From owner-chemistry@ccl.net Thu Jun 11 14:33:00 2020 From: "Leonardo De Maria demaria.leo(~)gmail.com" To: CCL Subject: CCL: Nordic Computational Chemistry Conference - February 2021 Message-Id: <-54092-200611054000-31389-FgpsrE6QyLVUcmKZmnBtAA^server.ccl.net> X-Original-From: "Leonardo De Maria" Date: Thu, 11 Jun 2020 05:39:59 -0400 Sent to CCL by: "Leonardo De Maria" [demaria.leo!A!gmail.com] Good morning, I sincerely hope you and your families are doing well in these difficult times. I would like to invite you to a Computational Chemistry Conference were organizing here in Gothenburg in February next year at our nice AstraZeneca site. The conference website is: https://www.lakemedelsakademin.se/produkt/1st- nordic-conference-on-computational-chemistry-2021/?lang=en Please distribute and consider attending or sending your students and lab members. Have a very good day, Leonardo From owner-chemistry@ccl.net Thu Jun 11 16:58:00 2020 From: "Niyas Ma niyasma0^gmail.com" To: CCL Subject: CCL:G: Free energy of complexation Message-Id: <-54093-200611155629-13352-Sb0z10isbJNNpKi+3zOBrw:+:server.ccl.net> X-Original-From: Niyas Ma Content-Type: multipart/alternative; boundary="000000000000b72dec05a7d45a3c" Date: Thu, 11 Jun 2020 21:56:08 +0200 MIME-Version: 1.0 Sent to CCL by: Niyas Ma [niyasma0-$-gmail.com] --000000000000b72dec05a7d45a3c Content-Type: text/plain; charset="UTF-8" Hi all, I am doing a computational investigation of binding energies for a noncovalent host-guest complex of two large polyaromatic hydrocarbons. Since I need Gibbs free energy of complexation, I did a frequency calculation and in Gaussian 16 with PM7 as the method (complex structure has 382 atoms). Separate optimizations and frequency calculations were done for a) host-guest complex, b) host, c) guest. Then, I took the 'Sum of electronic and thermal Free Energies (G)' value from the output for each of the structures to find the free energy of complexation (dG). dG = Gcomplex - (Ghost + Gguest) Problem started when I got an unrealistic compauted free energy of complexation which was also not comparable to the experimental values. Experimental free energy of complexation = 60 kJ/mol Computed free energy of complexation = 390 kJ/mol I am now struggling to find the error. It would be helpful if someone has any idea for the reasons why I am getting a huge and unrealistic energy in noncovalent complexation. Also, if anyone has any experience on the thermodynamics calculations with semiempirical methods, is it possible that the semiempirical methods are overestimating the energies? I also did the thermo calculations in MOPAC with COSMO (EPS = 4.81 for chloroform) for solvent effect and found that the dG reduces by 90 kJ/mol. But still the binding energy of 300 kJ/mol is still not unrealistic. Any suggestion is very helpful and greatly appreciated. Thanks and regards, Niyas --000000000000b72dec05a7d45a3c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,
=C2=A0I am doing a computational in= vestigation of binding energies for a noncovalent host-guest=C2=A0 complex = of two large polyaromatic hydrocarbons. Since I need Gibbs free energy of c= omplexation, I did a frequency calculation and in Gaussian 16 with PM7 as t= he method (complex structure has 382 atoms). Separate optimizations and fre= quency calcul= ations were done for a) host-guest complex, b) host, c) guest. Then, I took= the=C2=A0'Sum of electronic and thermal Free Energies (G)' valu= e from the output for each of the structures to find the free energy of com= plexation (dG).
dG =3D Gcomplex - (Ghost + Gguest)
Problem started when I got an unrealistic compauted free= energy of complexation which was also not comparable to the experimental v= alues.
Experimental free energy of complexation =3D 60= kJ/mol
Computed free energy of complexation =3D 390 k= J/mol
I am now struggling to find the error. It would = be helpful if someone has any idea for the reasons why I am getting a huge = and unrealistic energy in noncovalent complexation.
= Also, if anyone has any experience on the thermodynamics calculations wi= th semiempirical methods, is it possible that the semiempirical methods are= overestimating the energies?

I also did the thermo calculations in MOPAC with COSMO (EPS =3D 4.81 = for chloroform) for solvent effect and found that the dG reduces by 90 kJ/m= ol. But still the binding energy of 300 kJ/mol is still not unrealistic.

Any suggestion is very helpful= and greatly appreciated.
<= span style=3D"font-family:arial,sans-serif">
Th= anks and regards,
Niyas
=

--000000000000b72dec05a7d45a3c-- From owner-chemistry@ccl.net Thu Jun 11 23:19:01 2020 From: "Niyas Ma niyasma0-x-gmail.com" To: CCL Subject: CCL:G: Free energy of complexation Message-Id: <-54094-200611231808-13948-f3TgE8ROspssnyt6L7H72Q]^[server.ccl.net> X-Original-From: Niyas Ma Content-Type: multipart/alternative; boundary="0000000000005fe50005a7da8608" Date: Fri, 12 Jun 2020 05:17:51 +0200 MIME-Version: 1.0 Sent to CCL by: Niyas Ma [niyasma0,gmail.com] --0000000000005fe50005a7da8608 Content-Type: text/plain; charset="UTF-8" Hi all, Just an update. The dG values are all negative. Sorry for the mistake. Experimental free energy of complexation = -60 kJ/mol Computed free energy of complexation = -390 kJ/mol Computed free energy of complexation with solvent (Chloroform) = -300 kJ/mol Thanks for pointing this out Dr. Michael Gilson. With regards, Niyas On Fri, Jun 12, 2020 at 12:25 AM Niyas Ma niyasma0^gmail.com < owner-chemistry##ccl.net> wrote: > Hi all, > I am doing a computational investigation of binding energies for a > noncovalent host-guest complex of two large polyaromatic hydrocarbons. > Since I need Gibbs free energy of complexation, I did a frequency > calculation and in Gaussian 16 with PM7 as the method (complex structure > has 382 atoms). Separate optimizations and frequency calculations were > done for a) host-guest complex, b) host, c) guest. Then, I took the 'Sum > of electronic and thermal Free Energies (G)' value from the output for each > of the structures to find the free energy of complexation (dG). > dG = Gcomplex - (Ghost + Gguest) > Problem started when I got an unrealistic compauted free energy of > complexation which was also not comparable to the experimental values. > Experimental free energy of complexation = 60 kJ/mol > Computed free energy of complexation = 390 kJ/mol > I am now struggling to find the error. It would be helpful if someone has > any idea for the reasons why I am getting a huge and unrealistic energy in > noncovalent complexation. > Also, if anyone has any experience on the thermodynamics calculations with > semiempirical methods, is it possible that the semiempirical methods are > overestimating the energies? > > I also did the thermo calculations in MOPAC with COSMO (EPS = 4.81 for > chloroform) for solvent effect and found that the dG reduces by 90 kJ/mol. > But still the binding energy of 300 kJ/mol is still not unrealistic. > > Any suggestion is very helpful and greatly appreciated. > > Thanks and regards, > Niyas > > --0000000000005fe50005a7da8608 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,
=C2=A0 Jus= t an update.
=C2=A0 The dG values are all negative. = Sorry for the mistake.

<= span style=3D"font-family:arial,sans-serif;font-size:small">Experimental fr= ee energy of complexation =3D -60 kJ/mol
Computed free ener= gy of complexation =3D -390 kJ/mol
= Computed free energy of complexation with solvent (Chloroform) =3D -300 kJ/= mol

Th= anks for pointing this out Dr. Michael Gilson.

<= /div>
With regards,
Niyas

On Fr= i, Jun 12, 2020 at 12:25 AM Niyas Ma niyasma0^gmail.com <owner-chemistry##ccl.net> wrote:
Hi all,
=C2=A0I am doing a comp= utational investigation of binding energies for a noncovalent host-guest=C2= =A0 complex of two large polyaromatic hydrocarbons. Since I need Gibbs free= energy of complexation, I did a frequency calculation and in Gaussian 16 w= ith PM7 as the method (complex structure has 382 atoms). Separate optimizat= ions and frequency calculations were done for a) host-guest = complex, b) host, c) guest. Then, I took the=C2=A0'Sum of electronic and thermal Free Energies (G)= 9; value from the output for each of the structures to find the free energy= of complexation (dG).
dG =3D Gcomplex - (Ghost = + Gguest)
Problem started when I got an unrealistic= compauted free energy of complexation which was also not comparable to the= experimental values.
Experimental free energy of complexati= on =3D 60 kJ/mol
Computed free energy of complexation =3D = 390 kJ/mol
I am now struggling to find the error. It would b= e helpful if someone has any idea for the reasons why I am getting a huge a= nd unrealistic energy in noncovalent complexation.
Also= , if anyone has any experience on the thermodynamics calculations with semi= empirical methods, is it possible that the semiempirical methods are overes= timating the energies?

I also did th= e thermo calculations in MOPAC with COSMO (EPS =3D 4.81 for chloroform) for= solvent effect and found that the dG reduces by 90 kJ/mol. But still the b= inding energy of 300 kJ/mol is still not unrealistic.<= /div>

<= span style=3D"font-family:arial,sans-serif">Any suggestion is very helpful and greatly appreciated.

Thanks and regards,
Niyas
<= /span>

--0000000000005fe50005a7da8608-- From owner-chemistry@ccl.net Thu Jun 11 23:54:01 2020 From: "David Shobe shobedavid**gmail.com" To: CCL Subject: CCL:G: Free energy of complexation Message-Id: <-54095-200611232751-1961-cvuh8jkdr8gukmXmXD4pJg%server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="0000000000001d82b005a7daa9da" Date: Thu, 11 Jun 2020 22:27:33 -0500 MIME-Version: 1.0 Sent to CCL by: David Shobe [shobedavid/./gmail.com] --0000000000001d82b005a7daa9da Content-Type: text/plain; charset="UTF-8" Do you know whether the Delta H and/or Delta S values are anomalous? That might help you narrow down where the problem is. On Thu, Jun 11, 2020, 10:23 PM Niyas Ma niyasma0-x-gmail.com < owner-chemistry\a/ccl.net> wrote: > Hi all, > Just an update. > The dG values are all negative. Sorry for the mistake. > > Experimental free energy of complexation = -60 kJ/mol > Computed free energy of complexation = -390 kJ/mol > Computed free energy of complexation with solvent (Chloroform) = -300 > kJ/mol > > Thanks for pointing this out Dr. Michael Gilson. > > With regards, > Niyas > > On Fri, Jun 12, 2020 at 12:25 AM Niyas Ma niyasma0^gmail.com < > owner-chemistry%a%ccl.net > wrote: > >> Hi all, >> I am doing a computational investigation of binding energies for a >> noncovalent host-guest complex of two large polyaromatic hydrocarbons. >> Since I need Gibbs free energy of complexation, I did a frequency >> calculation and in Gaussian 16 with PM7 as the method (complex structure >> has 382 atoms). Separate optimizations and frequency calculations were >> done for a) host-guest complex, b) host, c) guest. Then, I took the 'Sum >> of electronic and thermal Free Energies (G)' value from the output for each >> of the structures to find the free energy of complexation (dG). >> dG = Gcomplex - (Ghost + Gguest) >> Problem started when I got an unrealistic compauted free energy of >> complexation which was also not comparable to the experimental values. >> Experimental free energy of complexation = 60 kJ/mol >> Computed free energy of complexation = 390 kJ/mol >> I am now struggling to find the error. It would be helpful if someone has >> any idea for the reasons why I am getting a huge and unrealistic energy in >> noncovalent complexation. >> Also, if anyone has any experience on the thermodynamics calculations >> with semiempirical methods, is it possible that the semiempirical methods >> are overestimating the energies? >> >> I also did the thermo calculations in MOPAC with COSMO (EPS = 4.81 for >> chloroform) for solvent effect and found that the dG reduces by 90 kJ/mol. >> But still the binding energy of 300 kJ/mol is still not unrealistic. >> >> Any suggestion is very helpful and greatly appreciated. >> >> Thanks and regards, >> Niyas >> >> --0000000000001d82b005a7daa9da Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Do you know whether the Delta H and/or Delta S values are= anomalous? That might help you narrow down where the problem is.

=
On Thu, Ju= n 11, 2020, 10:23 PM Niyas Ma niyas= ma0-x-gmail.com <owner-ch= emistry\a/ccl.net> wrote:
Hi all,
=C2=A0 Just an= update.
=C2=A0 The dG values are all negative. Sorr= y for the mistake.

Experimental free e= nergy of complexation =3D -60 kJ/mol
Computed free energy o= f complexation =3D -390 kJ/mol
Comp= uted free energy of complexation with solvent (Chloroform) =3D -300 kJ/mol<= /span>

Thanks= for pointing this out Dr. Michael Gilson.

With regards,
Niyas
On Fri, J= un 12, 2020 at 12:25 AM Niyas Ma niyasma0^gmail.com <owner-chemistry= %a%ccl.net> wrote:
= Hi all,
=C2=A0I am doing a computational investigation of binding= energies for a noncovalent host-guest=C2=A0 complex of two large polyaroma= tic hydrocarbons. Since I need Gibbs free energy of complexation, I did a f= requency calculation and in Gaussian 16 with PM7 as the method (complex str= ucture has 382 atoms). Separate optimizations and frequency c= alculations were done for a) host-guest complex, b) host, c) guest. Then, I= took the=C2=A0'Sum of ele= ctronic and thermal Free Energies (G)' value from the output for each o= f the structures to find the free energy of complexation (dG).
dG =3D Gcomplex - (Ghost + Gguest)
Pr= oblem started when I got an unrealistic compauted free energy of complexati= on which was also not comparable to the experimental values.<= /font>
Experimental free energy of complexation =3D 60 kJ/mol
Comp= uted free energy of complexation =3D 390 kJ/mol
<= div>I am now str= uggling to find the error. It would be helpful if someone has any idea for = the reasons why I am getting a huge and unrealistic energy in noncovalent c= omplexation.
Also, if anyone has any experience on the= thermodynamics calculations with semiempirical methods, is it possible tha= t the semiempirical methods are overestimating the energies?

I also did the thermo calculations in MOPAC with C= OSMO (EPS =3D 4.81 for chloroform) for solvent effect and found that the dG= reduces by 90 kJ/mol. But still the binding energy of 300 kJ/mol is still = not unrealistic.

Any suggestion is ver= y helpful and greatly appreciated.

=
Thank= s and regards,
Niyas

=
--0000000000001d82b005a7daa9da--