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

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
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
> Sent to CCL by: &quot;Lee=3DC2=3DA0 Jones&quot; [bunglinpie|,|= <a
href=3D3D"http:/=3D
<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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