From owner-chemistry@ccl.net Thu Sep 1 05:58:00 2022 From: "Bjoern Sommer bjoern[a]cellmicrocosmos.org" To: CCL Subject: CCL: DESIGN X BIOINFORMATICS workshop 09.09.2022, 1 pm Message-Id: <-54790-220901054344-17176-ZJlsyfeNbMsydqnUonUZig=-=server.ccl.net> X-Original-From: Bjoern Sommer Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 1 Sep 2022 10:43:17 +0100 MIME-Version: 1.0 Sent to CCL by: Bjoern Sommer [bjoern,,cellmicrocosmos.org] Dear all! We would like to invite you to the DESIGN X BIOINFORMATICS workshop which will happen on Friday, 9th September 2022, 1-5 pm (UK time) in a hybrid format. http://desxbioinf.i2d.uk/ There will be in-person events at the Royal College of Art (School of Design) in London and at the CNRS (IBPC) in Paris and a Zoom session. Registration is required, but free of charge! In-person places are limited - first come, first serve! Register NOW for free: https://www.eventbrite.com/e/design-x-bioinformatics-tickets-406083385337 If you think about Bioinformatics, probably not the first thing which comes to your mind is design, right? And vice versa. But wait - what about illustration - and visualization? Is this the same as design? What about network layouts? What about colors when visualizing microscopic structures? What about dynamics in simulations? What about pioneers like David Goodsell - combining the world of science and illustration while pushing the boundaries forward  like only very few did in biomedical history (1st KEYNOTE)? And the other way around, what implications might have approaches from the design world on Bioinformatics? What about the exciting work from people like Daria Jelonek from Studio Above&Below - designing and executing exhibitions - often data-driven and utilizing Augmented Reality technology - at renowned places in e.g. Hong Kong, Seoul, Wrocław, Milano, Berlin, and of course London (2nd KEYNOTE)? We will explore these questions in two sessions: * Bioinformatics 2 Design: A presentation session based on the just published DESIGN X BIOINFORMATICS special issue in the Journal of Integrative Bioinformatics. * Design 2 Bioinformatics: A hybrid interactive workshop session discussing future perspectives of DESIGN X BIOINFORMATICS based on the previous talks by using design methods! Registration Deadline: Wednesday, 7th September (midnight UK time) https://www.eventbrite.com/e/design-x-bioinformatics-tickets-406083385337 More info you can find here: http://desxbioinf.i2d.uk/ This workshop was made possible through a collaboration between the Royal College of Art (London), CNRS (Paris), and Kyushu University (Fukuoka)! We are looking forward to seeing you online or in-person! Bjorn, Daisuke, Marc & Louis From owner-chemistry@ccl.net Thu Sep 1 11:24:01 2022 From: "David Shobe shobedavid===gmail.com" To: CCL Subject: CCL: vinyl group twist Message-Id: <-54791-220901093052-32334-zvc/0W50e3k0kb9hUXh1FA_._server.ccl.net> X-Original-From: David Shobe Content-Type: multipart/alternative; boundary="000000000000adba5705e79d9e33" Date: Thu, 1 Sep 2022 08:30:28 -0500 MIME-Version: 1.0 Sent to CCL by: David Shobe [shobedavid^-^gmail.com] --000000000000adba5705e79d9e33 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Detlev-- I think you are correct about the triplet state being the lowest electronic state in twisted vinyl-X compounds, but would the reaction really proceed through *two* intersystem crossings (singlet to triplet then back to singlet)? --David Shobe On Mon, Aug 29, 2022, 4:09 PM Detlev Conrad Mielczarek detlevcm{:} googlemail.com wrote: > > Sent to CCL by: Detlev Conrad Mielczarek [detlevcm%googlemail.com] > If you are twisting through a double bond, I would expect at least one of > the bonds to break (forming. Asingle bond) and see the transition progres= s > from a singlet through a triplet state before reforming the double bond a= nd > becoming s singlet again. > (The ORCA manual contains an example of twisting an ethene molecule.) > > In this case, you would need to ideally treat this with a multi-reference > method such as CASSCF. > > Running a transition state search in a single multiplicity will invariabl= y > lead to incorrect results in such cases, even if some methods seem to wor= k > through them. > > You may be able to use two separate calculations to obtain a valid energy > value for the transition state. > > Detlev > > > > > Original Message > > > > From: owner-chemistry++ccl.net > Sent: 29 August 2022 21:21 > To: detlevcm++googlemail.com > Reply to: chemistry++ccl.net > Subject: CCL: vinyl group twist > > > CCL group-- > > > I am trying to find transition states for twisting the double bonds in > vinyl-X compounds (X is any group, not necessarily halogen), with the > torsion angle going from 0=C2=B0 to 180=C2=B0, through a transition state= that should > have a torsion angle of approximately 90=C2=B0. Of course, I expect these= to be > high-energy transition states. I have tried both opt=3Dts with a few valu= es > of X, and once tried opt=3Dqst3. > > > > The opt=3Dqst3 method generated something weird, in which the vinyl group > had a linear H-C=3DC angle (instead of 120=C2=B0). The other distal H on = the > vinyl's methylene group had a H-C=3DC angle of 96=C2=B0 It is a transiti= on state > (1 imag freq), but definitely not the one I am looking for. > > > Using opt=3D(usually along with noeigentest), I invariably end up with a > much-lower-energy transition state involving torsion of the vinyl group a= s > a whole in the vinyl-X molecule, or with a torsion of some subgroup withi= n > X. > > > Is it normal for attempts to calculate a high-energy transition state to > end up with a different, lower-energy transition state? More importantly, > is there any way to avoid this phenomenon and get the desired transition > state? > > > --David Shobe > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000000000000adba5705e79d9e33 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Detlev--

I think you are correct about the triplet state being = the lowest electronic state in twisted vinyl-X compounds, but would the rea= ction really proceed through *two* intersystem crossings (singlet to triple= t then back to singlet)?

--David Shobe=C2=A0

On Mon, Aug 29, 2022, 4:09 PM Detlev Conrad Mielczarek = detlevcm{:}googlemail.com <owner-chemistry..ccl.net> wrote:

Sent to CCL by: Detlev Conrad Mielczarek [detlevcm%google= mail.com]
If you are twisting through a double bond, I would expect at least one of t= he bonds to break (forming. Asingle bond) and see the transition progress f= rom a singlet through a triplet state before reforming the double bond and = becoming s singlet again.
(The ORCA manual contains an example of twisting an ethene molecule.)

In this case, you would need to ideally treat this with a multi-reference m= ethod such as CASSCF.

Running a transition state search in a single multiplicity will invariably = lead to incorrect results in such cases, even if some methods seem to work = through them.

You may be able to use two separate calculations to obtain a valid energy v= alue for the transition state.

Detlev




=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Original Message =C2=A0=C2=A0 =C2=A0

> From: owner-chemistry++ccl.net
Sent: 29 August 2022 21:21
To: detlevcm++googlemail.com
Reply to: chemistry++ccl.net
Subject: CCL: vinyl group twist


CCL group--


I am trying to find transition states for twisting the double bonds in viny= l-X compounds (X is any group, not necessarily halogen), with the torsion a= ngle going from 0=C2=B0 to 180=C2=B0, through a transition state that shoul= d have a torsion angle of approximately 90=C2=B0. Of course, I expect these= to be high-energy transition states. I have tried both opt=3Dts with a few= values of X, and once tried opt=3Dqst3.



The opt=3Dqst3 method generated something weird, in which the vinyl group h= ad a linear H-C=3DC angle (instead of 120=C2=B0). The other distal H on the= vinyl's methylene group had a H-C=3DC angle of=C2=A096=C2=B0=C2=A0 It = is a transition state (1 imag freq), but definitely not the one I am lookin= g for.


Using opt=3D(usually along with noeigentest), I invariably end up with a mu= ch-lower-energy transition state involving torsion of the vinyl group as a = whole in the vinyl-X molecule, or with a torsion of some subgroup within X.=


Is it normal for attempts to calculate a high-energy transition state to en= d up with a different, lower-energy transition state? More importantly, is = there any way to avoid this phenomenon and get the desired transition state= ?


--David Shobe



-=3D This is automatically added to each message by the mailing script =3D-=
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--000000000000adba5705e79d9e33-- From owner-chemistry@ccl.net Thu Sep 1 20:03:00 2022 From: "Detlev Conrad Mielczarek detlevcm]~[googlemail.com" To: CCL Subject: CCL: vinyl group twist Message-Id: <-54792-220901134616-13816-TcJFuqP0PcSvU/lz8Qz/Xw++server.ccl.net> X-Original-From: Detlev Conrad Mielczarek Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 1 Sep 2022 19:45:55 +0200 MIME-Version: 1.0 Sent to CCL by: Detlev Conrad Mielczarek [detlevcm .. googlemail.com] Good evening David. There really is no good alternative to breaking at least one of the bonds. Or if you didn't, you would end up with orbitals in an "x configuration" crossing each other's paths. Now you could consider breaking both bonds and going through a quintet state, but the energy barrier for such a transition should be much higher. Crossing from singlet to triplet and then back from triplet to singlet does not cause any problems. Breaking the bond initially will require an energy input. However, reforming the bond will liberate energy. - This bond formation also resembles a free radical termination in some ways which is generally considered to be barrierless. As a result, you really have an energy barrier/opposition to twisting the molecule and breaking the initial bond, while then continuing the rotation and reforming the bond will bring you back to the original lowest energy ground state. Incidentally, there is a lot of literature on this, such as for example: sciencedirect.com/topics/chemistry/bond-rotation I couldn't find anything on halogen bond rotation, but a quick google search turned up the following on bond dissociation energies, which should give you a good idea of the relative strengths of these bonds. Are carbon—halogen double and triple bonds possible? Robert Kalescky, Elfi Kraka, Dieter Cremer 27 February 2014 International Journal of Quantum Chemistry 10.1002/qua.24626 Detlev On Thu, 1 Sept 2022 at 18:25, David Shobe shobedavid===gmail.com wrote: > > Detlev-- > > I think you are correct about the triplet state being the lowest electronic state in twisted vinyl-X compounds, but would the reaction really proceed through *two* intersystem crossings (singlet to triplet then back to singlet)? > > --David Shobe > > On Mon, Aug 29, 2022, 4:09 PM Detlev Conrad Mielczarek detlevcm{:}googlemail.com wrote: >> >> >> Sent to CCL by: Detlev Conrad Mielczarek [detlevcm%googlemail.com] >> If you are twisting through a double bond, I would expect at least one of the bonds to break (forming. Asingle bond) and see the transition progress from a singlet through a triplet state before reforming the double bond and becoming s singlet again. >> (The ORCA manual contains an example of twisting an ethene molecule.) >> >> In this case, you would need to ideally treat this with a multi-reference method such as CASSCF. >> >> Running a transition state search in a single multiplicity will invariably lead to incorrect results in such cases, even if some methods seem to work through them. >> >> You may be able to use two separate calculations to obtain a valid energy value for the transition state. >> >> Detlev >> >> >> >> >> Original Message >> >> >> > From: owner-chemistry++ccl.net >> Sent: 29 August 2022 21:21 >> To: detlevcm++googlemail.com >> Reply to: chemistry++ccl.net >> Subject: CCL: vinyl group twist >> >> >> CCL group-- >> >> >> I am trying to find transition states for twisting the double bonds in vinyl-X compounds (X is any group, not necessarily halogen), with the torsion angle going from 0° to 180°, through a transition state that should have a torsion angle of approximately 90°. Of course, I expect these to be high-energy transition states. I have tried both opt=ts with a few values of X, and once tried opt=qst3. >> >> >> >> The opt=qst3 method generated something weird, in which the vinyl group had a linear H-C=C angle (instead of 120°). The other distal H on the vinyl's methylene group had a H-C=C angle of 96° It is a transition state (1 imag freq), but definitely not the one I am looking for. >> >> >> Using opt=(usually along with noeigentest), I invariably end up with a much-lower-energy transition state involving torsion of the vinyl group as a whole in the vinyl-X molecule, or with a torsion of some subgroup within X. >> >> >> Is it normal for attempts to calculate a high-energy transition state to end up with a different, lower-energy transition state? More importantly, is there any way to avoid this phenomenon and get the desired transition state? >> >> >> --David Shobe>> E-mail to subscribers: CHEMISTRY++ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use>> >> -- Detlev Conrad Mielczarek émail privé: detlevcm(-)googlemail.com téléphone: 0033 (0)648 151 995 From owner-chemistry@ccl.net Thu Sep 1 20:38:00 2022 From: "Soren Eustis soreneustis^gmail.com" To: CCL Subject: CCL: vinyl group twist Message-Id: <-54793-220901144652-18020-W95uO13H1U65NQryu5/i8Q]^[server.ccl.net> X-Original-From: Soren Eustis Content-Type: multipart/alternative; boundary="6310fe0d_66ef438d_bf89" Date: Thu, 1 Sep 2022 14:46:32 -0400 MIME-Version: 1.0 Sent to CCL by: Soren Eustis [soreneustis(!)gmail.com] --6310fe0d_66ef438d_bf89 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline David, =C2=A0=C2=A0I sense you are correct here.=C2=A0=C2=A0I think this is a ca= se of you can't get there from here... As my dad would say.=C2=A0=C2=A0Wh= ile the triplet state may be the lowest energy isolated structure with on= e of the bonds broken, that does not mean that is part of this process.=C2= =A0=C2=A0I would bet you actually have a singlet diradical that may need = a spin-flip treatment. Soren On Sep 1, 2022, 12:19 -0400, David Shobe shobedavid=3D=3D=3Dgmail.com , wrote: > Detlev-- > > I think you are correct about the triplet state being the lowest electr= onic state in twisted vinyl-X compounds, but would the reaction really pr= oceed through *two* intersystem crossings (singlet to triplet then back t= o singlet)=3F > > --David Shobe > > > On Mon, Aug 29, 2022, 4:09 PM Detlev Conrad Mielczarek detlevcm=7B:=7D= googlemail.com wrote: > > > > > > Sent to CCL by: Detlev Conrad Mielczarek =5Bdetlevcm%googlemail.com= =5D > > > If you are twisting through a double bond, I would expect at least = one of the bonds to break (forming. Asingle bond) and see the transition = progress from a singlet through a triplet state before reforming the doub= le bond and becoming s singlet again. > > > (The ORCA manual contains an example of twisting an ethene molecule= .) > > > > > > In this case, you would need to ideally treat this with a multi-ref= erence method such as CASSC=46. > > > > > > Running a transition state search in a single multiplicity will inv= ariably lead to incorrect results in such cases, even if some methods see= m to work through them. > > > > > > You may be able to use two separate calculations to obtain a valid = energy value for the transition state. > > > > > > Detlev > > > > > > > > > > > > > > > =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Original Message > > > > > > > > > > =46rom: owner-chemistry++ccl.net > > > Sent: 29 August 2022 21:21 > > > To: detlevcm++googlemail.com > > > Reply to: chemistry++ccl.net > > > Subject: CCL: vinyl group twist > > > > > > > > > CCL group-- > > > > > > > > > I am trying to find transition states for twisting the double bonds= in vinyl-X compounds (X is any group, not necessarily halogen), with the= torsion angle going from 0=C2=B0 to 180=C2=B0, through a transition stat= e that should have a torsion angle of approximately 90=C2=B0. Of course, = I expect these to be high-energy transition states. I have tried both opt= =3Dts with a few values of X, and once tried opt=3Dqst3. > > > > > > > > > > > > The opt=3Dqst3 method generated something weird, in which the vinyl= group had a linear H-C=3DC angle (instead of 120=C2=B0). The other dista= l H on the vinyl's methylene group had a H-C=3DC angle of=C2=A096=C2=B0=C2= =A0 It is a transition state (1 imag freq), but definitely not the one I = am looking for. > > > > > > > > > Using opt=3D(usually along with noeigentest), I invariably end up w= ith a much-lower-energy transition state involving torsion of the vinyl g= roup as a whole in the vinyl-X molecule, or with a torsion of some subgro= up within X. > > > > > > > > > Is it normal for attempts to calculate a high-energy transition sta= te to end up with a different, lower-energy transition state=3F More impo= rtantly, is there any way to avoid this phenomenon and get the desired tr= ansition state=3F > > > > > > > > > --David Shobe > > > > > > > > > > > > -=3D This is automatically added to each message by the mailing scr= ipt =3D- > > > > > > E-mail to subscribers: CHEMISTRY++ccl.net or use: > > > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fme= ssage > > > > > > E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use > > > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fme= ssage > > > > > > =C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub=5Funsub.shtml=> > > Conferences: http://server.ccl.net/chemistry/announcements/conferen= ces/= > > > > > > =C2=A0 =C2=A0 =C2=A0> > > > > > RT=46I: http://www.ccl.net/chemistry/aboutccl/instructions/ > > > > > > --6310fe0d_66ef438d_bf89 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
David,

&=23160;&=23160;I sense you are correct here.&=23160;&=23160;I think this= is a case of you can't get there from here... As my dad would say.&=2316= 0;&=23160;While the triplet state may be the lowest energy isolated struc= ture with one of the bonds broken, that does not mean that is part of thi= s process.&=23160;&=23160;I would bet you actually have a singlet diradic= al that may need a spin-flip treatment.&=23160;&=23160;

Soren
On Sep 1, 2022, 12:19 -0400, David = Shobe shobedavid=3D=3D=3Dgmail.com <owner-chemistry=40ccl.net>, wro= te:
Detlev--

I think you are correct about the triplet state bei= ng the lowest electronic state in twisted vinyl-X compounds, but would th= e reaction really proceed through *two* intersystem crossings (singlet to= triplet then back to singlet)=3F

--David Shobe&=23160;

On Mon, Aug 29, 2022, 4:0= 9 PM Detlev Conrad Mielczarek detlevcm=7B:=7Dgooglemail.com <owner-chemistry++ccl.net> wrote:

Sent to CCL by: Detlev Conrad Mielczarek =5Bdetlevcm%googlemail.com=5D
If you are twisting through a double bond, I would expect at least one of= the bonds to break (forming. Asingle bond) and see the transition progre= ss from a singlet through a triplet state before reforming the double bon= d and becoming s singlet again.
(The ORCA manual contains an example of twisting an ethene molecule.)

In this case, you would need to ideally treat this with a multi-reference= method such as CASSC=46.

Running a transition state search in a single multiplicity will invariabl= y lead to incorrect results in such cases, even if some methods seem to w= ork through them.

You may be able to use two separate calculations to obtain a valid energy= value for the transition state.

Detlev




&=23160; &=23160; &=23160; &=23160; &=23160; Original Message &=23160;&=23= 160; &=23160;


> =46rom: owner-chemistry++ccl.net
Sent: 29 August 2022 21:21
To: detlevcm++googlemail.com
Reply to: chemistry++ccl.net
Subject: CCL: vinyl group twist


CCL group--


I am trying to find transition states for twisting the double bonds in vi= nyl-X compounds (X is any group, not necessarily halogen), with the torsi= on angle going from 0=C2=B0 to 180=C2=B0, through a transition state that= should have a torsion angle of approximately 90=C2=B0. Of course, I expe= ct these to be high-energy transition states. I have tried both opt=3Dts = with a few values of X, and once tried opt=3Dqst3.



The opt=3Dqst3 method generated something weird, in which the vinyl group= had a linear H-C=3DC angle (instead of 120=C2=B0). The other distal H on= the vinyl's methylene group had a H-C=3DC angle of&=23160;96=C2=B0&=2316= 0; It is a transition state (1 imag freq), but definitely not the one I a= m looking for.


Using opt=3D(usually along with noeigentest), I invariably end up with a = much-lower-energy transition state involving torsion of the vinyl group a= s a whole in the vinyl-X molecule, or with a torsion of some subgroup wit= hin X.


Is it normal for attempts to calculate a high-energy transition state to = end up with a different, lower-energy transition state=3F More importantl= y, is there any way to avoid this phenomenon and get the desired transiti= on state=3F


--David Shobe



-=3D This is automatically added to each message by the mailing script =3D= -

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