Example: Charge transfer integrals: AT base pair¶
Download AT_transferintegrals.run
ADF can 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.
$ADFBIN/adf <<eor
TITLE Adenine fragment
ATOMS
1 N 0.000000000000 0.656191000000 4.473450000000
2 C 0.000000000000 1.850911000000 5.098850000000
3 N 0.000000000000 2.094911000000 6.411070000000
4 C 0.000000000000 0.951291000000 7.115010000000
5 C 0.000000000000 -0.355699000000 6.611740000000
6 C 0.000000000000 -0.487619000000 5.203330000000
7 N 0.000000000000 0.791131000000 8.484350000000
8 C 0.000000000000 -0.567649000000 8.729290000000
9 N 0.000000000000 -1.292469000000 7.631450000000
10 N 0.000000000000 -1.672349000000 4.572610000000
11 H 0.000000000000 2.715551000000 4.433920000000
12 H 0.000000000000 1.540301000000 9.166150000000
13 H 0.000000000000 -0.961519000000 9.739820000000
14 H 0.000000000000 -2.515699000000 5.129900000000
15 H 0.000000000000 -1.718459000000 3.541030000000
END
BASIS
type DZ
core None
END
ZlmFit
Quality good
End
eor
mv TAPE21 Adenine.t21
$ADFBIN/adf <<eor
TITLE Thymine fragment
ATOMS
1 N 0.000000000000 0.617991000000 1.666040000000
2 C 0.000000000000 1.851251000000 1.046260000000
3 N 0.000000000000 1.768641000000 -0.347380000000
4 C 0.000000000000 0.582611000000 -1.042160000000
5 C 0.000000000000 -0.621999000000 -0.417040000000
6 C 0.000000000000 -0.627269000000 1.045880000000
7 O 0.000000000000 -1.670479000000 1.720780000000
8 O 0.000000000000 2.924531000000 1.636600000000
9 C 0.000000000000 -1.937039000000 -1.138130000000
10 H 0.000000000000 0.635221000000 2.733380000000
11 H 0.000000000000 2.660141000000 -0.830100000000
12 H 0.000000000000 0.676731000000 -2.127100000000
13 H 0.880180000000 -2.533409000000 -0.860650000000
14 H 0.000000000000 -1.793509000000 -2.225780000000
15 H -0.880180000000 -2.533409000000 -0.860650000000
END
BASIS
type DZ
core None
END
ZlmFit
Quality good
End
eor
mv TAPE21 Thymine.t21
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.
$ADFBIN/adf <<eor
TITLE AT
ATOMS
1 N 0.000000000000 0.656191000000 4.473450000000 f=Adenine
2 C 0.000000000000 1.850911000000 5.098850000000 f=Adenine
3 N 0.000000000000 2.094911000000 6.411070000000 f=Adenine
4 C 0.000000000000 0.951291000000 7.115010000000 f=Adenine
5 C 0.000000000000 -0.355699000000 6.611740000000 f=Adenine
6 C 0.000000000000 -0.487619000000 5.203330000000 f=Adenine
7 N 0.000000000000 0.791131000000 8.484350000000 f=Adenine
8 C 0.000000000000 -0.567649000000 8.729290000000 f=Adenine
9 N 0.000000000000 -1.292469000000 7.631450000000 f=Adenine
10 N 0.000000000000 -1.672349000000 4.572610000000 f=Adenine
11 H 0.000000000000 2.715551000000 4.433920000000 f=Adenine
12 H 0.000000000000 1.540301000000 9.166150000000 f=Adenine
13 H 0.000000000000 -0.961519000000 9.739820000000 f=Adenine
14 H 0.000000000000 -2.515699000000 5.129900000000 f=Adenine
15 H 0.000000000000 -1.718459000000 3.541030000000 f=Adenine
16 N 0.000000000000 0.617991000000 1.666040000000 f=Thymine
17 C 0.000000000000 1.851251000000 1.046260000000 f=Thymine
18 N 0.000000000000 1.768641000000 -0.347380000000 f=Thymine
19 C 0.000000000000 0.582611000000 -1.042160000000 f=Thymine
20 C 0.000000000000 -0.621999000000 -0.417040000000 f=Thymine
21 C 0.000000000000 -0.627269000000 1.045880000000 f=Thymine
22 O 0.000000000000 -1.670479000000 1.720780000000 f=Thymine
23 O 0.000000000000 2.924531000000 1.636600000000 f=Thymine
24 C 0.000000000000 -1.937039000000 -1.138130000000 f=Thymine
25 H 0.000000000000 0.635221000000 2.733380000000 f=Thymine
26 H 0.000000000000 2.660141000000 -0.830100000000 f=Thymine
27 H 0.000000000000 0.676731000000 -2.127100000000 f=Thymine
28 H 0.880180000000 -2.533409000000 -0.860650000000 f=Thymine
29 H 0.000000000000 -1.793509000000 -2.225780000000 f=Thymine
30 H -0.880180000000 -2.533409000000 -0.860650000000 f=Thymine
END
Fragments
Adenine Adenine.t21
Thymine Thymine.t21
end
SYMMETRY NOSYM
TRANSFERINTEGRALS
ZlmFit
Quality good
End
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