This thesis analyzes computer simulations as a learning tool and assesses their impact on students' understanding of chemistry. To get an in-depth understudying of the use of computer simulations, a qualitative approach was adopted. The literature review section explores the use of computer animations and simulations in chemistry and presents the results of various studies in the areas of visualization, conceptual understanding, and conceptual problem-solving. The study section seeks to extend research on the representational and computational capabilities of computerized environments to improve students' conceptual understanding in chemistry and related practical applications. Effects of design of simulation and structure of the learning activity in enhancing student understanding of thermochemistry concepts were explored. Observations and 60-minute interview sessions with six undergraduate general chemistry students explored student thought processes while engaging in problem-solving and inquiry activities. The learning environment addressed a number of challenges in student understanding of thermochemistry concepts. Students were able to transition from algorithmic problem-solving to identifying concepts and justifying their answers. Interactions with the simulations helped students investigate concepts through the process of scientific experimentation and enhanced connections between lecture and laboratory sessions.