acs'08, 21-23 november, venice, italy designing organic reaction simulation engine using...
TRANSCRIPT
![Page 1: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/1.jpg)
ACS'08, 21-23 November, Venice, ITALY
Designing organic reaction simulation engine using
qualitative reasoning approach
Y.C. Alicia Tang Tenaga Nasional University Sharifuddin M. Zain (Chemistry Department, Malaya University)Noorsaadah A. Rahman (Chemistry Department, Malaya University)
MALAYSIA
![Page 2: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/2.jpg)
ACS'08, 21-23 November, Venice, ITALY
Contents (I)
Introduction Qualitative reasoning (QR) Problems and motivations
Organic reactions and mechanisms System methodology Previous works Functional components of QRIOM prototype
![Page 3: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/3.jpg)
ACS'08, 21-23 November, Venice, ITALY
Contents (II)
Reaction examples tested A reasoning scenario Qualitative reasoning algorithm Qualitative modeling algorithm A QPT process model Results Conclusion and future works
![Page 4: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/4.jpg)
ACS'08, 21-23 November, Venice, ITALY
Introduction (I)
This work presents a framework architecture that uses the QPT ontology as the knowledge representation scheme to model the behaviors of a number of organic reactions. We investigated qualitative representation and qualitative
simulation approaches The goal is to develop a learning tool that teaches
an organic chemistry course at the University of Malaya will undergo mental change so that they are able to
explain chemical phenomenon in a more elaborated way
![Page 5: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/5.jpg)
ACS'08, 21-23 November, Venice, ITALY
Qualitative Reasoning
Qualitative Reasoning (QR) research Attempts to model behavior of dynamic physical
systems without having to include a bunch of formulas and/or quantitative data
The research spans all aspects of the theory and applications Techniques, applications, task-level reasoning,
modeling, etc.
![Page 6: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/6.jpg)
ACS'08, 21-23 November, Venice, ITALY
Problems and Motivations (I)
Students faced problem in organic reaction mechanism courseThey learn the subject by memorizing the steps
and formulas of each reaction taught in classrooms
Poor conceptual understanding Not knowing the principles governing the
processes and the cause effect interaction among processes
![Page 7: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/7.jpg)
ACS'08, 21-23 November, Venice, ITALY
Problems and Motivations (II)
Simulation of chemical reactions that relied on pre-coded facts and rules cannot explain its results Since no tight coupling between concepts and their
embodiment in software
QPT describes processes in conceptual terms and embody notions of causality which is important to explain behavior of chemical
systems.
![Page 8: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/8.jpg)
ACS'08, 21-23 November, Venice, ITALY
Organic Reactions & Mechanisms
A reaction mechanism describes the sequence of steps (processes) that occur during the conversion of reactants to productsMechanism is used to explain how a reaction
takes place by showing what is happening to valence electrons during the making and breaking of bonds.
Organic chemists could work out the mechanisms by using knowledge developed from their chemical intuition and experience.
![Page 9: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/9.jpg)
ACS'08, 21-23 November, Venice, ITALY
System Methodology
Identifying chemical properties for organic reactions for model composition use
Classifying the possible reaction species and types Developing the automated model construction logic Developing the reasoning steps for predicting and
simulating the chemical behaviors of selected organic reactions
Designing the means for generating explanation
![Page 10: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/10.jpg)
ACS'08, 21-23 November, Venice, ITALY
Previous Works
From numerous substrates and reagents, we classify reacting species as either a nucleophile (charged/neutral) or an electrophile (charged/neutral)upon which chemical processes are selected
Two main reusable processes identifiedNamely, the “make-bond” and “break-bond”, for
the entire reaction mechanisms, specifically on SN1 and SN2.
![Page 11: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/11.jpg)
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
QRIOM:Functional Components
![Page 12: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/12.jpg)
ACS'08, 21-23 November, Venice, ITALY
Reaction examples Reasoning cases Mechanisms = 2 Reaction formulas = 3 Specific cases of simulation = 28
SN1 Tertiary alcohol + Hydrogen halide (CH3)3COH HX
CH3CH3CH3COH + HF CH3CH3CH3COH + HCl CH3CH3CH3COH + HBr CH3CH3CH3COH + HI
Alkyl halide (tertiary) + Water molecules (CH3)3CX 2H2O (in excess)
(CH3)3CF + 2H2O (CH3)3CCl + 2H2O (CH3)3CBr + 2H2O (CH3)3CI + 2H2O
![Page 13: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/13.jpg)
ACS'08, 21-23 November, Venice, ITALY
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-
![Page 14: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/14.jpg)
ACS'08, 21-23 November, Venice, ITALY
A QPT-basedreasoning scenario
![Page 15: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/15.jpg)
ACS'08, 21-23 November, Venice, ITALY
The production of alkyl halide
A = tert-Butyl alcohol, B = Hydrogen chloride
C= tert-Butyl chloride, D = Water molecule
(CH3)3COH + HCl (CH3)3CCl + H2O (1) A B C D
![Page 16: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/16.jpg)
ACS'08, 21-23 November, Venice, ITALY
Step 1: Protonation of tert-Butyl alcohol by H+. This is a “make-bond” process. .. .. .. ..
(CH3)3C – O: + H – Cl : (CH3)3C–O+–H + : Cl :
| .. | .. H H tert-butyl alcohol hydrogen chloride tert-butyloxonium ion chloride ion Step 2: Dissociation of tert-butyloxonium ion. This is a “break-bond” process. .. .. (CH3)3C O+ H CH3)3C
+ + : O–H | |
H H tert-butyloxonium tert-butyl cation water Step 3: Capturing of tert-butyl cation by chloride ion. This is a “make-bond” process. .. ..
(CH3)3C+ + : Cl :
(CH3)3C – Cl :
.. .. tert-butyl cation chloride ion tert-butyl chloride
![Page 17: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/17.jpg)
ACS'08, 21-23 November, Venice, ITALY
Qualitative Simulation
TopLevelDesign
QUALITATIVE SIMULATION ALGORITHM Q_Simulation(substrate, reagent, OUTPUT) 1. Recognizing substrate 2. Suggesting a chemical process 3. Constructing QPT models 4. Processes reasoning Initialize multiple data structures Perform quantity space analysis Check qualitative proportionalities in Relation-slot Refer to quantity spaces for each view used in the process Store propagated effects in data structures Store new individuals (intermediates) that produced Update all affected data structures 5. If view_structure <> EMPTY Then Go to step 2 Else Suggest mechanism used in the simulation Show overall reaction route Display final products End If 6. Generating explanations based on users’ queries
See next slide
![Page 18: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/18.jpg)
ACS'08, 21-23 November, Venice, ITALY
Qualitative Modeling
QPT VIEWS AND PROCESSES MODELING ALGORITHM Qualitative_Modeling(substrate, reagent, QPT_MODEL)
1. Examine user inputs (substrate and reagent) 1.1 Decompose inputs into functional units 2. Recognize functional units 2.1 Assign units to either nucleophile or electrophile group 3. Retrieve general properties of the groups Compose the Individual Views Put views in View Structure (VS) 4. Check Individual Views in the VS 4.1 Find a pair of individual views 4.2 Suggest a chemical process for the pair 5. Retrieve general properties for the selected process 5.1 Compose the slots for a QPT process 6. Stop
![Page 19: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/19.jpg)
ACS'08, 21-23 November, Venice, ITALY
Process “Protonation” (e.g. ((CH3)3C-OH) is protonated by H+) Individuals ;there is an electrophile (charged) 1. H ; hydrogen ion ; there is a nucleophile (neutral) that has lone pairs electron 2. O ; alcohol oxygen Preconditions 3. Am [no-of-bond(O)] = TWO 4. is_reactive(R3C-OH) 5. leaving_group(OH, poor) ;check KB for good/poor leaving group Quantity-Conditions 6. Am[non-bonded-electron-pair(O)] >= ONE 7. charges(H, positive) 8. electrophile(H, charged) 9. nucleophile(O, neutral) 10. charges(O, neutral) Relations 11. Ds[charges(H)]= -1 12. Ds[charges(O)]= 1
13. lone-pair-electron(O) P no-of-bond(O)
14. charges(O) P lone-pair-electron(O)
15. lone-pair-electron(H) P no-of-bond(H)
16. charges(H) P no-of-bond(H)
Influences 17. I+ (no-of-bond(O), Am[bond-activity])
Functional dependency implemented as
qualitative proportionality modeling construct
A “make-bond” process
in QPT terms
![Page 20: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/20.jpg)
ACS'08, 21-23 November, Venice, ITALY
Main interface of QRIOM
![Page 21: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/21.jpg)
ACS'08, 21-23 November, Venice, ITALY
A Qualitative Model
![Page 22: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/22.jpg)
ACS'08, 21-23 November, Venice, ITALY
![Page 23: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/23.jpg)
ACS'08, 21-23 November, Venice, ITALY
The ability to generate causal explanation has been one of the promises of the QR approach
Causal graph generated during
reasoning
![Page 24: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/24.jpg)
ACS'08, 21-23 November, Venice, ITALY
![Page 25: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/25.jpg)
ACS'08, 21-23 November, Venice, ITALY
![Page 26: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/26.jpg)
ACS'08, 21-23 November, Venice, ITALY
The approach enables prediction to be made, as well as causal explanation generation about theories of many chemical phenomena
Cause-effect chain can be explained by using only the ontological primitives of QPT
Results discussion (I)
![Page 27: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/27.jpg)
ACS'08, 21-23 November, Venice, ITALY
The explanation generation is causal in nature and is run-time based (not pre-coded)
Model inspection and reasoning can help to enhance a learner’s critical thinking and reasoning ability
Results discussion (II)
![Page 28: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/28.jpg)
ACS'08, 21-23 November, Venice, ITALY
Conclusions (I)
The qualitative models in QRIOM communicated knowledge that is common to chemistry people (via the QPT constructs).
The new computational approach can serve as alternative learning technology in developing educational software for subjects that require application of domain knowledge at intuitive level.
![Page 29: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/29.jpg)
ACS'08, 21-23 November, Venice, ITALY
Conclusions (II)
What the software can provide?the software can predict final productsthe software can explain its reasoningno pre-coded solution path or search path
From a learner’s point of viewconceptual understanding is improvedreasoning ability is sharpened
![Page 30: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/30.jpg)
ACS'08, 21-23 November, Venice, ITALY
Future works
To build a graphical interface that functions much as a protocol converter betweenReasoning shellGraphical outputs
To include user modeling in the softwareTowards an intelligent tutoring system
![Page 31: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/31.jpg)
ACS'08, 21-23 November, Venice, ITALY
The End.
Thank you GrazieTerima Kasih
![Page 32: ACS'08, 21-23 November, Venice, ITALY Designing organic reaction simulation engine using qualitative reasoning approach Y.C. Alicia Tang Tenaga Nasional](https://reader035.vdocuments.mx/reader035/viewer/2022062517/56649f075503460f94c1cc45/html5/thumbnails/32.jpg)
Questions?
COIT building, UNITEN
Faculty members