Computational Chemistry Commons^™

Predicting Rheology Of Uv-Curable Nanoparticle Ink Components And Compositions For Inkjet Additive Manufacturing, Cameron D. Lutz

Master's Theses

Inkjet additive manufacturing is the next step toward ubiquitous manufacturing by enabling multi-material printing that can exhibit various mechanical, electronic, and thermal properties. These characteristics are realized in the careful formulation of the inks and their functional materials, but there are many constraints that need to be satisfied to allow optimal jetting performance and build quality when used in an inkjet 3-D printer. Previous research has addressed the desirable rheology characteristics to enable stable drop formation and how the metallic nanoparticles affect the viscosity of inks. The contending goals of increasing nanoparticle-loading to improve material deposition rates while trying to …

A Molecular Dynamics Study On The Destruction Mechanism Of Per And Polyfluoroalkyl Substances Due To Ultrasound Technology, Bruno Bezerra De Souza

Dissertations

Per- and polyfluoroalkyl substances (PFAS) are a group of stable synthetic chemicals that are highly persistent and harmful pollutants to the environment and human health. PFAS have caused a strong public and regulatory response due to their ubiquitous presence in the environment and toxicity to humans. The application of ultrasound is one of the most effective treatment technologies for the mineralization of PFAS in contaminated water. However, this technology is treated as a black box causing the inability to be optimized. Therefore, there is a pressing need to investigate the intricate dynamics of PFAS degradation under ultrasound to unlock its …

Molecular-To-Continuum Scale Modeling Of Aerosols: Atmospheric Application And Beyond, Ella Ivanova

Dissertations

Aerosol modeling is critical for various applications, such as climate forecasting, air quality, and human health impact assessment. During their lifetime, aerosols undergo a complex evolution, usually divided into several stages — formation, processing, transport, and removal — that occur on different scales. Thus, the choice of modeling methods depends on the stage considered. For example, certain stages of particle formation may require nano-scale modeling while aerosol-cloud interactions span from microscale to mesoscale. This study examines the modeling of aerosol behavior over a wide range of scales, from nano to microscale, with implications to mesoscale.

This dissertation focuses on two …

The Investigation Of The Reaction Of 2,3-Dimethylfuran With O(³P) And The Estimate Of The Photoionization Cross Section Of C-Cl And Absolute Photoionization Cross Sections Of Chlorinated Organic Compounds, Yilan Lori Chen

Master's Theses

The work presented in this thesis focuses on gas-phase reactions, which are fundamental for reducing greenhouse gas emissions and mitigating climate change. The experiments are performed at the Advanced Light Source (ALS) of Lawrence Berkeley National Laboratory, where there is a time-of-flight mass spectrometer coupled with tunable synchrotron radiation at Beamline 9.0.2 to collect high-quality data.

Chapter 1 details the background and purpose of each project, along with an overview of the origins of synchrotron radiation and time-of-flight mass spectrometry. The adaptation of biofuels is a way to minimize carbon emission and air pollutants, so research surrounding the reaction dynamics …

Inchi Isotopologue And Isotopomer Specifications, Hunter N. B. Moseley, Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Emma L. Schymanski

Markey Cancer Center Faculty Publications

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically‑resolved chemi‑ cal entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically‑ resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry.

Scientific contribution

This new extension to the InChI standard …

Advancing Coupled Cluster Methods: Tensor Factorization And Analytic Gradient Implementation, Tingting Zhao

Chemistry Theses and Dissertations

With the rapid advancement of computing capabilities, computational chemistry has become increasingly indispensable in both experiment design and the interpretation of experimental outcomes. Wave-function-based quantum mechanistic methods are highly sought after for their ability to provide high-accuracy data and their potential for systematic improvement. However, to extend their applicability to larger molecules, it is essential to employ rank-reducing approximations to these methods. This dissertation dedicates Chapters Three and Four to the development of rank-reduced methodologies. Additionally, beyond single-point energies, molecular geometries and properties of molecule-excited states hold paramount importance across diverse fields of chemistry. Hence, Chapter Five presents the work …

Theoretical Spectroscopic Predictions Of Electronically Excited States, Noah R. Garrett

Honors Theses

The quest for faster computation of anharmonic vibrational frequencies of both ground and excited electronic states has led to combining coupled cluster theory harmonic force constants with density functional theory (DFT) cubic and quartic force constants for defining a quartic force field (QFF) utilized in conjunction with vibrational perturbation theory at second order (VPT2). This work shows that explicitly correlated coupled cluster theory at the singles, doubles, and perturbative triples level [CCSD(T)-F12] provides accurate anharmonic vibrational frequencies and rotational constants when conjoined with any of B3LYP, CAM-B3LYP, BHandHLYP, PBE0, and ωB97XD for roughly one-quarter of the computational time of the …

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 …

Selectivity Studies Of Cbds Against Cb1 And Cb2 Using Docking Approach, Brandon Villanueva Sanchez, Andy Zhong

Theses/Capstones/Creative Projects

Cannabis sativa is an herbal plant that is used for recreational and medicinal purposes. The two main components, ∆9-Tetrahydrocannabinol (THC) and Cannabidiol (CBD), are responsible for the two different uses. Both compounds have been heavily researched, with their mechanisms of action, docking site, and binding affinity and efficacy identified. Researchers have synthesized various analogs by altering the carbon side chains of THC/CBD’s molecular structures. These synthetic analogs have been created to study the structure-function relationship of different molecules to the endocannabinoid system receptors, CB1 and CB2. Here, we conduct a docking study of various THC/CBD analogs to both receptors using …

Design, Synthesis, And Optimization Of Allosteric Inhibitors Of Hiv-1 Integrase, Krunal H. Patel

Dissertations

The human immunodeficiency virus type 1 (HIV-1) infection remains a global health crisis, necessitating the development of innovative antiviral strategies. During the integration step, HIV-1 integrase (IN) interacts with viral DNA and the cellular cofactor LEDGF/p75 to effectively integrate the reverse transcript into the host chromatin. Recently, a novel class of antiretroviral agents called Allosteric Inhibitors of HIV-1 Integrase (ALLINI) compounds has emerged as a promising avenue in the fight against HIV-1. While originally designed to inhibit IN-LEDGF/p75 interactions, these compounds have been shown to also impact late-stage viral maturation severely through IN multimerization. Induction of IN multimerization interferes with …

Modelling Terrestrial And Potential Extraterrestrial Photopigments Via Density Functional Theory, Dorothea Illner

Theses and Dissertations

In the search for extraterrestrial life, biosignatures play a crucial role in identifying its putative traces. A commonly known and robust biosignature is the Vegetation Red Edge (VRE), which can be described as a sharp increase of reflectance observed from a planet and stems from the light absorption of photopigments in specific regions in the electromagnetic spectrum. For Earth, this VRE is known to occur around 700 nm, however, if the photopigments absorb light in different regions and have different structures the VRE could experience a wavelenght shift.

In this work, Chlorophyll a and a potential photopigment precursor called Phot0 …

Design And Application Of Smart Systems To Address Analytical Problems, Lucas B. Ayres

All Dissertations

This dissertation is a multidisciplinary effort that integrates low-cost analytical instrumentation, redox chemistry, and artificial intelligence to overcome existing limitations in the fields of wearable sensing technology, Deep Eutectic Solvents (DES), and antioxidant chemistry. The overall goal behind each implemented strategy is to enhance the accuracy, efficiency, and accessibility of analytical processes and technologies. A general overview of the thesis, along with the research outcomes is included in Chapter One. The theoretical framework of this dissertation is presented in Chapter Two. Chapter Three describes the development of a wearable platform (sensor and instrumentation) to rapidly detect (~20 minutes) S. aureus …

Modeling Sex-Specific Changes In Myocardial Fibrosis, Grace Martin

Chemical Engineering Undergraduate Honors Theses

Heart disease the leading cause of death for both men and women in the United States. Cardiac fibrosis, or accumulation of extracellular matrix proteins in the heart, can occur after a heart attack and increase the risk for further complications. Current treatments for heart disease do not include extracellular matrix regulators, partly due to the complicated signaling network responsible for the production of these proteins. By using a computational model of the signaling network in cardia fibroblasts, the relationship between particular molecules and downstream extracellular matrix production can be examined.

Biological sex is an important factor for cardiac health and …

Computational Investigation Of Transition Metal Photoredox Catalysis: Redox Property Tuning Via Ligand Modification, Christian Fernando Sandoval Pauker

Open Access Theses & Dissertations

In the last decade, photoredox catalysis has become a powerful tool in synthetic chemistry. It relies on the ability of catalytic systems that facilitate energy-demanding redox reactions thanks to photoinduced electron transfer processes. This dissertation focuses on the computational investigation of the redox properties of transition metal photoredox catalysts using density functional theory (DFT) calculations. The research systematically explores the effects of altering redox-active ligands on the thermodynamics of electron transfer events in the photoredox cycle. The electronic structure changes throughout oxidative and reductive quenching cycles are analyzed, with a particular focus on Cu(I) complexes. Through computational techniques, insights into …

Computational Study Of Fluorescent Molecular Probes For The Early Detection Of Alzheimer's Disease, Gabriela Elizabeth Molina Aguirre

Open Access Theses & Dissertations

Alzheimer's disease is a debilitating brain disorder that affects memory, thinking, and behavior. It is the most prevalent form of dementia and the seventh leading cause of death in the United States. As, researchers have identified biomarkers that can indicate the presence of the disease many years before the first symptoms appear, so there is an opportunity for early detection and treatment follow-ups, which could significantly improve the quality of life for those affected by this disease.This dissertation investigates the relationship between molecular structure and optical properties of donor-bridge-acceptor (DBA) fluorescent molecular probes designed for detecting Amyloid-β and p-Tau protein …

Methods For Computing Rovibrational Spectral Data With Applications To Inorganic Oxides And Hydrocarbons, Alexandria Watrous

Honors Theses

Computational chemistry focuses on finding solutions to the time-independent Schrödinger equation for systems of interest to study their molecular properties such as rovibrational spectral data. Any molecule containing more than one electron cannot be solved explicitly but coupled cluster theory offers one of the best approximations. One such application of this method is to molecules of astrochemical interest to support observation and experimental data. Chapters 2, 3, and 4 look at the performance of new couple cluster theory methods including composite and hybrid methods for ground and excited state rovibrational data. Chapters 5 - 9 use the previously mentioned methods …

Unlocking The Secret To Weight Loss: Discovering The Most Effective Green Tea Products, Seoyeon Kim

SACAD: Scholarly Activities

To find the most effective green tea product that can replace

weight loss drugs, we compared the amount of catechin in six

different green tea products. The result was green tea latte

powder contained a significantly small amount of catechin

compared to other products, and the dried pearl green tea leaves

had the highest amount of catechin. Also, the unexpected result

was that green tea supplements had less amount of catechin

compared to dried leaves or even tea bags that are commonly

sold in markets.

Decoding Molecular Recognition Mechanism Of Small Molecule Ligand-Rna Binding Pocket Systems Using Molecular Dynamics And Metadynamics, Zhixue Bai

Legacy Theses & Dissertations (2009 - 2024)

From my PhD research, under Amber99-Chen-Garcia force field, umbrella sampling and MD simulation helped us found that the 2’-5’ phosphodiester RNA backbone linkage modification on in vitro selected neomycin RNA aptamer can transfer it to ‘amikacin RNA aptamer’ by changing the conformation and backbone rigidity of the RNA binding pocket, which further influenced the binding mode and binding pathway of amikacin. Furthermore, under the same force field, metadynamics was found more powerful for simulating the binding pathway, binding mechanism and predicting binding modes of small molecule ligand recognizing its RNA target by filling up all energy basins on free energy …

Development Of On-The-Fly Quasi-Steady State Approximation For Chemical Kinetics In Cfd, Abhinav Balamurugan

Doctoral Dissertations and Master's Theses

This study analyzes the feasibility of On-The-Fly Quasi-Steady-State Approximation (OTF-QSSA) application for solving chemical kinetics within Computational Fluid Dynamics (CFD) simulations, aiming to reduce the computational demand of detailed mechanisms. An algorithm that dynamically identifies and designates Quasi-Steady-State (QSS) species at specific grid locations and instances during the simulation was developed. With this information, our method pseudo-delays the advancement of concentrations for these QSS species—effectively setting their rate of concentration change to zero for a set number iteration before updating using the detailed mechanism and thereby omitting the computationally intensive processes typically required for their calculation during those skipped iteration. …

Accurate Characterization Of Binding Kinetics And Allosteric Mechanisms For The Hsp90 Chaperone Inhibitors Using Ai-Augmented Integrative Biophysical Studies, Chao Xu, Xianglei Zhang, Lianghao Zhao, Gennady M. Verkhivker, Fang Bai

Mathematics, Physics, and Computer Science Faculty Articles and Research

The binding kinetics of drugs to their targets are gradually being recognized as a crucial indicator of the efficacy of drugs in vivo, leading to the development of various computational methods for predicting the binding kinetics in recent years. However, compared with the prediction of binding affinity, the underlying structure and dynamic determinants of binding kinetics are more complicated. Efficient and accurate methods for predicting binding kinetics are still lacking. In this study, quantitative structure–kinetics relationship (QSKR) models were developed using 132 inhibitors targeting the ATP binding domain of heat shock protein 90α (HSP90α) to predict the dissociation rate …