Hello,
still fairly new to NWChem I would like to use the program to assess ET coupling energies. Contrasting
to the manual's exercise with He, the preference is for small organic molecules. Three different dimers
of anthracene were chosen for an inital computation. Eventually, this should become a screening to sort
out dimers not very much interacting with each other with relatively few computational sources engaged.
So my question to the more experienced users of the NWChem is if the following instruction file is set up
correctly:
START ANT_EXAMPLE # anthracene_dimer_3.nw
# Block with coordinates about molecule_A starts:
GEOMETRY ANT1 NOCENTER NOAUTOZ NOAUTOSYM
C -1.51700 0.31900 3.45900
H -1.68300 0.63800 4.31599
C -2.05300 -1.04800 2.94500
H -2.61600 -1.54400 3.49500
C -1.72400 -1.54700 1.70900
H -2.03100 -2.37400 1.41500
C -0.91900 -0.75900 0.93800
C -0.48400 0.48800 1.36100
C 0.45300 1.25800 0.38600
H 0.77700 2.19300 0.68100
C 0.91900 0.75900 -0.93800
C 0.48400 -0.48800 -1.36100
C 0.79100 -0.99900 -2.55299
H 0.49401 -1.85500 -2.76600
C 1.51700 -0.31900 -3.45900
C 2.05300 1.04800 -2.94500
H 2.61600 1.54400 -3.49500
H 1.68300 -0.63800 -4.31599
C 1.72400 1.54700 -1.70900
H 2.03100 2.37400 -1.41500
C -0.45300 -1.25800 -0.38600
H -0.77700 -2.19300 -0.68100
C -0.79100 0.99900 2.55299
H -0.49401 1.85500 2.76600
END
# Block with coordinates about molecule_A ends.
# Block with coordinates about molecule_B starts:
GEOMETRY ANT2 NOCENTER NOAUTOZ NOAUTOSYM
C -1.51700 -5.70200 3.45900
H -1.68300 -5.38300 4.31599
C -2.05300 -7.06900 2.94500
H -2.61600 -7.56500 3.49500
C -1.72400 -7.56800 1.70900
H -2.03100 -8.39500 1.41500
C -0.91900 -6.78000 0.93800
C -0.48400 -5.53300 1.36100
C 0.45300 -4.76300 0.38600
H 0.77700 -3.82800 0.68100
C 0.91900 -5.26200 -0.93800
C 0.48400 -6.50900 -1.36100
C 0.79100 -7.02000 -2.55299
H 0.49401 -7.87600 -2.76600
C 1.51700 -6.34000 -3.45900
C 2.05300 -4.97300 -2.94500
H 2.61600 -4.47700 -3.49500
H 1.68300 -6.65900 -4.31599
C 1.72400 -4.47400 -1.70900
H 2.03100 -3.64700 -1.41500
C -0.45300 -7.27900 -0.38600
H -0.77700 -8.21400 -0.68100
C -0.79100 -5.02200 2.55299
H -0.49401 -4.16600 2.76600
END
# Block with coordinates about molecule_B ends.
# Block with coordinates about dimer (molecule_A and molecule_B) starts:
GEOMETRY DIMER NOCENTER NOAUTOZ NOAUTOSYM
# Now follow again coordinates about molecule_A:
C -1.51700 0.31900 3.45900
H -1.68300 0.63800 4.31599
C -2.05300 -1.04800 2.94500
H -2.61600 -1.54400 3.49500
C -1.72400 -1.54700 1.70900
H -2.03100 -2.37400 1.41500
C -0.91900 -0.75900 0.93800
C -0.48400 0.48800 1.36100
C 0.45300 1.25800 0.38600
H 0.77700 2.19300 0.68100
C 0.91900 0.75900 -0.93800
C 0.48400 -0.48800 -1.36100
C 0.79100 -0.99900 -2.55299
H 0.49401 -1.85500 -2.76600
C 1.51700 -0.31900 -3.45900
C 2.05300 1.04800 -2.94500
H 2.61600 1.54400 -3.49500
H 1.68300 -0.63800 -4.31599
C 1.72400 1.54700 -1.70900
H 2.03100 2.37400 -1.41500
C -0.45300 -1.25800 -0.38600
H -0.77700 -2.19300 -0.68100
C -0.79100 0.99900 2.55299
H -0.49401 1.85500 2.76600
# Now follow again coordinates about molecule_B:
C -1.51700 -5.70200 3.45900
H -1.68300 -5.38300 4.31599
C -2.05300 -7.06900 2.94500
H -2.61600 -7.56500 3.49500
C -1.72400 -7.56800 1.70900
H -2.03100 -8.39500 1.41500
C -0.91900 -6.78000 0.93800
C -0.48400 -5.53300 1.36100
C 0.45300 -4.76300 0.38600
H 0.77700 -3.82800 0.68100
C 0.91900 -5.26200 -0.93800
C 0.48400 -6.50900 -1.36100
C 0.79100 -7.02000 -2.55299
H 0.49401 -7.87600 -2.76600
C 1.51700 -6.34000 -3.45900
C 2.05300 -4.97300 -2.94500
H 2.61600 -4.47700 -3.49500
H 1.68300 -6.65900 -4.31599
C 1.72400 -4.47400 -1.70900
H 2.03100 -3.64700 -1.41500
C -0.45300 -7.27900 -0.38600
H -0.77700 -8.21400 -0.68100
C -0.79100 -5.02200 2.55299
H -0.49401 -4.16600 2.76600
END
# Block with coordinates about dimer (molecule_A and molecule_B) ends.
# start of basically invariant section:
BASIS
* LIBRARY 6-31g
END
SET geometry ANT1
CHARGE 0
SCF
UHF
SINGLET
VECTORS INPUT atom OUTPUT ANT1_N.movecs
END
TASK SCF
SET geometry ANT2
CHARGE 0
SCF
UHF
SINGLET
VECTORS INPUT atom OUTPUT ANT2_N.movecs
END
TASK SCF
SET geometry ANT1
CHARGE 1
SCF
UHF
DOUBLET
VECTORS INPUT atom OUTPUT ANT1_P.movecs
END
TASK SCF
SET geometry ANT2
CHARGE 1
SCF
UHF
DOUBLET
VECTORS INPUT atom OUTPUT ANT2_P.movecs
END
TASK SCF
SET geometry DIMER
CHARGE 1
SCF
SYM OFF
ADAPT OFF
NOPEN 1
UHF
VECTORS INPUT FRAGMENT ANT1_N.movecs ANT2_P.movecs OUTPUT ANT1_N_ANT2_P.mo
NOSCF
END
TASK SCF
SET geometry DIMER
CHARGE 1
SCF
NOPEN 1
UHF
VECTORS INPUT FRAGMENT ANT1_P.movecs ANT2_N.movecs OUTPUT ANT1_P_ANT2_N.mo
NOSCF
END
TASK SCF
SET geometry DIMER
CHARGE 1
ET
VECTORS REACTANTS ANT1_N_ANT2_P.mo
VECTORS PRODUCTS ANT1_P_ANT2_N.mo
END
TASK SCF ET
# This is the end of the instruction file.
As mentioned, the pattern above was used for two additional dimers. For the sake of brevity, I provide
only the changing information about molecule_A and molecule_B. Which is either
START ANT_EXAMPLE # anthracene_dimer_12.nw
# Block with coordinates about molecule_A starts:
GEOMETRY ANT1 NOCENTER NOAUTOZ NOAUTOSYM
C -1.51700 0.31900 3.45900
H -1.68300 0.63800 4.31599
C -2.05300 -1.04800 2.94500
H -2.61600 -1.54400 3.49500
C -1.72400 -1.54700 1.70900
H -2.03100 -2.37400 1.41500
C -0.91900 -0.75900 0.93800
C -0.48400 0.48800 1.36100
C 0.45300 1.25800 0.38600
H 0.77700 2.19300 0.68100
C 0.91900 0.75900 -0.93800
C 0.48400 -0.48800 -1.36100
C 0.79100 -0.99900 -2.55299
H 0.49401 -1.85500 -2.76600
C 1.51700 -0.31900 -3.45900
C 2.05300 1.04800 -2.94500
H 2.61600 1.54400 -3.49500
H 1.68300 -0.63800 -4.31599
C 1.72400 1.54700 -1.70900
H 2.03100 2.37400 -1.41500
C -0.45300 -1.25800 -0.38600
H -0.77700 -2.19300 -0.68100
C -0.79100 0.99900 2.55299
H -0.49401 1.85500 2.76600
END
# Block with coordinates about molecule_A ends.
# Block with coordinates about molecule_B starts:
GEOMETRY ANT2 NOCENTER NOAUTOZ NOAUTOSYM
C 3.57170 -2.69150 -12.65718
C 2.84570 -2.01150 -11.75118
C 2.53870 -2.52250 -10.55919
C 1.60170 -1.75250 -9.58419
C 1.13570 -2.25150 -8.26019
C 0.33070 -1.46350 -7.48919
C 0.00170 -1.96250 -6.25319
H -0.56130 -1.46650 -5.70319
C 0.53770 -3.32950 -5.73919
H 0.37170 -3.64850 -4.88220
C 1.26370 -4.00950 -6.64519
H 1.56069 -4.86550 -6.43218
H 0.02370 -0.63650 -7.78319
C 1.57070 -3.49850 -7.83719
C 2.50770 -4.26850 -8.81219
H 2.83169 -5.20350 -8.51719
H 1.27770 -0.81750 -9.87919
C 2.97370 -3.76950 -10.13619
C 3.77870 -4.55750 -10.90719
H 4.08570 -5.38450 -10.61319
H 2.54871 -1.15550 -11.96419
C 4.10770 -4.05850 -12.14319
H 4.67070 -4.55450 -12.69319
H 3.73770 -2.37250 -13.51418
END
# Block with coordinates about molecule_B ends.
and
START ANT_EXAMPLE # anthracene_dimer_31.nw
# Block with coordinates about molecule_A starts:
GEOMETRY ANT1 NOCENTER NOAUTOZ NOAUTOSYM
C -1.63519 0.15934 3.33354
H -1.95227 0.45526 4.22013
C -2.07589 -1.11599 2.87440
H -2.71363 -1.65332 3.44131
C -1.68221 -1.58324 1.66088
H -1.97289 -2.45602 1.31313
C -0.83269 -0.80450 0.81142
C -0.40393 0.48761 1.26604
C 0.41730 1.26455 0.44465
H 0.72569 2.12057 0.76977
C 0.83269 0.80450 -0.81142
C 0.40393 -0.48761 -1.26604
C 0.82798 -0.93149 -2.56287
H 0.49667 -1.80907 -2.88889
C 1.63519 -0.15934 -3.33354
C 2.07589 1.11599 -2.87440
H 2.71363 1.65332 -3.44131
H 1.95227 -0.45526 -4.22013
C 1.68221 1.58324 -1.66088
H 1.97289 2.45602 -1.31313
C -0.41730 -1.26455 -0.44465
H -0.72569 -2.12057 -0.76977
C -0.82798 0.93149 2.56287
H -0.49667 1.80907 2.88889
END
# Block with coordinates about molecule_A ends.
# Block with coordinates about molecule_B starts:
GEOMETRY ANT2 NOCENTER NOAUTOZ NOAUTOSYM
C -2.57201 -2.83581 -3.33354
C -3.37922 -2.06366 -2.56287
C -3.80327 -2.50754 -1.26604
C -4.62450 -1.73060 -0.44465
C -5.03989 -2.19065 0.81142
C -5.88941 -1.41191 1.66088
C -6.28309 -1.87916 2.87440
H -6.92083 -1.34183 3.44131
C -5.84239 -3.15449 3.33354
H -6.15947 -3.45041 4.22013
C -5.03517 -3.92664 2.56287
H -4.70387 -4.80422 2.88889
H -6.18009 -0.53913 1.31313
C -4.61113 -3.48276 1.26604
C -3.78990 -4.25970 0.44465
H -3.48151 -5.11572 0.76977
H -4.93289 -0.87458 -0.76977
C -3.37451 -3.79965 -0.81142
C -2.52499 -4.57839 -1.66088
H -2.23431 -5.45117 -1.31313
H -3.71053 -1.18608 -2.88889
C -2.13131 -4.11114 -2.87440
H -1.49357 -4.64847 -3.44131
H -2.25493 -2.53989 -4.22013
END
# Block with coordinates about molecule_B ends.
As expected, the numeric results of these computated with NWChem 3.8 depend on the intermolecular
distance, and orientation of the two molecules.
|------------------------------------------+----------------+----------------+----------------|
| property | dimer 3 | dimer 12 | dimer 31 |
|------------------------------------------+----------------+----------------+----------------|
| Electronic energy of reactants, H(RR) | -3315.2139 | -3122.8711 | -3420.0791 |
| Electronic energy of products, H(PP) | -3315.2139 | -3122.8731 | -3420.0888 |
| Reactants/Products overlap, S(RP) | 3.73D-03 | -7.28D-04 | 4.76D-03 |
|------------------------------------------+----------------+----------------+----------------|
| Reactants/Products interaction energy | | | |
| One-electron contribution H1(RP) | -21.9791 | 4.0067 | -28.9995 |
| Beginning calculation of 2e contribution | | | |
| Two-electron integral screening (tol2e) | 3.73D-10 | 7.28D-11 | 4.76D-10 |
| | | | |
| Two-electron contribution, H2(RP) | 9.5971 | -1.7322 | 12.7284 |
| Total interaction energy, H(RP) | -12.3819 | 2.2745 | -16.2711 |
| | | | |
| Electron Transfer Coupling Energy, V(RP) | 0.0017216585 | 0.0003717920 | 0.0016556628 |
| | 377.860 cm-1 | 81.599 cm-1 | 363.376 cm-1 |
| | 0.046849 eV | 0.010117 eV | 0.045053 eV |
| | 1.080 kcal/mol | 0.233 kcal/mol | 1.039 kcal/mol |
|------------------------------------------+----------------+----------------+----------------|
Following intuition, among the three dimers, anthracene dimer 3 has the most favourable blend
of proximity and orientation of the two molecules, while the relative tilt in dimer 31 lowers pi-pi
interaction. In case of dimer 12 there is much little interaction than in the case of the other two
dimers (illustration).
My questions:
+ Is the 6-31 functional a good tool if the aim at this stage of the analysis is to sort out dimers with
little electron coupling from those with strong electron coupling? If not, what were an other functional
better suited? How could I recognize that a particular functional is suited "sufficiently well" without
investing too much computation at the level of screening? Are there additional keywords a screening
computation should include (or: are there keywords I should not use here)?
+ Eventually, the aim is to advance to a higher level of computation, similar to this and this.
The authors used with FHI-Aims a different program altogether and it is obvious only a smaller number
of model dimers then may be scrutinized with a more demanding functional. Is such a fragment
molecular orbital FO-DFT accessible in NWChem? What functional were then to use?
|