Localized Protons Prevail, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

In this review in relation to some interesting arguments from Silverstein, it is now reaffirmed that the experimental demonstration of transmembrane-electrostatically localized protons (TELPs) was successfully accomplished through 1) using an aluminum film as a TELPs sensor in a biomimetic anode water-membrane-water cathode system, 2) analyzing the water-electrolysis current curve, and 3) measuring bulk liquid phase pH. Formation of induced TELPs was subsequently discovered in an anode water-membrane-water-membrane-water cathode system. The discovery of induced TELPs enabled clean experimental tests on the cation-TELPs exchange process by using sodium bicarbonate or potassium bicarbonate solution in the central liquid chamber. The sodium/TELPs exchange …

Application Of Telc Model To Better Elucidate Neural Stimulation By Touch, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Aim: This study is to better understand how the transient ion transport activity of touch receptors could change the graded potential to stimulate an action potential firing.

Methods: The latest transmembrane-electrostatically localized protons/cations charges (TELC) theory is employed for numerical analysis to calculate the neural touch signal transduction responding time required to fire an action potential spike.

Results: A neural action potential spike was constructed successfully using newly developed time-dependent TELC-based neural transmembrane potential integral equations (Equations 5, 6, and 7). The results explicated that the TELC curve has an inverse relationship with neural transmembrane potential since its curve appears …

The B³Π–A³Δ And B³Π–X¹Σ+ Band Systems Of Zro, Manish Bhusal, Peter F. Bernath, Jacques Liévin, Léo Lavy

Chemistry & Biochemistry Faculty Publications

The zirconium oxide (ZrO) b³Π–a³Δ system is a prominent source of opacity in the atmospheres of S-type stars in the near-infrared region. The emission spectra of ZrO, obtained at the National Solar Observatory located at Kitt Peak in Arizona, have been utilized to analyze this band system. A reanalysis of the 0–0 vibrational band of the b³Π–a³Δ transition has been carried out. For the first time, the vibrational bands with 1 ⩽ v ′ ⩽ 3 and v″ ≤ 4 for the same electronic transition have been rotationally analyzed using PGOPHER. Additionally, the 0–0 and 1–1 bands of the spin-forbidden …

Identification Of Π-Stacking Motifs In Naphthalene Diimides Via Solid-State Nmr, Jennifer E. Mejia, Hannah E. Butler-Au, Nalaya E. Thompson, Karcher D. Goodman, Elizabeth R. Zengel, Robert D. Pike, Jingdong Mao, Craig A. Bayse

Chemistry & Biochemistry Faculty Publications

Organic electronics, featuring π-conjugated small molecules and polymers, have gained significant attention for their potential in flexible, lightweight devices. However, characterization of the ordered, π-stacking domains within these materials using microscopy or X-ray diffraction (XRD) is challenging with complex systems or when crystallography is impractical. This study applied 1D ¹³C multiple cross-polarization magic angle spinning (multiCP/MAS) and 2D ¹H-¹³C heteronuclear correlation (HetCor) solid-state nuclear magnetic resonance (ssNMR) to systematically characterize π-stacking motifs in a series of N,N'-dialkyl naphthalene diimides (NDIs). These techniques were shown to distinguish between the electronic environments attributed to different π-stacking motifs adopted in these NDIs, such …

Oxidation Camouflages Terrestrial Organic Matter To Appear Marine-Like, Aleksandar I. Goranov, Susan J. Carter, Ann Pearson, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

The export of terrestrial organic matter (TOM) to the ocean has been traditionally viewed to be minimal or only of significance in near-coastal continental margins. The broadly accepted explanation for the widespread loss of terrestrial lignin biomarkers and apparent disappearance of the <-25‰ stable carbon isotopic signature (δ¹³C) of TOM is that TOM is almost fully degraded before reaching the open ocean. Oceanic carbon (δ¹³C value ≥ -22‰) is therefore thought to be derived primarily from algae. However, an alternative explanation for the different molecular and δ¹³C signatures in terrestrial and marine environments may be that oxidative processing transforms TOM to appear marine-like. To test this hypothesis, we subjected eight TOM samples to a strong oxidation gradient. At carbon losses typical of TOM degradation during transport and sedimentation (above 60%), the differentiators of provenance disappeared, leaving a residue that was marine-like both chemically (aliphatic- and nitrogen-rich) and isotopically (δ¹³C enrichment of 4 to 9‰). This challenges the validity of conventional two-endmember mixing models, suggesting that a much larger fraction than previously estimated of the organic matter found in the ocean may originate from terrestrial sources, impacting global models of carbon cycling and sequestration.

Amphiphilic Tripodal Metalloligands: Synthesis, Coordination Chemistry And Preliminary Catalysis, Austin W. Medley, Paul D. Miller, Craig A. Bayse, Robert D. Pike, Trandon A. Bender

Chemistry & Biochemistry Faculty Publications

Triscatecholate binding has been widely studied in the context of biological systems, supramolecular chemistry, and weak aggregate interactions. However, the utilization of the triscatecholate binding motif for the preparation of metalloligands remains unexplored. Herein, we report the synthesis, structural characterization, and functional studies of a triscatecholate ligand with an appended pyridyl residue as a candidate for such applications. Our findings reveal that the selective formation of cis-triscatecholate-based metalloligands is influenced by electronic effects on the catecholate anions, enabling the targeted synthesis of Al(III), Ga(III), and In(III) triscatecholate metalloligands capable of binding Zn(II) and Ru(II) at the appended pyridyl moiety for …

Twenty Years Of Global Stratospheric Fluorine Inventories From Atmospheric Chemistry Experiment Fourier Transform Spectrometer (Ace-Fts) Measurements, N. Raymond, P. Bernath, C. Boone, M. Chipperfield

Chemistry & Biochemistry Faculty Publications

We present fluorine inventories calculated for twenty years (2004–2023) and five latitude bands (82°–60°N, 60°–30°N, 30°N–30°S, 30°–60°S, and 60°–82°S) at altitudes from the surface up to 55 km. The inventories were calculated using the Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE‐FTS) version 5.2 retrievals of the volume mixing ratios (VMRs) of 15 fluorine‐containing species. Of these 15 species, 3 are product gases: HF, COF₂, COCIF, and 12 are source gases: SF₆, PFC-14 (CF₄), CFC-11 (CCl₃F), CFC-12 (CCl₂F₂), CFC-113 (CCIF₂CCl₂F), HCFC-22 (CHF₂CL), HCFC-141b(C₂H₃Cl₂F), HCFC-142b ( …

Cfd Analysis Of Hydrodynamic Cavitation Through An Orifice: Influence Of Different Inlet Pressures And Number Of Orifice Holes, Lemthong Chanphavong, Vongsavanh Chanthaboune, Keophousone Phonhalath

ASEAN Journal on Science and Technology for Development

Hydrodynamic cavitation (HC) is considered an energy-efficient process with high potential for utilization in many chemical processes. This study presents a computational fluid dynamics (CFD) analysis of cavitating flow through an orifice with a constant flow area. The Reynolds-Averaged Navier-Stokes (RANS) equations, coupled with turbulence and cavitation models, are employed to capture the complex flow behaviors. The effects of inlet pressures and number of orifice-holes on cavitation behavior are investigated. Result of the numerical simulation is validated with the existing experimental data from the literature. The CFD study revealed that cavitation initiates just behind the inlet edge of the orifice …

Effects Of Chain Length, Saturation, And Bases On Saponification, Sarah Fenik

Williams Honors College, Honors Research Projects

This project will analyze the effects of chain length and saturation of fatty acids on saponification processes, as well as the effects of the base used in the reaction. Stearic acid, lauric acid, and oleic acid will be used for the fatty acid comparisons, and sodium hydroxide and potassium hydroxide will be used for the base comparisons. Stearic acid is considered a long chain fatty acid, while lauric acid is considered a short chain fatty acid. Oleic acid is a monounsaturated fatty acid. Five soap products are be made: sodium stearate, sodium laurate, sodium oleate, potassium stearate, and potassium oleate. …

Synthesis Of Noval Hydroxy Chalcone And Study Of Fluorescent Properties, Margaret Hilliker

Williams Honors College, Honors Research Projects

Chalcones are a class of naturally occurring compounds found in plants, which have a general structure of Ar–CO–CH=CH–Ar’. They have shown significant potential as tunable organic fluorophores due to their extended π-conjugation and structural simplicity. In this study, a 2-hydroxy-substituted chalcone featuring a terminal dimethylamino group was synthesized via a pyrrolidine-catalyzed aldol condensation and characterized for its photophysical properties. The electron-donating and -accepting ends of the molecule establish an intramolecular charge transfer (ICT) pathway, while the hydroxyl group enables excited state intramolecular proton transfer (ESIPT), leading to complex emission behavior. Room temperature fluorescence analysis revealed broad, featureless emission, while low-temperature …

Light-Driven Chemistry: Photoswitch In Rna Activity Control And Development Of Photoredox Catalysis, Juncheng Li

Electronic Theses & Dissertations (2024 - present)

This dissertation is structured into two principal segments. The initial segment elucidates a series of synthetic works involving artificial molecules, specifically featuring the photosensitive azobenzene. These molecules facilitate remote control over the structure and functionality of biomolecules, with subsequent applications in regulating biological processes. The latter segment concentrates on the design and enhancement of organic photocatalysts, utilizing traditional acridine ions as a foundation. This section details the development of diverse organic photocatalyst-promoted processes, including photo Lewis acid catalysis, photo Brønsted acid catalysis, and photoredox reactions.

Phytochemistry Of Dalea Candida Var. Oligophylla, Ryan E. Galperin

All Master's Theses

The focus of this project was the plant Dalea candida and its phytochemistry. The plant compounds were isolated and purified by an array of chromatographic techniques. The structures of the pure compounds were determined by one-dimensional and two-dimensional ¹H and ¹³C NMR spectroscopy, supported by infrared and ultraviolet spectroscopy, experimental and calculated circular dichroism spectroscopy, and mass spectrometry. Plant parts were worked on separately since they typically differ in content. Purified compounds will be tested for biological activities. Based on our results, eight new or known compound were isolated, specifically four new compounds and four known compounds. Compound …

Investigation Of The Binding Mechanism Between The Supplemental And Tail Regions Of Mirna And Mrna Within Argonaute 2, Christina Ms Karadiakos

Electronic Theses & Dissertations (2024 - present)

MicroRNAs (miRNA) are a class of small non-coding RNAs that play a key role in gene silencing. miRNAs form an RNA-induced silencing complex (RISC) with the argonaute 2 (AGO2) protein in order to control gene expression through silencing messenger RNAs (mRNA). The ability for a miRNA-mRNA complex to fit into AGO2 and form the RISC is based on the location and characteristics of a central bulge, but the mechanism and interactions that lead to a functional RISC remain unknown. Using available experimental data, we modeled the miR-34 and NOTCH1 duplex inside of AGO2 with only the seed region base paired. …

Towards Developing Glut2 Specific Probes For Biochemical And Biomedical Applications, Abdelrahman Ismail

Dissertations, Master's Theses and Master's Reports

Facilitated Glucose transporters (GLUTs) are membrane proteins responsible for the uptake of simple sugars and other structurally similar metabolites in all mammalian cells. One of the hallmarks of cancer is dysfunctional sugar metabolism, known as the Warburg effect, and one of the manifestations of that effect is abnormal GLUT expression. There are 14 known GLUT proteins with different expression patterns in different tissues, and tumors tend to express certain GLUTs that are not present in surrounding healthy tissue. Therefore, selective targeting of GLUTs presents a potentially powerful tool for diagnostics and treatment of cancer and other diseases. This has been …

Near-Infrared Fluorescent Cyanine Probes For Monitoring Nad(P)H Dynamics In Living Cells And Drosophila Larvae, May Waters

Dissertations, Master's Theses and Master's Reports

Nicotinamide adenine dinucleotide (NAD+/NADH) plays a critical role in cellular metabolism, with abnormally elevated NADH levels linked to disrupted metabolic processes and cancer. In this study, we developed near-infrared fluorescent probes to selectively measure NADH concentrations. We present five cyanine-based probes, which were optimized by modifying the connection bridges to fine tune electronics. Two NAD(P)H-biosensing probes consisting of 1,3,3-trimethyl-3H-indolium and 3-quinolinium acceptors, linked by thiophene, A, and 3,4-ethylenedioxythiophene, B, bridges are detailed. They exhibit near-infrared fluorescence at 742.1 nm and 727.2 nm for probes A and B, respectively, and generate absorbance signals at 690.6 nm and 685.9 nm. Probe A …

Development Of Near-Infrared Probe For The Detection Of Nadh And Nad(P)H In Live Cells And D. Melanogaster Larvae, Sophia J. Jaeger

Dissertations, Master's Theses and Master's Reports

A near-infrared fluorescent probe, A, was designed by substituting the carbonyl group of the coumarin dye’s lactone with a 4-cyano-1-methylpyridinium methylene group and then attaching an electron-withdrawing NADH-sensing methylquinolinium acceptor via a vinyl bond linkage to the coumarin dye at the 4-position. The probe exhibits primary absorption maxima at 603, 428, and 361 nm, and fluoresces weakly at 703 nm. The addition of NAD(P)H results in a significant blue shift in the fluorescence peak from 703 to 670 nm, accompanied an increase in fluorescence intensity. This spectral shift is attributed to the transformation of A−π–A−π–D configuration to D−π–A−π–D pyridinium platform …

Cloud Condensation Nuclei Activity Of Fresh And Aged Phenolic Acid Aerosol Particles, Emily A. Nortmann

Honors Undergraduate Theses

In recent years, the incidence of wildfires has considerably increased, with fire seasons starting earlier and ending later than usual due to changes in snowpack, precipitation, and temperature, which are attributed in part to climate change. Wildfires are responsible for the emission of a variety of gases and organic aerosol particles in the atmosphere with profound impacts on air quality, visibility, and human health. The aerosol particles produced by wildfires can contribute to climate change by scattering or absorbing solar radiation, affecting the radiative balance of the planet through cooling or warming effects, or by acting as cloud condensation nuclei …

Biomechanics Of The Atherosclerotic Lipidome: (Un)Expected Statin Interactions And Membrane Remodelling, Ethan M. Fong

Pomona Senior Theses

Statins interact with lipid membranes in ways that shape their pharmacokinetics, off-target effects, and pleiotropic actions, yet these interactions' mechanical and biophysical consequences remain poorly understood. This thesis employs a combination of surface plasmon resonance (SPR), quartz crystal microbalance with dissipation monitoring (QCM-D), and rheological modelling to characterize how representative statins intercalate within biomimetic supported lipid bilayers (SLBs) of healthy and diseased composition. SPR reveals that lipophilic statins exhibit higher apparent affinities and slower dissociation kinetics, especially in cholesterol- and anionic lipid-rich membranes. QCM-D analyses demonstrate that statins alter membrane mass, dissipation, and interfacial stiffness in a statin- and membrane-dependent …

Light, Symbiosis, And The Biology Of Corals, Taylor R. Lindsay

Open Access Dissertations

Light is critical for the survival of most shallow water scleractinian corals. Corals are mixotrophs, acquiring energy via both feeding on water column plankton and photosynthesis via a symbiotic relationship with dinoflagellates living within their tissues. Corals rely heavily on photosynthetically derived metabolites through this symbiotic relationship, intrinsically linking their biology to light availability. Corals are known to modulate their biology to maximize light capture. However, there is a limited understanding of the interaction between morphology, physiology, and energetic strategy, as well as how light may affect these relationships. In Chapter 1, we quantified the morphology, physiology and energetic …

Beyond The Phonon Gas Model (Pgm): Unraveling The Unique Mechanistic Processes Dictating Thermal Transport In Highly Anharmonic And Disordered Materials, Sandip Thakur

Open Access Dissertations

Thermal transport in nonmetallic solids has traditionally been described by the phonon gas model (PGM), in which heat is carried by weakly interacting phonon quasiparticles in an ordered crystalline lattice. However, this model breaks down in materials characterized by strong anharmonicity, dynamic disorder, or structural complexity, features prevalent in many next-generation materials used in energy conversion, optoelectronics, and thermal management. This dissertation investigates thermal transport in such complex materials, including metal halide perovskites (MHPs), covalent organic frameworks (COFs), metal organic frameworks (MOFs), and 2D-3D heterostructures, through large-scale molecular dynamics (MD) simulations and frequency-resolved spectral analyses.

In MHPs, the work reveals …

Long Oligos: Direct Chemical Synthesis Of Genes With Up To 1728 Nucleotides, Yipeng Yin, Reed Arneson, Yinan Yuan, Shiyue Fang

Michigan Tech Publications

The longest oligos that can be chemically synthesized are considered to be 200-mers. Here, we report direct synthesis of an 800-mer green fluorescent protein gene and a 1728-mer Φ29 DNA polymerase gene on an automated synthesizer. Key innovations that enabled this breakthrough include conducting the synthesis on a smooth surface rather than within the pores of traditional supports, and the use of the powerful catching-by-polymerization (CBP) method for isolating the full-length oligos from a complex mixture. Conducting synthesis on a smooth surface not only eliminated the steric hindrance that would otherwise prevent long oligo assembly, but also, surprisingly, drastically reduced …

Enhancing Crispr-Cas12a Activity Through Guide Rna Methylation, Hilal Dagci

Electronic Theses & Dissertations (2024 - present)

CRISPR-Cas12a is a rapidly evolving technology for improved gene editing in cells, as well as in vivo. The system, consisting of Cas12a nuclease and approximately 40-nt long guide RNA (gRNA), can efficiently recognize and cut genomic double-stranded DNA (dsDNA). Chemical modifications to the gRNA can potentially improve its dsDNA binding and enhance Cas12a-mediated nuclease activity. In this work, 5-methyl cytidine (m5C) and N6-methyl adenosine (m6A) were explored to improve the binding between gRNA and target DNA. Phosphoramidites of m5C and m6A were used to construct a library of gRNAs using solid phase RNA synthesis. Tm studies were carried out …

Fabrication Of Functional Microparticles For Biological Analysis, Justin George

Electronic Theses & Dissertations (2024 - present)

To better advance our knowledge of cellular behavior, development of an organism, and disease mechanisms understanding cellular heterogeneity in the functional proteome is essential. Bulk measurements across a cell population often fail to capture the variations which exist between individual cells, however single cell proteomic technology has increasingly demonstrated the characterization of cellular heterogeneity. A single cell functional proteomics assay needs to be both high-throughput and multiplexed to effectively identify biomarkers and provide a quantitative correlation to better understand the interrelationships within complex protein networks. Janus particles have the ability to be engineered to have good compatibility and stability in …