Notes

Outline

An Open Standard for Chemical Structure Representation The IUPAC Chemical Identifier  S. E. Stein, S. R. Heller, D. V. Tchekhovskoi Physical & Chemical Properties Division NIST

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Communication of Chemical Identity Human Verbal – Common name Text – Systematic/Common name Pictorial – Structure diagram

Digital ‘Naming’ of Chemicals Chemical structure is the true ‘identifier’ But, structure representations are not unique or convenient for computers. So, convert structure to a unique ‘name’ by fixed algorithms The Iupac CHemical Identifier (IChI)

Customer Needs “Authors” Precise Convention-free Wide coverage “Readers” Robust Variable specificity Long life “Publishers” (Software) Ready access

Two Problems Chemicals Fast isomerization (tautomerization) Ill-defined connectivity Chemists Differing conventions Depends on discipline, education and convenience Imprecision/uncertainty

3 Steps to IChI Chemistry ‘Normalize’ Input Structure Implement chemical rules Math ‘Canonicalize’ (label the atoms) Equivalent atoms get the same label Format ‘Serialize’ Labeled Structure Output as character string (‘name’)

Normalize Simplify Divide structure into ‘layers’ Each layer ‘refines’ structure Ignore ‘Electron Density’ Use simple ‘connectivity’ only Ignore bond type and electron location Stereochemistry sp2 and sp3 only Free rotation around single bonds No Z/E stereo for small rings (default)

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4 Connectivity ‘Sublayers’ Disconnect metals and H-atoms Skeleton Reconnect fixed H-atoms Tautomerism Reconnect mobile H-atoms (optional) All connections fixed Reconnect metals (optional) Represent bonds to metals

Tautomer Sublayer

Stereochemical Sublayers sp2 – double bond sp3 – tetrahedral {others added later} relative, absolute or racemic

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Assume Free Rotation Around Single Bonds

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Nitrobenzene

MSG (tautomeric)

MSG (fixed)

Ferrocene

Byproducts: Stereogenic Centers and Equivalent Atoms Aids structure validation

Auxiliary Output Warnings/Errors Unusual valences Unrecognized input ‘Reversibility’ Coordinates Bond/Charge Location

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IChI FAQs How can you represent chemistry without electrons? Chemistry is not represented, just identity Whole molecule properties are easily added. Do big molecules have big IChIs? Yes, just like systematic names How to handle other tautomers, substructures,..? Other software Is IChI reversible? Partly - contains only data needed for ‘naming’ Auxiliary fields can carry other information Is IChI extensible? New layers can add refinement

IChI Capabilities Identify compounds at the known level of detail Convention-free (mostly) Generate quickly from structure Contains all essential connectivity information Simple ASCII representation

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Utility of Digital ‘Dictionary’ Traceability Clarity (especially for computers) Indexing Effective ‘keywording’ Accuracy Error checking Automated Processing

Goal Color Books as Source of Basic Chemical Terms in XML Why IUPAC? International Acceptance Comprehensive Open Process Long-standing Part of its mission

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The Gold Book is ‘Indexed’ on the Web

Gold Book in XML Provide uniform chemical terminology for XML documents Root for digital ‘tags’ in chemistry Model for future IUPAC recommendations

Gold Book – PDF to XML (implicit to explicit) Text ‘Tag’ data and relations Chemical Structures To connection tables/CML/SVG Equations To MathML Figures & Complex Schemes Redraw in SVG

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Green Book - Promise Template’ for numeric property validation Ensure proper units and representation Traceable  to IUPAC definition Basic Tags for Common Properties Covers 15 ‘fields’ of chemistry

Next Nov 12-14 Meeting at NIST IChI ‘Final’ Beta Nov. 2003 Dissemination Databases, Software Version 2 XML Data Dictionary Gold Book Conversion Maintenance Method Green Book

Thank you. I will be to answer any questions.