Research into Practice: Visualizing the molecular world for a deep understanding of chemistry

Research into Practice: Visualizing the molecular world for a deep understanding of chemistry 

Why is chemistry so difficult for novices?

A seminal paper by Johnstone (1982) offered an explanation for why science in general, and chemistry in particular, is so difficult to learn. He proposed that an expert in chemistry thinks seamlessly between three levels; the macro (referred to as the observable level in this article), the sub-micro (referred to as the molecular level here), and the representational (referred to as the symbolic level here). The observable level involves chemical changes that are visible, tangible, and often perceptible with other senses. The imperceptible molecular level of understanding consists of dynamic, imaginary mental images that chemists use to explain observations in terms of structures and processes involving atoms, ions and molecules. Observed phenomena, and molecular-level structures and processes are then represented using chemical notation, and rationalised mathematically, at the symbolic level. No wonder novices have difficulty with chemistry!

Figure 1 summarizes these three levels for the chemical reaction that occurs when silver nitrate solution is added to solid copper.  Dendritic silver crystals growing on the surface of the copper can be perceived at the observable level. At the molecular level an animation can portray the dynamic, but imperceptible, formation of silver atoms adhering to a growing cluster of silver atoms.  The equation summarises the reaction at the symbolic level. 

Johnstone (1991) suggests that much of the difficulty associated with learning science occurs because “so much of teaching takes place …. where the three levels interact in varying proportions and the teacher may be unaware of the demands being made on the pupils”. Many students find it difficult to see the relationships between the levels and therefore, find it practically impossible to switch their thinking spontaneously between them. Understanding the relationships between the three levels does, however, vary from student to student, regardless of academic success (Hinton & Nakhleh, 1999). When students fail to see these relationships their knowledge is ultimately fragmented (Gabel, 1999) and many concepts may have only been learnt at a superficial level.

Gabel (1999) also suggests that problems arise because chemistry teaching has traditionally concentrated on the abstract, symbolic level and that teachers often have not considered the three levels in their own thinking. It is likely that teachers do not realise that they are routinely moving from one level to another during their teaching. However, presenting the three levels simultaneously to a novice is likely to overload his or her working memory (Johnstone, 1991; Gabel, 1999). If the levels are introduced together, numerous opportunities should be given to relate them, so that linkages are formed in the long-term memory.

Why is visualisation at the molecular level so important?

Nakhleh (1992) defined the term "misconception" as "any concept that differs from the commonly-accepted scientific understanding of the term". There is convincing evidence in the literature that many student difficulties and misconceptions in chemistry result from inadequate or inaccurate models at the molecular level. Moreover, many of the misconceptions are common to students all over the world, and at different educational levels. Lack of meaningful learning is demonstrated by the fact that many students can solve traditional-style chemistry problems without understanding the underlying molecular processes (Nurrenbem & Pickering, 1987; Nakhleh, 1993). The most important finding is that many misconceptions are extraordinarily resistant to change.

How can we help students to visualise the molecular level?

Until the early 1990s there was a shortage of resources that portrayed the dynamic molecular level so teaching and learning was restricted to the observable and symbolic levels, in the hope that students’ mental models of the molecular world would “develop naturally”. Students were then left to construct these models from the static, often oversimplified, two-dimensional diagrams in textbooks, or from their own imaginative interpretation of chemical notation—for example, does the chemical formula “Na₂CO₃(aq)” mean that sodium carbonate solution contains “Na₂CO₃ molecules” among the water molecules (Figure 3)?

 Physical models like those depicted in Figure 4 are static, and can be misleading models of substances like

·         solid sodium chloride, that does not have directional bonds or significant spaces between ions

·         ice, where the distinction between intramolecular and intermolecular bonds is not clear because both are shown with sticks (albeit of different lengths).

My recommendation is to only use ball and stick models to portray single molecules.

However, physical models do provide a tactile, kinaesthetic dimension to appreciation of shape and angles. This can be more convincing than 2-D representations (perspective or orthogonal) of 3-D models on a computer screen, particularly without any previous experience with physical models. This can be likened to failure to navigate efficiently in virtual gaming environments without enough physical experience of the real world.

Since the molecular world is always dynamic it would be reasonable to assume that computer animations would be a more effective medium for depicting this world. However, animations also have pedagogical weaknesses—some obvious (use of ‘artistic license’ such as colour, shiny “hard” surfaces, and slow motion), some not so obvious but revealed through interviews with students, as described in the next two sections.

The VisChem project – visualising the molecular level with animations

In the early 1990s the VisChem project (see www.vischem.com.au) was funded to produce a suite of molecular animations, depicting the structures of substances, and selected chemical and physical changes, to address student misconceptions identified in the literature (Tasker et al., 1996, Tasker, R., & Dalton, R., 2008). These misconceptions have been identified among students, from various age groups and different educational systems, regarding the nature of matter, molecular and ionic substances, aqueous solutions, and chemical reactions at the molecular level.

VisChem animations are novel in that they portray the vibrational movement in solid substances. This is important because the degree of movement is correlated with temperature, and students need to understand this correlation to interpret the significance of melting and boiling points in molecular-level terms.

Many diagrams in textbooks depicting particles in the solid, liquid and gaseous states are misleading because the relative spacing between particles is inaccurate. Little wonder that students develop poor mental models of states of matter. The VisChem animations are more accurate in this respect.

Few students have a ‘feel’ for the average distance between ions in a solution of a given concentration. VisChem animations portray ionic solutions at a concentration of about 1 mol/L, with ions separated from each other by, on average, about three water molecules. This brings meaning to the magnitude of the number expressing molarity, in much the same way that people have a ‘feel’ for a length of one metre. Students are also encouraged to imagine dilution of a solution in terms of separation of ions by more water molecules.

The VisChem animations are freely available for non-commercial purposes on the VisChem Project web site at www.vischem.com.au. They have also been incorporated into online learning resources associated with university-level chemistry textbooks, most comprehensively and strategically in one in particular (Mahaffy et al, 2014).

The animations portray substances, some in different states of matter, some undergoing physical changes, and some involved in common chemical reactions, as summarised in Figure 5. All the building blocks – individual atoms, molecules, ions, and hydrated ions – are available as separate graphics or animations for use as ‘symbol legends’.

Effective use of VisChem animations in chemistry teaching

We have teaching experience and research findings with students over 20 years on what and how they learn from these animations. The most effective way to use molecular visualisation to promote deep understanding of chemistry concepts is to

·         use an explicit learning design (see a YouTube demonstration of the VisChem Learning Design on vischem.com.au) informed by an audiovisual information processing model (Tasker & Dalton, 2006; Johnstone & El-Banna, 1986)

·         use animations in this constructivist way in a sustained manner over the whole course, so students gradually enrich their mental model of the molecular world with constant reflection. Figure 5 summarizes the progression of animations portraying states of water, phase changes, ionic and molecular substances, to the common types of reactions.

Potential and pitfalls of animations

The VisChem animations were designed to be useful mental models of substances and processes at the molecular level. The challenge was to balance the often-competing demands of:

·         scientific accuracy – such as very little space between adjacent molecules in the liquid state; complicated internal molecular bond vibrations; and the diffuse nature of electron cloud surfaces of atoms

·         ‘artistic license’ required for clear communication – such as depicting slightly less than realistic crowding in the liquid state to enable visibility beyond the nearest molecules; the absence of internal molecular bond vibrations to reduce the degree of movement; use of reflective boundary surfaces on atoms at their van de Waals radii; and greatly reduced speed of molecules in the gaseous state

·         technical computing constraints on rendering times and file size – such as the close-up view to limit the number of moving objects to be rendered; and the depiction of non-trivial events in minimum time to reduce the number of animation frames.

Animations of the molecular world can stimulate the imagination, bringing a new dimension to learning chemistry. One can imagine being inside a bubble of boiling water, or at the surface of silver chloride as it precipitates, as depicted in Figures 6 and 7 respectively.

Most molecular-level processes involve competition between conflicting processes. Atkins (1999) has recommended that this is one of the most important ‘big ideas’ that we should communicate to students. Consequently VisChem animations portray the ‘tug-of-war’ competition for a proton between a base, like ammonia, and a water molecule (Figure 8); and between lattice forces and ion-dipole interactions when sodium chloride dissolves in water (Figure 9).

Like all molecular-level animations, VisChem animations can also generate misconceptions about processes at this level. One of the most serious examples is the clear perception of ‘directed intent’ in molecular-level processes, instead of a more scientifically accurate, probabilistic behaviour, governed by thermodynamics and kinetics.

We discovered this flaw in one particular animation during interviews with students. One perceptive student thoughtfully drew this to our attention in the animation portraying silver chloride precipitation (Figure 7):

“This animation ... shows water molecules ... sort of carrying this structure [AgCl ion pair] along … like a bunch of little robots … The animation depicts something that … I think really happens by chance, as a very deliberate sort of process and I think that’s slightly misleading … Surely it must be possible to make it look less deliberate, less mechanical, maybe by showing ... the odd one or two going into the structure but not all of them.”

The reasons that animation frames are not usually ‘wasted’ on depicting unsuccessful encounters (the majority) are related to the technical imperative to reduce rendering times, the animation time period, and to minimise file size to enable rapid delivery over the web. However, we need to explicitly point out to students that this is a form of ‘artistic license’, and can be likened to the conventional use of a chemical equation to summarize a reaction, rather than to list all the elementary steps in the reaction mechanism.

In contrast to choreographed animations, theory-driven simulations (e.g., the most impressive being in Odyssey by Wavefunction, Inc.; see www.wavefun.com) offer a more accurate depiction of structures and processes at the molecular level. However, a limitation of simulations is that they often do not show key features of molecular events clearly because they occur only rarely (sometimes taking years in the slowed-down timescale used), at random, and usually with intervening solvent molecules blocking the view! Clearly simulations and animations should be used to complement one another.

Finally, we have found that if visualisation is to be taken seriously by students as a learning strategy, it is essential that they are encouraged to practise their new skills with new situations, and assess their visualisation skills in formal assessment. In addition to questions that probe qualitative and quantitative understanding of concepts at the symbolic level, we need to design questions that require students to articulate their mental models of molecular-level structures and processes.

Conclusion

The need for a chemistry student to move seamlessly between Johnstone’s three ‘thinking-levels’ is a challenge, particularly for the novice. Our work in the VisChem project indicates that animations and simulations can communicate many key features about the molecular level effectively, and these ideas can link the observable level to the symbolic level. However, we have also shown that new misconceptions can be generated.

To use animations effectively, we need to direct our students’ attention to their key features, avoid overloading working memory, and promote meaningful integration with prior knowledge, over the whole chemistry course. We can do this by using constructivist learning designs that exploit our knowledge of how students learn. A demonstration of our VisChem learning design can be seen at the VisChem Project web site at vischem.com.au.

‘Scarring’ misconceptions are those that inhibit further conceptual growth. To identify these misconceptions we need a strategic approach to assist our students to visualise the molecular level, to encourage students to communicate their mental models through drawing as well as their writing, and to assess their deep understanding of structures and processes at this level.

Acknowledgement

The author wishes to acknowledge that this work was partially supported by the National Science Foundation under Grant No. 0440103. Any opinions, findings, and conclusions or recommendations expressed in this chapter are those of the authors and do not necessarily reflect the views of the National Science Foundation.

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