From owner-chemistry@ccl.net Sun Jul  1 07:31:01 2018
From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor_+_fluor.quimica.uniovi.es" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Cl became unbonded after DFT GO
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Date: Sun, 1 Jul 2018 13:24:37 +0200
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Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor||fluor.quimica.uniovi.es]
* Ghazwan Fadhil ghazwan_fadhil a yahoo.co.uk <owner-chemistry===ccl.net> [2018-06-30 02:54:15 -0400]:
> 
> Sent to CCL by: "Ghazwan  Fadhil" [ghazwan_fadhil---yahoo.co.uk]
> I am doing geometry optimization using Gaussian 09 software to a fused 
> cyclic rings with chlorine atom on fused carbon atom. The DFT with 6-311G 
> dp(++) and ab initio give optimized structure with no negative frequency 
> but the chlorine atom got elongated and became unbonded. However, GO with 
> semi-empirical PM 6 does not give  such elongation and un-bonded chlorine 
> is not observed, i.e. normal result obtained. I request explanation and a 
> suggestion to overcome this problem.

Fadhil,

Knowing the compound you try to examine would be most helpful and
aomeone could think on your problem.

You have several options to presents your problem:

1) Provide your initial geometry from the gaussian input.
2) Provide a regular chemical formulation of your compund.
3) Provide a smiles (or similar) description of your compound.

My proposed best options is (3).

If you are not familiar about what smiles is think of a graph
based language that describe the traditional bonding patterns in
a compound. For instance "c1ccccc1" desscribes benzene.

In wikipedia (https://en.wikipedia.org/) you may find smiles for *many*
compounds.  See, for instance <https://en.wikipedia.org/wiki/Caffeine>
and show the smiles code for caffeine: "CN1C=NC2=C1C(=O)N(C(=O)N2C)C".

Molecular geometry tools like avogadro recognize the smiles code, and I
find it useful as the initial geometry for an optimization. Avogadro's
capabilities are based on open babel, so many computational tools can
use the same.

Best regards,
             Víctor Luaña
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