1. Molecular modeling in chemistry instruction
    • The potential and challenges of molecular modeling
    • Technological pedagogical content knowledge (TPCK) in molecular modeling
    • Streamlined using of molecular modeling
  2. From desktop software to web applications: The historical analysis of molecular modeling tools used in Finnish chemistry education
    • Theory of blended learning
    • The use of ICT in the 1990s
    • The use of ICT in 2000–2010
    • The use of ICT from 2011 onward
  3. Edumol
    • The history and central technologies of Edumol
    • JSmol
    • JSME
    • Edumol features designed to support chemistry learning and teaching
      • Retrieving structures
      • 2D sketching
      • Molecular mechanics
      • Geometry optimization
      • Visualizations
      • Measurement tools
      • File tools
      • Social interaction
  4. Computer-based molecular models
    • Supporting visualization skills: Model types and rotation tools
      • Model types
      • Wire and tube
      • Ball-and-stick
      • CPK model
      • Dot surface
    • Exercise 1. Model types
    • Exercise 2. Rotation tools
  5. Molecular visualizations and informal chemistry learning
    • Informal learning in chemistry
    • Exercise 3. Organic compound groups in magazines and newspapers
      • Example student task
    • Exercise 4. Information retrieval
      • Teacher tips
      • Example Student task
  6. Partial charges and electrostatic potential surface
    • Exercise 5. Partial charges and solubility
      • Answers
    • Exercise 6. Visualizing acid strengths
      • Implementation
  7. Visualizing chemical bonding
    • Exercise 7. Intermolecular and intramolecular forces
      • Ionic bonds
      • Covalent bonds – small molecules
      • Dipole–dipole forces – intermolecular forces
      • Dispersion forces – intermolecular forces
      • Giant covalent structures
      • Metallic bonding
    • Exercise 8. Similarities between ionic, covalent and polar covalent bonding
    • Exercise 9. Bond length
  8. Visualizing hybridization
    • Exercise 10. Hybridization of carbon atoms
      • Warming up
      • sp3
      • sp2
      • sp
    • Exercise 11. Hybridization of nitrogen and oxygen
      • Nitrogen
      • Oxygen
    • Exercise 12. Hybridization of benzene
  9. Isomerism
    • Exercise 13. Visualizing constitutional isomerism
    • Exercise 14. Geometrical isomerism and energy
    • Exercise 15. Enantiomers
      • Alanine
      • Thalidomide
      • Extra – Other interesting molecules
    • Exercise 16. Conformational isomerism
  10. Introduction to cheminformatics: Biomodels and databases
    • The history of cheminformatics
      • Success stories of cheminformatics and Edumol
    • Visualizing biomodels
      • Retrieving biomodels
      • Biomodel menu
    • Exercise 17. Retrieving data in different ways
    • Exercise 18. Visualizing biomodels
      • Compare possibilities and limitations
    • Exercise 19. Molecule of the Month articles
  11. Next step: Design your own visualization exercises
    • Exercise 20. Other JSmol sites
    • Exercise 21. JSmol web development
      • Your first JSmol page
      • Build your own user interface
      • Checkboxes
      • Buttons
      • Links
    • Exercise 22. Designing molecular visualization exercises
  • Authors
  • Index


Welcome to learn molecular modeling in the context of chemistry instruction.

The goal of this book is to offer theoretical insights and hands-on activities so that chemistry teachers can implement molecular modeling in teaching.

This book includes 22 hands-on modeling exercises. They can be performed using the web application, which is a JSmol-JSME-based molecular modeling and visualization environment.

Users can do the exercises via any device that has a modern web browser and access to the internet. It is vital that all exercises can be done via minimal resources. Our research group has spent over a decade working with commercial software. Our experience is that schools don’t have the funds to purchase equipment and software, let alone update them every three years. Free open source solutions are the only way to support the integration of molecular modeling into schools.

In this book, the level of the theory and the exercises are designed to support the work of primary, upper-secondary and high school chemistry teachers all over the world. Molecular modeling is a crucial part of chemistry instruction and chemistry educational research.

We wish you a great modeling experience with our book.

Johannes, Maija & Shenelle

Helsinki, March 2017


Our sincere thanks to Teemu Arppe for his accurate preliminary reading and hundreds of ideas how to improve the book. It was a pleasure to work with you again.

Thanks to all the graphical designers in e-Oppi Ltd. The book layout is awesome.

The book has been supported by The Finnish Association of Non-fiction Writers. Thank you for your important support.


The first three chapters illustrate why molecular modeling is vital in modern chemistry education. In the first chapter, we explain what molecular modeling is and why it is an important tool in chemistry instruction. How can molecular modeling support chemistry learning? The second chapter presents a technical account of molecular modeling software development. Chapter three introduces Edumol, the software used in the exercises. In the third chapter we discuss the technology and pedagogical features of Edumol.

Chapters 411 constitute the hands-on part of the book. The focus of the exercises is to produce concrete ideas for teaching. Many of the chapters include information regarding chemistry education: chapter 5, for example, describes informal contextual learning. Other chapters include discussions on how to model or visualize certain chemistry topics, such as isomerism, bonding, hybridization. The book ends with chapter 11, which encourages teachers to start building their own visualization exercises by providing them with the basic technical information.


Computer-aided molecular modeling which is used in chemistry research can also be an effective educational tool at different stages from basic education to universities and teacher training (e.g. Aksela & Lahtela-Kakkonen, 2001; Pernaa, 2011; Aksela & Lundell, 2008). From a chemistry teacher’s point of view, computer-aided modeling is one of the most useful uses of information and communications technology (ICT) in chemistry teaching (Helppolainen & Aksela, 2015).

This chapter first examines molecular modeling, its possibilities and challenges in light of research knowledge. After the theoretical background, we will discuss the usage of molecular modeling in the planning and application of chemistry teaching. In order to understand the real world possibilities and challenges, we use a model called technological pedagogical content knowledge (TPCK).


Models and modeling are an essential part of chemistry and its teaching (e.g. Gilbert & Justi, 2016). In the research of chemistry, models are exploited at every stage of the process: forming hypotheses, observing the action of a phenomenon, explaining research results or formulating new predictions based on models. The models unite theoretical and experimental chemistry by visualizing connections between the three levels of chemical knowledge. (Justi & Gilbert, 2002). By using different models of chemistry – analogical models and computer graphics – an invisible phenomenon may be made visible, which then makes it easier to understand chemistry (Barnea, 2000). Molecular modeling is a so called metacognitive tool (Tversky, 2005) that helps us to communicate, to present information about chemistry and to process that information.

A chemistry model is used to describe a visualization of a specific phenomenon in chemistry. These visualizations help to represent thinking: they make it easier to remember and to process information, as well as to cooperate with others (Jones et al., 2005). A model in chemistry can be a concrete model like a scale model or a molecular model made of plastic, a verbal figure of speech used in an oral or a written description, a mathematical model like the general gas law, a visual model like a picture or a graph or a gestural model like the movement of a hand (Gilbert, Boulter & Elmer, 2000). Electronic molecular models can take the following forms: wire, tube, ball-and-stick, space-filling and dot surface.

Computer-aided molecular modeling is advanteageous in teaching because:

  • it helps students understand chemistry on three different levels: macroscopic (a visible phenomenon), submicroscopic (e.g. electron density) and symbolic (e.g. a formula or a template) (Barak & Dori, 2005; Frailich, Kesner, & Hofstein, 2008)
  • it helps to understand chemistry as a modern field of science (Aksela & Lundell, 2009)
  • it helps to improve skills in visualization and to understand the concept of a model and three-dimensional molecular structures (Barnea, 2000, Pernaa et al., 2009)
  • it supports the elucidation and learning of many concepts in chemistry (Aksela & Lundell, 2008; Kozma & Russell, 2005; Russell & Kozma, 2005), for example chemical bonds (Barnea, 2000; Pernaa et al., 2009), isomerism (Dori & Barak, 2001), orbitals (Flemming, Hart & Savage, 2000; Pernaa et al., 2009), functional groups (Dori & Barak, 2001), electrochemistry (Yang, Greenbowe & Andre, 2004), the structure of a substance and the proceeding of a chemical reaction (Williamson & Abraham, 1995), infrared spectroscopy (Aksela & Lundell, 2008), electron density (Aksela & Lundell, 2008), chemical equilibrium and solution chemistry (Russell & Kozma, 2005) and phenomena in biochemistry (Pernaa et al., 2009).
  • it supports higher-order thinking skills (Webb, 2005; Aksela & Lundell, 2008; Dori & Kaberman, 2012)
  • it improves the making of questions and the skills in inquiry-based learning and modeling, and it makes it easier to shift from three-dimensional models to structural formulas (Dori & Kaberman, 2012)
  • it inspires towards learning concepts of chemistry (Barnea & Dori, 1996; Webb, 2005; Aksela & Lundell, 2008)
  • it supports the handling of experimentally achieved phenomena and discussions about them (Kozma, 2003; Aksela & Lundell, 2008).

With the help of molecular modeling, it is possible to practice practice spatial skills (visual-spatial ability) that are extremely important skills in the teachi...