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-= > >
> E-mail to subscribers: k">CHEMISTRY]~[ccl.net or use:
> =C2=A0 =C2=A0 =C2=A0 sage" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi- bin/ccl/s= > end_ccl_message
>
> E-mail to administrators: et=3D"_blank">CHEMISTRY-REQUEST]~[ccl.net or use
> =C2=A0 =C2=A0 =C2=A0 sage" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi- bin/ccl/s= > end_ccl_message
> > =C2=A0 =C2=A0 =C2=A0 l" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/sub_un= > sub.shtml
>
> Before posting, check wait time at: oreferrer" target=3D"_blank">http://www.ccl.net
>
> Job: k">http://www.ccl.net/jobs
> Conferences: rences/" rel=3D"noreferrer" target=3D"_blank">http://server.ccl.net/chemist= > ry/announcements/conferences/
>
> Search Messages: tml" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/sear= > chccl/index.shtml
> > =C2=A0 =C2=A0 =C2=A0 eferrer" target=3D"_blank">http://www.ccl.net/spammers.txt
>
> RTFI: =3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/aboutccl/ins= > tructions/
>
>
>


--
mail_signature">If you think you can, you are right.
> > --000000000000a2e42d058c6e9ce7-- > >