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saeed_E

Member

Registered: 2019-12-21

Posts: 157

About calculating mutual penetration (a specific case)

Dear Professor Lu,

First of all, please let me say you merry Christmas and happy new year 2020; I wish you and your honorable family all the best.

If you kindly let me, I would like to ask a question regarding calculating mutual penetration. Please, suppose the XB (halogen-bond) interaction between F-Cl and the pi-system of acetylene in a T-shape approach: F-Cl...HCCH. When we are going to calculate the value of mutual penetration between Cl and pi-electrons of acetylene in the corresponding dimer complex, we also need the vdw radius of acetylene pi-electrons in its isolated and fully optimized structure. While this quantity can easily be calculated for Cl atom (through sub-function 10 of main-function 12) how should this value be calculated for the acetylene pi-system while, in this case, we have no a certain atom?

In advance too many thanks for your kind attention.

Sincerely,
Saeed

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,628

Website

Re: About calculating mutual penetration (a specific case)

In your case, the actual interaction distance can be defined as the distance between nucleus of Cl and midpoint of C-C in the complex.
The "vdW radius" for pi bond in HCCH as acceptor may be defined as the distance between the midpoint of the C-C bond and the surface vertice, which is lying in the plane perpendicular to the C-C bond and crossing the C-C midpoint.

Best,

Tian

saeed_E

Member

Registered: 2019-12-21

Posts: 157

Re: About calculating mutual penetration (a specific case)

Dear Tian,
Thank you very much.
Indeed, considering the x,y, and z coordinates of two carbon atoms of acetylene we can find coordinates of mid point as:
X=(x1+x2)/2, Y=(y1+y2)/2, and Z=(z1+z2)/2. Then, we can put a Bq atom at this point and calculate the value of "the closest distance to the point" for this Bq by entering its index. Do you confirm the validity of my approach?

Sincerely,
Saeed

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,628

Website

Re: About calculating mutual penetration (a specific case)

You can have a try, but I am not sure if this idea works. Currently I am out of office, I can give you definitive reply only after Jun 2, 2020.

saeed_E

Member

Registered: 2019-12-21

Posts: 157

Re: About calculating mutual penetration (a specific case)

Dear Tian,
OK. As you nicely indicated, I will try it but I am waiting your definitive reply after 2th Jun, as you mentioned.

Sincerely,
Saeed