Chemistry Commons^™

Solvation Thermodynamic Mapping Approaches For Computer-Aided Drug Discovery, Vjay Molino

Dissertations, Theses, and Capstone Projects

The drug discovery process is inherently long and costly, prompting the development and integration of computational tools to mitigate these challenges. One of area explored in computer-aided drug discovery is to understand the role of solvation in protein-drug binding and to develop computational tools and methods that can be integrated in the drug discovery process. Grid Inhomogeneous Solvation Theory (GIST) is a tool that provides a framework for mapping solvation thermodynamiproperties of water molecules on the protein surface.This thesis explores the use of GIST in generating pharmacophore models and elucidates the role of solvation in protein structural fluctuations.

One of …

Novel Alchemical Methodologies For Modeling Molecular Binding, Solmaz Azimi

Dissertations, Theses, and Capstone Projects

Molecular recognition is fundamental to all biological and biochemical processes. Understanding the interactions between molecules is the foundation for drug discovery and development, for understanding biological processes, and for the design of biosensors and nanomaterials. There is tremendous interest in the development of computer models to predict molecular association equilibria. In structure-based drug discovery enterprises, predicting the strength and selectivity of a small molecule to a biological target can advance target identification, aid ligand design, and accelerate high-throughput screening of drug compounds. This work focuses on free energy models, a class of computational methodologies grounded on the fundamental physical and …

The Role Of Confined Hydration And Water Reorganization In Molecular Binding, Joe Z. Wu

Dissertations, Theses, and Capstone Projects

An important factor in guiding the development of drug discovery efforts is the comprehensive assessment of a ligand or drug’s ability to bind its receptor. The metric used to measure this interaction strength is by calculating the binding free energy (BFE). To achieve this accurately, we combine two concepts: (1) Grid Inhomogeneous Solvation Theory (GIST) returns the local water thermodynamic and structural contributions to free energy; and the (2) Alchemical Transfer Method (ATM) obtains the absolute (ABFE) and relative binding free energy (RBFE) estimates between ligand pairs. In this work, we employ Alchemical Water-Transfer to tether bridging water(s) during the …

Introduction To Epr, Gareth R. Eaton

TeachEPR Submissions

A very brief introduction to the scope of EPR at the beginning of a workshop in 2019.

Anisotropy Of Nitroxide Radicals, Gareth R. Eaton

TeachEPR Submissions

The special utility of nitroxide radicals for probing orientation and motion depends on the anisotropy of g-values and hyperfine values, especially the ¹⁴N hyperfine.

Workshop On Rapid Scan Epr, Gareth R. Eaton, Arthur H. Heiss, Deborah Gale Mitchell, Joshua R. Biller, Richard W. Quine, George A. Rinard, Mark Tseitlin, Sandra S. Eaton

TeachEPR Submissions

An introduction to the method of rapid scan EPR is given with emphasis on the design of rapid scan coils, selection of scan parameters, and the reasons that the method improves signal to noise per unit time.

Concentration Effects On Nitroxides, Gareth R. Eaton

TeachEPR Submissions

We need to distinguish line broadening due to restricted motion from line broadening due to concentration of the same or other paramagnetic species. For example, if you increase the concentration of nitroxyl to get better S/N, the lines will broaden due to collisions with other nitroxyl molecules.

Copper Line Shapes, Gareth R. Eaton

TeachEPR Submissions

The spectrum of Cu²⁺ has 4 lines, since I = 3/2. Cu has two major isotopes, ⁶³Cu (69.2%) and ⁶⁵Cu (30.8%). The magnetic moment of ⁶⁵Cu is 7% larger than that for ⁶³Cu, so the hyperfine coupling is 7% larger. If the lines are narrow enough, one can observe superposition of spectra due to complexes of the two isotopes.

Workshop On Selecting An Epr Resonator, Gareth R. Eaton

TeachEPR Submissions

Guidance is presented to help select a resonator to optimize a measurement. Different resonator types are described with information about resonator Q and microwave power efficiency.

Workshop presented at the 28th International EPR Symposium on July 31, 2005.

Understanding Anionic Hyperporphyrins: Tddft Calculations On Peripherally Deprotonated Meso-Tetrakis(4-Hydroxyphenyl)Porphyrin., Jeanet Conradie, Carl C. Wamser, Abhik Ghosh

Chemistry Faculty Publications and Presentations

Presented herein is a DFT/TDDFT study of -tetrakis(4-hydroxyphenyl)porphyrin (H[THPP]) and its Meso-deprotonated tetraanionic form; the latter was modeled as both a free tetraanion and with various counterions. Based on our calculations, the experimentally observed hyperporphyrin spectra are attributed to an admixture of phenol/phenoxide character into the a-type HOMO of tetraphenylporphyrin. The admixture results in an elevation of the orbital energy of the HOMO in relation to other frontier orbitals, which accounts for the observed spectral redshifts. The calculations underscore differences in the performance of different exchange-correlation functionals. Thus, while the popular hybrid functional B3LYP greatly exaggerates the redshift of …

An Effective Secure Multi-Objective Task Scheduling Algorithm In Multi-Cloud Environment, V K S K Sai Vadapalli, Ramesh Babu Gurujukota, Phaneendra Varma Chintalapati, Satyanarayana Murty, G. Sai Chaitanya Kumar, Satish Kumar Kode

Karbala International Journal of Modern Science

In cloud environments, task scheduling is essential for improving performance. Nevertheless, the existence of several heterogeneous clouds makes scheduling extremely difficult, requiring increasingly advanced algorithms to manage these environments' diversity and dynamic nature. To solve this, numerous authors have created a variety of task schedulers utilizing heuristic and metaheuristic techniques. Nevertheless, it remains dynamic and challenging because task scheduling is an NP-hard issue. Furthermore, in many complicated situations, it is still problematic to guarantee security throughout the task’s execution. Therefore, this paper introduces a multi-objective security-aware task scheduler using the Crayfish Mud Ring Optimization Algorithm for a multi-cloud environment. This …

In Memoriam - Nora Sabelli: Master Orchestrator Of Grant Programs And Mentor For Advancing The Interdisciplinary Learning Sciences Field, Eric Hamilton, Jeremy Roschelle, Roy Pea, Barbara Means, Louis Gomez, Kim Gomez, Nancy Butler Songer

Education Division Scholarship

On Friday, September 6, 2024, the learning sciences field lost a giant in Dr. Nora Sabelli, 87 years old, a personal mentor to many researchers and an inspiration to so many learning scientists and STEM leaders. Nora’s first professional career was as a computational chemist, and later she became a passionate leader in research for improving STEM education. Nora’s time as a senior program officer at the National Science Foundation’s (NSF) Education and Human Resources (EHR) directorate was legendary; she was a force of nature who reshaped funding priorities for stronger science and a stronger connection of science to education …

Development And Evaluation Of Butyl Norbornene Based Cross-Linked Anion Exchange Membranes For Enhanced Nonaqueous Redox Flow Battery Efficiency, M. Motiur Mazumder, Hazel Gerber, Paul A. Kohl, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Nonaqueous redox flow batteries (NARFBs) have been plagued by the lack of appropriate separators to prevent crossover. In this article, the synthesis and characterization of poly(norbornene) (PNB) anion-exchange membranes (AEMs) were studied. PNB is a copolymer of butyl norbornene (BuNB) and bromobutyl norbornene (BrBuNB) with varying amounts of tetramethyl hexadiamine cross-linker. The performance of the AEMs was investigated in nonaqueous redox flow batteries under ideal conditions. Performance evaluation encompassed several key factors, including durability in a nonaqueous solvent, charge-carrying ions permeability, electric cell resistance, crossover of redox-active molecules, and mechanical properties. The BuNB-based AEMs outperformed the commercial Fumasep membrane in …

A Cnt Intercalated Co Porphyrin-Based Metal Organic Framework Catalyst For Oxygen Reduction Reaction, Pei-Pei He, Jin-Hua Shi, Xiao-Yu Li, Ming-Jie Liu, Zhou Fang, Jing He, Zhong-Jian Li, Xin-Sheng Peng, Qing-Gang He

Journal of Electrochemistry

The poor electronic conductivity of metal-organic framework (MOF) materials hinders their direct application in the field of electrocatalysis in fuel cells. Herein, we proposed a strategy of embedding carbon nanotubes (CNTs) during the growth process of MOF crystals, synthesizing a metalloporphyrin-based MOF catalyst TCPPCo-MOF-CNT with a unique CNT-intercalated MOF structure. Physical characterization revealed that the CNTs enhance the overall conductivity while retaining the original characteristics of the MOF and metalloporphyrin. Simultaneously, the insertion of CNTs generated adequate mesopores and created a hierarchical porous structure that enhances mass transfer efficiency. X-ray photoelectron spectroscopic analysis confirmed that the C atom in CNT …

New Insights Into Controlling The Functional Properties Of Tin Oxide-Based Materials, Alexandra Kuriganova, Nina Smirnova

Journal of Electrochemistry

Development of methodologies for fabrications of nanostructured materials that provide control over their microstructural features and compositions represents a fundamental step in the advancement of technologies for productions of materials with well-defined functional properties. Pulse electrolysis, a top-down electrochemical approach, has been demonstrated to be a viable method for producing nanostructured materials with a particular efficacy in the synthesis of tin oxides. This method allows for significant control over the composition and shape of the resulting tin oxides particles by modifying the anionic composition of the aqueous electrolyte, obviating the need for additional capping agents in the synthesis process and …

Nanostructured Graphitic Carbon Nitride For Photocatalytic And Electrochemical Applications, Muhammad Abdul Qadeer, Iqra Fareed, Asif Hussaine, Muhammad Asim Farid, Sadia Nazir, Faheem K. Butt, Ji-Jun Zou, Muhammad Tahir, Shang-Feng Du

Journal of Electrochemistry

Graphitic carbon nitride (g-C₃N₄) exhibits great mechanical as well as thermal characteristics, making it a valuable material for use in photoelectric conversion devices, an accelerator for synthesis of organic compounds, an electrolyte for fuel cell applications or power sources, and a hydrogen storage substance and a fluorescence detector. It is fabricated using different methods, and there is a variety of morphologies and nanostructures such as zero to three dimensions that have been designed for different purposes. There are many reports about g-C₃N₄ in recent years, but a comprehensive review which covers nanostructure dimensions …

Interaction Of N-Methylmesoporphyrin Ix With A Hybrid Left-/Right-Handed G-Quadruplex Motif From The Promoter Of The Slc2a1 Gene, Paul Seth , '23, Eric Xing , '26, Andrew D. Hendrickson , '27, Kevin Li , '22, R. Monsen, J. B. Chaires, S. Neidle, Liliya A. Yatsunyk

Chemistry & Biochemistry Faculty Works

Left-handed G-quadruplexes (LHG4s) belong to a class of recently discovered noncanonical DNA structures under the larger umbrella of G-quadruplex DNAs (G4s). The biological relevance of these structures and their ability to be targeted with classical G4 ligands is underexplored. Here, we explore whether the putative LHG4 DNA sequence from the SLC2A1 oncogene promoter maintains its left-handed characteristics upon addition of nucleotides in the 5′- and 3′-direction from its genomic context. We also investigate whether this sequence interacts with a well-established G4 binder, N-methylmesoporphyrin IX (NMM). We employed biophysical and X-ray structural studies to address these questions. Our results indicate that …

Immuno-Bioinformatics Study Of Secondary Metabolites From Watercress Nasturtium Officinale As Immunostimulant In Whiteleg Shrimp Litopenaeus Vannamei By Targeting Peroxinectin And Scavenger Receptor Class B, Qurrota A’Yunin, Muhaimin Rifa’I, Maftuch Maftuch, Yoga Dwi Jatmiko, Muhammad Hermawan Widyananda, Triyanto Triyanto, Muhammad Tegar Handrianto

Karbala International Journal of Modern Science

The viral disease affects the whiteleg shrimp (Litopenaeus vannamei) and causes losses. Immunostimulants are recognized as a more environmentally friendly approach to disease management and antimicrobial properties of aquatic organisms. Watercress (Nasturtium officinale) is an aquatic plant species that contains antioxidant properties that can protect the organism from disease and boost the immune system. Shrimp rely heavily on innate immunity to combat infectious agents due to their absence of adaptive immunity. Peroxinectin and scavenger receptor class B (SRB) play essential roles in the shrimp defense system. This research employs a bioinformatic to assess the immunostimulatory potential …

Selectivity Effects Of Hydrogen Acceptors And Catalyst Structures In Alcohol Oxidations Using (Cyclopentadienone)Iron Tricarbonyl Compounds, Timothy Funk, Melanie Hempel, Auden Cameron Lampariello, Nicolle Elahian Lopez, Cole Springer, Kimberly Mccaskey, Sneha Jayaram, Kathryn Wnuk-Fink, Bryn Werley

Chemistry Faculty Publications

Oppenauer-type oxidations are catalyzed by air- and moisture-stable, sustainable, (cyclopentadienone)iron carbonyl compounds, but the substrate scope is limited due to the low reduction potential of acetone, which is the most commonly used hydrogen acceptor. We discovered that furfural, an aldehyde derived from cellulosic biomass, is an effective hydrogen acceptor with this class of catalysts. In general, reactions using furfural as the hydrogen acceptor led to higher isolated yields of ketones and aldehydes compared to those using acetone. Importantly, primary benzylic and allylic alcohols─typically a challenging class of alcohols to oxidize with these catalysts─could be oxidized. The selectivity for primary vs …

Chemistry Of Metalloguanines: An Overview Of Their Synthesis Routes And Their Implementations For The Period 2000-2024, Farah Saadoon Jaafar, Mahasin F. Alias

Karbala International Journal of Modern Science

Guanine has a variety of roles in chemistry, from its basic function in the storing and transferring genetic information to its usages in synthetic chemistry and other fields. Because of its distinct structure and biological importance, it is a fundamental component of contemporary study in organic chemistry and molecular biology.

In this review, we focused on covering the synthetic pathways of various derivatives of guanine from the year 2000 until the present. As a result of the guanine molecule containing multiple functional groups, this gives us the ability to prepare several guanines such as O⁶-alkylating guanines, O^{6 …}

A Sensitivity Analysis Of The Modeling Of Polycyclic Aromatic Hydrocarbon Emission In Galaxies, A. Maragkoudakis, C. Boersma, P. Temi, J. D. Bregman, L. J. Allamandola, Vincent J. Esposito, A. Ricca, E. Peeters

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We have conducted a sensitivity analysis on the mid-infrared spectral decomposition of galaxies and the modeling of the polycyclic aromatic hydrocarbon (PAH) emission spectrum with the NASA Ames PAH Infrared Spectroscopic Database (PAHdb) to assess the variance on the average galaxy PAH population properties under a grid of different modeling parameters. We find that the short-low and short-low+long-low Spitzer-IRS decomposition with PAHFIT provides consistent modeling and recovery of the 5–15 μm PAH emission spectrum. For PAHdb modeling, application of a redshift to the calculated spectra to account for anharmonic effects introduces a 15%–20% variance on the derived parameters, while its …

Computational Investigation Of The Unveils Nsd2 Inhibition Potential Of Berberis Vulgaris, Sambucus Nigra, And Morus Alba Through Virtual Screening, Molecular Docking, Md Simulation, And Dft Analyses, Supriyo Saha, Vanshita Gupta, Ahad Hossain, Prinsa Prinsa, Jannatul Ferdous, Kiran Bharat Lokhande, Vikash Jakhmola, Sarkar M. A. Kawsar

Karbala International Journal of Modern Science

Nuclear receptor binding set domain protein 2 (NSD2) plays a key role in chromatin regulation and is associated with different cancers and other developmental problems. Berries are rich in major secondary metabolites with anticancer properties. Here, we virtually screened 145 berry phytochemicals as putative NSD2 inhibitors via structure-based virtual screening, molecular docking, MD simulations, and DFT and ADMET analyses. Among them, α-carotene had the maximum docking score of -9.9 kcal/mol, followed by sulfuretin and β-amyrin. MD simulation analysis revealed that the dynamic behavior of the ligand‒NSD2 complexes was within the limit, indicating no significant changes in the structural integrity of …

Antimicrobial Effect Of Herbs Extracted With Ethanol Compared To Ampicillin, Brianna Neilan, Laura Rowe

Posters-at-the-Capitol

Antibiotics are commonly used to treat bacterial infections within the medical field, however there are growing concerns of antibiotic resistance. Before the introduction of antibiotics herbs were commonly used to treat infections, and herbal medicine is still used in many communities and cultures. Bacteria’s increasing resistance to traditional antibiotics has caused herbal medicines to become a significant research topic recently. Methods of herbal medicine preparation include preparing teas using hot water, and tinctures that soak herbs in alcohol for several weeks. Previous research has shown significant antimicrobial effects of some herbs when soaked in water and other liquids. The aim …

Photolysis And Sublimation Chemistry Of Ammonium Cyanide With Relevance To Cometary Environments, O. H. Wilkins, K. M. Yocum, Vincent J. Esposito, E. Harel, S. N. Milam, P. A. Gerakines

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Bulk nitrogen is depleted in solar system objects, including the terrestrial planets, chondritic meteorites, and comets. Recently, it was suggested that cometary nitrogen may be locked up in ammonium salts—ionic solids comprising ammonia (NH₃) and an acid such as hydrogen cyanide (HCN)—based on Rosetta/ROSINA data from comet 67P/Churyumov–Gerasimanko. Among the proposed salts to have been found in 67P were ammonium cyanide (NH₄CN) and ammonium cyanate (NH₄OCN), which were inferred from identifying HCN, cyanamide (NH₂CN), and isocyanic acid (HNCO) in the mass spectrometry data collected in the coma of 67P. However, the relationship …

Associations Between Social Determinants Of Health And Mental Health Disorders Among U.S. Population: A Cross-Sectional Study, S. Tanarsuwongkul

Faculty Publications

Aims

The impact of social determinants of health (SDOH) on mental health is increasingly realized. A comprehensive study examining the associations of SDOH with mental health disorders has yet to be accomplished. This study evaluated the associations between five domains of SDOH and the SDOH summary score and mental health disorders in the United States.

Methods

We analyzed data from a diverse group of participants enrolled in the All of Us research programme, a research programme to gather data from one million people living in the United States, in a cross-sectional design. The primary exposure was SDOH based on Healthy …

Umbrella Sampling Md Simulations For Retention Prediction In Peptide Reversed-Phase Liquid Chromatography., Pablo M Scrosati, Evelyn H Mackay-Barr, Lars Konermann

Chemistry Publications

Reversed-phase liquid chromatography (RPLC) is an essential tool for separating complex mixtures such as proteolytic digests in bottom-up proteomics. There is growing interest in methods that can predict the RPLC retention behavior of peptides and other analytes. Already, existing algorithms provide excellent performance based on empirical rules or large sets of RPLC training data. Here we explored a new type of retention prediction strategy that relies on first-principles modeling of peptide interactions with a C18 stationary phase. We recently demonstrated that molecular dynamics (MD) simulations can provide atomistic insights into the behavior of peptides under RPLC conditions (Anal. …

Tribological, Thermal, Kinetic, And Surface Microtextural Characterization Of Prime P-Type <100> Silicon Wafer Cmp For Direct Wafer Bonding Applications, Michelle Yap, Catherine Yap, Yasa Sampurno, Glenn Whitener, Jason Keleher, Len Borucki, Ara Philipossian

Chemistry Department Faculty Articles

We investigated the tribological, thermal, kinetic, and surface microtextural characteristics of chemical mechanical polishing (CMP) of 300 mm p-type <100> prime silicon wafers (and their native oxide) at various pressures, sliding velocities, and starting platen temperatures. Results showed the dominant tribological mechanism for both native oxide and silicon polishing to be boundary lubrication. Using frictional data, we pinpointed the exact time that corresponded to the total removal of the native oxide and the onset of silicon polishing. This allowed us to separately characterize removal rates of each layer. For native oxide, while the rate depended on temperature, the presence of a …

Synthesis And Characterization Of Bimetallic Plasmonic Nanoparticles Using Linear And Nonlinear Spectroscopy, Daniel Babayode

LSU Doctoral Dissertations

Recent exploration in the field of nanomaterials has led to the investigation of noble metal nanoparticles for various nanomedical applications. The spectroscopy of these nanoparticles is studied using both linear and nonlinear optical processes such as second harmonic generation (SHG), two-photon fluorescence (TPF), and extinction spectroscopy. Details pertaining to the growth dynamics of silver-gold core-shell (Ag@Au CS) nanoparticles (NPs) and gold-silver-gold core-shell-shell (Au@Ag@Au CSS) nanoparticles (NPs) are currently being investigated in order to obtain better control and optimization of the nanoparticle size and surface morphology. Transmission electron microscopy (TEM) images show that the nanoparticles have tunable core and shell sizes …

Development Of Momordica Saponin-Based Vaccine Adjuvants, Hyunjung Kim

All ETDs from UAB

Vaccine adjuvants are indispensable substances that help induce a fast, potent, and durable immune response when administered with vaccine antigens. Among the FDA-approved vaccine adjuvants for human use, three of the most recently approved ones contain saponin adjuvant QS-21. To address QS-21’s inherent drawbacks, we investigated the adjuvant activity of a series of saponin-based semisynthetic vaccine adjuvants, including VSA-1 and VSA-2, prepared from natural Momordica saponins I and II in one-step. The natural saponins precursors are isolated from the widely available and inexpensive seeds of Momordica cochinchinensis SPRENG. In general, VSA adjuvants can enhance both humoral and cellular immune responses …

Targeting Streptococcus Mutans Diadenylate Cyclase For The Prevention Of Dental Caries, Edwin Miguel Rojas

All ETDs from UAB

Streptococcus mutans (S. mutans) is the primary etiological agent involved in the initiation and progression of dental caries. S. mutans forms robust biofilms on the tooth surface, and current preventative treatments, such as oral rinses, eliminate both pathogenic and commensal oral species. Therefore, there is an urgent need for therapeutics which selectively inhibit S. mutans biofilms while keeping the oral microbiome intact. The diadenylate cyclase (DAC) enzyme in S. mutans plays a key role in biofilm formation. DAC converts adenosine triphosphate (ATP) into cyclic di-AMP (c-di-AMP), a secondary messenger involved in several cellular pathways. Increased levels of c-di-AMP have shown …