From owner-chemistry@ccl.net Fri Dec 15 10:25:00 2023 From: "Belma Nallbani belmagjergjizi^_^gmail.com" To: CCL Subject: CCL:G: Transition State Not Optimized for Neutral Nucleophilic Attacks Message-Id: <-55064-231215101633-18684-JS9b6Y1Q5T3Q76NulgrzjQ]![server.ccl.net> X-Original-From: "Belma Nallbani" Date: Fri, 15 Dec 2023 10:16:32 -0500 Sent to CCL by: "Belma Nallbani" [belmagjergjizi~~gmail.com] Thank you Mr. Ferreira, Incorporating SMD calculations have solved the issue, however, I will consider adding Rydberg functions as well. Best regards, Belma > "Antonio Ferreira amferreira68!A!gmail.com" wrote: > > Sent to CCL by: Antonio Ferreira [amferreira68\a/gmail.com] > --0000000000003dfff5060c7f83b0 > Content-Type: text/plain; charset="UTF-8" > > Have you tried adding Rydberg functions to your basis set? You don't have > many diffuse/long-range functions to allow overlap, which might keep the > lonely pair electrons too local for the TS. > > Antonio M. Ferreira, PhD > > "He who will not risk cannot win." > - John Paul Jones > > I must go down to the seas again, > to the lonely sea and the sky, > And all I ask is a tall ship > And a star to steer her by. > - John Masefield > > > On Thu, Dec 14, 2023, 2:05 PM Belma Nallbani belmagjergjizi^^gmail.com < > owner-chemistry^^^ccl.net> wrote: > > > > > Sent to CCL by: "Belma Nallbani" [belmagjergjizi|*|gmail.com] > > Dear Mr. Shobe, > > > > Thank you very much for your valuable response. I have already optimized > > the TS geometry by > > incorporating SMD calculations. > > > > Best regards, > > Belma > > > > > > > "David Shobe shobedavid^gmail.com" wrote: > > > > > > Sent to CCL by: David Shobe [shobedavid!=!gmail.com] > > > --00000000000090d6af060c6b8fc9 > > > Content-Type: text/plain; charset="UTF-8" > > > > > > Like CH3SH + NH3 --> CH3S- + NH4+? > > > > > > There might not be a transition state in the gas phase. After all, you > > are > > > taking a neutral system and trying to separate charges. Solvation helps > > > that kind of reaction proceed. > > > > > > On Wed, Dec 13, 2023, 2:56 PM Belma Nallbani belmagjergjizi!^!gmail.com > > < > > > owner-chemistry * ccl.net> wrote: > > > > > > > > > > > Sent to CCL by: "Belma Nallbani" [belmagjergjizi\a/gmail.com] > > > > Dear All, > > > > > > > > I am trying to optimize a transition state geometry for amine catalyzed > > > > thiolate formation. I have already optimized the transition state > > geometry > > > > of > > > > Hydrogen transfer from methanethiol to anionic species. Thus, if an > > > > anionic > > > > nucleophile attacks, TS can be optimized for proton transfer, but if a > > > > neutral > > > > nucleophile attacks, I could not optimize the TS geometry. I have done > > my > > > > calculations with Gaussian 16 B.01, M06-2X/6-31+G(d) level of theory. > > > > Thank you in advance for your responses. > > > > > > > > Sincerely, > > > > Belma> > > > > > > > > > > > > > > --00000000000090d6af060c6b8fc9 > > > Content-Type: text/html; charset="UTF-8" > > > Content-Transfer-Encoding: quoted-printable > > > > > >
Like CH3SH + NH3 --> CH3S- + > > NH= > > > 4+?

There might not be a transition > > state = > > > in the gas phase. After all, you are taking a neutral system and trying > > to = > > > separate charges. Solvation helps that kind of reaction > > proceed.

> > v class=3D"gmail_quote">
On Wed, > > Dec 1= > > > 3, 2023, 2:56 PM Belma Nallbani belmagjergjizi!^! > http://gmail.co= > > > m">gmail.com < > ">owner-chemi= > > > stry * ccl.net> wrote:
> class=3D"gmail_quote" styl= > > > e=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
> > > Sent to CCL by: "Belma=C2=A0 Nallbani" [belmagjergjizi\a/ > href= > > > =3D"http://gmail.com" rel=3D"noreferrer noreferrer" > > target=3D"_blank">gmail= > > > .com]
> > > Dear All,
> > >
> > > I am trying to optimize a transition state geometry for amine catalyzed > > > > > > > > thiolate formation. I have already optimized the transition state > > geometry = > > > of
> > > Hydrogen transfer from methanethiol to anionic species. Thus, if an > > anionic= > > >
> > > nucleophile attacks, TS can be optimized for proton transfer, but if a > > neut= > > > ral
> > > nucleophile attacks, I could not optimize the TS geometry. I have done > > my <= > > > br> > > > calculations with Gaussian 16 B.01, M06-2X/6-31+G(d) level of theory.
> > > Thank you in advance for your responses.
> > >
> > > Sincerely,
> > > Belma
> > >
> > >
> > >
> > > -=3D This is automatically added to each message by the mailing script > > =3D-= > > > > > >
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> > > > > > --00000000000090d6af060c6b8fc9--> > > > > > > --0000000000003dfff5060c7f83b0 > Content-Type: text/html; charset="UTF-8" > Content-Transfer-Encoding: quoted-printable > >
Have you tried adding Rydberg functions to your basi= > s set?=C2=A0 You don't have many diffuse/long-range functions to allow = > overlap, which might keep the lonely pair electrons too local for the TS. div>

Antonio M. Ferre= > ira, PhD

=C2=A0"He who will not risk cannot win."
=C2= > =A0=C2=A0=C2=A0=C2=A0 - John Paul Jones

=C2=A0I must go down to the = > seas again,
to the lonely sea and the sky,
And all I ask is a tall sh= > ip
And a star to steer her by.
=C2=A0=C2=A0=C2=A0=C2=A0 - John Masefi= > eld
=C2=A0=C2=A0=C2=A0

ir=3D"ltr" class=3D"gmail_attr">On Thu, Dec 14, 2023, 2:05 PM Belma Nallban= > i belmagjergjizi^^gmail.com < "mailto:owner-chemistry^^^ccl.net">owner-chemistry^^^ccl.net> wrote:
= >
eft:1px #ccc solid;padding-left:1ex">
> Sent to CCL by: "Belma=C2=A0 Nallbani" [belmagjergjizi|*| =3D"http://gmail.com" rel=3D"noreferrer noreferrer" target=3D"_blank">gmail= > .com]
> Dear Mr. Shobe,
>
> Thank you very much for your valuable response. I have already optimized th= > e TS geometry by
> incorporating SMD calculations.
>
> Best regards,
> Belma
>
>
> > "David Shobe shobedavid^ errer noreferrer" target=3D"_blank">gmail.com"=C2=A0 wrote:
> >
> > Sent to CCL by: David Shobe [shobedavid!=3D! m" rel=3D"noreferrer noreferrer" target=3D"_blank">gmail.com]
> > --00000000000090d6af060c6b8fc9
> > Content-Type: text/plain; charset=3D"UTF-8"
> >
> > Like CH3SH + NH3 --> CH3S- + NH4+?
> >
> > There might not be a transition state in the gas phase. After all, you= > are
> > taking a neutral system and trying to separate charges. Solvation help= > s
> > that kind of reaction proceed.
> >
> > On Wed, Dec 13, 2023, 2:56 PM Belma Nallbani belmagjergjizi!^! =3D"http://gmail.com" rel=3D"noreferrer noreferrer" target=3D"_blank">gmail= > .com <
> > owner-chemistry * rer" target=3D"_blank">ccl.net> wrote:
> >
> > >
> > > Sent to CCL by: "Belma=C2=A0 Nallbani" [belmagjergjizi\= > a/ nk">gmail.com]
> > > Dear All,
> > >
> > > I am trying to optimize a transition state geometry for amine cat= > alyzed
> > > thiolate formation. I have already optimized the transition state= > geometry
> > > of
> > > Hydrogen transfer from methanethiol to anionic species. Thus, if = > an
> > > anionic
> > > nucleophile attacks, TS can be optimized for proton transfer, but= > if a
> > > neutral
> > > nucleophile attacks, I could not optimize the TS geometry. I have= > done my
> > > calculations with Gaussian 16 B.01, M06-2X/6-31+G(d) level of the= > ory.
> > > Thank you in advance for your responses.
> > >
> > > Sincerely,
> > > Belma>
> > >
> > >
> >
> > --00000000000090d6af060c6b8fc9
> > Content-Type: text/html; charset=3D"UTF-8"
> > Content-Transfer-Encoding: quoted-printable
> >
> > <div dir=3D3D"auto"><div><div dir=3D3D"a= > uto">Like CH3SH + NH3 --&gt; CH3S- + NH=3D
> > 4+?</div><div dir=3D3D"auto"><br></div&= > gt;There might not be a transition state =3D
> > in the gas phase. After all, you are taking a neutral system and tryin= > g to =3D
> > separate charges. Solvation helps that kind of reaction proceed.<br= > ><br><di=3D
> > v class=3D3D"gmail_quote"><div dir=3D3D"ltr"= > class=3D3D"gmail_attr">On Wed, Dec 1=3D
> > 3, 2023, 2:56 PM Belma Nallbani belmagjergjizi!^!<a href=3D3D"= > >http://gmail.co=3D
> > m"> target=3D"_blank">gmail.com</a> &lt;<a href=3D3D"mail= > to:= > owner-chemistry * er" target=3D"_blank">ccl.net">owner-chemi=3D
> > stry * =3D"_blank">ccl.net</a>&gt; wrote:<br></div><b= > lockquote class=3D3D"gmail_quote" styl=3D
> > e=3D3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:= > 1ex"><br>
> > Sent to CCL by: &quot;Belma=3DC2=3DA0 Nallbani&quot; [belmagje= > rgjizi\a/<a href=3D
> > =3D3D" target=3D"_blank">http://gmail.com" rel=3D3D"noreferrer noref= > errer" target=3D3D"_blank">gmail=3D
> > .com</a>]<br>
> > Dear All,<br>
> > <br>
> > I am trying to optimize a transition state geometry for amine catalyze= > d <br=3D
> > >
> > thiolate formation. I have already optimized the transition state geom= > etry =3D
> > of <br>
> > Hydrogen transfer from methanethiol to anionic species. Thus, if an an= > ionic=3D
> >=C2=A0 <br>
> > nucleophile attacks, TS can be optimized for proton transfer, but if a= > neut=3D
> > ral <br>
> > nucleophile attacks, I could not optimize the TS geometry. I have done= > my <=3D
> > br>
> > calculations with Gaussian 16 B.01, M06-2X/6-31+G(d) level of theory.&= > lt;br>
> > Thank you in advance for your responses.<br>
> > <br>
> > Sincerely,<br>
> > Belma<br>
> > <br>
> > <br>
> > <br>
> > -=3D3D This is automatically added to each message by the mailing scri= > pt =3D3D-=3D
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> > --00000000000090d6af060c6b8fc9--
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