Physical Sciences and Mathematics Commons^™

Visualizing Phytochemical-Protein Interaction Networks: Momordica Charantia And Cancer, Yumi L. Briones, Alexander T. Young, Fabian M. Dayrit, Armando Jerome De Jesus, Nina Rosario L. Rojas

Chemistry Faculty Publications

The in silico study of medicinal plants is a rapidly growing field. Techniques such as reverse screening and network pharmacology are used to study the complex cellular action of medicinal plants against disease. However, it is difficult to produce a meaningful visualization of phytochemical-protein interactions (PCPIs) in the cell. This study introduces a novel workflow combining various tools to visualize a PCPI network for a medicinal plant against a disease. The five steps are 1) phytochemical compilation, 2) reverse screening, 3) network building, 4) network visualization, and 5) evaluation. The output is a PCPI network that encodes multiple dimensions of …

Comparative Toxicity, Phytochemistry, And Use Of 53 Philippine Medicinal Plants, Lydia M. Clemen-Pascual, Rene Angelo S. Macahig, Nina Rosario L. Rojas

Chemistry Faculty Publications

The study compares the toxicity of 53 selected medicinal plants commonly used in the Philippines to treat various diseases. It uses as a benchmark Vitex negundo L., which was approved by the Philippine Food and Drug Administration as an herbal drug for cough and asthma after passing clinical trials for safety and efficacy. The methods were chosen for their simplicity and accessibility even for resource-limited laboratories. Extracts (95 % ethanol) of the medicinal parts of the plants were (1) chemically profiled using qualitative phytochemical tests that detect the presence of key classes of bioactive compounds; and (2) evaluated for toxicity …

A Tribute To Professor Gaetano Granozzi And His Contributions To Surface Science On The Occasion Of His 70th Birthday, Kurt W. Kolasinski

Chemistry Faculty Publications

On the occasion of his 70th birthday, we celebrate the career of our Editor-in-Chief, Professor Gaetano Granozzi. Prof. Granozzi’s work is marked by his dedication to the fundamental understanding of technologically relevant systems through the lens of surface science.

Aberrant Crosstalk Between Insulin Signaling And Mtor In Young Down Syndrome Individuals Revealed By Neuronal-Derived Extracellular Vesicles, Marzia Perluigi, Anna Picca, Elita Montanari, Riccardo Calvani, Federico Marini, Roberto Matassa, Antonella Tramutola, Alberto Villani, Giuseppe Familiari, Fabio Di Domenico, D. Allan Butterfield, Kenneth J. Oh, Emanuele Marzetti, Diletta Valentini, Eugenio Barone

Chemistry Faculty Publications

INTRODUCTION: Intellectual disability, accelerated aging, and early-onset Alzheimer-like neurodegeneration are key brain pathological features of Down syndrome (DS). Although growing research aims at the identification of molecular pathways underlying the aging trajectory of DS population, data on infants and adolescents with DS are missing.

METHODS: Neuronal-derived extracellular vesicles (nEVs) were isolated form healthy donors (HDs, n = 17) and DS children (n = 18) from 2 to 17 years of age and nEV content was interrogated for markers of insulin/mTOR pathways.

RESULTS: nEVs isolated from DS children were characterized by a significant increase in pIRS1^Ser636, a marker of …

Premade Nanoparticle Films For The Synthesis Of Vertically Aligned Carbon Nanotubes, Abdul Hoque, Ahamed Ullah, Beth S. Guiton, Noe T. Alvarez

Chemistry Faculty Publications

Carbon nanotubes (CNTs) offer unique properties that have the potential to address multiple issues in industry and material sciences. Although many synthesis methods have been developed, it remains difficult to control CNT characteristics. Here, with the goal of achieving such control, we report a bottom-up process for CNT synthesis in which monolayers of premade aluminum oxide (Al₂O₃) and iron oxide (Fe₃O₄) nanoparticles were anchored on a flat silicon oxide (SiO₂) substrate. The nanoparticle dispersion and monolayer assembly of the oleic-acid-stabilized Al₂O₃ nanoparticles were achieved using 11-phosphonoundecanoic acid …

Biotinylation As A Tool To Enhance The Uptake Of Small Molecules In Gram-Negative Bacteria, Ankit Pandeya, Ling Yang, Olaniyi Alegun, Chamikara Karunasena, Chad Risko, Zhenyu Li, Yinan Wei

Chemistry Faculty Publications

Antibiotic resistance is a major public health concern. The shrinking selection of effective antibiotics and lack of new development is making the situation worse. Gram-negative bacteria more specifically pose serious threat because of their double layered cell envelope and effective efflux systems, which is a challenge for drugs to penetrate. One promising approach to breach this barrier is the “Trojan horse strategy”. In this technique, an antibiotic molecule is conjugated with a nutrient molecule that helps the antibiotic to enter the cell through dedicated transporters for the nutrient. Here, we explored the approach using biotin conjugation with a florescent molecule …

The Primarily Undergraduate Nanomaterials Cooperative: A New Model For Supporting Collaborative Research At Small Institutions On A National Scale, Steven M. Huges, Mark P. Hendricks, Katherine M. Mullaugh, Mary E. Anderson, Anne K. Bently, Justin G. Clar, Clyde A. Daly Jr., Mark D. Ellison, Z. Vivian Feng, Natalia I. Gonzalex-Pech, Leslie S. Hamachi, Christine L. Heinecke, Joseph D. Keene, Adam M. Maley, Andrea M. Munro, Peter N. Njoki, Jacob H. Olshansky, Katherine E. Plass, Kathryn R. Riley, Matthew D. Sonntag, Sarah K. St. Angelo, Lucas B. Thompson, Emily J. Tollefson, Lauren E. Toote, Korin E. Wheeler

Chemistry Faculty Publications

The Primarily Undergraduate Nanomaterials Cooperative (PUNC) is an organization for research-active faculty studying nanomaterials at Primarily Undergraduate Institutions (PUIs), where undergraduate teaching and research go hand-in-hand. In this perspective, we outline the differences in maintaining an active research group at a PUI compared to an R1 institution. We also discuss the work of PUNC, which focuses on community building, instrument sharing, and facilitating new collaborations. Currently consisting of 37 members from across the United States, PUNC has created an online community consisting of its Web site (nanocooperative.org), a weekly online summer group meeting program for faculty and students, …

3d-Printable And Open-Source Modular Smartphone Visible Spectrophotometer, Brandon Winters, Nick Banfield, Cassandra Dixon, Anna Swensen, Dakota Holman, Braxton Fillbrown

Chemistry Faculty Publications

The past four decades have brought significant and increasingly rapid changes to the world of instrument design, fabrication, and availability due to the emergence of 3D printing, open-source code and equipment, and low-cost electronics. These, along with other technological advances represent a nexus in time ripe for the wide-spread production and availability of low-cost sophisticated scientific equipment. To that end, the design of a 3D printable and open-source, modular spectrometer is described. This specific instrument is distinctly different from others that have been reported in recent years in that it was designed outside of the “black box” paradigm of …

Aqueous Photochemistry Of 2-Oxocarboxylic Acids: Evidence, Mechanisms, And Atmospheric Impact, Marcelo I. Guzman, Alexis J. Eugene

Chemistry Faculty Publications

Atmospheric organic aerosols play a major role in climate, demanding a better understanding of their formation mechanisms by contributing multiphase chemical reactions with the participation of water. The sunlight driven aqueous photochemistry of small 2-oxocarboxylic acids is a potential major source of organic aerosol, which prompted the investigations into the mechanisms of glyoxylic acid and pyruvic acid photochemistry reviewed here. While 2-oxocarboxylic acids can be contained or directly created in the particles, the majorities of these abundant and available molecules are in the gas phase and must first undergo the surface uptake process to react in, and on the surface, …

Fabrication Of Electrospun Nanofiber Composite Of G-C3n4 And Au Nanoparticles As Plasmonic Photocatalyst, Dipendu Saha, Pasquale Gismondi, Kurt W. Kolasinski, Samantha L. Shumlas, Sylvie Rangan, Babak Eslami, Amy Mcconnell, Taevaughn Bui, Kayla Cunfer

Chemistry Faculty Publications

In this research, we have fabricated a composite nanofiber mat of plasmonic photocatalyst consisting of g-C3N4, gold nanoparticles (AuNPs) and random nanofibers of polyvinylidene fluoride (PVDF) by electrospinning. The structure and chemical properties of the nanofiber mat were investigated in detail by ESEM, TEM, AFM, XPS, FTIR, XRD, TGA, PL spectroscopy and UV-Vis reflectance spectra. Imaging of the composite map confirmed that the fiber diameter was in the range of 100-400 nm with the g-C3N4 size in the range of 2-8 μm. Backscattered (Zcontrast) electron imaging in ESEM revealed that the AuNP particle size is in the range of 60-160 …

Insight Into The Acrab-Tolc Complex Assembly Process Learned From Competition Studies, Prasangi Rajapaksha, Isoiza Ojo, Ling Yang, Ankit Pandeya, Thilini Abeywansha, Yinan Wei

Chemistry Faculty Publications

The RND family efflux pump AcrAB-TolC in E. coli and its homologs in other Gram-negative bacteria are major players in conferring multidrug resistance to the cells. While the structure of the pump complex has been elucidated with ever-increasing resolution through crystallography and Cryo-EM efforts, the dynamic assembly process remains poorly understood. Here, we tested the effect of overexpressing functionally defective pump components in wild type E. coli cells to probe the pump assembly process. Incorporation of a defective component is expected to reduce the efflux efficiency of the complex, leading to the so called “dominant negative” effect. Being one of …

Metal-Assisted Catalytic Etching (Mace) For Nanofabrication Of Semiconductor Powders, Kurt W. Kolasinski

Chemistry Faculty Publications

Electroless etching of semiconductors has been elevated to an advanced micromachining process by the addition of a structured metal catalyst. Patterning of the catalyst by lithographic techniques facilitated the patterning of crystalline and polycrystalline wafer substrates. Galvanic deposition of metals on semiconductors has a natural tendency to produce nanoparticles rather than flat uniform films. This characteristic makes possible the etching of wafers and particles with arbitrary shape and size. While it has been widely recognized that spontaneous deposition of metal nanoparticles can be used in connection with etching to porosify wafers, it is also possible to produced nanostructured powders. Metal-assisted …

Donnan Potential Across The Outer Membrane Of Gram-Negative Bacteria And Its Effect On The Permeability Of Antibiotics, Olaniyi Alegun, Ankit Pandeya, Jian Cui, Isoiza Ojo, Yinan Wei

Chemistry Faculty Publications

The cell envelope structure of Gram-negative bacteria is unique, composed of two lipid bilayer membranes and an aqueous periplasmic space sandwiched in between. The outer membrane constitutes an extra barrier to limit the exchange of molecules between the cells and the exterior environment. Donnan potential is a membrane potential across the outer membrane, resulted from the selective permeability of the membrane, which plays a pivotal role in the permeability of many antibiotics. In this review, we discussed factors that affect the intensity of the Donnan potential, including the osmotic strength and pH of the external media, the osmoregulated periplasmic glucans …

Formulating 3-Chloropropyltriethoxysilane Modified Silica Nanoparticle Sprays As Hydrophobic Transparent Coatings Onto Cotton Textiles, Mikaela C. S. Mendoza, Gilbert U. Yu

Chemistry Faculty Publications

Cotton textiles were transformed into hydrophobic fabrics via the application of 3-chloropropylthriethoxysilane-functionalized silica nanoparticle spray coatings. Silica particles were measured to be < 50 nm, as determined by dynamic light scattering (DLS). The incorporation of hexadecyltrimethylammonium bromide (HTAB), a surfactant, into the nanosilica alcohol-based sprays resulted in a suspension that was stable for at least a week. Stability and turbidity tests of samples point to smaller particle size (silica nanoparticles = 24.3 ± 8.5 nm) as the main contributor to possibly providing transparency, as evidenced when sprayed in colored (black) textiles, while still contributing to hydrophobicity/ superhydrophobicity of the cloth.

From Disease Description And Gene Discovery To Functional Cell Pathway: A Decade-Long Journey For Tmco1, Helen Batchelor-Regan, Baozhong Xin, Aimin Zhou, Heng Wang

Chemistry Faculty Publications

A decade has passed since transmembrane coiled-coil domains 1 (TMCO1) defect syndrome was identified in 11 undiagnosed patients within the Old Order Amish of Northeastern Ohio-a disorder characterized by a distinctive craniofacial dysmorphism, skeletal anomalies and global developmental delay. Twenty seven patients, from diverse ethnic groups, have been reported with pathogenic TMCO1 variants now recognized to cause cerebrofaciothoracic dysplasia (CFTD). The implication of previously uncharacterized TMCO1 within disease has instigated a 10-year journey to understand the function of TMCO1 protein in Ca2+ homeostasis. TMCO1 is an ER Ca2+ leak channel which facilitates Ca2+ leak upon ER "overload" through the novel …

Synthesis And Crystal Structures Of 3,6-Di­Hy­Droxy­Picolinic Acid And Its Labile Inter­Mediate Dipotassium 3-Hy­Dr­Oxy-6-(Sulfonato­­Oxy)Pyridine-2-Carboxyl­Ate Monohydrate, Edward J. Behrman, Sean R. Parkin

Chemistry Faculty Publications

A simplified two-step synthesis of 3,6-di­hydroxy­picolinic acid (3-hy­droxy-6-oxo-1,6-di­hydro­pyridine-2-carb­oxy­lic acid), C₆H₅NO₄ (II), an inter­mediate in the metabolism of picolinic acid, is described. The crystal structure of II, along with that of a labile inter­mediate, dipotassium 3-hy­droxy-6-(sulfonato­oxy)pyridine-2-carboxyl­ate monohydrate, 2K⁺·C₆H₃NO₇S²⁻·H₂O (I), is also described. Compound I comprises a pyridine ring with carboxyl­ate, hydroxyl (connected by an intra­molecular O—H⋯O hydrogen bond), and sulfate groups at the 2-, 3-, and 6-positions, respectively, along with two potassium cations for charge balance and one water …

Suppressing Bias Stress Degradation In High Performance Solution Processed Organic Transistors Operating In Air, Hamna F. Iqbal, Qianxiang Ai, Karl J. Thorley, Hu Chen, Iain Mcculloch, Chad Risko, John E. Anthony, Oana D. Jurchescu

Chemistry Faculty Publications

Solution processed organic field effect transistors can become ubiquitous in flexible optoelectronics. While progress in material and device design has been astonishing, low environmental and operational stabilities remain longstanding problems obstructing their immediate deployment in real world applications. Here, we introduce a strategy to identify the most probable and severe degradation pathways in organic transistors and then implement a method to eliminate the main sources of instabilities. Real time monitoring of the energetic distribution and transformation of electronic trap states during device operation, in conjunction with simulations, revealed the nature of traps responsible for performance degradation. With this information, we …

Direct Detection Of 5-Mev Protons By Flexible Organic Thin-Film Devices, Ilaria Fratelli, Andrea Ciavatti, Enrico Zanazzi, Laura Basiricò, Massimo Chiari, Laura Fabbri, John E. Anthony, Alberto Quaranta, Beatrice Fraboni

Chemistry Faculty Publications

The direct detection of 5-MeV protons by flexible organic detectors based on thin films is here demonstrated. The organic devices act as a solid-state detector, in which the energy released by the protons within the active layer of the sensor is converted into an electrical current. These sensors can quantitatively and reliably measure the dose of protons impinging on the sensor both in real time and in integration mode. This study shows how to detect and exploit the energy absorbed both by the organic semiconducting layer and by the plastic substrate, allowing to extrapolate information on the present and past …

The Zinc-Binding Domain Of Mammalian Prolyl-Trna Synthetase Is Indispensable For Catalytic Activity And Organism Viability, Kommireddy Vasu, Iyappan Ramachandiran, Fulvia Terenzi, Debjit Khan, Arnab China, Krishnendu Khan, Aayushi Chechi, Camelia Baleanu-Gogonea, Valentin Gogonea, Paul L. Fox

Chemistry Faculty Publications

Aminoacyl-tRNA synthetases (AARS) participate in decoding the genome by catalyzing conjugation of amino acids to their cognate tRNAs. During evolution, biochemical and environmental conditions markedly influenced the sequence and structure of the 20 AARSs, revealing adaptations dictating canonical and orthogonal activities. Here, we investigate the function of the appended Zn2+-binding domain (ZBD) in the bifunctional AARS, glutamyl-prolyl-tRNA synthetase (GluProRS). We developed GluProRS mutant mice by CRISPR-Cas9 with a deletion of 29 C-terminal amino acids, including two of four Zn2+-coordinating cysteines. Homozygous ZBD mutant mice die before embryonic day 12.5, but heterozygous mice are healthy. ZBD disruption profoundly reduces GluProRS canonical …

Modes Of Transmission Of Severe Acute Respiratory Syndrome-Coronavirus-2 (Sars-Cov-2) And Factors Influencing On The Airborne Transmission: A Review, Mahdieh Delikhoon, Marcelo I. Guzman, Ramin Nabizadeh, Abbas Norouzian Baghani

Chemistry Faculty Publications

The multiple modes of SARS-CoV-2 transmission including airborne, droplet, contact, and fecal–oral transmissions that cause coronavirus disease 2019 (COVID-19) contribute to a public threat to the lives of people worldwide. Herein, different databases are reviewed to evaluate modes of transmission of SARS-CoV-2 and study the effects of negative pressure ventilation, air conditioning system, and related protection approaches of this virus. Droplet transmission was commonly reported to occur in particles with diameter >5 µm that can quickly settle gravitationally on surfaces (1–2 m). Instead, fine and ultrafine particles (airborne transmission) can stay suspended for an extended period of time (≥2 h) …

N-Type Charge Transport In Heavily P-Doped Polymers, Zhiming Liang, Hyun Ho Choi, Xuyi Luo, Tuo Liu, Ashkan Abtahi, Uma Shantini Ramasamy, J. Andrew Hitron, Kyle N. Baustert, Jacob L. Hempel, Alex M. Boehm, Armin Ansary, Douglas R. Strachan, Jianguo Mei, Chad Risko, Vitaly Podzorov, Kenneth R. Graham

Chemistry Faculty Publications

It is commonly assumed that charge-carrier transport in doped π-conjugated polymers is dominated by one type of charge carrier, either holes or electrons, as determined by the chemistry of the dopant. Here, through Seebeck coefficient and Hall effect measurements, we show that mobile electrons contribute substantially to charge-carrier transport in π-conjugated polymers that are heavily p-doped with strong electron acceptors. Specifically, the Seebeck coefficient of several p-doped polymers changes sign from positive to negative as the concentration of the oxidizing agents FeCl3 or NOBF4 increase, and Hall effect measurements for the same p-doped polymers reveal that …

Computational Analysis Beyond The Monomer Frontier Orbitals For Photovoltaic Donor-Polymer Candidates, Mitchell E. Lahm, Megan M. Niblock, John M. Migliore, Kendra M. Mckenzie, Hans P. Lüthi, Rollin A. King

Chemistry Faculty Publications

Scharber et al. proposed an efficiency model for organic photovoltaic cells based on the orbital energies of the monomers of the donor- and acceptor- polymers [Advanced Materials 18 (2006) 789–794]. We report theoretical extensions of this approach. First, the frontier-orbital energies and electronic spectra of n-length oligomers (n = 1 − 5) of 3-butylthiophene have been determined. The results show reasonable convergence with respect to system size at the point of a trimer with alkyl end caps. The HOMO-LUMO gap well matches computed excitation energies. Second, the structures and electronic spectra of dimers formed by three different monomers, with various …

Philippine Medicinal Plants With Potential Immunomodulatory And Anti-Sars-Cov-2 Activities, Fabian M. Dayrit, Armando M. Guidote Jr, Nina Gloriani, Sheriah Laine M. De Paz-Silava, Irene M. Villaseñor, Rene Angelo S. Macahig, Mario A. Tan, John Ross N. Chua, Isidro C. Sia

Chemistry Faculty Publications

Coronavirus disease 2019 (COVID-19) continues to devastate the world’s health and economy, affecting all aspects of life leading to widespread social disruption. Even as several vaccines have been developed, their availability in developing countries is limited and their efficacy against the variants of SARS-CoV-2 (severe acute respiratory syndrome–coronavirus 2) needs to be continuously assessed. The World Health Organization (WHO) has acknowledged that vaccines alone will not overcome the global challenges of COVID-19. Medicinal plants may provide the needed support. Herein, we identify Philippine medicinal plants that possess phytochemicals with potential anti-SARS-CoV-2 activity and/or immunomodulatory properties that may strengthen one’s immune …

One-Pot Synthesis Of 2-Methylfurans From 3- (Trimethylsilyl)Propargyl Acetates Promoted By Trimethylsilyl Trifluoromethanesulfonate, Danielle E. Sklar, Alex V. Helbling, Yiqi Liu, C. Wade Downey

Chemistry Faculty Publications

In the presence of trimethylsilyl trifluoromethanesulfonate (TMSOTf) and triethylamine, 3-(trimethylsilyl)propargyl carboxylates undergo a one-pot alkylation-cyclization- desilylation reaction with ketones to produce 2-methylfurans. Alkylation at 0 °C in methylene chloride, followed by acid-catalyzed cyclization at room temperature, provides the furans in 52-86% yield. Cyclization and desilylation appear to be promoted by triflic acid generated in situ from the exposure of the reaction mixture to water upon completion of the initial substitution reaction.

Friedel–Crafts Addition Of Indoles To Nitrones Promoted By Trimethylsilyl Trifluoromethanesulfonate, Zachary Z. Oracheff, Helen L. Xia, Christopher D. Poff, Scott E. Isaacson, C. Wade Downey

Chemistry Faculty Publications

N-alkylindoles undergo Friedel–Crafts addition to aryl and secondary alkyl nitrones in the presence of trimethylsilyl trifluoromethanesulfonate and a trialkylamine to produce 3-(1- (silyloxyamino)alkyl)indoles. Spontaneous conversion to the bisindolyl(aryl)methanes, which is thermodynamically favored for nitrones derived from aromatic aldehydes, is suppressed under the reaction conditions. The silyloxyamino group can be deprotected with tetrabutylammonium fluoride to yield the hydroxylamine.

The Application Of 13c Nmr And Untargeted Multivariate Analysis For Classifying Virgin Coconut Oil, Lolita G. Lagurin, Mark Joseph Garrovillas, Fabian M. Dayrit

Chemistry Faculty Publications

Virgin coconut oil (VCO) is produced from fresh mature coconut meat without the use of chemicals or high heat. VCO can be made using three processes: fermentation, centrifuge, and expeller. To determine quality, it is important to be able to differentiate control VCO (fresh) from old VCO, refined bleached and deodorized coconut oil (RBDCO), and VCO which has been adulterated with RBDCO. Differentiating these types of samples has remained a challenge because of their chemical similarity. This study investigated the ability of 13C NMR and multivariate analysis to differentiate these different coconut oil samples. The methodology used the standard 13C …