From owner-chemistry@ccl.net Thu Jul 11 01:56:01 2019 From: "Pierre Archirel pierre.archirel(~)u-psud.fr" To: CCL Subject: CCL: SDD basis and polarisation functions Message-Id: <-53788-190711015347-1867-YdLAKeclsz81pc6UEe4i3A#,#server.ccl.net> X-Original-From: "Pierre Archirel" Date: Thu, 11 Jul 2019 01:53:45 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel(a)u-psud.fr] This is an example of my data: #t b3lyp sddall extrabasis opt ..... P 0 d 1 0.70 **** O 0 d 1 0.55 **** C 0 d 1 0.9 **** Best wishes, Pierre Archirel, LCP, Universite d'Orsay pierre.archirel_+_u-psud.fr From owner-chemistry@ccl.net Thu Jul 11 06:17:01 2019 From: "mo.fateh-.-yahoo.com mo.fateh-.-yahoo.com" To: CCL Subject: CCL: SDD basis and polarisation functions Message-Id: <-53789-190711044607-7145-H3J9QTKegMI+7uMqJKAu0A..server.ccl.net> X-Original-From: "mo.fateh|yahoo.com" Content-Type: multipart/alternative; boundary="----=_Part_8756171_2013342998.1562834749186" Date: Thu, 11 Jul 2019 08:45:49 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: "mo.fateh(0)yahoo.com" [mo.fateh(0)yahoo.com] ------=_Part_8756171_2013342998.1562834749186 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear=C2=A0Pierre, Thanks for your answer. However, can you please let me know the reference f= or these numbers: 0.7, 0.55 and 0.9 for P, O, and C, respectively? ThanksMo On Thursday 11 July 2019, 08:24:24 GMT+2, Pierre Archirel pierr= e.archirel(~)u-psud.fr wrote: =20 =20 =20 Sent to CCL by: "Pierre=C2=A0 Archirel" [pierre.archirel(a)u-psud.fr] This is an example of my data: #t b3lyp sddall extrabasis opt ..... P 0 d 1 0.70 **** O 0 d 1 0.55 **** C 0 d 1 0.9 **** Best wishes, Pierre Archirel, LCP, Universite d'Orsay pierre.archirel,+,u-psud.fr -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20 ------=_Part_8756171_2013342998.1562834749186 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Pierre,

Thanks for your answ= er. However, can you please let me know the reference for these numbers: 0.= 7, 0.55 and 0.9 for P, O, and C, respectively?

=
Thanks
Mo
=20
=20
On Thursday 11 July 2019, 08:24:24 GMT+2, Pierre Archir= el pierre.archirel(~)u-psud.fr <owner-chemistry|*|ccl.net> wrote:



Sent to CC= L by: "Pierre  Archirel" [pierre.archirel(a)u-psud.fr]
This is an example of my data:

#t b3lyp sddall extrabasis opt

.....

P 0
d 1
0.70
****
O 0
<= /div>
d 1
0.55
****
C 0
d= 1
0.9
****
=

Best wishes,
Pierre Archirel, LCP, Universite d'Orsay
pierre.archirel,+,u-psud.fr



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------=_Part_8756171_2013342998.1562834749186-- From owner-chemistry@ccl.net Thu Jul 11 06:52:00 2019 From: "Susi Lehtola susi.lehtola!^!alumni.helsinki.fi" To: CCL Subject: CCL:G: How to add polarization and diffuse functions to SDD in Gaussian 09? Message-Id: <-53790-190711062325-16358-s3hrwNSm4GrcXcwn+fHAaw[#]server.ccl.net> X-Original-From: Susi Lehtola Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Thu, 11 Jul 2019 13:23:13 +0300 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola!A!alumni.helsinki.fi] On 7/11/19 12:21 AM, Mo Fateh mo.fateh-x-yahoo.com wrote: > > Sent to CCL by: "Mo Fateh" [mo.fateh{}yahoo.com] Dear CCL membetrs, > > How to add polarization and diffuse functions to SDD in Gaussian 09? > I have checked these website but I couldnot find a solution for this > severe problem. Instead of SDD you can use e.g. the Karlsruhe def2 basis sets which come at several levels of precision, including polarization and diffuse functions, which are available out-of-the-box in Gaussian, e.g. def2svp for split-valence polarization, def2tzvp for triple-zeta valence polarization, and def2qzvp for quadruple-zeta valence polarization. (The diffuse sets you may have to download from basissetexchange.org) -- ------------------------------------------------------------------ Mr. Susi Lehtola, PhD Junior Fellow, Adjunct Professor susi.lehtola-$-alumni.helsinki.fi University of Helsinki http://susilehtola.github.io/ Finland ------------------------------------------------------------------ Susi Lehtola, dosentti, FT tutkijatohtori susi.lehtola-$-alumni.helsinki.fi Helsingin yliopisto http://susilehtola.github.io/ ------------------------------------------------------------------ From owner-chemistry@ccl.net Thu Jul 11 07:27:01 2019 From: "Benoit Gearald ablux13-x-gmail.com" To: CCL Subject: CCL: Barrierless channel Message-Id: <-53791-190711072150-11746-wsnC1oRmKSkmT5b0vLTfnQ:-:server.ccl.net> X-Original-From: "Benoit Gearald" Date: Thu, 11 Jul 2019 07:21:48 -0400 Sent to CCL by: "Benoit Gearald" [ablux13(a)gmail.com] Dear CCLers, I'm studying a multichannel reaction. I've found a barrierless channel i.e. the transition state is below the intermediate and I have confirmed that by different methods of calculation. My question is whether I have to locate a molecular complex that links the intermediate to the TS or it's ok as it is? I'm really confused on that point and need some explanations and clarifications. Best regards, Benoit From owner-chemistry@ccl.net Thu Jul 11 09:10:00 2019 From: "Pierre Archirel pierre.archirel_._u-psud.fr" To: CCL Subject: CCL: polarisation for SDD basis Message-Id: <-53792-190711090755-16115-tSo50dVHMTWD/JjU7tZCOQ-.-server.ccl.net> X-Original-From: "Pierre Archirel" Date: Thu, 11 Jul 2019 09:07:53 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel%a%u-psud.fr] Dear Mo, These numbers have been optimised by myself! The data I gave is for a methylphosphate molecule, I have varied them and chosen the set which minimises the DFT energy of the molecule. This must be done whenever polarisation functions have not been published. Note that this must be done in principle for every new system. I hope this is clear to you? Best wishes, Pierre Pierre Archirel, LCP, Orsay, France pierre.archirel]-[u-psud.fr From owner-chemistry@ccl.net Thu Jul 11 09:44:00 2019 From: "Pierre Archirel pierre.archirel:+:u-psud.fr" To: CCL Subject: CCL: SDD bases again Message-Id: <-53793-190711094025-300-vNSa7DCgudEa2QpaN1J7LQ(!)server.ccl.net> X-Original-From: "Pierre Archirel" Date: Thu, 11 Jul 2019 09:40:23 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel###u-psud.fr] Dear colleagues, I take this opportunity for advertising the SDD bases, even if polarisation functions must be guessed or best, optimised. These bases are little and very efficient, much more than the old Lanl2 bases. I show in a paper (to be published) that they mimic very well the results with the large aug-cc-pvdz basis. Pierre Archirel, LCP, Orsay, France pierre.archirel()u-psud.fr From owner-chemistry@ccl.net Thu Jul 11 13:31:00 2019 From: "Eric V. Patterson eric.patterson**stonybrook.edu" To: CCL Subject: CCL: Barrierless channel Message-Id: <-53794-190711113011-23763-P0GL1OO8xxROfCAbCpILZA*o*server.ccl.net> X-Original-From: "Eric V. Patterson" Content-Type: multipart/alternative; boundary="Apple-Mail=_080CE90A-3962-473E-8D70-953B83EAB3AC" Date: Thu, 11 Jul 2019 11:30:03 -0400 Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Sent to CCL by: "Eric V. Patterson" [eric.patterson]|[stonybrook.edu] --Apple-Mail=_080CE90A-3962-473E-8D70-953B83EAB3AC Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Benoit, I offer a very observations in no particular order. 1) Have you confirmed the TS via IRC calculations? If not, you should. = This will tell you if it is the TS you hoped to locate and also give you = reasonable starting geometries for optimizing the pre- and post-TS = complexes. 2) Pre- and post-TS complexes (minima) are very commonly found as = stationary points on the Born-Oppenheimer surface. My personal protocol = is to look for them every time, using the end points from IRCs as my = initial geometries. 3) You=E2=80=99ve not said what type of energy (electronic, enthalpic, = Gibbs=E2=80=A6). This makes a difference, especially if entropy is a = factor. For example, consider a pre-TS complex that is a minimum on the = BO surface, with an electronic energy lower than separated reactants. = Once corrected to Gibbs free energy, you may find that the complex is = higher in energy than the separated reactants. Similar may be true for = post-TS complexes. 4) If your intermediate is higher in energy than the TS and higher than = separated reactants, you have not found a barrierless process. You have = a found a process where the barrier is equivalent to the difference = between intermediate and reactants. A barrierless process would have = reactants as the highest point with everything else lying below. 5) How big is the energy difference? Is it within the accepted error = bars of your method? 6) Finally, this is a common shortcoming of BO calculations. Unless you = are comparing to experiments conducted near absolute zero, the BO = surface, even corrected to Gibbs free energy, is a crude approximation = of reality. Nuclear dynamics can prove to be the determining factor = when considering competing channels. =20 Cheers, Eric > On Jul 11, 2019, at 7:21 AM, Benoit Gearald ablux13-x-gmail.com = wrote: >=20 >=20 > Sent to CCL by: "Benoit Gearald" [ablux13(a)gmail.com] > Dear CCLers, >=20 > I'm studying a multichannel reaction. I've found a barrierless channel = i.e.=20 > the transition state is below the intermediate and I have confirmed = that by=20 > different methods of calculation. =20 > My question is whether I have to locate a molecular complex that links = the=20 > intermediate to the TS or it's ok as it is? >=20 > I'm really confused on that point and need some explanations and=20 > clarifications. >=20 > Best regards, >=20 > Benoit >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 --Apple-Mail=_080CE90A-3962-473E-8D70-953B83EAB3AC Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Benoit,

I = offer a very observations in no particular order.
1) Have you confirmed the TS via IRC = calculations?  If not, you should.  This will tell you if it = is the TS you hoped to locate and also give you reasonable starting = geometries for optimizing the pre- and post-TS complexes.

2) Pre- and post-TS = complexes (minima) are very commonly found as stationary points on the = Born-Oppenheimer surface.  My personal protocol is to look for them = every time, using the end points from IRCs as my initial = geometries.

3) = You=E2=80=99ve not said what type of energy (electronic, enthalpic, = Gibbs=E2=80=A6).  This makes a difference, especially if entropy is = a factor.  For example, consider a pre-TS complex that is a minimum = on the BO surface, with an electronic energy lower than separated = reactants.  Once corrected to Gibbs free energy, you may find that = the complex is higher in energy than the separated reactants. =  Similar may be true for post-TS complexes.

4) If your intermediate is higher in energy than the TS and higher than separated reactants, you have not = found a barrierless process.  You have a found a process where the = barrier is equivalent to the difference between intermediate and = reactants.  A barrierless process would have reactants as the = highest point with everything else lying below.

5) How big is the energy difference? =  Is it within the accepted error bars of your method?

6) Finally, this is a = common shortcoming of BO calculations.  Unless you are comparing to = experiments conducted near absolute zero, the BO surface, even corrected = to Gibbs free energy, is a crude approximation of reality.  Nuclear = dynamics can prove to be the determining factor when considering = competing channels.  

Cheers,
Eric


On Jul 11, 2019, at 7:21 AM, Benoit Gearald ablux13-x-gmail.com = <owner-chemistry!A!ccl.net> wrote:


Sent to CCL by: "Benoit  Gearald" [ablux13(a)gmail.com]
Dear = CCLers,

I'm studying a multichannel = reaction. I've found a barrierless channel i.e.
the = transition state is below the intermediate and I have confirmed that by =
different methods of calculation.  
My = question is whether I have to locate a molecular complex that links the =
intermediate to the TS or it's ok as it is?

I'm really confused on that point and need = some explanations and
clarifications.

Best regards,

Benoit



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