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
# =============================================================================================