Molecular Vibrations

Plot an IR spectrum and animate vibrational modes using quantum chemistry results

This example shows how to import harmonic normal mode analysis results from an electronic structure package and use those results to plot the infrared absorption spectrum. Then we take the Cartesian displacement vectors for the individual normal modes and use them to animate molecular normal modes.

Import a Gaussian log file as a

Molecule

In[1]:=

mol=Import["ExampleData/bisCWdhpe2Cl_13benz_c1_freq.log","GaussianLog"]

Out[1]=

The optimized molecular geometry is stored in the molecule's

AtomCoordinates

, and the electronic structure results are in the

MetaInformation

. Both can be retrieved via

MoleculeValue

In[2]:=

coords=MoleculeValue[mol,"AtomCoordinates"]meta=MoleculeValue[mol,"MetaInformation"]

Out[2]=

QuantityArray

Dimensions: {64,3}

Unit: Angstroms



Out[3]=

HeaderGaussian 03 #p TPSSTPSS genecp 5d 7f pop=nbo freq geom=check guess=check nosymm,DipoleMoment{

-0.6716

0.0002

-3.1644

},AlphaOrbitalEnergiesQuantityArray

Dimensions: {547}

Unit: HartreeEnergy

,AlphaOrbitalOccupationsNumericArray

Type: Real32

Dimensions: {547}

,RotationalConstants{

0.13848

GHz

0.02876

GHz

0.02714

GHz

},RotationalSymmetryNumber1,RotorTypeAsymmetric,VibrationalFrequenciesQuantityArray

Dimensions: {186}

Unit: Wavenumbers

,InfraredIntensitiesQuantityArray

Dimensions: {186}

Unit:

Kilometers

Moles

,CartesianDisplacementVectorsQuantityArray

Dimensions: {186,64,3}

Unit: Angstroms

,ProgramGaussian 03, Revision C.02

Assume a Lorentzian line shape for each mode, and plot the calculated infrared absorption spectrum:

In[4]:=

{intensities,frequencies}=Lookup[meta,{"InfraredIntensities","VibrationalFrequencies"}];σ=5;spectrum=TotalMapThread#1(

(ω-#2)

)&,QuantityMagnitude[{intensities,frequencies}];Plotspectrum,{ω,0,3300},

plotting options



Out[4]=

Use the Cartesian displacement vectors to make functions to animate the normal vibrational modes:

In[5]:=

{displacements,frequencies}=Lookup[mol["MetaInformation"],{"CartesianDisplacementVectors","VibrationalFrequencies"}];atomCoordinates[ωt_,mode_]:=(coords+Sin[ωt]displacements〚mode〛);molPlot3D[ωt_,mode_]:=MoleculePlot3D[mol,AtomCoordinates(coords+Sin[ωt]displacements〚mode〛),SphericalRegionSphere[{0,0,0},8],ViewPoint{Top,Left}];animation[mode_]:=ListAnimate[Table[molPlot3D[ωt,mode],{ωt,0,2π,.1}],AnimationRate300frequencies〚mode〛/Max[frequencies]];

Animate the asymmetric chlorine stretching mode:

In[6]:=

animation[34]

Out[6]=

Animate the symmetric chlorine stretching mode:

In[7]:=

animation[35]

Out[7]=

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Contributed by: Jason Biggs

Molecular Vibrations

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