Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Physical Chemistry Rotation Talks
Thursday, December 12, 2024
2:00pm in Pacific Hall, Room 30
Hosted by Julia Widom
SPEAKERS
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, December 6, 2024
3:00 pm, WIL 110
Christopher Hendon
Assistant Professor
Chemistry and Biochemistry
Hendon Lab
Celeste Melamed
Assistant Professor – Fall 2025
Chemistry and Biochemistry
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Andrew H. Marcus, University of Oregon
December 2, 2024 — 2:00pm
Tykeson 140
Title: Studies of local DNA structure and dynamics by nonlinear spectroscopy and single-molecule optical approaches
DNA contains the ‘genetic information’ that is encoded as specific DNA base sequences, and which is ‘read’ and ‘processed’ by proteins that interact with DNA at specific sites. The local conformations of DNA bases and sugar-phosphate backbones near single-stranded (ss) – double-stranded (ds) DNA junctions undergo thermally activated fluctuations (termed DNA ‘breathing’) within an unknown distribution of macrostates to permit the proper binding of proteins involved in core biochemical processes.
In this talk, I will discuss novel spectroscopic methods and analyses – both at the ensemble and single-molecule levels – to study structural and dynamic properties of exciton-coupled molecular dimer-labeled DNA constructs in which the dimer probes are inserted at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as ‘sensors’ of the local conformations adopted by the DNA bases and backbones immediately adjacent to the probes. These methods can be used to study the biochemical mechanisms of protein-DNA recognition, complex assembly, and function in biological processes.
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
Professor Robert Strongin, Portland State University
3:30 pm, 110 Fenton Hall
December 5, 2024
Hosted by NRT
Title: Advances in Abiotic Biosensors and Targeted Molecular Probes
For the past three decades our group has addressed fundamental challenges in biomedical diagnostics. Applications have included the detection of cancer, cardiovascular disease and redox-related disorders. The general approach involves the development of design principles for transforming relatively simple pH dyes into inherently targeted, highly selective long wavelength and NIR-active agents that function without the need for conjugation to biomolecules. This has allowed us to develop abiotic chemical indicators to detect intriguing disease biomarkers such as specific sugars, amino acids and low-abundant phospholipids. In addition, molecular probes that target human pancreatic cancer tissue have been synthesized and evaluated.
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
Ben Bythell, Hazardous Materials Manager, Chemical Safety Officer
November 22, 2024
3:00 pm, WIL 110
Q & A Session to Follow
Hosted by the Chemistry and Biochemistry Department
Title: Hazardous Waste Determinations and New TSCA Legislation at University of Oregon
New federal TSCA legislation for dichloromethane/ methylene chloride (DCM) requires the University of Oregon and other research-use employers to generate a monitoring program to ensure employee safety. I shall discuss why the law has changed, how the monitoring program will help keep you safe, and what this means for your research and teaching.
Hazardous waste determinations are legally required to occur at the point of generation, i.e., by the lab generator. Most labs do a great job of labeling hazardous waste containers with an accurately filled-in tag. Each lab (PI-responsible) must document how hazardous waste determinations occur for each major process. i.e., with SOPS, SDSs, and chemical knowledge. Dr. Bythell will guide you and your students through completing this process using an online form (~ 2 minutes to complete). I will cover how this reduces lab (PI and institutional) liability, how often to fill in the form, and how to avoid unnecessary work/duplication. Dr. Bythell will audit each of these hazardous waste determination documents promptly and provide PIs, students, and staff copies to show legal compliance has occurred.
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Evan R. Williams – UC Berkeley
November 18, 2024 —2:00pm
Tykeson 140
Hosted by Jim Prell
Title: Overcoming Molecular Complexity One Ion at a Time
Heterogeneous materials can be challenging to analyze especially when the masses of individual components extend beyond 100 kDa. With mass spectrometry, individual charge states produced by electrospray ionization can be difficult to resolve due to overlaps in m/z from other components or from adduction of salts or other non-specific molecular interactions. One demonstrated solution to this problem of sample heterogeneity for high mass analytes is to measure the charge as well of the m/z of individual ions so that the mass of each ion can be determined without interference from other ions. Single ion mass measurements have been performed with a variety of instrument types, but charge detection mass spectrometry with electrostatic ion traps have the advantage of virtually unlimited mass range, single charge accuracy, and the ability to make dynamic measurements. A primary challenge is to acquire single ion data sufficiently rapidly to make this method practical. Solutions to this challenge, as well as state of the art capabilities of charge detection mass spectrometry and applications to viral and nanoparticle analysis will be discussed. Results from experiments aimed at understanding the chemistry and physics of charged droplets will also be presented.
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, November 8, 2024
3:00 pm, WIL 110
Carl Brozek
Assistant Professor
Chemistry and Biochemistry
Brozek Lab
Darren Johnson
Professor
Chemistry and Biochemistry
DW Johnson Lab
Amanda Cook-Sneathen
Assistant Professor
Chemistry and Biochemistry
Cook Lab
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Teresa Rapp, University of Oregon
November 4, 2024 —2:00pm
Tykeson 140
Title: Photo-scissile Ruthenium Compounds for Tissue Engineering and Drug Delivery
Biology is complex. Any biological process we may wish to replicate, modulate, or direct exhibits complexity in both space and time. Spatial gradients of soluble proteins direct cell migration and proliferation. Cell populations must increase and decrease over various timescales. Any disruption to this order leads to a disordered state which is indicated in various diseases, chronic wounds, or tumorigenesis. If we wish to study these disordered systems, we need a platform that affords us control over biological events in both space and time.
Light offers both the researcher and clinician control over biological events in space and time. We leverage the uniquely powerful photochemistry of ruthenium polypyridyl compounds to trigger complex events in biological systems, from changing material environments to releasing drug cargoes on demand.
In this presentation I will discuss how we design and leverage ruthenium’s photochemistry and synthetic accessibility to produce the next generation of photodynamic biomaterials.
Department of Chemistry and Biochemistry
Organic-Inorganic-Materials Chemistry Seminar Series
Professor Nicholas D. Ball, Pomona College
November 1, 2024
3:00 pm, WIL 110
Hosted by the Alliance for Diversity in Science and Engineering (ADSE)
Title: Synthetic Strategies toward Fluorosulfurylation of Organic Molecules and Lewis-Acid Catalyzed Sulfur-Fluoride Exchange (SuFEx)
Sulfur-fluoride exchange (SuFEx) chemistry is emerging as a promising synthetic tool in chemical biology, material science, and synthetic chemistry. In synthesis, sulfur (VI) fluorides show unique promise as synthons in organic chemistry due to their stability versus other sulfur (VI) halogen analogues. The key to adopting SuFEx chemistry is the development of efficient modes to synthesize and react to sulfur (VI) fluorides. Research initiatives employing Lewis acids, and transition-metal chemistry toward synthesizing sulfonyl fluorides will be described. New SuFEx methods that react a broad set of S(VI) fluorides with carbon, oxygen, and nitrogen-based nucleophiles towards structurally diverse S(VI) compounds will also be presented.
Our study introduces a novel SuFEx reaction that synthesizes nitrogen-based sulfonylated compounds from various S(VI) fluorides, mediated via a Lewis acidic calcium salt. This reaction, conducted under a unified set of reaction conditions, allows for coupling sulfonyl fluorides, fluorosulfates, and sulfamoyl fluorides with various amines. The result is the synthesis of a wide array of aryl and alkyl sulfonamides, sulfamides, and sulfamates in good to excellent yield. We will also discuss computational and NMR kinetic studies that aim to elucidate the mechanism of Ca-activation and the lessons learned from these mechanistic studies that have led to new catalytic SuFEx reactions that work across an array of Lewis acids.
Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series
Professor Dhiman Ray, University of Oregon
October 28th, 2024 —2:00pm
Tykeson 140
Title: Deep Learning Augmented Simulation of Biomolecules
Molecular dynamics (MD) simulations are used extensively to study the mechanisms of biological processes in atomistic resolution. Most physiological events, e.g. drug-target binding and protein folding, occur at beyond millisecond timescales. But, we can simulate only up to a few microseconds at an affordable computational cost. Enhanced sampling algorithms such as umbrella sampling, metadynamics, etc. can accelerate conformational sampling by applying external biasing potential. The accuracy and efficiency of these algorithms are sensitive to the choice of collective variable (CV), a low dimensional space along which the bias is applied. Intuitive CVs, e.g. distances, angles, etc. are often insufficient to adequately sample the conformational landscape.
Machine learning algorithms can play a key role in addressing these challenges. We demonstrated that collective variables constructed using deep neural networks with a generic and system-agnostic feature space provide accurate free energy surface for complex molecular systems e.g. protein folding and ligand binding. Using it in combination with the novel On-the-fly probability enhanced sampling (OPES) flooding algorithm, the kinetic properties can also be recovered. Integrating them with explainable artificial intelligence (XAI) methods such as surrogate models can help interpret mechanisms while further improving the sampling efficiency.
The Ray group works on the development and application of these algorithms to study complex biomolecular processes relevant to drug discovery, antibiotic resistance, and rational design of monoclonal antibodies.
