The first EVER JAWSChem Webinar will take place via the internet on Tuesday November 24th, 2020 at 11am EST/4pm GST. Please note that every week the seminar time will alternate to accommodate presenters and attendees from different time zones. Sign up on our mailing list to receive the zoom link!
Our featured speakers this week are Haryana Thomas (graduate student; Oklahoma State University), Jenya Semenova (graduate student; University of Florida), and Dr. Victoria Barber (postdoctoral researcher; MIT).
LEARN MORE ABOUT THE SPEAKERS AND THEIR TALKS BELOW
HARYANA THOMAS (on twitter @19hary96)
Biography: Haryana Thomas is a Chemical Engineering PhD student at Oklahoma State University doing research in the field of computational biology. Haryana is doing research in the field of computational biology. Prior to attending Oklahoma State University, Haryana completed his undergraduate degree in chemical engineering from Calvin University where he was the recipient of multiple scholarships and awards including the Jansma family award which enabled him to become a summer research scholar. This opportunity led Haryana to begin a journey in computational research where he is currently working on developing computational tools to enable the prediction of the onset and progression of diabetic kidney damage.
Title of Talk: Modeling the spatial distribution of collagen in mesangial fibrosis during diabetic kidney disease
Abstract: In the U.S. alone over 250,000 people use dialysis or have received a kidney transplant due to diabetic kidney failure. Although we have come a long way in the treatment of diabetes, kidney failure due to diabetic kidney damage is still prevalent, and the need for increasing our understanding of kidney damage to enable the development of better treatment methods is ever present. Thus the goal of this research is to develop computational models to better understand the kidney damage that occurs due to diabetic kidney disease. In the kidney glomerulus, the filtration unit of the kidney, lies a network of capillaries that are surrounded by interstitial tissue called the mesangium. In health, the mesangium acts as a support for the capillaries; however, during diabetic kidney disease, the mesangium undergoes excess deposition of collagen leading to irreparable damage to the environment around it. This damage occurs in stages that have marked spatial distribution patterns. Initially, the deposition is just diffuse collagen deposition which progresses onto nodular formations then segmental collagen deposition until the final stage of globular collagen deposition. Our goal is to understand the factors that affect the spatial distribution of collagen in mesangial fibrosis. Thus, we have developed an agent based model of mesangial fibrosis, using fundamental biological principles of collagen fiber growth, to enable the prediction of spatial deposition patterns and in doing so develop models to predict the progression of diabetic kidney damage.
JENYA SEMENOVA (on twitter @xhimichka)
Biography: Jenya was born in Stavropol, Russia and immigrated to the United States in 2006. She received her bachelor’s degrees in chemistry and psychology from Lake Forest College in 2017 before moving to Gainesville, Florida to pursue graduate studies in organic chemistry under the supervision of Dr. Alexander Grenning. She is currently in her 4th year developing Cope rearrangement and olefin metathesis methodologies for analog synthesis.
Title of Talk: Exploration of olefin metathesis on unique bicyclic tetraenes
Abstract: Explored was the competitive ring-closing metathesis vs. ring-rearrangement metathesis of bicyclo[3.2.1]octenes prepared by a simple and convergent synthesis from bicyclic alkylidenemalono-nitriles and allylic electrophiles. It was uncovered that ring-closing metathesis occurs exclusively on the tetraene-variant, yielding unique, stereochemically and functionally rich polycyclic bridged frameworks, whereas the reduced version (a triene) undergoes ring-rearrangement metathesis to 5–6–5 fused ring systems resembling the isoryanodane core. The ring-closing metathesis products also undergo an unexpected [3,3] sigmatropic rearrangement to yield cyclopenta-fused dihydrofurans or pyrroles.
DR. VICTORIA BARBER (on twitter @vbarber820)
Biography: Dr. Barber began her chemistry career as an undergraduate at Swarthmore College, where she studied the spectroscopy of natural products. She did her PhD at the University of Pennsylvania under the guidance of Prof. Marsha Lester, where she studied the spectroscopy and unimolecular reactions of Criegee intermediates, important intermediates in atmospheric chemistry. For the past year, she has been a postdoctoral researcher at MIT with Prof. Jesse Kroll, where her current research focuses on the chemistry of organic radicals in the atmosphere.
Title of Talk: Automating the Search for New Pathways in Atmospheric Oxidation Chemistry
Abstract: Reactive organic carbon (ROC) is emitted into the atmosphere from a variety of sources and in large quantities. Most ROC subsequently undergoes radical-initiated oxidation in a highly complex, multigenerational process. Standard descriptions of this chemistry have existed for many years, but there remains a great deal of uncertainty in the mechanisms involved. In recent years, a number of "exotic" transformations not found in standard atmospheric oxidation mechanisms (e.g. Peroxy radical isomerization, epoxide formation) have been shown to be of great atmospheric importance. These discoveries suggest that there may be other non-traditional mechanisms that play a role in atmospheric organic oxidation, and point to the need for a systematic way to look for such processes. The Reaction Mechanism Generator (RMG) is an open-source program, typically applied to combustion systems, which automatically develops reaction networks. Here, we use RMG to systematize and automate the search for new mechanisms in atmospheric organic oxidation. Reaction networks are generated for the OH-initiated gas-phase oxidation of a set of approximately 200 substituted pentanes under atmospherically relevant conditions. In addition to the canonical reactions expected for organic radicals in the atmosphere, a number of "exotic" reactions are identified. These include the recently explored reaction mechanisms described above, as well as examples of novel organic radical chemistry. The results demonstrate the utility of RMG as a tool for atmospheric reaction discovery, and provide several interesting targets for further study.