Seminar

Dr. Ronald L. Koder (Physical Seminar)

Title "Leveraging disorder in designed biosensor proteins and protein materials"

Dr. Ronald L. Koder, James Peace Chair of Physics

Koder Lab, The City College of New York

Dr. Amrit Venkatesh (Physical Seminar)

Hosted By: Dr. Aaron Rossini 

Title: Pathways for Better Dynamic Nuclear Polarization NMR Polarizing Agents

Dr. David Kaphan (Inorganic Seminar)

Hosted by: Dr. Fred Perras

Title: Metal-Surface Stereoelectronic Communication in Surface Organometallic Catalysis

Dr. Kurt Brorsen (Physical Seminar)

Hosted by: Mark Gordon

Title: "Calculating Vibrationally Averaged Molecular Properties with Multicomponent Methods"

Abstract

Multicomponent methods are a rapidly emerging class of quantum-chemistry methods that inherently and directly include nuclear quantum effects such as zero-point energy and nuclear delocalization in quantum-chemistry calculations. Such nuclear quantum effects are often important when comparing experimentally measured molecular properties to those calculated theoretically. As an example, theoretically calculated rotational constants commonly change by 0.5% when vibrational averaging effects arising from zero-point energy are included. As accuracy with 0.1% of the measured value is normally needed to assist experimental studies, their inclusion in calculations is essential. In this talk, we will pedagogically introduce the multicomponent formalism, discuss our recent implementations of wave function-based multicomponent methods, and demonstrate how these methods can calculate accurate vibrationally averaged molecular properties such as geometries and rotational constants. Finally, we will show how multicomponent methods have the same computational scaling with respect to system size and similar working equations as the standard methods of quantum chemistry. These similarities make multicomponent methods ideally suited to include nuclear quantum effects in computationally chemistry calculations for a wide range of systems and by a diverse cohort of computational chemistry users.

Biography

Kurt R. Brorsen is an Assistant Professor of Chemistry at the University of Missouri. He received his Ph.D. in Physical Chemistry from Iowa State University in 2014 in the group of Mark S. Gordon. He was a postdoctoral research associate at the University of Illinois Urbana-Champaign from 2014-2018. His research focuses on the development of new theoretical quantum-chemistry methods. Current research interests include the development of new multicomponent methods for the inclusion of nuclear quantum effects in computational-chemistry calculations, the application of selected configuration interaction methods to novel systems, and computational studies of precursors for oxidative molecular layer deposition. 

Dr. Michael A. Reynolds (Inorganic Seminar)

Hosted By: Dr. Aaron Sadow 

Title: Achieving Net Zero by Flipping for Hydrogen and Soaring on Soybeans.

Dr. Eszter Boros (Organic/Chemical Biology Seminar)

Hosted by: Brett VanVeller

Title: “Catch and Release: Manipulating the Chemistry of Radioactive Metal Ions to Develop the Next Generation of Metal-based Medicines.”

Abstract:

Stable and radioactive metal ions possess attractive properties for biomedical imaging and therapy. Our lab applies a cross-disciplinary approach that combines physical inorganic chemistry, coordination chemistry, chemical biology and preclinical imaging to transform aqua ions into tools for non-invasive diagnostic imaging, optical probes for image-guided surgical resection and targeted radiotherapy of cancers.

Dr. Jacqueline Applegate (Physical Seminar)

Hosted by: Dr. Theresa Windus

Title: ISU - Foundation of Your Future

Dr. Sonya Hanson (Physical Seminar)

Hosted by: Dr. Davit Potoyan

Title: "Biomolecules aren’t rocks:  Perspective on biological temperature sensors and protein ensembles"

Dr. Maxx Arguilla (Inorganic Seminar)

Hosted by: Dr. Kirill Kovnir 

Title: Through thick and thin: Chemical strategies towards unique electronic and optical landscapes in atomically precise one-dimensional solids."

Karena Chapman - Stonybrook (Physical/Inorganic)

Karena Chapman

Stony Brook University

Inorganic/Physical

Hosted by: Aaron Rossini

Abstract:

X-ray visions: Insights into functional energy materials

Abstract:   Our need for clean energy drive widespread materials research, from energy storage in lithium-ion batteries to efficient catalytic conversions of chemical fuels to  the capture of CO2 from the air. Breakthroughs can be driven by discoveries of new materials or advances in the tools that we use to understand how these materials function and fail. We exploit advanced characterization tools to probe the atomic structure of energy materials in situ, as they function or react. This allows us to identify how their functional behaviors are governed by their structure and chemistry. These fundamental insights serve as a road map towards next-generation clean energy solutions. This presentation will describe recent insights into the structure-function relationship in energy-relevant materials derived from operando high energy synchrotron X-ray scattering and pair distribution function analysis. 

Bio:

Karena Chapman is the Endowed Chair in Materials Chemistry in the Department of Chemistry at Stony Brook University. Before moving the Stony Brook University, she was a chemist at Argonne National Laboratory, building first dedicated Pair Distribution Function instrument at the Advanced Photon Source. She received her undergraduate and graduate degrees at the University of Sydney, Australia. Her research focuses on understanding the coupling of structure and reactivity in energy-relevant materials for which she develops new operando characterization tools and analytics. She is currently engaged in projects on nanoporous materials for catalysis and CO2 capture and advanced materials synthesis. Her work has been recognized as one of American Chemical Society's Talented 12 in 2016, was awarded the 2015 MRS Outstanding Young Investigator Award and the 2023 Hanawalt Award. She has served as a main editor of the Journal of Applied Crystallography and is currently an Associate Editor for ACS Energy Letters.

Paul Robustelli - "Targeting Intrinsically Disordered Proteins and Biomolecular Condensates with Small Molecule Drugs" (BioPhysical)

Paul Robustelli

Dartmouth College

Hosted by: Vincenzo Venditti

**BioPhysical Seminar**

Targeting Intrinsically Disordered Proteins and Biomolecular Condensates with Small Molecule Drugs

Abstract:

Intrinsically disordered proteins (IDPs), which represent ~40% of the human proteome, play crucial roles in a variety of biological pathways and biomolecular assemblies and have been implicated in many human diseases. IDPs do not fold into a well-defined three-dimensional structure under physiological conditions. Instead, they populate a dynamic conformational ensemble of rapidly interconverting structures. As a result, IDPs are extremely difficult to experimentally characterize and are largely considered “undruggable” by conventional structure-based drug design methods.  Our laboratory utilizes a combination of computational and biophysical methods to characterize the molecular recognition mechanisms of intrinsically disordered proteins in atomic detail.  Here I will discuss recent progress in our efforts to characterize the interactions of IDPs with small molecule drugs, understand molecular mechanisms that drive the formation of biomolecular condensate, and understand how small molecule drugs modulate biomolecular condensate stability. 

Bio:

Paul Robustelli, PhD. is an assistant professor of chemistry at Dartmouth College, where his research focuses on the integration of computational and experimental methods to study dynamic and disordered proteins. Dr. Robustelli utilizes computer simulations and nuclear magnetic resonance (NMR) spectroscopy to model the conformational ensembles of intrinsically disordered proteins at atomic resolution to understand how small molecule drugs bind and inhibit disordered proteins and rationally design novel disordered protein inhibitors. Dr. Robustelli has made contributions to the development of physical models (“force fields”) that enable accurate simulations of disordered proteins and computational methods to integrate NMR data as restraints in molecular simulations.

Dr. Robustelli earned his B.A. in chemistry from Pomona College and his Ph.D. in chemistry from the University of Cambridge in the laboratory of Michele Vendruscolo.  Before joining the chemistry faculty at Dartmouth, Paul worked as a postdoctoral fellow at Columbia University in the laboratory of Arthur Palmer III and as a scientist at D.E. Shaw Research.

Seminar: Boone M. Prentice

Boone M. Prentice, Ph.D.

Assistant Professor

University of Florida

Hosted by: Young-Jin Lee

Abstract

Imaging with high chemical and spatial resolutions using mass spectrometry

Imaging mass spectrometry is a powerful analytical technique for analyzing the spatial lipidome. This technology enables the visualization of molecular pathology directly in tissues by combining the specificity of mass spectrometry with the spatial fidelity of microscopic imaging. This label-free methodology has proven exceptionally useful in research areas such as cancer diagnosis, diabetes, and infectious disease. However, state-of-the-art experiments stress the limits of current analytical technologies, necessitating improvements in molecular specificity and sensitivity in order to answer increasingly complicated biological and clinical hypotheses. Especially when studying lipids, many isobaric (i.e., same nominal mass) and isomeric (i.e., same exact mass) compounds exist that complicate spectral analysis, with each structure having a potentially unique cellular function. The Prentice Lab develops instrumentation and novel gas-phase reactions to provide unparalleled levels of chemical resolution. These gas-phase transformations are fast, efficient, and specific, making them ideally suited for implementation into imaging mass spectrometry workflows. For example, these workflows have enabled the identification of multiple sn-positional phosphatidylcholine isomers, the separation of isobaric phosphatidylserines and sulfatides, and the identification of fatty acid double bond isomers using a variety of charge transfer and covalent ion/ion reactions as well as ion/electron and ion/photon reactions. Working with biologists and clinicians, we then leverage these novel imaging technologies to understand the molecular events associated with important problems in human health, including infectious disease, diabetes, and neurodegenerative diseases.

Bio

Boone Prentice is Assistant Professor in the Department of Chemistry at the University of Florida. He received his B.S. in Chemistry from Longwood University (Farmville, VA), and completed his Ph.D. in Chemistry at Purdue University (West Lafayette, IN) under the mentorship of Prof. Scott McLuckey studying gas-phase ion/ion reactions and ion trap instrumentation. He then completed his postdoctoral work in the Department of Biochemistry at Vanderbilt University (Nashville, TN) as an NIH NRSA fellow under the guidance of Prof. Richard Caprioli before joining the faculty at UF in 2018. He was awarded an NIH Focused Technology Research and Development R01 grant in 2020 and a JDRF Innovation Award in 2023 to support his research developing gas-phase reactions and imaging mass spectrometry technologies to study the molecular pathology of diabetes, infectious disease, neurodegeneration, and neuropharmacology. He was also awarded the 2022 Young Investigator Award from Eli Lilly and Company, which is an unsolicited award given annually by Eli Lilly’s Analytical Chemistry Academic Contacts Committee to recognize a “rising star” in analytical chemistry, and was highlighted as a 2023 Emerging Investigator by the Journal of the American Society for Mass Spectrometry and as a 2023 Young Investigator in (Bio-)Analytical Chemistry by Analytical and Bioanalytical Chemistry.

Jason Chen - "Beyond the Round Bottom: Transforming Academic Synthesis"

Professor Jason Chen

Scripps Research - Former ISU Professor (2011-2016)

Hosted by: Wenyu Huang, Levi Stanley and Brett VanVeller

Abstract:

Beyond the Round Bottom: Transforming Academic Synthesis

The Automated Synthesis Facility at Scripps Research provides hardware, software, and services in
support of data-rich synthetic organic chemistry. Founded in 2017, the facility operates $7 million in
equipment in support of diverse projects including reaction discovery, kinetics studies, and natural
products total synthesis. The facility helps scientists to speed up research and improve data quality with
the long-term goal of enabling innovative projects and transforming organic synthesis research. Towards
these ends, the facility staff works with Scripps chemists to develop project-specific solutions and with
instrument vendors to deliver enabling technologies. Vignettes illustrating how the facility works towards
these goals will include examples from chiral reaction development, DNA-encoded library research,
isotopic labeling studies, and chemistry involving gaseous reagents.

Bio:

Dr. Chen participated in International Chemistry Olympiad in high school, 2nd place in 1997. He
received his undergrad and master’s at Harvard with Matthew Shair. Dr. Chen then worked two
years at Enanta Pharmaceuticals as a medicinal chemist working on analogs of the
immunosuppressant cyclosporin A, mostly by olefin metathesis. He then obtained his Ph.D. from
The Scripps Research Institute with K.C. Nicolaou including postdoctoral studies, with work
including total synthesis of uncialamycin (route used by BMS in antibody-drug conjugate
program), asymmetric dichlorination, and co-authorship of the book Classics in Total Synthesis
III. Dr. Chen then went to Iowa State University as an Assistant Professor working on reaction
development, total synthesis, and biorenewable materials research, where he received an NSF
CAREER and an ISU honors program teaching award. Dr. Chen then returned to Scripps
Research where he built the Automated Synthesis Facility from scratch and obtained an NIH S10
equipment grant. He is now the Senior Director overseeing the collective core facilities at
Scripps Research.

George Lisi - "Allosteric and Redox-dependent Regulation of MIF through Molecular Space and Time"

Professor George Lisi, Brown University, BioPhysical

Macrophage migration inhibitory factor (MIF) is a multifunctional immunoregulatory protein that is a key player in the innate immune response. Despite its symmetric trimer structure composed of small, identical protein subunits, MIF contains three enzymatic active sites, a pro-inflammatory receptor binding site, and is implicated in more than 30 protein-protein interactions and diseases.  MIF is implicated in nearly all inflammatory diseases and several cancers, though the mechanism by which MIF engages in promiscuous interactions with substrates and partner proteins is unclear at the biophysical level, hampering the visualization and targeting of MIF disease states. This talk will describe the structural and dynamic factors that facilitate multi-domain crosstalk and control multiple biological activities in MIF and its homologs. Primarily using solution NMR, the highly dynamic MIF structure will be connected to rearrangements that tune its specific catalytic and pro-inflammatory functions.

A secondary focus will be on efforts to leverage biochemical stimuli such as redox conditions and mutations to understand altered MIF structures and signatures of its “disease states.” NMR spectroscopy will reveal real-time, redox-dependent alterations to the MIF solution structure, and through mass spectrometry, detect residue-level modifications that acts as “molecular switches” for selective binding. Biophysical studies implicate redox-dependent structural dynamics as a means to toggle the MIF functions, and these motions are leveraged in the discovery of latent allosteric sites through mutational analysis. A disruption of redox-dependent structural triggers within MIF attenuate its pro-inflammatory CD74 receptor activation in vivo, suggesting sites of redox sensitivity can be targets for structure-based drug design aimed at modulating MIF its pathological function.

Severin Schneebeli - Supramolecular Chemistry to Advance Pharmaceutical Peptide/Protein Biotechnology (Organic)

Professor Severin T. Schneebeli, Purdue University

Peptide drugs represent a rapidly growing segment of the pharmaceutical market. Like antibody drugs, peptides can target key protein-protein interactions, which is difficult to accomplish with small-molecule drugs. Additional key advantages of peptide drugs include their modular synthesis, their metabolism into generally non-toxic amino acids, their relatively low immunogenicity, and the ability to readily prepare libraries. Yet, major challenges remain with peptide drugs that are mostly related to their proteolytic stability and reduced ability to cross cellular membranes. These major ADME-related challenges have not only made it difficult for peptide drugs to reach intracellular targets but have also limited desirable oral formulations of peptide drugs. To meet these challenges, research in the Schneebeli lab is focused on discovering new high-throughput selection approaches for identifying optimal peptide sequences that are not only able to selectively bind their therapeutic targets but also display more favorable ADME properties. To reach this goal, we make use of new sequencing tools driven by supramolecular chemistry advances in our laboratory. This seminar will provide an overview of our new supramolecular tools with a highlight on how to synthetically access them, while also providing a road map outlining their applications for next-generation sequencing of pharmaceutical peptide/protein libraries.

Innovation + Entrepreneurship Academy

Rebecca Runyon

Director of Liberal Arts & Sciences Innovation + Entrepreneurship Academy

Cong Liu - "Understanding the Heterogeneity and Dynamic Evolution of Supported Catalysts via Combined XANES Simulations and First-principle Mechanistic Studies." Argonne National Lab

Professor Cong Liu, Argonne National Laboratory, Physical/Inorganic

Single-site heterogeneous catalysts (e.g., single-atom catalysts, supported organometallics and metal hydrides, etc.) have gained increasing attention in both industry and academia, integrating crucial aspects of homogeneous catalysis (high activity and selectivity) with the stability of heterogeneous catalysts. Because high-surface-area supports are usually preferred in synthesizing these catalysts, a lot of these catalysts often present high heterogeneity in the catalytic sites, resulting in a distribution of active-site structures and site-specific activities. Meanwhile, some of these catalysts may not be stable under reaction condition and can experience dynamic evolution during catalysis. In situ spectroscopic characterization (e.g., X-ray absorption spectroscopy (XAS)) is an effective technique to characterize supported catalysts under reaction conditions. In XAS, X-ray Absorption Near Edge Spectroscopy (XANES) spectra contains key information on the local coordination environment of the metal atom(s), and thus the analysis of which is more challenging. Some key characteristics of the metal centers and their coordination environment can be directly extracted from the experimental XAS, such as average oxidation state and coordination number. However, certain bonding interactions that are key to catalysis, such as metal-hydride, often present only subtle features in XANES spectra, and these are challenging to interpret directly from experimental spectra. In addition, interpreting XANES spectra of supported catalysts with high site heterogeneity is particularly difficult. This is because XAS measures all the catalytic sites, and the response from this technique is dominated by the sites with the highest volumetric density. However, the overall activity is dominated by the sites with the highest turnover frequencies, not necessarily those with the highest density. Computational XANES simulations offer a powerful technique for interpreting experimental spectra, providing a one-to-one correspondence between the molecular structure and spectral features. In this talk, we will discuss about our recent work on a supported organovanadium catalyst and a supported single-atom Cu catalyst to demonstrate that when integrated in situ and computational XANES analyses are combined with systematic mechanistic simulations, the most active catalytic site in dynamic and disordered catalytic systems can be identified. 

Andrew George Roberts - "Natural product-inspired peptide cyclization strategies and their therapeutic applications"

Professor Andrew G. Roberts, University of Utah

Peptide cyclization methods are useful in the development of therapeutic peptide leads with improved metabolic stability properties. To develop residue-selective peptide cyclization strategies, we draw inspiration from cyclic and lassoed peptide natural product scaffolds that exhibit diverse biological activities. For example, the reactive phenolic linkages found in both the arylomycin and vancomycin families of antibacterial natural products motivated us to develop simple-to-perform oxidative methods that generate electrophilic 1,2,4-triazoline-3,5-dione moieties on native peptides to ultimately achieve residue-selective cyclizations (Keyes et al. J. Am. Chem. Soc. 2023, 145, 10071). In awe of lasso peptides, non-covalently interlocked and proteolytically-stable bioactive natural products, we are working in collaboration with the Swanson laboratory to develop and understand strategies for reversible isopeptide bond formation that could enable the sequence-independent chemical synthesis of lasso peptides. Detailed accounts of these developments and their applications will be presented.

Shinae Kim - "Exploring decomposition mechanism of Hydroxylamine on Cu(111) and Iridium(111) surface using Pynta – Workflow code for heterogeneous catalysis reaction."

Exploring decomposition mechanism of Hydroxylamine on Cu(111) and Iridium(111) surface using Pynta – Workflow code for heterogeneous catalysis reaction