chem-news

Let’s Get Kraken

May 10, 2021

the sigman Group launches open-access tool for chemists

An open-access tool for chemists that promises to save time and money in the discovery of chemical reactions has been launched this week by the research group of Distinguished Professor Matt Sigman of the University of Utah Department of Chemistry and the Matter group of professor Alán Aspuru-Guzik at the University of Toronto.

Kraken—created in a collaboration between the Matter lab, the Sigman group, IBM Research and AstraZeneca—is a library of virtual, machine-learning calculated organic compounds, roughly 300 thousand of them, with 190 descriptors each.

“This collaborative project changes how researchers will approach reaction optimization both in industry and academics,” Sigman says. “It will provide unforeseen opportunities to investigate new reactions while also the ability to know why the reactions work.”

“The world has no time for science as usual,” says Aspuru-Guzik, “Neither for science done in a silo. This is a collaborative effort to accelerate catalysis science that involves a very exciting team from academia and industry.”

“It takes a long time, a lot of money and a whole lot of human resources to discover, develop and understand new catalysts and chemical reactions,” says co-lead author and Banting Fellow Dr. Gabriel dos Passos Gomes. “These are some of the tools that allow molecular scientists to precisely develop materials and drugs, from the plastics in your smartphone to the probes that allowed for humanity to achieve the COVID-19 vaccines at an unforeseen pace. This work shows how machine learning can change the field.”

When developing a transition-metal catalyzed chemical reaction, a chemist must find a suitable combination of metal and ligand. Despite the innovations in computer-optimized ligand design led by the Sigman group, ligands would typically be identified by trial and error in the lab. With kraken, chemists will eventually have a vast data-rich collection at their fingertips, reducing the number of trials necessary to achieve optimal results.

The Kraken library features organophosphorus ligands, what Tobias Gensch—one of the co-lead authors of this work—recalls as “some of the most prevalent ligands in homogeneous catalysis.”

“We worked extremely hard to make this not only open and available to the community, but as convenient and easy to use as we possibly could,” says Gomes, who worked with graduate student Theophile Gaudin in the development of the web application. “With that in mind, we created a web app where users can search for ligands and their properties in a straightforward manner.”

The team also notes that while 330,000 compounds will be available at launch, a bigger-scale library of over 190 million ligands will be made available in the future. In comparison, similar libraries have been limited to compounds in the hundreds with far fewer properties.

“This is very exciting as it shows the potential of AI for scientific research,” says Aspuru-Guzik. “In this context, the University of Toronto has launched a global initiative called the Acceleration Consortium which hopes to bring academia, government, and industry together to tackle AI-driven materials discovery. It is exciting to have Professor Matthew Sigman on board with the consortium and seeing results of this collaborative work come to fruition.”

Kraken can be freely accessed here. The preprint describing how the dataset was elaborated and how the tool can be used for reaction optimization can be accessed at ChemRxiv.

Story originally published in @theU

Camille-Dreyfus Award

May 5, 2021

Luisa Whittaker-Brooks recognized with the Camillle-Dreyfus Teacher Scholar Award

Luisa Whittaker-Brooks, an assistant professor in the department of chemistry, is among 16 early career chemists named as a 2021 Camille Dreyfus Teacher-Scholar. Selected by the Camille and Henry Dreyfus Foundation, Camille Dreyfus Teacher-Scholars receive an unrestricted $100,000 research grant.

“I was actually having a meeting with my undergraduate students when I received a text message from my Ph.D. advisor with the news,” Whittaker-Brooks says. “The only thing I could think about after the text was how instrumental my undergrads were in getting this award.”

Camille Dreyfus Teacher-Scholars, according to the Dreyfus Foundation, “are within the first five years of their academic careers, have each created an outstanding independent body of scholarship, and are deeply committed to education.”

Whittaker-Brooks’ award cites her research in “designer hybrid organic-inorganic interfaces for coherent spin and energy transfer.” Her research group, their website says, is “driven by two of the greatest challenges of our time –sustainable energy and low cost electronics for daily use applications. We plan to embark in these new endeavors by synthesizing and elucidating the functional properties of well-defined and high-quality materials for applications in photovoltaics, thermoelectrics, batteries, spintronics, and electronics.”

Story originally published in @theU

Sloan Research Fellow

March 11, 2021

LUISA WHITTAKER-BROOKS AWARDED PRESTIGIOUS SLOAN AWARD

Assistant Professor of Chemistry Luisa Whittaker-Brooks is one of the recipients of the prestigious 2021 Sloan Research Fellowship, given to researchers “whose creativity, innovation, and research accomplishments make them stand out as the next generation of scientific leaders.”

The awards are open to scholars in eight scientific and technical fields: chemistry, computational and evolutionary molecular biology, computer science, Earth system science, economics, mathematics, neuroscience and physics. Candidates must be nominated by their fellow scientists, and winners are selected by independent panels of senior scholars on the basis of a candidate’s research accomplishments, creativity and potential to become a leader in his or her field. More than 1000 researchers are nominated each year for 128 fellowship slots. Winners receive a two-year, $75,000 fellowship which can be spent to advance the fellow’s research.

Whittaker-Brooks, a 2007 Fulbright fellow, earned her doctorate from the State University of New York at Buffalo before a L’Oreal USA for Women in Science Postdoctoral fellowship at Princeton University. Among other awards, Whittaker-Brooks has received a Department of Energy Early Career Award, a Cottrell Research Scholarship, a Marion Milligan Mason Award for Women in the Chemical Sciences and was named one of C&EN’s Talented 12 in 2018.

“I was very excited as this award is a testament to all the great work that my students have accomplished throughout these years,” Whittaker-Brooks said. “I am happy to see that their endless creativity and research work ethics are highly recognized in the field.”

Her research studies the properties and fabrication processes of nanomaterials for potential applications in solar energy conversion, thermoelectrics, batteries and electronics. She and her research group are also testing hybrid concepts to simultaneously integrate multiple functions, such as a nanosystem that scavenges its own energy.

The Fellowship is funded by the Alfred P. Sloan Foundation, a not-for-profit dedicated to improving the welfare of all through the advancement of scientific knowledge. Founded in 1934 by industrialist Alfred P. Sloan Jr., the foundation disburses about $80 million in grants each year in four areas: for research in science, technology, engineering, mathematics and economics; initiatives to increase the quality and diversity of scientific institutions and the science workforce; projects to develop or leverage technology to empower research and efforts to enhance and deepen public engagement with science and scientists.

Since the first fellowships were awarded in 1955, 44 faculty from University of Utah have received a Sloan Research Fellowship.

 

first published @ chem.utah.edu

Mission Unstoppable

January 8, 2021

 

Mission Unstoppable

Watch chemistry professor and mixed martial artist, Dr. Janis Louie, on CBC television's Mission Unstoppable. Dr. Louie uses exercise to show how science solutions play an important role in our bodies.

Born and raised in San Francisco.– Dr. Louie earned degrees and honed her chemistry skills at University of California, Los Angeles (UCLA), Yale University, and the California Institute of Technology (CalTech) before settling in Salt Lake City and joining the faculty in the University of Utah Department of Chemistry. Her research is centered on the discovery, development, and utilization of transition metal catalyzed reactions to overcome obstacles in traditional synthetic approaches.  Dr Louie's honors include the Cope Scholar Award, the Camille-Dreyfus Teacher Scholar Award, and the inaugural AAAS If/Then Ambassadorship.

Student Spotlights

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COVID Connections

January 4, 2021

Creating a Virtual Symposium

Tanya Vickers

Rising to the Challenge

Science is about preparing the next generation of innovators, explorers, and connoisseurs of curiosity. For the last 29 years the College of Science ACCESS program has been the “first step” on this journey of discovery. The ACCESS program runs from June to August and is open only to first-year students freshmen and transfers).

A cornerstone of the ACCESS experience is the opportunity for the student cohort to share their work with faculty and peers during a research poster symposium. The symposium is a powerful learning experience that mirrors professional science conferences and a career in the field, and plays a key role in the program.

When COVID-19 hit the U.S., the longstanding tradition of the Spring Research Symposium was in jeopardy. As the director of ACCESS , I was driven to find a way to continue the capstone symposium, and provide talented first-year student scientists the opportunity to showcase their research, in spite of social distancing.

With just six weeks until the event we decided to design, build, and launch a novel virtual research symposium platform. The sudden shift and short time-frame presented a real challenge, but it was also an opportunity to pursue and explore innovative approaches to current standards that, if not for CO VID-19, would have been stagnant.

It’s been six months since the Virtual Symposium, and we are still surprised by its success. The merits and results of the virtual platform challenged the notion that in-person is best. The in-person symposium normally saw about 200 guests. In contrast, the virtual symposium reeled in nearly 6,000-page views in three days and 260 guests attended the live zoom presentations.

Thinking Differently

COVID-19 upended and reshaped our everyday lives and challenged everyone to find new approaches to routine activities and novel fixes for nascent problems, much like scientists do on a regular basis.

When the on-campus student research experience was cut short in March, it didn’t mark the end of learning for the 2019-2020 ACCESS cohort. Research faculty agreed to continue mentoring remotely, which included helping the students report their research in a scientific poster they would present virtually. Unfortunately, the technology for a virtual research poster presentation did not exist.

That’s when I began the process of envisioning and creating the Virtual Symposium platform, as it’s now known. I started with identifying the critical elements of an in-person research symposium and considering how to transpose them to a virtual model. My experience teaching and using Canvas (used to deliver course content) shaped the content, and with the collaboration and support of Micah Murdock, Associate Director of Teaching and Learning Technologists (TLT ), a novel virtual research symposium was fully realized.

Embracing Technology

The platform was a lofty goal that required three defining features: a webpage for students to introduce their project, a message board for peers, guests, and mentors to pose questions, and a live Zoom presentation with question and answer.

Each student had a personal webpage that included their research poster, a 3-minute video summary of their research project, and a short personal bio. These elements provided guests with an introduction and interactions analogous to an in-person symposium.

In-person symposia can feel rushed, but the virtual platform offered the advantage of providing guests more time to preview projects on their own, before using one, or both, forum tools—the student scientist’s discussion board, or the 30-minute Zoom live session scheduled on the last day—to ask questions or comment.

Building For the Future

Throughout this process, we wanted to build a tool with the future, as well as other disciplines and applications, in mind. We are proud to announce that the platform has already seen use for the School of Biological Sciences Virtual Retreat, ACCESS Alumni Career Panel, and a number of campus-wide projects. Most recently, the Virtual Symposium was chosen to serve as the cornerstone of the new College of Science high school outreach platform SCIENCE NO W—engaging students, presenters, and elite scientists from across the U.S. and around the world.

As a species and as scientists, we always look forward to new ideas and what can be done. In our darkest hours, we find a space for new forms of unity and growth, and can challenge ourselves to create and expand. CO VID has been undeniably difficult, but the development of new platforms and technologies, like the Virtual Research Symposium, show that sometimes, when we are forced to make changes to long held traditions, the outcome goes beyond finding an equivalent, making what we thought was “best” even better.

Special thanks to Dean Peter Trapa, ACCESS Program Manager, Samantha Shaw, and to the ACCESS students and mentors for believing in the vision of a Virtual Research Symposium.

For more information on the Virtual Symposium platform contact: tanya.vickers@utah.edu.

 

by Tanya Vickers

 

A Catalyst for Safety

December 8, 2020

A Catalyst for Safety

In June 2019, a chemical spill in a Department of Chemistry laboratory led to a full department shutdown until a comprehensive safety assessment could be completed. Within days, most laboratories re-opened. Within weeks, the department had put into motion an unprecedented safety makeover in partnership with the Office of Environmental Health and Safety (EHS) and the College of Science. Since then, the college and EHS have enacted creative solutions to rebuild a culture of lab safety from the ground up—and it has paid dividends in implementing safeguards related to COVID-19.

Tommy Primo

“Everyone from the department level up to the President’s Office has made significant changes to how the U regulates laboratory safety,” said Peter Trapa, dean of the College of Science. “By the time COVID-19 hit, we had the right infrastructure, the right coordination between EHS and our own folks, so that we could quickly lead out in the COVID era.”

Committed committees

Matthew Sigman

At the time of the spill, the U’s laboratory safety culture had been through a series of internal and external audits, including one by the Utah State Legislature. The reports identified crucial gaps in safety and made recommendations for improvement. The U has made significant progress addressing these recommendations, including establishing and expanding the number and authority of college and departmental-level safety committees. Within the College of Science, the Departments of Chemistry, Mathematics, Physics & Astronomy and the School of Biological Sciences all have committees made up of staff and faculty who performed routine lab inspections and reported violations. The previous safety system’s structure allowed some violations to remain unresolved. Now, the committees are empowered to recommend how violations get addressed. They’ve also expanded their scope to include postdocs and graduate students who can make suggestions for outdated practices or areas that need attention. In the coming weeks, safety committees will be required in all University colleges.

“To change the safety culture, there has to be the motivation, and it has to be a grassroots effort,” said Matthew Sigman, Peter J. Christine S. Stang Presidential Endowed Chair of Chemistry. “This is a success because it’s collaborative, it’s conversational, and it’s pragmatic. It’s about building relationships and getting buy-in from the top down.”

Sarah Morris-Benavides

In January, EHS and the College of Science jointly hired Sarah Morris-Benavides as the first associate director of safety for the College. Morris-Benavides facilitates communication between researchers, and helps translate regulatory protocols between the college and EHS. She also heads the College of Science’s safety committee that is made up of the department committee chairs. She and the committees have worked closely to ensure that classes and research are conducted safely in light of the coronavirus restrictions.

“I can’t tell you how valuable they’ve been,” said Morris-Benavides of the response to COVID-19. “We had a great benefit that these committees were already established and in place.”

Every month, the college safety committee meets to discuss each department’s safety protocols. “We have the ability to say, ‘Well, here’s something that they’re doing in biology. Does that make sense for physics?” she said. “Chemistry learned a lot from their amazing safety turnaround, and they’ve shared their best practices. It all benefits every department.”

Precipitating solutions

Selma Kadic

The U overhauled the previous laboratory safety system by restructuring EHS directly under the Vice President for Research Office, and Frederick Monette became its new director. This helped rebuild trust between the EHS and researchers, who had historically been at odds.

“Fred Monette was all in right away. His willingness to sit down with people, listen to their concerns, and back it up financially meant a lot to the people in the department,” said Holly Sebahar, professor of chemistry who was the chair of the chemistry safety committee at the time of the shutdown.

Safety violations can be complicated; some are easy fixes, such as ensuring lab members wear proper PPE, but other issues are expensive, such as electrical or ventilation upgrades within older buildings. Traditionally, the burden of arranging infrastructure upgrades and their cost often fell solely on the principal investigator (PI) of the laboratory in question.

Angus Wu

To change that, EHS and the College of Science lobbied for an infrastructure improvement project to fund overdue, expensive safety upgrades in College of Science buildings, many of which were identified as deficiencies during the chemistry shutdown. The resulting $1 million capital improvement project will address electrical upgrades, seismic bracing, and ventilation improvements in several buildings, beginning in January 2021. Addressing these deficiencies in one comprehensive project will be much quicker, more economical, and result in less disruption to laboratory operations compared with the past approach of fixing each issues one by one at the request of individual laboratories.

Working with the College of Science, the VPR Office facilitated the purchase of 20 new refrigerator/freezers rated for storage of flammable chemicals to replace units that failed to meet regulatory requirements, sharing the cost 50/50 with the PIs. These initiatives demonstrated the administration’s commitment to promoting a culture of safety across the university.

From the ground up

As another example of a changed safety culture, the Department of Chemistry aims to incorporate safety in all aspects of academic life. Every speaker, seminar and many group meetings now incorporate a ‘safety moment,’ with each presenter asked to share an example of a safety incident and how they addressed it.

Shelley Minteer

“We have upwards of 30 or 40 external visitors a year. That’s a lot of safety moments. They’ll walk through that experience, then walk through the lab procedures to fix the problem,” Sigman said. “It’s a lessons learned, but also it’s an open conversation. We want to have the lowest risk, but we know when you sign up to be a chemist, you have the danger. Even when you cross the t’s, dot the i’s, something can happen.”

The collaborations go beyond the science—last year, EHS, the College of Science and the College of Mines and Earth Sciences co-hosted a two-day lab safety symposium with speakers and training sessions that addressed all types of issues, from chemical storage to creating effective safety committees. More than 400 staff, students and faculty attended the mandatory event to emphasize that every individual is responsible to making their environment safe. The U is applying that same philosophy for COVID-19.

“As we started going through the safety culture changes, we realized that it’s not that students or post docs or faculty won’t follow safety protocols, they will, if they know where they are, if they can find the paperwork,” said Shelley Minteer, associate chair for faculty for the Department of Chemistry and COVID-19 coordinator for the department. “We learned a lot from the safety ramp up. We need clear guidelines and good communication. We’ve been applying those same principles to COVID.”

 

by Lisa Potter - first published in @theU

 

Michelle Williams

November 17, 2020

Michelle Williams

Michelle’s story sounds like it must have been deliberately calculated and executed. How else does someone go from Jamaica at an all-girls boarding school to college in New York City to graduate school at the University of Utah to Global Group President of Arkema, a billion-dollar subsidiary of Altuglas International? Turns out, Michelle had zero plans whatsoever to lead an international company along her career path. Instead, she thought she might like teaching. As she says, “Plan A never works out, and sometimes it’s Plan H or Plan G that finally works!”

She came to the University of Utah after breezing through college so much so that it was all a blur, and she found herself in Dr. David Grant’s research group at the age of 19. “I had no idea what I was getting into.” She, like most 19-year-olds, was looking for adventure and eagerly said goodbye to her teary-eyed mother at the airport. Michelle was checking off her adulting list: she rented an apartment--her ​own​ place; figured out her schedule; supported herself on her tiny teaching and research stipend; and she made her way, “I mucked my way through it.”

Michelle is emphatic that “this is where I grew up.” Only second to her decision to have children, coming to the University of Utah Chemistry Department was the best decision she ever made. Despite her overwhelm when she began her graduate research, she was quick and willing to ask for help, and she’s continued to do so throughout her entire career. “The reality is that I have always found that there are people who will help you. There are always people who see something in you.”

As she was completing her PhD research and dissertation defense, Michelle began casually interviewing with companies while she waited for her experiments to finish. She turned down a job offer from Dow Chemical though the interview was one of the most impactful conversations she would have about her career. The interviewer advised her, “young lady,” at which Michelle rolled her eyes, “you’re going to have opportunities and opportunities, and you need to find a company that has the right personality to match your personality.” She turned down the Dow Chemical position, and, instead, accepted a job at Rohm and Haas.

The job at Rohm and Haas was a continuation of the sense of community she had come to love at the University of Utah. It was a small enough, family-owned company where she could build relationships, and the focus was on learning, training, development and growing people. From a young age, Michelle has developed and followed her core values through every step of the way.

 
by Anne Vivienne
 

Bill Jack

July 20, 2020

Bill Jack’s undergraduate experience at the University of Utah’s Chemistry Department was foundational and flavored his graduate school and professional path. In hindsight, Bill also recognizes the influence of the few humanities courses he participated in where discussions on James Joyce and American Literature altered his perspective on the world. His only regret about his undergraduate years here at the U, is that he did not slow down and take advantage of broader educational opportunities to learn as much as he could in both the humanities as well as in chemistry.

During one undergraduate summer, Bill was inspired by a single sentence in a physics course that would influence the way he approached the world. The instructor, Dr. Swaggart, began his class by telling the students, “I’m going to teach you about a new way to look at the world.” Bill integrated this sentiment in a variety of different subjects since then, whether in math, social studies, literature, chemistry, anything really. “It’s a different way to see the world, and that broad background just increases your appreciation of the world,” says Bill.

Bill’s educational foundation lead him to a graduate program at Duke University where he thought he would begin a career as a physical biochemist after “tailing” Sidney Velick all summer, but, in an effort to simplify his newlywed life, he asked to work in a lab which quickly altered his path. He ended up being a graduate student with Paul Modrich researching an enzyme that ended up being one of the enzymes that is foundational at New England Biolabs--the only “real” job he’s ever had after he completed his graduate and postdoc work.

Bill has been working at NEB for the past 31 years, and now enjoys the freedom to take risks in his research. He confirms that the company’s founder is absolutely right when he claims that, “New England Biolabs scientists can’t wait to get to work each morning to see how their experiments turned out.” Bill’s latest project is admittedly risky, but that’s what makes it so exciting. The possibility that something might work as he tries to wrap his mind around different ways of analyzing and changing the environment to find a solution for such a fascinating biological phenomena keeps him pushing new boundaries.

Bill is collaborating with a team at Columbia University with an expertise in the biology of the DNA sequence he’s investigating. They’re growing, breaking, and piecing back together the sequences to try to replicate in a test tube the DNA splicing that happens naturally. “I believe that there will be steps along the way that we will have insights into other organisms, other processes whether they be normal ones or ones that cause disease, and there’s also even prospects from a commercial perspective that some of the enzymes involved will be useful in advancing other molecular biology techniques. The company I work for takes enzymes that occur in nature, pulls them out, and characterizes them so they’re available in other workflows to prepare DNA sequences.”

 
by Anne Vivienne
 

Kurt Zilm

July 5, 2020

As Yale’s current Chair of the Chemistry Department, it seems clear that Kurt has always understood what the foundation of a successful chemistry department is built on: human connection, collaborative research, and investment in students. As a graduate student at the University of Utah, Kurt took advantage of Professor Ted Eyring’s time, knowledge, and generosity as much as Ted would endure his endless questions and curiosity. He’s spent the past 16 years as the Director of Undergraduate Studies at Yale University, and has committed to create an environment for students that allows them to indulge their curiosity--just as he was able to do with Professor Eyring.

After being at Yale for 38 years, Kurt has recently been part of a renaissance in their college of science as they renovate and build facilities that give all students the opportunities and experiences they need in order to establish themselves as serious chemists and innovators. The department’s investments have made it possible for every undergraduate in organic chemistry to have their own hood with an updated condenser system that delivers chilled water back through a seperate gravity-fed drain system--saving 150,000 gallons of water per year. Kurt has moved his lab three times in the past few years with all the renovating, but of course, is already seeing the extensive benefits to student research.

Since 1995, Yale has made a big push to provide more opportunities for women, minority, economically underprivileged, and other historically underrepresented students in STEM through their STARS Program. Zilm has seen the impact of this program on the science community, and the stats reveal that students who participate in this program continue on in the sciences with a significant impact.

Kurt’s own research is on the cusp of exciting results that he will be publishing in the near future. For one project, he’s been collaborating with a team at Dartmouth trying to figure out what it is that makes infectious prions infectious and how to differentiate them from non-infectious prions. He’s also been working with a team at Yale’s Medical School to understand the molecular mechanism of Alzheimer’s Disease--which he thinks they now understand, and have drugs that seem to work with mice.

These research projects have been 90% of Kurt’s work over the past five years, and it’s all finally starting to bear some fruit. He is quick to talk about the importance of collaboration:

“These projects are really starting to bear fruit only because we’re collaborating with these two teams, and we have the right people and the right facilities to work on this. None of us could have done it on our own.”

For Zilm, it’s all connected: from the similar molecular origins of his two projects, to the investment in students and facilities, to his beginnings at the University of Utah, and the collaborations he’s been part of in the past, present, and future.

 
by Anne Vivienne