From owner-chemistry@ccl.net Sun Jan 24 04:10:01 2021 From: "Igors Mihailovs igorsm_+_cfi.lu.lv" To: CCL Subject: CCL:G: DFT Solvent Calculations With Small Molecules Message-Id: <-54260-210124040838-4216-ukTunfjnm+qrDsvLwUZNXA(0)server.ccl.net> X-Original-From: Igors Mihailovs Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary="----UIALQZQ40TMZR3CHI3TNLMN12OO74X" Date: Sun, 24 Jan 2021 11:08:25 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm,cfi.lu.lv] ------UIALQZQ40TMZR3CHI3TNLMN12OO74X Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Mr=2E Sobral, I think what You described is pretty much normal? Surely if the molecule i= s not completely rigid (such as pyrene or so) there will be differences bet= ween the gas phase and the solvent phase=2E As what regards finding the transition state, maybe this would be helpful: https://joaquinbarroso=2Ecom/2016/05/26/the-art-of-finding-transition-stat= es-part-1/ Best wishes, Igors Mihailovs On 23 January 2021 21:25:08 EET, "Lu s Sobral lsobral!=3D!hovione=2Ecom" <= owner-chemistry/./ccl=2Enet> wrote: > >Sent to CCL by: "Lu s Sobral" [lsobral=2E/./=2Ehovione=2Ecom] >I am doing PCM solvent calculations in methanol of a molecule whose >geometry=20 >was previously optimized in the gas phase=2E The calculations are being >performed=20 >at the B3LYP/6-31G(d) level of theory=2E This specific molecule is a >transition=20 >state and the geometry changed during PCM (IEFPCM) calculations=2E The >output=20 >structure presents a geometry different from the input structure and it >is not=20 >a transition state=2E The software I am using is Gaussian 16=2E > >Thank you, >Lus Sobral > > > >-=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 >the strange characters on the top line to the /./ sign=2E You can also >look up the X-Original-From: line in the mail header=2E > >E-mail to subscribers: CHEMISTRY/./ccl=2Enet or use: > http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message > >E-mail to administrators: CHEMISTRY-REQUEST/./ccl=2Enet or use > http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message > >Subscribe/Unsubscribe:=20 > http://www=2Eccl=2Enet/chemistry/sub_unsub=2Eshtml > >Before posting, check wait time at: http://www=2Eccl=2Enet > >Job: http://www=2Eccl=2Enet/jobs=20 >Conferences: http://server=2Eccl=2Enet/chemistry/announcements/conference= s/ > >Search Messages: http://www=2Eccl=2Enet/chemistry/searchccl/index=2Eshtml > >If your mail bounces from CCL with 5=2E7=2E1 error, check: > http://www=2Eccl=2Enet/spammers=2Etxt > >RTFI: http://www=2Eccl=2Enet/chemistry/aboutccl/instructions/ --=20 Sent from my Android device with K-9 Mail=2E Please excuse my brevity=2E ------UIALQZQ40TMZR3CHI3TNLMN12OO74X Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Mr=2E Sobral,

I think what You describ= ed is pretty much normal? Surely if the molecule is not completely rigid (s= uch as pyrene or so) there will be differences between the gas phase and th= e solvent phase=2E

As what regards finding the transition state, may= be this would be helpful:

https://joaquinbarro= so=2Ecom/2016/05/26/the-art-of-finding-transition-states-part-1/
Best wishes,
Igors Mihailovs


On 2= 3 January 2021 21:25:08 EET, "Lu s Sobral lsobral!=3D!hovione=2Ecom" <ow= ner-chemistry/./ccl=2Enet> wrote:

Sent to CCL by: "Lu  s  Sobral" [lsobral=2E/./=2Eh=
ovione=2Ecom]
I am doing PCM solvent calculations in methanol of a molec=
ule whose geometry 
was previously optimized in the gas phase=2E The cal=
culations are being performed 
at the B3LYP/6-31G(d) level of theory=2E =
This specific molecule is a transition 
state and the geometry changed d=
uring PCM (IEFPCM) calculations=2E The output 
structure presents a geom=
etry different from the input structure and it is not 
a transition stat=
e=2E The software I am using is Gaussian 16=2E

Thank you,
Lus Sob=
ral



-=3D This is automatically added to each message by the =
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--
Sent from my Android = device with K-9 Mail=2E Please excuse my brevity=2E ------UIALQZQ40TMZR3CHI3TNLMN12OO74X-- From owner-chemistry@ccl.net Sun Jan 24 09:22:01 2021 From: "=?UTF-8?Q?kamila=2Emaria=2Ekazmierczak=40tlen=2Epl?= kamila.maria.kazmierczak^tlen.pl" To: CCL Subject: CCL:G: =?UTF-8?Q?Odp=3A_CCL=3AG=3A_DFT_Solvent_Calculations_With_Small_Molecules?= Message-Id: <-54261-210124075804-27515-joAwiw4mXw3XMt/+penfQA{=}server.ccl.net> X-Original-From: =?UTF-8?Q?kamila=2Emaria=2Ekazmierczak=40tlen=2Epl?= Content-Type: multipart/alternative; boundary="2MIUGRPGSLBCKWSUCGESOnhgwp" Date: Sun, 24 Jan 2021 13:57:51 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?kamila=2Emaria=2Ekazmierczak=40tlen=2Epl?= [kamila.maria.kazmierczak^tlen.pl] --2MIUGRPGSLBCKWSUCGESOnhgwp Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Dear Lus, as you are using Gaussian 16 I have a feeling you might have enc= ountered a problem connected with changing the default solvent description = > from non-symmetric into symmetric PCM model in software parameters, as it h= appened to me. (It does not happened for all types of structures, but in th= e case of my organometallic complexes I could not reach convergence and I c= ould not find transition states. The issue was cross-checked with Gaussian = 09 where the default settings were different, and with it there was no prob= lem.) You can try to add in the input file, in the additional parameter s= ection the following: NonSymmetricPCM surface=3Dsas Hope it will help = you. Best wishes, Kamila Ka=C5=BAmierczak Dnia 23 stycznia 2021 22:19 = Lu s Sobral lsobral!=3D!hovione.com <owner-chemistry[a]ccl.net> napisa= =C5=82(a): Sent to CCL by: "Lu =C2=A0s =C2=A0Sobral" [lsobral.[a].ho= vione.com] I am doing PCM solvent calculations in methanol of a molecule w= hose geometry was previously optimized in the gas phase. The calculations = are being performed at the B3LYP/6-31G(d) level of theory. This specific m= olecule is a transition state and the geometry changed during PCM (IEFPCM)= calculations. The output structure presents a geometry different from the= input structure and it is not a transition state. The software I am using= is Gaussian 16. Thank you, Lus Sobral -=3D This is automatically ad= ded to each message by the mailing script =3D- To recover the email addres= s of the author of the message, please change the strange characters on th= e top line to the [a] sign. You can also look up the X-Original-From: line i= n the mail header.= =C2=A0=C2=A0=C2=A0=C2=A0 www.ccl.net www.ccl.net E-mail to administrators= : CHEMISTRY-REQUEST[a]ccl.net or use =C2=A0=C2=A0=C2=A0=C2=A0 www.ccl.net= www.ccl.net=C2=A0=C2=A0=C2=A0=C2=A0 www.ccl.net= www.ccl.net Before posting, check wait time at: www.ccl.net www.ccl.net= Job: www.ccl.net www.ccl.net Conferences: server.ccl.net server.ccl.n= et Search Messages: www.ccl.net www.ccl.net If your mail bounces from = CCL with 5.7.1 error, check: =C2=A0=C2=A0=C2=A0=C2=A0 www.ccl.net www.ccl.= net RTFI: www.ccl.net www.ccl.net=0D --2MIUGRPGSLBCKWSUCGESOnhgwp Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=UTF-8
Dear Lus,
as you are using Gaussian 16 I have a feeling = you might have encountered a problem connected with changing the default so= lvent description from non-symmetric into symmetric PCM model in software p= arameters, as it happened to me. (It does not happened for all types of str= uctures, but in the case of my organometallic complexes I could not reach c= onvergence and I could not find transition states. The issue was cross-chec= ked with Gaussian 09 where the default settings were different, and with it= there was no problem.)

You can try to add in = the input file, in the additional parameter section the following:

NonSymmetricPCM
surface=3Dsas
<= div>
Hope it will help you.

Best= wishes,
Kamila Ka=C5=BAmierczak

Dnia 23 stycznia 2021 22:19 Lu s Sobral lsobral!=3D!hovione.com= <owner-chemistry[a]ccl.net> napisa=C5=82(a):

Sent to CCL by: "Lu  s  Sobr= al" [lsobral.[a].hovione.com]
I am doing PCM solvent calculatio= ns in methanol of a molecule whose geometry
was previously op= timized in the gas phase. The calculations are being performed
at the B3LYP/6-31G(d) level of theory. This specific molecule is a transi= tion
state and the geometry changed during PCM (IEFPCM) calcu= lations. The output
structure presents a geometry different f= rom the input structure and it is not
a transition state. The= software I am using is Gaussian 16.

Thank you= ,
Lus Sobral



=
-=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
the strange characters on the top lin= e to the [a] sign. You can also
look up the X-Original-From: li= ne in the mail header.

E-mail to subscribers: = CHEMISTRY[a]ccl.net= or use:

E-mail to= administrators: CHEMISTRY-REQUEST[a]ccl.net or use
Before posting, check wait time at: http://www.ccl.net

=


If your mail bounce= s from CCL with 5.7.1 error, check:
    <= a href=3D"http://www.ccl.net/spammers.txt" =3D"" target=3D"_blank">http://w= ww.ccl.net/spammers.txt


--2MIUGRPGSLBCKWSUCGESOnhgwp-- From owner-chemistry@ccl.net Sun Jan 24 10:04:00 2021 From: "Antarip Halder antarip.halder],[gmail.com" To: CCL Subject: CCL:G: DFT Solvent Calculations With Small Molecules Message-Id: <-54262-210123203222-7620-EJ4m2V8823Mu+aqG9j+44A_+_server.ccl.net> X-Original-From: Antarip Halder Content-Type: multipart/alternative; boundary="0000000000003ea55005b99b6475" Date: Sun, 24 Jan 2021 07:02:09 +0530 MIME-Version: 1.0 Sent to CCL by: Antarip Halder [antarip.halder:-:gmail.com] --0000000000003ea55005b99b6475 Content-Type: text/plain; charset="UTF-8" If geometry optimization is carried out in the solvent phase, the final optimized will definitely diverge from the initial geometry, which is the gas phase optimized geometry in this case. If the objective is to study solvent screening effects on the electrostatic interaction in the system, a single point energy calculation using PCM on the gas phase optimized geometries can be performed. Thanks, Antarip On Sun, Jan 24, 2021 at 2:39 AM Lu s Sobral lsobral!=!hovione.com < owner-chemistry:ccl.net> wrote: > > Sent to CCL by: "Lu s Sobral" [lsobral.:.hovione.com] > I am doing PCM solvent calculations in methanol of a molecule whose > geometry > was previously optimized in the gas phase. The calculations are being > performed > at the B3LYP/6-31G(d) level of theory. This specific molecule is a > transition > state and the geometry changed during PCM (IEFPCM) calculations. The > output > structure presents a geometry different from the input structure and it is > not > a transition state. The software I am using is Gaussian 16. > > Thank you, > Lus Sobral> > > -- Research Associate Solid State and Structural Chemistry Unit Indian Institute of Science Bengaluru, Karnataka, India. --0000000000003ea55005b99b6475 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
If geometry optimization is carried out in the solvent pha= se, the final optimized will definitely diverge from the initial geometry, = which is the gas phase optimized geometry in this case. If the objective is= to study solvent screening effects on the electrostatic interaction in the= system, a single point energy calculation using PCM on the gas phase optim= ized geometries can be performed.
Thanks,
Antarip
=
On Sun= , Jan 24, 2021 at 2:39 AM Lu s Sobral lsobral!=3D!hovione.com <owner-= chemistry:ccl.net> wrote:

Sent to CCL by: "Lu=C2=A0 s=C2=A0 Sobral" [lsobral.:.hovione.com] I am doing PCM solvent calculations in methanol of a molecule whose geometr= y
was previously optimized in the gas phase. The calculations are being perfo= rmed
at the B3LYP/6-31G(d) level of theory. This specific molecule is a transiti= on
state and the geometry changed during PCM (IEFPCM) calculations. The output=
structure presents a geometry different from the input structure and it is = not
a transition state. The software I am using is Gaussian 16.

Thank you,
Lus Sobral



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--
Research Associate
Solid State and Structural Chemistry Unit
Indian Institute= of Science
Bengaluru, Karnataka, India.
--0000000000003ea55005b99b6475--