A Simulator For Explaining Organic Reactions Through
Qualitative Reasoning
Introduction (I)
• We implemented qualitative reasoning based on QPT ontology in a software tool (QRiOM)
• The main educational goals of the tool are that:– The students will undergo mental change so that they are
able to explain chemical phenomenon in a more elaborated way
– The students would benefit from it in terms of improving their reasoning skills and enhancing their understanding of the organic processes
Introduction (II)• The main focus of the design of QRiOM is on
the generation of explanation (causal and behavioral aspects of organic reactions)
• The results of a simulation is presented in five main forms:– Names of the final product (most stable form), and organic
mechanism used to predict the output– QPT processes (for inspection)– Causal diagram for tracing parameter dependency during a
make-bond/break-bond organic process– The entire reaction route (from initial substrate to the final
products)– Reacting species (view pairs) used in each reaction step and
their chemical parameters’ states change
Inputs 1 (Substrates &
Reagents)
2 Substrates Recognizer
4 QPT model constructor
3 Chemical
Knowledge Base 1. Chemical facts 2. Chemical theories 3. OntoRM 4. QPT process models
5 Qualitative Simulator
1. Quantity space analyzer 2. Molecule update routine
6 Explanation Generator (Causal and behavioral)
7
Outputs 1. Final products 2. Reaction routes 3. mechanism used 4. explanation notes
This module checks user selection, and returns the “type”
of the inputs as either a nucleophile or an electrophile. From here, an organic reaction
may be determined
This module will automate the construction of a
process model using QPT modeling constructs
The actual reasoning and simulation starts here. The task
is handled by several sub-modules. These include QSA
and MUR
This module will generate explanation to justify the
simulated result
Functional components of QRiOM
Functional components of QRiOM
Main interface of QRiOM simulator prototype
A B C
More learning activities and explanation can be viewed by clicking A, B and C buttons
Input selection Predicted products
Learners may inspect the automated
models
QPT processes
QPT model inspection page
Brief explanation of QPT slots is provided
Check how twoparameters are relatedin a given bond activity
The series of organic reactionsoccurred are stored in special purpose
data structures during reasoning in orderto generate causal graph;
like this one
Causal diagram inspection page
This button will display thepop-up window to tell the user how to read the causal diagram
More snapshots are provided for learners to examine the chemical parameter states’
changes
The entire reaction route is displayed after a simulation is completed
Basic properties of each atom
involved in a reaction are
recorded for user inspection
More learning activities and explanation
Learners can select any reacting species to study their
parameter history (from the first reaction step until the entire simulation is ended)
During simulation each chemical state change is recorded
Contents of the View Structure give the pairs of reacting species used in each small reaction step
Editor page for adding/deleting chemical facts and theories
Some organic chemistry terms are also provided; the page can be accessed from the main interface
Examples used are:Reasoning casesOrganic Mechanisms = 2 (SN1 and SN2)General Reaction formulas = 3
SN1Tertiary alcohol + Hydrogen halide(CH3)3COH HX
• CH3CH3CH3COH + HF• CH3CH3CH3COH + HCl• CH3CH3CH3COH + HBr• CH3CH3CH3COH + HI• CH3CH3CHOH + HF• CH3CH3CHOH + HCl• CH3CH3CHOH + HBr• CH3CH3CHOH + HI
Alkyl halide (tertiary) + Water molecules(CH3)3CX 2H2O (in excess)
• (CH3)3CF + 2H2O• (CH3)3CCl + 2H2O• (CH3)3CBr + 2H2O• (CH3)3CI + 2H2O
SN2
Alkyl Halide (primary) + incoming nucleophileCH3CH2X Hydroxyl functional group
CH3F + HO-CH3Cl + HO-CH3Br + HO-CH3I + HO-CH3CH2F + HO-CH3CH2Cl + HO-CH3CH2Br + HO-CH3CH2I + HO-CH3CH2CH2F + HO-CH3CH2CH2Cl + HO-CH3CH2CH2Br + HO-CH3CH2CH2I + HO-CH3CH2CH2CH2F + HO-CH3CH2CH2CH2Cl + HO-CH3CH2CH2CH2Br + HO-CH3CH2CH2CH2I + HO-
Other reaction formulas tested are:
1. CH3CH3CH3COH + HO-2. CH3CH3CH3COH + H2O 3. CH3OH + HO-4. CH3OH + H2O5. CH3CH3CHOH + HO-6. CH3CH3CHOH + H2O7. CH3CH2X + H2O8. CH3X + H2O9. CH3CH2X + X-10. CH3X + X-11. CH3CH2CH2CH2X + H2O12. CH3CH2CH2CH2X + HO-13. CH3CH2CH2X + H2O14. CH3CH2CH2X + HO-15. (CH3)3CX + HO-16. (CH3)3CX + X-
Conclusion (I)
• The simulation has been successfully tested with positive results– The QR approach enables prediction to be made, as
well as causal explanation generation about theories of a number of organic chemistry phenomena
– Cause-effect chain can be explained by using only the ontological primitives of QPT
• A study of learners’ feedback using the software was carried out– Overall, there was general understanding that the new
means of learning through qualitative simulation and explanation had proved valuable
Conclusions (II)
• The software – can predict final products– can explain its reasoning
• Unlike other chemistry software, QRiOM is implemented without having any pre-coded solution path in the knowledge base
• From a learner’s point of view– conceptual understanding is nurtured– reasoning ability is improved
Alicia Tang (University of Tenaga Nasional, MALAYSIA)Email: [email protected] Tel: +603 89212336
Sharifuddin Mohd. Zain (Dept. of Chemistry, Malaya University)
Noorsaadah Abd. Rahman (Dept. of Chemistry, Malaya University)
Rukaini Abdullah (Dept. of AI, Malaya University)