From owner-chemistry@ccl.net Thu Dec 14 12:38:00 2023 From: "Belma Nallbani belmagjergjizi^^gmail.com" To: CCL Subject: CCL:G: Transition State Not Optimized for Neutral Nucleophilic Attacks Message-Id: <-55062-231214123601-7591-ccJjf5hqMvIjVPZk7weT9Q]~[server.ccl.net> X-Original-From: "Belma Nallbani" Date: Thu, 14 Dec 2023 12:36:00 -0500 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!^! m">gmail.com <owner-chemi= > stry * ccl.net> wrote:
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/ =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
>
>
>
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> > --00000000000090d6af060c6b8fc9-- > > From owner-chemistry@ccl.net Thu Dec 14 19:37:01 2023 From: "Antonio Ferreira amferreira68!A!gmail.com" To: CCL Subject: CCL:G: Transition State Not Optimized for Neutral Nucleophilic Attacks Message-Id: <-55063-231214170753-20396-MViIdhx4uG6AFGQWrhHVkw- -server.ccl.net> X-Original-From: Antonio Ferreira Content-Type: multipart/alternative; boundary="0000000000003dfff5060c7f83b0" Date: Thu, 14 Dec 2023 17:07:30 -0500 MIME-Version: 1.0 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.

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

On Thu, Dec 14, 2023, 2:05 PM Belma Nallban= i belmagjergjizi^^gmail.com <owner-chemistry^^^ccl.net> wrote:
=

Sent to CCL by: "Belma=C2=A0 Nallbani" [belmagjergjizi|*|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^gmail.com"=C2=A0 wrote:
>
> Sent to CCL by: David Shobe [shobedavid!=3D!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!^!gmail= .com <
> owner-chemistry * ccl.net> wrote:
>
> >
> > Sent to CCL by: "Belma=C2=A0 Nallbani" [belmagjergjizi\= a/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">gmail.com</a> &lt;<a href=3D3D"mail= to:= owner-chemistry * ccl.net">owner-chemi=3D
> stry * 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"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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