Visualize Atomic Charge and Steric Effects in Caffeine

Analyze caffeine by computing basic molecular properties and visualizing atom-level electronic descriptors such as oxidation state, partial charge and a charge-to-steric-effect ratio

Caffeine is a methylxanthine molecule containing carbon, hydrogen, nitrogen and oxygen atoms. This example uses molecular property values to highlight how oxidation states and partial charges vary across the atoms of caffeine then compares the same derived descriptor with a related molecule, theophylline.

Load the caffeine molecule and compute its atom count and molecular formula:

In[1]:=

mol=Molecule["caffeine"];mol["AtomCount"]mol["MolecularFormula"]

Out[1]=

Out[2]=

Visualize the oxidation state assigned to each atom in the two-dimensional molecular structure:

In[3]:=

MoleculeValuePlot[mol,"OxidationState"]

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-3

-2

oxidation states

Display the same oxidation state values on a three-dimensional molecular structure:

In[4]:=

MoleculeValuePlot3D[mol,"OxidationState"]

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-3

-2

oxidation states

Visualize the Gasteiger partial charge, an estimated electric charge assigned to each atom, to show how charge is distributed across the caffeine molecule:

In[5]:=

MoleculeValuePlot[mol,"GasteigerPartialCharge"]

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Gasteiger partial charge

Combine partial charge with the topological steric effect index to create a normalized atom-level descriptor:

In[6]:=

MoleculeValuePlot[mol,#GasteigerPartialCharge/#TopologicalStericEffectIndex&]

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Extract atom symbols and molecular property values, then organize them into a dataset for direct inspection:

In[7]:=

symbols=mol["AtomicSymbols"];oxStates=MoleculeValue[mol,"OxidationState"];partialCharge=N@MoleculeValue[mol,"GasteigerPartialCharge"];stericIndex=N@MoleculeValue[mol,"TopologicalStericEffectIndex"];chargePerSteric=partialCharge/stericIndex;Dataset@MapThread["Atom"#1,"OxidationState"#2,"PartialCharge"#3,"ChargePerSteric"#4&,{symbols,oxStates,partialCharge,chargePerSteric}]

Out[7]=

Atom	OxidationState	PartialCharge	ChargePerSteric
C	-2	0.019485	0.00991465
N	-3	-0.261474	-0.0660186
C	3	0.281677	0.0823425
O	-2	-0.266675	-0.153861
C	1	0.151769	0.040548
C	2	0.167412	0.0463561
N	-3	-0.218377	-0.0780515
C	2	0.0975023	0.0378878
N	-3	-0.327863	-0.0840222
C	-2	0.0129584	0.00665163
N	-3	-0.279181	-0.0697866
C	-2	0.017865	0.0090292
C	4	0.331703	0.0998123
O	-2	-0.247497	-0.144879
H	1	0.0463569	0.0139909
H	1	0.0463569	0.0139909
H	1	0.0463569	0.0139909
H	1	0.104408	0.0300786
H	1	0.046108	0.0139525
H	1	0.046108	0.0139525
rows 1–20 of 24

Define a normalized charge descriptor by dividing the Gasteiger partial charge by the topological steric effect index, then use it to compare atom-level charge patterns in caffeine and theophylline:

In[8]:=

chargeStericFn=#GasteigerPartialCharge/#TopologicalStericEffectIndex&;GraphicsRow[{MoleculeValuePlot[Molecule["caffeine"],chargeStericFn,PlotLabel"Caffeine"],MoleculeValuePlot[Molecule["theophylline"],chargeStericFn,PlotLabel"Theophylline"]}]

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Contributed by: Wolfram Staff

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This work is licensed under a Creative Commons Attribution 4.0 International License

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Visualize Atomic Charge and Steric Effects in Caffeine

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Visualize Atomic Charge and Steric Effects in Caffeine

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