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alessiomacorano

Member

Registered: 2023-12-19

Posts: 9

Nucleophilic idenx calculation in Multiwfn

Dear Prof Tian Lu

First of all thank you so much for all your work of Multiwfn.

Actually, in collaboration with an experimental lab we are working on the dissociation reaction (retro michael reactions) of some thiols and some unsaturated aldehyde compounds such as crotonaldehyde. The experimental conditions are set at a temperature of 37° Celsius at pH 7.4 to study the dissociation reactions. I'm performing DFT calculations to support experiments.

I have a set of some thiolates molecule that I have optimized using the folowing level of theory:  'opt=calcfc freq=noraman wb97xd/6-311+g(d,p) scrf=(cpcm,solvent=water)', I have done the same also for TCE molecule as reference for calculate the nucleophilicity index.
I have used the implicit solvent and I have carried out the calculation of the nucleophilic index on the atttached thiolate (cysteamine) in the protonated form since the experiemental condition is pH 7.4 becuase we wanted to correlated kinetic constant as kon with nucleophilicity index so,

If possible, I have a couple of questions: 

1) Since I wanted to correlate with experimental data is right to include the implicit solvent in the calculation for the Nucleophilic index ? or  just considering the gas phase ?

2) Is it correct to calculate the nucleophilicity index considering the experimental conditions (for example considering the protonated amine NH3 since it's the same compund in the experiemntal lab), given that I want to compare it with experimental data? Is the nucleophilic index accurate for charged molecules ? or should I use another index?

Thank you so much,
My best
Alessio

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 2,058

Website

Re: Nucleophilic idenx calculation in Multiwfn

Dear Alessio,

1 In principle, considering implicit solvent should be more rigorous, but it doesn't necessarily improve fitting quality. So you can try both cases, with and without implicit solvation model.

2 Nucleophilicity index should only be calculated for reactant molecule, protonated amine NH3 should be ignored. Nucleophilic index is not necessarily limited to neutral species, though you can simultaneously consider other descriptors, such as Hirshfeld atomic charge of key atom(s), average local ionization energy (ALIE), etc.

Best regards,

Tian