Invert the Local Geometry Around a Chiral Atom

Modify the local stereochemistry of a molecule by inverting the geometry around a selected atom

Open in Cloud
Download Notebook

Invert the stereochemistry (the spatial arrangement of atoms) around a specific atom in a molecule while leaving the rest of the structure unchanged. In this example, D-glucose is converted to D-mannose by inverting the local geometry around atom 3.

Use the molecular entity for D-glucose as the starting structure for the stereochemical modification:

In[1]:=

glucose=Molecule["D-glucose"]

Out[1]=

Molecule

Formula:

Atoms: 24 Bonds: 23



Apply a local geometry inversion at atom 3 to obtain the corresponding stereoisomer (a molecule with the same atoms and bonds but a different three-dimensional arrangement):

In[2]:=

mannose=MoleculeModify[glucose,{"InvertAroundAtom",3}]

Out[2]=

Molecule

Formula:

Atoms: 24 Bonds: 23



Visualize the neighborhood of atom 3 in both molecules to see how the local geometry changes after inversion:

In[3]:=

MoleculePlot3D#,3,ImageSizeSmall,

viewOptions

&/@{glucose,mannose}//Row[#,Spacer[20]]&

Out[3]=

Extract the chiral atoms and their assigned configurations to confirm that the inversion changes the stereochemistry at atom 3:

In[4]:=

AtomList[#,Atom["AtomChirality"Except[None]],{"AtomIndex","AtomChirality"}]&/@{glucose,mannose}//Column

Out[4]=

{{3,R},{5,S},{7,R},{9,R}}

{{3,S},{5,S},{7,R},{9,R}}

Related Symbols

MoleculeModify
Molecule
MoleculePlot3D
AtomList
Atom

Publisher Information

Contributed by: Wolfram Staff

Wolfram Language Example Repository

Invert the Local Geometry Around a Chiral Atom

See Also

Publisher Information