Notes

Outline

The IUPAC Chemical Identifier Steve Stein, Steve Heller, Dmitrii Tchekhovskoi National Institute of Standards and Technology Gaithersburg, MD, USA   U.S. Government Chemical Databases Frederick, MD July 22, 2003

Too Many Identifiers Structure diagrams various conventions contain ‘too much’ information Connection Tables MolFiles, Smiles, ROSDAL, .. Pronounceable names IUPAC, CAS, trivial Index Numbers EINECS, FEMA, DOT, RTECS, CAS, Beilstein, USP, RTECS, EEC, RCRA, NCI, UN, USAF

What kind of Identifier is needed? Derived from structure by algorithm Accepts common drawing conventions Exactly one Identifier per structure Comprehensive Openly available

Requirements Different compounds have different identifiers All distinguishing structural information is included

Requirements One compound has only one identifier Include only necessary information

IChI First Version Discrete, bonded compounds Include ‘dot disconnected’ compounds Stereochemistry sp3 - tetrahedral Z/E - double bond Tautomers

3 Steps to IChI ‘Normalize’ Input Structure Defined input structure required Remove conventions with chemical rules Divide into ‘layers’ ‘Canonicalize’ (label the atoms) Equivalent atoms get the same label ‘Serialize’ the Labeled Structure A unique series of bytes

NORMALIZATION

Simplifications Ignore ‘Electron Density’ Double/Triple/Coordination bonds Odd-electrons/Charges Free Rotation Around Single Bonds Separate structure information into ‘layers’

Ignore Electron Density Not required for compound identification Represent ‘excited states’ Simplify representations Delocalization, aromaticity, zwitterions, coordination …

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Assume Free Rotation Around Single Bonds

LAYERS

Divide into ‘Layers’ Formula Connectivity Disconnect metals Connect metals Isotopes Stereochemistry Tautomers (on/off)

Basic Layer Non-Metals Only Just atoms and their neighbors Ignore everything else Non-Metals: CHNO SPSi Halogens

Metals Layer Bonds to ‘Metals’ All bonds to metals Ignore bond type Empty if no bonds to metals Use when bonding is known and significant

Isotopes

Stereochemistry Double Bond (Z/E) Coordinates Defined parity Tetrahedral (sp3) ‘in/out’ bonds x,y,z coordinates Defined parity

Varieties of Double Bond Isomers

sp3 (tetrahedral) stereoisomers

Identify Stereogenic Centers Speed up processing Helpful for chemists

Basic Tautomer Layer

Tautomers

‘Salt’ Tautomers

Electronic Layer Net Charge

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IChI Output 9 possible fields Basic – non-metal ## Metal ## Isotopic ## Stereo ## Stereo ## Tautomer – non-metal ## Metal ## Isotopic ## Stereo ## Stereo ## Electronic ##

Output Format      Example: Benzene Represent atoms as sequence number in formula      C6H6   =  C  C  C  C  C  C  H  H  H  H  H  H      tags          1  2   3  4   5   6   7  8   9 10 11 12      Basic Layer:      <basic>C6H6 1-2-7 2-3-8 3-4-9 4-5-10 5-6-11 7-12</basic>

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Non-IChI Output Information Only For user verification Label true stereogenic atoms Identify equivalent atoms Warnings Unusual valences Unrecognized input ‘Reversibility’ Information Coordinates Electron density Positions of double/triple bonds, charges, odd electrons

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Future Extensions Other Stereo Forms Non-atom centered Conformations Hydrogen Bonding Polymers/Macromolecules Compound Classes Markush structures