Reaction classification, an enduring success story
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1 1 / 31 Reaction classification, an enduring success story J. Eiblmaier, H. Kraut, H. Saller, H. Matuszczyk, P. Loew InfoChem GmbH, Landsberger Strasse 408, Munich, 81241, Germany 50 Years of Computers in Organic Chemistry: Symposium in Honor of James B. Hendrickson ACS National Meeting Anaheim Spring 2011
2 2 / 31 Outline» CLASSIFY an overview» The driving force» The idea» The solution» Scope of application
3 3 / 31» CLASSIFY an overview marabou / PIXELIO
4 4 / 31 SciFinder Web Version, summer 2009 Copyright American Chemical Society (ACS). All Rights Reserved.
5 5 / 31 Reaxys, November 2010 Copyright Elsevier. All Rights Reserved.
6 6 / 31 Isentris 3.2: Transformation search Search finds all reactions that match query based on Medium reaction similarity Copyright Accelrys. All Rights Reserved.
7 7 / what probably users don t know:
8 8 / 31» The driving force
9 9 / mil. RXNs» ORAC (6.5): 25,000 reactions» SynLib (2.2): 39,000 reactions» REACCS (6.1 - Current Literature + Theilheimer): 19, ,000 reactions» ChemInform development in progress, approx. 65,000 reactions/year from 1991 onwards» InfoChem acquired 1.8 million reactions from ZIC/VINITI 25k 39k 66k 65k/y ORAC (6.5) SynLib (2.2) REACCS (6.1) ChemInform (>=1991) ZIC/InfoChem
10 10 / tapes of data (ORWO 430, 40 MB) Tape drive: Kennedy model 9401
11 11 / 31 Great but...» The available in-house systems (REACCS, ORAC) could handle approx. 100,000 Reactions!» How to provide this precious data to customers?» 1.8 million reactions worthless???
12 12 / 31» The idea hofschlaeger/ PIXELIO
13 13 / 31 The idea» Develop a concept similar to the way how chemistry is published» Represent a series of different, specific reactions having the same transformation type with one general representation» Main challenge: automatic identification of different transformation types
14 14 / 31 The idea: fundamentals» Reactions can be characterized by their transformations» Reactions which have the same reaction centers and share the same environment close to the reaction centers are similar reactions» Calculate a unique hash code for each particular transformation type» Select/define one relevant representative for database
15 15 / 31» The solution Rolf van Melis/ PIXELIO
16 16 / 31 Definition and determination of the reaction center» A bond is defined as a reaction center if it is made or broken» An atom is defined as a reaction center if it changes number of implicit hydrogens number of valencies number of -electrons atomic charge» or if at least one connecting bond is a reaction center
17 17 / 31 How is the Reaction Classification Code calculated?» Hashcodes are calculated for all reaction centers (incl. atom properties) atom type valence state total number of bonded hydrogens (implicit plus explicit) number of -electrons aromaticity formal charges reaction center information» The sum of all reaction center hashcodes of all reactants and one product of a reaction provides the unique overall reaction hashcode called: InfoChem Reaction Classification Code (15 digits numeric)
18 18 / 31 BROAD, MEDIUM, NARROW C N C N H 0-Sphere (BROAD) Reaction centers only NH NH H C C N NH C C N NH H H 1-Sphere (MEDIUM) Reaction centers plus alpha atoms, excluding hydrogens C C N NH C C N NH H H 2-Sphere (NARROW) Reaction centers plus beta atoms, excluding hydrogens and consecutive sp 3 -atoms
19 19 / 31 Results 2.3 mil. CLASSIFY (NARROW) 1991: 2.3 million ZIC RXNs => 400,000 reaction types (CHEMREACT) 400k
20 20 / 31 InfoChem products» CHEMREACT» CHEMSYNTH» CHEMSELECT» CHEMREACT32» CHEMREACT41» CHEMREACT68
21 21 / 31» Scope of application hpgruesen/ PIXELIO
22 22 / 31 Reaction similarity search (same transformation)» Scifinder Web (summer 2009)» REAXYS (Nov. 2010)» Discovery Gate (v. 2.5)» Isentris (v. 3.2)» SPRESI web (v. 2.2)
23 23 / 31 Reaction Type Search (RTS)» ICCARTRIDGE / ICFSE» SPRESI web
24 24 / 31 Reaction Type Search (Isentris 3.x: Transformation Search )
25 25 / 31 Post search hit list clustering (Isentris 3.x)
26 26 / 31 Linking of reaction databases (cross database): MDL / InfoChem Integrated Major Reference Works RXN ClassCodes IMRW RXN Databases DiscoveryGate RXN Databases RXL Browser
27 Count of reactions per ClassCode 27 / 31 Analysis of diversity of RXN databases (E.g. SPRESI Version 2.8, 4.1 Million RXNs, NARROW) 13,794 examples 8,989 examples ClassCodes
28 28 / 31 Analysis of diversity of RXN databases: What do the singletons tell me?» Erroneous manual data entry?» Inadequate/incorrect Mapping (e.g. complex rearrangements)?» Weird (but valid) chemistry?
29 29 / 31 Spresi Doc-ID * 13 step reaction!!! *Da-Ming Gou and Ching-Shih Chen: Synthesis of L- -phosphatidyl-d-myo-inositol 3,4,5-trisphosphate, an important intracellular signalling molecule, J. Chem. Soc., Chem.Commun., 1994, 2125
30 30 / 31 Acknowledgements Accelrys Carmen Nitsche Russ Hillard CAS Kirk Schwall Robert S. Sadowski P. Storz / PIXELIO, Elsevier Jochen Tannemann InfoChimia Klaus Borchardt Günter Grethe The InfoChem Team
31 31 / 31 Thank you!
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