Molecule
MoleculeModify
MoleculeProperty
MoleculeValue
MoleculePlot3D
QuantityMagnitude

Chemistry

Torsional Potential Energy Surface of Butane

Explore the conformational energy of butane by systematically varying the torsion angle around the central carbon-carbon bond

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Create a molecule for butane:

In[1]:=

butane=Molecule["butane"]

Out[1]=

Molecule

Formula:

Atoms: 14 Bonds: 13



Define a function to obtain the plane containing certain atoms in a molecule:

In[2]:=

planeFrom3Atoms[mol_,atoms_]:=InfinitePlane[QuantityMagnitude[mol[{"AtomCoordinates",atoms}]]];

The torsion angle for atoms C1-C2-C3-C4 is the angle between the plane containing atoms C1-C2-C3 and the plane containing atoms C2-C3-C4. Visualize these planes along with the ball-and-stick model of butane:

In[3]:=

ShowMoleculePlot3D[butane],Graphics3D

,planeFrom3Atoms[butane,{1,2,3}],

...

,planeFrom3Atoms[butane,{2,3,4}],



Out[3]=

The Wolfram Language uses an MMFF94 force field implementation to minimize the energy for all automatically generated coordinates. Use

MoleculeModify

to vary the torsion angle, keeping the result for each step in a table:

In[4]:=

carbonIndices={1,2,3,4};relaxedScan=Table[butane=MoleculeModify[butane,{"EnergyMinimizeAtomCoordinates",carbonIndicesang}],{ang,-180,180,5}];relaxedScan〚1;;3〛

Out[4]=

Molecule

Formula:

Atoms: 14 Bonds: 13

,Molecule

Formula:

Atoms: 14 Bonds: 13

,Molecule

Formula:

Atoms: 14 Bonds: 13



Plot the energy computed using the MMFF94 force field versus torsion angle:

In[5]:=

ListLinePlotMoleculeValue[relaxedScan,"MMFFEnergy"],

plot options



Out[5]=

Find the lowest- and highest-energy conformations, typically referred to as "synperiplanar" and "antiperiplanar":

In[6]:=

MoleculePlot3D/@Part[SortBy[relaxedScan,MoleculeProperty["MMFFEnergy"]],{1,-1}]

Out[6]=

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Molecule
MoleculeModify
MoleculeProperty
MoleculeValue
MoleculePlot3D
QuantityMagnitude

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Torsional Potential Energy Surface of Butane

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