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

flyer with seminar information

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


Organic/Inorganic/Materials Seminar – La’Shaye Cobley, June 7th

Flyer with event info and a smiling woman wearing a white shirt and black jacket

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

Dr. La’Shaye Cobley, California Air Resources Board
Friday, June 7th, 2024
3:00pm, Willamette 110 via Zoom
Hosted by the Alliance for Diversity in Science and Engineering (ADSE)

Navigating the Impacts of Human Activity on the Environment

Dr. Cobley is very passionate about public health, the environment, and mentoring diverse students in STEM. She received her PhD in Biology from the University of Utah and her BA in Biology and Africana Studies from Bowdoin College. During her graduate studies, Dr. Cobley used the leaf chemistries of urban plants to tell stories about air pollution in cities. Her research led her to pursue a career in science policy and she is currently a Staff Air Pollution Specialist at the California Air Resources Board. Dr. Cobley is also a board member of the nonprofit ADDSTEAM. In addition to talking about her dissertation research, Dr. Cobley will discuss various topics such as working in science policy, navigating STEM as a person of color, and how to smoothly changing career paths.

Physical Chemistry Seminar – John Hardwick, June 3rd

flyer with event info and photo of a smiling man in a pink shirtDepartment of Chemistry and Biochemistry
Physical Chemistry Seminar Series

Professor John Hardwick, University of Oregon
Monday, June 3, 2024—2:00pm
Tykeson 140
Hosted by: Jeff Cina

Electron detachment in the infrared: the spectrum and structure of HNO– in the infrared

Over the past few decades, the importance of ions in both common and exotic chemical processes has become obvious. The chemistry of flames, atmospheres, and astronomical objects all involve ion-molecule and ion-ion reactions, some of which are critical in understanding the complex reaction kinetics in those systems. In many such environments, the best way of observing the abundance of molecular ions is high resolution spectroscopy.

The spectra of positive ions are often observed in emission or absorption in laboratory discharges, since positive ions can survive in high temperature environments. Negative ions, on the other hand, often will detach an electron under moderate thermal conditions, since molecular electron affinities are rarely above 1 or 2 electron volts. Rotationally resolved spectra of molecular anions are, as a result, relatively rare.

The HNO– ion is known to have an electron detachment energy of 0.338 eV (about 2776 cm–1). We have recorded the rotationally resolved vibrational spectra of H14NO– and H15NO– near 3000 cm–1. The rotational analysis indicates that the origin of the vibrational band is only about 20 cm–1 above this limit. The analysis requires a determination of the geometry that can be compared with previous experimental and computational studies.

O-I-M Seminar – Illuminating the Patent Examination Process – May 29th

flyer with event informationOrganic/Inorganic/Materials Chemistry – Special Seminar

Illuminating the Patent Examination Process
Presented by: Patent Examiners from the United States Patent and Trademark Office
Wednesday, May 29th @ 12:30PM
Beetham Family Seminar Room, Knight Campus
Sponsored by the Department of Chemistry & Biochemistry and the Office of Innovation Partnership Services

The role of a patent examiner at the United States Patent and Trademark Office is to serve as advocate and protector of the public interest with respect to intellectual property, provide service and assistance to inventors, and evaluate the patentability of claimed inventions. In this presentation, we will describe the patent examination process and the laws applicable to determining patentability of inventions. Afterwards, we welcome a robust Q&A session from audience members. The patenting process can sometimes feel a bit like the Wizard of Oz, in that one does not know what goes on “behind the curtain” after the application is filed. This talk seeks to demystify the processes in evaluating patent applications.

O-I-M Boekelheide Lecture Series – Graham Boswell, May 29th and 31st

Organic/Inorganic/Materials Chemistry Seminars
Boekelheide Lecture Series

Professor Graham Bodwell, Memorial University of Newfoundland
Hosted by Mike Haley

May 29, 2024 ·  2:00 pm, 115 Lawrence Hall

Synthesis, Properties and Chemistry of  Cyclophanes Containing Nonplanar  Polycyclic Aromatic Hydrocarbons

Nonplanar aromatic compounds are interesting molecules because they provide opportunities to learn how chemical and physical properties are affected by changes in structure.  Such compounds are challenging synthetic targets due to fact that they are strained, and the level of synthetic challenge typically increases with the amount of strain.  As a result, powerful synthetic methodology and effective general strategies are required to enable the synthesis of such compounds, especially those that are at more highly strained.  Details of our work aimed at the synthesis and study of cyclophanes that contain bent aromatic systems will be presented.

May 31, 2024 • 3:00 pm, 110 WIL Hall

[n](2,11) Teropyrenophanes: Models for Probing Armchair Edge Chemistry in Nanocarbons and a Platform for the Design of Mixed Cyclophanes with Unusual Properties

Teropyrene, a C36 PAH, is the largest PAH to have been systematically bent out of planarity through its incorporation into a series of [n]cyclophanes (those that consist of a single aromatic system and a single aliphatic bridge).[1] In this series of cyclophanes (1, n = 7-10), the end-to-end bend in the teropyrene ranges from q = 145° to 178°. The teropyrene system undergoes highly regioselective electrophilic aromatic substitution (bromination) and this can be understood in terms of a combination of steric and electronic effects. Furthermore, the chemical reactivity of the teropyrene system toward bromination increases substantially as it becomes more bent.[2] The K-regions can also be oxidized to afford diones that have been π-extended to afford a series of [n]heterocyclophanes. APEX chemistry has also been achieved with high regioselectivity in the synthesis of a cyclophane with C84 aromatic system.

More recently, a large, strained (SE = 44.2 kcal/mol) and conformationally flexible mixed [3.3]cyclophane of pyridine and teropyrene (2) was synthesized using two intramolecular Wurtz coupling reactions and an unprecedented Scholl reaction between the unreactive 2 positions of the pyrene systems in a triply-bridged pyrenophane.[3] Protonation of the pyridine unit results in a greatly enhanced preference for nesting in the cavity of the highly bent teropyrene system (qcalc = 162.6°) and emergence of a charge transfer absorption band (lmax = 592 nm) due to a long range (5.0-5.5 Å), through-space intramolecular transition between the teropyrene and pyridinium units, which does not exist in the neutral cyclophane

References
1. Unikela, K. S.; Ghods Ghasemabadi, P.; Houska, V.; Dawe, L. N.; Zhao, Y.; Bodwell, G. J. “Chem. – Eur. J. 2021, 27, 390–400
2. Unikela, K. S.; Roemmele, T. L.; Houska, V.; McGrath, K. E.; Tobin, D. M.; Dawe, L. N.; Boeré, R. T.; Bodwell, G. J. Angew. Chem. Int. Ed. 2018, 57, 1707–1711.
3. Ghods Ghasemabadi, P.; Tabasi, Z. A.; Salari, P.; Zhao, Y.; Bodwell, G. J. Chem. – Eur. J. 2023, 29, e202302404

Organic/Inorganic/Materials Seminar – Michael Ruggiero, May 24th

flyer with event information

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

Professor Michael Ruggiero, University of Rochester

Friday, May 24, 2024
3:00 pm, WIL 110
Hosted by Chris Hendon

Designing Next-Generation Organic Semiconductors Through Phonon Engineering

Organic semiconductors (OSCs) are an exciting class of materials for advanced electronics. In contrast to inorganic semiconductors, OSCs can be processed in solution under benchtop conditions, enabling them to be engineered for a variety of applications, including flexible devices. However, OSCs are exhibit low charge-carrier mobilities (1-102 cm2 V-1 s-1) compared to their inorganic counterparts (103-105 cm2 V-1 s-1), limiting their utility. The origins of the reduced mobility in OSCs arise from a number of factors, but one of the most significant is electron-phonon coupling – particularly from low-frequency vibrations that are highly-excited at ambient conditions. In this work, recent efforts to generate a mode-resolved picture of electron-phonon coupling through a combined experimental and theoretical approach will be discussed, which provides insight into precisely which vibrational dynamics most strongly influence charge-carrier mobility. Such vibrations, termed ‘killer modes’ suggest that it is often only one or two mode-types that ultimately hinder charge transport in solids. Subsequently, this insight can be leveraged to mitigate detrimental phononic effects in OSCs by ‘phonon engineering’. The results of these efforts will be highlighted, and will showcase the powerful utility – as well as the supramolecular design pitfalls – that arise when subtle intermolecular forces are altered by chemical modification. Overall, this work highlights the powerful interplay between supramolecular design, electronic structure calculations, and vibrational spectroscopy for understanding electronic effects in OSCs, and suggests multiple paths forward for future work.

Physical Chemistry Seminar – Kallol Gupta, May 20th

flyer with event informationDepartment of Chemistry and Biochemistry
Physical Chemistry Seminar Series

Professor Kallol Gupta, Yale University
May 20, 2024—2:00pm
Tykeson 140
Hosted by: Jim Prell

A Nanmeter-Scale Macromolecular Cartography of the Cellular Membrane

The local molecular environment of the native membrane profoundly influences all aspects of membrane protein biology. Despite this, the most prevalent method of studying membrane  proteins uses detergent-like molecules that remove this critical local membrane context. This impedes our ability to quantitatively decipher the local molecular context and how it regulates structure, function, and biogenesis of membrane proteins. Addressing this, combining a  embrane-active-copolymers (MAP) library with MS based quantitative proteomics, lipidomics,  and native mass spectrometry, we present a quantitative molecular platform to determine macromolecular organization of membrane proteins and lipids in the cellular membrane with  nanoscale spatial resolution. Interfacing such capabilities with a range of bioanalytical  approaches, such as singlemolecule microscopy, EM-imaging, and biochemical assays, we aim to render a quantitative molecular view of how the local membrane context regulates the function of membrane proteins in human health and disease.

Physical Chemistry Seminar – Anastassia Alexandrova, May 13th

flyer with event information

Department of Chemistry and Biochemistry
Physical Chemistry Seminar Series

Anastassia Alexandrova, UCLA
May 13, 2024
2:00pm in Tykeson 140
Hosted by: Alexander Batelaan

Enzymes as Molecular Capacitors

Proteins have been shown to produce intramolecular electric fields, preorganized to help enzymatic catalysis. Using IR probes placed in proteins, and measuring their Stark shift, it became possible to assess the local fields at the location of the probe, and correlate those with the reactivity. The talk will show that in fact, 3-D fields in the entirety of the active site (as opposed to a particular bond) are relevant to catalysis.

I will show that the diverging reactivity of the natural Fe-heme proteins is strongly regulated by the electric field from the protein, outside of the primary coordination sphere of the Fe. Next, I will use Protoglobin as a model, which was evolved to efficiently catalyze carbene transfer reactions, to show that what directed evolution developed is a highly strategic electric field that facilitates the reaction. The field is strongly heterogeneous and curvy, aligned opposite to the direction of the electron flow in the reaction. I will demonstrate that electric fields are dynamic. Each protein can visit several characteristic fields, only some of which are strongly catalytic, and some may promote different reaction mechanisms.

The talk will highlight several methods for field analysis, directly as a vector object, and indirectly via the scalar field of electronic charge density. These ideas and methods pertain to our understanding f how enzymes work, how they evolve toward acquiring a function, and how they should be designed to be competitive with natural enzymes.

Organic-Inorganic-Materials Seminar – Grace Han, May 10th

flyer with event informationOrganic-Inorganic-Materials Chemistry Seminar Series
Department of Chemistry and Biochemistry

Grace Han, Brandeis University
May 10 2024
3:00 pm in WIL 110
Hosted by Carl Brozek

Light-Responsive Materials for a Sustainable Future: Exploring Optically-Controlled Functional Organic Systems

Light-responsive materials hold immense potential in revolutionizing various fields including solar energy conversion and storage, recyclable catalysis, single-molecule sensing, and reversible nanomaterial assembly. These materials exhibit phase transitions, changes in solubility, and nanoscale mechanical alterations triggered by external stimuli, particularly light, through molecular-level structural changes. While the photo-switching of molecules has primarily been studied in dilute solutions, understanding this process in condensed liquid or solid environments is crucial for successful real-world applications. Currently, there is a lack of fundamental knowledge regarding the interaction between light and molecules in condensed phases, as well as the impact of photomechanical switching on intermolecular interactions.

This presentation aims to elucidate the design principles behind optically-controllable materials that integrate organic photoswitches or solid-state photochromes. Extensive exploration of various photochromic core structures and functional groups has been conducted to gain insights into the structure-property relationship of these stimuli-responsive material systems. Additionally, the talk will introduce the application of photo-controlled materials in solar photon and thermal energy storage as well as sustainable catalysis.