From owner-chemistry@ccl.net Mon Jul 1 07:10:01 2019 From: "John Simmie john.simmie..nuigalway.ie" To: CCL Subject: CCL: BSSE correction for transition states Message-Id: <-53777-190701024234-609-SYDJ03d/5BHVm8EDcoDvKA a server.ccl.net> X-Original-From: "John Simmie" Date: Mon, 1 Jul 2019 02:42:32 -0400 Sent to CCL by: "John Simmie" [john.simmie++nuigalway.ie] The original post was concerned with bimolecular reactants & transition states and whether corrections are required. AFAIK the conclusion reached by Lendvay and Mayer [https://doi.org/10.1016/S0009-2614(98)01191-9]: "We performed a theoretical and numerical analysis of the different `counterpoise correction' (CP) schemes potentially applicable to correct for the basis set superposition error (BSSE) in the neighborhood of transition structures of chemical reactions. The analysis proved that neither of them is satisfactory: all CP versions result in either discontinuous potential surfaces or yield different energies for the same species in different reactions. Standard CP correction is unavoidable and satisfactory when loosely bound pre- or post-reaction complexes are studied. For transition structures, however, doing no correction is better than any available CP method." Has never been countermanded and most if not all practicing kineticists would apply a counterpoise correction to pre-reaction and post-reaction complexes if necessary but that's all. Of course swamping with basis functions is also a good idea if that is feasible for the particular system being studied. John M. Simmie//School of Chemistry//National Univ. of Ireland, Galway From owner-chemistry@ccl.net Mon Jul 1 07:45:01 2019 From: "Lee Jones bunglinpie---googlemail.com" To: CCL Subject: CCL: BSSE Counterpoise correction Message-Id: <-53778-190701042753-11974-bP80qyjeyaNQQXdqqsnzsg/a\server.ccl.net> X-Original-From: "Lee Jones" Date: Mon, 1 Jul 2019 04:27:51 -0400 Sent to CCL by: "Lee Jones" [bunglinpie**googlemail.com] Hi Thanks for your reply. I think I have it now, but just to make sure i'm following you correctly, I should perform CP correction calculations on the Transition state AB* and the bonded addition product AB, but would calculate the energies of the individual reactants A and B in the normal way without any CP corrections? Is it best to perform a geometry optimisation+freq with CP correction active, or should I optimise first, then perform a single point CP correction on the optimised structure? The basis set size can have an effect on the geometry and frequencies so I guess it would make sense for CP to be active throughout. Thanks > "Antarip Halder antarip.halder:_:gmail.com" wrote: > > Sent to CCL by: Antarip Halder [antarip.halder++gmail.com] > --000000000000a2e42d058c6e9ce7 > Content-Type: text/plain; charset="UTF-8" > > Hi, > > BSSE comes into picture when you want to calculate the interaction energy > of a molecular assembly (say XY). Interaction energy of a molecular > assembly is defined as electronic energy of the complete assembly XY (E_XY) > minus the sum of the electronic energies of individual monomer (E_X + E_Y). > The problem is, to construct the wave function for XY we use more number of > basis set functions than for X or Y. Therefore, the energy difference (E_XY > - E_X -E_Y) gets overestimated. All the three energies should be calculated > using same number number of basis set functions and that is taken care of > by the counterpoise method. > > Now in your case, if you want to find out the correct interaction energy of > the bio-molecular assembly AB then run CP calculation on AB to get the BSSE > correction (say E_BSSE). So your final interaction energy should be, E_AB - > E_A - E_B + E_BSSE. Similarly if you are interested to find out how stable > your intermediate (AB)* is, then calculate its interaction energy as, > E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is the correction energy > obtained from the counterpoise calculation performed on (AB)*. > > Hope this helps. > > Thanks, > Antarip > > On Sat, Jun 29, 2019 at 5:01 AM Lee Jones bunglinpie[*]googlemail.com < > owner-chemistry]~[ccl.net> wrote: > > > > > Sent to CCL by: "Lee Jones" [bunglinpie|,|googlemail.com] > > Hi. I'm after a little guidance regarding Basis Set Superposition Error. > > > > I understand what BSSE is and how to perform a counterpoise correction > > using ghost atoms, but my question is a little more fundamental. > > > > Considering a bimolecular addition reaction where you have reactants A > > and B that proceed to form a single molecule AB via a transition state > > AB*, what species do you actually perform the CP correction on? > > > > I read the following article which contains the following passage: > > > > https://scicomp.stackexchange.com/questions/3/what-is-counterpoise- > > correction > > > > "This correction will depend on the geometries of the reactants. When > > they are very far from one another, it will be very small: they don't > > influence one another. When they are very close, this effect will be > > small, for the same reasoning. It's the intermediate distances that have > > the largest BSSE. These are the distances at or approaching the > > transition state, which serves as the bottleneck for the reaction. If you > > are not accounting for the artificial improvement near the transition > > state, then you will get an incorrect approximation of the activation > > energy, the energy difference between this transition state and the > > separated-reactant limit." > > > > > > This seems to suggest that, to a first approximation, I would only need > > to CP correct the transition state AB* and can effectively ignore BSSE > > for the reactants A and B at infinite distance and for the final product > > AB (i.e. the BSSE only has a small effect on the overall reaction > > energy/enthalpy) is this correct. > > > > > > Thanks> > > > > > > -- > If you think you can, you are right. > > --000000000000a2e42d058c6e9ce7 > Content-Type: text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > >
Hi,

BSSE comes into picture = > when you want to calculate the interaction energy of a molecular assembly (= > say XY). Interaction energy of a molecular assembly is defined as electroni= > c energy of the complete assembly XY (E_XY) minus the sum of the electronic= > energies of individual monomer (E_X + E_Y). The problem is, to construct t= > he wave function for XY we use more number of basis set functions than for = > X or Y. Therefore, the energy difference (E_XY - E_X -E_Y) gets overestimat= > ed. All the three energies should be calculated using same number number of= > basis set functions and that is taken care of by the counterpoise method.<= > /div>

Now in your case, if you want to find out the corr= > ect interaction energy of the bio-molecular assembly AB then run CP calcula= > tion on AB to get the BSSE correction (say E_BSSE). So your final interacti= > on energy should be, E_AB - E_A - E_B + E_BSSE. Similarly if you are intere= > sted to find out how stable your intermediate (AB)* is, then calculate its = > interaction energy as, E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is the c= > orrection energy obtained from the counterpoise calculation performed on (A= > B)*.

Hope this helps.

Tha= > nks,
Antarip

ir=3D"ltr" class=3D"gmail_attr">On Sat, Jun 29, 2019 at 5:01 AM Lee Jones b= > unglinpie[*]googlemail.com < f=3D"mailto:owner-chemistry]~[ccl.net">owner-chemistry]~[ccl.net> wrote:= >
ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
> Sent to CCL by: "Lee=C2=A0 Jones" [bunglinpie|,| /googlemail.com" rel=3D"noreferrer" target=3D"_blank">googlemail.com] r> > Hi.=C2=A0 I'm after a little guidance regarding Basis Set Superposition= > Error.
>
> I understand what BSSE is and how to perform a counterpoise correction
> using ghost atoms, but my question is a little more fundamental.
>
> Considering a bimolecular addition reaction where you have reactants A
> and B that proceed to form a single molecule AB via a transition state
> AB*, what species do you actually perform the CP correction on?
>
> I read the following article which contains the following passage:
>
> se-" rel=3D"noreferrer" target=3D"_blank">https://scicomp.stackexchange.com= > /questions/3/what-is-counterpoise-
> correction
>
> "This correction will depend on the geometries of the reactants. When = >
> they are very far from one another, it will be very small: they don't <= > br> > influence one another. When they are very close, this effect will be
> small, for the same reasoning. It's the intermediate distances that hav= > e
> the largest BSSE. These are the distances at or approaching the
> transition state, which serves as the bottleneck for the reaction. If you <= > br> > are not accounting for the artificial improvement near the transition
> state, then you will get an incorrect approximation of the activation
> energy, the energy difference between this transition state and the
> separated-reactant limit."
>
>
> This seems to suggest that, to a first approximation, I would only need > > to CP correct the transition state AB* and can effectively ignore BSSE
> for the reactants A and B at infinite distance and for the final product r> > AB (i.e. the BSSE only has a small effect on the overall reaction
> energy/enthalpy) is this correct.
>
>
> Thanks
>
>
>
> -=3D This is automatically added to each message by the mailing script =3D-= > >
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--
mail_signature">If you think you can, you are right.
> > --000000000000a2e42d058c6e9ce7-- > > From owner-chemistry@ccl.net Mon Jul 1 14:22:01 2019 From: "Tobias Kraemer Tobias.Kraemer###mu.ie" To: CCL Subject: CCL: BSSE Counterpoise correction Message-Id: <-53779-190701100701-28134-DMaBY7VuaJZ0VAMhiq/Tog|*|server.ccl.net> X-Original-From: Tobias Kraemer Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 1 Jul 2019 14:06:54 +0000 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [Tobias.Kraemer{}mu.ie] Hi, Yes, CP corrections should be beformed on both the transition state (since this can be considered a supermolecule made of two fragments A and B) and the bonded addition product AB. For the individual fragments A and B you don't need and CP correction, it would in fact be difficult to do so anyways. You need knowledge of the position of both fragments for this type of calculation, and for the isolated fragments you don't have this information. The BSSE does not come into effect here. Tobias Dr. Tobias Krämer Lecturer in Inorganic Chemistry Department of Chemistry Maynooth University, Maynooth, Co. Kildare, Ireland. E: tobias.kraemer%x%mu.ie   T: +353 (0)1 474 7517 -----Original Message----- > From: owner-chemistry+tobias.kraemer==mu.ie%x%ccl.net On Behalf Of Lee Jones bunglinpie---googlemail.com Sent: 01 July 2019 09:28 To: Tobias Kraemer Subject: CCL: BSSE Counterpoise correction Sent to CCL by: "Lee Jones" [bunglinpie**googlemail.com] Hi Thanks for your reply. I think I have it now, but just to make sure i'm following you correctly, I should perform CP correction calculations on the Transition state AB* and the bonded addition product AB, but would calculate the energies of the individual reactants A and B in the normal way without any CP corrections? Is it best to perform a geometry optimisation+freq with CP correction active, or should I optimise first, then perform a single point CP correction on the optimised structure? The basis set size can have an effect on the geometry and frequencies so I guess it would make sense for CP to be active throughout. Thanks > "Antarip Halder antarip.halder:_:gmail.com" wrote: > > Sent to CCL by: Antarip Halder [antarip.halder++gmail.com] > --000000000000a2e42d058c6e9ce7 > Content-Type: text/plain; charset="UTF-8" > > Hi, > > BSSE comes into picture when you want to calculate the interaction > energy of a molecular assembly (say XY). Interaction energy of a > molecular assembly is defined as electronic energy of the complete > assembly XY (E_XY) > minus the sum of the electronic energies of individual monomer (E_X + E_Y). > The problem is, to construct the wave function for XY we use more > number of > basis set functions than for X or Y. Therefore, the energy difference (E_XY > - E_X -E_Y) gets overestimated. All the three energies should be calculated > using same number number of basis set functions and that is taken care > of by the counterpoise method. > > Now in your case, if you want to find out the correct interaction > energy of > the bio-molecular assembly AB then run CP calculation on AB to get the BSSE > correction (say E_BSSE). So your final interaction energy should be, > E_AB - > E_A - E_B + E_BSSE. Similarly if you are interested to find out how stable > your intermediate (AB)* is, then calculate its interaction energy as, > E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is the correction energy > obtained from the counterpoise calculation performed on (AB)*. > > Hope this helps. > > Thanks, > Antarip > > On Sat, Jun 29, 2019 at 5:01 AM Lee Jones bunglinpie[*]googlemail.com > < owner-chemistry]~[ccl.net> wrote: > > > > > Sent to CCL by: "Lee Jones" [bunglinpie|,|googlemail.com] Hi. I'm > > after a little guidance regarding Basis Set Superposition Error. > > > > I understand what BSSE is and how to perform a counterpoise > > correction using ghost atoms, but my question is a little more fundamental. > > > > Considering a bimolecular addition reaction where you have reactants > > A and B that proceed to form a single molecule AB via a transition > > state AB*, what species do you actually perform the CP correction on? > > > > I read the following article which contains the following passage: > > > > https://scicomp.stackexchange.com/questions/3/what-is-counterpoise- > > correction > > > > "This correction will depend on the geometries of the reactants. > > When they are very far from one another, it will be very small: they > > don't influence one another. When they are very close, this effect > > will be small, for the same reasoning. It's the intermediate > > distances that have > > the largest BSSE. These are the distances at or approaching the > > transition state, which serves as the bottleneck for the reaction. > > If you > > are not accounting for the artificial improvement near the > > transition state, then you will get an incorrect approximation of > > the activation energy, the energy difference between this transition > > state and the separated-reactant limit." > > > > > > This seems to suggest that, to a first approximation, I would only > > need to CP correct the transition state AB* and can effectively > > ignore BSSE for the reactants A and B at infinite distance and for > > the final product > > AB (i.e. the BSSE only has a small effect on the overall reaction > > energy/enthalpy) is this correct. > > > > > > Thanks> > > > > > > -- > If you think you can, you are right. > > --000000000000a2e42d058c6e9ce7 > Content-Type: text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > >
Hi,

BSSE comes into picture = > when you want to calculate the interaction energy of a molecular > assembly (= > say XY). Interaction energy of a molecular assembly is defined as electroni= > c energy of the complete assembly XY (E_XY) minus the sum of the electronic= > energies of individual monomer (E_X + E_Y). The problem is, to > construct t= > he wave function for XY we use more number of basis set functions than for = > X or Y. Therefore, the energy difference (E_XY - E_X -E_Y) gets overestimat= > ed. All the three energies should be calculated using same number > number of= > basis set functions and that is taken care of by the counterpoise method.<= > /div>

Now in your case, if you want to find out the corr= > ect interaction energy of the bio-molecular assembly AB then run CP calcula= > tion on AB to get the BSSE correction (say E_BSSE). So your final interacti= > on energy should be, E_AB - E_A - E_B + E_BSSE. Similarly if you are intere= > sted to find out how stable your intermediate (AB)* is, then calculate its = > interaction energy as, E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is > the c= > orrection energy obtained from the counterpoise calculation performed > on (A= > B)*.

Hope this helps.

Tha= > nks,
Antarip

class=3D"gmail_quote">
ir=3D"ltr" class=3D"gmail_attr">On Sat, Jun 29, 2019 at 5:01 AM Lee > Jones b= > unglinpie[*]googlemail.com > < f=3D"mailto:owner-chemistry]~[ccl.net">owner-chemistry]~[ccl.net&g > t; wrote:= >
0px 0.8= > ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
> Sent to CCL by: "Lee=C2=A0 Jones" [bunglinpie|,| /googlemail.com" rel=3D"noreferrer" > target=3D"_blank">googlemail.com] r> > Hi.=C2=A0 I'm after a little guidance regarding Basis Set Superposition= > Error.
>
> I understand what BSSE is and how to perform a counterpoise correction
> using ghost atoms, but my question is a little more fundamental.
>
Considering a bimolecular addition reaction where you have > reactants A
> and B that proceed to form a single molecule AB via a transition state
> AB*, what species do you actually perform the CP correction on?
>
I read the following article which contains the following > passage:

href=3D"https://scicomp.stackexchange.com/questions/3/what-is- counterpoi= > se-" rel=3D"noreferrer" target=3D"_blank">https://scicomp.stackexchange.com= > /questions/3/what-is-counterpoise-
> correction
>
> "This correction will depend on the geometries of the reactants. When = >
> they are very far from one another, it will be very small: they > don't <= > br> > influence one another. When they are very close, this effect will be >
small, for the same reasoning. It's the intermediate > distances that hav= > e
> the largest BSSE. These are the distances at or approaching the
> transition state, which serves as the bottleneck for the reaction. If > you <= > br> > are not accounting for the artificial improvement near the transition
> state, then you will get an incorrect approximation of the activation
> energy, the energy difference between this transition state and the >
separated-reactant limit."


This seems to > suggest that, to a first approximation, I would only need > > to CP correct the transition state AB* and can effectively ignore BSSE
> for the reactants A and B at infinite distance and for the final > product r> > AB (i.e. the BSSE only has a small effect on the overall reaction
> energy/enthalpy) is this correct.
>
>
> Thanks
>
>
>
> -=3D This is automatically added to each message by the mailing script =3D-= > >
> E-mail to subscribers: k">CHEMISTRY]~[ccl.net or use:
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--
mail_signature">If you think you can, you are right.
> > --000000000000a2e42d058c6e9ce7--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jul 1 23:31:00 2019 From: "Antarip Halder antarip.halder],[gmail.com" To: CCL Subject: CCL: BSSE Counterpoise correction Message-Id: <-53780-190701230653-658-fwbd616JxCCIVBSj8pwLhQ]^[server.ccl.net> X-Original-From: Antarip Halder Content-Type: multipart/alternative; boundary="000000000000e5fa51058caa08c4" Date: Tue, 2 Jul 2019 08:38:07 +0530 MIME-Version: 1.0 Sent to CCL by: Antarip Halder [antarip.halder(a)gmail.com] --000000000000e5fa51058caa08c4 Content-Type: text/plain; charset="UTF-8" Hi, Let me summarize the procedure for interaction energy calculation of a molecular assembly AB in the ground state. Geometry optimize the complex AB and the isolated monomers A & B. Perform the so called 'Frequency calculation' on the optimized geometries of AB, A and B, to confirm that all the frequencies are real. Now if you calculate E(AB) - E(A) - E(B), then you will get the preliminary interaction energy. Note that E(AB), E(A) & E(B) are the electronic energies corresponding to the optimized geometries of AB, A and B, respectively. Next perform counterpoise calculation on the optimized geometry of AB. This will give the correction energy due to BSSE, say E(BSSE). Now add E(BSSE) to the preliminary interaction energy to get the BSSE corrected interaction energy, i.e., E(AB) - E(A) - E(B) + E(BSSE). This interaction energy can further be modified by adding deformation correction and zero point vibrational energy correction. For that you may have a look at the supporting information (page S5 onwards) of the following article https://pubs.acs.org/doi/abs/10.1021/acsomega.8b03689 Best wishes, Antarip Halder Research Associate SSCU, IISc On Mon, Jul 1, 2019 at 7:16 PM Lee Jones bunglinpie---googlemail.com < owner-chemistry__ccl.net> wrote: > > Sent to CCL by: "Lee Jones" [bunglinpie**googlemail.com] > Hi > > Thanks for your reply. > > I think I have it now, but just to make sure i'm following you correctly, > I > should perform CP correction calculations on the Transition state AB* and > the bonded addition product AB, but would calculate the energies of the > individual reactants A and B in the normal way without any CP corrections? > > Is it best to perform a geometry optimisation+freq with CP correction > active, or should I optimise first, then perform a single point CP > correction on the optimised structure? The basis set size can have an > effect on the geometry and frequencies so I guess it would make sense for > CP to be active throughout. > > Thanks > > > > "Antarip Halder antarip.halder:_:gmail.com" wrote: > > > > Sent to CCL by: Antarip Halder [antarip.halder++gmail.com] > > --000000000000a2e42d058c6e9ce7 > > Content-Type: text/plain; charset="UTF-8" > > > > Hi, > > > > BSSE comes into picture when you want to calculate the interaction energy > > of a molecular assembly (say XY). Interaction energy of a molecular > > assembly is defined as electronic energy of the complete assembly XY > (E_XY) > > minus the sum of the electronic energies of individual monomer (E_X + > E_Y). > > The problem is, to construct the wave function for XY we use more number > of > > basis set functions than for X or Y. Therefore, the energy difference > (E_XY > > - E_X -E_Y) gets overestimated. All the three energies should be > calculated > > using same number number of basis set functions and that is taken care of > > by the counterpoise method. > > > > Now in your case, if you want to find out the correct interaction energy > of > > the bio-molecular assembly AB then run CP calculation on AB to get the > BSSE > > correction (say E_BSSE). So your final interaction energy should be, > E_AB > - > > E_A - E_B + E_BSSE. Similarly if you are interested to find out how > stable > > your intermediate (AB)* is, then calculate its interaction energy as, > > E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is the correction energy > > obtained from the counterpoise calculation performed on (AB)*. > > > > Hope this helps. > > > > Thanks, > > Antarip > > > > On Sat, Jun 29, 2019 at 5:01 AM Lee Jones bunglinpie[*]googlemail.com < > > owner-chemistry]~[ccl.net> wrote: > > > > > > > > Sent to CCL by: "Lee Jones" [bunglinpie|,|googlemail.com] > > > Hi. I'm after a little guidance regarding Basis Set Superposition > Error. > > > > > > I understand what BSSE is and how to perform a counterpoise correction > > > using ghost atoms, but my question is a little more fundamental. > > > > > > Considering a bimolecular addition reaction where you have reactants A > > > and B that proceed to form a single molecule AB via a transition state > > > AB*, what species do you actually perform the CP correction on? > > > > > > I read the following article which contains the following passage: > > > > > > https://scicomp.stackexchange.com/questions/3/what-is-counterpoise- > > > correction > > > > > > "This correction will depend on the geometries of the reactants. When > > > they are very far from one another, it will be very small: they don't > > > influence one another. When they are very close, this effect will be > > > small, for the same reasoning. It's the intermediate distances that > have > > > the largest BSSE. These are the distances at or approaching the > > > transition state, which serves as the bottleneck for the reaction. If > you > > > are not accounting for the artificial improvement near the transition > > > state, then you will get an incorrect approximation of the activation > > > energy, the energy difference between this transition state and the > > > separated-reactant limit." > > > > > > > > > This seems to suggest that, to a first approximation, I would only need > > > to CP correct the transition state AB* and can effectively ignore BSSE > > > for the reactants A and B at infinite distance and for the final > product > > > AB (i.e. the BSSE only has a small effect on the overall reaction > > > energy/enthalpy) is this correct. > > > > > > > > > Thanks> > > > > > > > > > > -- > > If you think you can, you are right. > > > > --000000000000a2e42d058c6e9ce7 > > Content-Type: text/html; charset="UTF-8" > > Content-Transfer-Encoding: quoted-printable > > > >
Hi,

BSSE comes into > picture = > > when you want to calculate the interaction energy of a molecular > assembly > (= > > say XY). Interaction energy of a molecular assembly is defined as > electroni= > > c energy of the complete assembly XY (E_XY) minus the sum of the > electronic= > > energies of individual monomer (E_X + E_Y). The problem is, to > construct > t= > > he wave function for XY we use more number of basis set functions than > for = > > X or Y. Therefore, the energy difference (E_XY - E_X -E_Y) gets > overestimat= > > ed. All the three energies should be calculated using same number number > of= > > basis set functions and that is taken care of by the counterpoise > method.<= > > /div>

Now in your case, if you want to find out the > corr= > > ect interaction energy of the bio-molecular assembly AB then run CP > calcula= > > tion on AB to get the BSSE correction (say E_BSSE). So your final > interacti= > > on energy should be, E_AB - E_A - E_B + E_BSSE. Similarly if you are > intere= > > sted to find out how stable your intermediate (AB)* is, then calculate > its = > > interaction energy as, E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is > the > c= > > orrection energy obtained from the counterpoise calculation performed on > (A= > > B)*.

Hope this helps.

>
Tha= > > nks,
Antarip

class=3D"gmail_quote">
d= > > ir=3D"ltr" class=3D"gmail_attr">On Sat, Jun 29, 2019 at 5:01 AM Lee > Jones > b= > > unglinpie[*]googlemail.com < hre= > > f=3D"mailto:owner-chemistry]~[ccl.net">owner-chemistry]~[ccl.net> > > wrote:= > >
0.8= > > ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
> > Sent to CCL by: "Lee=C2=A0 Jones" [bunglinpie|,| href=3D"http:/= > > /googlemail.com" rel=3D"noreferrer" target=3D"_blank">googlemail.com > ] > > r> > > Hi.=C2=A0 I'm after a little guidance regarding Basis Set > Superposition= > > Error.
> >
> > I understand what BSSE is and how to perform a counterpoise correction >
> > using ghost atoms, but my question is a little more fundamental.
> >
> > Considering a bimolecular addition reaction where you have reactants A >
> > and B that proceed to form a single molecule AB via a transition state >
> > AB*, what species do you actually perform the CP correction on?
> >
> > I read the following article which contains the following passage:
> >
> > counterpoi= > > se-" rel=3D"noreferrer" > target=3D"_blank">https://scicomp.stackexchange.com= > > /questions/3/what-is-counterpoise-
> > correction
> >
> > "This correction will depend on the geometries of the reactants. > When = > >
> > they are very far from one another, it will be very small: they > don't > <= > > br> > > influence one another. When they are very close, this effect will be
> > small, for the same reasoning. It's the intermediate distances that > hav= > > e
> > the largest BSSE. These are the distances at or approaching the
> > transition state, which serves as the bottleneck for the reaction. If > you > <= > > br> > > are not accounting for the artificial improvement near the transition >
> > state, then you will get an incorrect approximation of the activation >
> > energy, the energy difference between this transition state and the
> > separated-reactant limit."
> >
> >
> > This seems to suggest that, to a first approximation, I would only need > > > > > to CP correct the transition state AB* and can effectively ignore BSSE >
> > for the reactants A and B at infinite distance and for the final product > > r> > > AB (i.e. the BSSE only has a small effect on the overall reaction
> > energy/enthalpy) is this correct.
> >
> >
> > Thanks
> >
> >
> >
> > -=3D This is automatically added to each message by the mailing script > =3D-= > > > >
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--
class=3D"g= > > mail_signature">If you think you can, you are right.
> > > > --000000000000a2e42d058c6e9ce7--> > > -- If you think you can, you are right. --000000000000e5fa51058caa08c4 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,

Let me summarize the pro= cedure for interaction energy calculation of a molecular assembly AB in the= ground state.

Geometry optimize the complex AB an= d the isolated monomers A & B. Perform the so called 'Frequency cal= culation' on the optimized geometries of AB, A and B, to confirm that a= ll the frequencies are real. Now if you calculate E(AB) - E(A) - E(B), then= you will get the preliminary interaction energy. Note that E(AB), E(A) &am= p; E(B) are the electronic energies corresponding to the optimized geometri= es of AB, A and B, respectively. Next perform counterpoise calculation on t= he optimized geometry of AB. This will give the correction energy due to BS= SE, say E(BSSE). Now add E(BSSE) to the preliminary interaction energy to g= et the BSSE corrected interaction energy, i.e., E(AB) - E(A) - E(B)=C2=A0+ = E(BSSE).

This interaction energy can further be modified = by adding deformation correction and zero point vibrational energy correcti= on. For that you may have a look at the supporting information (page S5 onw= ards) of the following article https://pubs.acs.org/doi/abs/10.1021/acsomega.8b03689=

Best wishes,
Antarip Halder
Research Associate
SSCU, IISc

On Mon, Jul 1, 2019 at = 7:16 PM Lee Jones bunglinpie= ---googlemail.com <owner-= chemistry__ccl.net> wrote:

Sent to CCL by: "Lee=C2=A0 Jones" [bunglinpie**googlemail.com] Hi

Thanks for your reply.

I think I have it now, but just to make sure i'm following you correctl= y, I
should perform CP correction calculations on the Transition state AB* and <= br> the bonded addition product AB, but would calculate the energies of the individual reactants A and B in the normal way without any CP corrections?<= br>
Is it best to perform a geometry optimisation+freq with CP correction
active, or should I optimise first, then perform a single point CP
correction on the optimised structure?=C2=A0 The basis set size can have an=
effect on the geometry and frequencies so I guess it would make sense for <= br> CP to be active throughout.

Thanks


> "Antarip Halder antarip.halder:_:gmail.com"=C2=A0 wrote:
>
> Sent to CCL by: Antarip Halder [antarip.halder++gmail.com]
> --000000000000a2e42d058c6e9ce7
> Content-Type: text/plain; charset=3D"UTF-8"
>
> Hi,
>
> BSSE comes into picture when you want to calculate the interaction ene= rgy
> of a molecular assembly (say XY). Interaction energy of a molecular > assembly is defined as electronic energy of the complete assembly XY <= br> (E_XY)
> minus the sum of the electronic energies of individual monomer (E_X + =
E_Y).
> The problem is, to construct the wave function for XY we use more numb= er
of
> basis set functions than for X or Y. Therefore, the energy difference =
(E_XY
> - E_X -E_Y) gets overestimated. All the three energies should be
calculated
> using same number number of basis set functions and that is taken care= of
> by the counterpoise method.
>
> Now in your case, if you want to find out the correct interaction ener= gy
of
> the bio-molecular assembly AB then run CP calculation on AB to get the=
BSSE
> correction (say E_BSSE). So your final interaction energy should be, E= _AB
-
> E_A - E_B + E_BSSE. Similarly if you are interested to find out how stable
> your intermediate (AB)* is, then calculate its interaction energy as,<= br> > E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is the correction energy > obtained from the counterpoise calculation performed on (AB)*.
>
> Hope this helps.
>
> Thanks,
> Antarip
>
> On Sat, Jun 29, 2019 at 5:01 AM Lee Jones bunglinpie[*]googlemail.com = <
> owner-chemistry]~[ccl.net> wrote:
>
> >
> > Sent to CCL by: "Lee=C2=A0 Jones" [bunglinpie|,|googlemail.= com]
> > Hi.=C2=A0 I'm after a little guidance regarding Basis Set Sup= erposition
Error.
> >
> > I understand what BSSE is and how to perform a counterpoise corre= ction
> > using ghost atoms, but my question is a little more fundamental.<= br> > >
> > Considering a bimolecular addition reaction where you have reacta= nts A
> > and B that proceed to form a single molecule AB via a transition = state
> > AB*, what species do you actually perform the CP correction on? > >
> > I read the following article which contains the following passage= :
> >
> > https://scicomp.stackex= change.com/questions/3/what-is-counterpoise-
> > correction
> >
> > "This correction will depend on the geometries of the reacta= nts. When
> > they are very far from one another, it will be very small: they d= on't
> > influence one another. When they are very close, this effect will= be
> > small, for the same reasoning. It's the intermediate distance= s that
have
> > the largest BSSE. These are the distances at or approaching the > > transition state, which serves as the bottleneck for the reaction= . If
you
> > are not accounting for the artificial improvement near the transi= tion
> > state, then you will get an incorrect approximation of the activa= tion
> > energy, the energy difference between this transition state and t= he
> > separated-reactant limit."
> >
> >
> > This seems to suggest that, to a first approximation, I would onl= y need
> > to CP correct the transition state AB* and can effectively ignore= BSSE
> > for the reactants A and B at infinite distance and for the final =
product
> > AB (i.e. the BSSE only has a small effect on the overall reaction=
> > energy/enthalpy) is this correct.
> >
> >
> > Thanks>
> >
> >
>
> --
> If you think you can, you are right.
>
> --000000000000a2e42d058c6e9ce7
> Content-Type: text/html; charset=3D"UTF-8"
> Content-Transfer-Encoding: quoted-printable
>
> <div dir=3D3D"ltr"><div>Hi,</div><div&g= t;<br></div><div>BSSE comes into
picture =3D
> when you want to calculate the interaction energy of a molecular assem= bly
(=3D
> say XY). Interaction energy of a molecular assembly is defined as
electroni=3D
> c energy of the complete assembly XY (E_XY) minus the sum of the
electronic=3D
>=C2=A0 energies of individual monomer (E_X + E_Y). The problem is, to c= onstruct
t=3D
> he wave function for XY we use more number of basis set functions than=
for =3D
> X or Y. Therefore, the energy difference (E_XY - E_X -E_Y) gets
overestimat=3D
> ed. All the three energies should be calculated using same number numb= er
of=3D
>=C2=A0 basis set functions and that is taken care of by the counterpois= e
method.<=3D
> /div><div><br></div><div>Now in your case, = if you want to find out the
corr=3D
> ect interaction energy of the bio-molecular assembly AB then run CP calcula=3D
> tion on AB to get the BSSE correction (say E_BSSE). So your final
interacti=3D
> on energy should be, E_AB - E_A - E_B + E_BSSE. Similarly if you are <= br> intere=3D
> sted to find out how stable your intermediate (AB)* is, then calculate=
its =3D
> interaction energy as, E_(AB)* - E_A - E_B + E*_BSSE. Here E*_BSSE is = the
c=3D
> orrection energy obtained from the counterpoise calculation performed = on
(A=3D
> B)*.</div><div><br></div><div>Hope this = helps.</div><div><br></div>
<div>Tha=3D
> nks,</div><div>Antarip<br></div></div>&l= t;br><div class=3D3D"gmail_quote"><div
d=3D
> ir=3D3D"ltr" class=3D3D"gmail_attr">On Sat, Jun= 29, 2019 at 5:01 AM Lee Jones
b=3D
> unglinpie[*]<a href=3D3D"http://googlemail.com">googlemail= .com</a> &lt;<a
hre=3D
> f=3D3D"mailto:owner-chemistry]~[ccl.net">owner-chemistry]~[ccl.net</a>&gt;
wrote:=3D
> <br></div><blockquote class=3D3D"gmail_quote"= style=3D3D"margin:0px 0px 0px
0.8=3D
> ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">&l= t;br>
> Sent to CCL by: &quot;Lee=3DC2=3DA0 Jones&quot; [bunglinpie|,|= <a
href=3D3D"http:/=3D
> /googlemail.com" rel=3D3D"noreferrer" target=3D3D"= _blank">googlemail.com</a>]
<b=3D
> r>
> Hi.=3DC2=3DA0 I&#39;m after a little guidance regarding Basis Set =
Superposition=3D
>=C2=A0 Error.<br>
> <br>
> I understand what BSSE is and how to perform a counterpoise correction=
<br>
> using ghost atoms, but my question is a little more fundamental.<br= >
> <br>
> Considering a bimolecular addition reaction where you have reactants A=
<br>
> and B that proceed to form a single molecule AB via a transition state=
<br>
> AB*, what species do you actually perform the CP correction on?<br&= gt;
> <br>
> I read the following article which contains the following passage:<= br>
> <br>
> <a href=3D3D"https://scicomp.stac= kexchange.com/questions/3/what-is-
counterpoi=3D
> se-" rel=3D3D"noreferrer"
target=3D3D"_blank">https://scicomp.stackexchange.com<= /a>=3D
> /questions/3/what-is-counterpoise-</a><br>
> correction<br>
> <br>
> &quot;This correction will depend on the geometries of the reactan= ts.
When =3D
> <br>
> they are very far from one another, it will be very small: they don&am= p;#39;t
<=3D
> br>
> influence one another. When they are very close, this effect will be &= lt;br>
> small, for the same reasoning. It&#39;s the intermediate distances= that
hav=3D
> e <br>
> the largest BSSE. These are the distances at or approaching the <br= >
> transition state, which serves as the bottleneck for the reaction. If = you
<=3D
> br>
> are not accounting for the artificial improvement near the transition =
<br>
> state, then you will get an incorrect approximation of the activation =
<br>
> energy, the energy difference between this transition state and the &l= t;br>
> separated-reactant limit.&quot;<br>
> <br>
> <br>
> This seems to suggest that, to a first approximation, I would only nee= d
<br=3D
> >
> to CP correct the transition state AB* and can effectively ignore BSSE=
<br>
> for the reactants A and B at infinite distance and for the final produ= ct
<b=3D
> r>
> AB (i.e. the BSSE only has a small effect on the overall reaction <= br>
> energy/enthalpy) is this correct.<br>
> <br>
> <br>
> Thanks<br>
> <br>
> <br>
> <br>
> -=3D3D This is automatically added to each message by the mailing scri= pt
=3D3D-=3D
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> --000000000000a2e42d058c6e9ce7--
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