Research Projects and Mentors

Our group develops and utilizes new light sources and techniques to follow the motions of electrons, holes, and nuclei in molecular and condensed matter systems on ultrafast time scales. Developing new technologies and physics ideas go hand in hand with gaining insight into ultrafast molecular dynamics. PChem II or Modern Physics are good prerequisites to this project.

Surita Bhatia

Nanostructure of Polymer Solutions and Gels for Delivery Applications

Several types of pharmaceutical formulations include polymers that assemble into larger structures such as micelles, vesicles, and networked gels. These structures can aid in solubilizing the active agent and controlling the rate of release within the body. We can probe these structures through small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) experiments. The REU student will work with graduate students in the Bhatia group to either perform and analyze DLS experiments or analyze and fit SAXS spectra. No prior lab experience or knowledge of coding is required. Students wishing to work on data analysis should have access to a computer to download and run the relevant software.

Chris Johnson

Mass Spectrometry and Laser Spectroscopy with Environmental Applications

Students placed in the Johnson group will use mass spectrometry and laser spectroscopy to study the possible structures and thermodynamics of molecular clusters involved in atmospheric new particle formation (NPF), the process by which atmospheric trace gases cluster and grow into climatically-relevant aerosol particles. This project focuses on the surface structure and acid-base chemistry that stabilizes incoming molecules involved in particle growth at the surface, with a particular emphasis on the interplay between proton transfer and hydrogen bonding in clusters composed primarily of sulfuric acid, amines, and organic acids. Recently, iodic acid has been identified as a potent accelerant of NPF in polar regions - the student will perform quantum chemical calculations to predict the most likely cluster structures and their interactions with water vapor and compare these results to more well-understood sulfuric acid clusters. These experiments will help to define a chemical mechanism for the formation and growth of iodic acid-containing particles.

Ben Levine

Computational Design of Materials for Energy Applications

The design of materials for use in energy conversion and storage applications is essential to a sustainable future. Design efforts are most efficient when guided by knowledge of the relationship between the atomistic structure of a material and its function. Computational electronic structure theory enables researchers to discover such relationships without ever setting foot in a traditional wet laboratory. Recent work in the Levine group has elucidated the relationship between the chemical structure of amine-substituted cyanine dyes and their Stokes shifts. Optimization of the Stokes shift is essential to avoiding reabsorption losses in transparent solar luminescent concentrators (TSLCs; windows that act as solar panels). An undergraduate student in the Levine group will utilize computational electronic structure methods to search the range of possible dye molecules for those with ideal properties for application in TSLCs. Toward this end, the student will benchmark the accuracy of ab initio methods for this purpose, in the process gaining familiarity with the approximate nature of quantum chemical calculations. Then they will design their own computational experiment(s) in order to identify structure-function relationship(s). In the process, they will learn about solar energy conversion and the physics of light-matter interactions while developing important design principles for materials for next-generation solar windows.

Amy Marschilok

Batteries are ubiquitous in our everyday lives, but the chemistry that governs their function is diverse and complicated. The A. Marschilok group is interested in electrochemically-based and electrochemistry-coupled approaches to study functional materials and systems, with an emphasis on battery systems. UG researchers will expand their knowledge of physical chemistry, inorganic chemistry, materials science, and electroanalytical chemistry through these projects. Local probes to bulk probes ranging from ultramicroelectrode measurements to systems level impedance will be used to understand factors governing productive and non-productive electrochemistry function. Complementary spectroscopy and diffraction measurements at SBU and Brookhaven National Lab may be employed to gain full insight into the systems.

Ken Takeuchi

The K. Takeuchi group develops synthetic strategies to control both crystallite size on the nanometer scale and non-stoichiometric chemical compositions of inorganic materials, for use of these inorganic materials in energy storage. We emphasize earth-abundant materials and scalable sustainable synthesis approaches, where specific inorganic materials of interest include: iron-containing spinels and inverse spinels, and bimetallic layered or channeled manganese oxide materials. The structure/function relationships among crystallite size, particle size, and the electrochemistry of inorganic materials are of interest to our group. UG researchers have been involved in materials synthesis and characterization, including mechanistic study with application toward electrochemical energy storage (battery) uses for the materials. This includes measurements using advanced characterization tools at BNL, including x-ray absorption spectroscopy and diffraction at the National Synchrotron Light Source II and electron microscopy and x-ray photoelectron spectroscopy at the Center for Functional Nanomaterials.

Biological Chemistry

Figure 1. AlphaFold predicted structure of the heme-based NO sensor NosP from Pseudomonas aeruginosa, a principal pathogen in hospital-acquired infections.

Elizabeth Boon

Heme and Nitric Oxide Binding by NosP

Biofilms, surface-adhered bacterial communities, are widespread, persistent, and extremely resistant to antibiotics; new strategies for biofilm prevention are desperately needed. Our group aims to understand the fundamental mechanisms of biofilm regulation with the goal of preventing biofilm-based infections. When we began our work, several reports had documented NO dispersion of biofilms through an unknown pathway. Our group has since identified two bacterial sensors of NO, H-NOX and NosP. NosP proteins are significantly less well understood than H-NOX proteins, including the basics of structure and heme-binding properties. Using AlphaFold we have generated a predicted structure of NosP (Figure 1). This structure has led us to several hypotheses for structure/function relationships in this protein family. REU students will test these hypotheses by making amino acid mutations in NosP and characterizing those mutants in structural and functional assays, both in vitro and in vivo.

Scott Laughlin

Chemistry for Exploring the Brain

REU students under Laughlin’s mentorship will use chemistry to better understand the brain by creating new strategies for visualizing and manipulating the brain’s cells. The brain contributes more to what makes us human than any other organ system. The challenge of understanding the brain, and the impetus for much of the Laughlin Lab’s research, stems from the brain’s incredible complexity. As we have learned more about the brain, it has become apparent that other types of brain cells in addition to neurons directly contribute to the brain’s computations. For example, cells called astrocytes, have emerged as key participants in the function of neurons and the circuits they compose. Few tools exist for visualizing astrocytes and their interactions with neurons, which prompted the Laughlin lab to develop molecules that can deliver fluorophores and drugs specifically to astrocytes.

Maria Nagan

Computational RNA Folding

The Nagan lab employs computational methods to better understand ribonucleic acid structure and recognition. In the cell, 75% of the genome is transcribed (the transcriptome) but only 2% of ribonucleic acid molecules (RNAs) code for proteins. These sequences that are not expressed, known as long non-coding RNAs (lncRNAs), are greater than 200 nucleotides and variants of lncRNAs are found in genetic disorders, cancer, and diseases related to inflammation. The Nagan lab studies the three-dimensional structure of lncRNAs. REU students will use molecular dynamics methods to fold subsections of lncRNA molecules and structurally characterize the ensemble.

Targeted protein degradation (TPD) is a hot new area of drug discovery in which the protein drug target is physically removed from the cell. TPD differs fundamentally from traditional strategies that normally involve inhibiting enzyme activity, and has the potential to tackle ‘undruggable’ targets. We are applying TPD to drug targets in oncology and infectious diseases including the cancer target Bruton’s tyrosine kinase (Btk) and the COVID-19 target Mpro. Btk is a target for treating B cell malignancies and autoimmune diseases such as MS, while the SARS-CoV-2 main protease Mpro is essential for viral replication and is a target for treating COVID-19 infection. To achieve these goals, we are developing heterobifunctional small molecules known as proteolysis targeting chimeras (PROTACs) that recruit an E3 ligase to the protein of interest leading to ubiquitination and hence selective degradation of the target protein (Figure 1). The PROTACs will be synthesized and compounds that degrade Btk or Mpro will be identified using a combination of biochemical and cell-based assays. Students may use different techniques that are at the interface of chemistry and biology.

Peter Tonge

Targeted Degradation of SARS-CoV-2 Protease Mpro

Figure 1: PROTAC Mechanism of Action. PROTAC’s function by hijacking the endogenous ubiquitination/proteolysis system.

Synthesis

Quinton Bruch

Electrocatalysts and Alkene Difunctionalization

Figure 1. Organometallic tools for control CO2 reduction to ≥C2 products (left) and controlling alkene difunctionalization (right).

Project 1: The Bruch lab develops organometallic tools to exert control over catalysis for the sustainable production of molecular fuels and small molecules. Currently, one area of focus is the development of new bimetallic platforms for electrocatalytic CO2 reduction to valuable ≥C2 products. In this project, the undergraduate researcher will synthesize new ligand backbones with differing electronic properties. In turn, they will then investigate how the electronic tuning influences redox potentials and catalyst activity of bimetallic complexes. These studies will provide insight into structure-function analyses and allow for improved catalyst design. Through this project, the undergraduate researcher will develop skills in organic and inorganic synthesis, air-free/glovebox work, electrochemistry, and characterization techniques such as NMR, GC, and X-ray crystallography.

Project 2: In a separate thrust, the Bruch lab is working to understand how secondary coordination sphere effects can be used to control the regioselectivity of alkene difunctionalization. In this project, the undergraduate researcher will investigate whether structure-function analyses developed in arylamination reactions can be used to predict selectivity in disparate difunctionalizations. The key finding of this work will be either (1) selectivity is conserved and can be used to predict future transformations or (2) selectivity is not conserved and subsequent investigations will determine why that is the case. Through this project, the undergraduate researcher will develop skills in organic and inorganic synthesis, air-free/glovebox work, catalysis, and characterization techniques such as NMR, GC-MS, and LC-MS.

Barney Grubbs

Research projects in Grubbs’ research group are focused on the controlled synthesis and characterization of degradable polymers, with a specific focus on polyacetals and polylactide block copolymers (with the Bhatia group). REU participants will work on short-term projects involving the polymerization of cyclic esters and aldehydes for the preparation of degradable materials. Participants will learn air- and water-free synthetic techniques, glove box use, and a range of characterization techniques, including nuclear magnetic resonance spectroscopy, size-exclusion chromatography, matrix-assisted laser-desorption ionization time-of-flight mass spectrometry.

Figure 1. Schematic illustration of nanocellulose (NC) production from abundant and underutilized biomass feedstocks, followed by their characterization and applications for sustainable water purification (Hsiao and colleagues 2021, Chem. Rev.).

Ben Hsiao

Nanocellulose Templated Nanoparticles Growth for Water Purification

REU students trained in the Hsiao lab will grasp to use nanostructured cellulosic materials, comprising of cellulose nanofibrils (CNF) and cellulose nanocrystals (CNC) for different metals and/or metal oxide nanoparticles growth through less complex, cost-effective and eco-friendly wet chemical methods. Students placed in our group will have the opportunity to understand basic science, which governs the nucleation of different metal ions at CNF/CNC interface. Following that, we tune the versatile functionalities of CNF/CNC, such as hydroxyl or its derivatives including carboxyl, sulfate etc. to reach the desired properties. We use advanced characterization facilities especially X-ray scattering and advanced spectroscopy techniques to characterize nanocellulose-nanoparticle hybrid. These hierarchical systems may simultaneously promote the trapping of pollutants through coagulation/flocculation, adsorption, photocatalysis and membrane filtration; empowering people to tackle varying freshwater crises across the globe.

Jeff Lipshultz

Templated Charge-Transfer Catalysis for Selective Decarboxylative Upgrading of Amino Acids

The Lipshultz group is broadly interested in leveraging "photocatalyst-free" photochemically-active systems for selective single-electron transfer activation of abundant functional groups. One approach we utilize is the reversible "templating" of charge-transfer (CT) complexes between simple organocatalysts and functionality-rich substrates. In this project, the undergraduate researcher will explore the structure-activity relationship between Templated Charge-Transfer (TCT) catalyst structure and activity in the decarboxylative functionalization of simple amino acids. This will enable both catalyst structure optimization and scope exploration, as we explore the boundaries of selectivity-governing parameters in the system. The undergraduate researcher will also gain extensive experience in organic synthesis, purification, and characterization, in the exciting area of visible light photocatalysis.

Iwao Ojima

Computer-Aided Drug Design and Synthesis of Medicinally Active Compounds

Research in the Ojima laboratory broadly focuses on synthetic organic and medicinal chemistry at the biomedical interface, including computer-aided drug design (CADD), as well as chemical and cell biology. This summer, REU students will be engaged in the fundamentals of drug discovery by studying the background of a drug target in medicine, structural biology of the target and computer-aided design of potential drugs. Computational predictions of pharmacological properties (ADME) of the designed potential drugs will also be performed. Then, REU students will investigate a possible (best) synthesis of the designed drug molecule through retrosynthetic analysis, propose a feasible synthetic route to the designed molecule, and then actually be engaged in (a part of) the chemical synthesis. Each REU student will choose the drug target among cancer therapy, infectious diseases control and pain control, depending on his/her interest.

Stan Wong

Investigations of Nanomaterials for Energy applications

We are interested in chemical synthesis and characterization of novel types of nanomaterials for diverse applications in energy such as batteries and fuel cells.

This program is funded by the National Science Foundation. Award No. CHE-2050541.

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