I am trying to work with some metal (Fe,Zn,Pb,Hg,Cd) complexes of Cysteine in Gaussian16. I tried B3LYP/6-311++G for Fe & Zn and B3LYP/LanL2DZ for other complexes. Am I in the right track? Again I am confused about using polarization functions for Fe and Zn complex. Can anyone suggest me with best ones?
Dear Titon,
There is no simple rule, the choice of proper theoretical model (functional + basis set) depends on system, phase, methodology, properties of interest and more...So, to find a suitable model, I strongly recommend that you follow literature, take some functionals and basis sets that seem appropriate for your system, then test them to obtain your own reliable combination.
In your case, use of simple split-valence (6-31G(d)...) or correlation-consistent (cc-pVDZ...) basis sets for main atoms , in conjunction with Effective core potentials ECPs (SDD, LANL2DZ ...) for metal atoms is probably a suitable model commonly employing for metal complexes.
Concerning the additional functions (polarization and diffuse basis functions) please refer to below RG discussion: https://www.google.com/amp/s/www.researchgate.net/post/When_do_I_add_polarization_and_diffuse_basis_functions_in_Gaussian_theoretical_calculations/amp
Dear Titon,
Just to add up on what Melek said: one good way to further test your DFT method is optimizing the geometries of crystals from the CCDC database. Then, you can compare the DFT and crystal structures to check that no big errors are made in bond lengths or angles. Bear in mind that crystal structures are obtained in a bulk crystal, so the media is different than gas or solvent phase from your DFT calculations (small changes are expected).
For your case including cysteine-metal complexes, I've seen some examples that you can use: https://www.ccdc.cam.ac.uk/structures/Search?Compound=cysteine&DatabaseToSearch=Published
If you want an example of how to carry out this DFT vs crystal comparison, check out the computational part of the supporting information in this article: https://science.sciencemag.org/content/362/6416/799.editor-summary
Please read literature.
You can follow the link but it always not help.
https://www.basissetexchange.org/
Thanks to all, specially to @MelekHajji. I have go through several papers and now working with a mix basis set using GENECP on Gaussian16 considering ECP for heavier atoms. Can anyone say, if I need to use APFD in this case? If not then please tell me what's the function of APFD in G16?
Titon Saha I would be cautious when using the APFD functional, there are cases where it doesn't perform well. Take a look at this benchmarking study for example:
https://pubs.rsc.org/en/content/articlelanding/2017/cp/c7cp04913g#!divAbstract
When compared to other DFT functionals that include dispersion, one of the conclusions of the study is that: "... We also note that the APFD approach, which had been recommended as an alternative to DFT-D3 and other dispersion corrections, cannot compete with them at all. It ranks 41st on the WTMAD-1 and 27th on the WTMAD-2 list. ..."
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