Wolfram Chemistry | Things to Try

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Molecular and Chemical Modeling & Analysis. For students, engineers and researchers—visualize, analyze and model molecular structures, chemical reactions and more with specialized functions tightly integrated with built-in or publicly available data.

Specify Molecules

Specify a molecule using curated data:
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Molecule
caffeine
CHEMICAL
Specify common molecules by their common names:
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Molecule["caffeine"]
Specify a molecule using systematic chemical names:
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MoleculeName["caffeine"]​​Molecule["1,3,7-trimethylpurine-2,6-dione"]
Specify a molecule using a SMILES string:
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caffeine
CHEMICAL
["SMILES"]​​Molecule["CN1C=NC2=C1C(=O)N(C(=O)N2C)C"]
Import molecular data from standard file formats:
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Import["ExampleData/caffeine.xyz"]
Specify a molecule using lists of atoms and bonds:
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Molecule[{"H","O","H"},{Bond[{1,2},"Single"],Bond[{2,3},"Single"]}]

Find Properties of Molecules

Use
MoleculeValue
to obtain properties of specific molecules:
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MoleculeValue[Molecule["caffeine"],"ElementMassFraction"]
You can directly extract properties of molecules as well:
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Molecule["caffeine"]["MolarMass"]
Obtain properties that depend on specific atoms or bonds in a molecule:
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Molecule["water"][{"BondLength",{2,1}}]​​Molecule["water"][{"BondAngle",{2,1,3}}]
Obtain a list of isomers in a specified form:
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FindIsomers
C
8
H
10
N
4
O
2
,"Entity"

Visualize Molecules

Create a 2D representation of a molecule:
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MoleculePlot[Molecule["caffeine"]]
Highlight and label specified molecular patterns:
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MoleculePlot[​​Molecule["caffeine"],​​<|​​"aromatic bonds"->Bond[_,"Aromatic"],​​"double bonds"->Bond[_,"Double"],​​"carbon atoms"->Atom["C"]​​|>​​]
Create a rotatable 3D representation of a molecule:
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MoleculePlot3D[Molecule["caffeine"],PlotLegends->Automatic]

Balance a Chemical Reaction

Balance an unbalanced chemical reaction:
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ReactionBalanceChemicalReaction
H
2
+
O
2
⟶
H
2
O
Interpret a string as a chemical formula:
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ReactionBalance["H2 + O2 -> H2O"]
Interpret common names of compounds to generate a balanced reaction:
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ReactionBalance["Hydrogen + Oxygen -> Water"]

Specify a Pattern for a Reaction

A
PatternReaction
is used to apply chemical reactions to a collection of reactants. Specify a molecule pattern in much the same way you would specify a molecule:
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reactantpatterns={​​MoleculePattern[{"H","H"},{Bond[{1,2},"Single"]}],MoleculePattern[{"H","H"},{Bond[{1,2},"Single"]}],MoleculePattern[{"O","O"},{Bond[{1,2},"Double"]}]​​};​​productpatterns={​​MoleculePattern[{"H","O","H"},{Bond[{1,2},"Single"],Bond[{2,3},"Single"]}],MoleculePattern[{"H","O","H"},{Bond[{1,2},"Single"],Bond[{2,3},"Single"]}]​​};
Represent a chemical reaction using a rule for lists of patterns:
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PatternReaction[reactantpatterns->productpatterns]
You can also specify a chemical reaction using a SMARTS string:
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PatternReaction["[H][H].[H][H].[O]=[O]>>[H][O][H].[H][O][H]"]

Apply a Reaction

Specify a
PatternReaction
:
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In[]:=
reaction=PatternReaction["[H][H].[H][H].[O]=[O]>>[H][O][H].[H][O][H]"]
Create a list of molecules to be the reactants (each molecule must be explicitly present in the list):
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In[]:=
reactants=Molecule
Formula:
H
2
Atoms: 2 Bonds: 1
,Molecule
Formula:
H
2
Atoms: 2 Bonds: 1
,Molecule
Formula:
O
2
Atoms: 2 Bonds: 1
;
Find the molecules produced by applying a reaction to a list of reactants:
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products=ApplyReaction[reaction,reactants]
Quickly visualize the products and reactants in 3D:
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GraphicsColumn[MoleculePlot3D/@reactants]->GraphicsColumn[MoleculePlot3D/@products]
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