In 2007, Khalili joined the University of Washington. Her research makes use of ultrafast spectroscopies to understand the structural dynamics of molecules. Photoinduced charge transfer depends on an interplay between atomic and electronic processes on multi-dimensional energy surfaces. She develops 3D electronic-vibrational femtosecond spectroscopies to understand vibrational and electronics motions on femtosecond timescales. In particular, she is interested in how solvents (e.g. water in photosynthesis) impact the electron transfer processes.
Khalil was made chair of the department of chemistry in 2020.