The mental models students have after engaging in an activity designed to teach infrared (IR) spectroscopy without reliance on IR absorption tables, were characterized. Qualitative analysis of semi-structured interviews, through open coding, allowed the classification of the mental models as Molecules as Dynamic (MAD), Bonds as Dynamic (BAD), Molecules as Static (MAS), External Energy (EE), and Internal Energy (IE). Assumptions students have about structure, dynamics, and spectra when solving IR spectra were identified and grouped as intuitive, valid, and spurious. A connection was found between participants with more sophisticated mental models and those who used multi-variate reasoning. Participants were also more likely to be successful when they compared spectra. The results of the analysis suggest IR spectroscopy should be taught through a conceptual lens to guide learning about the interaction of energy and matter.