1 / 10

Knowledge Based Reactions

Knowledge Based Reactions. Outside of quantum mechanical modeling, typical method is to explicitly specify the participating reactant atoms and how bonds are rearranged as a reaction profile. O. O. H. NH 2 -R 2. +. + H 2 O. OH. R 1. NH 2 -R 2. R 1. Sample Reaction Profile.

Download Presentation

Knowledge Based Reactions

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Knowledge Based Reactions • Outside of quantum mechanical modeling, typical method is to explicitly specify the participating reactant atoms and how bonds are rearranged as a reaction profile O O H NH2-R2 + + H2O OH R1 NH2-R2 R1 Sample Reaction Profile

  2. Knowledge Based Limitations • Requires manual pre-specification of many different known reaction profiles to achieve any degree of generalization + + + + +

  3. Knowledge Based Limitations A B C D A B C D • A very generic reaction profile can cover everything from previous slide and indeed about 50% of all known organic reactions • Still, a screening or ranking method is needed to filter many unrealistic reactions proposed above • Many reactions with more sophisticated profiles are not covered without manually specifying more knowledge based profiles • Diels-Alder • Azide + Alkyne aromatic cyclization

  4. Reaction Favorability Scoring • Simple scoring method to suggest predicted reaction feasibility and favorability based on a simplification of Hess’ law DHreaction = S(BDEbroken) – S(BDEformed) • Estimate change in enthalpy by looking up bond-dissociation energies (BDE) • Apply additional bonuses and penalties for aromaticity and ring strain

  5. Pseudo-Mechanistic Reactions • First step towards more generalized, pseudo-mechanistic reaction modeling is the introduction of “intermediates” • Model breaking a bond in each reactant by separating charge, representative of the bond electrons moving to one atom • Closing the intermediates is then just a matter of matching + and - charges A B C D A+ B- C- D+ A B C D

  6. Pseudo-Mechanistic Reactions O- H+ O H O O - H+ • Applying general electron-shifting rules on the intermediates before closing them into products provides a lot of power and chemically intuitive results

  7. Azide + Alkyne Example R1 N N+ N- R2 C C R3 R1 N N N R1 N+ N N- C C R2 R3 R2 C- C+ R3

  8. Diels-Alder Example C C C C + C C C- C C+ C + C- C+ C C C+ C- + C- C+

  9. ChemDB Architecture finger.ics.uci.edu 2. Similarity Query 1. HTTP Request 3. Similarity Results cdb.ics.uci.edu Client 4. DB Query 6. HTML Results 5. DB Results chemdb.ics.uci.edu

  10. ChemDB Architecture • cdb.ics.uci.edu • Linux, 1GB • Primary Integration Point • Web Server (Apache) • Image Server (internal smi2gif.py script) • Issue Tracker (Scarab, Tomcat JSP, PostgreSQL DB) • chemdb.ics.uci.edu • MS Windows Server 2003 • Database Server (PostgreSQL) • finger.ics.uci.edu • Linux, 4GB • Similarity Search Server (Internal FINGER module)

More Related