Molecule
MoleculeModify
MoleculePlot
ValenceErrorHandling

Chemistry

Modify Molecule Properties and Structures

Change atomic properties like charge and mass number or add and remove entire substructures

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Use

MoleculeModify

to add a ring-closing bond to

-hexane to form cyclohexane:

In[1]:=

MoleculeModify[Molecule["n-hexane"],{"AddBond",Bond[{1,6},"Single"]}]

Out[1]=

Molecule

Formula:

Atoms: 18 Bonds: 18



Add a double-bonded oxygen atom to make cyclohexanone:

In[2]:=

MoleculeModify[%,{"AddBond",Bond[{1,"O"},"Double"]}]

Out[2]=

Molecule

Formula:

Atoms: 17 Bonds: 17



Convert phenol to phenolate by adding a negative charge to the oxygen atom:

In[3]:=

MoleculeModify[Molecule["phenol"],{"SetFormalCharge",1-1}]

Out[3]=

Molecule

Formula:

Atoms: 12 Bonds: 12



When the charge on the oxygen atom was changed, the number of attached hydrogen atoms was changed accordingly. Disable this using the

ValenceErrorHandling

option:

In[4]:=

MoleculeModify[Molecule["phenol"],{"SetFormalCharge",1-1},ValenceErrorHandlingFalse]

Out[4]=

Molecule

Formula:

Atoms: 13 Bonds: 13



Replace a carbon atom with nitrogen:

In[5]:=

MoleculePlot[MoleculeModify[Molecule["benzene"],{"ReplaceAtom",1"N"}]]

Out[5]=

Related Symbols

Molecule
MoleculeModify
MoleculePlot
ValenceErrorHandling

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Modify Molecule Properties and Structures

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