Stereochemistry Elements of Molecules

Detect, depict and modify the arrangement of atoms in a molecule with respect to chiral centers and non-rotatable double bonds

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Show the chiral centers of Dithiothreitol:

In[1]:=

m=Molecule["dithiothreitol"];MoleculePlot[m,m["PossibleStereocenters"]]

Out[1]=

Display the molecule's stereochemistry elements in a

Dataset

In[2]:=

m["StereochemistryElements"]//Dataset

Out[2]=

To visualize the result, define the view vector for viewing the molecule along the vector from atom 1 to atom 2:

In[3]:=

viewVector=QuantityMagnitude@m[{"AtomCoordinates",{1,2}}];viewVector〚1〛=viewVector〚2〛-20Normalize[viewVector〚2〛-viewVector〚1〛];

Get a 3D plot of the molecule and show the stereochemistry element. Atoms 3, 5 and 10 are arranged in a counterclockwise direction when viewed along the vector from atom 1 to atom 2:

In[4]:=

MoleculePlot3Dm,ViewVectorviewVector,



Out[4]=

Use

MoleculeModify

with a

ReflectionTransform

to create the mirror image:

In[5]:=

m2=MoleculeModify[m,{"TransformAtomCoordinates",ReflectionTransform[{0,0,1}]}]

Out[5]=

Molecule

Formula:

Atoms: 18 Bonds: 17



Show the stereochemistry element in the mirror image. The atoms 3, 5 and 10 are now arranged in clockwise order:

In[6]:=

viewVector=QuantityMagnitude@m2[{"AtomCoordinates",{1,2}}];viewVector〚1〛=viewVector〚2〛-20Normalize[viewVector〚2〛-viewVector〚1〛];MoleculePlot3Dm2,ViewVectorviewVector,