Applying Folding@home to coronavirus research

chem.cst.temple.edu

Chair’s message During the COVID-19 pandemic, Temple chemistry’s resilience meant this spring’s extremely challenging semester was also quite productive. Faculty brought their in-person classes online in a matter of days. Our resourceful and talented students adapted well to this new and, for many, unfamiliar mode of instruction. True to Temple’s motto, Perseverance Conquers, our graduating seniors emerged at the end of the semester with bachelor degrees in chemistry and biochemistry, and our graduate students with masters and doctorates. We hope they will enjoy a graduation ceremony in the near future.

Currently, faculty are developing further expertise in online instruction to be ready for this fall. Meanwhile, the department’s world-class research eff ort continues to transition from a remote work environment back to our more familiar on-campus laboratory environment.

While our path forward faces challenges, there is no doubt that we can overcome anything thanks to the commitment and resilience of our students, staff and faculty. The latter will soon include recently hired Assistant Professor Daniel Kim, an organic chemist. His presence will further strengthen our teaching and research mission to meet the challenges ahead.

I hope you enjoy reading about our department’s growing success.

Daniel StronginProfessor and Chair

CHEMISTRYCollege of Science and Technology

UPDATE SUMMER 2020

Associate Professor Vincent Voelzhas been working with an international team of researchers to computationally screen potential inhibitors of the coronavirus’s main protease, an attractive target for new antiviral drugs. They’re using the distributed computing network Folding@home to do it. Folding refers to the processes by which a protein structure assumes its shape so that it can perform its biological functions.

“Our group uses the tools of molecular simulation and statistical mechanics to investigate the structure and function of biomolecules,” says Voelz, who has worked with Folding@home since 2007 while he was a postdoc at Stanford University, where the distributed computing network started. “It’s a quick jump from that work to using our expertise in biomolecular simulation to help fi ght COVID-19.”

For the coronavirus research, Voelz is partnering with researchers at Memorial Sloan-Kettering Cancer Center and Diamond Light Source. An X-ray crystallography group in the U.K., Diamond Light Source has done groundbreaking work in solving more than a thousand diff erent crystal structures of the coronavirus main protease and discovering several drug fragments that bind to sites on the protein.

You can contribute to the continued success of the College of Science and Technology and the Department of Chemistry by supporting scholarships, undergraduate research and innovative programs. Make your gift at giving.temple.edu/givetocst.

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“When the virus gets inside a cell, it co-opts the machinery of the cell to assemble more copies of itself and replicate,” explains Voelz. “If you can inhibit the protease, you can inhibit a necessary step in the virus’s lifecycle.”

The combined computing power of Folding@home’s users is being used to virtually screen a huge number of potential drug compounds. In early March, about 30,000 users were active participants in the COVID-19 project. As of June 15, there were more than 1 million people participating. “Combined, we are now the largest supercomputer in the world,” says Voelz. “We’ve broken the exaFLOP barrier, a measurement of operations per second that is the equivalent of ten times the computing power of the world’s fastest supercomputer.”

According to Voelz, the speed of the coronavirus’s spread around the world has inspired many researchers to remove “bottlenecks” in how scientific knowledge is developed, analyzed and shared.

“Scientific organizations are sharing information in an unprecedented way, and people around the world are banding together to solve a very difficult problem,” says Voelz. “Folding@home’s kind of citizen science or crowdsourced science can be very powerful. The more people get turned on to this idea, the more vitally important basic science we can do.”

Want to help find new drug therapies to fight COVID-19? Go to foldingathome.org to download the software.

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Folding@home Can’t get enough of research in GermanyStringent, sequenced curricula often make it harder for STEM students to study abroad. But that hasn’t stopped Olivia Stepanic, CST ’19, whose grandfather served in the U.S. Army in Germany, where her mother also spent time as a toddler.

With a referral from Professor Ann Valentine, in whose lab the then-undergraduate fell in love with research, Stepanic spent three months of her junior year engaged in X-ray spectroscopy research in Germany. That research was funded by a $3,000 Temple University Creative Arts, Research and Scholarship grant. She worked with an acquaintance of Valentine’s, Serena DeBeer, an American inorganic chemist who is director of the Max Planck Institute for Chemical Energy Conversion in Germany. She then spent several months taking general education classes, and one inorganic chemistry class, in German at the University of Hamburg.

Stepanic loved the experience so much that, after graduating she returned to the Max Planck Institute and Ruhr-University Bochum to pursue MS and PhD degrees in chemistry. She is using X-ray emission and absorption spectroscopies to explore phosphorus, biological zinc and zinc salts.

“I came back specifically to work with Serena because I thought I could learn a lot more from her,” says Stepanic, whose ultimate goals include teaching and pursuing academic research. “Temple prepared me really well for working in an international research setting. I really enjoy communicating with the wide range of scientists at the institute, and I work with several amazing scientists from around the world.”

Chemistry Department offers popular general education coursesStudents from throughout the university, including non-science majors, have flocked to two 3-credit general education courses:

The Chemistry of WineThis fall course, which regularly draws 100 students, begins with a large-scale fermentation of red and white grapes and continues with team-based analyses of the two-month process of turning grape juice into wine.

The course was pioneered by Robert Levis, professor and now senior associate dean of the College of Science and Technology, when he chaired the Chemistry Department. For the past six years, it has been taught by Robert Rarig, associate professor of instruction.

“Mostly, the students are curious about alcoholic beverages and are attracted to the class because it talks about science in that context,” says Rarig. “Many of them haven’t even had a high school chemistry class, but the course allows me to expose them to the chemistry that surrounds them every day.”

The Chemistry of Global Environmental Issues

Global warming, alternative power sources and ocean acidification are some of issues explored by this course, which attracted more than 60 students during the past two semesters.

“We focus on the chemistry involved in these processes, such as how the increase of carbon dioxide in the atmosphere has led to potential increases in acidity in the ocean and the effects on coral and shellfish,” says Elizabeth Cerkez, assistant professor of instruction, who began teaching the course last fall after developing the curriculum with Rarig.

Students also read current news to become more discerning: Do authors cite sources readers can verify? Who funds a particular study?

Says Cerkez, “The goal is to increase scientific literacy by giving students tools to think critically about the science they see and hear in the news.”

NEW FACULTY

Daniel K. Kim joins the Chemistry Department as an assistant professor of organic/biological chemistry. He earned his PhD from the University of California, Irvine, and for the past two years was a postdoctoral researcher at Princeton University.

His research group will focus on developing new synthetic methodologies to tackle challenges in organic synthesis and in biological systems. “Our main efforts will be to develop novel biocatalysts and transition metal catalysts for applications in the pharmaceutical industry, petroleum industry, and to other fine chemicals such as

fragrances, agrochemicals and small molecule synthesis,” he says.

Newly Funded Grants

Rodrigo Andrade• Synthesis and Evaluation of Narrow-

Spectrum Antibiotics Targeting MRSA, NIH

Eric Borguet• MRI: Development of a Timeresolved,

High-resolution Nonlinear Optical Microscope for Interfacial Studies, NSF

Hai-Lung Dai• Chemical Mechanisms of Biodeterioration

of Aircraft Fuel Studied by Nonlinear Light Scattering, Air Force Office of Scientific Research

Michael L. Klein• Computational Chemical Science

Center: Chemistry in Solution and at Interfaces, DOE

Ronald M. Levy• Mapping Fitness and Free Energy

Landscapes of Proteins, NIH

Spiridoula Matsika• Quantum Chemical Methods for Studying

Photon and Electron Driven Process, NSF

Christian Schafmeister• Development of Intelligent Systems for

Macromolecular Catalysts, Atomically Precise Membranes and Therapeutics, ThirdLaw, LLC

• Developing Nanometer Scale, Atomically Precise Metallocatalysts with Molecular Lego, U.S. Department of Energy

• Molecular Lego Based Organophospha-tase Mimics, Department of Defense

• Atomically Precise Membranes for Gas Separations, Mainstream Engineering Corporation

Francis Spano• Modeling Molecular Aggregate

Photophysics in Free Space and in Optical Microcavities, NSF

Yugang Sun• EAGER: Imaging of Element-Specific

3D Distribution Dynamics in Working Bimetallic Catalysts by in situ Anomalous Small-Angle X-Ray Scattering, NSF

Susan Jansen-Varnum• REU Site, NSF

FACULTY AWARDS

Robert-André Rarig, associate professor of instruction, won the Provost Award for Teaching in General Education and the Dean’s Distinguished Teaching Award.

Vincent Voelz, associate professor, won the William Caldwell Memorial Distinguished Teaching Award.

Daniele Ramella, assistant professor of instruction, won the Dean’s Distinguished Excellence in Mentoring Award.

Kevin Cannon won Temple’s Part-Time Faculty Excellence in Teaching and Instruction Award

TENURE AND PROMOTION

Tenured and promoted to associate professor: Graham Dobereiner

Promoted to associate professor of instruction: Robert-André Rarig

Promoted to professor: Michael Zdilla and Katherine Willets

Retired: Professor Brad Wayland, after teaching and doing research in the department since 2008. Brad’s many important contributions to the advancement of the department’s educational and research mission will be felt for years to come. We wish him well.

IDing new psychoactive drugsAlex Krotulski, CST ’19, is a forensic toxicologist and chemist who utilizes mass spectrometry to identify new psychoactive substances (NPS). These synthetic drugs, including novel, more powerful opioids, are designed to circumvent prosecution for the manufacture, distribution and use of listed illegal drugs, such as cocaine, heroin and fentanyl.

Krotulski, as a research scientist and the program director, oversees operations of NPS Discovery, a flagship program for the nonprofit Center for Forensic Science Research and Education (CFSRE) at the Frederic Rieders Family Foundation in Pennsylvania.

CFSRE collaborates with federal agencies—including the U.S. Department of Justice and the CDC—as well as state and local law enforcement agencies and medical examiners throughout the country to identify new drugs and specific drug combinations responsible for overdose deaths.

Krotulski earned BS and MS degrees in forensic science from Loyola University New Orleans and Arcadia University, respectively—then earned his Temple chemistry PhD in just three and half years while also working full time at CFSRE.

“At Temple, I started to develop and modify certain methods we now use to rapidly identify emerging substances in blood and urine toxicology samples,” says Krotulski, who has published in both the Journal of Analytical Toxicology and Journal of Forensic Science. “Those experiences at Temple, combined with guidance from Professor Susan Jansen-Varnum, my advisor, enabled me to become an expert in this field.”

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For more news, go to chem.cst.temple.edu

Rongsheng Wang• Novel Protein Agents for

Image-guided Cancer Immunotherapy, Fox Chase Cancer Center

• Novel Stapled Peptides to Target Leukemia-Related Protein-Protein Interactions, University of Texas M.D. Anderson Cancer Center

• Steric-free Labeling Strategies to Study Disease-related Non-histone Substrates of Posttranslational Modifications, NIH

Katherine Willets• OP: Super-resolution

Imaging of Plasmon-molecule Interactions, NSF

Stephanie Wunder• I-Corps, NSF

Michael Zdilla• Maximizing Redox

Frustration in Hybrid Organic-Inorganic Energetic Materials to Pursue New Realms of Energy Density, Office of Naval Research

New class preps doctoral candidates to develop research proposalsAs part of their progress towards their degree, PhD students are required to complete and orally defend an original research proposal (ORP). Students must write a 10- to 15-page proposal, present it to the department and answer questions about it from their doctoral advisory committee members.

Last fall, the department introduced a new one-credit ORP class to help students develop so-called “soft skills,” such as communication, necessary to help them write and successfully present their proposals.

“The class focuses on developing ideas, writing clear problem statements, crafting strong hypotheses, setting experimental goals, and defining expected outcomes,” says Associate Professor Katherine Willets, who developed and teaches the course. “We also provide more general guidance on good practices for scientific writing, making strong figures, and writing clear oral presentations.

“The students seem to really appreciate learning how to structure a proposal, including what content to include, as well as seeing examples of other successful proposals as part of our peer-review process.”

Creating new nanoparticle materials for photosynthetic chemistryAssociate Professor Yugang Sun’s research focuses on the potential of novel nanomaterials for utilizing solar energy—rather than heat—to catalyze important chemical reactions.

His research, currently NSF funded, has three thrusts: developing a strategy to synthesize high-performance nanoscale catalyst materials; analyzing these materials’ formation and transformation; and utilizing these catalysts to harvest light energy that drives important chemical reactions.

“We’re trying to use solar energy to drive chemical reactions with improved activity and selectivity on quantum-sized metal nanoparticle catalysts,” he says. “Once we understand why the nanoparticles are behaving the way they are, we can use that information as feedback to design better performing catalysts. If we’re successful, we might be able to overcome the limitations of reaction selectivity determined by thermodynamics.”

The potential applications of photocatalysis on quantum-sized metal nanoparticle catalysts range from reducing carbon dioxide emissions to manufacturing novel pharmaceuticals.

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