QuantumChemistry
ChargesPlot
display the atomic charges of a molecule
Calling Sequence
Parameters
Description
Examples
ChargesPlot(molecule, method, options)
molecule
-
list of lists; each list has 4 elements, the string of an atom's symbol and atom's x, y, and z coordinates
method
(optional) method = name/procedure where name is one of 'HartreeFock' (default), 'DensityFunctional','RDMFunctional', 'ActiveSpaceCI', 'ActiveSpaceSCF', 'CoupledCluster', 'FullCI', 'MP2', 'Variational2RDM', 'Parametric2RDM', 'ContractedSchrodinger'
options
(optional) equation(s) of the form option = value where option is any valid option of the chosen method
The procedure ChargesPlot displays the charges of each atom based on atomic-orbital populations.
Colors of the atoms in a ball-and-stick model convey the charges of the atoms.
Positive charges in the range from 0 to 0.4 are indicated by shades of red, changing from white at 0 to dark red at 0.4.
Negative charges in the range from 0 to -0.4 are indicated by shades of blue, changing from white at 0 to dark blue at -0.4.
The options include the options available for both PlotMolecule and the selected method.
The keyword viewpoint generates a molecular fly-through animation. It can be set to one of the following strings "flythrough", "flythrough2", "flythrough3", "flythrough4", "circleleft", and "circleright". It can also be set to a custom fly-through animation as described on the help page for viewpoint.
withQuantumChemistry:
Consider the hydrogen peroxide molecule
mol≔ O, 0.7247, 0.0, 0.0, O, −0.7247, 0.0, 0.0, H, 0.8233, −0.7, −0.6676,H, −0.8233, −0.6175, 0.7446;
mol≔O,0.72470000,0.,0.,O,−0.72470000,0.,0.,H,0.82330000,−0.70000000,−0.66760000,H,−0.82330000,−0.61750000,0.74460000
Plot the atomic charges
ChargesPlotmol, method=HartreeFock;
Consider the 1,3-dichlorobenzene molecule
mol≔ MolecularGeometry1,3-dichlorobenzene;
mol≔Cl,−2.69870000,−1.16790000,−0.00070000,Cl,2.69910000,−1.16770000,−0.00030000,C,0,−1.00570000,0.00050000,C,−1.20800000,−0.30820000,0.00050000,C,1.20800000,−0.30820000,0.00010000,C,−1.20800000,1.08670000,0.00020000,C,1.20780000,1.08680000,−0.00030000,C,−0.00010000,1.78420000,−0.00020000,H,0,−2.09370000,0.00050000,H,−2.14160000,1.64350000,−0.00010000,H,2.14140000,1.64360000,−0.00060000,H,−0.00020000,2.87030000,−0.00050000
Generate a fly-through animation of the molecule and its charges
ChargesPlotmol, method='Variational2RDM',viewpoint=flythrough3;
See Also
Charges
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