Exciton calculation
Contents
Exciton calculation¶
Objectives
Learn how to run an ab initio exciton model calculation.
Keypoints
Run an ab initio exciton model calculation.
Plot the UV-Vis absorption and ECD spectra.
Analyze the character of the excitations.
Introduction¶
In this exercise we will use an ab initio exciton model to compute the UV-Vis absorption and electronic ciruclar dichroism (ECD) of stacked base-pairs.
The Frenkel exciton model describes the electronic structure of multi-chromophoric system by dividing the system into subgroups. It has been most successful in the weak-coupling limit where the excitons are localized on inidividual chromophores. The ab initio exciton model expands the Frenkel exciton model by taking into account charge-transfer between the chromophores, and is therefore more useful for studies of singly excited states. You may read more in this paper [LPL+17]
In the exciton model, the Hamiltonian adopts the following matrix form
where \(N\) is the total number of excited states, \(\phi_I\) is the \(I\)-th excitonic basis function, and \(E\) and \(V\) are the excitation energies and couplings, respectively. Diagonalization of the Hamiltonian gives the eigenvalues and eigenvectors for the excited states.
System: stacked base-pairs¶
Input file¶
Below is the input file for ab initio exciton model calculation of stacked base-pairs. You can read more about the VeloxChem input keywords in this page.
@jobs
task: exciton
@end
@method settings
xcfun: b3lyp
basis: cc-pvdz
@end
@exciton
fragments: 4
atoms_per_fragment: 18
nstates: 5
ct_nocc: 1
ct_nvir: 1
@end
@molecule
charge: 0
multiplicity: 1
xyz:
!
C -6.660852 -0.537882 1.153909
N -5.464736 -1.279376 0.755959
C -5.401171 -2.560318 0.247397
N -4.174046 -3.023620 0.133321
C -3.381917 -1.986143 0.602941
C -1.992881 -1.833262 0.772320
N -1.082150 -2.773804 0.430539
N -1.561016 -0.663937 1.284758
C -2.433159 0.310896 1.615380
N -3.755877 0.269284 1.515634
C -4.169954 -0.898312 1.003955
H -6.251667 0.367975 1.602217
H -6.307739 -3.093503 0.000510
H -0.105552 -2.647436 0.711625
H -1.428402 -3.703654 0.256126
H -1.977553 1.222109 1.990935
H -7.232028 -0.272547 0.264277
H -7.198697 -1.104105 1.914241
!
C 2.851050 2.995046 2.599348
N 2.527756 1.602753 2.308882
C 3.532227 0.664719 2.312269
C 3.334055 -0.650927 2.042128
C 4.427868 -1.675290 2.122996
C 1.991369 -1.073522 1.662818
O 1.695829 -2.225702 1.304567
N 1.033632 -0.081482 1.723397
C 1.202795 1.237840 2.079265
O 0.267775 2.020999 2.194386
H 2.038764 3.665857 2.318009
H 4.514450 1.063598 2.536881
H 4.468845 -2.269173 1.208202
H 5.402713 -1.203674 2.275485
H 4.243922 -2.374298 2.949162
H 0.028442 -0.344669 1.510910
H 3.059650 3.104482 3.663610
H 3.756601 3.276716 2.061996
!
C -4.314093 3.585540 -0.745962
N -3.776236 2.345248 -1.222725
C -4.429311 1.234574 -1.724072
N -3.619950 0.263430 -2.082104
C -2.355203 0.754373 -1.794323
C -1.062681 0.209500 -1.941029
N -0.829700 -1.011471 -2.484749
N -0.016323 0.966928 -1.550945
C -0.232699 2.193134 -1.027881
N -1.398793 2.802091 -0.844023
C -2.426789 2.040798 -1.247281
H -3.476672 4.252611 -0.541847
H -5.507670 1.210043 -1.788692
H 0.097505 -1.414764 -2.327103
H -1.616525 -1.643972 -2.460000
H 0.667576 2.728356 -0.738854
H -4.949051 4.025189 -1.515114
H -4.870540 3.409636 0.174609
!
C 5.998154 1.457635 -0.884522
N 4.880476 0.546557 -1.110671
C 5.131080 -0.800139 -1.218262
C 4.175422 -1.720603 -1.495703
C 4.420389 -3.200491 -1.511467
C 2.819732 -1.249071 -1.750005
O 1.900417 -1.986038 -2.139201
N 2.619774 0.100602 -1.531205
C 3.575740 1.051488 -1.217952
O 3.304363 2.231635 -1.062168
H 5.639472 2.486207 -0.926066
H 6.167047 -1.075919 -1.059977
H 4.077679 -3.645564 -2.450382
H 5.481281 -3.429544 -1.370436
H 3.845849 -3.678198 -0.708469
H 1.625787 0.452603 -1.593169
H 6.431836 1.263647 0.096542
H 6.752907 1.304911 -1.655985
@end
Exercise¶
Submit a job
Runs the above example. On Beskow this calculation can finish within 15 minutes on 2 nodes. You can choose to run on more nodes.
Plot the spectrum
The excitation energies, oscillator strengths, and rotatory strengths will be printed at the end of the output file. You can plot the UV-Vis and ECD spectra by line broadening using e.g. Gaussian function.
Examine the character of the excitations
The character of the excitations will also be printed at the end of the output file. Find out the characters of the important excitations.
Compare with full TDDFT-TDA result
Compare the spectra from exciton model and from full TDDFT-TDA calculation (
link to TDDFT-TDA output file).