In undergraduate science education, laboratory courses stand as essential cornerstones of experiential learning. Chemistry laboratory courses offer students unique hands-on experiences that bridge the gap between theoretical knowledge and practical application. The journey through the undergraduate chemistry curriculum is paved with a series of conceptual gateways known as threshold concepts that can dramatically shape a student's understanding and success. We identified the idea of intermolecular forces (IMFs) as a threshold concept to students' ability to link molecular structures, properties, and applications to real-world problems such as extraction and separation of compounds. The development of course-specific pedagogical tools can provide students with the scaffolding necessary for the transition from novice to expert-level disciplinary comprehension. This work presents the development process of a Threshold Concept Assessment Rubric (TCAR) based on Johnstone's triangle framework and discusses its application for evaluating students' progress in overcoming a threshold concept. The rubric is used in a 200-level multilayer laboratory course that is intentionally designed with intermolecular forces as the central theme. We analyze the role and structure of different questions to provide a holistic assessment of students' learning processes using sample assignments. Furthermore, we demonstrate how insights from statistical analyses can highlight areas in which students struggle to gain expert or exemplary-level understanding of IMFs. This rubric development approach can be applied to other threshold concepts.