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customize energyE() parameters?
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Bob

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Link to postPosted: Wed Mar 23, 2016 9:13 pmPost subject: customize energyE() parameters? Reply with quote

We're using the energyE() parameter in Reactor to calculate the products of electrophilic aromatic substitution reactions of substituted benzenes. Some inconsistent results have led us to the conclusion that one or more of the values you use to calculate energyE() is off a bit. I know you're using literature values, but it's possible that the literature values are inaccurate in a few cases. My question is, is it possible for programmers to replace some of your energyE() parameters with their own? If not, could you add such a feature? We're specifically interested in the HMO parameters for the methyl group.

Daniel
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Link to postPosted: Tue Mar 29, 2016 10:17 amPost subject: Reply with quote

Hi, 

Currently there is no way to do what you would like to do, even not through the calculators API. We are currently not planning to implement such feature for the Hückel Plugin. 

Best regards, 

Daniel

Bob

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Link to postPosted: Tue Mar 29, 2016 2:07 pmPost subject: Reply with quote

I would very much appreciate it if you would add this feature to your list of requests. I understand that it might not be a high priority for you, but for those of us who do use these parameters, there is no way of working around the problem of inaccuracy. I understand that you obtained your parameters from the literature, but the literature is not perfect, and it may be necessary to revise other values in the future in light of further research.

An API method would be sufficient; no need to require implementing it in the GUI. Even a chemical terms method would be helpful. 

For your reference, here is an email trail on the subject that I exchanged with Hans-Ulrich Wagner.

Hi Bob,
after discussion of these results, we find the values for the
para bromobenzoic acid not so bad. We think the problem is in
the values of toluene.
Considering the bromobenzoic acid the ortho to COOH position having
2.5568 is deactivated by the COOH group and the Br substituent.
The meta to COOH position is deactivated by COOH and activated
by the Br substituent. 2.5190 is resonable relative to the
benzene value 2.5359.
The values for toluene are not good.
The para-position is too high, 2.5354 is very near to benzene 2.5359.
But the methyl substituent activates the nucleophilicity in para
and ortho nearly to the same result, isn't it ? So it seems the
parameters for the methyl group are not so good.
The values of bromobenzene, benzoic acid and benzaldehyde are all
reasonable. So the really problematic example here is the para position
in toluene. Which parameters uses Marvin/Jchem ? Do you know where
we can find the manual of JChem ? And the HMO-parameters.
we only found the hint "Streitwieser's" parameters are used.
Best regards, Hans-Ulrich and Julia
Am 2014-10-07 23:05, schrieb Grossman, Robert B:
bob@epoch-virtual:~$ evaluate -e "energyE()" "c1ccccc1" -p 4 (benzene)
2.5359;2.5359;2.5359;2.5359;2.5359;2.5359
bob@epoch-virtual:~$ evaluate -e "energyE()" "Brc1ccccc1" -p 4
(bromobenzene)
3.0326;2.5685;2.5061;2.5366;2.5104;2.5366;2.5061
bob@epoch-virtual:~$ evaluate -e "energyE()" "O=Cc1ccccc1" -p 4
(benzaldehyde)
3.7774;4.4979;3.0338;2.5887;2.5512;2.6928;2.5512;2.5887
bob@epoch-virtual:~$ evaluate -e "energyE()" "OC(=O)c1ccccc1" -p 4
(benzoic acid)
4.3027;4.0032;2.8625;2.9619;2.5546;2.5468;2.6241;2.5468;2.5546
bob@epoch-virtual:~$ evaluate -e "energyE()" "OC(=O)c1ccc(Br)cc1" -p 4
(4-bromobenzoic acid)
4.3021;3.8994;2.8585;2.9398;2.5568;2.519;2.66;3.036;2.519;2.5568
bob@epoch-virtual:~$ evaluate -e "energyE()" "O=Cc1ccc(Br)cc1" -p 4
(4-bromobenzaldehyde)
3.7719;4.396;3.0136;2.5912;2.5245;2.7307;3.0378;2.5245;2.5912
  From: Hans-Ulrich Wagner <Hans-Ulrich.Wagner@cup.uni-muenchen.de>
  Date: Tue, 7 Oct 2014 21:26:43 +0200
  To: Robert Grossman <robert.grossman@uky.edu>
  Subject: Re: weird ChemAxon energy calculation result
Hi Bob,
nice to hear from you and let us continue our interaction:
To evaluate these JChem results it would be fine to get the JChem
values for
benzene, bromobenzene, benzoic acid and benzaldehyde.
You could send simply the result line below the JChem command line.
This can be easily interpretated corresponding the molecule string.
It would be nessesary to have all energy results for all positions.
Best regards, Hans-Ulrich
Am 2014-10-07 15:01, schrieb Grossman, Robert B:
Hi Hans-Ulrich,
This is Bob Grossman, we’ve interacted on the ChemAxon forum in
the
past. I’ve come across a strange result of a JChem calculation, at
least I think it is strange, and I wanted to bounce it off of you
before I go to the ChemAxon forum and risk incurring the wrath of
Zsolt.
I was calculating the nucleophilicity of the different ring atoms in
para-bromobenzoic acid, and I was surprised to see that the values
for
the two kinds of aromatic H-bearing C atoms were very close:
bob@epoch-virtual:~$ evaluate -e "energyE()" "OC(=O)c1ccc(Br)cc1"
-p
4
4.3021;3.8994;2.8585;2.9398;2.5568;2.519;2.66;3.036;2.519;2.5568
ortho to CO2H: 2.5568
ortho to Br: 2.5190
Much closer, in fact, than the values for the ortho and para C atoms
in toluene:
bob@epoch-virtual:~$ evaluate -e "energyE()" "Cc1ccccc1" -p 4
2.9809;3.9168;2.4682;2.546;2.5354;2.546;2.4682
ortho to Me: 2.4682
para to Me: 2.5354
Might this be a flaw in the parameters that JChem uses, or do I
really
just not understand what controls electrophilic aromatic
substitution
very well?
— Bob
Daniel
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Link to postPosted: Tue Mar 29, 2016 4:04 pmPost subject: Reply with quote

Hi Bob, 

Thank you for sending us the details ! We put this issue on our request list and in our backlog.

Daniel

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