Upcoming Seminars & Events

Professor Ambika Bhagi-Damodaran
Department of Chemistry
University of Minnesota
Abstract

Exploring and Engineering Iron Enzymes: Six Years of Bhagi-Damodaran Lab

From respiration to nitrogen fixation, iron-containing enzymes catalyze some of the most critical biological processes. These enzymes exploit their complex protein architecture to manipulate the chemical properties of their iron center and execute a diverse array of biochemical reactions. The Bhagi-Damodaran lab is dedicated to elucidating the structural and mechanistic foundations of iron enzyme function and developing small-molecule discovery and computational protein engineering strategies to optimize their biological capabilities. These enzyme engineering endeavors, while central to biological and inorganic chemistry, hold immense promise for advancing therapeutics and sustainable catalysis. In this seminar, Professor Bhagi-Damodaran will delve into her lab’s research on (A) deciphering the molecular underpinnings of iron enzyme-mediated redox signaling pathways in cells, (B) rationally engineering iron enzymes for precise and adaptable C(sp3)-H functionalization reactions, and (C) redox selectively inhibiting iron enzymes for the development of next-generation antibiotics. This talk will appeal to a broad audience of Biological, Inorganic, Computational, and Analytical Chemists.

Ambika Bhagi-Damodaran

Ambika Bhagi-Damodaran is an Assistant Professor of Chemistry at the University of Minnesota, Twin Cities. Ambika completed her Ph.D. at the University of Illinois, Urbana- Champaign in 2016 focusing on structure- function relations of iron and copper enzymes involved in respiration and denitrification processes. Ambika’s postdoctoral work at the University of California, San Francisco focused on understanding structural basis of protein- protein interactions in an enzymatic cancer drug target. In 2018, Ambika started her independent career at the University of Minnesota. She leads the Bhagi-Damodaran lab which focuses on engineering metalloenzymes towards sustainable catalysis and new therapeutics. Throughout her career, Ambika has received numerous awards. Most notable amongst them are the Young Investigator Award from American Chemical Society, NIH Ruth L. Kirschstein postdoctoral fellowship, Faculty for the Future award from Schlumberger foundation, NIH MIRA award, NSF CAREER Award, 3M NTF Award, RCSA Cottrell Scholar Award, McKnight Land-Grant Professorship, and ACS Jon Sessler Award for Emerging Leaders in Bioinorganic and Medicinal Inorganic Chemistry.

Hosted by Professor Mark Distefano

Professor David R. Williams
Department of Chemistry
Indiana University
Abstract

Inspiration and Discovery in Natural Product Synthesis

The presentation will discuss the generation of ideas, and aspects of strategy that led to experimentation and execution of a route for the total synthesis of cyathin D and related terpenes. Our retrosynthetic analysis is intended to provide a platform for discoveries of new methods. A fusion of ideas and novel applications stemming from the traditions of natural product synthesis will incorporate leading elements of transition-metal catalysis. Stereocontrolled and regiocontrolled transformations require careful attention to detail and a concept for mechanistic understanding of complex reactions.

David R. Williams

David R. Williams received his B.S. degree (Magna Cum Laude, Phi Beta Kappa Honors) at St. Lawrence University (Canton, New York). He went on to graduate studies at the Massachusetts Institute of Technology and was awarded the Ph.D. in organic chemistry in 1976 under the direction of Professor George Büchi. Subsequently, he was awarded the National Institutes of Health Postdoctoral Fellowship for studies at Harvard University with Professor E. J. Corey (Nobel laureate), and also served as an NIH Fellow at Harvard under the mentorship of Professor R. B. Woodward (Nobel laureate). Prof. Williams began his academic career at IU in 1980. His research has resulted in over 160 scholarly publications. To date, 130 graduate students and postdoctoral associates have studied in his laboratories. Prof. Williams’ research interests lie in the development of methodologies and strategies for the total synthesis of biologically active natural products. The Williams’ laboratories have made leading contributions of synthetic chemistry in areas of marine natural products, including macrocycles, antibiotics, and alkaloids. To date, these efforts have described new pathways to approximately 50 natural product syntheses of importance completed as potential therapeutic agents to advance treatments for cancer, as well as other diseases. 

Prof. Williams was named a Fellow of the American Chemical Society in 2024. In addition, he was the recipient of the ACS Ernest Guenther Award in the Chemistry of Natural Products (2018) and was recognized with the ACS Edward Leete Award (2005) for mentorship and scholarship in his research.

Hosted by Professor Chris Douglas

Professor Courtney Roberts
Department of Chemistry
University of Minnesota
Abstract

Access to “Inaccessible” Arynes and Redox Chemistry Using Transition Metal Complexes 

Research in the Roberts group involves looking at unsolved problems in organic synthesis through the perspective of organometallic/inorganic chemistry. One main area of interest for the group is the synthesis of heterocycles through aryne intermediates. Despite their useful reactivity, a number of challenges still remain in the use of arynes including problems with regioselectivity and the synthesis of N-heterocyclic arynes. Using fundamental principles of Ni chemistry, our group is the first to be able to access previously “inaccessible” 5-membered heterocyclic arynes for the first time since they were hypothesized to exist 120 years ago. We are also the first group to demonstrate catalyst controlled regioselectivity in arynes, where all previous examples operated under substrate control. Another challenge in organic synthesis lies in alkyl–alkyl cross-coupling. This is due to challenges with oxidative addition and off cycle pathways such as beta-hydride elimination. Our group has pioneered the use of Group 3 metal catalysts supported by redox-active ligands to overcome some of these challenges. Using 10 mol% of a Sc, Y, or Lu tris(amido) catalyst, coupling partners that both have beta-hydrogens can be successfully cross- coupled for the first time using early transition metals. These improvements related to organic synthesis can only be accessed using inorganic/organometallic chemistry.

Courtney Roberts

Prof. Courtney C. Roberts is an assistant professor and the 3M-Alumni Professor of Chemistry and McKnight Land-Grant Professor at the University of Minnesota. She obtained her B.S. in chemistry from Pepperdine University in Los Angeles, CA. She then pursued her graduate studies at the University of North Carolina at Chapel Hill, becoming the first graduate student in the laboratory of Prof. Simon Meek. During graduate school, Courtney developed rhodium olefin hydrofunctionalization catalysts using a new class of ligands called carbodicarbenes. After completing her Ph.D. in 2016, Courtney became a postdoctoral research fellow in the laboratory of Prof. Melanie Sanford at the University of Michigan where she explored C–H functionalization reactions using high valent Ni. Courtney began her career as an Assistant Professor at the University of Minnesota in the Fall of 2019. The Roberts group focuses on the development of d 0 metal catalysts for alkyl–alkyl cross coupling as well as harnessing heterocyclic aryne intermediates for medicinally relevant building blocks. While at UMN, she has been the recipient of the Amgen Young Investigator Award, a Thieme Chemistry Journal Award, the NSF CAREER Award, the NIH Maximizing Investigators Research Award, ICCC Rising Star Award, the 3M-Alumni Professorship in Chemistry, and McKnight Land-Grant Professorship.

Hosted by Professor Ian Tonks

Professor Sapna Sarupria
Department of Chemistry 
University of Minnesota 
Abstract

Simulations and Advanced Methods for Probing Energy Landscapes (SAMPEL) – Pushing the frontiers of computational simulations for molecular engineering of materials 

Molecular simulations provide atomistic details that enable uncovering the fundamental interactions that govern material behavior. They are a critical tool in completing the structure-property-dynamics-function relationship for materials. SAMPEL lab has two synergistic research thrusts – Area 1 focuses on developing and applying path sampling methods to study rare events. Additionally, we build machine learning-based methods to enable sampling and analysis of the simulation trajectories. We are particularly focused on crystallization. Area 2 combines molecular simulations, advanced sampling, machine learning-based analysis and sampling approaches, and experiments to design biomolecules with desired functionalities. Active projects include enzyme engineering, peptide hydrogels for drug delivery, and vaccine formulations. In my talk, I will discuss the novel approaches we have developed to study nucleation with a focus on integrating machine learning with molecular simulations to identify and characterize transient structures during nucleation. Our approach enables us to see those structures that were previously invisible to the standard metrics used to characterize structures. I will also discuss our efforts in designing vaccine formulations based on small (excipient) molecules to eliminate the cold chain requirement for vaccine storage and distribution. We have uncovered the molecular interactions that lead to the unique behavior of arginine on biomolecular stability. Arginine has been reported to have stabilizing or destabilizing effects on biomolecules based the solution conditions and the reason for this has remained elusive. Our simulations provide the framework to understand this behavior based on which we design binary excipient solutions that can lead to better stabilizing effects. Through both these stories, I will illustrate the synergy of molecular simulations, machine learning, and experiments enabling the molecular engineering of materials.

Sapna Sarupria

Dr. Sapna Sarupria is an associate professor in the department of Chemistry at the University of Minnesota, Twin Cities (UMN). Before joining UMN in Fall 2021, she was an associate professor in the department of Chemical and Biomolecular Engineering at Clemson University. She received her Master’s from Texas A & M University and her Ph.D. from Rensselaer Polytechnic Institute. She was a postdoctoral researcher in Princeton University. Her research focuses on using molecular simulations to tease out the underlying phenomena governing material behavior. Her passion for computational molecular science comes from her love to answer the question “why” and her love for programming. Sarupria research lab is involved in a broad range of projects – ice and hydrate nucleation, development of simulation methods to study rare events, modeling of water purification membranes, and modeling biomolecular assemblies. She received the NSF CAREER award, ACS COMP Outstanding Junior Faculty Award, Clemson’s Board of Trustees Award of Excellence and the CoMSEF Impact Award. Along with research, Sarupria is passionate about enhancing diversity, inclusion, and equity in academia and more broadly in the society. She has actively mentored students and faculty from various backgrounds and enjoys building bridges across different cultures. She is the co-founder of the NSF-funded Institute of Computational Molecular Science Education (I-CoMSE), which is focused on creating a sustainable ecosystem for training the next generation in molecular simulation cyberinfrastructure while enhancing education accessibility and equity. She co-organizes a virtual seminar series “Statistical Thermodynamics and Molecular Simulations (STMS)” that has been successfully running since 2020 and attracts over 80+ participants at every event! So far STMS has hosted 82 seminars with 164 speakers. She is the past-Chair of the Computational and Molecular Science and Engineering Forum (CoMSEF) in AIChE and the chair of the Theory subdivision of Physical Chemistry division at ACS. Additionally, Sarupria is an elected trustee of the not-for-profit Computer Aids for Chemical Engineering (CACHE), and member-at-large of the Executive Board of the Program Committee (EBPC) of AIChE. She is the associate editor for LiveCoMS -- Living Journal of Computational Molecular Simulation, a modern and innovative peer-reviewed home for manuscripts which share best practices in molecular modeling and simulation. She is also the co-Director of the recently established NSF-funded National Research Traineeship program (NRT) Data-Driven Discovery and Engineering from Atoms to Processes (3DEAP) housed in the CEMS and Chemistry department at UMN.

Hosted by Professor Ilja Siepmann

Professor Yang Yang
Department of Chemistry
University of Wisconsin- Madison
Abstract

Constrained Nuclear-Electronic Orbital (CNEO) Framework: Accurate Vibrational Spectra and Hydrogen Transfer Reaction Rates from Efficient Incorporation of Nuclear Quantum Effects

Nuclear quantum effects play a crucial role in various chemical and biological processes, but accurately incorporating them into large-scale molecular simulations remains challenging. Recently, we developed a new quantum chemistry and molecular dynamics framework called constrained nuclear- electronic orbital (CNEO) framework, which enables the accurate and efficient inclusion of nuclear quantum effects in quantum chemistry calculations and molecular dynamics simulations. Using CNEO molecular dynamics (CNEO- MD), we calculated the vibrational spectra of a series of molecular systems and found that it significantly outperforms conventional ab initio molecular dynamics (AIMD), especially for vibrational modes characterized by substantial hydrogen motion. Moreover, by integrating the CNEO framework with transition state theory (TST), we demonstrated that the resulting CNEO-TST significantly outperforms conventional TST in predicting hydrogen transfer reaction rate constants, while maintaining a similar computational cost. Additionally, our recent development of CNEO excited-state theories and CNEO hybrid quantum mechanics/molecular mechanics (QM/ MM) approaches demonstrated the strong potential of the CNEO framework for accurately describing nuclear quantum effects in more complex chemical processes and biological systems.

Yang Yang

Professor Yang is currently an Assistant Professor in the Department of Chemistry at the University of Wisconsin-Madison. He earned his bachelor’s degrees in chemistry and physics from Peking University in 2011, followed by a Ph.D. in 2016 under Dr. Weitao Yang at Duke University. Afterward, he performed postdoctoral research with Dr. Sharon Hammes-Schiffer at the University of Illinois Urbana-Champaign and Yale University before joining the faculty at UW-Madison in 2019. Professor Yang’s research primarily focuses on the development of methods within multicomponent quantum theory to describe systems with significant nuclear quantum effects. His group has recently pioneered a novel framework for molecular dynamics simulations that accurately and efficiently incorporates nuclear quantum effects. In recognition of his innovative contributions, Yang received the NSF CAREER Award in 2022.

Hosted by Professor Don Truhlar

Professor Mark Levin
Department of Chemistry
University of Chicago
Abstract

Replacing Atoms

Transformations that allow for the replacement of one atom for another in a ring system will be presented. Key takeaways include the strategies and concepts that enable site-selective replacements without perturbation of the remaining molecular skeleton. Though the chemical modalities employed to accomplish such transformations are diverse, photochemistry and reagent design are a significant focus.

Professor Yamuna Krishnan
Department of Chemistry, Institute for Biophysical Dynamics, Grossman Institute for Neuroscience
University of Chicago
Abstract

Intracellular electrophysiology

I have been interested in exploring how the ionic milieu within an organelle facilitates its lumenal biochemistry and thereby, organelle function. To map these lumenal chemistries, my lab developed a DNA-based, fluorescent reporter technology to quantitatively map ions such as H + ,
Cl - and Ca 2+ within organelles (1). We can now interrogate organelles of cells in culture, in live organisms (2) and in human patient cells (3,4). Our most recent reporter for absolute membrane potential ended a previous misconception by showing that many organelles do in fact, have membrane potential (4). Today I will discuss two new reporters for organellar Na + and K + : the final pieces needed to build an electrochemical model for organelle membranes (5,6). The only existing electrochemical model of a biological membrane is that of the neuronal cell membrane, first developed by Hodgkin and Huxley in 1952 (7). To accomplish this for organelles we will need input from physicists, cell biologists and electrophysiologists.

References:

1. Krishnan, Y. et. al. “Quantitative imaging of biochemistry in situ and at the nanoscale.” ACS Cent. Sci., 2020, 6, 1938–1954.
2. Narayanaswamy, N. et. al. "A pH-correctable, DNA-based fluorescent reporter for organellar Calcium." Nature Methods, 2019, 16, 95-102.
3. Leung, K., et. al. “A DNA Nanomachine chemically resolves lysosomes in live cells.” Nature Nanotechnology, 2019, 14, 176-183.
4. Saminathan, A., et. al. “A DNA-based voltmeter for organelles.” Nature Nanotechnology, 2021, 16, 96-103.
5. Anees, P. et al. “DNA nanodevices measure the organelle-specific activity of potassium channels.” Nature Biotechnology 2024, 42, 1065-74.
6. Zou, J. et al. “A DNA nanodevice maps sodium at single organelle resolution” Nature Biotechnology 2024, 42, 1075-83.
7. Hodgkin A.L., Huxley A.F. "A quantitative description of membrane current and its application to conduction and excitation in nerve." J. Physiol. 1952, 117, 500–44.

Yamuna Krishnan 

Prof. Yamuna Krishnan is The Louis Block Professor of Chemistry and the College at the University of Chicago. She has pioneered the interface between DNA nanotechnology and cell biology. Her lab has developed a versatile chemical imaging technology to quantitatively image second messengers in real time, in living cells and genetic model organisms. While her lab is engaged in basic biology - discovering new organellar channels and transporters – she has co-founded two companies –Esya Inc & Macrologic Inc, that utilize her organelle-targeting technology for diagnostics and therapeutics respectively. She is a recipient of the NIH Director’s Pioneer Award, the Ono Pharma Breakthrough Science Award, the Infosys Prize for Physical Sciences, Shanti Swarup Bhatnagar Prize in the Chemical Sciences and the Sun Pharma Foundation Award for Basic Medical Research. She is a fellow of the American Association for the Advancement of Science, featured on LSDP’s top 100 global thinkers (2014), and Cell’s 40 under 40 list of scientists shaping current and future trends in biology. She is an Editor for Chemical Reviews, on the scientific advisory/review boards for Angewandte Chemie, Nanoscale, Cell Chemical Biology, to name a few journals and the Max Planck Institute of Cell Biology and Genetics and the Brain Research Foundation to name a few institutions.

Hosted by Professor William C.K. Pomerantz

Professor Osvaldo Gutierrez
Department of Chemistry
Texas A&M University
Abstract

Dreamer’s Pathway to Become a Professor: Tips and Tricks

This talk will be based on my own experience as an undocumented immigrant in this country for more than 25 years and navigating through the school and university system to fund my Ph.D. and beyond. Challenges to address diversity and the role of the Alliance for Diversity in Science in Engineering in addressing these issues will be covered briefly.

Osvaldo Gutierrez

Osvaldo was born in Mexico and raised in Sacramento, California. He attended Sacramento City College and transferred to UCLA in 2006 where he worked as an undergraduate at the laboratories of Prof. Houk where his research focused on the use of quantum mechanical calculations to study organocatalysis. He obtained his B.S./M.S. in 2009 and completed his Ph.D. in 2012 (UC Davis) under the guidance of Prof. Tantillo. From 2012-2016 he worked as a postdoc with Prof. Kozlowski at the University of Pennsylvania where he used computational and experimental tools to study transition metal-catalyzed processes. In 2016 he started his independent position at the University of Maryland College Park as an Assistant Professor, and then promoted to Associate Professor in Summer 2021. In the Fall 2021, he moved to Texas A&M University and recently promoted to Full Professor. His research combined computational and experimental approaches to advance our understanding of iron- and photo- catalyzed reaction mechanisms. In addition to research interests, Osvaldo is involved in a series of initiatives to increase diversity in STEM including serving as president of the Alliance for Diversity in Science and Engineering (ADSE) and organizer of the annual Young Researchers Conference (YRC) and Breaking Barriers Through Chemistry (BBTC).

Hosted by Alexander Umanzor

Professor Osvaldo Gutierrez
Department of Chemistry
Texas A&M University
Abstract

The advent and recent developments of Fe-catalyzed multicomponent cross-coupling reactions 

Despite advances in high-throughput screening methods leading to a surge in the discovery of catalytic reactions, our knowledge of the molecular-level interactions in the rate- and selectivity- determining steps of catalytic reactions, especially those involving highly unstable and reactive open-shell intermediates, is rudimentary. These knowledge gaps prevent control, suppression or enhancement, of competing reaction channels that can drive development of unprecedented catalytic reactions. In this talk, I will focus on our use of high-level quantum mechanical calculations, rigorously calibrated against experimental data, to interrogate the mechanisms and to guide the development of new catalysts and reagents for currently sluggish or unselective reactions. In particular, I will focus on our use of combined experimental and computational tools to understand and develop new (asymmetric) three-component iron-catalyzed radical cascade/cross- coupling reactions.

Osvaldo Gutierrez

Osvaldo was born in Mexico and raised in Sacramento, California. He attended Sacramento City College and transferred to UCLA in 2006 where he worked as an undergraduate at the laboratories of Prof. Houk where his research focused on the use of quantum mechanical calculations to study organocatalysis. He obtained his B.S./M.S. in 2009 and completed his Ph.D. in 2012 (UC Davis) under the guidance of Prof. Tantillo. From 2012-2016 he worked as a postdoc with Prof. Kozlowski at the University of Pennsylvania where he used computational and experimental tools to study transition metal-catalyzed processes. In 2016 he started his independent position at the University of Maryland College Park as an Assistant Professor, and then promoted to Associate Professor in Summer 2021. In the Fall 2021, he moved to Texas A&M University and recently promoted to Full Professor. His research combined computational and experimental approaches to advance our understanding of iron- and photo- catalyzed reaction mechanisms. In addition to research interests, Osvaldo is involved in a series of initiatives to increase diversity in STEM including serving as president of the Alliance for Diversity in Science and Engineering (ADSE) and organizer of the annual Young Researchers Conference (YRC) and Breaking Barriers Through Chemistry (BBTC).

Hosted by Professor Courtney Roberts

Professor Matt Golder
Department of Chemistry
University of Washington
Abstract

Masquerading Soft Materials: Anomalous Behavior in Macromolecular Design

The Golder Research Team utilizes fundamental principles of molecular structure to control synthetic polymer function. Many of society’s greatest advancements spanning health, sanitation, construction, electronics, and transportation have been enabled by the invention and application of plastics. Simultaneously, these materials have created significant concerns about global sustainability, climate impact, and environmental pollution. My laboratory aims to discover new materials and methods that unveil unexpected phenomena on the macroscopic scale; this overarching strategy will produce next-generation designer plastics and reform how commodity plastics are utilized. In this talk, the team’s efforts towards these common goals will be outlined in the context of recent work centered on: (1) synthetic transformations fueled by initiator and methodology development, and (2) molecular design of new soft materials.

Matt Golder

Matt received his BS in Chemistry from the University of Rochester (NY) in 2010 where he conducted organometallic catalysis research with Prof. Patrick Holland. He was also DAAD RISE Scholar at HU Berlin with Prof. Stefan Hecht during his time as an undergraduate. Following graduation, he moved back to his home city of Boston, MA where he began graduate school in the lab of Prof. Ramesh Jasti at Boston University. He relocated with the lab to the University of Oregon in 2014, where he ultimately earned his PhD in Chemistry in 2015. His work on carbon nanohoop synthesis was recognized by a 2016 IUPAC-Solvay International Award for Young Chemists. Matt was then an NIH NRSA Postdoctoral Fellow in Prof. Jeremiah Johnson’s laboratory at the Massachusetts Institute of Technology where he worked on the synthesis of polymer drug delivery agents and unimolecular macromolecules. He began his independent career in the Department of Chemistry at the University of Washington in 2019. His group works at the interface of physical organic chemistry and polymer science to explore novel structural motifs to solve broad challenges centered on sustainability, engineering, and energy. He is the recipient of a Thieme Chemistry Journal Award, NSF CAREER Award, & Army Research Office Young Investigator Program Award, and is an ACS Division of Organic Chemistry Young Investigator and an ACS PMSE Early Investigator.

Hosted by Professor Alexander Grenning