Project-based learning (PBL), which is increasingly supported by information technologies (IT), contributes to fostering student-directed scientific inquiry of problems in a real-world setting. This study investigated the integration of PBL in an IT environment into three undergraduate chemistry courses, each including both experimental and control students. Students in the experimental group volunteered to carry out an individual IT-based project, whereas the control students solved only traditional problems. The project included constructing computerized molecular models, seeking information on scientific phenomena, and inquiring about chemistry theories. The effect of the PBL was examined both quantitatively and qualitatively. The quantitative analysis was based on a pretest, a posttest, and a final examination, which served for comparing the learning gains of the two research groups. For the qualitative analysis, we looked into the experimental students' performance, as reflected by the projects they had submitted. In addition, "think aloud" interviews and observations helped us gain insight into the students' conceptual understanding of molecular structures. Students who participated in the IT-enhanced PBL performed significantly better than their control classmates not only on their posttest but also on their course final examination. Analyzing the qualitative findings, we concluded that the construction of computerized models and Web-based inquiry activities helped promote students' ability of mentally traversing the four levels of chemistry understanding: symbolic, macroscopic, microscopic, and process. More generally, our results indicated that incorporating IT-rich PBL into freshmen courses can enhance students' understanding of chemical concepts, theories, and molecular structures.