Chemistry Research Projects 2024

Anna Gray Ashton

Advisor: Jonas Goldsmith

Synthesis and Assembly of Polymeric Transition Metal Complexes for use in the Production of Clean Hydrogen Fuel via Photocatalytic Electron Relay

Hydrogen-powered fuel cells present an appealing alternative energy source due to their lack of harmful emissions. However, the most common method for producing hydrogen gas, steam reforming, uses methane and results in greenhouse gas emissions. One alternative method for producing hydrogen gas is water electrolysis, which can be energy inefficient and costly. This research aims to develop a novel method for water electrolysis using a polymer composed of transition metal complexes. This polymer contains both a photosensitizer (PS) complex and an electron relay (ER) complex. When the PS is excited by a light source, it can pass electrons to the ER, which then relays electrons to reduce the hydrogen atoms in water and generate hydrogen gas. The energetic advantage of this process is that linking the transition metals together in a polymer film allows for highly efficient electron transfer in the relay. This approach differs from the current method, which relies on the molecules randomly coming into close proximity with each other in solution to transfer electrons. This research aims to synthesize ruthenium, iridium, cobalt, and rhodium transition metal complexes containing vinyl bipyridine ligands, which can be linked together through electropolymerization. The polymers can then be assembled into layers to form the PS/ER water reduction system.

Juanita Beenyi

Advisor: Yan Kung

Structural analysis of the ternary complex of an archaeal mevalonate kinase.

Mevalonate kinase is a key enzyme in the mevalonate pathway found across bacteria, archaea, and eukaryotes, catalyzing the phosphorylation of mevalonate to mevalonate-5-phosphate using ATP. Despite its ubiquity, MK homologs vary significantly in their responses to feedback inhibition and in the structures of their ATP-binding regions. However, in some archaea, downstream metabolites do not inhibit MK, unlike in many other organisms. In addition, although crystal structures of MK bound to either substrate—mevalonate or ATP—have been solved, no structure of the ternary complex yet exists, leaving key questions about MK’s catalytic mechanism unanswered. This summer, I will conduct the kinetic and structural characterization of MK from the archaeon Methanocaldococcus jannaschii (MjMK) with the goal of generating new three-dimensional crystal structures, including the structure of the ternary complex, to provide insight into the MK mechanism. By exploring the structure of MjMK and its ATP-binding architecture, we also hope to gain an understanding of why MK in some archaea is resistant to feedback inhibition. This will yield a better understanding of how the structure of MK governs its activity and regulation.

Sachiko Bower

Advisor: Ashlee Plummer-Medeiros

Investigation of electrostatic interactions of membrane proteins and lipids

PqiA and YebS are proteins found embedded in the inner membrane of E. coli and other Gram negative bacteria, that are associated with the transport of phospholipids from the inner to the outer membrane. The mechanisms of PqiA/YebS and the phospholipid-protein interactions involved with lipid trafficking have not been widely studied, and the structures of PqiA/YebS remain unsolved. This project will investigate the roles of highly conserved polar and charged residues within the transmembrane domains of these proteins, which may contribute to the substrate binding site. Using AlphaFold predicted structures of both proteins, simulation systems will be constructed to investigate these key interactions of PqiA/YebS with membrane phospholipids. Phospholipid-protein interactions will be characterized by lipid residence time, bond distance, bonding atoms, lipid specificity, and type of interaction, using computational analysis. In addition to the analysis of wild type PqiA/YebS, simulations with proteins modified at the aforementioned residues will be constructed to observe lipid activity without key amino acids present. This determination of the mechanism of substrate selection will assist in the characterization of protein function that are critical to bacterial survival, contributing to the field’s understanding of bacterial life.

Abby Champlin

Advisor: Ashlee Plummer-Medeiros

Investigation of the role of the N-terminal extension of YebS on lipid and protein interactions

Gram-negative bacteria contain both an inner membrane and an outer membrane and bacterial growth relies on the efficient transport of phospholipids to the outer membrane. In Escherichia coli there are two protein complexes involved in lipid transfer (i.e., PqiABC and YebST). This research will be focused on the YebST complex or more specifically on YebS. YebS is an inner membrane protein while YebT, also known as LetB, is the bridging protein which physically connects the two membranes. The goal of this research is to further investigate possible interactions between YebS and phospholipids on an atomic level through molecular dynamics simulations using the predicted structure of YebS from AlphaFold. YebS has an N-terminal extension approximately 27 amino acids long that is predicted to be unstructured. Previous simulations of YebS in a phospholipid bilayer have shown that the N-terminal extension adsorbs to the cytosolic regions of YebS and potentially adsorbs to the phospholipid bilayer. This research will investigate the interactions between the YebS N-terminal extension, the phospholipid membrane, and the cytosolic regions of YebS. Phospholipid transfer to the outer membrane of E. coli is integral to the structural stability of the outer membrane and cell growth, thus since YebS is an integral member of the YebST lipid transfer complex it is also important to membrane stability and cell growth. An understanding of the structure and function of YebS, could lead to the development of more specifically targeted antibacterial drugs as the lipid transport complexes could potentially be targeted.

Carmen Gitchell

Advisor: Jonas Goldsmith

The Synthesis of Bimetallic Catalysts and Their Uses in Hydrogen Based Energy

The way that energy is created in the US usually produces carbon dioxide as a byproduct which is harmful to the atmosphere. Hydrogen energy can be made in a more green process though. The goal of the experiment in the future is renewable hydrogen-based energy as opposed to carbon-based energy. This project is focused on synthesizing a bimetallic molecule which works as a catalyst for the reduction of water using light energy, which produces hydrogen gas. One of the metal centers works as a photosynthesizer (absorbs energy and gets excited) which then transfers the electron to the electron relay. The electron is then transferred to an acid creating hydrogen gas. The transition metal complexes need to be close together for this to happen. One of the complexes will have an amine on it and the other will have a carboxylic acid. The two complexes are then connected through an amide bond. The work will involve synthesizing bipyridine molecules with amines and carboxylic acids to make the complexes.

Simone Gorman

Advisor: Bill Malachowski

Enantioselective Synthesis Using Birch-Hydroamination Reactions

Drugs that contain sp3 carbons are more successful in clinical trials than those that contain flat molecules due to the lack of solubility of flat molecules in the body and their tendency to react with many proteins. However, it is difficult to synthesize these quaternary carbons, and it is even more difficult to do so in an enantioselective manner. The Malachowski group has used the Birch-Heck sequence to achieve this goal in the past, but I’ll be looking to extend the strategy to hydroamination reactions. The Birch reduction-alkylation reaction produces a symmetrical diene, and an intramolecular hydroamination reaction would simultaneously generate a quaternary carbon stereocenter and a nitrogen-containing ring, which are incredibly common in successful drugs. The use of a chiral ligand in the hydroamination reaction would allow for the enantioselective creation of a chiral carbon during hydroamination. My research this summer will explore the use of different amines, different reaction conditions, and different chiral ligands in the Birch-hydroamination sequence.

Alex Harmon

Advisor: Patrick Melvin

Novel Synthesis of Fluoroformates Using a Sulfone Iminium Flouride Reagent

Fluorine plays a crucial role in drug development. It is often incorporated into pharmaceuticals to change a drug’s properties such as bioavailability and potency. The Melvin Group focuses on the production and applications of a novel sulfone iminium fluoride (SIF) reagent, which has been used to incorporate fluorine into molecules in under 60 seconds at room temperature. This project continues the investigation of SIF and its potential applications through the production of fluoroformates.  Currently, there are various methods to synthesize fluroroformates, but many of these techniques require highly toxic reagents, feature low yields, or require overnight reactions. The aim of this project is to first synthesize and isolate a scope of alpha-nitrile keto ester substrates. Our novel SIF reagent will then be applied to these substrates to yield various fluoroformates, in the hopes of increasing yields and decreasing reaction times. Easier synthesis of fluoroformates would allow for wider investigation into the applications of this highly useful class of organic molecule.

Suli Kamholtz-Roberts

Advisor: Ashlee Plummer-Medeiros

Investigation of YebS Transport System in Escherichia coli

Gram negative bacteria, such as Escherichia coli (E. coli), have a double membrane system to protect themselves from outside threats and keep functioning properly. The transport pathway of lipids to the outer membrane is important because it provides structural integrity for the bacteria. This project centers on the bacterial membrane protein YebS and understanding how it moves lipids between membranes. YebS is found in the inner membrane and works with YebT to form a lipid transport system. Together, YebS and YebT transport phosphatidylethanolamine (PE) and phosphatidylglycerol (PG), two major lipids in bacterial membranes. This function promotes outer membrane stability and subsequent cell growth. Without YebS functioning properly, the structural stability of the cell would be lost and the bacteria would not survive. YebS will be purified using affinity and size exclusion chromatography in detergent, then a Bradford assay will be conducted to further purify YebS from E. coli before testing it. Synthetic vesicles will then be used, these mimic the inner and outer membrane structure of gram negative bacteria. YebS will be reconstituted into synthetic vesicles and the lipid trafficking between vesicles will be measured to determine the function of the protein and the role it plays in lipid trafficking. PE and PG lipids will be transported from donor vesicle to acceptor vesicle by the YebS system. In E. coli, 75% of lipids are PE and 25% are PG. It is hypothesized that YebS will transport PE to the acceptor vesicle at a higher rate than PG because it is more abundant in E. coli. Future experiments will include testing the rate of lipid transport when adenosine triphosphate (ATP) is added and under various pH conditions. This research will further scientific understanding of the YebS transport system and aid in future development of antibiotics that target lipid transport.

Jude Kim

Advisor: Yan Kung

Structural basis of GGPP inhibition in Saccharomyces cerevisiae (yeast) MK

The mevalonate pathway uses seven enzymes to synthesize precursors for a variety of molecules, including steroids and isoprenoids. Mevalonate kinase (MK), the fourth enzyme of the pathway, binds substrates mevalonate and ATP to catalyze the phosphorylation of mevalonate. MK is competitively inhibited with respect to ATP by various downstream products of the pathway, including isoprenoid precursors and isomers isopentenyl pyrophosphate (IPP, C5) and dimethylallyl pyrophosphate (DMAPP, C5) as well as isoprenoid intermediates geranyl pyrophosphate (GPP, C10), farnesyl pyrophosphate (FPP, C15­), and geranylgeranyl pyrophosphate (GGPP, C20). However, these inhibitors have notably different structures than ATP, raising the question of how MK accommodates such different structures of varying sizes in the ATP-binding site. Previous work by the Kung lab has obtained structures of MK from Saccharomyces cerevisiae (ScMK) bound to IPP, DMAPP, GPP, and FPP, but the structure of ScMK bound to GGPP has not yet been solved. Solving the structure of ScMK bound to GGPP will complete the current structural data of ScMK bound to its inhibitors. GGPP is also of particular interest because its carbon chain is the longest of all known inhibitors, yet it is unclear how ScMK adjusts for the longer chain. Inhibition data exists for GGPP, but without a solved structure of GGPP bound to ScMK, it is unclear exactly how structure correlates with binding affinity. Understanding this information will allow for better insight into the inhibition profile of MK and would be useful in the development of MK-inhibiting drugs. To answer these questions, I will first express and purify ScMK and confirm its activity using kinetics experiments, comparing results to previous data obtained by the Kung lab. I will then crystallize ScMK with GGPP to obtain its structure using X-ray crystallography. 

Maya Kumar

Advisor: Bill Malachowski

Development of Enantioselective Drug Intermediates Through Birch Alkylation Reduction

Completely flat carbon structures don’t make very good drugs. Research has shown that tetrahedral carbons and chiral centers in molecules allow for more selectivity and better bioavailability. This summer in the Malachowski Lab I will work on different methods of efficiently synthesizing tetrahedral chiral carbon structures that through desymmetrizing reactions can, if adapted, produce different enantioselective derivatives. The initial structures are made starting with commercially available ethyl benzoate and conducting a Birch reduction-alkylation reaction to add an alkyl chain with a nitrile group. The nitrile group will then be reduced. The molecule will then be potentially be desymmetrized using a transition metal catalyst to produce a chiral carbon and potentially create stereoselectivity through the use of chiral ligands on the catalyst.

Nuha Mohammed

Advisor: Patrick Melvin

Synthesis of Primary Carbamoyl Fluorides via a Modified Lossen Rearrangement

Fluorine plays a significant role in the pharmaceutical industry. Its incorporation in drug design can influence a molecule's acidity, conformation, lipophilicity, and metabolic stability. Despite fluorine’s crucial role in drug development, installing fluorine atoms still poses a difficult challenge. Given this concern, the Melvin Lab Group has created a novel sulfone iminium fluoride reagent, known as SIF, which is capable of performing effective deoxyfluorination reactions at room temperature in less than 60 seconds. Using this fluorinating reagent, I will ultimately be synthesizing primary carbamoyl fluorides following a modified Lossen rearrangement of hydroxamic acids. My work specifically focuses on developing a variety of hydroxamic acids that can participate in the Lossen rearrangement as well as optimizing the reaction conditions to maximize the yield of primary carbamoyl fluorides.

Charli Parsons

Advisor: Bill Malachowski

Exploration of the Intramolecular Pd-Catalyzed Hydroamination of a Birch Ester Cyclohexadiene

Heterocycles, especially those containing nitrogen, are structures commonly found in pharmaceuticals; therefore, developing efficient and selective synthetic pathways to generate them is crucial. Previous work in the Malachowski lab has explored the possibility of synthesizing these nitrogen-containing heterocycles by conducting hydroamination reactions on the products of the Birch reduction-alkylation, the hallmark reaction of our lab. Building on this work, we will attempt to expand the scope of the hydroamination reaction, yielding a variety of bicyclic structures with quaternary carbons, a particularly challenging carbon to create. Additionally, we hope to carry out mechanistic studies in order to better understand the reaction pathway, rendering it a more useful tool for our lab in the future.

Anna Roumiantsev

Advisor: Yan Kung

Structural Analysis of Substrate Binding in Human Mevalonate Kinase

The mevalonate pathway is a metabolic pathway that is responsible for the production of the precursors to isoprenoids, the largest and most diverse class of natural products that are used as drugs to treat different diseases. Mevalonate kinase (MK) catalyzes the ATP-dependent phosphorylation of mevalonate and is a key enzyme of the mevalonate pathway as it is a primary target of regulation. Although crystal structures of various MK homologs are available, none depict both mevalonate and ATP substrates bound to the enzyme. For human MK, structures of the enzyme bound to either ATP or mevalonate have also not been determined. In this work, I will crystallize MK from Homo sapiens (HsMK) to determine its structure bound to mevalonate and ATP or ATP analogs. Studying the crystal structure of the HsMK active site bound to these substrates will allow us to have a better understanding of MK catalysis and regulation.

Bernie Schintz

Advisor: Jonas Goldsmith

Investigation of Photoreduction Via the Electropolymerization of Ruthenium, Iridium, and Cobalt Transition Metal Complexes 

The Thin Layer Team in the Goldsmith lab focuses on producing hydrogen gas without the dependence on nonrenewable resources. Previously, hydrogen production via water photoreduction has been performed using catalytic systems composed of metal complexes which act as photosensitizers (PS) and a separate electron relay (ER) molecule. The ER quenches the excited PS through electron transfer, creating a reactive species which will reduce protons to hydrogen gas. These components have been studied in solution; however, electron transfer rates depend on distance. This project focuses on the synthesis of iridium, cobalt, rhodium, and ruthenium complexes containing vinyl substituents allowing for electropolymerization. Layering the synthesized polymers allows the complexes to be in close proximity, increasing electron transfer rates. Research aims to investigate how to structure the photosystem through cyclic voltammetry to ensure efficient photosensitizer and electron relay behavior from metal complexes. Since the complex’s photophysical and electrochemical properties depend on its ligands, ligands containing monovinyl and divinyl substituents in different positions will continue to be synthesized and investigated. Research aims to create an efficient photosystem via electropolymerization, techniques that have never been combined in such a manner, highlighting a new avenue of synthesis for hydrogen production.

Eujeong (Sal) Shin

Advisor: Patrick Melvin

Expanding the Use of Sulfone Iminium Fluoride Reagents in the Synthesis of Diverse Fluorinated Molecules

Fluorine is widely used in pharmaceutical and medicinal chemistry for introducing significant modifications to the molecule’s conformation, lipophilicity, solubility, pKa, and metabolic stability. These unique and beneficial properties that fluorine imparts has seen the incorporation of this powerful element into various drug motifs. The Mevin group has previously developed novel sulfone iminium fluoride (SIF) reagents that facilitate efficient deoxyfluorination reaction with high yields in only 60 seconds. Recently, I contributed to a project that took amidoxime substrates and rearranged those to novel fluoroformamidines using SIF reagents. The project this summer will focus on expanding the usage of those same fluoroformamidine products and the exploration of other interesting fluorinated products.

 

Tiffany Xue

Advisor: Jonas Goldsmith

Synthesis of bimetallic transition metal macromolecules for photosensitizer and electron relay pre-connection

The transition towards a low-carbon future necessitates the development of environmentally friendly energy sources, including green hydrogen. However, current hydrogen production methods emit substantial amounts of greenhouse gases, rendering them unsustainable. Electrolysis of water offers promise as a green hydrogen production method, but it suffers from high costs and low output. To address these challenges, our laboratory aims to enhance the photocatalytic water reduction system, thereby increasing hydrogen output. In this system, a light-trapping Photosensitizer (PS) rapidly excites and transfers electrons to an Electron Relay (ER). To establish an effective connection between PS and ER within a limited timeframe, we bring together PSs and ERs through amide coupling, accomplished by synthesizing transition metal macromolecules, with carboxylic acid one carbon away on either PS or ER and amine on the other. Previously we have achieved carboxymethylation. This summer we aim to achieve aminomethylation and improve the procedure with better purity and yield. This research has the potential to make a significant impact on the energy sector and the environment by reducing greenhouse gas emissions and contributing to global climate goals. Additionally, the mechanism employed to attach groups onto the original molecule to establish connections holds further potential for application in other synthesis cases.

Zahraa Zamir

Advisor: Yan Kung

Structural Modification of Cofactor Specificity in HMG-CoA reductase​

The mevalonate pathway is a major metabolic pathway in biology consisting of 7 enzymes responsible for the formation of isoprenoid precursors. Isoprenoids are a diverse class of natural products that can be utilized in many different industries, including but not limited to drug development. HMG-CoA reductase (HMGR) is the third enzyme of the pathway and catalyzes the committed step, the reduction of HMG-CoA to mevalonate. This reaction requires redox cofactors, either NADH or NADPH, where cofactor preference varies between different HMGR homologs. My research aims to develop a molecular understanding of the structural basis of cofactor preference. Previous research in the lab has shown that switching a short ‘cofactor helix’ between two HMGR homologs with different cofactor specificities also switches cofactor preference. Here, we have attempted to identify which amino acid residue(s) in the cofactor helix play a determining role in conferring cofactor specificity. We have performed site-directed mutagenesis of HMGR from Streptococcus pneumoniae (SpHMGR), which has a cofactor preference for NADPH. Our mutagenesis results indicate that changing specific amino acid residues does indeed change cofactor preference, with different mutants showing greater activity using NADH than NADPH. Through this work, we have identified specific amino acids of the cofactor helix that play key roles in conferring cofactor specificity in HMGR.