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CSC 599: Computational Scientific Discovery

Lecture 6: The Mechem System. CSC 599: Computational Scientific Discovery. Overview. Domain: Chemistry Mechanisms Basic Mechem Problems with Basic Mechem Mechem with TEST-STEP and INFER-STRUCTURES. The Domain. Chemistry is a unique science:

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CSC 599: Computational Scientific Discovery

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  1. Lecture 6: The Mechem System CSC 599: Computational Scientific Discovery

  2. Overview Domain: Chemistry Mechanisms Basic Mechem Problems with Basic Mechem Mechem with TEST-STEP and INFER-STRUCTURES

  3. The Domain Chemistry is a unique science: • The “rules” of the science are worked out (we think!)‏ • Stoichiometry: conservation of mass/energy/charge • Valences of atoms • Patterns in molecules • Benzene rings • Complexity due to combinatorics • Infinite number of possible organic compounds • Many possible chemical mechanisms

  4. Example Mechanism 6CH4 + 3O2 -> 5H2+CH3CH3+H2O+CH3OH+CH2O+CO+CO2 • CH4 + M -> CH3M + H • CH3M -> M + CH3 • O2 + CH3M -> CH3O2M • 2H -> H2 • CH3 + CH3M -> M + CH3CH3 • H + CH3O2M -> H2O + CH2OM (Not finished yet!)‏

  5. Example Mechanism (2)‏ 6CH4 + 3O2 -> 5H2+CH3CH3+H2O+CH3OH+CH2O+CO+CO2 • CH3 + CH3O2M -> CH3OH + CH2OM • CH2OM -> M + CH2O • CH3O2M -> H + CH2O2M • CH2O + CH2O2M -> CH3O2M + CHO • CH2O2M + CHO -> CH3O2M + CO • CO + CH2O2M -> CH2OM + CO2 (Whew!)‏

  6. Example Mechanism (3)‏ Let's step back and look at what we did: • It's “easy” because: • Apply rules of chemistry to posit legal steps • Assemble legal steps to accomplish overall reaction • It's “hard” because: • Combinatorics of all the reactions that COULD have been done • Why not, for example: 2CH3O2M -> CH3O4CH3O (chemists might think unlikely)‏ • How would you search space of mechanisms? • Is it worth automating?

  7. Basic Mechem: the Big Picture MECHEM searches space of reactions • Exhaustive search • From simplest to increasingly more complex Inputs: all reagents, at least one product Outputs: first (i.e.) simplest mechanism from reagents to product(s)‏ MECHEM will: • Search space of reaction pathways • Recall DENDRAL searched space of chemical structures

  8. Basic MECHEM, Issues • What is “simplicity” for mechanisms? • Number of “species” (atoms, molecules, or radicals) allowed • Number of reaction steps • Space is combinatorially huge! • Use rules of chemistry to limit search • Each reaction may have at most 2 reactants and 2 products • Disallow violations like C2H6O-1 • search formulas, not structures C2H6O can be either Ethyl alcohol: CH3CH2O Dimethyl ether: CH3OCH3

  9. MECHEM Algorithm (1)‏ findPathways(reagents, prods) { for ( maxSpeciesCount = reagents.count() + prods.count(); ; maxSpeciesCount++, prods.addNewVariable()‏ ) { sequenceList.setToEmpty(); extendNum = ceiling((maxSpeciesCount-num(reagents))/2); do { sequenceList=sequenceList.extendBy(extendNum,reagents,prods); if ( sequenceList.hasSolution() )‏ return( sequenceList.getSolution() ); extendNum = 1; } while ( !sequenceList.isEmpty() )‏ } }

  10. MECHEM Algorithm (2)‏ sequenceList::extendBy(downCount, reactants,prods) { if (downCount == 0)‏ return(this.sequenceList); newSequenceList.setToEmpty(); for ( seq in this.sequenceList) do for ( react in reactants) do for (prod in prods) do { newSeqence = seq.append(makeStep(react,prod)); newSeqence.inferAndInstantiateVarValues(); if ( newSequence.getIsLegal() )‏ newSequenceList.add(newSequence); } return(newSequenceList.extendBy(downCount-1,reactants,prods)); }

  11. Example: n1(C7H9N) + n2(CH2O) --> n3(C17H18N2) + n4(H20)‏ maxSpeciesCount = 6; initMaxReactionSteps = 3 • Initialize reactions as half steps: CH2O -> . . . C7H9N -> . . . 2CH2O -> . . . 2C7H9N -> . . . CH2O + C7H9N -> . . . (RECALL: 1 and 2 reagent reactions only)‏ • Reject full step reactions that are illegal • Example: Reject C7H9N -> H2O

  12. Example (2): Legal Whole Steps • CH2O -> H2O + X • CH2O -> X + Y • 2(CH2O) -> X • 2(CH2O) -> H2O + X • 2(CH2O) -> X + Y • 2(C7H9N) -> X • 2(C7H9N) -> X + Y • CH2O + C7H9N -> X • CH2O + C7H9N -> H2O + X • CH2O + C7H9N -> X + Y • C7H9N -> X + Y

  13. Legal 2 Step Reactions Only 2 reagents, only 2 reactions • 91 legal two-step reactions (Yikes!)‏ Here are the 4 that can be extended: CH2O + C7H9N -> H2O + X CH2O + X -> H2O + Y CH2O + C7H9N -> H2O + X CH2O + X -> Y CH2O + C7H9N -> H2O + X 2X -> C7H9N + X CH2O + C7H9N -> H2O + X 2X -> Y

  14. Basic MECHEM analysis Found 5 solutions, 6 steps each Another example: C3H8 (propane) + O2 (oxygen) -> C2H4O2 (acetic acid) + C3H6O (acetone)‏ + C3H8O (isopropanol) + C2H4O (acetaldehyde)‏ + C4H8O2 (ethyl acetate) + CH4O (methanol)‏ + CO2 (carbon dioxide)‏ • 16 pathways, 10 species, 6 steps • Several hours on DecStation 3100 (14 MIPS)‏ Yikes!

  15. What would you do? 10 species, 6 steps --> several hours That reaction ain't all that big How would you speed it up? Other forms of knowledge to reduce search? (What information did we ignore in Basic Mechem?)‏

  16. What would you do? 10 species, 6 steps --> several hours That reaction ain't all that big How would you speed it up? Other forms of knowledge to reduce search? (What information did we ignore in Basic Mechem?)‏ • Search formulas, not structures BINGO!

  17. Mechem with Structural Help Idea: Keep track of structure of molecules and radicals Heuristics: Let N = max. number of (topological) bonds created/destroyed By default, for all steps N <= 3

  18. Mechem with Structural Help (2)‏ Example • Notation: [(#Cs) (#Hs) (#Os) (#Ms)] M = “metal” (catalyst)‏ • Reaction has: . . . . W[1 3 2 1] -> V[0 1 0 0] + Y[1 2 2 1] . . . . With N = 2 No possible Y With N = 3 Y could be 2 things: MCH2OO or MCHOOH With N = 4 Y could be 18 things! • Handles 12 step reactions (hrs on Si Graphic Indigo)‏

  19. Other Ideas for Speeding Mechem • Max # of atoms/element, oxidation state, etc. • Bi-directional search • List of “compounds” that should not appear • Can do spectroscopy to see if they really do occur, even if transient • A.I. notion of “easy”  chemist notion of “easy” • AI. researcher: “Minimize number of steps!” • Chemists: “Minimize energy of rate determining step!” • Compare “cost” of bond-breakings • Mechem (rxn step proposer) + ChemNet (reaction network)‏

  20. Take Home Message: About Combinatorial Search • Finds “all” solutions? Finds “the best” solution? Yes, when scientists' notion of “simplest” == CSD researcher's notion of “simplest” • Takes forever! / only for toy problems Use domain knowledge Domain knowledge usage • Started simply (initially no structures)‏ • Used more when needed to solve harder problems (structure knowledge -> solve bigger problems)‏ • Eventually added so much knowledge that architecture changed (time to redesign algorithm?)‏ • HOW WOULD YOU DO BETTER THAN MECHEM?

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