From owner-chemistry@ccl.net Thu Oct 8 11:55:01 2015 From: "Fredrick Mutunga fredrick.mutunga++gmail.com" To: CCL Subject: CCL: Potential energy surface with ZPEs appended Message-Id: <-51807-151008115419-1600-qF3qK1u6hfjICkLJp+iYyw/./server.ccl.net> X-Original-From: Fredrick Mutunga Content-Type: multipart/alternative; boundary=089e013d0bbae3d342052199df90 Date: Thu, 8 Oct 2015 09:54:13 -0600 MIME-Version: 1.0 Sent to CCL by: Fredrick Mutunga [fredrick.mutunga#gmail.com] --089e013d0bbae3d342052199df90 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Victor, I know all these details. I also know how to scan for PES and how to get IRC. I am trying to develop a PES using single point energy computed for points along the IRC using high level method CCSD(T)/aug-cc-pVTZ and ZPEs calculated using B3LYP/6-311++G(d,p). I am wondering how I should add ZPEs to these single point energies! Should I add to the stationary points only or is there another way? There are a couple of papers out there but they just mention appended ZPEs so it's not clear how they have done it. Fred On Wed, Oct 7, 2015 at 6:18 PM, V=C3=ADctor Lua=C3=B1a Cabal victor . fluor.quimica.uniovi.es wrote: > > Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor* > fluor.quimica.uniovi.es] > On Wed, Oct 07, 2015 at 05:05:35PM -0600, Fredrick Mutunga > fredrick.mutunga++gmail.com wrote: > > I have computed single point energies along the potential energy surfac= e > > using CCSD(T). I also have DFT calculated ZPEs for the stationary point= s > > (this is an isomerization reaction cis-A ->trans-A) how do I append Zer= o > > point energies to generate more accurate PES? > > Frdederik, > > Remember what the ZPE are. Check Wilson-Decius-Cross, Molecular > vibrations if you are in doubt. > > As for a method you need the vibration energies of your molecule. Use > python or whatever script language you prefer. Is just enough. > > For stationary points all your frequencies should be positive escept > the translations and rotation modes that you will identify quite close > to zero. For a transition state in your PES one more of the modes will > be the one corresponding to the reaction coordinate and the normal > constant will be negative, so the frequency clearly imaginary (except > that most electronic structure software does not use complex arithmetic > and it says negative frequencies). > > Good luck, > Dr. V=C3=ADctor Lua=C3=B1a > -- > . . "In science a person can be convinced by a good argument. > / `' \ That is almost impossible in politics or religion" > /(o)(o)\ (Adapted from Carl Sagan) > /`. \/ .'\ "Lo mediocre es peor que lo bueno, pero tambi=C3=A9n es peo= r > / '`'` \ que lo malo, porque la mediocridad no es un grado, es una > | \'`'`/ | actitud" -- Jorge Wasenberg, 2015 > | |'`'`| | (Mediocre is worse than good, but it is also worse than > \/`'`'`'\/ bad, because mediocrity is not a grade, it is an attitude) > =3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > ! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"I have two kinds= of > problems, > ! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! the urgent = and the > important. > ! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not > important, > ! e-mail: victor(_)fluor.quimica.uniovi.es ! and the important are > never > ! phone: +34-985-103491 fax: +34-985-103125 ! urgent. > +--------------------------------------------+ (Dwight D. > Eisenhower) > GroupPage : http://azufre.quimica.uniovi.es/ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --089e013d0bbae3d342052199df90 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Victor,

I know all these details. I= also know how to scan for PES and how to get IRC. I am trying to develop a= PES using single point energy computed for points along the IRC using=C2= =A0 high level method CCSD(T)/aug-cc-pVTZ and ZPEs calculated using B3LYP/6= -311++G(d,p). I am wondering how I should add ZPEs to these single point en= ergies! Should I add to the stationary points only or is there another way?= There are a couple of papers out there but they just mention appended ZPEs= so it's not clear how they have done it.

Fred

On Wed, Oct 7, 2015= at 6:18 PM, V=C3=ADctor Lua=C3=B1a Cabal victor . fluor.quimica.uniovi.es <owner-chemistry**ccl.= net> wrote:

Sent to CCL by: =3D?iso-8859-1?Q?V=3DEDctor_Lua=3DF1a?=3D Cabal [victor*fluor.quimica.uniovi.es]
On Wed, Oct 07, 2015 at 05:05:35PM -0600, Fredrick Mutunga= fredrick.mutunga++gmail.com wrote:
> I have computed single point energies along the potential energy surfa= ce
> using CCSD(T). I also have DFT calculated ZPEs for the stationary poin= ts
> (this is an isomerization reaction cis-A ->trans-A) how do I append= Zero
> point energies to generate more accurate PES?

Frdederik,

Remember what the ZPE are. Check Wilson-Decius-Cross, Molecular
vibrations if you are in doubt.

As for a method you need the vibration energies of your molecule. Use
python or whatever script language you prefer. Is just enough.

For stationary points all your frequencies should be positive escept
the translations and rotation modes that you will identify quite close
to zero. For a transition state in your PES one more of the modes will
be the one corresponding to the reaction coordinate and the normal
constant will be negative, so the frequency clearly imaginary (except
that most electronic structure software does not use complex arithmetic
and it says negative frequencies).

Good luck,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Dr. V=C3=ADctor Lua=C3=B1a
--
=C2=A0 =C2=A0 =C2=A0.=C2=A0 .=C2=A0 =C2=A0 "In science a person can be= convinced by a good argument.
=C2=A0 =C2=A0 / `' \=C2=A0 =C2=A0That is almost impossible in politics = or religion"
=C2=A0 =C2=A0/(o)(o)\=C2=A0 (Adapted from Carl Sagan)
=C2=A0 /`. \/ .'\=C2=A0 "Lo mediocre es peor que lo bueno, pero ta= mbi=C3=A9n es peor
=C2=A0/=C2=A0 =C2=A0'`'`=C2=A0 =C2=A0\ que lo malo, porque la medio= cridad no es un grado, es una
=C2=A0|=C2=A0 \'`'`/=C2=A0 | actitud" -- Jorge Wasenberg, 2015=
=C2=A0|=C2=A0 |'`'`|=C2=A0 | (Mediocre is worse than good, but it i= s also worse than
=C2=A0 \/`'`'`'\/=C2=A0 bad, because mediocrity is not a grade,= it is an attitude)
=3D=3D=3D(((=3D=3D)))=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D+=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
! Dr.V=C3=ADctor Lua=C3=B1a, in silico chemist & prof. !"I have tw= o kinds of problems,
! Departamento de Qu=C3=ADmica F=C3=ADsica y Anal=C3=ADtica ! the urgent an= d the important.
! Universidad de Oviedo, 33006-Oviedo, Spain ! The urgent are not important= ,
! e-mail:=C2=A0 =C2=A0victor(_)fluor.quimica.uniovi.es=C2=A0 =C2= =A0! and the important are never
! phone: +34-985-10= 3491=C2=A0 fax: +34-985-103125 ! urgent.
+--------------------------------------------+=C2=A0 =C2=A0 =C2=A0 =C2=A0 (= Dwight D. Eisenhower)
=C2=A0GroupPage : http://azufre.quimica.uniovi.es/



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY**ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST**ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/



--089e013d0bbae3d342052199df90--