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Insights into Molecular Visualization Design


Resa M. Kelly, San Jose State University, CA

05/08/15 to 05/14/15

The first customer that a visualization designer has to please is the instructor. Are you surprised that it is not the student? The instructor decides whether to use the tools and judges whether the animation will actually fit with his/her instructional needs, thereby determining whether the tool will even reach their students. However, the students are the ones we, as designers, want to assist in their learning progress and we ponder, how will we make the information in our visuals more meaningful? Both instructors and students critique animations. Instructors tell us when the tools lack accuracy in depicting chemical concepts, when the representation is too simplistic or in some cases too complex. In contrast, students tend not to critique the tools based on their accuracy, they trust that the designers are the experts and that they simply have to learn the concepts. Instead students tell us whether the tools are difficult to use, understandable or just plain boring. The purpose of this ConfChem paper is to share my experience with the design process and how I try to listen to the voices of both instructors and students to inform what is depicted. Finally, results gathered on visuals assigned in a naturalistic setting, as a pre-lab exercise, will be shared. 



The purpose of this paper is to provide an overview of how an Electronic Learning Tool (ELT) on precipitation reactions was designed with input from both instructors and students. It is important to note that the research conducted with students was previously published (Kelly et al, 2010), and this paper will emphasize the instructors’ perspectives and the overall design process.

The process of developing the tool began with first thinking about what the molecular animations should emphasize and how the content would actually be unpacked. Since instructors are the ones who ultimately decide whether to use the tool, they were interviewed to learn ways that the tool could be made more appealing to them. For example, what would they want an animation about atomic level details associated with precipitation reactions to show? More importantly, the hope was that by interviewing instructors to learn the features on which they wanted their students to focus and by also being mindful of how students understand the reactions, a scaffold could be developed to assist students in adapting their understanding to fit with their instructors’ vision. Thus a sample population of instructors at a University located in the Western United States was interviewed to learn what they expected students to be able to convey about precipitation reactions to show mastery of atomic level details associated with precipitation reactions. In addition to interviewing instructors, as mentioned, students were also interviewed to learn how they viewed the atomic level and the kinds of misconceptions they held. This work informed the design of the atomic level visualizations. Later, the framework was built around the visualizations to build context and connections to the macroscopic and symbolic levels and to make the tool more interactive and reflective.

In the fall of 2005, eleven chemistry instructors (7 males and 4 females of diverse ethnicity) all with doctorate degrees in chemistry disciplines were interviewed to examine how they segmented their understanding of precipitation reactions to teach first year, General Chemistry students.  The instructors were asked to draw their submicroscopic level understanding of three molecular equations presented to them on worksheets.  The worksheets consisted primarily of four blank box frames for drawing submicroscopic events for each of three molecular equations; however, instructors were told that they could use as many boxes as they felt were necessary.  The three equations were:

                        1) AgNO3(aq) + NaCl(aq) AgCl(s) + NaNO3(aq)

                        2) KNO3(aq) + NaCl(aq) No Rxn

                        3) MnCl2(aq) + 2 AgNO3(aq) 2 AgCl(s) + Mn(NO3)2(aq)

The first equation had only monovalent ions. The second reaction provided an example of a situation in which no reaction occurs. The third reaction showed more complicated formulas and coefficients.  The specific research question was: How do instructors segment these reaction equations and what key features do they incorporate in their segments?


Constructivism was used as the theoretical framework guiding this qualitative study. According to Fergusen (2007), constructivism is best suited for studies that focus on sense- or meaning-making, concept construction, or elucidation of alternative concepts.  Instructors’ drawings were analyzed to ascertain how the instructors communicated molecular-level understandings of the given equations. Special attention was paid to learn how the instructors organized their understanding. The worksheet drawings were coded and examined using a constant comparison method of analysis (Merriam, 2001). 


Informing the Segmentation of Precipitation Reactions

The findings indicated that instructors drew three segments to convey changes in time as the reaction progressed from reactants to products.  The first segment (Figure 1) consisted of events that occurred prior to the start of the reaction. Seven instructors emphasized the nature of the aqueous reactant solutions prior to mixing while two depicted how the aqueous solutions were made.

Figure 1. An example of an instructor's depiction of how aqueous solutions were made.

The second segment illustrated the nature of the reaction solution at the moment of mixing.  Seven instructors drew a step at the initiation of the reaction just after mixing, at which point the solution consisted entirely of unreacted aqueous ions.  Some drew pictures that consisted of events that occurred during the reaction, such as collisions between the various species.  Eight instructors depicted the dynamics of the processes that occurred during the reaction in which some collisions resulted in the formation of a precipitate while others did not (Figure 2).

Figure 2. An instructor's depiction of collision dynamics in the reaction.

The third and final segment illustrated the nature of the species at the conclusion of the reaction (Figure 3).  Eleven instructors drew the make-up of the precipitate and ten drew the aqueous product solution. 

Figure 3. An instructor’s depiction of precipitate aggregate formation.

Additional findings from this research indicated ways that experts used elements of graphic language to simplify complex reaction features to communicate the essential features of the reaction. For example, many used lines to create separation between the reactant solutions. In some instances wavy lines were used to indicate the nature of a solution instead of drawing water molecules or boxes to separate the precipitate from the aqueous solution environment.  Nine of the eleven professors simplified the role of water in the reaction by drawing: a cloud around ions to indicate the presence of water, circles to represent water molecules, or graphic features such as a beaker filled with a liquid or a wavy line to represent water’s presence. Six instructors drew only water molecules involved in the hydration of the ions.  To depict the species involved in the reaction, ten instructors used the symbolic representation of the species with the element symbol and charge and four of these drew a circle around the symbol to represent the ions.  Only two instructors drew geometric shapes to represent the species and provided a legend to clarify the identity of the shapes. 


Students’ Explanations

In addition to studying the experts, 21 General Chemistry students were interviewed to learn how they understood the particulate nature of the reaction events to occur (Kelly, Barrera and Mohamed, 2010). To summarize, several misconceptions were uncovered. Most importantly it was revealed that students tended to map their atomic level understanding onto their symbolic portrayal of chemical equations. In the case of precipitation reactions, they believed that the ionic compounds existed as molecules, which broke apart when they were mixed together, then changed partners, before they formed molecular products. Students also had a weak understanding of the term aqueous. When students are taught formulas and chemical equation, they are often provided with affirmation when their symbolic representations are correct, thus when students map their understanding of the atomic level onto their “correct” symbolic representations, they trust and infer that their atomic pictures are also “correct”. This makes it very challenging to convince them that a dilute aqueous salt solution does not consist of ion pairs. 


How do you design it?

To design the learning tool a learning cycle approach was adopted. The storyboard for the learning cycle design began with an exploration video in which the questions – why is it that when two aqueous solutions are mixed, sometimes a precipitate is formed yet when other solutions are mixed nothing happens? How do we account for this? This was an attempt to tap into students’ curiosity and get them to consider a “why” type question to frame their viewing experience. In addition, an effort was made to start with the familiarity of the macroscopic representation of the reaction and to ask students to consider what could account for this result at the atomic level? Care was taken to represent at most two levels at a time. After the exploration phase, the next phase of the learning cycle was concept development. This section was informed by the interviews with the instructors and students and consisted of an atomic level animation section as well as cartoon tutorials to help students connect the symbolic and submicroscopic levels. Finally, the tool ended with a concept application section in which students were given a laboratory context with which to connect their atomic level understanding. 


Who Designs it?

When the project began, two animation artists, students enrolled in the Bachelor of Fine Arts (BFA) program at SJSU, were hired to develop the first prototype based on the author’s research and guidance. The team soon grew to consist of five animation artists (students in the SJSU BFA program). One of the artists was able to construct Maya animations to create the atomic level animations, while the other artists were skilled in Flash animation and video. The artists constructed the major components of the tools, but in order to allow navigation to the different components and to make it interactive a programmer was needed. Therefore, a student majoring in computer programming was hired to create: the navigation between the tool components, interactive features, and data entry and feedback components. Rounding out the team was a student majoring in graphics design, and a narrator with an authentic British accent, which was desired by the animation team. 


Design Aspects

Simple and Intuitive. The ELT employs the use of simple interactive features consisting of buttons and click-and-drag type tools. The design team tried to make these as intuitive as possible by using pictorial icons and highlighting labels. Supplemental animations were presented through links next to the main animations to highlight the importance of water molecules in the processes. 


Friendly Cartoon Tutor (Advocate for Learning). A cartoon character was created to introduce the ELT and this offered a more personable experience (Figure 4). When the tool was first constructed, a character named “Billy” was designed to represent a student who was confused and the information in the tool was meant to help him, but many students disliked this character. They felt that it implied that they were Billy and obviously lacking intelligence. Thus one of my animation team members, Virgil Serrano came up with a test tube character named Dr. NRG (pronounced “Energy”). He also decided that the character he constructed was British, which presented a challenge to find narration prospects. Dr. NRG became a friendly tutor to ease tension, through humorous mannerisms such as morphing from a test tube on the table into a cartoon tutor, and he sips tea while he waits for the student to select from the main menu. The character allowed us to instruct the students through the tool experience, making it easy for us to emphasize key features and teach how the atomic level connected to the symbolic representations.


Concept Development. The Concept Development section was designed initially to assist students with their atomic level understanding. However, once we completed our study of how students tended to connect the chemical equation to the atomic level events, we recognized that we needed to create tutorials to teach students how the three equations (molecular, total ionic and net ionic) specifically related to the atomic level.  We approached this in two stages. First an atomic level perspective was delivered to address how solutions that reacted were sometimes able to form a precipitate, while some solutions were unable to react. Next, tutorials featuring Dr. NRG were made to teach the chemical equations and how they connected to the atomic level.  Again care was taken to focus first on the atomic level before bridging to the symbolic level

1. Atomic Level View – In this section, the students were first asked to construct their understanding of aqueous sodium chloride and solid silver chloride using a click and drag tool Figure 5). This was done because students do not always recognize when they have changed their understanding.


Figure 5. Screen shot of the Click-and-Drag Metacognition tool.


Some students believe that their mental models do not differ noticeably from animation models, even though experts reviewing their work may find them drastically different (Kelly, 2014). As a result, metacognitive reflection activities helped some students notice differences between their understanding and what the animation showed. Upon completion of the click and drag exercise, students were allowed to view an introductory video in which they could see the most complicated view of the animation (Figure 6).


Figure 6a: Still image pictures showing complex view of the atomic level precipitation reaction.


Figure 6b: Embedded Video showing complex view of the atomic level precipitation reaction.

This was done purposefully so that students could recognize the complicated nature of the reaction environment. Viewing a more complex animation prior to showing simplistic components may help students better focus and understand critical features of the complex visualization.

Following the complex view the students were taken back to the main menu where they could choose to view one of two situations: 1) when a reaction occurs and 2) when no reaction occurs. The reason both reaction and non-reaction events were included was due to findings from an initial study in which we learned that many students thought that ionic pairs that did not react, first switched partners, in essence reacting, but then broke apart (Kelly, Barrera & Mohamed, 2010).  In both the reaction and non-reaction sections the events were segmented in accordance with the segments uncovered from the interviews with instructors (Figure 7)

Figure 7a. Still image showing the segmentation of the precipitation reaction.


Figure 7b. Embedded video showing the segmentation of the precipitation reaction

In the case of the reaction between aqueous solutions of sodium chloride and silver nitrate the reaction was segmented into reactants, with animations of each reactant solution: aqueous sodium chloride and aqueous silver nitrate prior to mixing together, then the reaction between the two solutions and finally an animation that focused on the products of the reaction. Additional animations were provided as links to further account for the nature of the species involved. For example, a hydrated sodium ion and a hydrated chloride ion were represented to highlight the orientation of water molecules in the initial layer of hydration surrounding the ion. In addition, an animation that showed the presence of solvent water molecules was also included so that students would have a more realistic perspective of the interactions between the aqueous ions and water. In the case of the products, a 3-d representation of the silver chloride aggregate was shown, but students could also click on a picture that allowed them to see that water would be attracted to the aggregate, but unable to pull it apart. 


Upon examining both sets of animations for the reaction and non-reaction events, students were once again tasked with analyzing their conceptual understanding. They were shown an example of their initial drawing of aqueous sodium chloride and solid silver chloride and they were asked once again to construct their understanding after they had gained new insights from the animations. They were also required to type a description of the misconceptions they had before and how changes were made to correct them (Figure 8).


Figure 8. An example of a student’s pre and post conception pictures.


2.  Chemical Equations. In this section, Dr. NRG leads students through four tutorials on how to represent reactions with symbols and how to represent the three types of ionic equations molecular, total ionic and net ionic (Figure 9). Kelly et al. 2010 noted that many students incorrectly incorporated features of both the molecular equation and the total ionic equation in their drawn depictions, suggesting that they viewed the total ionic equation as an intermediate step in the reaction.  Thus, this section specifically addressed the function of the equations for conveying the nature of the reactions. The primary goal was to connect the symbolic level to the atomic level portrayal of reactions and assessment questions followed each of the sections to allow students to test their understanding.


Figure 9a. A screenshot from a tutorial with Dr. NRG.

Figure 9b. Embedded video from a tutorial with Dr. NRG.


Concept Application. In this section, students were provided with a table of reactants and asked to predict whether a reaction would occur. If they decided that a reaction occurred, they were asked to balance the equation and construct a picture of the reactants and products. This was done to provide students with practice connecting symbolic and atomic levels and also provided the students a way to predict the number of reactions that they could expect to see should these solutions be mixed. After they completed the table, the students were provided with a table of actual reactions; however, the reactants did not have labels and the students were challenged to identify the reactant solutions responsible for the resulting precipitates (Figure 10). Upon completion of the third part of the ELT, students were able to see a chart of their progress on the main page. 

Figure 10. A screenshot of the reaction table and a chart for identifying the reactant solutions.

Feedback. In order to provide students with feedback on their progress, a star system was developed and students were awarded gold, silver and bronze stars when they attempted to complete a task. The gold star indicated that they had completed the tasks perfectly or nearly perfectly (missing only a few items). A silver star was assigned if the student missed more than three items, but less than 5 items. For example, when balancing equations, if a phase was entered incorrectly or subscripts and coefficients were entered incorrectly, the student might receive a silver star. A bronze star was awarded if more than five items were missed, but less than 10 items. If the student did not complete a section, the star would be dark gray. Typically, most students received either gold or silver stars if they attempted the tasks. The dark gray star was important because it allowed us to see when students did not complete a section of the tool. Many students liked the star system because it gave them immediate feedback, but they disliked it when they missed an equation and they were unable to tell which one it was. This caused some students to make numerous attempts to get all gold stars, which many vocally conveyed to be frustrating. On the final grade report, students’ work was mostly automatically scored through the computer program, but the pictures and comments were hand graded by their Teaching Assistants (TAs) who used a 5-point rubric to award points. In addition to the points the TAs could also include brief comments (bottom of Figure 8). The comments made by the TA’s varied: some were quite detailed and explicit, while others simply left the comment box blank. 


Naturalistic Analysis

During the Fall 2011 semester, nineteen Introductory Chemistry lab sections, consisting of approximately 500 total students, were assigned to complete the ELT on precipitation as a pre-lab exercise. Most of the students, 379 of 500, completed the pre and post conceptions pictures. In order to examine how effective the atomic level animations were toward changing students’ mental models, pre- and post- treatment pictures from all students who completed the ELT for their pre-lab, were coded for the presence of key features and misconceptions for reactant solution, aqueous sodium chloride, and the precipitate, solid silver chloride (Table 1). 


Table 1. Key features and misconceptions coded from students’ ELT progress report.


Atomic Level Events

Pre- Treatment


Post- Treatment




Key Features of NaCl(aq)




Separated ions of sodium and chloride are present

202 (53.3%)

318 (83.9%)


Hydration Waters – waters that immediately surround the ions

83 (21.9%)

350 (92.3%)


Solvent Waters – water molecules are present in the solvent

148 (39.1%)

102 (26.9%)



Ion pairs of NaCl are present in solution

169 (44.6%)

49 (12.9%)


Key Features of AgCl(s)




Lattice of ions makes up the precipitate

100 (26.4%)

241 (63.6%)


Hydration Waters – water molecules attract to the precipitate



225 (59.4%)


Solvent Water – water molecules in the solvent are present

110 (29.3%)

49 (12.9%)



Ion Pair(s) make up the precipitate

245 (64.9%)





In general, students improved on the number of key features that they represented for both aqueous sodium chloride and solid silver nitrate. Most notably, more students recognized that aqueous sodium chloride was composed of separated ions that were surrounded by waters of hydration. Interestingly, fewer students chose to depict the presence of solvent water. This is likely due to the enhanced focus on the hydration spheres that were represented in the animations and perhaps recognizing that additional solvent waters would be unnecessary to depict, rendering them nonessential. In addition, this finding fits with the simplified animations, which did not depict solvent water molecules and only represented the water molecules next to the ions or one-layer of hydration surrounding the ions. It is also important to notice that the number of students expressing the misconception that aqueous sodium chloride existed as ion pairs decreased substantially. In the case of solid silver chloride, the biggest learning gain was depicting that the precipitate consisted of a lattice arrangement of ions and that water molecules could still be attracted to the precipitate, but they would not pull it apart. Once again, fewer students felt compelled to depict solvent water molecules even though the precipitate was formed in an aqueous environment. However, this was consistent with the simplified animations that the students viewed, which also did not depict solvent water molecules. The major misconception that students held initially, that of the precipitate consisting of ion pairs, also noticeably decreased. 



The ELT helps students better understand the atomic level of precipitation reactions based on their pictorial constructions and completion of the tool. It is difficult to know whether the experience of using the tool will help students improve their ability to make connections between the macroscopic and symbolic levels or if the changes that they made to their pictures are reflective of lasting changes to their mental models. Further studies in which we examine the longitudinal effect of using visualization tools should be considered. 



The author wishes to acknowledge that the National Science Foundation under Grant No. 0941203 supported this work. Any opinions, findings, and conclusions or recommendations expressed in this paper are those of the author and do not necessarily reflect the views of the National Science Foundation.



1. Kelly, R. M., Barrera, J. H., & Mohamed, S. C. (2010) An Analysis of Undergraduate General Chemistry Students’ Explanations of the Submicroscopic Level of Precipitation Reactions. Journal of Chemical Education 87(1), 113-118. Publication date(Web): December 18, 2009.
2. Ferguson, R. L. Constructivism and Social Constructivism. In Theoretical Frameworks for Research in Chemistry/Science Education; Pearson Education, Inc.: Upper Saddle River, NJ, 2007.
3. Merriam, S. B. Qualitative Research and Case Study Applications in Education; Jossey-Bass Publishers: San Francisco, CA, 2001.
4. Lincoln, Y. S.; Guba, E. G. Naturalistic Inquiry; SAGE Publications:London, 1985.
5. Kelly, R.M. (2014) "Using variation theory with metacognitive monitoring to develop insights into how students learn from molecular visualizations." Journal of Chemical Education DOI: 10.1021/ed500182g. Publication date (Web) June 13, 2014.

To see the ELT visit and email Resa Kelly (resa.kelly) to gain access.
To view a sample of the ELT visit YouTube (all videos were accessed on April 4, 2015).

1. Introduction to ELT- Precipitation -
2. View of Complex Atomic Level Animation -
3. View of Segmented Precipitation Reaction NaCl(aq) -
4. Hydrated Sodium -;
5. Hydrated Chloride - \
6. Tutorial 1 on Chemical Equations –
7. Tutorial 2 on Molecular Equations -
8. Tutorial 3 on Total Ionic Equations -
9. Tutorial 4 on Net Ionic Equations -


Emily Moore's picture

Hi Resa,

Thanks so much for this contribution to ConfChem. I particularly appreciated the descriptions of the design process you go through in making the ELTs, and the focus on the role of the instructor in informing your process and designs. While reading your paper, I had a few questions:

1) In your description of the instructor interviews, I was curious about the framing of the question/task, and whether you think instructors were answering based on their personal understanding of precipitation reactions, or based on their teaching of precipitation reactions. Are the instructor drawings indicative of how the instructors think about precipitation reactions, or how they teach them? If the instructors were engaged in the drawing task from a teaching perspective, were you able to gain any information useful for ELT design based on any verbal descriptions they gave about their drawings?
2) I found the range of simplifications in the teacher’s drawings very interesting. For example, it seemed like there were multiple ways teachers included (or did not include) water molecules in their drawings. Do you have a sense of why teachers were selecting particular simplifications, or where some of these stemmed (e.g., I have never used the “cloud around the ions” example)? Do you think there were particular simplifications that instructors where choosing for pedagogical reasons, or ones that might be considered conventions (but not necessarily pedagogically motivated)?
3) Regarding the design and development team – I applaud your work involving a diverse group of undergraduate students. I am sure the development of this ELT was a valuable experience for them. Could you share any insights you may have from leading teams of undergraduates to develop interactive tools? Do you have any “do’s and don’ts” for folks following along that may be interested in developing online materials with undergraduate students?

Thanks again for this contribution! I look forward to your response.

From my findings, I learned that even though I framed the question to focus instructors to think about how their students learn, many instructors would start from their teaching experiences and then connected to how they, themselves, learned the concepts. Often when they shared experiences from teaching the concepts, they discussed one-on-one interactions they had with their students or how students responded to test questions. They seemed to refer to experiences and generalized from these experiences to discuss how they think most students learn, which I think is common. Oh and just to add – when I first began this work, I simply went in and asked instructors how they taught precipitation reactions to their students. This was a big mistake because there was so much variation in response. Now, of course, I recognize that I was a bit too open-ended in my questioning strategies (smile) and this helped me frame how to narrow the questions to get tighter responses that could actually inform the animation design process.

In my research, I always use a blend of picture construction (drawn explanations) and oral explanations with a great deal of questions brought in to find out the “why’s” of their explanations. I cannot discern what specific aspects I learned from their pictures and what aspects I learned from their oral explanations as both were done to inform how instructors wished their students to be able to explain the reactions. In the design process, I purposefully tried to bridge between the different instructors’ perspectives when constructing the storyboards for the animation. The most complicated animation was actually a blend of instructors’ constructions. The simplified animations involved simply reducing the solvent water, and then offering additional animations that assisted in explaining some of the complexities associated with ion hydration and precipitate formation. I noticed from my research that many students thought that when any reactant solutions were mixed that there was a sort of reaction that occurred (based on how they switched the atoms with different partners) before then the ion pairs broke apart – resulting in no reaction. As a result, of this research, we also animated what it would look like if two solutions were mixed and did not result in a reaction.

I think professors are purposeful in their intent to simplify the complexity for two or three reasons – they wish to address key features of the reaction events to ease the learning experience or maybe to help focus students on what's important to know. In addition, they don’t have time to draw the most accurate pictures and/or they are limited by their artistic abilities to construct pictures that reflect what they picture. Often times, they use their talents to construct a picture that is one part symbolic and one part submicroscopic, a hybrid of sorts. For example, in the figures you might notice that many drew the symbol of the elements as if they were atoms or ions. (Aside -Now some of you might wish to discuss how this really shows that experts work seamlessly between the levels made famous by Alex Johnstone, and as a result they are so immersed in these two worlds that they don’t distinguish between them. Maybe? I am not sure.) Again, I notice that instructors tend to orally describe the details and leave them out of the pictures (I guess this is counter to my answer to Q1 – I have an idea of what the oral and drawn explanations reveal). The drawings also reflect the instructors’ beliefs about what is important to teach. Some are trying to relate to the equations and some try to account for the macroscopic connection. Some do both. This alone is complicated, but consider that once the animation is designed now the instructors are critics of what was made. This reflects their pedagogical aim, as well as what they believe are scientific accuracies that should be included regardless of the educational training of the student. I find that these suggestions for change usually come out after the animation is designed, because the animation is a conversation starter and I believe this causes instructors to compare and contrast to their mental models. Perhaps as we move forward, I would now ask instructors what they like or dislike about the existing animations? What do they find useful for their instruction and what would they like changed to better meet their instructional needs. I might also ask them how the animation is similar or different to how they picture the event verses how they teach the event. This is all part of the iterative process of animation design. And it is sort of on par with looking at your student evaluations at the end of the semester – it takes a bit of courage to do this and a stiff drink probably doesn't hurt either (joke).

Here are a few do's and don'ts
Do seek a collaborative group of animation artists.
Do obtain someone with awesome programming skills.
Do find out how much time it takes the artist to construct the animation and how you should pay them. Same goes for the programmer.
Do be sure that you obtain not only the final animation product, but also the code that goes into the design.
Don't be afraid to try.

Hi Resa,
Could you tell me what you mean by ion pair, and why you think so many students have a misconception about it and water molecules in the solvent?

How are you using animations with your students? How much time do they average per week using the animations? How has the use of animations affected class grades is there a difference between the students who are heavy users of the animations versus those we don't use the animations?

Hi Brian,
In my studies, some students will represent an aqueous ionic solution of sodium chloride with the cation and anion bonded together, almost like a covalent bond or two circles touching. They will also do this for the silver chloride precipitate. Sometimes they do not include the charges in their structures, but they may represent the anion as a larger circle to indicate that there are charge differences as observed by the size of the ion. Sometimes they do not include any charges or they do not vary the size and will simply pair atoms together. From my research, when I have asked students why they construct their aqueous salt solutions or the precipitate in this manner, they tend to tell me that the formula is written together and the formula is correct so they are keeping the ions together to fit with the formula. Basically, they seem to map their atomic level conception onto the formula. I realize that if the solution were a concentrated salt solution, it is quite possible for these ion pairs or even clusters of ions to exist, but usually students aren't considering how ions might attract and cluster together despite being attracted to water molecules or entropy factors. So I try to describe how students represent their mental models in pictures and to me they look like ion pairs, but in some cases molecule might be a better term to use or maybe just ionic compound. As far as the water molecules, most students tend to leave it out and consider it an unnecessary detail. A few students might include a few water molecules just to convey its presence, but very few recognize the ion-dipole attraction or the orderly arrangement of the water molecules about the ions, and the disorganization/organization of the water molecules in the solvent.

How do I use animations? When I teach, I typically ask students to first simply view the animation or take it in. I will ask that they jot down notes of what they consider key features of the animations. Then I will ask them to focus on some specific aspects - perhaps the interactions, the mechanism or structural details. I am interested in whether they believe the animation is an acceptable model, but I try to also get them to think about the limitations of the model - so this adds to the discussion. Once I show the animation, I will usually take screen shots from the animation and use these for discussion. I guess ultimately, what I ask them to think about depends on the concepts that I am teaching and what I hope to emphasize with the animation. I do not use animations every time I teach so as far as an average per week, that really varies and would actually be quite small compared to the other things I do in my lessons. Usually I show the animation in class, have a discussion and then I will pose some clicker questions or I will have them draw a picture and turn it in (although I rarely grade these) and some times I simply have them do a think-pair-share activity. As far as differences among students that are heavy users and students that don't use as often, I have not noticed big differences here. I know Roy Tasker talks about this and he discusses the importance of training students to use animations. I haven't had that experience as much. Many of my students will tell me that they search for YouTube videos or Kahn Academy clips to make sense of chemistry, but then there are some that do not. Some will tell me that it doesn't matter what they picture, because they don't know what they are doing. They view the animation as another didactic method of instruction, in which they must keep track of all that they see so that they can recall it later. This is why I like to have them compare the animation to experimental evidence as often as I can, and I try to get them to critique the model.

Thanks for your questions!

Hi Resa,

I partially agree with Roy and I have found it worthwhile to take the time to help students understand what they are seeing in animations. It sounds as if you do something similar. I'm somewhat surprised that you find no correlation between learning an amount of use of animations.

What do you think of this definition from Wikipedia of ion pairs?

There are three distinct types of ion-pair, depending on the extent of solvation of the two ions.
Schematic representations of ion-pairs

fully solvated

solvent-shared or solvent-separated

In the schematic representation above, the circles represent spheres. The sizes are arbitrary and not necessarily similar as illustrated. The cation is coloured red and the anion is coloured blue. The green area represents solvent molecules in a primary solvation shell: secondary solvation is ignored. When both ions have a complete primary solvation sphere the ion-pair may be termed fully solvated. When there is about one solvent molecule between cation and anion, the ion-pair may be termed solvent-shared. Lastly when the ions are in contact with each other the ion-pair is termed a contact ion-pair. Even in a contact ion-pair, however, the ions retain most of their solvation shell. The nature of this solvation shell is generally not known with any certainty. In aqueous solution and in other donor solvents, metal cations are surrounded by between four and nine solvent molecules in the primary solvation shell,[1] but the nature of solvation of anions is mostly unknown.

Hi Brian,
I don't really delve into animation use, because I think this has been studied and there is probably a threshold number of viewings that is optimal (assuming the student is actively engaged or at least reflective during the process). But students are not always so self-motivated or disciplined to view animations 3 or 4 times (I may be off on the "magic" number). I prefer to study how students make sense of what they view. I don't think there is a right or wrong here, and I certainly don't intend to challenge your belief in viewing repetition, because I think you are probably correct. Practice is a good thing.

I find your Wikipedia reference interesting! Thank you for sharing. But I worry that you may be misunderstanding that I am only using the term ion pair to describe how students (beginning, first semester students) depict aqueous salt solutions. I am aware that there is a great deal of complexity associated with solvated ions, and I know that my animations may be horribly simplistic, but it opens the door for discussion. That's what I want. I'm glad that there are additional models that allow us to reconsider our viewpoints. That's exciting! I also like that this is a different model and a still image. I would be open to sharing it with my students to see how they might compare and contrast the models. How might they redesign my animations to show a broader range of interactions between water molecules and ions. I think this could be fun to explore with them! I might just try that.

Thanks again for sharing this and for your thoughtful critique of my animations.



I enjoyed reading your paper, I believe this is a wonderful way to address many misconceptions related to different general chemistry topics. Have you done further research for a different gen chem topic?


Hi Zack,
Thanks for the kind note! I have examined students' conceptions of substances tested for electrical conductivity (JCE paper 2014) and I have unpublished work examining acid-base neutralization reactions and redox reactions. I'm analyzing data right now and hoping (fingers crossed) that I can get something out in the near future.

Hi Resa,

Thank you very much for your paper it is very insightful! I create educational media for a living and am very interested in how I can design better learning experiences. Although much of the ELT was designed to address specific misconceptions that you had identified for precipitation reactions, as I read your paper I also tried to see what lessons could be generalized to other molecular visualizations/interactives:

First, it seems the learning cycle approach could be applied, and be useful to, almost any topic: first arouse curiosity by presenting a mystery, develop the concepts using animations and illustrations (ideally informed by student and teacher interviews), and then have the student carry out an experiment, either real or virtual, to answer the initial question.

Second, in general it might be beneficial for the animation style to progress from more complex to simple. By presenting a more complex or realistic animation first, you allow the student to appreciate the true nature of the process, and then to focus on the salient features of the process when shown a simplified version afterward.

Third, the click-and-drag exercise helped track changes in student understanding, but do you think going through the exercise of visualizing their understanding also helped them to actually improve their understanding? I.e. might we want to think about simply embedding tools that enables students to construct visualizations of a topic periodically while learning a topic?

Would you agree with these generalized take aways or have any others to add? As well, do you have any suggestions for quick and dirty ways we might go about learning what misconceptions students might have about a topic when we have limited time and budgets?

Thanks again,

Hi Melanie,
I think you did a great job of summarizing this work into three take aways. The only one I would modify a little is #3 - only because I am not an expert here. Designing animations is tricky for professionals to do and some of the tools that exist are great, but still a bit clunky when it comes to portraying the interactivity between chemical species so having students design could be great or it could be problematic. I do not want you to think that I am discouraging this, because I know there are a few researchers who study this very area and I think they might be better qualified to make a recommendation. Vickie Williamson, Sevil Akaygun and Mike Stieff come to mind- they would be able to offer some excellent suggestions. I like the click and drag because it removes the movement and it's very simple to use, yet provides good insight into the students' mental model. But I should caution that even though it is good, it's only one piece of evidence into how students think and it is limited by students taking liberty to only express the most salient features.

As for your last question - I am convinced that misconceptions are not the enemy. Look out - I may get on a soap box here, it's just that so many of us have labored over students' misconceptions only to find that students will retain misconceptions, and as they practice and keep studying chemistry they will begin to form better conceptions. It takes a lot of time and practice to overturn a misconception depending on how ingrained it is. This is why I think we are better off not to target the misconceptions, because even if we design tools to point right at the student and tell them - you are wrong! They probably won't be inspired to suddenly align their understanding. I'm pretty sure I still have misconceptions, but that's another story! I recommend trying to animate the key characteristics you want students to learn and how you might present something that the students haven't thought about before. I think Roy Tasker is masterful at this! Look at VisChem animations if you get a chance. I also recommend asking students to consider whether experimental evidence can be used to support or refute these models - any models good or bad. Actually going back to the design your own animations, I think it would be really useful to have students critique each other's models - what are the strengths, what are places for growth?

Anyway, I hope this helps! Thank you again for your interest and questions.

Doug Ragan's picture

Thank you for responding on how you use animations with your students. As a HS teacher, I too have faced similar misconceptions with my students with the dissolving of ionic salts and have used animations as a tool for instructional purposes. I have had some success with a Target Inquiry lab I wrote entitled "Where's My Salt" and have also recently with a little more success had students use unifix cubes to build the ionic salts and then break them apart to represent what is happening as the salts dissolve. Again thanks for the insight on how you use the animations. It truly becomes more of an interaction than just watching. I will be sure to include those tips in my teaching.

malkayayon's picture

Hi Resa,
Thank you for sharing this paper and for letting me experience the tool.
I think that the comparison between the first atomic view model and the final one is very powerful, it is easy to draw the model. I have been a HS teacher for many years, as Doug mentioned, I too have faced similar misconceptions with my students with the dissolving of ionic salts and have used animations as a tool for instructional purposes, your tool is different because students can reflect on what their mistakes.
Maybe there could be an option of multiplication of the number of particles when the student finishes to draw the simplest ratio..or a question asking to estimate how many of those particles are there in a "real solution".
The idea of the menu and letting students skip parts is good because if they know something they can skip that part. Did you see students skipping a part even if they didn't know that part?
Also, in Israel we do not teach the "molecular" type reaction for ionic solutions, we can skip that part with our students.
I found the tool very systematic, explanations were good and it is great to have the sound combined. Do you work with headphones in class? Can you elaborate on students' ideas regarding the cartoon of Mr. NRG (BTW - great name!!)
Maybe the final table could be divided in class so each pair of students answers only two or three of the squares (one with a 1:1 mole ratio, one with another ratio , one that doesn't react) and then students present their answers in class. This could solve the frustration of not having the correct answer when they fail, and it is less "heavy" work.
I was happy to see animations dealing with other topics.
Thank you again,

Doug, could you share the "Where's My Salt" lab?

Hi Malka,
Glad you enjoyed the tool. I really like your suggestions! Molecular equations can be a bit of a pain, but I think that they have a use - I'm fairly lazy, I mean efficient, yes, efficient - and I will write a molecular equation over a total ionic any time. The trick is helping our students understand them, but I do realize that it can seem like an uphill battle. You said that you can skip those types of reactions, but are they taught somewhere else? I wonder if writing these types of equations is more of the proverbial - well, we've always done it, how can we stop? I have no answers here, only more questions. (smile)

As I work to design new tools, perhaps I could have you test them with your students? Let me know if you would be interested. I would so enjoy getting your feedback and observations, and I think it's important to study how tools work across cultures.

Oh and you asked about Dr. NRG - we actually had a contest, and this little test tube man won. Our next character is Dr. Ann Ion - yes, we love the puns. She even has a cat named Ion and as you can imagine they are quite inseparable - oh groan! Dr. Ann Ion is shaped like an Erlenmeyer flask and she has bubbles for hair. We wanted a female tutor, and unfortunately she's a bit frumpy, but a good balance for Dr. NRG. We had a contest for her as well. Most college students tend to like the cartoon characters; this may be because they are used to characters like the Simpsons and SpongeBob Square Pants. There are a few students who find it childish, but they will tell me that the content is definitely not childish.


malkayayon's picture

Hi Resa,
In Israel students are taught to write only ionic equations for ionic compounds. I agree that it is less confortable, but we learned to cope with it :)
We can be in touch and see if I can try some animations in my class next year. I am on Sabbatical now.
Language might be an obstacle, but maybe it could be a challenge to overcome!
My students find my name suitable for a chemistry teacher "Ya yon" :)

Oversby's picture

I do have some issues with this idea of ionic compounds. For example, sodium hydroxide has a covalent bond between O and H, and an ionic nature in the structure (not between one OH and one Na). I am also ignoring ideas about partial character of bonds here.
Resa, I have enjoyed reading your paper, which I find very stimulating and thoughtful, as well as provoking new thinkinf for me. Well done and long may you continue to develop these ideas. John

Yes, that's a good point John - polyatomic ions present some challenges too. In some of my interviews students express frustration that "we chemistry instructors" keep changing the rules on them. To quote a student from memory - There's all these exceptions. You start out telling us one thing and then you wave your hands and say, but not always. That's why I don't like chemistry. --this was from a very bright student who actually learned to play the student game and earned an excellent mark in the course. When I reflect on this, I think yeah, he's right. I know I am guilty of simplifying and then later saying, remember when I said this, well it was a bit of a simplification (shrug shoulders, grin). In defense of instructors, we have to start somewhere and scaffolding is a huge part of instruction. I wonder what the learning progression folks would say about this? Perhaps the key is giving students just a few tools and then asking them to apply them in a greater variety of contexts? Or keep in mind, one could start with an animation about aqueous sodium chloride and then ask - what would it look like if we dissolved sodium hydroxide in pure water? How would it be similar to dissolving aqueous sodium chloride? How is it different? Perhaps the more we can ask our students to consider these situations the better off they will be.

Thanks for the kind note! It's quite flattering to know that you found the article stimulating and thoughtful!

Oversby's picture

A thought that comes to my mind, Resa, is how the interactions change with high concentration. In a saturated sodium chloride solution, every water molecule is influenced by one ion or other, or by many at once. It is almost as though there are no 'solvent water molecules' i.e. water molecules that are not affected by ions. How dilute the solution has to be before such solvent water molecules exist I do not know. For multi-charged ions the impact on the water structure will be even more significant. When I was teaching chemistry to prospective primary science specialist teachers, through the topic of dissolving, a pedagogical question for me was how much complexity to include.
In the meantime, I do rember your insightfulness from when we first met in Oxford so many years ago, and your great sense of humour!

SDWoodgate's picture

I have been thinking about the comment about ionic compounds, and wonder if it would be better if we taught students that some compounds (NaOH for example) exist as ions instead of calling them ionic compounds. The former description does not presuppose the bonding IN the ions.

The other thing that I have been thinking in recent years is that the concept of a lattice (for ionic solids and metals) isn't pushed enough. It is my opinion that we should be teaching something about degree of aggregation (I am sure that somebody can think of a more catchy description), namely atoms, molecules and lattices at the same time that we teach about elements and compounds. The students first need to be comfortable with how the various reactants exist before they can visualise the events leading to reaction.

One other point is that in my experience teaching beginning organic chemistry, students find drawing three-dimensional objects hard. They need to have conventions to assist them in their representations - like the hash and wedge that is used in organic chemistry.

Thanks to both authors for interesting papers.

Hi Sheila!
Great to hear from you! I find myself nodding in agreement with your suggestions. I especially like the idea of teaching aggregation and providing practice with 3d representations. I think that could be quite useful. Hope all is well in New Zealand!


Doug Ragan's picture

Target inquiry keeps track of the labs downloaded. They are all free just request a password at under teaching materials.

I think physical models are very important and useful for our students. I need to check out unifix cubes and your lab! Thank YOU for sharing. Best to you as the school year draws to a close.

There is a lot here that is interesting. Have you looked at the students who, after the intervention, still hold misconceptions about the ion pairs both in solution and in the precipitate? It seems likely that there would be some significant overlap between the two groups. Maybe looking at the group that is confused about both would help provide a path to removing the confusion. It is a really complex topic, and there are lots of places for students to get hung up. Like the fact that some books that call NaCl a molecular formula which students will translate to "it's a molecule". And I would support the notion that lattices and unit cells should probably get more attention than they do.

Hi Lou,
I have modestly studied students who have misconceptions related to both solid sodium chloride and aqueous sodium chloride after an animation and video treatment. My findings indicate that students who retain misconceptions may feel that it's an unimportant detail - what they have is close enough, and sometimes they continue to believe that the atomic level needs to reflect the formula. Sometimes, in the case of aqueous NaCl, they draw a mixture of free ions and paired ions, because they are reluctant to believe that all of the ions would be dissociated. I refer to this as a transitional state in which students are beginning to fit correct conceptions to their existing mental models. I think this goes back to the idea that misconceptions are tricky and repairing them sometimes is not an all or none kind of thing. This actually makes me feel a bit better about my teaching practice, because it's likely that students are learning to fit new ideas to their existing schemas regardless of their test performance. There is a quote about running that says, "The race is not always to the swiftest, but to those who keep running." I think the same is true of learning chemistry. It takes a lot of practice.
Thanks for your question Lou!

Hi Resa,

I really did enjoy reading your paper. I like how you monitored the over success with the Pre-Treatment and Post-Treatment of the students misconceptions. I typically refer my students to online videos and the PHET website to supplement the different topics that we cover in an attempt to help them develop their perception skills.