Multiwfn forum

Quark

Member

Registered: 2020-06-24

Posts: 15

ESP of a charged molecule

Dear Dr. Tian Lu,
I would be grateful if you answer my questions
How to build ESP for a charged molecule? Is it correct to optimize the whole molecule, and to use separate cation and anion to calculate the ESP surface?  As far as I know, the basis function should contain diffuse functions, so I plan to use PBE0 dеf2-TZVPD to calculate ESP. However, for optimization, can I use a def2-TZVP to shorten the computation time?

Best regards
Eugene

Last edited by Quark (2020-11-15 00:06:08)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,954

Website

Re: ESP of a charged molecule

I don't fully know why you intend to "use separate cation and anion" to calculate ESP. For a charge system, in otherwords, a cation or anion, you can use exactly the same procedure to conduct quantum chemistry calculations and then use Multiwfn to perform ESP analysis. The only point that should be paid attention to is the choice of basis set, for anion you must use a basis set containing diffuse functions, otherwise the loosely bounded electrons cannot be properly represented. Using def2-TZVPD is fully reasonable for anion; decreasing to def2-TZVP is usually acceptable for optimization and frequency analysis purposes (however, some critical referees may make comment on this treatment. A safer way is using 6-31+G* instead, which also contains diffuse functions and is significantly cheaper than def2-TZVPD and def2-TZVP).

Quark

Member

Registered: 2020-06-24

Posts: 15

Re: ESP of a charged molecule

Dear Dr. Tian Lu,
Thank you very much for your reply. As for my first question, I cannot understand the algorithm for constructing surfaces ESP for charged molecules. If I use the whole molecule [A- and K +], then I have a single ESP surface covering part of the K+ molecule. Please tell me how I can build two surfaces ESP separate for ions A- and K +. Should I optimize separately anion and cation or the whole molecule [A- and K +], and then make single calculations of the wave function for the obtained geometry of anions and cations? Thus, I planned to evaluate the sigma holes on the iodine atom

Best regards
Eugene

Last edited by Quark (2020-11-16 00:46:12)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,954

Website

Re: ESP of a charged molecule

You should optimize geometry and perform ESP analysis respectively for the cation and anion.

Quark

Member

Registered: 2020-06-24

Posts: 15

Re: ESP of a charged molecule

Dear Dr. Tian Lu,
Thanks for answering my questions.

Best regards
Eugene

gottlib

Member

Registered: 2019-10-24

Posts: 9

Re: ESP of a charged molecule

Hello
I tried the mentioned procedure, but there is a problem with ESP script to generate pdb (surfanalysis and vtx) file for anion in particular. The unit is eV while for cation and neutral molecule is always in kcal/mol. I can not find any settings to change the unit in Multiwfn. Is there something I do incorrectly? Thanks!

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,954

Website

Re: ESP of a charged molecule

For a charged system, you should manually modify upper and lower limits of color scale in VMD, so that different colors can distinguish ESP in various surface areas. It is irrelevant to setting of Multiwfn.

gottlib

Member

Registered: 2019-10-24

Posts: 9

Re: ESP of a charged molecule

I mean that mutlwfn generates ESP potential in different units, for anion in eV and cation in kcal/mol. It affects the visualization of charged system. Do I have to apply my proper script to convert all data in eV to kcal/mol?

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,954

Website

Re: ESP of a charged molecule

The unit of ESP directly generated by Multiwfn is independent of charged state of the system. Only when you ask Multiwfn to export surface extrema or vertices as pdb file (in which B-factor field records ESP), the unit will be different for neutral and charged systems, because for charged systems, the ESP value on vdW surface is significantly larger than neutral systems, while the number of columns for recording B-factor in pdb format is very limited, so eV should be used instead of kcal/mol in this situation.

You can easily manually convert the unit. In addition, if you choose option "8 Export all surface vertices and surface extrema as vtx.pqr and extrema.pqr", then ESP will always be recorded in a.u. in the exported files, irrespective of charged state.