Drawing Molecular Sequences

Helen Zhang would like students to be able to draw simple sequences of annotated molecular reactions for LOOPS activities involving Chemical Reactions.

Initially Helen's request was to have the students use Chem Sense Animator. ChemSense Animator has a large number of customized molecular drawing

After a discussion in December 2009 between Stephen Bannasch, Bob Tinker and Helen where Helen used ChemSense Animator to show in detail just what she wanted the students to do and what data she'd like back as a researcher we realized that a much simpler component was necessary. ChemSense Animator is both quite complex, and has a confusing non-standard UI.

Here's a link to the 23 minute screencast of Helen, Stephen Bannasch, Bob Tinker, and Dan Damelin exploring drawing molecular sequences with ChemSense Animator.

• chemsense_ideas.mov 23 minutes, 49.53 MB

Our plan instead is to develop a simple OTrunk molecular drawing component using Molecular Workbench. The DrawMolecules component will be similar to the current drawing component with at least the following additional features:

1. Atoms: Add and subtract atoms of various types. (Each type has chemical symbol, size, color, and allowed number of bonds.)
   Initially the list is limited to the elemental forms of: Hydrogen, Carbon, Oxygen, and Nitrogen.
2. Bonds: create single, double, and triple bonds between a pair of adjacent atoms (if allowed).
   Each kind of atom has a maximum number of allowed bonds. (A bond is made only if each atom has the available bonds.)
   A magic wand for creating one covalent bond. Select the tool, touch one atom and then the other where a bond is desired. If there is already one bond, make it a double bond. If there is already a double bond, make it triple bond. If they are too far apart or no free electrons, put up a suitable error message.)
3. Scissors for eliminating a bond. Select a bond and click to break one bond. If it is a double bond, make it single. If it is triple, make it double.
4. Move atoms and molecules (atoms with bonds joining them).
5. Rotate molecules.
6. Directional arrow
7. Label tool.

In addition the DrawMolecules component would allow a sequential series of molecular drawings to be made, both the drawings and the sequence itself will be editable.

1. Make a sequence of drawings that can be individually edited and annotated.
2. Arrange the sequence in any order
3. Delete and add drawings.
4. Arrows to sequence one drawing forward or backwards.
5. "Play" button to show the sequence from the beginning to end with a user selectable pause time between frames.

At any point the existing sequence can be "played" from start to finish.

The author needs to set what tools are available and to be able to populate a drawing or drawings with starting conditions that include atoms and molecules. One option would be to NOT allow a student to add or delete atoms and molecules.

Use case

Students would be asked to:

1. Make an animation of possible steps in the creation two water molecules from oxygen and hydrogen molecules. Each step in the reaction must involve breaking or making one bond.
2. Use an annotation to describe whenever a new molecule is made.

A student response would be an ordered sequence of molecular drawings.

They might show H2 breaking up into 2H, one H attacking and O2 to make HO2. This might combine with the other free H to make H2O2 with might make H2O and a free O. The free O might attack the other H2 to make OH and H, which would then combine into H2O. This is not the only possible sequence.

chemsense_ideas.mov (video/quicktime)
MW_Sense_10.11.doc (application/msword)

From chemsense_ideas.mov: Goals Allow students to make several frames or snapshots in a sequence and attach text or audio. Make the UI much cleaner and simpler than Chem Sense Animator Student Use Scenario Students are engaged with some chemistry curriculum. Then, to illustrate their understanding, they create a short sequence (~3 frames) from scratch to show a chemical change. Each frame is annotated with text, audio, or both. Tools Students Need selector tool text inserter with changeable border (square, diamond, circle, etc.) element selector with bigger button, lists Hydrogen, Carbon, Oxygen, and maybe Nitrogen need circle for some students (not sure why, Helen didn't say...perhaps as a generic atom?) single/double bond tool draw arrow tool to point to products of reactions Also Need dynamically associated objects (ie, moving one moves all associated with it) fewer buttons, shorter/fewer menus slower/manual sequence maybe attach audio narration to the sequence (there may be an issue with file sizes...) Notable Divergencies (this vs. Bob's Draft) several frames vs. 20 or so single/double bonds only vs. triple bonds too User Narrative: Fully student-made vs. teacher prepared for student manipulation Posted by abean at Mar 11, 2009 13:15

An updated version of Bob's Draft can now be found here: MW_Sense_10.11.doc Posted by abean at Mar 11, 2009 13:17

I admit, triple bonds are unusual. But two important cases are nitrogen gas (N2) and ethylene (HCCH). Having enough frames (20, say) to show a series of partial reactions is very important. This is the way reactions really happen and they are modeled in MW. Helen wasn't thinking about this when she was being interviewed. In some future version, it would be most valuable to have a meter that showed the free energy. Breaking a bond would reduce it and making one would increase it. This should be coupled with the capacity to calculate the minimum energy configuration (already in MW.) The system could have a button for energy minimization that would move bonded atoms into the most favorable positions. Other tools for the future: Dots for un-paired electrons. A background grid. A spline with N ticks for making smooth animations--not shown in the movie. Tweening. Putting N steps between student drawn frames. Resonances. Students could show alternative bond assignments for a molecule (i.e. double bonds in benzene) and the software would alternate between the two or show shared bonds. Important b/c resonances like this are lower energy. Posted by rtinker at Mar 13, 2009 11:52