Author: Leah O'Brien
Physical Chemistry Seminar – Evan Williams, November 18th
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.
Dissertation Defense – Matthew Yglesias, November 14th
Chemistry and Biochemistry Department
Upcoming Thesis Defense
Matthew Yglesias
DeRose Lab
Thursday, November 14th, 2024
12 PM in 116 Education
The title of his thesis is “Disruption of Ribosome Biogenesis and Induction of Nucleolar Stress by Platinum(II)-based Chemotherapeutics”
Dissertation Defense – Liam Twight, November 12th
Chemistry and Biochemistry Department
Upcoming Thesis Defense
Liam Twight
Boettcher Lab
Tuesday, November 12th, 2024
9am in 240D Willamette Hall and via Zoom
contact Chemistry and Biochemistry office for Zoom link
The title of his thesis is
“Advancing understanding of oxygen evolving active sites formed by iron adsorption and surface reconstruction of transition metal (hydr)oxide electrocatalysts for high performance alkaline water electrolysis”
Jasti and Dalton Labs’ Collaboration Creates Glowing Implants
Organic/Inorganic/Materials Faculty Introductions – November 8th
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
Physical Chemistry Seminar – Teresa Rapp, November 4th
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.
Organic-Inorganic-Materials Seminar – Nicholas Ball, November 1st
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.
Physical Chemistry Seminar – Dhiman Ray, October 28th
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.
Organic/Inorganic/Materials Faculty Introductions – October 25th
Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series
O-I-M Faculty Introductions – Fall 2024
Friday, October 25, 2024
3:00 pm, WIL 110
Ramesh Jasti
Professor
Chemistry and Biochemistry
Jasti Lab
Romila Mascarenhas
Assistant Professor
Chemistry and Biochemistry
Research
Teresa Rapp
Assistant Professor
Chemistry and Biochemistry
Rapp Lab
Mike Pluth
Professor
Chemistry and Biochemistry
Pluth Lab