From owner-chemistry %-% at %-% 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-= > > > >
> > E-mail to subscribers: target=3D"_blan= > > k">CHEMISTRY]~[ccl.net or use:
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> >
> > E-mail to administrators: > targ= > > et=3D"_blank">CHEMISTRY-REQUEST]~[ccl.net or use
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> > Before posting, check wait time at: rel=3D"n= > > oreferrer" target=3D"_blank">http://www.ccl.net
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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
> <br<br=3D<br<br>
> <br>
> E-mail to subscribers: <a href=3D3D"mailto:CHEMISTRY]~[ccl.net"
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> <br>
> <br>
> </blockquote></div><br clear=3D3D"all"><= ;br>-- <br><div dir=3D3D"ltr"
class=3D3D"g=3D
> mail_signature">If you think you can, you are right.<br>= </div>
>
> --000000000000a2e42d058c6e9ce7--
>
>



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If you think you can, you are right.
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