Other Chemistry Commons^™

Taking A Deeper Look: Attributing Tonal Values Of Photolumens To Their Emulsions Using Scanning Electron Microscopy, Anna M. Moore

All Theses

This thesis examines whether tonal variation in photolumens made with historic silver gelatin photographic papers can be linked to differences in elemental composition. Photolumens are cameraless photographic images created by placing objects directly on light-sensitive paper and exposing them to ultraviolet light. Because expired and historic darkroom papers often produce unpredictable colors and tones, this study asks whether visually defined tonal groups also show measurable chemical differences.

Twenty historic paper samples were exposed, documented, and sorted into five tonal groups based on visible image characteristics. Each sample was then analyzed using scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS) …

Form And Fusion: The Art And Science Of Ceramics And Glass, Juniper J. Bauroth-Sherman, Kaleigh Evans

Interdivisional Studies Presentations

The first Ceramics & Art class (IDS-110-F: ST: Ceramics) has completed an immersive, interdisciplinary exploration of stained glass and we’re excited to showcase it now. Through hands-on studio work, experiments, and design projects, we combined artistic expression with the science of glass—learning how physics and chemistry shape everything from color to strength and light interaction. The students have developed practical skills in cutting, grinding, foiling, soldering, and assembling stained-glass pieces, while also experimenting with thermal stress, light transmission, and color chemistry. Glass is now understood as not just as an art form, but as a dynamic material grounded in scientific …

Insights Into The Radiation Chemistry Of Flash Radiation Therapy, Alan E. Lopez Hernandez

Dissertations and Theses (Open Access)

Purpose: FLASH radiation therapy (FLASH-RT) is an emerging modality that delivers radiation at ultra-high dose rates (UHDR) and has shown consistent normal tissue sparing while preserving tumor control compared to conventional RT—a phenomenon termed the FLASH effect. Despite promising results, the mechanisms behind the FLASH effect remain unclear. Many hypotheses point to radiolytic interactions, but experimental validation is limited. This work aims to develop a robust experimental platform to evaluate the relationship between radiolytic species production and physical beam parameters relevant to FLASH-RT, alongside dosimetry tools for reliable UHDR beam characterization.

Methods: A beam collector (BC) Faraday cup detector was …

Structural Optimization And Stability Enhancement Of Uba(2) And Ntl9 Using The Computational Tool: Emcast, Bahar Ghazi Esfahani

Graduate Student Theses, Dissertations, & Professional Papers

This study enhances protein stability prediction by refining EmCAST (Empirical C-Alpha Stability Tool), a computational tool used to identify stabilizing mutations in protein domains. We applied EmCAST to two model proteins: the α-helical ubiquitin-associated domain 2 (UBA(2)) and the α/β N-terminal domain of ribosomal protein L9 (NTL9). Protein stability is critical for proper function, and mutations can lead to misfolding and disease. To validate EmCAST’s predictions, guanidine hydrochloride-induced denaturation was monitored using circular dichroism (CD) spectroscopy for both wild-type and mutant variants. Results guided refinements to EmCAST’s algorithm, incorporating new experimental datasets to improve accuracy. Additionally, we examined the assumption …

Myeloid-Derived Suppressor Cell Mitochondrial Fitness Governs Chemotherapeutic Efficacy In Hematologic Malignancies, Saeed Daneshmandi, Jee Eun Choi, Qi Yan, Cameron R. Macdonald, Manu Pandey, Mounika Goruganthu, Nathan Roberts, Prashant K. Singh, Richard M. Higashi, Andrew N. Lane, Teresa W-M Fan, Jianmin Wang, Philip L. Mccarthy, Elizabeth A. Repasky, Hemn Mohammadpour

Markey Cancer Center Faculty Publications

Myeloid derived suppressor cells (MDSCs) are key regulators of immune responses and correlate with poor outcomes in hematologic malignancies. Here, we identify that MDSC mitochondrial fitness controls the efficacy of doxorubicin chemotherapy in a preclinical lymphoma model. Mechanistically, we show that triggering STAT3 signaling via β2-adrenergic receptor (β2-AR) activation leads to improved MDSC function through metabolic reprogram- ing, marked by sustained mitochondrial respiration and higher ATP generation which reduces AMPK signaling, altering energy metabolism. Furthermore, induced STAT3 signaling in MDSCs enhances glutamine consumption via the TCA cycle. Metabolized glutamine generates itaconate which downregulates mitochondrial reactive oxygen species via regulation of …

Photoisomerizable Membrane Active Peptides, Cristina Ventura

Seton Hall University Dissertations and Theses (ETDs)

Membrane active peptides (MAPs) bind and partition into the cell membrane thus causing permeabilization. Many α-helical membrane active peptides contain central proline residues that distinguish the hydrophobic and hydrophilic faces of the helix. The proline induces a bend that produces a helix-hinge-helix motif. Mutation of these proline residues has a significant effect on the activity of the MAP. Azobenzene is a photoisomerizable molecule that switches from its trans to cis isomer upon excitation with ultraviolet (UV) light and from its cis to trans isomer upon excitation with visible light (VL). In this work it is hypothesized that the hinge function …

Inhibitors Of Alpha-Synuclein Aggregation, Jemil Ahmed

Electronic Theses and Dissertations

Alpha-Synuclein (αS) – a neuronal, disordered, presynaptic protein – aggregates into amyloid fibrils and accumulates in the substantia nigra pars compacta of Parkinson's Disease (PD) patients. The aggregation and accumulation of αS amyloid fibrils leads to death of dopaminergic neurons; a hallmark of PD. Although it’s not clear why αS aggregates, prior studies have found that intrastriatal injection of fibril alone is sufficient to cause PD pathology in mouse and non-human primates models. These observations implicate αS as a therapeutic target against PD.

Unfortunately, there are three caveats when attempting to target αS. First, αS is a neuronal protein expressed …

Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih

Makara Journal of Science

Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …

A Theoretical Study Of Synchronous Proton Transfer In (Hf)N, (H2O) N, And (Hcl) N Where N = 3, 4, 5, Johnny Yang

Honors Theses

For (HF)_n, (H₂O)_n, and (HCl)_n (n = 3 − 5), we have rigorously characterized the structures for the minima and transition states for synchronous proton transfer (SPT) with the CCSD(T) method and aug-cc-pVTZ basis set. The electronic barrier heights (∆E^†) associated with these transition states have also been computed with the explicitly correlated CCSD(T)-F12 method and the aug-cc-pVQZ-F12 basis set (abbreviated aQZ-F12). (HCl)_n (n = 3 − 5) SPT transition states have not been previously identified to the best of our knowledge, and they have been found …

Predicting The Hydration Free Energy Of Small Alkanes And Alcohols From Custom, Electronic Structure-Based Force Fields, T. Ryan Rogers

Graduate Theses and Dissertations

Mathematical theories reveal the fundamental physics involved in experimentalphenomena. Computer models of such theories are routinely used to corroborate or explain experiments and predict properties of chemical systems. Therefore, an important effort in computational chemistry is the development of more accurate and efficient chemical models. Current-generation models are only beginning to approach experimental-quality predictions of hydration free energies (HFEs).Using computations of quantum mechanical (QM) forces and classical simulations based on these forces, I investigate models to predict several properties of solutes and solutions. This dissertation is a collection of projects exemplifying methods used to gain insight into chemical systems.

Simulations …

Single-Reference Coupled Cluster Theory For Multi-Reference Problems, Johannes T. Margraf, Ajith Perera, Jesse J. Lutz, Rodney J. Bartlett

Faculty Publications

Coupled cluster (CC) theory is widely accepted as the most accurate and generally applicable approach in quantum chemistry. CC calculations are usually performed with single Slater-determinant references, e.g., canonical Hartree-Fock (HF) wavefunctions, though any single determinant can be used. This is an attractive feature because typical CC calculations are straightforward to apply, as there is no potentially ambiguous user input required. On the other hand, there can be concern that CC approximations give unreliable results when the reference determinant provides a poor description of the system of interest, i.e., when the HF or any other single determinant ground state has …

"Probing The Transition State Region In Catalytic Co Oxidation On Ru" Data Files, H. Öström, H. Öberg, H. Xin, Jerry L. Larue, M. Beye, M. Dell'angela, J. Gladh, M. L. Ng, J. A. Sellberg, S. Kaya, G. Mercurio, D. Nordlund, W. F. Schlotter, A. Föhlisch, M. Wolf, W. Wurth, M. Persson, J. K. Nørskov, F. Abild-Pedersen, H. Ogasawara, L. G. M. Pettersson, A. Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Data Sets

Femtosecond x-ray laser pulses are used to probe the CO oxidation reaction on Ru initiated by an optical laser pulse. On a timescale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and O on the surface allowing the reactants to collide and, with a transient close to a picosecond (ps), new electronic states appear in the O K-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond-formation between CO and O with a distribution of OC—O bond lengths close to the transition state (TS). After …

Probing The Transition State Region In Catalytic Co Oxidation On Ru, H. Öström, H. Öberg, H. Xin, Jerry L. Larue, M. Beye, M. Dell'angela, J. Gladh, M. L. Ng, J. A. Sellberg, S. Kaya, G. Mercurio, D. Nordlund, M. Hantschmann, F. Hieke, D. Kühn, W. F. Schlotter, G. L. Dakovski, J. J. Turner, M. P. Minitti, A. Mitra, S. P. Moeller, A. Föhlisch, M. Wolf, W. Wurth, M. Persson, J. K. Nørskov, F. Abild-Pedersen, H. Ogasawara, L. G. M. Pettersson, A. Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Femtosecond x-ray laser pulses are used to probe the CO oxidation reaction on Ru initiated by an optical laser pulse. On a timescale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and O on the surface allowing the reactants to collide and, with a transient close to a picosecond (ps), new electronic states appear in the O K-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond-formation between CO and O with a distribution of OC—O bond lengths close to the transition state (TS). After …

Hydration Of The Sulfuric Acid−Methylamine Complex And Implications For Aerosol Formation, Danielle J. Bustos, Berhane Temelso, George C. Shields

Faculty Journal Articles

The binary H₂SO₄−H₂O nucleation is one of the most important pathways by which aerosols form in the atmosphere, and the presence of ternary species like amines increases aerosol formation rates. In this study, we focus on the hydration of a ternary system of sulfuric acid (H₂SO₄), methylamine (NH₂CH₃), and up to six waters to evaluate its implications for aerosol formation. By combining molecular dynamics (MD) sampling with high-level ab initio calculations, we determine the thermodynamics of forming H₂SO₄(NH₂CH₃)(H …

Dipole Bound Excited States Of Polycyclic Aromatic Hydrocarbons Containing Nitrogen And Their Relation To The Interstellar Medium, Mallory L. Theis

Honors College Theses

Polycyclic aromatic hydrocarbons (PAHs) are the most abundant type of molecule present in the interstellar medium (ISM). It has been hypothesized that nitrogen replacement within a ring is likely for PAHs present in the ISM. Additionally, electrons, protons, and hydrogen atoms are readily added to or removed from PAHs creating a truly diverse set of chemistries in various interstellar regions. The presence of a nitrogen within a PAH (called a PANH herein) that is additionally dehydrogenated leads to a neutral radical with a large dipole moment. It has recently been shown through the use of high-level quantum chemical computations for …

Cloning And Characterization Of Sas0754, A Hypothetical Protein From Community Associated Staphylococcus Aureus, Unknown Unknown

Symposium 2012

Community associated Staphylococcus aureus (strain MSSA476) is a gram positive cocci capable of infecting many different parts of the body and known to cause serious infections that can be fatal, such as bacterial arthritis and acute endocarditis. To find effective ways of fighting against CA-MRSA strains we must learn more about their ability to infect. The focus of this study was cloning and characterization of a protein referred to as SAS0754. The size of SAS0754 is 340 amino acids and the gene sequence is 1023 nucleotides. The hypothetical function of this protein is that it is an extracellular matrix binding …

A Convenient Synthesis Of 2,6-Dichlorohomonicotinic Acid, Chase Buchanan, Richard W. Fitch

Symposium 2012

In our synthetic efforts toward the alkaloid phantasmidine, we required a convenient source of the title compound. Herein, we describe a short synthesis of 2,6-dichlorohomonicotinic acid by direct allylation of 2,6-dichloropyridine with LDA/allyl chloride, followed by permanganate oxidation of the side chain [figure1]. Yields for the allylation are high, while permanganate oxidation required more adjustment. Successful conditions require the modest acidification of the mixture with acetic acid and cleanup by acid base workup. No chromatography is needed.

Convenient Parallel Synthesis Of Alkyl- And Aryl-S-Tert-Butyl Thiothers, Rebecca Norcross, Jessica Stanfield, Richard W. Fitch

Symposium 2012

While preparing novel cysteine derivatives as oxidation catalysts, we needed S-tert-butylcysteine. We also examined acid-promoted tert-butylation of thiols using tert-butanol as reagent and solvent. While cysteine and aminoethanethiol work well using tBuOH in 4M HCl, other thiols fail in the aqueous environment and aerobic conditions. We examined a variety of aliphatic and aromatic thiols in tBuOH with H2SO4 catalysis and found that argon sparging and the use of 1 eq of acid led to good yields in a parallel format.

Communication: Bubbles, Crystals, And Laser-Induced Nucleation, Brandon C. Knott, Jerry L. Larue, Alec M. Wodtke, Michael F. Doherty, Baron Peters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Short intense laser pulses of visible and infrared light can dramatically accelerate crystal nucleation from transparent solutions; previous studies invoke mechanisms that are only applicable for nucleation of ordered phases or high dielectric phases. However, we show that similar laser pulses induce CO₂bubblenucleation in carbonated water. Additionally, in water that is cosupersaturated with argon and glycine, argon bubbles escaping from the water can induce crystal nucleation without a laser. Our findings suggest a possible link between laser-induced nucleation of bubbles and crystals.

Site-Specific Photocatalytic Splitting Of Methanol On Tio2(110), Chuanyao Zhou, Zefeng Ren, Shijing Tan, Zhibo Ma, Xinchun Mao, Dongxu Dai, Hongjun Fan, Xueming Yang, Jerry L. Larue, Russell Cooper, Alec M. Wodtke, Zhou Wang, Zhenyu Li, Bing Wang, Jinlong Yang, Jianguo Hou

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Clean hydrogen production is highly desirable for future energy needs, making the understanding of molecular-level phenomena underlying photocatalytic hydrogen production both fundamentally and practically important. Water splitting on pure TiO₂ is inefficient, however, adding sacrificial methanol could significantly enhance the photocatalyzed H₂ production. Therefore, understanding the photochemistry of methanol on TiO₂ at the molecular level could provide important insights to its photocatalytic activity. Here, we report the first clear evidence of photocatalyzed splitting of methanol on TiO₂ derived from time-dependent two-photon photoemission (TD-2PPE) results in combination with scanning tunneling microscopy (STM). STM tip induced molecular manipulation …

A Surface Femtosecond Two-Photon Photoemission Spectrometer For Excited Electron Dynamics And Time-Dependent Photochemical Kinetics, Zefeng Ren, Chuanyao Zhou, Zhibo Ma, Chun-Lei Xhao, Xinchun Mao, Dongxu Dai, Jerry L. Larue, Russell Cooper, Alec M. Wodtke, Xueming Yang

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A surface femtosecond two-photon photoemission (2PPE) spectrometer devoted to the study of ultrafast excited electron dynamics and photochemical kinetics on metal and metal oxide surfaces has been constructed. Low energy photoelectrons are measured using a hemispheri- cal electron energy analyzer with an imaging detector that allows us to detect the energy and the angular distributions of the photoelectrons simultaneously. A Mach-Zehnder interferom- eter was built for the time-resolved 2PPE (TR-2PPE) measurement to study ultrafast surface excited electron dynamics, which was demonstrated on the Cu(111) surface. A scheme for measuring time-dependent 2PPE (TD-2PPE) spectra has also been developed for studies of …

The Effective Potential Energy Surfaces Of The Nonadiabatic Collision B(2PJA) + H2(1Σ+G,Ν,J) ↔ B(2PJ'A) + H2(1Σ+G,Ν',J'), Matthew B. Garvin

Theses and Dissertations

Effective potential energy surfaces (PESs) are calculated for a nonadiabatic collision . This calculation employed 1 ²A', 2 ²A' and 1 ²A" adiabatic PESs numerically calculated at the state-averaged multiconfigurational self-consistent field (SA-MCSCF)/configuration interaction (CI) level for several values of the H₂ bond length, H₂ orientation angle, and boron distance. The associated nonadiabatic coupling terms (NACTs) were calculated from the SA-MCSCF/CI wave functions using analytic gradient techniques. A line integral through the NACTs was then used to determine the adiabatic-to-diabatic mixing angle required to transform from the 1 ²A' and 2 ²A' …

Inverse Velocity Dependence Of Vibrationally Promoted Electron Emission From A Metal Surface, N. H. Nahler, J. D. White, Jerry L. Larue, Daniel J. Auerbach, Alec M. Wodtke

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

All previous experimental and theoretical studies of molecular interactions at metal surfaces show that electronically nonadiabatic influences increase with molecular velocity. We report the observation of a nonadiabatic electronic effect that follows the opposite trend: The probability of electron emission from a low–work function surface—Au(111) capped by half a monolayer of Cs—increases as the velocity of the incident NO molecule decreases during collisions with highly vibrationally excited NO(X²π_½, V = 18; V is the vibrational quantum number of NO), reaching 0.1 at the lowest velocity studied. We show that these results are consistent with a vibrational …

Use Of Quantum Mechanical Calculations To Investigate Small Silicon Carbide Clusters, Jean W. Henry

Theses and Dissertations

Density Functional Theory (DFT) method was employed to model silicon carbide small clusters. Comparing the DFT calculation results with experimental results that observed by using photoelectron spectroscopy (PES), DFT predicts the same structures that experiment observed. For electron affinity, DFT results are in good agreement with experimental results, the root mean square negative offset 0.1 eV found using medium size of basis set (cc-pVDZ+) calculation. DFT results for vibrational frequencies are in good agreement with experiment results; the root mean square error is 72.5 cm^-1 wave number. 16 ground state structures of Si_mC_n (m ≤ 4, …

Pressure Dependence Of Fluorescent And Photolytic Interferences In Ho Detection By Laser-Excited Fluorescence, Thomas M. Hard, Robert J. O'Brien, T. B. Cook

Chemistry Faculty Publications and Presentations

In the measurement of HO concentrations by laser-excited fluorescence, expansion of the sampled air offers a way to reduce fluorescent and photolytic interference by other species. The decrease in [HO] upon expansion is balanced by an increase in HO fluorescence yield over a wide range of pressures. Background air fluorescence is reduced if the responsible species have fluorescence yields higher than those of HO. Preliminary experiments indicate that most of the fluorescence observed in laboratory air is due to such species. Upon expansion, the suppression of fluorescent interference can be no greater than the reduction in pressure, whereas the suppression …

Some Contributions Of Pure Math To Science, Herbert B.E. Case

Student and Lippitt Prize Essays

An examination of the connection between math and science through discoveries in the subjects of astronomy, mechanics, physics and chemistry.