Explore Conformations of Cyclohexane

Obtain the symmetries, energies and other properties of the different conformations of cyclohexane

Import the

"SDF"

data from a

CloudObject

In[1]:=

data=CloudImport

CloudObject[

]

,"SDF";

Label the distinct conformations::

In[2]:=

labels={"planar","chair","twist-boat","boat","half-boat","half-chair"};conformers=AssociationThread[labelsdata]

Out[2]=

planarMolecule

Formula:

Atoms: 18 Bonds: 18

,chairMolecule

Formula:

Atoms: 18 Bonds: 18

,twist-boatMolecule

Formula:

Atoms: 18 Bonds: 18

,boatMolecule

Formula:

Atoms: 18 Bonds: 18

,half-boatMolecule

Formula:

Atoms: 18 Bonds: 18

,half-chairMolecule

Formula:

Atoms: 18 Bonds: 18



Define a function using

MoleculePlot3D

to create 3D models of the molecules with their labels:

In[3]:=

labeledPlot[label_,mol_]:=MoleculePlot3Dmol,

options



Show the plots of conformations in a grid:

In[4]:=

plots=KeyValueMap[labeledPlot,conformers];Grid[Partition[plots,3],DividersCenter]

Out[4]=

Use

MoleculeProperty

to determine the point group of each conformation:

In[5]:=

MoleculeProperty["PointGroupString"]/@conformers

Out[5]=

planarD6h,chairD3d,twist-boatD2,boatC2v,half-boatCs,half-chairC2

Use

FiniteGroupData

to get the total number of elements in each group. Observe that the planar structure with point group

has the highest symmetry, while the half-chair and half-boat have much lower symmetry:

In[6]:=

FiniteGroupData[#,"Order"]&/@%

Out[6]=

planar24,chair12,twist-boat4,boat4,half-boat2,half-chair2

Use the MMFF94 force field to compare the energetics for these conformations:

In[7]:=

Sort[MoleculeProperty["MMFFEnergy"]/@conformers]

Out[7]=

chair

-2.69161

kcal

/mol

,twist-boat

3.37698

kcal

/mol

,boat

4.08168

kcal

/mol

,half-chair

7.97938

kcal

/mol

,half-boat

7.99279

kcal

/mol

,planar

21.6114

kcal

/mol



Illustrate point-group subduction, removing symmetry elements from the maximal symmetry group to smaller symmetric groups, with a labeled

Graph

In[8]:=

edges={"planar""chair","planar""boat","planar""twist-boat","boat""half-chair","twist-boat""half-boat"};Graphedges,

options



Out[8]=

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Contributed by: Wolfram Staff

Wolfram Language Example Repository

Explore Conformations of Cyclohexane

See Also

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Explore Conformations of Cyclohexane

See Also

Related Symbols

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