Electron transfer between two different conjugated molecules

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Posts 3
  1. Dear NWchem people,

  1. I am new to NWchem and I would like to learn more about how to use the electron transfer module. I find some posts on electron transfer but I didn't find then really clear for the specific case of (localized) charge transfer between two different organic molecules.
  2. What I really when to do is to compute charge transfer integrals (for both positive and negative charges) between two different Pi-conjugated molecules. To do so, we need to localize the charge on a give molecular fragment to generate the reactants and products states required to compute the transfer integral. To illustrate this post let me consider two face to face anthracene molecules. In the second molecule one C-C distance has been slightly increase to get two "different" molecular fragments.

geometry Ant1 nocenter noautoz
C -3.6498210 -0.7128910 0.0000000
C -2.4733540 -1.4043670 0.0000000
C -1.2176100 -0.7143810 0.0000000
C -1.2176100 0.7143810 0.0000000
C -2.4733540 1.4043670 0.0000000
C -3.6498210 0.7128910 0.0000000
C 0.0000000 -1.4035360 0.0000000
C 0.0000000 1.4035360 0.0000000
C 1.2176100 0.7143810 0.0000000
C 1.2176100 -0.7143810 0.0000000
C 2.4733540 -1.4043670 0.0000000
H 2.4596240 -2.5047250 0.0000000
C 3.6498210 -0.7128910 0.0000000
C 3.6498210 0.7128910 0.0000000
C 2.4733540 1.4043670 0.0000000
H 0.0000000 -2.5044860 0.0000000
H -4.6158010 -1.2390670 0.0000000
H -2.4596240 -2.5047250 0.0000000
H -2.4596240 2.5047250 0.0000000
H -4.6158010 1.2390670 0.0000000
H 0.0000000 2.5044860 0.0000000
H 4.6158010 -1.2390670 0.0000000
H 4.6158010 1.2390670 0.0000000
H 2.4596240 2.5047250 0.0000000
end

geometry Ant2 nocenter noautoz
C -3.6498210 -0.7128910 3.0000000
C -2.4733540 -1.4043670 3.0000000
C -1.2176100 -0.7143810 3.0000000
C -1.2176100 0.7143810 3.0000000
C -2.4733540 1.4043670 3.0000000
C -3.6498210 0.7128910 3.0000000
C 0.0000000 -1.4035360 3.0000000
C 0.0000000 1.4035360 3.0000000
C 1.2176100 0.7243810 3.0000000
C 1.2176100 -0.7243790 3.0000000
C 2.4733540 -1.4043670 3.0000000
H 2.4596240 -2.5047250 3.0000000
C 3.6498210 -0.7128910 3.0000000
C 3.6498210 0.7128910 3.0000000
C 2.4733540 1.4043670 3.0000000
H 0.0000000 -2.5044860 3.0000000
H -4.6158010 -1.2390670 3.0000000
H -2.4596240 -2.5047250 3.0000000
H -2.4596240 2.5047250 3.0000000
H -4.6158010 1.2390670 3.0000000
H 0.0000000 2.5044860 3.0000000
H 4.6158010 -1.2390670 3.0000000
H 4.6158010 1.2390670 3.0000000
H 2.4596240 2.5047250 3.0000000
end

geometry AntDimer nocenter noautoz
C -3.6498210 -0.7128910 0.0000000
C -2.4733540 -1.4043670 0.0000000
C -1.2176100 -0.7143810 0.0000000
C -1.2176100 0.7143810 0.0000000
C -2.4733540 1.4043670 0.0000000
C -3.6498210 0.7128910 0.0000000
C 0.0000000 -1.4035360 0.0000000
C 0.0000000 1.4035360 0.0000000
C 1.2176100 0.7143810 0.0000000
C 1.2176100 -0.7143810 0.0000000
C 2.4733540 -1.4043670 0.0000000
H 2.4596240 -2.5047250 0.0000000
C 3.6498210 -0.7128910 0.0000000
C 3.6498210 0.7128910 0.0000000
C 2.4733540 1.4043670 0.0000000
H 0.0000000 -2.5044860 0.0000000
H -4.6158010 -1.2390670 0.0000000
H -2.4596240 -2.5047250 0.0000000
H -2.4596240 2.5047250 0.0000000
H -4.6158010 1.2390670 0.0000000
H 0.0000000 2.5044860 0.0000000
H 4.6158010 -1.2390670 0.0000000
H 4.6158010 1.2390670 0.0000000
H 2.4596240 2.5047250 0.0000000
C -3.6498210 -0.7128910 3.0000000
C -2.4733540 -1.4043670 3.0000000
C -1.2176100 -0.7143810 3.0000000
C -1.2176100 0.7143810 3.0000000
C -2.4733540 1.4043670 3.0000000
C -3.6498210 0.7128910 3.0000000
C 0.0000000 -1.4035360 3.0000000
C 0.0000000 1.4035360 3.0000000
C 1.2176100 0.7243810 3.0000000
C 1.2176100 -0.7243790 3.0000000
C 2.4733540 -1.4043670 3.0000000
H 2.4596240 -2.5047250 3.0000000
C 3.6498210 -0.7128910 3.0000000
C 3.6498210 0.7128910 3.0000000
C 2.4733540 1.4043670 3.0000000
H 0.0000000 -2.5044860 3.0000000
H -4.6158010 -1.2390670 3.0000000
H -2.4596240 -2.5047250 3.0000000
H -2.4596240 2.5047250 3.0000000
H -4.6158010 1.2390670 3.0000000
H 0.0000000 2.5044860 3.0000000
H 4.6158010 -1.2390670 3.0000000
H 4.6158010 1.2390670 3.0000000
H 2.4596240 2.5047250 3.0000000
end

  1. Lets define a small basis set.

basis
* library 6-31g
end

  1. To use the electron transfer module we have first to prepare the reactants and products states. To do so we have to use "vector" to merge together the MOs of the two molecular fragments. First we prepare the MOs of each molecular fragment in the charged and neutral states.

set geometry Ant1
charge 0
scf
uhf             
singlet
vectors input atom output Ant1_N.mo
end
task scf

set geometry Ant1
charge 1
scf
uhf             
doublet
vectors input atom output Ant1_P.mo
end
task scf

set geometry Ant1
charge -1
scf
uhf             
doublet
vectors input atom output Ant1_M.mo
end
task scf

set geometry Ant2
charge 0
scf
uhf             
singlet
vectors input atom output Ant2_N.mo
end
task scf

set geometry Ant2
charge 1
scf
uhf             
doublet
vectors input atom output Ant2_P.mo
end
task scf

set geometry Ant2
charge -1
scf
uhf             
doublet
vectors input atom output Ant2_M.mo
end
task scf

  1. Then we have to merge together the MOs of the molecular fragments to prepare the reactants and the products states. At this point the problem is that with "vector" we just set the initial guess for the SCF procedure and then a SCF calculation is perform. Therefore, after this new electronic optimization the charge is not anymore localized on one molecule (Am I right?).

set geometry AntDimer
charge 1
scf
doublet             
uhf
vectors input fragment Ant1_N.mo Ant2_P.mo output Ant1_N_Ant2_P.mo
maxiter 100
end
task scf

set geometry AntDimer
charge 1
scf
doublet             
uhf
vectors input fragment Ant1_P.mo Ant2_N.mo output Ant1_P_Ant2_N.mo
maxiter 100
end
task scf

set geometry AntDimer
charge -1
scf
doublet             
uhf
vectors input fragment Ant1_N.mo Ant2_M.mo output Ant1_N_Ant2_M.mo
maxiter 100
end
task scf

set geometry AntDimer
charge -1
scf
doublet             
uhf
vectors input fragment Ant1_M.mo Ant2_N.mo output Ant1_M_Ant2_N.mo
maxiter 100
end
task scf

  1. Is there a way to contrain the charge to be localized on one molecule? I have tryed the following (set maxiter to 0 in the scf calculation) but then I am in trouble to compute the tranfer integral using the electron transfer module.

set geometry AntDimer
charge 1
scf
nopen 1             
print "initial vector analysis"
uhf
vectors input fragment Ant1_N.mo Ant2_P.mo output Ant1_N_Ant2_P.mo
maxiter 0
print mulliken
end
task scf ignore

set geometry AntDimer
charge 1
scf
nopen 1
print "initial vector analysis"
uhf
vectors input fragment Ant1_P.mo Ant2_N.mo output Ant1_P_Ant2_N.mo
maxiter 0
print mulliken
end
task scf ignore

  1. Once we have these "constrained" reactants and products states I try to calculate the transfer integral as follow:

set geometry AntDimer
et
vectors reactants Ant1_N_Ant2_P.mo
vectors products Ant1_P_Ant2_N.mo
end
task scf et

  1. Here the problem is the at the end of the SCF calculations for which we set maxiter to 0 the energy of the system is not saved because the calculation doesn't converged (I have added the "ignore" keyword to avoid error messages when the calculation doesn't converged).

  1. I have also tryed to use the constrained DFT to localized the charge but it seems that the "et" module for cdft desn't have been yet implemented in nwchem.

  1. Do you think that it is feasible to do what I am trying to do with nwchem ?
  2. Thank you in advance.

  1. Julien

  • Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Threads 1
Posts 185
Hi Julien,

I think you want to use the "noscf" keyword when constructing the dimer wavefunctions (see below). This gets around the issues related to the code thinking that the SCF did not converge.

 set geometry AntDimer
charge 1
scf
nopen 1
print "initial vector analysis"
uhf
vectors input fragment Ant1_N.mo Ant2_P.mo output Ant1_N_Ant2_P.mo
noscf
print mulliken
end
task scf

 set geometry AntDimer
charge 1
scf
nopen 1
print "initial vector analysis"
uhf
vectors input fragment Ant1_P.mo Ant2_N.mo output Ant1_P_Ant2_N.mo
noscf
print mulliken
end
task scf

Having said that I did have trouble getting something reasonable out of your test case. Essentially I got only 0 for the electron transfer coupling energy. So I am not sure whether you would expect that or not.

Best wishes, Huub

Just Got Here
Threads 2
Posts 3
Thank you Huub for your reply. The "noscf" keyword was actually what I was looking for. Like you, with my example above I can not get any transfer integral value (Only zero...) which is not normal for such Pi-conjugated molecules. After some tests, I finally get something more resonable. I thought that my new example could help other NWChem users then I decided to post it. This example can also be used for the calculation of transfer integrals between two different molecules. The problem was that by default NWChem always try to use symmetry. I have added some keywords to switch off all these features. The most important are probably the "SYM OFF" and the "ADAPT OFF". The following new example works pretty well. I have been able to reproduce the evolution of the transfer integral with the translation (and rotation) of one of the two anthracene molecules as a respect to the other, as it has been done at the VB/HF level in the following paper (Execpt that as the VB/HF transfer integral are usually under-estimate I get lager values in comparison to this paper):
Physical Review B 77, 115210 (2008).
Hopping that it will help...

Julien


START ANT_EXAMPLE

GEOMETRY ANT1 NOCENTER NOAUTOZ NOAUTOSYM
C -3.6498210 -0.7128910 0.0000000
C -2.4733540 -1.4043670 0.0000000
C -1.2176100 -0.7143810 0.0000000
C -1.2176100 0.7143810 0.0000000
C -2.4733540 1.4043670 0.0000000
C -3.6498210 0.7128910 0.0000000
C 0.0000000 -1.4035360 0.0000000
C 0.0000000 1.4035360 0.0000000
C 1.2176100 0.7143810 0.0000000
C 1.2176100 -0.7143810 0.0000000
C 2.4733540 -1.4043670 0.0000000
H 2.4596240 -2.5047250 0.0000000
C 3.6498210 -0.7128910 0.0000000
C 3.6498210 0.7128910 0.0000000
C 2.4733540 1.4043670 0.0000000
H 0.0000000 -2.5044860 0.0000000
H -4.6158010 -1.2390670 0.0000000
H -2.4596240 -2.5047250 0.0000000
H -2.4596240 2.5047250 0.0000000
H -4.6158010 1.2390670 0.0000000
H 0.0000000 2.5044860 0.0000000
H 4.6158010 -1.2390670 0.0000000
H 4.6158010 1.2390670 0.0000000
H 2.4596240 2.5047250 0.0000000
END

GEOMETRY ANT2 NOCENTER NOAUTOZ NOAUTOSYM
C -3.6498210 -0.7128910 3.0000000
C -2.4733540 -1.4043670 3.0000000
C -1.2176100 -0.7143810 3.0000000
C -1.2176100 0.7143810 3.0000000
C -2.4733540 1.4043670 3.0000000
C -3.6498210 0.7128910 3.0000000
C 0.0000000 -1.4035360 3.0000000
C 0.0000000 1.4035360 3.0000000
C 1.2176100 0.7143810 3.0000000
C 1.2176100 -0.7143810 3.0000000
C 2.4733540 -1.4043670 3.0000000
H 2.4596240 -2.5047250 3.0000000
C 3.6498210 -0.7128910 3.0000000
C 3.6498210 0.7128910 3.0000000
C 2.4733540 1.4043670 3.0000000
H 0.0000000 -2.5044860 3.0000000
H -4.6158010 -1.2390670 3.0000000
H -2.4596240 -2.5047250 3.0000000
H -2.4596240 2.5047250 3.0000000
H -4.6158010 1.2390670 3.0000000
H 0.0000000 2.5044860 3.0000000
H 4.6158010 -1.2390670 3.0000000
H 4.6158010 1.2390670 3.0000000
H 2.4596240 2.5047250 3.0000000
END

GEOMETRY DIMER NOCENTER NOAUTOZ NOAUTOSYM
C -3.6498210 -0.7128910 0.0000000
C -2.4733540 -1.4043670 0.0000000
C -1.2176100 -0.7143810 0.0000000
C -1.2176100 0.7143810 0.0000000
C -2.4733540 1.4043670 0.0000000
C -3.6498210 0.7128910 0.0000000
C 0.0000000 -1.4035360 0.0000000
C 0.0000000 1.4035360 0.0000000
C 1.2176100 0.7143810 0.0000000
C 1.2176100 -0.7143810 0.0000000
C 2.4733540 -1.4043670 0.0000000
H 2.4596240 -2.5047250 0.0000000
C 3.6498210 -0.7128910 0.0000000
C 3.6498210 0.7128910 0.0000000
C 2.4733540 1.4043670 0.0000000
H 0.0000000 -2.5044860 0.0000000
H -4.6158010 -1.2390670 0.0000000
H -2.4596240 -2.5047250 0.0000000
H -2.4596240 2.5047250 0.0000000
H -4.6158010 1.2390670 0.0000000
H 0.0000000 2.5044860 0.0000000
H 4.6158010 -1.2390670 0.0000000
H 4.6158010 1.2390670 0.0000000
H 2.4596240 2.5047250 0.0000000
C -3.6498210 -0.7128910 3.0000000
C -2.4733540 -1.4043670 3.0000000
C -1.2176100 -0.7143810 3.0000000
C -1.2176100 0.7143810 3.0000000
C -2.4733540 1.4043670 3.0000000
C -3.6498210 0.7128910 3.0000000
C 0.0000000 -1.4035360 3.0000000
C 0.0000000 1.4035360 3.0000000
C 1.2176100 0.7143810 3.0000000
C 1.2176100 -0.7143810 3.0000000
C 2.4733540 -1.4043670 3.0000000
H 2.4596240 -2.5047250 3.0000000
C 3.6498210 -0.7128910 3.0000000
C 3.6498210 0.7128910 3.0000000
C 2.4733540 1.4043670 3.0000000
H 0.0000000 -2.5044860 3.0000000
H -4.6158010 -1.2390670 3.0000000
H -2.4596240 -2.5047250 3.0000000
H -2.4596240 2.5047250 3.0000000
H -4.6158010 1.2390670 3.0000000
H 0.0000000 2.5044860 3.0000000
H 4.6158010 -1.2390670 3.0000000
H 4.6158010 1.2390670 3.0000000
H 2.4596240 2.5047250 3.0000000
END

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

Just Got Here
Threads 1
Posts 3
ET coupling matrix elements.
Hi,
Calculated matrix ET coupling element is 0.92 eV.
Usually the above number is in meV.
Anything wrong with the calculation ?

Just Got Here
Threads 1
Posts 3
ET coupling is large
I am trying to calculate the diabatic coupling between an organic molecule (donor) and oxygen (triplet ground state) molecule with
that in the charge transfer state (donor+) and (oxygen -). The total spin of the system is triplet.
When I calculate the coupling in nwchem using et module, I got very large values (> 20 eV).
Can anybody tell me what is going wrong?


title "Donor molecule"
memory stack 750 mb heap 1500 mb global 1500 mb
geometry da units angstroms noautoz noautosym
H -0.795156758 0.000000000 -2.227654133
C -0.795156758 0.487597890 -1.256117947
C -0.795156758 1.860916946 -1.165576758
C -0.795156758 2.493399263 0.102084608
C -0.795156758 1.739878824 1.253783303
C -0.795156758 0.320033769 1.195949286
C -0.795156758 -0.320033769 -0.086914861
C -0.795156758 -1.739878824 -0.144748877
C -0.795156758 -2.493399263 1.006949817
C -0.795156758 -1.860916946 2.274611184
C -0.795156758 -0.487597890 2.365152373
H -0.795156758 2.466184811 -2.067366236
H -0.795156758 3.577893185 0.160790532
H -0.795156758 2.222891720 2.227607108
H -0.795156758 0.000000000 3.336688558
H -0.795156758 -2.466184811 3.176400661
H -0.795156758 -3.577893185 0.948243894
H -0.795156758 -2.222891720 -1.118572683
O 0.450902565 -1.273158752 0.405804063
O 0.486697153 -0.727754909 1.781177974
end

basis
* library 6-31G*
    • library 3-21G*
end

  1. Fragments for Donor-Acceptor
set geometry da
charge 0
dft
xc b3lyp
iterations 100
grid xfine
mult 3
odft
cdft 1 18 charge 0.0 # On the Neutral geometry
cdft 19 20 charge 0.0
cdft 1 18 spin 0.0 # Donor in the singlet state
cdft 19 20 spin 2.0 # Oxygen in the triplet state
vectors output reactant.movecs
convergence nolevelshifting
end
  1. Fragments for Donor-Acceptor in charge transfer state
set geometry da
charge 0
dft
xc b3lyp
iterations 100
grid xfine
mult 3
cdft 1 18 charge +1.0 # Donor with positive charge
cdft 19 20 charge -1.0 # Oxygen with negative charge
cdft 1 18 spin 1.0 # Donor with unpaired electron
cdft 19 20 spin 1.0 # Oxygen with unpaired electron
vectors output product.movecs
convergence nolevelshifting
end
task dft

set geometry da
charge 0
et
vectors reactants  reactant.movecs
vectors products product.movecs
end
task scf et


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