Chemistry Commons^™

College Of Natural Sciences Newsletter, September 2021, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 2, Issue 9.

Page 1 Dean's Message
Page 2 Awards and Recognition
Page 3 Student Clubs in Natural Science
Page 4 Media Coverage of CNS
Page 5 Hobo Day Festivities
Page 6 Open PRAIRIE Data; Grants Awarded in CNS
Page 7 One Day for State Recap

Utah - Perry Port Of Entry 2020, University Of Denver

FEAT Heavy-Duty Vehicle Measurements

Relevant Publications

Environmental Science & Technology publication.

Utah DEQ Final Report

Washington - Feat Bridge Based Train Measurements 2012, University Of Puget Sound

Non-Road Vehicle Data

Relevant Publications

Atmospheric Environment Publication (2019)

Mechanically Transduced Immunosorbent Assay To Measure Protein-Protein Interactions, Christopher J. Petell, Kathyrn Randene, Michael Pappas, Diego Sandoval, Brian Dstrahl, Joseph S. Harrison, Joshua P. Steimel

College of the Pacific Faculty Articles

Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus …

Laboratory Capabilities, University Of North Dakota. Energy And Environmental Research Center

EERC Brochures and Fact Sheets

Fact sheet about the Energy & Environmental Research Center’s laboratory capabilities including reservoir characterization, organic geochemistry, fluid sampling, and material analysis. A list of publications and laboratory information is also included.

Instrumentation For Routine Analysis Of Acrylamide In French Fries: Assessing Limitations For Adoption, Mark M. Skinner, Jared T. Seale, Maranda S. Cantrell, Joseph M. Collins, Matthew W. Turner, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

The purpose of this experimental review was to detect acrylamide in French fries using methods most adaptable to the food process industry for quality control assessment of products. French fries were prepared at different cook times using the same fryer oil over a five-day period to assess the influence of oil degradation and monitor trends in acrylamide formation. Acrylamide detection was performed using LC-MS, GC-MS and FT-NIR. The low levels of acrylamide produced during frying, low molecular weight of the analyte, and complexity of the potato matrix make routine acrylamide measurement challenging in a well-outfitted analytical lab with trained personnel. …

Genotype, Age, Genetic Background, And Sex Influence Epha2-Related Cataract Development In Mice, Alpana Dave, Jamie E. Craig, Mohammad Alamein, Karina Skrzypiec, Justin Beltz, Annalise Pfaff, Kathryn P. Burdon, Nuran Ercal, Robb U. De Iongh, Shiwani Sharma

Chemistry Faculty Research & Creative Works

PURPOSE. Age-related cataract is the leading cause of blindness worldwide. Variants in the EPHA2 gene increase the disease risk, and its knockout in mice causes cataract. We investigated whether age, sex, and genetic background, risk factors for age-related cataract, and Epha2 genotype influence Epha2-related cataract development in mice.

METHODS. Cataract development was monitored in Epha2⁺/⁺, Epha2^+/-, and Epha2^-/- mice (Epha2^{Gt(KST085)Byg}) on C57BL/6J and FVB:C57BL/6J (50:50) backgrounds. Cellular architecture of lenses, endoplasmic reticulum (ER) stress, and redox state were determined using histological, molecular, and analytical techniques.

RESULTS. Epha2^-/- and Epha2^{+/- …}

Molecular Dynamics Simulations Of Self-Assemblies In Nature And Nanotechnology, Phu Khanh Tang

Dissertations, Theses, and Capstone Projects

Nature usually divides complex systems into smaller building blocks specializing in a few tasks since one entity cannot achieve everything. Therefore, self-assembly is a robust tool exploited by Nature to build hierarchical systems that accomplish unique functions. The cell membrane distinguishes itself as an example of Nature’s self-assembly, defining and protecting the cell. By mimicking Nature’s designs using synthetically designed self-assemblies, researchers with advanced nanotechnological comprehension can manipulate these synthetic self-assemblies to improve many aspects of modern medicine and materials science. Understanding the competing underlying molecular interactions in self-assembly is always of interest to the academic scientific community and industry. …

Evaluation Of The Potential Of Automated Sem-Eds Analysis For The Discrimination Of Inorganic Soil Particles, Anna S. Duggar

Dissertations, Theses, and Capstone Projects

Soil, that complex mixture of minerals, organic particles, chemicals, and anthropogenic materials, is ubiquitous and easily transferred, which gives it forensic relevance. Forensic soil analysis has traditionally included the identification and comparison of both organic and inorganic components, the inorganic portion being most commonly examined by light microscopy and other instrumental techniques. Predominantly, the inorganic materials in soil are naturally-occurring minerals, contributed as grains from the surrounding bedrock, which gives a soil its regional character. That parent material then undergoes physical, chemical, and anthropogenic changes producing wide geographic variation within a single region. This variation forms the basis for potential …

Automated Code Engine For Tensor Hypercontraction: Derivation, Optimization And Implementation Of Rank-Reduced Coupled Cluster Theories, Yao Zhao

Dissertations, Theses, and Capstone Projects

The ultimate goal of electronic structure theory is solving the electronic Schr¨odinger Equation. However, even accurate approximations of solving Schr¨odinger Equation, such as high order coupled cluster theories, require computational efforts that are too demanding to be applied on large chemical systems. This thesis tackles the problem of curse of dimensionality: how to reduce the time complexity of high-accuracy coupled cluster methods in order to accelerate computations of molecular energy. On one hand, we believe that low-rank approximation (i.e. Tensor HyperContraction) of high-order tensors appearing in coupled cluster theory is a promising way to achieve rank-reduced coupled cluster theory. On …

Development Of An Lcms Analytical Method With Applicability To Determination Of Trace Level Explosives In Environmental Waters, Cristina I. Veresmortean

Dissertations, Theses, and Capstone Projects

Traces of explosives and their degradation products present in explosives contaminated sites from military sources, such as training facilities, impose a great concern over the public health and our eco-system. This work is centered around finding an efficient way to extraction of these chemicals from water samples and their analysis using advanced separation technology: LC-MS/MS Shimadzu Prominence 8050 and AB Sciex Trap 4000 LC-MS/MS. Different extraction methods will be proposed, along with chromatographic and mass spectroscopy method development. Dependent on the target analyte polarity, thermal degradation, solubility and type of matrix, an appropriate method of analysis will be established. The …

Enhanced Platinum (Ii) Drug Delivery For Anti-Cancer Therapy, Marek T. Wlodarczyk

Dissertations, Theses, and Capstone Projects

Over the years, anti-cancer therapies have improved the overall survival rate of patients. Nevertheless, the traditional free drug therapies still suffer from side effects and systemic toxicity, resulting in low drug dosages in the clinic. This often leads to suboptimal drug concentrations reaching cancer cells, contributing to treatment failure and drug resistance. Among available anti-cancer therapies, metallodrugs are of great interest. Platinum (II)-based agents are highly potent and are used to treat many cancers, including ovarian cancer (OC). Cisplatin (cis-diaminedichloroplatinum (II)) is the first Food and Drug Administration (FDA)-approved metallodrug for treatment of solid tumors, and its mechanism …

Tools And Strategies For The Patterning Of Bioactive Molecules And Macromolecules, Daniel J. Valles

Dissertations, Theses, and Capstone Projects

Hypersurface Photolithography (HP) is a printing method for fabricating structures and patterns composed of soft materials bound to solid surfaces and with ~1 micrometer resolution in the x, y, and z dimensions. This platform leverages benign, low intensity light to perform photochemical surface reactions with spatial and temporal control of irradiation, and, as a result, is particularly useful for patterning delicate organic and biological material. In particular, surface- initiated controlled radical polymerizations can be leveraged to create arbitrary polymer and block- copolymer brush patterns. Chapter 1 will review the advances in instrumentation architectures from our group that have made these …

Dissecting Monomer-Dimer Equilibrium Of An Rnase P Protein Provides Insight Into The Synergistic Flexibility Of 5’ Leader Pre-Trna Recognition, Danyun Zeng, Ainur Abzhanova, Benjamin P. Brown, Nicholas J. Reiter

Chemistry Faculty Research and Publications

Ribonuclease P (RNase P) is a universal RNA-protein endonuclease that catalyzes 5’ precursor-tRNA (ptRNA) processing. The RNase P RNA plays the catalytic role in ptRNA processing; however, the RNase P protein is required for catalysis in vivo and interacts with the 5’ leader sequence. A single P RNA and a P protein form the functional RNase P holoenzyme yet dimeric forms of bacterial RNase P can interact with non-tRNA substrates and influence bacterial cell growth. Oligomeric forms of the P protein can also occur in vitro and occlude the 5’ leader ptRNA binding interface, presenting a challenge in accurately defining …

Differential Effects Of Polyphenols On Insulin Proteolysis By The Insulin-Degrading Enzyme, Qiuchen Zheng, Micheal T. Kebede, Bethany Lee, Claire A. Krasinski, Saadman Islam, Liliana A. Wurfl, Merc M. Kemeh, Valerie A. Ivancic, Charles E. Jakobsche, Donald E. Spratt, Noel Lazo

Chemistry

The insulin-degrading enzyme (IDE) possesses a strong ability to degrade insulin and Aβ42 that has been linked to the neurodegeneration in Alzheimer’s disease (AD). Given this, an attractive IDE-centric strategy for the development of therapeutics for AD is to boost IDE’s activity for the clearance of Aβ42 without offsetting insulin proteostasis. Recently, we showed that resveratrol enhances IDE’s activity toward Aβ42. In this work, we used a combination of chromatographic and spectroscopic techniques to investigate the effects of resveratrol on IDE’s activity toward insulin. For comparison, we also studied epigallocatechin-3-gallate (EGCG). Our results show that the two polyphenols affect the …

Synthesis, Characterization And Applications Of Europium Based Perovskite Oxide Nanoparticles, Nasim Farahmand

Dissertations, Theses, and Capstone Projects

The synthesis and characterization of nanocrystalline transition and rare-earth metal oxides have been studied widely over the past years. These materials possess unique physical, chemical, magnetic and dielectric properties which make them potential candidates for a wide range of applications such as electronics, energy storage and photocatalysis. There are a number of synthesis methods for preparing these materials, where most of them require stringent conditions such as high pressure and high temperature. However, in this study, a modified sol-gel synthesis has been used with a lower calcination temperature to make uniform nanocrystals of the transition/rare-earth metal oxide family. The focus …

Don't Sell Them Short, There's More To Bacterial Natural Products Than Antibiotics, Alison Clare Domzalski

Dissertations, Theses, and Capstone Projects

Recent genomic studies of microbiomes have revealed an overwhelming number of biosynthetic genes of unknown function. Most of these “cryptic” biosynthetic genes are not expressed in laboratory monocultures of individual microbes. Thus, there remains tremendous untapped potential for natural products discovery. Here we employ mixed microbial culture (MMC) as a simple yet powerful approach to awaken cryptic biosynthetic gene clusters. Our preliminary studies demonstrated that arrays of metabolites could be induced in MMCs upon environmental cues, such as surface adhesion. Using this system, we have screened, identified, and isolated bioactive bacterial metabolites, which were characterized structurally and biologically. Of the …

Electronic Structures And Spectroscopic Signatures Of Diiron Intermediates Generated By O2 Activation Of Nonheme Iron(Ii)–Thiolate Complexes, Danushka M. Ekanayake, Dao Pham, Andrew L. Probst, Joshua R. Miller, Cordina V. Popescu, Adam T. Fiedler

Chemistry Faculty Research and Publications

The activation of O₂ at thiolate–ligated iron(II) sites is essential to the function of numerous metalloenzymes and synthetic catalysts. Iron–thiolate bonds in the active sites of nonheme iron enzymes arise from either coordination of an endogenous cysteinate residue or binding of a deprotonated thiol-containing substrate. Examples of the latter include sulfoxide synthases, such as EgtB and OvoA, that utilize O₂ to catalyze tandem S–C bond formation and S-oxygenation steps in thiohistidine biosyntheses. We recently reported the preparation of two mononuclear nonheme iron–thiolate complexes (1 and 2) that serve as structural active-site models of substrate-bound EgtB …

Evaluation Of Wind Data Reliability By Using Logarithmic And Power Laws: A Case Study In Southern Iraq, Ahmed B. Khamees, Saif F. Yaseen, Khalid S. Heni, Mudar Ahmed Abdulsattar

Karbala International Journal of Modern Science

In this study, two sites were investigated in the southern region of Iraq: Ali AL-Gharbi and AL-Salman in Mesan and AL-Muthana provinces, respectively. A theoretical extrapolation between wind speed and height was carried out for both locations each month using the Logarithmic Law. Power Law was also applied to achieve calculations of wind shear coefficient (α) by using the actual data collected from the meteorological mast installed in each site at three levels of 10 m, 30 m, and 50 m, at an interval of ten minutes. To compare the effects of each law, two laws are employed.

Polystyrene Molecular Weight Determination Of Submicron Particles Shell, Airat Z. Sakhabutdinov, Safaa.M.R.H. Hussein, Alsu R. Ibragimova Ph.D., Vladimir Kuklin Ph.D., Maxim Petrovich Danilaev, L.Y. Zaharova

Karbala International Journal of Modern Science

The method of determination of the molecular weight of the polystyrene, which is formed as the shell on the surfaces of submicron aluminum oxide particles is considered in the paper. This method is based on the sedimentation of submicron particles, covered by polymer molecules, in a solvent for polystyrene. It is shown that the average polystyrene molecular weight is 39500±11250 amu, when the polymer shells on the surfaces of submicron particles (Al2O3) are formed by the vapor-phase method.

Adaptive Reconstruction Of The Heterogeneous Scan Line Etm+ Correction Technique, Heba Kh. Abbas, Salema S. Salman, Rash Awad Abtan, Anwar H. Al-Saleh, Ali A. Al-Zuky

Karbala International Journal of Modern Science

ETM+ is a land-imaging sensor with great and wide use in many fields, however, after May 2003, because of a technical defect in the sensor´s system scan line corrector SLC, it started giving images of earth containing black gap lines at a 22% rate. These gaps made the process of analyzing and extracting accurate information from these images difficult and complicated. Therefore, scientists have developed many techniques to remove the gap lines from all ETM+ band-images and complete the missing data. In this study, three different ETM+ time images with a 16-day interval between them were used to fill gap …

Two-Dimensional Quantitative Profiling Of Cell Morphology With Serous Effusion By Unsupervised Machine Learning Analysis, Safaa Al-Qaysi Ph.D., Ding Dai Md Ph.D., Heng Hong Md Ph.D., Yuhua Wen Ph.D., X.H. Hu Ph.D.

Karbala International Journal of Modern Science

Cytological evaluation of serous effusion specimens is an important part of cancer diagnosis. In this study we performed two-dimensional (2D) morphometric features and clustering analysis for development of useful techniques for identification and differentiation of malignant and begin cells in serous effusion specimens extracted from ten patients with clinical symptoms of pleural and peritoneal effusion. Our findings show that the two-dimensional (2D) morphometric features and clustering analysis are useful techniques for identification and differentiation of malignant and begin cells in serous effusion specimens, which can lead to development of new methods for rapid cells profiling in clinical application.

Modeling Vitexin And Isovitexin Flavones As Corrosion Inhibitors For Aluminium Metal, Abdullahi Muhammad Ayuba, Umaru Umar

Karbala International Journal of Modern Science

Theoretically, the aluminium corrosion inhibitive performance of vitexin (VTX) and isovitexin (SVT) were evaluated with a view of establishing the mechanism of the inhibition process. Calculations which include the consideration of several global descriptors were studied to describe and correlate the reactivity of the molecules with the computed descriptors. First and second-order condensed Fukui functions were employed to analyze local reactivity parameters, while simulations involving the adsorbed molecules on Al (1 1 0) surface were conducted through quench dynamic simulations and the mechanism of physical adsorption was established with SVT relatively been a better inhibitor on Al surface than VTX.

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

High Speed Impact On Graphene Composites, Giovanny A. Espitia

Symposium of Student Scholars

Since the isolation of Graphene occurred in 2004, numerous studies attempting to exploit the properties of this carbon allotrope have been conducted. Graphene exists in a 2-D manner with sp2 bonds, which provides the allotrope with great electrical, conductive, and mechanical properties. In this paper however, we will focus on the latter in order to examine the feasibility of graphene composites for bulletproof material in the military. Pure graphene sheets count with high porosity density that leads to structural defects as well as poor mechanical properties due to physical contact being sole retainer. For this reason, the selected composite is …

Investigating The Proton Transfer Dynamics And Vibrational Spectrum Of Hydrogen Oxalate Using Driven Molecular Dynamics Simulations, Martina Kaledin, Dominick Pierre-Jacques, Olivia Cochran, Dayana Salazar, Dalton Boutwell, Martina Kaledin

Symposium of Student Scholars

In this computational chemistry work, we describe ab initio calculations and assignment of infrared (IR) spectra of an intramolecular H-bonding system hydrogen oxalate, C₂O₄H^–. The mechanism and dynamics of proton transfer are of fundamental importance in chemistry and biology. In C₂O₄H^–, proton transfer occurs along the non-linear path. Previous experimental studies are signaling very strong coupling between OH stretch mode and low frequency motions. We calculated IR spectra at 300 K using the direct molecular dynamics (MD) method at the MP2/ aug-cc-pVDZ level of theory and assigned the …

Molecular Vibrations Of Symmetric Molecules: Raman Scattering Driven Molecular Dynamics Method, Martina Kaledin, Dominick Pierre-Jacques, Ciara Tyler, Jason Dyke

Symposium of Student Scholars

This project focuses on developing a novel computational technique to study molecular vibrations through infrared (IR) and Raman scattering Driven Molecular Dynamics (DMD) method. While the main criterion for IR absorption is a net change in the dipole moment in a molecule as it vibrates, presently we wish to predict and analyze vibrational spectra to study symmetric vibrational modes that are IR inactive or weakly active while strongly Raman active. A newly developed method was tested on CO₂, H₂O, CH₄, and C₂₀ molecules. Students optimized the molecular structures, obtained vibrational frequencies, and IR …

Investigating Cathode Dissolution By Homogenous Sol-Gel Coating On Manganese Dioxide Nanofibers To Extend Battery Performance, Milan Haddad

Symposium of Student Scholars

The cathode dissolution is a known phenomenon for manganese dioxide (MnO₂) based cathode materials in both aqueous and non-aqueous batteries. Upon battery discharge, reduced Mn³⁺ species disproportionate (2Mn³⁺→ Mn⁴⁺ + Mn²⁺) and Mn²⁺ dissolves into the electrolyte causing the loss of active material. While MnO₂ is a promising cathode for rechargeable aqueous zinc ion batteries (ZIB) due to its availability and low toxicity, the electrochemical performance is limited during battery cycling due to the dissolution of the cathode. In this work, a homogeneous sol-gel SiO₂ coatings with various thicknesses …

Probing Structure And Energetics Of Proton-Bound Complexes N2…Hco+ And N2h+…Oc Using Computational Chemistry Methods, Antonio Barrios, Dalton Boutwell, Onyi Okere, Monique Olocha, Oluwaseun Omodemi, Alexander Toledo, Antonio Barrios

Symposium of Student Scholars

N₂…HCO⁺ and N₂H⁺…OC are predicted to exist in interstellar clouds. These complexes involve HCO⁺ and N₂H⁺ fragments that are bound to N₂ and CO, respectively using hydrogen-bonded interaction. The reason these molecules are important is that the existence of nitrogen can be measured indirectly through ion-molecular complexes studied in this work. The measured vibrational spectra of molecules is an excellent way to characterize and detect molecules. We used B3LYP, MP2, and CCSD(T) computational methods to predict the structure and vibrational frequencies of N₂…HCO⁺ and N …

Theoretical Study On The Isomerization And Detection Of N2h+…Oc Complex In Interstellar Clouds, Dalton Boutwell, Martina Kaledin

Symposium of Student Scholars

In this study, we characterize N₂H⁺…OC linear complex using Driven Molecular Dynamics (DMD) and Vibrational Self-Consistent Field Theory (VSCF) methods due to its relevance in astrochemistry. A central challenge is the detection of the molecular complex in interstellar media (ISM). Computational chemistry approaches can predict vibrational spectra, hence facilitate prediction of its existence and stability in the ISM. N₂H⁺…OC involves the proton transfer process via hydrogen bonding interaction. Proton motion is highly anharmonic, therefore facing a significant challenge to characterize it accurately. Quantum mechanical variational methods are popular among many theoretical chemists …