Summer Centered: Scott Kaiser '22 Gets With the (Chemistry) Program

This summer, with support from the Koshland Integrated Natural Sciences Center, chemistry major Scott Kaiser '22 is pursuing his passion for chemistry in the lab of Assistant Professor Clyde Daly, where he is using computational chemistry programs to investigate the behavior of molecules in different chemical systems. 

Kaiser reached out to Daly shortly after he joined the Haverford faculty last fall, knowing Daly would be on the lookout for students to work in his lab during the summer. “I knew his research somehow involved computers and theoretical chemistry, and I had some background in the former, but was fairly intimidated by the latter,” said Kaiser. “I was excited by the prospect of helping to found a new lab and help establish the infrastructure and culture of a successful lab, and I was also interested in learning more coding skills.” 

Kaiser’s work, which will serve as the foundation of his senior thesis, focuses on carbon dioxide in ionic liquids. Mainly, he uses molecular dynamics (MD) simulations to make “molecular movies” of various chemical systems, which can be analyzed using quantum mechanics to extract useful properties. “Simulations can provide a lot of detail about chemical systems that aren't apparent from real-world experiments,” he explained. 

Before this summer, he had experience implementing MD simulations in Open MM, a computational chemistry program. With Daly, he’s introduced quantum mechanics into the program. “More recently, I've been working on processes to refine the data from these MD simulations into data we can plug into a quantum chemistry program to calculate properties like vibrational frequencies,” said Kaiser.  

He began the summer, refining data from MD simulations he completed last semester. With those results, he used a quantum chemistry program to calculate properties such as vibrational frequencies. Then, he learned the theory behind the program so he could figure out how to use the system more efficiently. 

“I got a lot of help from Professor Daly and from the work of Sara Hunsberger '22, who wrote much of the code I needed to do the calculations I wanted,” said Kaiser. “In the past week or so, everything has started to come together and we've started to get some vibrational frequencies! The eventual goal is to figure out what properties from the simulations result in frequency shifts so we can make predictions about systems we haven't simulated.”

The best parts of his job, he said, are the skills he’s developed—Python and Shell scripting and computational chemistry programming in particular—as well as the independence he was given working on his own project. Above all else, the problem-solving he’s done will surely help him in the long run. “Effective problem solving is a skill that isn't taught very much in classes, especially in intro classes, but I think it's one of the most important skills to learn in the long term,” he said. “On the day-to-day, I sometimes feel like my job is fixing one problem just to see what will break next—computational chemistry programs can be a little finicky!”

Research in Daly’s lab focuses primarily on simulations of molecular processes where atomic motion is the dominant factor, such as protein-protein interactions, protein-nanomaterial interactions, and vibrational spectroscopy. Other members of this summer's lab team include Sunny Truslow '21, Genevieve C. Uy '22, Sara Hunsberger '22, Scott Kaiser '22, Ali M. Altamimi '22, Daniela Moreira '23, Avi Patel '23, and Logan Smith '23.

“If you're interested in joining the lab or want to learn more about our projects, visit our website or reach out to Professor Daly,” said Kaiser. “We're always looking for new members, including and especially first-year and sophomore students!”

“Summer Centered” is a series exploring our students’ campus-supported summer work.