PhET Build A Molecule

PhET (Physics Education Technology Project)
Type Category
Instructional Materials
Interactive Simulation
This resource, vetted by NSTA curators, is provided to teachers along with suggested modifications to make it more in line with the vision of the NGSS. While not considered to be “fully aligned,” the resources and expert recommendations provide teachers with concrete examples and expert guidance using the EQuIP rubric to adapted existing resources. Read more here.



Students will have fun constructing simple molecules with this simulation, while also gaining insight into molecular structure and chemical nomenclature. The activity gives learners tasks to build molecules from “kits” of elements. The tasks increase in complexity step-by-step, as students click & drag atoms to make specific molecules to match a molecular formula . Tasks include building diatomic molecules, molecular compounds, and construction of larger molecules without explicit direction. After a molecule is built, it can be viewed in 3D either as a ball-and-stick or a space-filling model. This resource is appropriate for the early phases of a unit on molecular structure.

Teachers:  The main library link goes to the HTML simulation itself. To access an excellent set of lesson materials created by a middle school teacher to support this simulation, click on the “For Teachers” tab.  Look for the lesson written by Jackie Esler. Her lesson includes pre-test, two post-tests, Student Guide, and lesson plan specifically developed to use with “Build A Molecule”. You must be a registered user on the PhET website to access the add-on materials, but registration is FREE.

Intended Audience

Educational Level
  • Middle School
Access Restrictions

Free access - The right to view and/or download material without financial, registration, or excessive advertising barriers.

Performance Expectations

MS-PS1-1 Develop models to describe the atomic composition of simple molecules and extended structures.

Clarification Statement: Emphasis is on developing models of molecules that vary in complexity. Examples of simple molecules could include ammonia and methanol. Examples of extended structures could include sodium chloride or diamonds. Examples of molecular-level models could include drawings, 3D ball and stick structures, or computer representations showing different molecules with different types of atoms.

Assessment Boundary: Assessment does not include valence electrons and bonding energy, discussing the ionic nature of subunits of complex structures, or a complete description of all individual atoms in a complex molecule or extended structure is not required.

This resource is explicitly designed to build towards this performance expectation.

Comments about Including the Performance Expectation
While the “Build A Molecule” activity offers an inquiry-based experience, teachers may wish to introduce some of the language of chemical formulas up front, such as “diatomic molecule”, “element”, and “chemical compound”.  Through using the model, students should be able to figure out independently what the coefficients and subscripts signify, without much direction.  Note: The model offers three levels of increasing complexity. The first two levels give specific tasks for using buckets of atoms to build simple molecules.  In the third level, “Larger Molecules” students can develop their own models.

Science and Engineering Practices

This resource appears to be designed to build towards this science and engineering practice, though the resource developer has not explicitly stated so.

Comments about Including the Science and Engineering Practice
To fully meet this Practice, teachers may wish to introduce a formative assessment asking learners to describe their digital molecular creations in writing.  Ask students to click the 3D box next to each created molecule and closely examine the structure. Example questions could include: 1) How do diatomic molecules stick together? 2) What does the water molecule look like in the 3D image? 3) Describe the difference between the 3D model of the water molecule and the carbon dioxide molecule. 4) Describe in your own words what is happening when you place two hydrogen atoms next to an oxygen atom. (They are highly attracted to each other: this helps build a foundation to understand chemical bonds.) What pattern do you notice when hydrogen bonds with another atom? 5) What are you observing in the model that we can’t see with our eyes? To keep students focused and on task in meeting learning goals, registered users of PhET can access a Student Guide and assessment, written by a middle school teacher specifically to supplement the “Build A Molecule” simulation.  You’ll find it under “For Teachers”.

Disciplinary Core Ideas

This resource is explicitly designed to build towards this disciplinary core idea.

Comments about Including the Disciplinary Core Idea
Students in the middle grades may need scaffolding to understand the difference between chemical compounds and diatomic/triatomic molecules. They will be building each of these types of molecules in the model. Diatomic and triatomic molecules are composed of the same kind of atoms. Chemical compounds are substances made up of two or more different elements.  Note to Teachers: The DCI statement, as written, states “from two to thousands of atoms”. Middle school molecular models rarely encompass “thousands” of atoms. Teachers may want to embed a textbook excerpt to cover this concept, which likely refers to ionic crystal structures like table salt.

Crosscutting Concepts

This resource appears to be designed to build towards this crosscutting concept, though the resource developer has not explicitly stated so.

Comments about Including the Crosscutting Concept
The driving purpose of this activity is to give students the opportunity to discover how atoms can combine to form molecules. As they work through the various digital molecule-building “Kits”, learners will figure out that certain atoms like to bond with other atoms, some don’t, and some atoms like to form pairs. It’s important to let them work through the model without expert guidance. To assess the level of student understanding about how the function of molecules depends on shape and composition, teachers will need to supplement the model with conceptual discussions about the importance of the carbon atom as the basis of life, the nature of the oxygen we breathe (it occurs in the atmosphere as a diatomic molecule), and why certain atoms are more likely to bond than others.

Resource Quality

  • Alignment to the Dimensions of the NGSS: This interactive model integrates the three dimensions in the following ways: 1) Explicitly meets a both a PE and DCI within Middle School Physical Science-Structure and Properties of Matter -- students construct digital models of various small molecules by choosing correctly from "kits" of atoms. 2) Meets the Science Practice, “Using and Developing Models” through a robust set of digital tools for students to construct their own models of diatomic molecules and chemical compounds, including simple molecular building tools, cut/slice tool, viewing in 2D or 3D, and tasks that begin very simply and gradually increase in complexity. Level 3 (Larger Molecules) allows students to develop their own molecules. 3) Meets the basics of the CCC within “Structure and Function” that allows students to easily visualize molecular shapes and differentiate one from another, however, conceptual support will be optimal for best outcomes. Scaffolding will be required to help learners recognize that attractions among atoms have discernible patterns that can be determined both by using models and by analyzing the placement of the atoms in the Periodic Table.

  • Instructional Supports: The model is highly relevant to a middle school physical science curriculum, with challenging tasks that will promote understanding of molecular structure. However as a stand-alone resource, it does not provide opportunities for students to connect their experience to an explanation of macro-scale phenomena. The PhET website also offers teacher-contributed supplemental lessons with student guides that provide explicit guidance. By clicking "For Teachers", users can locate an excellent lesson with assessment written by a middle school teacher specifically for use with the "Build A Molecule" simulation. Look for the lesson written by Jackie Esler, which gives tips on how to elicit prior understanding and assess student progress while using the model. While the model featyres different levels, it does not provide specific guidance to support differentiated instruction. It does provide numerous versions in languages other than English (i.e., Spanish, Chinese, German, French, Arabic, and many more).

  • Monitoring Student Progress: “Build A Molecule” allows teachers to see limited evidence of progress: students cannot progress from one “Kit” to the next level unless their molecular structures are accurately constructed. But, as a stand-alone, it does not embed assessment, rubrics, or vocabularies. However, the teacher-created supplemental materials provide the following:  Pre-Test to elicit prior understanding, two Post-Lab assessments, Student Guide, and teaching tips. To find this lesson, click "For Teachers" and open the link to Jackie Esler's lesson plan titled, "Molecules Are Made Up of Atoms".

  • Quality of Technological Interactivity: This model is highly interactive. Students have access to multiple tools for building their digital molecules. They can click and drag atoms from "buckets", view a correctly-assembled molecule in 3D, and view as space-filling or ball-and-stick. If a learner incorrectly constructs a molecule, there's a tool to slice out one atom at a time (rather than resetting the entire sequence). The simulation progresses from very simple to tasks of greater complexity. In the top level, users can create larger molecules from scratch, using a "refill" tool, which is essential for building a larger molecule from scratch.