*From*: Tobias Kraemer <Tobias.Kraemer===mu.ie>*Subject*: CCL: BSSE Counterpoise correction*Date*: Mon, 1 Jul 2019 14:06:54 +0000

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 <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 <Tobias.Kraemer%x%mu.ie> 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 > > <div dir=3D"ltr"><div>Hi,</div><div><br></div><div>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><div><br></div><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)*.</div><div><br></div><div>Hope this helps.</div><div><br></div> <div>Tha= > nks,</div><div>Antarip<br></div></div><br><div > class=3D"gmail_quote"><div d= > ir=3D"ltr" class=3D"gmail_attr">On Sat, Jun 29, 2019 at 5:01 AM Lee > Jones b= > unglinpie[*]<a href=3D"http://googlemail.com";>googlemail.com</a> > <<a hre= > f=3D"mailto:owner-chemistry]~[ccl.net";>owner-chemistry]~[ccl.net</a>&g > t; wrote:= > <br></div><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px > 0px 0.8= > ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><br> > Sent to CCL by: "Lee=C2=A0 Jones" [bunglinpie|,|<a href=3D"http:/= > /googlemail.com" rel=3D"noreferrer" > target=3D"_blank">googlemail.com</a>] <b= > r> > Hi.=C2=A0 I'm after a little guidance regarding Basis Set Superposition= > 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> > <br> I read the following article which contains the following > passage:<br> <br> <a > 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-</a><br> > correction<br> > <br> > "This correction will depend on the geometries of the reactants. When = > <br> > 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 > <br> small, for the same reasoning. It's the intermediate > distances that hav= > 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 <= > 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 > <br> separated-reactant limit."<br> <br> <br> This seems to > suggest that, to a first approximation, I would only need <br= > > > 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 > product <b= > 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> > -=3D This is automatically added to each message by the mailing script =3D-= > <br<br=<br<br> > <br> > E-mail to subscribers: <a href=3D"mailto:CHEMISTRY]~[ccl.net"; target=3D"_blan= > k">CHEMISTRY]~[ccl.net</a> or use:<br> > =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi- bin/ccl/send_ccl_mes= > sage" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi- bin/ccl/s= > end_ccl_message</a><br> > <br> > E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST]~[ccl.net"; targ= > et=3D"_blank">CHEMISTRY-REQUEST]~[ccl.net</a> or use<br> > =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/cgi- bin/ccl/send_ccl_mes= > sage" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/cgi- bin/ccl/s= > end_ccl_message</a><br> > <br<br> > =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtm= > l" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/sub_un= > sub.shtml</a><br> > <br> > Before posting, check wait time at: <a href=3D"http://www.ccl.net"; rel=3D"n= > oreferrer" target=3D"_blank">http://www.ccl.net</a><br> > <br> > Job: <a href=3D"http://www.ccl.net/jobs"; rel=3D"noreferrer" target=3D"_blan= > k">http://www.ccl.net/jobs</a> <br> > Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe= > rences/" rel=3D"noreferrer" target=3D"_blank">http://server.ccl.net/chemist= > ry/announcements/conferences/</a><br> > <br> > Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh= > tml" rel=3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/sear= > chccl/index.shtml</a><br> > <br<br> > =C2=A0 =C2=A0 =C2=A0 <a href=3D"http://www.ccl.net/spammers.txt"; rel=3D"nor= > eferrer" target=3D"_blank">http://www.ccl.net/spammers.txt</a><br> > <br> > RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/"; rel= > =3D"noreferrer" target=3D"_blank">http://www.ccl.net/chemistry/aboutccl/ins= > tructions/</a><br> > <br> > <br> > </blockquote></div><br clear=3D"all"><br>-- <br><div dir=3D"ltr" class=3D"g= > mail_signature">If you think you can, you are right.<br></div> > > --000000000000a2e42d058c6e9ce7--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp-:-//www.ccl.net/chemistry/sub_unsub.shtmlhttp-:-//www.ccl.net/spammers.txt