MoleculeModify
MoleculeValue
MoleculeProperty
MoleculePlot3D

Chemistry

Generate Atomic Coordinates

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Create a hundred random conformations for adenosine and find the lowest-energy structure

Get the molecule for adenosine:

In[1]:=

m=Molecule["adenosine"]

Out[1]=

Molecule

Formula:

Atoms: 32 Bonds: 34



Use

MoleculeModify

to generate a list of 100 molecules with different randomly generated coordinates:

In[2]:=

(conformers=MoleculeModify[m,{"GenerateConformers",100}])//Short[#,.5]&

Out[2]//Short=

Molecule

Formula:

Atoms: 32 Bonds: 34

,Molecule

Formula:

Atoms: 32 Bonds: 34

,97,Molecule

Formula:

Atoms: 32 Bonds: 34



Visualize the molecules as closely packed together as possible:

In[3]:=

Show[Map[MoleculePlot3D,conformers]]

Out[3]=

Use

MoleculeValue

to find and visualize the force-field energy for the different conformations:

In[4]:=

HistogramMoleculeValue[conformers,"MMFFEnergy"],

...



Out[4]=

Now optimize the energy conformations using the MMFF force field:

In[5]:=

optimized=Map[MoleculeModify["EnergyMinimizeAtomCoordinates"],conformers];

Visualize the result. Note that the energy spread is smaller and the overall energies have decreased:

Out[5]=

Use

TakeSmallestBy

to find the molecule with the lowest-energy conformation:

In[6]:=

MoleculePlot3D[First[TakeSmallestBy[optimized,MoleculeProperty["MMFFEnergy"],1]]]

Out[6]=

Related Symbols

MoleculeModify
MoleculeValue
MoleculeProperty
MoleculePlot3D

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Contributed by: Wolfram Staff

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Generate Atomic Coordinates

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