introduction to smiles & smatrs

7/31/2019 Introduction to SMILES & SMATRS

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An Introduction to LineNotations

SMILES and SMARTS

By Bhushan Bapat


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CONTENTS

Line notations to represent molecular structures

SMILES

Specification Rules Isomeric SMILES

General conventions Reaction SMILES

SMARTSSpecifications

Recursive SMARTS

SMILES vs SMARTS

Acknowledgements


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Line Notations

International Chemical Identifier (InChI)

ROSDAL

Wiswesser Line Notation (WLN)

Simplified Molecular Input Line Entry Specification(SMILES)

SMILES Arbitrary Target Specification (SMARTS)

SYBYL Line Notation (SLN)


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SMILES

Simplified Molecular-Input Line-Entry System

Describes the structure of molecules using shortASCII strings

Conversion into two-dimensional drawings or three-dimensionalmodels of the molecules.

By Arthur Weininger and David Weininger in the late 1980s

Modified and extended by Daylight Chemical Information SystemsInc

In 2007, an open standard called "Open SMILES" was developed bythe Blue Obelisk open-source chemistry community.


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Rules for Encoding

Five rules for specifying atoms, bonds, branching, ring closures anddisconnections.

Rule for specifying Atoms Denoted by their atomic symbols in Square brackets []

[Se] , [Au]

B, C, N, O, P, S, P, F, Cl, Br and I do not need []

C methane, O water

Within brackets attached H and charges must be specified

[H+] proton, [OH-] hydroxyl ion[Fe+2] iron (II) cation

Aliphatic atom by capital symbol, aromatic by lower case symbol


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Rules for specifying Bonds

Single bond by - or can be omitted

CC ethane CH2CH3 Double bond by =

C=C ethene CH2CH2 Triple bond by #

C#N hydrogen cyanide

Aromatic bond by : or can be omitted

cccccc - benzene

For linear structures, SMILES notation is simple diagrammatic notationwith Hydrogen and single bonds omitted

C=CCC=CC - 1,4-Hexadiene

Rules for specifying Branches

Branches shown in parenthesis on the right

CCN(CC)CC -


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Rules for specifying Cyclic structures

by breaking one bond in each ring, ring opening (closing) atoms denoted by anumber following them

For cubane where more than one ring closure is present

SMILE for cubane is C12C3C4C1C5C4C3C25


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Rules for specifying Disconnected structures

Written as individual structures separated by .

Example Sodium Phenoxide

Atoms separated by . are not connected / bonded to each other

But

C1.C1 means CC i.e. Ethane


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Isomeric SMILES Used to specify isotopism, configuration around = bonds and chirality

Isotopic specification Desired atomic mass followed by atomic symbol

[12C] carbon-12

[13C] carbon-13

[13CH4] carbon-13 methane

Configuration around double bond Denoted by / and \ called directional bonds

F/C=C/F F/C=C\F

F\C=C\F F\C=C/F


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Chiral specification

Configuration around Tetrahedral Centers Tetrahedral structure is commonest chiral structure with four different

structures attached to C atom Indicated by @ and @@ @ - when neighboring atoms listed anticlockwise

- N[C@](C)(F)C(=O)O

@@ when neighboring atoms listed clockwise

- N[C@@](F)(C)C(=O)O


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Hydrogens

Denoted as explicit when

1) Charged hydrogen proton [H+]

2) Hydrogen molecule [H][H]

3) Bridging hydrogen H connected to two atoms

4) Isotopic hydrogen heavy water

Aromaticity

Uses Huckel rule to identify aromaticity

1) All C sp2 hybrtidized

2) Pi electrons satisfy 4n+2 rule

C1=COC=C1

c1cocc1

C1=CN=C[NH]C(=O)1

c1cnc[nH]c(=O)1

General conventions inSMILES


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Aromatic Nitrogen compounds

All can be represented as lower case atomic symbol, n

1) Pyridine

n1ccccc1

2) Pyridine-N-oxide

O=n1ccccc1

[O-][n+]1ccccc1

3) Mthyl and 1H-pyrrole

Cn1cccc1

[nH]1cccc1


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Reaction SMILES

Reactions written as

reactant > agent > product

Examples

C=CCBr>>C=CCI

C=CCBr.[Na+].[I-]>CC(=O)C>C=CCI.[Na+].[Br-]


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SMARTS

SMILES Arbitrary Target Specification

Language that allows searching of substructure within a structure

Extension of SMILES rules

Includes logical operators with nodes and edges Specifications

Atomic and Bond Primitives

Logical operators and Recursive SMARTS


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Atomic Primitives

Symbol Symbol name Atomic property

requirements

Default

* wildcard any atom (no default)

a aromatic aromatic (no default)

A aliphatic aliphatic (no default)

D degree explicit connections exactly one

H total-H-count attached hydrogens exactly one

h implicit-H-count implicit hydrogens at least one

R ring membership in SSSR rings any ring atom

r ring size in smallest SSSR ring of size

any ring atom

v valence total bond order exactly one

X connectivity total connections exactly one


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x ringconnectivity

total ring connections at least one

- negativecharge

- charge -1 charge (-- is -2, etc)

+ positivecharge

+ formal charge +1 charge (++ is +2,etc)

#n atomic number atomic number (no default)

@ chirality anticlockwise anticlockwise, defaultclass

@@ chirality clockwise clockwise, default class

@ chirality chiral class chirality

(nodefault)

@? chiral or unspec

chirality orunspecified

(no default)

atomic mass explicit atomic mass unspecified mass


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Bond Primitives

Symbol Atomic property requirements

- single bond (aliphatic)

/ directional bond "up"

\ directional bond "down"

/? directional bond "up or unspecified"

\? directional bond "down or unspecified"

= double bond

# triple bond

: aromatic bond

~ any bond (wildcard)

@ any ring bond1


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Logical operators

Atom and Bond specifications combined to form expressions

Example

[CH2] - aliphatic carbon with two hydrogens (methylene carbon) [!C;R] - ( NOT aliphatic carbon ) AND in ring

[X3&H0]atom with 3 total bonds and no H's

[35*]any atom of mass 35

Symbol Expression Meaning

exclamation !e1 not e1

ampersand e1&e2 a1 and e2 (high precedence)

comma e1,e2 e1 or e2

semicolon e1;e2 a1 and e2 (low precedence)


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ACKNOWLEDGEMENT

Daylight Chemical Information System Inc

Wikipedia

Thank You!

introduction to smiles & smatrs

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