From owner-chemistry@ccl.net Wed May 26 03:56:00 2021 From: "Nico green nicogreen6[-]gmail.com" To: CCL Subject: CCL: UV-Vis Message-Id: <-54344-210526035445-26543-UwJMVNrQYySJg9nH+0aaeg _ server.ccl.net> X-Original-From: "Nico green" Date: Wed, 26 May 2021 03:54:44 -0400 Sent to CCL by: "Nico green" [nicogreen6^_^gmail.com] Hello all, I have been asked by an experimental colleague to assist them to explain the lack of UV of a compound. They have the starting material with 2 Ph ring and it is UV, however after an oxidative addition/reductive elimination which adds another aromatic ring, the molecule loses its UV. How can I model and rationalize this observation via calculations? Thanks to everybody Nico From owner-chemistry@ccl.net Wed May 26 06:59:00 2021 From: "Herbert Fruchtl herbert.fruchtl||st-andrews.ac.uk" To: CCL Subject: CCL:G: UV-Vis Message-Id: <-54345-210526065604-21070-MbExGHM2xcvXajC4Wr82cA~~server.ccl.net> X-Original-From: Herbert Fruchtl Content-Language: en-GB Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Wed, 26 May 2021 11:55:24 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl=-=st-andrews.ac.uk] The default method for electronically excited states is TD-DFT. There are higher precision methods available, but they are considerably more expensive and need more user input. For choice of functionals, look for benchmark studies or publications on systems chemically similar to yours. If you ask on CCL, you may get some strong opinions, some of them correct :-). For a quick and qualitative picture on simple molecules (no metals...), you might get away with ZINDO (ORCA has a more complete set of parameters for this than Gaussian, from what I remember), or DFTB or 3c based approaches. See https://doi.org/10.1007/s40097-020-00334-0 for a recent comparison. Hope this helps, Herbert On 26/05/2021 08:54, Nico green nicogreen6[-]gmail.com wrote: > > Sent to CCL by: "Nico green" [nicogreen6^_^gmail.com] > Hello all, > > I have been asked by an experimental colleague to assist them to explain the > lack of UV of a compound. > They have the starting material with 2 Ph ring and it is UV, however after an > oxidative addition/reductive elimination which adds another aromatic ring, the > molecule loses its UV. > How can I model and rationalize this observation via calculations? > > Thanks to everybody > > Nico> > -- Herbert Fruchtl Senior Scientific Computing Officer / HPC Administrator School of Chemistry, IT Services University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed May 26 10:21:00 2021 From: "Bijan Mondal mondal.bijan(-)gmail.com" To: CCL Subject: CCL:G: generating or plotting electrostatic potential surface with gaussview Message-Id: <-54346-210526101819-20710-zaV6vzaiPKgXAPzcPTRMGg===server.ccl.net> X-Original-From: Bijan Mondal Content-Type: multipart/alternative; boundary="00000000000021292e05c33c5054" Date: Wed, 26 May 2021 16:18:02 +0200 MIME-Version: 1.0 Sent to CCL by: Bijan Mondal [mondal.bijan:-:gmail.com] --00000000000021292e05c33c5054 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello, I need help with the above. I did a MO calculation with POP=3DFULL keyword in a SP calculation. Then I used cubegen keyword (since gaussian is only installed away from us at the central facility) and the following command line to generate the SCF density as well as potential density. However, I failed to generate the ESP on full electron density (this is how I should generate the electrostatic potential surface, I guess!) Neither I could generate the HOMO, LUMO, and other MOs from the .cube files. Please help me in this regard. Or if anyone knows any tricks! I get the following error: surface build failed! reading cube file writing grid data opening grid file no data to plot isovalue may be out of range cubegen 0 density L1.fchk L1_dens.cube 80 cubegen 0 potential L1.fchk L1_esp.cube 80 I also tried other combinations like.. cubegen 1 density=3Dscf L1.fchk another.cube -3 h cubegen 1 density=3Dscf L1.fchk another.cube -3 100 h regards, --=20 ----------------------------------------------------- Dr. Bijan Mondal Universit=C3=A4t Regensburg, Germany [image: ORCID iD icon]orcid.org/0000-0002-7359-8926 ------------------------------------------------------ --00000000000021292e05c33c5054 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,
I need help with the above.
I did a M= O calculation with POP=3DFULL keyword in a SP calculation. Then I used cube= gen keyword (since gaussian is only installed away from us at the central f= acility) and the following command line to generate the SCF density as well= as potential density. However, I failed to generate the ESP on full electr= on density (this is how I should generate the electrostatic potential surfa= ce, I guess!) Neither I could generate the HOMO, LUMO, and other MOs from t= he .cube files. Please help me in this regard. Or if anyone knows any trick= s!

I get the following error:=C2=A0

=
surface build failed!=C2=A0
reading cube file=C2=A0
writing grid data=C2=A0
opening grid file=C2=A0
no da= ta to plot=C2=A0
isovalue may be out of range

cubegen 0 density L1.fchk L1_dens.cube 80

cubegen 0 potential L1.fchk L1_esp.cube 80
<= br>
I also tried other combinations=C2=A0like..

=C2=A0 cubegen 1 density=3Dscf L1.fchk another.cube -3 h
= =C2=A0 cubegen 1 density=3Dscf L1.fchk another.cube -3 100 h =C2=A0

regards,

--
-----------------------------------------------------
Dr. = Bijan Mondal
Universit=C3=A4t Regensburg, Germany
<= a href=3D"https://orcid.org/0000-0002-7359-8926" rel=3D"noopener noreferrer= " style=3D"font-size:14px;font-family:initial;outline:0px;width:218px;margi= n-top:5px;vertical-align:top;display:inline" target=3D"_blank">3D"ORCIDorcid.org= /0000-0002-7359-8926
--------------------------------------------= ----------


<= /div> --00000000000021292e05c33c5054-- From owner-chemistry@ccl.net Wed May 26 21:02:00 2021 From: "Victor Rosas Garcia rosas.victor++gmail.com" To: CCL Subject: CCL: UV-Vis Message-Id: <-54347-210526210025-24725-8NTTzATiSW/akUrf4lgNMA_-_server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary="0000000000004851c105c345481a" Date: Wed, 26 May 2021 20:00:05 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor/./gmail.com] --0000000000004851c105c345481a Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello Nico, Could it be that the extra aromatic ring reduces the solubility so much that it is very hard to measure a UV-Vis spectrum? Just a thought. Victor El mi=C3=A9, 26 may 2021 a las 4:34, Nico green nicogreen6[-]gmail.com (< owner-chemistry]-[ccl.net>) escribi=C3=B3: > > Sent to CCL by: "Nico green" [nicogreen6^_^gmail.com] > Hello all, > > I have been asked by an experimental colleague to assist them to explain > the > lack of UV of a compound. > They have the starting material with 2 Ph ring and it is UV, however afte= r > an > oxidative addition/reductive elimination which adds another aromatic ring= , > the > molecule loses its UV. > How can I model and rationalize this observation via calculations? > > Thanks to everybody > > Nico > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --0000000000004851c105c345481a Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Nico,

Could it be that= the extra aromatic ring reduces the solubility so much that it is very har= d to measure a UV-Vis spectrum?

Just a thought.

Victor

El mi=C3=A9, 26 may 2021 a las 4:34,= Nico green nicogreen6[-]gmail.com (<owner-chemistry]-[ccl.net>) e= scribi=C3=B3:
Sent to CCL by: "Nico=C2=A0 green" [nicogreen6^_^gmail.com]
Hello all,

I have been asked by an experimental colleague to assist them to explain th= e
lack of UV of a compound.
They have the starting material with 2 Ph ring and it is UV, however after = an
oxidative addition/reductive elimination which adds another aromatic ring, = the
molecule loses its UV.
How can I model and rationalize this observation via calculations?

Thanks to everybody

Nico



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