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Re: How invoke g16 in linux in parallel mode?

dummy@example.com (sobereva) — Sat, 02 May 2020 11:07:20 +0000

Your interpretation of f- and f+ is right. However, the meaning of f0 in fact is somewhat tricky. Essentially, it represents the local activity during the reaction in which no evident electron transfer is occured, some people argued that it is suitable for predicting the favorable site under radical attack (they assumed that in this process electron transfer is small, but this is not always true).

The O* doesn't necessarily have high f+, the situation also depends on other part of the system, your consideration is somewhat too ideal.

Re: How invoke g16 in linux in parallel mode?

dummy@example.com (rezabma) — Sat, 02 May 2020 09:45:17 +0000

To be sure, let me check:
f-: how much the site is ready to donate its electron. means that how much the site is nucleophile.

f0: how much the site is ready for sharing electron and forming covalent bond.

f+: how much the site like to get more electrons. For example, by leaving H+ and getting minus charge.

So, O* atom in strong acids containing COO*H group should have high f+ and low f-.

Is it right?

Re: How invoke g16 in linux in parallel mode?

dummy@example.com (sobereva) — Sat, 02 May 2020 07:46:14 +0000

"accept electrophilic attack" implies that this systems will donate electron during reaction, so, I don't think the interpretation in your mentioned papers is wrong.

Re: How invoke g16 in linux in parallel mode?

dummy@example.com (rezabma) — Sat, 02 May 2020 05:19:38 +0000

Thanks.
I have more question about Fukui index. In the Multiwfn manual, there is an example for calculating f- f0 f+ for phenol. The data in manual shows that f- is larger for ortho and para sites. This is in line with experiments (especially in organic chemistry) which says that ortho and para sites in phenol have more electron density and ready for doing electrophilic attack (they are nucleophiles).
However, I see in some papers that interpret f- as the index that shows sites are more favorable to accept electrophilic attack (means they are positive sites and accept electrons,i.e., they are electrophiles)!!
The formula shows that f-=rho(N) - rho(N-1) which shows the molecules in these sites is ready to donate its electron. Please clarify this. It seems that in some papers (even Q1) it was misunderstood.

Thank You

Re: How invoke g16 in linux in parallel mode?

dummy@example.com (sobereva) — Thu, 30 Apr 2020 07:40:27 +0000

The E(HOMO) of TCE is a bulit-in data in Multiwfn. If you are interested in nucleophilicity index and you employed other calculation level, you should manually calculate the E(HOMO) of TCE at current level by Gaussian, and then manually calculate nucleophilicity index based on E(HOMO) of TCE and that of your molecule.

The xyz coordinate of TCE optimzed at B3LYP/6-31G* level is given below, you can use it as initial geometry to perform TCE optimization at your level
C 0.00011970 0.68617321 0.00000000
C -0.00011970 -0.68617321 0.00000000
C -1.21903081 -1.43328689 -0.00000000
N -2.19872201 -2.05958097 0.00000000
C 1.21881925 -1.43338329 0.00000000
N 2.19872201 -2.05934263 0.00000000
C 1.21903081 1.43328689 0.00000000
N 2.19872201 2.05958097 0.00000000
C -1.21881925 1.43338329 0.00000000
N -2.19872201 2.05934263 -0.00000000

Re: How invoke g16 in linux in parallel mode?

dummy@example.com (rezabma) — Thu, 30 Apr 2020 05:47:24 +0000

Thanks. Solved.
Now I finished calculating three wfn files by running parallel job by invoking g16. I calculated quantitative indices (Number 2 in list). the program saved me a file named CDFT.txt.

I used B3LYP/6-31++G** for calculating WFNs. But in CDFT.txt I see following comment at the top of the file:

Note: the E(HOMO) of TCE used for evaluating nucleophilicity index is the value evaluated at B3LYP/6-31G* level

Well, I defined B3LYP/6-31++G** during all steps whenever it needed. I want to report the data in paper. How can force Multiwfn to use my level (B3LYP/6-31++G**) for above comment? Please note that I successfully defined my level in previous invoking steps, and I checked it in generated GJF files before running by G16.

Thanks

Re: How invoke g16 in linux in parallel mode?

dummy@example.com (sobereva) — Wed, 29 Apr 2020 20:21:55 +0000

1 Please manually edit the three .gjf files prior to making Multiwfn to calculate them. Alternatively, editing the Default.Route file in Gaussian folder, so that Gaussian uses 44 cores and 200GB by default.

2 It seems that the "gaupath" parameter in settings.ini file was not properly set, or Multiwfn didn't find the settings.ini file when booting up. In the latter case, please properly set "Multiwfnpath" environment variable as shown in Section 2.1.2 of manual, so that Multiwfn can always locate the settings.ini file.

How invoke g16 in linux in parallel mode?

dummy@example.com (rezabma) — Wed, 29 Apr 2020 11:28:41 +0000

Hi,
I run multiwfn in linux to obtain f-, f0, and f+ (Fukui functions). It needs that g16 invoked to calculate N-1.gjf, N+1.gjf, and N.gjf. I can generate three above files. I set g16 path by "/home/g16/g16". I have 2 problems:

1- in gjf files I see that multiwfn wants ti use 1 processor. How can I force it to use commands such as %nprocshared=44 %mem=200GB?

2-After generating three gjf file it could not invoke g16, and prints error:

Running: "N.gjf" "N.out"
sh: N.gjf: command not found
forrtl: No such file or directory

My gjf file is in /home/runs
My g16 id in /home/g16
My Multiwfn is in /home/Multiwfn

I run the multiwfn from my runs directory. I set g16 environment variables by "source /home/g16/bsd/g16.profile"

Thanks