Atomic and molecular concepts are fundamental topics in chemistry that are often perceived as abstract and challenging, particularly for engineering students. Conventional instructional approaches that rely heavily on textual explanations and limited visualization tend to be insufficient in supporting students’ conceptual understanding. This study investigated the effectiveness of integrating the PhET interactive simulations Build an Atom and Build a Molecule into chemistry instruction in improving engineering students' learning outcomes in atomic and molecular concepts. A pre-experimental approach employing a one-group pretest–posttest design was adopted. The study involved 32 engineering students enrolled in a Basic Chemistry course. Learning outcomes were assessed using a 15-item multiple-choice test administered before and after the implementation of instruction supported by the PhET simulations Build an Atom and Build a Molecule. The collected data were analyzed using descriptive statistics, the Shapiro–Wilk normality test, the Wilcoxon Signed-Rank Test, and N-Gain analysis. Descriptive analysis revealed that the mean score increased substantially from 51.46 on the pretest to 92.08 on the posttest. The Wilcoxon Signed-Rank Test revealed a statistically significant difference between the pretest and posttest scores (p < 0.05). In addition, the average N-Gain score of 0.82 was classified as high, indicating substantial improvement in students' learning outcomes. These findings demonstrate that integrating the Build an Atom and Build a Molecule PhET simulations into chemistry instruction effectively enhances engineering students' understanding of atomic and molecular concepts and provides empirical support for the use of interactive, simulation-based learning in engineering education.
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