How does a molecule get solvated?
(Dr. Josh Newby with students:  Kone Mamourou, Anna Dubany, Jeremy Swartz, Isiah McMurray, and Aaron Uzelmeier)



The goal of this work is to better understand  the process of solvation. Our research will focus on how the first water molecule attaches to another molecule. Students learned how to use computational chemistry to complete a structural analysis of a molecular complex. This was done using computing resources remotely accessed at the San Diego Supercomputer Center. Students also performed FTIR studies of simple to experimentally verify computational results. These studies make use of a matrix isolation cell that operates at 15 K (-420 F). Student projects have focused on the microsolvation of petroleum impurities, drug precursors, and flavoring agents. 

Using Enzymes to Make Human Milk Sugars
(Dr Jessica Stachowski with students:  Kyra Couglin, Reece Wieder, Sandra Perkins, Lydia Coombs, and Bianca Hernandez Salazar)

Human milk oligosaccharides (HMOs) are a family of sugars that are a major component in human milk and impart many immediate and long-term health benefits to breastfed infants.  Although there is a large demand for HMOs for clinical research studies, chemical synthesis of these molecules is too complex for large-scale production.  Our group is investigating the use of engineered enzymes as a tool to make HMOs in a more efficient manner.  Students had The opportunity to be a part of an interdisciplinary research group working in the areas of biochemistry (DNA cloning and protein expression), organic chemistry (carbohydrate synthesis), and computational chemistry (molecular docking simulations).

A variety of research projects took place during the summer of 2022.

Story: "Invaluable" experiences for Naz students immersed in research

More Summer 2022
During summer 2022, Annabelle and Emily continued their work to better understand the interactions of lactones (a common drug precursor) with water; Brian, Hallie, Jacob explore isomers of methoxystyrene (used as a fragrance and flavoring); and Joey continued his work on oxazole complexes (found in biologic antimicrobials).

The Newby Research Group, summer 2022. (l to r) Jacob Alvira, Brian Chong, Emily Weaver, Joey Nettles, Anabelle Carney, and Hallie Todd.

The group also learned to use the matrix isolation system so that they record spectra of their complexes at 15 K. This low temperature is needed to stabilize the complexes long enough to study them using FTIR spectroscopy. Spectra and analyses of Annabelle and Emily’s lactone complexes were presented at the 2022 International Symposium on Molecular Spectroscopy held at the University of Illinois Urbana-Champaign to significant interest.

The matrix isolation chamber operating at 14.7 K!

Spring 2022
The Newby Research Group always has something exciting going on!

In the spring of 2022, Annabelle, Emily and Xavier traveled to the national ACS meeting in San Diego to present their work on weakly bound complexes as studied using computational chemistry.

(L to R) Annabelle, Xavier, and Emily at their posters at ACS San Diego

While in San Diego, we also visited UC San Diego where the San Diego Supercomputing Center (SDSC) is located. SDSC is where many of our calculations are run, as they are too complex for a basic lab computer.

Newby Research Group
Summer 2021


(L-R: Rachael Vasilchenko, Emily Weaver, Annabelle Carney, Kenny Mogauro, Xavier Solivan,  and Dr. Newby)
21_Summer_recap.pdf

Summer 2021
Abby Manning (BCH) participated in a SPARK Research Grant with Dr. Amber Charlebois.  The research project explored the interactions between cresyl violet and nucleic acid molecules.

Charlebois Research Group
Fall 2020 Research "Covid-19 Style"

Students: Seth Terzo, Jenna Phillips, & Maggie O’Conner ·
Previous Research Students: Olivia Guerrette, Meredith Rasey, Tenaya Chaney and Ben Butler 

Project 1: Hydrogenation. The synthesis of stercobilin, from bilirubin, a potential biomarker of childhood autism involves a two-step process of hydrogenation followed by oxidation. We produced stercobilin under multiple reaction conditions and analyzed the products using NMR & IR (at Naz) and MS (at University at Buffalo). It was highly successful experience and we confirmed that we can make stercobilin, but in doing so we have discovered the that mechanism is not what we expected. Moving forward we are looking at smaller model molecules to investigate the specific reactivity of different types of double bonds in hydrogenation. We explored limonene and a- phellandrene.

Project 2: HPLC of Proteins. This research involves protein structure interrogation using HPLC for development of a new undergraduate laboratory experiment. We looked at the retention time for several proteins under native, denatured and reduced conditions. The first protein was lysozyme, a protein that catalyzes the destruction of the cell walls of certain bacteria, and the second was Bovine Pancreatic Trypsin, is a serine protease found in the digestive system of many vertebrates, where it hydrolyzes proteins. This was done in effort to explore the differences in structure and therefore interaction with the hydrophobic stationary phase in chromatography. Results show that the more tightly packed the protein is folded, the shorter time it spends bound to the column. We are now working on writing this up for publication.

Current Students: Madyson Marks & Jessica Granchelli (not in photo, Hannah Smith) · Previous Students: Lan Nguyen, Emily Welch & Jacob Dougal   

Project 3: Cresyl Violet. In this research we are investigation of binding of cresyl violet (CV) to nucleic acid molecules. It has been shown that CV is blue when bound to DNA and purple when bound to RNA, and this fall we delved into why this might be the case. We looked at CV bound to multiple different sequences of DNA and RNA both in the gel and in solution. We looked at the interaction in the gel and in solution. We investigated the local environment within the CV when bound to the nucleic acid by exploring the role of pH and concentration (both CV and nucleic acids) and we continue to analyze all of the spectroscopic data the data using peak fit.

Current Students: Jessica Granchelli, Abby Manning & Megan Griffin ·
Previous Students: Frank Gaffney, Nicole Waild & Mitchell Duvall     

Projects 4. Development of microwave assisted esterification and synthesis of amides reactions using unknowns for use in the organic chemistry curriculum.  We have established a protocol for the microwave that allows us to perform several different reactions in the microwave simultaneously. We were successful and therefore the students in Organic lab courses will be required to determine the identity of both their products and starting materials. Moving forward this spring we will continue to collect student data and begin preparing a manuscript.

Current Student: Abby Manning · Previous Student: Bryanna Roos

Projects 5. Art and Chemistry This is a new project for me and I will let you know all about it once we get started! I see the artistic side of chemistry all the time and wanted to see if I could capture it to share. Stay tuned.

Current Student: Emma Golden

Dr. Charlebois and her summer research group worked on five projects during the summer of 2019:

A. Synthesis of stercobilin, from bilirubin, a potential biomarker of childhood autism. This involves a two-step process of hydrogenation followed by oxidation. We produced stercobilin under multiple reaction conditions and analyzed the products using NMR and IR  (at Naz) and MS (at University at Buffalo). It was highly successful experience and we confirmed that we can make stercobilin, but in doing so we have discovered the that mechanism is not what we expected. Moving forward we are looking for a smaller model molecule to investigate the specific reactivity of different types of double bonds in hydrogenation.

Summer Student: Meredith Rasey     Previous Students: Tenaya Chaney and Ben Butler

 B. Protein structure interrogation using HPLC for development of a new undergraduate laboratory experiment. We looked at the retention time for lysozyme, a protein that catalyzes the destruction of the cell walls of certain bacteria, under native, denatured and reduced conditions. This was done in effort to explore the differences in structure and therefore interaction with the hydrophobic stationary phase in chromatography. Results show that the more tightly packed the protein is folded, the shorter time it spends bound to the column. We plan to write this up for publication once we reproduce it on a different protein, trypsin inhibitor.

Summer Students: Emily Welch and Jacob Dougal    Previous Students: Lan Nguyen

 C. Investigation of binding of cresyl violet (CV) to nucleic acid molecules. It has been shown that CV is blue when bound to DNA and purple when bound to RNA, and this summer we delved into why this might be the case. We looked at CV bound to multiple different sequences of DNA and RNA both in the gel and in solution. We gathered a whole bunch of data and so moving forward we will analyze the data using peak fit to see what it all means.

Summer Student: Mitchell Duvall      Previous Students: Frank Gaffney and Nicole Waild

D. Development of microwave assisted esterification reactions using potential unknowns for use in the organic chemistry curriculum.  We have established a protocol for the microwave that allows us to perform several different reactions in the microwave simultaneously. We were successful and therefore the students in Organic lab will be required to determine the identity of both their alcohol and their carboxylic acid starting materials in this experiment starting this fall. Moving forward we will be working on a similar amide synthesis using the microwave.

Summer Student: Bryanna Roos

E. Creation of videos as pre-lab lectures for organic chemistry laboratory. In effort to keep the multiple sections of Organic Chemistry Laboratory consistent, we have recorded about half of the videos for the fall semester including a full safety video. Hopefully this effort will help the students with the reactions as well as the execution of the experimental protocols.

Summer Student: Samantha Druce

Dr. Sanela Lampa-Pastirk
2017 Summer Research Project

In recent years, the application of quantum dots (QD) in a number of technologies including biomedical imaging and detection, QD based solar cells or as light emitting devices has led to the industrial level scale-up of their synthesis reactions. With scale-up of these reactions came the raised concern about related environmental issues such as increased levels of toxic metals and their long term effect on the genetics of exposed organisms. As a result, there is a growing interest in developing bio-based methods for aqueous, low-cost, green synthesis of inorganic QD materials. QDs created through biosynthesis have the advantage of being water soluble and environmentally friendly. Not only that the use of toxic surfactants and chemicals are unnecessary, the toxic materials already present in the bacterial surrounding can be utilized for production of useful inorganic nanoparticles.

Our research focuses on developing new strategies for controlled biosynthesis of Cd and Zn QDs using proteobacterium Shewanella oneidensis MR-1. This well-studied metal-reducing bacterium has a great potential to be utilized as a biological factory for production of QDs due to its naturally high resistivity to toxic metals that is directly related to Shewanella's unique respiration mechanism.

Summer 2017 research students learned anaerobic culturing, synthetized Cd QDs and implemented spectroscopic techniques to determine their quality and efficiency.

Dr. Stephen Tajc
2017 Summer Research Project

Water treatment has been an important and often overlooked component of the hydraulic fracturing process. Currently, the primary method of hydraulic fracturing flowback water disposal is deep underground injection into caverns using EPA Class II disposal methods. There is an urgent need for new methods of removing total dissolved solids (TDS) from hydraulic fracturing flowback water. Affordable and environmentally friendly methods should be a high priority as to preserve our drinking water and fragile ecosystem. Our research explores the structure activity relationships of pyridine-based small molecules that can bind and sequester metals in water, in addition to exploring the small molecule:metal complex as a nutrient source for soil bacterial.

This summer, our research students gained hands-on experience on a variety of state-of-the-art instruments including:

• IIsothermal Titration Calorimetry (ITC), small molecule:metal binding analysis
• Flame Atomic Absorbance, metal analysis
• Proton and Carbon NMR, structure determination and binding analysis
• UV-vis titration, binding analysis
• Analytical HPLC, synthesis and purityPrep HPLC, compound purification
  
  

Dr. Stephen Tajc

The Marcellus Shale has been known to contain usable natural gas for over 75 years, however previous drilling methods were not adequate for releasing the trapped natural gas from the shale.  The development of horizontal fracture drilling (hydraulic fracturing) and slick-water fracturing fluids now makes drilling these difficult areas a reality. Hydraulic fracturing uses a large volume of slick-water that is composed of freshwater, sand, and chemical additives.  A volume of 7-15 million gallons of water may be required to produce a sufficient horizontal fracture in a single natural gas well.  Flowback wastewater is collected, and much of this water is contaminated with halogens and metals, which are classified as total dissolved solids (TDS).  There are reports that hydraulic fracturing drilling produces flowback water exceeding 200,000 mg/L of TDS.  The United States Environmental Protection Agency considers any amount over 500 mg/L of TDS for drinking water to be contaminated.

Water treatment has been an important and often overlooked component of the hydraulic fracturing process.  Currently, the primary method of hydraulic fracturing flowback water disposal is deep underground injection into caverns using EPA Class II disposal methods.  There is a urgent need for new hydraulic fracturing flowback water purification methods to combat the increasing demand for natural gas drilling in shale.  Affordable and environmentally friendly methods should be a high priority as to preserve our drinking water and fragile ecosystem. My research group explores the structure activity relationships of pyridine-based small molecules that can sequester metals in water, in addition to the capabilities of the small molecules:metal complex to be used as a source of nutrition by bacterial found in soil.

Dr. Lynn O'Brien

“Let’s Go Green!”
Finding alternative energy sources is the goal of research across a variety of scientific disciplines.  One biochemical approach to developing a renewable fuel has been the production of ethanol from plants such as corn and sugar cane.  Some of the concerns to this approach include an increase in food costs and the loss of natural habitats, as large amounts of land are required to grow these crops.  One solution is to produce the fuel from the inedible parts of plants and non-food crops such as corn stalks, fast-growing grasses, and more recently algae.  The challenge is overcoming the chemical and engineering barriers to producing this fuel from cellulosic materials.  Certain fungi and bacteria can produce cellulases, the enzymes required to break down cellulose to glucose that can then be fermented to produce ethanol. Our project will focus on the identification and characterization of stable and efficient cellulase enzymes isolated from microorganisms in soil.   

“Let’s Not Go!”

Enteropathogenic and enterohemorrhagic E. coli (EPEC and EHEC) cells that attach to human intestinal epithelium result in the formation of effacing lesions.  This lesion formation is the precursor of intestinal cell membrane disruption and diarrhea in infected individuals.  Two proteins, intimin and the translocated intimin receptor (TIR) play an essential role in attachment to intestinal epithelial cells.  E. coli first expresses TIR which is translocated to the host cell via a type-III secretion system.  TIR then becomes immobilized in the intestinal epithelium with its intimin binding domain exposed on the intestinal cell surface.  Intimin, from the E. Coli surface, then binds TIR and attaches the E. coli cell to the intestinal epithelium, which leads to lesion formation.

Currently EPEC and EHEC infections take a minimum of 24 hours to diagnose.  Developing a small molecule that is capable of disrupting the intimin/TIR binding association could potentially lead to immediate identification of EPEC and EHEC infections and faster treatments.  Our project involves expression of the recombinant intimin protein and its purification.

Expression of recombinant intimin and translocated intimin receptor proteins in E.coli cells

Kayla Page, Christopher Redmond, Claire Sobraske, and Dr. Lynn O'Brien

Abstract: Enteropathogenic and enterohemorrhagic E.coli (EPEC and EHEC) cells that attach to human intestinal epithelium result in the formation of effacing lesions, which is the precursor of intestinal cell membrane disruption and diarrhea in infected individuals. Two proteins, intimin and the translocated intimin receptor (TIR), play an essential role in attachment to intestinal epithelial cells.

E. coli first expresses TIR, which is translocated to the host cell via a type‐III secretion system. TIR then becomes immobilized in the intestinal epithelium with its intimin binding domain exposed on the intestinal cell surface. Intimin, from the E.coli surface, then binds TIR and attaches the E. coli cell to the intestinal epithelium, which leads to lesion formation. These types of infections can take up to 24 hours to diagnose and there has not yet been a small molecule developed to speed up this diagnostic process, prevent further infection, or allow sooner initiation of treatment. The initial expression of recombinant TIR and Intimin proteins and their purification will be discussed.

Effect of Educational Videos in the Classroom

Emily Loiodice, Sarah Forney, and Dr. Kelly Hutchinson-Anderson

This project investigated creative methods to teach science in city schools so as to engage students and make a positive impact on their view of science. In particular, we examined the way that solar energy can be taught in the classroom using short educational videos in addition to interactive lessons. We have partnered with the team at Prove Your World in an effort to research students’ misconceptions of the topic of solar energy and find a variety of methods to overcome these conceptions and explain the topic including a short video clip with puppets. Currently the video is in the process of being scripted and filmed, and we hope to have the lessons and video out to schools in the fall of 2015.

Synthesis of small molecule receptors for binding cations

Allison O'Neil, Jacob H Murray, Jacob D Murray, Steven Lewis, and Dr. Stephen Tajc

Abstract: Heavy metal pollution has been causing problems with the purity of our fresh water supplies. A history of mining has led to heavy-metal contamination of both ground and surface water in many areas of the United States^. Small molecule receptors that bind cations in aqueous solution may have potential as a water purification technique. Dipicolinic acid (DPA) is a small molecule formed in bacteria spores and is known to chelate calcium. DPA, which has been found to aid in heat resistance for the bacteria endospores,may also have potential as a small molecule that binds larger heavy metal cations. Our research focuses on the structure activity relationship of DPA and DPA derivatives to determine the fundamental binding characteristics of DPA:cation interactions in aqueous solution.

Investigation of the effect of alcohol size on the methylation kinetics of eleic acid catalyzed by SnBr₂

Goodwell Nzou, Elana Tontarski, and Dr. Richard Hartmann

_{Abstract: Previous work in our group has shown SnX2 (X=F, Cl, Br, I) as effective catalysts with a reaction rate trend of I>Br>Cl>F. In an effort to deduce the mechanistic pathway, we have designed a series of experiments to investigate the steric effect of different alcohols. We are evaluating the effect of the steric bulk of methanol, ethanol, propanol, isopropanol, and butanol in order to understand the trend.}

1H NMR analysis of the methylation of acetic acid catalyzed by tin (II) bromide:  A kinetic study.

Nandini Singh, Nicole Bayona, Jaissy Sekhon, and Dr. Richard Hartmann

Abstract: Biodiesel made from waste cooking oil is a popular substitute for petroleum diesel. However, due to its high content of free fatty acids (FFA), waste oil must undergo an initial acid catalyzed esterification. This process typically employs concentrated H2SO4 but we chose a milder Lewis acid, tin (II) bromide, as our catalyst. Our investigation is part of a larger project which employs acetic acid, and tin II bromide as catalyst at various temperatures to verify computational derived activation energy and mechanistic data acquired from a collaborator. The preliminary data suggest the formation of a methanol-tin complex as the acidic species in this reaction. This poster will present our interpretation of the data and discussion of the mechanistic pathway it supports.

Dipicolonic acid with metal cations as a nutrient source for soil microorganisms

Cara R Czechowki, Sarah Getsy, and Dr. Stephen Tajc

Abstract:Water contamination of heavy metals from hydraulic fracturing is an increasing threat to environmental and human safety, and an effort to find ways to remediate these waste waters is necessary. It has been suggested that the compound dipicolinic acid (DPA) that is naturally produced by Bacillus subtilis spores is able to chelate to metal cations, specifically Ca2+. In this research we explore the possibility of other soil microorganisms such as Bacillus licheniformis to utilize Ca2+-DPA as a nutrient source. The metabolism of metal ions with DPA by soil bacteria will then allow further insight into the bioremediation of waste waters polluted by heavy metals.

Study of small molecules and their chelating capabilities in an aqueous solution

Hannah E Garlick, Nicole R Delello, Stacy Yazo, and Dr. Stephen Tajc

Abstract: It is known that some small molecules naturally chelate to cations in water. One small molecule of interest is Dipicolinic acid (DPA). DPA is found naturally in certain species of bacterial spores and is well-known that DPA chelates calcium ions. Further research is being done to observe chelation to larger cations with DPA and synthetic derivatives of DPA. Using UV-VIS titrations, DPA's chelating ability was studied with other heavy metals. The binding capabilities of DPA to magnesium, silver, strontium, cobalt and iron in aqueous solution have been measured. In addition, the stoichiometry of DPA has been measured with larger cations via Job's plot.

Synthesizing DPA derivatives to identify effective cation scavengers

Nick Polito and Dave Studin

Abstract: Dipicolinic acid (pyridine-2,6-dicarboxylic acid)(DPA) is a pyridine-based compound produced by gram-positive, spore producing bacteria. DPA has been shown to successfully chelate Calcium metal ions in aqueous solution.[i] DPA-derivatives may have the ability to act as heavy metal scavengers in aqueous solutions making them a novel alternative for the purification of contaminated water. My research involves synthesizing DPA-derivatives to create more feasible schemes for the production of derivatives. Several successful synthetic routes have been confirmed. The resulting derivatives were tested for their structural activity relationship for binding. Using various organic synthesis schemes to produce new compounds and UV-titration to test the binding ability of these compounds, we hope to identify DPA derivatives that will successfully scavenge metal ion contaminants in water.

[i] Lewis, J. C. (1967). Determination of dipicolinic acid in bacterial spores by ultraviolet spectrometry of the calcium chelate. Analytical biochemistry, 19(2), 327-337.

Modifying small molecule HIV-1 viral entry inhibitors to bind glycoprotein qp120 on a solid surface

Cara Czechowski with Dr. Stephen Tajc

Abstract: According to the World Health Organization, 34 million people are currently living with HIV. Small molecule HIV viral entry inhibitor drugs are interesting compounds as they target protein complexes involved in viral membrane fusion that could be used for HIV diagnostics. The small molecule drug BMS-806 binds to the HIV-1 envelope glycoprotein gp120 and is a potent HIV-1 viral entry inhibitor. In this research we explore adding a synthetic linker using solid surface techniques to BMS-806 focusing on the portion of 7-azaindole with amine molality. The linker on BMS-806 will then allow for solid surface binding analysis with gp120. These studies will provide further insight of HIV-1 viral protein interactions with small molecules.

Towards the analysis of small molecule HIV-1 viral entry inhibitor with qp120 on a solid surface

Goodwell Nzou with Dr. Stephen Tajc

Abstract: The number of people dying from HIV/AIDS infection continues to escalate throughout the world. There is a critical need for smaller, inexpensive molecules for the diagnosis of the virus to help minimize the proliferation of this pandemic. Currently, a rapid HIV test that utilizes antibodies is available for diagnosing an HIV infection1. However, a large antibody protein is less stable and cost more to produce large quantities than a small molecule with similar binding capabilities. This project is geared towards the exploration of NBD-556, which binds to the HIV-1 envelope glycoprotein gp1202. Understanding the solid surface binding capabilities of this small molecule HIV-1 viral entry inhibitor may lead to fast and affordable diagnosing tools for lower income areas both domestic and worldwide.

Systematic modification of electron density on a series of tungsten based Lewis acid catalysts with minimal structural changes

Molly Kingsley and James Chambers with Dr. Richard Hartmann

Abstract: The results of recent experiments in our group have shown that tungsten compounds (WCl6 and WCl4(PPh3)2) are successful Lewis acid catalysts in the methylation of oleic acid. While it is clear the oxidation state of tungsten influences the rate of reaction, we are unsure of its specific role because both structural and electronic changes were made. In an attempt to investigate the sole effect of electronic changes, we have systematically synthesized a group of compounds of the general formula: WCl4(PPh3-X)2 (X = H, F, Cl, O-CH3, and CH3, all in the para position). These compounds present a scenario where no appreciable change to the structure has been made, yet the electron density of tungsten is influenced from afar. We report here the synthesis, and characterization of these compounds along with a 1H NMR study of their ability to catalyze the methylation of oleic acid.

Tin(II) halides as catalysts for the methylation of eleic acid

Elana Tontarski with Dr. Richard Hartmann

Abstract: Although biodiesel is known to be an effective and environmentally sound replacement for petroleum diesel, it has remained a marginal fuel because of high production costs. The majority of this cost could be eliminated if high free fatty acid (FFA) waste oils were employed as the starting material rather than virgin oils. Because these kinds of oils require acid catalyzed pretreatment, we have been investigating a variety of mild Lewis acids as replacements for the highly caustic and sulfur containing H2SO4 which is the standard catalyst employed. Using oleic acid as a model FFA we have found SnX2 (X = F, Cl, Br, and I) to be an effective catalyst for this reaction and have also observed an interesting trend in reaction rates (I>Br>Cl>F). This poster will present our findings along with a discussion of their significance and the unique use of 1HNMR to determine the rates of these reactions.

Investigation of the kinetic isotope effect with tin(II) bromide for the esterification of oleic acid

Nandini Singh and Nicole Bayona

Abstract: Biodiesel made from waste cooking oil is a popular substitute for petroleum diesel. However, due to its high content of free fatty acids (FFA), waste oil must undergo an initial acid catalyzed esterification. This process typically employs concentrated H2SO4 but we chose a milder Lewis acid, tin (II) bromide, as our catalyst. Our investigation is part of a larger project which uses oleic acid as a model FFA, and the tin(II) halides (SnF2, SnCl2, SnBr2, and SnI2) as catalysts.

Our investigation primarily focuses on the tin(II) halides SnCl2 and SnBr2, because previous research suggests that these two halides are most appropriate for the methylation of oleic acid. Methanol-D was substituted for methanol in order to assess the role of this species in the overall mechanism. Through the use of NMR, we have determined that methanol-D does eventually make methyl ester, but it takes substantially more time for the reaction to occur and it also occurs best at 60ᵒC. Our investigation is done at 55ᵒC and 60ᵒC with both the SnCl2 and SnBr2 halides compare the percent methyl ester created from the different temperature of the two different tin(II) halides. This poster will present our interpretation of the data, how it relates to potential mechanisms, involved in determining the rate limiting steps and the broader impact for the series of tin(II) halides.

Activation energy determination for the esterification of free fatty acids in oleic acid for biodiesel synthesis using Lewis acid tin (II) iodide

Kristin Nichols with Dr. Richard Hartmann

Abstract: Biodiesel is a readily produced and commonly used alternative fuel source. Biodiesel can be synthesized from renewable resources, such as used cooking oil, through esterification of free fatty acids (FFA) or transesterification of triglycerides. Because used oils are often contaminated with FFA's we have chosen oleic acid as a model system for investigating reactions that convert FFA into methyl esters. An acid catalyst is used to treat the FFA's and create fatty acid methyl esters (FAME). Tin halides are common Lewis acid catalysts and are readily available. Preliminary results show that the rate constants for these reactions fit the following trend: SnF2 < SnCl2 < SnBr2 < SnI2, monitoring the reaction progress using 1H NMR. Based on these results, we have undertaken a series of experiments to determine the activation energies of the reactions. This poster will present my methods and results on the use of tin (II) iodide to catalyze the methylation of oleic acid.

Synthesis of tin (II) halide-phosphine complexes and characterization via ^119, Sn, ³¹P, and ¹⁹F NMR spectroscopy

Briana Laubacker with Dr. Richard Hartmann

Abstract: Recent work in our labs has shown SnX2 (X = F, Cl, Br, and I) to be effective Lewis acid catalysts for the methylation of oleic acid. The results show a clear trend in reaction rates, with SnI2 being the best catalyst and SnF2 the worst. However, we are unable to determine if this result is due to changes in electron density at the metal center, or the steric bulk introduced by the halide ligands. In an effort to systematically modulate the electron density on the tin center we have undertaken the synthesis of several phosphine derivatives of each tin (II) halide using the following phosphines: triphenylphosphine, tris(4-chlorophenyl)phosphine, tris(4-fluorophenyl)phosphine, tris(4-methoxyphenyl)phosphine, tri(p-tolyl)phosphine, 1,2-bis(diphenylphosphino)ethane, and trioctylphosphine. 119Sn, 31P, and 19F NMR studies verify the formation of several novel compounds and this poster will discuss the interpretation of these spectra and the possible identity of the compounds that were formed.

Investigating the effect of steric bulk on the catalytic activity of substituted tin(II) chlorides in the esterification of a free fatty acid

Emily Benton with Dr. Richard Hartmann

Abstract: Recent work in our group has shown tin(II) halides to be effective Lewis acid catalysts for the esterification of a free fatty acid (FFA) with an unusual pattern of reaction rates (I> Br> Cl >F). To confirm that this effect is due to steric bulk, substituted tin(II) chlorides of the form SnCl2X2 (X= Me, Et, t-Butyl) were used as catalysts under the same reaction conditions as the original halides. Reaction rates for the substituted halides follow a similar trend (t-Buytl> Et > Me). We present here the methods used to obtain and analyze our data, our potential mechanisms of this reaction, and our planned future work.

Structural analysis of HIV-1 inhibitor drug candidate BMS-378806:  The role of benzyl derivatives

McKenna Murphy and Emily Triplett with Dr. Stephen Tajc

Abstract: Since the discovery of HIV in 1981, AIDS has caused the deaths of millions of people. The current treatment requires high dosages and results in unfavorable side effects that discourage long-term use. BMS-378806 is a small molecule HIV-1 inhibitor that is preferable to the current therapy. However, little is known about the mechanism of this drug. This research aims to identify the most effective functional groups by attaching structural variations to the piperzine-adjacent phenyl ketone. These structural variants may be analyzed by isothermal titration calorimetry (ITC) to determine thermodynamically favorable binding conditions. This data may be used to construct an even more effect HIV-1 inhibitor.

Development of small molecule linkers towards solid surface analysis of HIV-1 viral envelope proteins

Sarah Wazenkewitz, Jennah Wolcott, and Goodwell Nazou with Dr. Stephen Tajc

Abstract: There are millions of people that are currently infected with HIV/AIDS, yet countless contagious individuals remain unaware that they are infected. The Center for Disease Control is presently supporting a two-year study on a free HIV antibody rapid screen test for Americans to examine if increased availability and convenience will promote HIV diagnostics and awareness1. The antibody protein used in this test however, is less stable and costs more to produce large quantities than a small molecule with similar binding capabilities. Small molecule HIV viral entry inhibitors have been found to be a promising new class of drugs due to the ways in which they can target protein complexes that are involved in the process of viral membrane fusion, specifically the HIV-1 glycoprotein gp120. This research is designed to gain a fundamental understanding of small molecule HIV-1 viral entry inhibitors with synthetic linkers towards solid surface analysis of gp120.

Modifying small molecule BMS-806 to bind glycoprotein qp120 on solid surface

Moudi Hubeishy with Dr. Stephen Tajc

Abstract: HIV infection continues to be a prevalent stress in the nation. About 1.2 million people are living with HIV in the United States but approximately 240,000 are unaware of their infection. The Center for Disease Control and Prevention (CDC) is studying to rapidly screen for HIV by using antibodies.1 However, antibodies are large proteins that cost more and are less stable than small molecules, we are interested in using a small molecule drug that is proven to bind to the HIV-1 envelope glycoprotein gp120 such as that of BMS-806.2 In this research, we explore the addition of a synthetic linker to create an amine on the 7-azaindole portion of BMS-806 in solution. This amine will allow us to covalently attach a linker to BMS-806. The linker will allow for solid surface binding analysis so then we might have more information about how the HIV-1 viral protein interacts with small molecules.

Examination of dipicolinic acid scaffolds containing cis-cyclopenta-1,3-dial under aquatic conditions

Nepherteria Wright with Dr. Stephen Tajc

Abstract: Typically dipicolinic acid (DPA) is noted for its association with calcium in spores. It has also been reported to associate as a bidentate ligand with iron, copper, and cobalt. Previous studies had shown the association between derivatives of DPA scaffolds and zinc. We are exploring DPA binding potential with scaffolds during aquatic mono-association. We have begun investigation towards bridging two DPA molecule with cis-cyclopenta-1,3-dial. It has been hypothesized that the cup-shaped DPA molecule will chelate well with the cation in water.

Optimization of solubility and chelating effects of dipicolinic acid

Alan Lee Connor and Jacob Murray

Abstract: Dipicolinic acid (DPA) has been shown to have strong chelating capabilities in polar solvents with various metals. DPA lacks hydrophilicity therefore it is pertinent to modify the structure in order to maximize chelating effects. Structure activity relationships (SAR) will allow us to identify the fundamental bonding characteristics of DPA through various modifications aiding in the optimization of DPA solubility in polar solvents, in turn improving binding to metals. In this research we utilized synthetic chemistry to modify DPA for SAR studies in aqueous solutions.

Investigation of dipicolinic acid-derivatives using structural activity relationships

James Chambers with Dr. Stephen Tajc

Abstract: Some bacteria spores release dipicolinic acid (DPA) is a naturally occurring compound released that is known to chelate to calcium, copper, cobalt and iron. DPA has multiple parts on the molecule that could be used for chelation, and although the location of the interaction has been extensively studied the binding could be optimized. Testing DPA and its derivatives with other cations will help to determine the optimal binding for cations and the essential aspects for optimization. Performing a structural activity relationship test on the DPA molecule will allow us to find compounds with better chelation as well as allow us to further understand the mechanism of binding allowing us to improve the binding capabilities.

Kamal Chappell (BMS)
Buffalo Research Innovation in Genomic and Healthcare Technology (BRIGHT) Program
University at Buffalo - Buffalo, NY

Kamal conducted research in the BRIGHT program alongside a faculty mentor that helped him develop useful computational and statistical skills. His project furnished him with research experience, as well as building skills for a career in biomedical informatics research.


Sofie Fischler (BCH, PBH)
Research Experience for Undergraduates (REU)
University of Connecticut - Farmington, CT

Sofie participated in a biomedical research internship/REU at UCONN in Farmington, CT.  She was paired with the Bartley Lab in the Center on Aging, studying the impact of senolytics on flu vaccination responses in mice in an effort to determine new ways to better protect older adults from the flu.

Noah Suave

Summer 2019 - Noah Suave was part of an REU internship at the University of Delaware. Noah spent 10 weeks in an organic synthesis lab. There he derived a viable synthesis plan for an inhibitor of the enzyme ADAM9. This compound has been used before in previous research, however, it’s creation was either not documented, or they did not have access to the synthesis details.  Noah also created derivatives of the inhibitor, which along with the normal inhibitor, are going to be sent to the Biology Department for testing. This will allow additional properties of ADAM9 to be examined so more effective inhibitors can be created. ADAM9 is an enzyme that has been linked to the severity of cancer.

Lan Nguyen

During the summer of 2019, Lan was an intern at Dr. Somarelli’s lab at Duke Cancer Institute, specifically, genomic techniques.  He studied the genes in marine mammals to discover new treatments for humans to overcome hypoxia during cancers. More particularly, using the technique of siRNA-meditated knockdown, Lan turned down the expression of the ALOX5 gene that was upregulated in dolphin cells under hypoxia. Subsequently, he performed RNA extractions, reverse transcriptions (RT), and quantitative polymerase chain reactions (qPCR) to validate the knockdown’s results molecularly. In addition, he conducted immunofluorescence staining (IF) to validate the knockdown’s results phenotypically. During the school year, Lan will be under the co-mentorship of Dr. Somarelli and a faculty partner at Nazareth College to analyze the gathered data as a part of a final research project. Learning about the nexus of medicine and marine science, Lan realized that the potential positive uses of creativity in science are truly without limit. Therefore, as a student who pursues osteopathic medicine, she looks forward to being more creative in not only her study strategies but also her diagnoses, treatments, and care plans for future patients. 

Abby Krysztofowicz (BMS '18)
University of Rochester
"Biochemical characterization of YbeY from E. coli"
with Dr. Gloria Culver, Dean, School of Arts and Sciences and Dr. Brian Smith, Post Doctoral Fellow

Mark Lysiak (BMS '19) and Kayla Sinclair (BMS '18)
Universidad De Concepcion, Chile

 
Erin Stryker ('19, BMS and CHM)
Virginia Commonwealth University, School of Engineering
Program Head: B. Frank Gupton, Ph.D.
Advisors: Hari Mangunuru, Ph.D., Eric Yu

Erin was in the Medicines for All Institute. This project as a whole focuses on improving access to medicine by lowering the cost of the active pharmaceutical ingredient (API). The high cost of APIs is a major cost driving factor of medical treatment in the developing world. (http://medicines4all.vcu.edu).

More specifically, she worked with tenofovir disoproxil fumarate, a drug used to treat chronic hepatitis B and to prevent and treat HIV. The current process for making tenofovir uses very expensive starters, so finding a new process that avoided those was the first goal in the project. When she came on to the project, they had already devised a new synthesis for the first half of the drug, so she spent her summer working on the first step of the second half. Currently, the first half of the synthesis can be done as a semi-continuous process, so the goal would be to maintain that throughout the rest of the new method.

Universidad De Concepcion, Chile
Andrew Cross (BCH '18) and Shane Fuentes (BCH '18)

Shane Fuentes researching nano-particle polymers in Dr. Urbano's laboratory.

Shane Fuentes, Andrew Cross, and Eduardo (the head of the Chemistry department at Universidad de Concepcion) in the lobby of their science building.

University of Rochester - Rochester, NY
Kathryn Proe
Biological electron donor project. The group is working to get deeper into bioelctrochemistry and microbiology as they work to identify a sustainable supply of electrons for photochemically driving hydrogen evolution from water.

Mentor:  Dr. Sanela Lampa-Pastrik

University of Rochester - Rochester, NY
Kevin Denny
Making CdSe nanoplatelets.

Mentor:  Dr. Todd D. Krauss

Penn State University - University Park, PA
Jacob Murrary - Research Experience for Undergraduates (REU) program working on efficient catalysis in modern synthesis.

University of Rochester Medical Center - Rochester, NY
Department of Biochemistry and Biophysics, Department of Dermatology

Mentor: Dr. Benjamin L. Miller

Tom Dwyer - Examining the Binding Potential of RAGE Inhibitors: Towards New Anti-Alzheimer's Therapeutics

University of California, San Diego - La Jolla, CA
UCSD Skaggs School of Pharmacy & Pharmaceutical Sciences
The Handel Laboratory

Goodwell Nzou - Optimization of Chemokine Receptor Expression in Spodoptera frugiperda 9 Cells.

University of Rochester Medical Center - Rochester, NY
Department of Chemistry, Department of Biochemistry and Biophysics, and Department of Dermatology

Mentor: Dr. Benjamin L. Miller

Moudi Hubeishy - Enhancing the Bioavailability of RAGE Inhibitors: Towards New Anti-Alzheimer's Therapeutic

Abstract: In the past ten years there has been a 68 percent increase of people dying with Alzheimer's disease (AD). AD is a neurodegenerative disease characterized by the progressive loss of brain function. The causative agent of AD is the amyloid- (A) peptide, which has been directly linked to increased levels of apoptosis in neurons. The receptor for advanced glycation end products (RAGE) has been shown to be up regulated in Alzheimer's disease to transport A peptide into the blood brain barrier. Previous research has defined a pharmacophore and designed a lead molecule, which inhibits RAGE from transporting A into the brain. In this research we set out to optimize the bioavailability of the lead compound by enhancing its hydrophilic properties by adding multiple hydrogen bonding groups. I synthesized three different analogs of the lead compound and was able to then characterize and test binding affinities for two of the analogs.

University of South Dakota - Vermillion, SD

Briana Laubacker - Modification of surface ligands coordinated to β-NaYF4: Yb, Er/Tm nanocrystals for use in security printing applications

Faculty Advisor: Dr. Stanley May

University of South Dakota - Vermillion, SD

James Chambers - Investigation into the reactivity of anilinomagnesium halides with carboxylic esters using the Bodroux reaction.

Faculty Advisor: Dr. David Hawkinson

SUNY Upstate Medical University - Syracuse, NY

Molly Kingsley - Characterization of Domain-Swapping Proteins for Design of Self-Assembling Hydrogels

Dr. Loh's biochemistry laboratory

Applying to SUNY Upstate Summer Research Program

Abstract: Molly's work focused on characterizing (and first purifying) six new protein constructs made from ribose binding protein (RBP) and ubiquitin (Ub) which both provided the lever and assembler domain. These proteins were designed to domain swap and ultimately form protein oligomers and hydrogels through the unique forced unfolding mechanism. To domain swap, the lever domain unfolds the assembler domain when it is inserted into a surface loop and the assembler domain swaps with a neighboring assembler.

She characterized the six constructs based on their solubility, stability, ability to bind ribose, and oligomerization. For use in a hydrogel, which is the ultimate goal, the constructs must be extremely soluble and have high oligomerization. Five of the six constructs were highly soluble, stable, could still bind ribose and domain swapped; two of these are moving forward to be used to make hydrogels. Protein based hydrogels have a huge potential in many biomedical uses such as tissue engineering and drug delivery.

Rashid Saleh (BMS, PreMed)
Summer Health Professional Education Program (SHPEP)|
New York, NY

The Summer Health Professions Education Program (SHPEP) is a free summer program for students to explore their interests in medicine, dentistry, nursing, optometry, pharmacy, physical therapy, public health, and more. The program takes place at our 12 partner institutions and offers students a chance to develop healthcare skills, plan academic journeys, get clinical exposure, and network.

Joseph (Joey) Nettles (BMS)
Duke University - Visiting Undergraduate Scholar
Durham, NC

Through this internship Joey developed many research skills he did not have before summer 2023. He is now proficient in cell culture techniques, pipetting incredibly small volumes, using an incucyte system, and doing qPCR. Furthermore, Joey told us he learned new life skills as he had to move to Durham for this internship and need to learn things such as meal prep, shopping for himself and using public transportation. 

Maïka Paquin (BMS)

Centre de Répit Théo Vallières,  Rue Saint-Georges Windsor QC

Amanda Rourke (BCH, PBH minor)
Amanda participated in a PBH internship at Saint Regis Mohawk Health Services, Hogansburg, NY.

Andrew DiMaria (CHM.ADOL, HON)
Andrew completed a Career Exploration Internship at Bay Trail Middle School, Penfield, NY. 

Carlie Smith (BMS, CLS minor)
Carlie participated in a Career Exploration Internship at Oriskany Central School District, Oriskany, NY, while exploring the human and social services field.

Marissa Berghorn (BMS, PMED, HON) 
Marissa completed an Exploratory Internship at Womens OBGYN Associates, Johnson City, NY

Highland Hospital - Hospital Elder Life Program (HELP)
Rochester, NY

Gweynneth Lloyd (BMS) and Lan Nguyen (BMS)


SUNY Downstate Medical Center - clinical research on Afro American and Caribbean patients who had chronic heart disease. Aija tested two different methods, ejection fraction and global longitudinal strain to see which test was more efficient in diagnosing chronic heart failure.
Brooklyn, NY

Aija Jones (BMS)

FF Thompson Hospital
Canandaigua, NY

Alyssa Benziger (CLS)

Medicines for All (M4ALL)
Virginia Commonwealth University
Richmond, VA

Erin Stryker (CHM)

Wegmans - Tim worked as a quality assurance intern at the Wegman's Bakeshop located at 1500 Brooks Avenue. Rochester NY. While there, he worked with another intern in shifts collecting specification data for finished goods produced at the Wegman's Bakeshop to help the company comply with FDA regulations. Along with this, he also helped determine shelf-life dates for new products and assisted the quality assurance technicians with longer term projects

Tim Vinton (CHM)

Bausch and Lomb (Valeant)
Rochester, NY

Vy Bui (CLS)

New Vanderbilt Rehabilitation and Care Center
Staten Island, NY

Tia Moore (BMS)

Highland Hospital - Hospital Elder Life Program (HELP)
Rochester, NY

Tia Moore, BMS, Class of 2020
DeVyne Parks, BMS, Class of 2020
David Powlowski, BMS, Class of 2019



Tia Moore


David Powlowski

Highland Hospital - Hospital Elder Life Program (HELP)
Rochester, NY


Alexis Bell (Biochemistry, '18)

Sophia Qureshi, Biochemistry '19 (No photo)



Roberto Jaquez, Biochemistry '19 (pictured with Naz student Ahmad Jackson)

The Hospital Elder Life Program is part of an innovative and comprehensive health care service for older adults. This program brings together hospital staff and volunteers to provide regular assessment, supportive visits and recreation and exercise opportunities for seniors at risk of delirium and other cognitive or physical difficulties.