I generated cube files for (a) Surface (b) Molecule and (c) Surface + Molecule.
Forumula: Charge Transfer = Bader Charge of (c) - Bader Charge of (a) - Bader Charge of (b).
But it gives change in the individual charges. How do i get the total charge transfer (some number) from surface to molecule.
Kindly see the attached file. They have reported a charge transfer from graphene to organic molecule.
Dear Chandra,
You can calculate the charge transfer in VASP according to the following steps:
1. Use special flags to get the correct CHGCAR that can be used in Bader analysis.
2. Calculate Bader Charge.
3. Do Step 1 & 2 for (a) Surface Only, (b) Molecule Only and (c) Surface + Molecule.
4. Charge Transfer = Bader Charge of (c) - Bader Charge of (a) - Bader Charge of (b)
I have read the attached paper and the study's method is the same as described above:
" For the energetically most stable configuration, we compute the charge transfer (CT), between molecule and graphene, using the Bader charge analysis method43 with the code developed by the Henkelman’s group.44 The results are listed in Table I, we observe a charge transfer flowing from the graphene carbon atoms to the molecules. For the most stable configurations, we find CTs of 0.43 e/molecule (1.28×1013 e/cm2 ) and 0.60 e/molecule (1.79 × 1013 e/cm2 ) for single-TCNQ/ and
single-F4-TCNQ/graphene. The electron transfer to the F4- TCNQ is larger than to the TCNQ molecule, with a difference of 0.17 e/molecule".
(a) gives charge for the surface; (b) gives charge for the molecule and (c) gives the charge of molecule + surface. Please note, that the total charge transfer is equal to charge (surface---molecule) minus [charge (molecule alone + surface alone)]. This is exactly what was done in the work of the attached paper.
Hoping this will be helpful,
Rafik
Thank you Sir. What we get from the VASP or Gaussian is the charges on the individual atoms of a molecule or surface. If i understand correctly after subtracting the individual charges on atoms of the molecule and surface from their respective atomic charges in the complex i need to sum up all the charges and that gives the total charge. Am I write.
Dear Chandra,
Yes. You do have to sum up the charges of all atoms.
Rafik
Sum up all the charges on atoms of a molecule pre and post adsorption on the surface....and take the diffrenece of them....u will get the charge difference which is charge transfered.....
We happen to get total charge on an atom. Can we also get charges of the individual orbitals like s, p, etc of the atom using Bader Charge analysis ?
You can simplify the above procedure. Normally you will know the net charges for the isolated surface and isolated molecule without having to do any calculation. For example, if you have a carbon monoxide (CO) molecule adsorbed on the surface, then you know the net charge of an isolated CO molecule is zero. Therefore, you don't have to do calculation on isolated surface and isolated molecule. You get their net charges from inspection. In this case, the only calculation you have to do is for the combined system. Then, follow same procedure as described in the original question.
To compute the net atomic charges of the combined system, I recommend using the free Chargemol program (http://ddec.sourceforge.net) which computes the bond orders, atomic spin moments (for magnetic materials), atomic dipoles and quadrupoles, etc. in addition to the net atomic charges.
What about if you extract and determine the sum of the respective atomic charges for the molecule within the complex, then you find the charge difference from the isolated molecule all from chargemol program.
I am doing the following way, based on reading of some reference, methods suggested by many people. its also suggested in one of the VASP community question and answers. So, if i understood correctly or not, please comment.
For example i have a combined system just a hypothetical one A.B (say A= compound containing C, H and N; and B=compound containing Pb, O)
1. Do geometry Optimisation for A.B
2. After geometry optimised then Copy INCAR, CONTCAR, POTCAR, KPOINTS, and jobscript file to another folder
3. Add or Change INCAR tags as LAECHG = .TRUE., LCHARG = .TRUE.
add NGX, NGY, NGZ, NGXF, NGYF, NGZF tags and values . (Take these values from OUTCAR file from geometry step)
4. then after job submitted and finished, do Bader commands as per
http://theory.cm.utexas.edu/henkelman/code/bader/
5. Then i use only the ACF.dat file for analysis.
6. Open ACF.dat in excel and convert to columns.
7. now I segregate the elements/atoms as per A and B.
8. Calculate net charge from each atom (i.e. Say Carbon has 4 valence electrons and the ACF file if it shows the charge for a specific Carbon atom as '2.3454' then net charge is 4 - 2.3454 = 1.6546 (positive value, that means this carbon has lost some charge in the combined system to some other atoms) ; means synonymous to 'hole transport'.
Similarly say, Pb atom has Bader charge as '5.6544' and as the valence of Pb is 4, then net charge is 4 - 5.6544 = - 1.6544 (negative value, that means this Lead atom has gained charge from another atom in the combined system) ; means synonymous to 'electron Transport'.
So, i can sum up such net charge for each component i.e. A and B, and then check further the difference between A and B to find out net charge transfer from A to B or B to A.
Please can anyone, confirm, if my method is correct? or any issues? or improvements?
Thank you.
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