Atom
Molecule
MoleculeModify
MoleculePlot
Entity
ToEntity

Chemistry

Generate the Isomers of Decane

Add carbon atoms to methane one by one to exhaustively list all alkanes with up to 10 carbon atoms

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Start with a carbon atom:

In[1]:=

carbonPattern=Atom["C","HydrogenCount"GreaterThan[0]];

Write a function to take a molecule and replace each unique

group with a

group, returning the results as a list:

In[2]:=

addCarbons[mol_]:=MoleculeModify[mol,{"ReplaceSubstructureList",carbonPattern"CC"}];

Use the function to add a carbon atom to

-butane. Note that there are two positions in

-butane where the carbon atom can be added:

In[3]:=

addCarbons[Molecule["n-butane"]]

Out[3]=

Molecule

Formula:

Atoms:

Bonds:

,Molecule

Formula:

Atoms:

Bonds:



Find these molecules in the Wolfram Knowledgebase represented as

"Chemical"

entities:

In[4]:=

ToEntity/@%

Out[4]=



N-pentane

isopentane



Now add a carbon atom to each of the resulting alkanes. Note this procedure can produce the same molecule from different routes, so delete any duplicates:

In[5]:=

addCarbonsList[mols_]:=DeleteDuplicates[Flatten[addCarbons/@mols],MoleculeMatchQ];

In[6]:=

addCarbonsList[addCarbons[Molecule["n-butane"]]]

Out[6]=

Molecule

Formula:

Atoms:

Bonds:

,Molecule

Formula:

Atoms:

Bonds:

,Molecule

Formula:

Atoms:

Bonds:

,Molecule

Formula:

Atoms:

Bonds:

,Molecule

Formula:

Atoms:

Bonds:



In[7]:=

ToEntity/@%

Out[7]=



3-methylpentane

2-methylpentane

N-hexane

2,3-dimethylbutane

2,2-dimethylbutane



Now use this function with

Nest

to generate all isomers of decane:

In[8]:=

decanes=Nest[addCarbonsList,{Molecule["methane"]},9];

Verify that all 75 isomers were found:

In[9]:=

Length[decanes]

Out[9]=

Visualize the structure diagrams using

ImageCollage

In[10]:=

ImageCollageTable[MoleculePlot[m,ColorRules{_White}],{m,decanes}],

...



Out[10]=

Related Symbols

Atom
Molecule
MoleculeModify
MoleculePlot
Entity
ToEntity

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Generate the Isomers of Decane

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