Organic/Inorganic/Materials Seminar – Ben Bythell, November 22nd

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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.


Physical Chemistry Seminar – Evan Williams, November 18th

flyer with event informationDepartment 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.


Organic/Inorganic/Materials Faculty Introductions – November 8th

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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

flyer with event informationDepartment 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

flyer with event informationDepartment 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

flyer with event informationDepartment 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

flyer with event infoDepartment 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


Organic/Inorganic/Materials Faculty Introductions – October 18th

flyer with event informationDepartment of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series

O-I-M Faculty Introductions – Fall 2024
Friday, October 18, 2024
3:00 pm, WIL 110

Victoria DeRose
Department Head, Professor
Chemistry and Biochemistry
DeRose Lab

Matthias Agne
Assistant Professor
Chemistry and Biochemistry

Gary Harlow
Research Assistant Professor
Chemistry and Biochemistry
Harlow Lab

Paul Kempler
Assistant Professor
Chemistry and Biochemistry
Kempler Lab


Physical Chemistry Seminar – Julia Widom, October 14th

flyer with eevent information and a picture of smiling personDepartment of Chemistry and Biochemistry
Physical Chemistry Seminar Series

Professor Julia Widom, University of Oregon
October 14th, 2024 —2:00pm
Tykeson 140

Title: Spectroscopic Studies of Nucleic Acid structure, Dynamics and Photophysics

RNA performs a diverse set of biological functions, many of which require it to fold into specific structures. Many techniques have been developed to study RNA folding, a number of which are based on fluorescence detection.
I will present work in which we used fluorescent analogues of the natural RNA bases to selectively probe the structures of different conformational subpopulations of RNA.

We investigated the photophysical properties of base analogues in different structural contexts using a combination of time-resolved fluorescence measurements and fluorescence-detected circular dichroism spectroscopy, which circumvents the ensemble averaging that typically limits the power of bulk spectroscopic methods such as CD.

Ensemble averaging can also be avoided by performing measurements on single molecules. I will present work in which we utilized single-molecule microscopy to investigate the ensemble of structures adopted by RNA
“switches”. These studies reveal how the 3D structure of RNA is impacted by intrinsic factors such as base sequence and extrinsic factors such as the
binding of small molecules.


Organic/Inorganic/Materials Seminar – Dirk M. Guldi, October 4th

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Department of Chemistry and Biochemistry
Organic/Inorganic/Materials Seminar Series

Dirk M. Guldi, Friedrich Alexander University Erlangen-Nürnberg
October 4, 2024 ~ 3:00 pm, WIL 110
Hosted by Mike Haley

Title: Towards Adaptive Light Capture, Conversion, and Storage

The sun is an abundant and sustainable source of energy that is vital for the on-going energy transition. However, while abundant, the solar radiation reaching the earth’s surface covers a broad range of energies, from high-energy ultraviolet, through the visible region, to low-energy infrared. This poses significant challenges for efficient capturing and converting solar energy.

For photons with energies well-above the bandgap of the absorbing material, excess energy is lost predominantly by thermalization in the form of heat. In contrast, photons with energies below the optical bandgap are not absorbed at all. Even at peak efficiencies, both thermalization and sub-bandgap losses account for over 50% of incident solar power. Therefore, single-junction solar cells are limited to a maximum performance of 33%, which is known as the detailed balance limit. It is therefore imperative to find strategies to reduce thermalization and sub-bandgap losses to achieve efficiencies beyond the detailed balance limit. Here, down- and up-conversion processes could, theoretically, increase solar-energy conversion efficiencies beyond current limitations by reaching 39% and 49%, respectively. Additionally, the integration of down- and up-shifters with the aforementioned elements will aid in controlling light throughout the solar radiation spectrum, spanning from the ultraviolet up to the infrared.

The spectral conversion enables modifying the incident solar spectrum such that a better match is obtained with the wavelength-dependent conversion efficiency of, for example, the photoactive layer of photovoltaics. We thereby demonstrate to harness down- and/or up-converting or down- and/or up-shifting of the spectrum, meaning that the energy of photons is modified at demand to either lower or higher energy. Hereby, we systematically vary the electronic coupling in molecular dimers and oligomers to tune the dynamics of all relevant down- and up-conversion steps and, in turn, deciphering not only the full mechanisms of singlet-fission (SF) and triplet-triplet-annihilation up-conversion (TTA-UC), but also all bottlenecks enroute towards the conversion targets of 200% down-converted triplets at minimum driving forces and 50% up-converted singlets at maximum anti Stokes shifts. All of our down- and up-converters will be combined with complementary absorbers to round off the optimal spectral overlap across the solar spectrum by either down- or up-shifting of the spectrum. Crucially, we achieve this not only in solution, but also in the solid state with optimized arrangement and panchromatic absorption from 300 to 1000 nm.

Publications & Resources

Guldi Group, Friedrich-Alexander University

Dirk Guldi, Citations

Dirk Guldi, Electrochemical Society

Dirk Guldi, ResearchGate