> 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 >>> >>> --00000000000030c7f105a7de0158 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Thank you Dr. Shobe for the reply.

=C2=A0 I have tabul= ated the values in the following table for the complexation A + 2B -> C.= B is coronene and A is an organic receptor larger than coronene. This calc= ulation is done with PM7 in MOPAC with COSMO solvent (EPS =3D 4.81 for chloroform) at 29= 8 K.

	H (kJ/mol)	S (kJ/K/mol)	H-TS (kJ/mol)
C	-164.431= 2	3.418112= 524	-1183.02= 8732
A	-337.883= 104	3.163188= 098	-1280.51= 3157
B	342.1173= 12	0.471864= 826	201.5015= 94

If we take the H-TS =3D G the total dG for t= he complexation is calculated as

C-(A+2B) =3D -305.519 kJ/mol

Here the stabilization due to enthalpy is high, but I= am not sure whether any of the values are anomalous.

It would be= very nice if you have some comments on the values.

Thanks and=C2=A0regards,

Niyas

On Fri, Jun 12, 2020 at 7:3= 2 AM David Shobe shobedavid**gmail.com <= ;owner-chemistry]^[ccl.net>= wrote:

Do you know whether the Delta H and/or Delta S values are anomalo= us? That might help you narrow down where the problem is.

On Thu, Jun 11, 20= 20, 10:23 PM Niyas Ma niyasma0-x-gmail.com <owner-chemistry]![ccl.net> wrote:
= Hi all,
=C2=A0 Just an update.
=C2=A0 The dG values are all negative. Sorry for the mistake.

Experimental free energy of complexation = =3D -60 kJ/mol
Computed free energy of complexation =3D -39= 0 kJ/mol
Computed free energy of co= mplexation with solvent (Chloroform) =3D -300 kJ/mol

Thanks for pointing this out= Dr. Michael Gilson.

Wit= h regards,
Niyas

On Fri, Jun 12, 2020 at 12:25 A= M Niyas Ma niyasma0^gmail.com <owner-chemistry%a%ccl.net> wr= ote:
Hi all,
=C2=A0I am doing a computational investigation= of binding energies for a noncovalent host-guest=C2=A0 complex of two larg= e 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) gue= st. Then, I took the=C2=A0'= ;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).
<= span style=3D"font-family:arial,sans-serif">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 complexation =3D 60 kJ/mol
Computed free energy of complexation =3D 390 kJ/mol
I= am now struggling to find the error. It would be helpful if someone has an= y idea for the reasons why I am getting a huge and unrealistic energy in no= ncovalent complexation.
<= span style=3D"font-family:arial,sans-serif">Also, if anyone has any experie= nce on the thermodynamics calculations with semiempirical methods, is it po= ssible that the semiempirical methods are overestimating the energies?
<= /span>
=
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/mol. But still the binding energy of 300 kJ/m= ol is still not unrealistic.
<= span style=3D"font-family:arial,sans-serif">
=
Any suggest= ion is very helpful and greatly appreciated.

Thanks and regards,
Niyas

--00000000000030c7f105a7de0158-- From owner-chemistry@ccl.net Fri Jun 12 12:10:00 2020 From: "Prof P Ramasami ramchemi-$-intnet.mu" To: CCL Subject: CCL: CALL FOR ABSTRACTS: VIRTUAL CONFERENCE ON CHEMISTRY AND ITS APPLICATIONS (VCCA-2020) Message-Id: <-54098-200612014428-22984-sSf71vWAguoQUUQXXAHEzw!A!server.ccl.net> X-Original-From: "Prof P Ramasami" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01D6409D.F2D5CF70" Date: Fri, 12 Jun 2020 09:43:38 +0400 MIME-Version: 1.0 Sent to CCL by: "Prof P Ramasami" [ramchemi^intnet.mu] This is a multi-part message in MIME format. ------=_NextPart_000_0031_01D6409D.F2D5CF70 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear Scientists, =20 Greetings from Mauritius.=20 A VIRTUAL Conference on Chemistry and it Applications (VCCA-2020) will = be held from 1st to 31st August 2020. The website of the conference is: = http://sites.uom.ac.mu/vcca2020 The VIRTUAL conference will cover all topics of Chemistry and = Interdisciplinary Sciences. The theme of the VIRTUAL conference is =E2=80=9CResearch and Innovations = in Chemical Sciences: Paving the Way Forward=E2=80=9D. There will be no need to travel. There will not be live presentations and thus one does not have to be = always online. There will be Nobel Prize presentations including; Prof Robert Huber (1988 Nobel Prize Winner in Chemistry) Sir (Prof) Richard Roberts (1993 Nobel Prize Winner in Physiology or = Medicine) Prof Ada Yonath (2009 Nobel Prize Winner in Chemistry) Prof Jean-Pierre Sauvage (2016 Nobel Prize Winner in Chemistry) You are invited to submit an abstract for VCCA-2020. Deadline to submit abstract is 15th June 2020. All abstracts will be reviewed and accepted abstracts will be collected = in the books of abstracts. There will be awards for three best presentations. After the VIRTUAL conference, there will be a call for full papers for = the book of proceedings to be published by De Gruyter (this is = optional). Kindly forward this email to those who may be interested. Looking forward to your participation. Kind regards, Prof Ponnadurai Ramasami Chairman of VCCA-2020. =20 ------=_NextPart_000_0031_01D6409D.F2D5CF70 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable

Dear Scientists,

Greetings = > from Mauritius. =

A = VIRTUAL Conference on Chemistry and it Applications (VCCA-2020) will be = held from 1^st to 31^st August = 2020.

The website of the conference is: http://sites.uom.ac.mu/vcca2020

The VIRTUAL conference will cover all topics = of Chemistry and Interdisciplinary Sciences.

The theme of the VIRTUAL conference is = =E2=80=9CResearch and Innovations in Chemical Sciences: Paving the Way = Forward=E2=80=9D.

There will be no need to = travel.

There will not be live presentations and thus = one does not have to be always online.

There will be Nobel Prize presentations = including;

Prof Robert Huber (1988 Nobel Prize Winner in = Chemistry)

Sir (Prof) Richard Roberts (1993 Nobel Prize = Winner in Physiology or Medicine)

Prof Ada Yonath (2009 Nobel Prize Winner in = Chemistry)

Prof Jean-Pierre Sauvage (2016 Nobel Prize = Winner in Chemistry)

You are invited to submit an abstract for = VCCA-2020.

Deadline to submit abstract is = 15^th June 2020.

All abstracts will be reviewed and accepted = abstracts will be collected in the books of = abstracts.

There will = be awards for three best presentations.

After the VIRTUAL conference, there will be a = call for full papers for the book of proceedings to be published by De = Gruyter (this is optional).

Kindly forward this email to those who may be = interested.

Looking forward to your = participation.

Kind regards,

Prof Ponnadurai = Ramasami

Chairman of = VCCA-2020.

------=_NextPart_000_0031_01D6409D.F2D5CF70-- From owner-chemistry@ccl.net Fri Jun 12 14:06:00 2020 From: "Niyas Ma niyasma0(!)gmail.com" To: CCL Subject: CCL:G: Free energy of complexation Message-Id: <-54099-200612140436-4019-pnhNFH78MBahL8PQMyJ3aA*o*server.ccl.net> X-Original-From: Niyas Ma Content-Type: multipart/alternative; boundary="0000000000009c76de05a7e6e849" Date: Fri, 12 Jun 2020 20:04:19 +0200 MIME-Version: 1.0 Sent to CCL by: Niyas Ma [niyasma0#%#gmail.com] --0000000000009c76de05a7e6e849 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Dr. Pierre Archirel, Thank you for the comment. I have used COSMO for solvation with PM7 in MOPAC. I couldn't find the CPCM keyword in MOPAC. From what I understood, MOPAC only has the COSMO method for solvation. Please correct me if I am wrong. Also the PM7 semiempirical method has inbuilt dispersion correction (D2 type). So, the dispersion is considered during calculation. This large energy is mostly coming from dispersion contribution as you can see below. Computed total enthalpy of complexation (with solvent chloroform) =3D -510.78272 kJ/mol Computed dispersion contribution to the total enthalpy (with solvent chloroform) =3D -490.614 kJ/mol Could it be an overestimation of dispersion? Also, thanks for the reference. With regards, Niyas On Fri, Jun 12, 2020 at 8:25 AM Pierre Archirel pierre.archirel|| universite-paris-saclay.fr wrote: > > Sent to CCL by: Pierre Archirel [pierre.archirel|| > universite-paris-saclay.fr] > This is an answer to Niyas, about complexation free energies. > Your reaction is of the type: > A+B -> C > if you use the PCM method > (you mention CPCM with MOPAC but not with GAUSSIAN) > your entropy balance is very poor and spuriously very positive. > This is an intrinsic drawback of the PCM method, > which can be empirically corrected, for example with > the Wertz formula, see for example: > P.Archirel et al. J. Phys. Chem. B 2012, 116, 1467=E2=88=921481 > Note that other errors may interfere: lack of dispersion in PM7? > Best wishes, > Pierre Archirel > > -- > > ______________________________________________________________ > > Pierre Archirel > Groupe Th=C3=A9osim: Th=C3=A9orie et Simulation > Laboratoire de Chimie Physique Tel: 01 69 15 63 86 > B=C3=A2t 349 Fax: 01 69 15 61 88 > 91405 Orsay C=C3=A9dex > France pierre.archirel-.-universite-paris-saclay.fr > ______________________________________________________________ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --0000000000009c76de05a7e6e849 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi Dr.=C2=A0 Pierre Archirel,

=C2=A0=C2=A0 Thank you for the comment.

I have used COSMO for solvation with PM7 in MOPAC. I couldn't fi= nd the CPCM keyword in MOPAC. From what I understood, MOPAC only has the CO= SMO method for solvation. Please correct me if I am wrong.

A= lso the PM7 semiempirical method has inbuilt dispersion correction (D2 type= ). So, the dispersion is considered during calculation. This large energy i= s mostly coming from dispersion contribution as you can see below.

Computed total enthalpy of complexation (with solvent chloro= form) =3D -510.78272 kJ/mol

Computed dispersion contribution to the total enthalpy (with sol= vent chloroform) =3D -490.614 kJ/mol

Could it be an overestimation of dispersion?
<= /div>

Also, thanks for the reference.

With reg= ards,

Niyas

On Fri, Jun 12, 2020 at 8:25 AM Pierre Archi= rel pierre.archirel||universite-paris-saclay.fr <owner-chemistry_+_ccl.net> wrote:
=

Sent to CCL by: Pierre Archirel [pierre.archirel||universite-paris-= saclay.fr]
This is an answer to Niyas, about complexation free energies.
Your reaction is of the type:
A+B -> C
if you use the PCM method
(you mention CPCM with MOPAC but not with GAUSSIAN)
your entropy balance is very poor and spuriously very positive.
This is an intrinsic drawback of the PCM method,
which can be empirically corrected, for example with
the Wertz formula, see for example:
P.Archirel et al. J. Phys. Chem. B 2012, 116, 1467=E2=88=921481
Note that other errors may interfere: lack of dispersion in PM7?
Best wishes,
Pierre Archirel

--

______________________________________________________________

=C2=A0 Pierre Archirel
=C2=A0 Groupe Th=C3=A9osim: Th=C3=A9orie et Simulation
=C2=A0 Laboratoire de Chimie Physique=C2=A0 =C2=A0 =C2=A0 Tel: 01 69 15 63 = 86
=C2=A0 B=C3=A2t 349=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Fax: 01 69 15 61 88
=C2=A0 91405 Orsay C=C3=A9dex
=C2=A0 France=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 pierre.archirel-.-universite-paris-saclay.fr
______________________________________________________________

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--0000000000009c76de05a7e6e849-- From owner-chemistry@ccl.net Fri Jun 12 16:08:00 2020 From: "Stefan Grimme grimme^^thch.uni-bonn.de" To: CCL Subject: CCL: Free energy of complexation Message-Id: <-54100-200612160637-16725-DMaBY7VuaJZ0VAMhiq/Tog .. server.ccl.net> X-Original-From: "Stefan Grimme" Date: Fri, 12 Jun 2020 16:06:36 -0400 Sent to CCL by: "Stefan Grimme" [grimme[-]thch.uni-bonn.de] Dear Niyas, I very strongly recommend the GFN2-xTB QM method freely available in the xtb code (see https://github.com/grimme-lab/xtb/releases). It features a proper treatment of dispersion, comes with the robust GBSA solvation model and is well tested for various supramolecular complexes (C. Bannwarth, S. Ehlert, S. Grimme, GFN2-xTB - An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion Contributions, J. Chem. Theory Comput. (2019), 15, 1652-1671) Best Stefan Grimme From owner-chemistry@ccl.net Fri Jun 12 18:30:01 2020 From: "Niyas Ma niyasma0^_^gmail.com" To: CCL Subject: CCL: Free energy of complexation Message-Id: <-54101-200612182918-1306-ea5Dt9q/HLqFTCtdMK6FSw===server.ccl.net> X-Original-From: Niyas Ma Content-Type: multipart/alternative; boundary="000000000000427ced05a7ea9b6b" Date: Sat, 13 Jun 2020 00:29:01 +0200 MIME-Version: 1.0 Sent to CCL by: Niyas Ma [niyasma0 .. gmail.com] --000000000000427ced05a7ea9b6b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Prof. Grimme, Thank you for the suggestion of the GFN2-xTB QM method. I will surely give it a try after reading carefully. I have a small query regarding the free energy method shown in your 2012 paper (S. Grimme , *Chem. Eur. J.* *2012*, 18, 9955=E2=80=93 9964 ). I haven't fully understood the dGRRHO term described in the paper to account for the entropic contribution to the free energy of complexation. Is the term GRRHO computed by taking total entropy difference from frequency analyses and calculating -TS? It would be very helpful if you can give a comment on this query when you have time? Thanks and regards, Niyas On Fri, Jun 12, 2020 at 11:25 PM Stefan Grimme grimme^^thch.uni-bonn.de < owner-chemistry[*]ccl.net> wrote: > > Sent to CCL by: "Stefan Grimme" [grimme[-]thch.uni-bonn.de] > Dear Niyas, > I very strongly recommend the GFN2-xTB QM method freely available in > the xtb code (see https://github.com/grimme-lab/xtb/releases). > It features a proper treatment of dispersion, comes with the robust > GBSA solvation model and is well tested for various supramolecular > complexes (C. Bannwarth, S. Ehlert, S. Grimme, GFN2-xTB - An Accurate and > Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Metho= d > with Multipole Electrostatics and Density-Dependent Dispersion > Contributions, J. Chem. Theory Comput. (2019), 15, 1652-1671) > Best > Stefan Grimme > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000000000000427ced05a7ea9b6b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Dear Prof. Grimme,

=C2=A0 Thank you for the= suggestion of the=20 GFN2-xTB QM method. I will surely give=C2=A0it a try after reading careful= ly.

=C2=A0 I have a small query regarding the=C2= =A0free energy method shown in your 2012 paper= (S. Grimme, Chem. Eur. J= . 2012, 18, 9955=E2=80=93 9964). I haven't= fully understood the dGRRHO term described in the = paper to account for the entropic contribution to the free energy of comple= xation. Is the term GRRHO computed by taking total = entropy difference from frequency analyses and calculating -TS? It would be= very helpful if you can give a comment on this query when you have time?

Thanks and regards,

Niyas

=C2=A0

On Fri, Jun 12, 2020 at 11:25 PM Stefan Grimme grimme^^thch.uni-bonn.de <owner-chemistry[*]ccl.net> wrote:

Sent to CCL by: "Stefan=C2=A0 Grimme" [grimme[-]thch.uni-bonn.de]
Dear Niyas,
I very strongly recommend the GFN2-xTB QM method freely available in
the xtb code (see https://github.com/grimme-lab/xtb/releas= es).
It features a proper treatment of dispersion, comes with the robust
GBSA solvation model and is well tested for various supramolecular
complexes (C. Bannwarth, S. Ehlert, S. Grimme, GFN2-xTB - An Accurate and B= roadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method w= ith Multipole Electrostatics and Density-Dependent Dispersion Contributions= , J. Chem. Theory Comput. (2019), 15, 1652-1671)
Best
Stefan Grimme

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