Example: Charge transfer integrals: AT base pair

Download AT_transferintegrals.run

#! /bin/sh


# ADF can calculate charge transfer integrals, that are needed in
# approximate methods that model charge transport properties. The molecular
# system typically should be build from 2 fragments. In this example charge
# transfer integrals are calculated between Adenine and Thymine. First these two
# molecules are calculated. In the fragment calculation full symmetry can be
# used. For precision reasons the ZlmFit quality is set to good.

AMS_JOBNAME=Adenine $AMSBIN/ams <<eor
System
  symmetrize
  atoms
     N       0.000000000000       0.656191000000       4.473450000000
     C       0.000000000000       1.850911000000       5.098850000000
     N       0.000000000000       2.094911000000       6.411070000000
     C       0.000000000000       0.951291000000       7.115010000000
     C       0.000000000000      -0.355699000000       6.611740000000
     C       0.000000000000      -0.487619000000       5.203330000000
     N       0.000000000000       0.791131000000       8.484350000000
     C       0.000000000000      -0.567649000000       8.729290000000
     N       0.000000000000      -1.292469000000       7.631450000000
     N       0.000000000000      -1.672349000000       4.572610000000
     H       0.000000000000       2.715551000000       4.433920000000
     H       0.000000000000       1.540301000000       9.166150000000
     H       0.000000000000      -0.961519000000       9.739820000000
     H       0.000000000000      -2.515699000000       5.129900000000
     H       0.000000000000      -1.718459000000       3.541030000000
  end
end

Task SinglePoint

Engine ADF
  title Adenine fragment
  basis
    core None
    type DZ
  end
  zlmfit
    quality good
  end
EndEngine
eor


AMS_JOBNAME=Thymine $AMSBIN/ams <<eor
System
  symmetrize
  atoms
     N       0.000000000000       0.617991000000       1.666040000000
     C       0.000000000000       1.851251000000       1.046260000000
     N       0.000000000000       1.768641000000      -0.347380000000
     C       0.000000000000       0.582611000000      -1.042160000000
     C       0.000000000000      -0.621999000000      -0.417040000000
     C       0.000000000000      -0.627269000000       1.045880000000
     O       0.000000000000      -1.670479000000       1.720780000000
     O       0.000000000000       2.924531000000       1.636600000000
     C       0.000000000000      -1.937039000000      -1.138130000000
     H       0.000000000000       0.635221000000       2.733380000000
     H       0.000000000000       2.660141000000      -0.830100000000
     H       0.000000000000       0.676731000000      -2.127100000000
     H       0.880180000000      -2.533409000000      -0.860650000000
     H       0.000000000000      -1.793509000000      -2.225780000000
     H      -0.880180000000      -2.533409000000      -0.860650000000
  end
end

Task SinglePoint

Engine ADF
  title Thymine fragment
  basis
    core None
    type DZ
  end
  zlmfit
    quality good
  end
EndEngine
eor


# Next the the base pair is calculated that consists of Adenine and Thymine. To
# calculate the charge transfer integrals, spatial overlap integrals and site
# energies, include the key TRANSFERINTEGRALS in the input for ADF. Symmetry
# NOSYM should be used.


$AMSBIN/ams <<eor
System
  atoms
     N       0.000000000000       0.656191000000       4.473450000000  adf.f=Adenine
     C       0.000000000000       1.850911000000       5.098850000000  adf.f=Adenine
     N       0.000000000000       2.094911000000       6.411070000000  adf.f=Adenine
     C       0.000000000000       0.951291000000       7.115010000000  adf.f=Adenine
     C       0.000000000000      -0.355699000000       6.611740000000  adf.f=Adenine
     C       0.000000000000      -0.487619000000       5.203330000000  adf.f=Adenine
     N       0.000000000000       0.791131000000       8.484350000000  adf.f=Adenine
     C       0.000000000000      -0.567649000000       8.729290000000  adf.f=Adenine
     N       0.000000000000      -1.292469000000       7.631450000000  adf.f=Adenine
     N       0.000000000000      -1.672349000000       4.572610000000  adf.f=Adenine
     H       0.000000000000       2.715551000000       4.433920000000  adf.f=Adenine
     H       0.000000000000       1.540301000000       9.166150000000  adf.f=Adenine
     H       0.000000000000      -0.961519000000       9.739820000000  adf.f=Adenine
     H       0.000000000000      -2.515699000000       5.129900000000  adf.f=Adenine
     H       0.000000000000      -1.718459000000       3.541030000000  adf.f=Adenine
     N       0.000000000000       0.617991000000       1.666040000000  adf.f=Thymine
     C       0.000000000000       1.851251000000       1.046260000000  adf.f=Thymine
     N       0.000000000000       1.768641000000      -0.347380000000  adf.f=Thymine
     C       0.000000000000       0.582611000000      -1.042160000000  adf.f=Thymine
     C       0.000000000000      -0.621999000000      -0.417040000000  adf.f=Thymine
     C       0.000000000000      -0.627269000000       1.045880000000  adf.f=Thymine
     O       0.000000000000      -1.670479000000       1.720780000000  adf.f=Thymine
     O       0.000000000000       2.924531000000       1.636600000000  adf.f=Thymine
     C       0.000000000000      -1.937039000000      -1.138130000000  adf.f=Thymine
     H       0.000000000000       0.635221000000       2.733380000000  adf.f=Thymine
     H       0.000000000000       2.660141000000      -0.830100000000  adf.f=Thymine
     H       0.000000000000       0.676731000000      -2.127100000000  adf.f=Thymine
     H       0.880180000000      -2.533409000000      -0.860650000000  adf.f=Thymine
     H       0.000000000000      -1.793509000000      -2.225780000000  adf.f=Thymine
     H      -0.880180000000      -2.533409000000      -0.860650000000  adf.f=Thymine
  end
end

Task SinglePoint

Engine ADF
  title AT
  fragments
     Adenine Adenine.results/adf.rkf
     Thymine Thymine.results/adf.rkf
  end
  symmetry NOSYM
  TransferIntegrals
  zlmfit
    quality good
  end
EndEngine
eor

# After the calculation has finished in the output one will find the charge
# transfer (overlap integrals and site energies) that are needed to calculate
# hole mobility or electron mobility calculations:

# =============================================================================================
# Electronic coupling V (also known as effective (generalized) transfer integrals J_eff)
# V = (J-S(e1+e2)/2)/(1-S^2)
# 
# V for hole transfer:           0.000 eV
# V for electron transfer:      -0.036 eV
# 
# The effective transfer integral, or electronic coupling, is calculated from these components:
# 
# e1(hole) Site energy HOMO fragment 1:      -6.88 eV
# e2(hole) Site energy HOMO fragment 2:      -6.46 eV
# J(hole) Charge transfer integral HOMO fragment 1 - HOMO fragment 2:       0.000 eV
# S(hole) Overlap integral HOMO fragment 1 - HOMO fragment 2:       0.000
# 
# e1(electron) Site energy LUMO fragment 1:      -2.24 eV
# e2(electron) Site energy LUMO fragment 2:      -2.62 eV
# J(electron) Charge transfer integral LUMO fragment 1 - LUMO fragment 2:      -0.046 eV
# S(electron) Overlap integral LUMO fragment 1 - LUMO fragment 2:       0.004
# =============================================================================================