From owner-chemistry@ccl.net Fri Jun 10 07:57:00 2011
From: "Krishna Kuben Govender kk.govender]|[gmail.com" <owner-chemistry a server.ccl.net>
To: CCL
Subject: CCL: Parameterization of semi-empirical methods
Message-Id: <-44874-110610075557-26262-GsHsO4tbpoyhlrEOqGZcxw a server.ccl.net>
X-Original-From: "Krishna Kuben Govender" <kk.govender*o*gmail.com>
Date: Fri, 10 Jun 2011 07:55:56 -0400


Sent to CCL by: "Krishna Kuben Govender" [kk.govender*_*gmail.com]
Good day CCL users,

I am currently working on reparameterization of some semi-empirical methods.

I wish to find out if it is possible for anyone, who has already worked on parameterization of such methods, can provide me with some scripts that I maybe able to use as a starting point to begin the reparameterization process.
I would appreciate any assistance with this matter, because as alot of you might already know parameterization of semi-empirical methods is a considerably difficult process and I would just like an idea of how to go about doing this.



Regards,
Krishna Kuben Govender
University of Cape Town
Scientific Computing Research Unit
Rondebosch
Cape Town
7701


From owner-chemistry@ccl.net Fri Jun 10 08:32:00 2011
From: "=?ISO-8859-1?Q?Juan_Arag=F3?= juan.arago{:}uv.es" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL:G: Correctly Determining Binding Energies Using Counterpoise
Message-Id: <-44875-110610050637-4719-cJ33iu7WORPfWEq0nbDjDQ-,-server.ccl.net>
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Hi Sam,

I would like to clarify you some points. For instance, in a complex 
formed by two fragments (A and B) counterpoise correction in G09 uses 
five single-point energy calculations:

    * The energy of the complex AB with the basis set X, E(AB).
    * The energy of the fragments A and B with the basis set X, E(A) and
      E(B).
    * The energy of the fragments A and B, but now with the basis set of
      the complex, E(A') and E(B').

With these energies you can compute the counterpoise-corrected energy of 
complex as follows:
Counterpoise-corrected energy of complex= E(AB)-E(A')-E(B');
Basis set superposition error (BSSE) energy = E(A)+E(B)-E(A')-E(B');

In this sense, you cannot talk about "counterpoise corrected energy 
fragment 1 or 2"the only counterpoise-corrected energy is the complex one.
You can find each single-point energy in the output after each SCF. For 
instance, in a dimer computed with wB97X-D the energies follow this order:
  SCF Done:  E(RwB97XD) =  -2335.23274970     A.U. after   21 cycles *E(AB)*
  SCF Done:  E(RwB97XD) =  -1656.67203385     A.U. after   16 cycles *E(A')*
  SCF Done:  E(RwB97XD) =  -678.537009287     A.U. after   15 cycles *E(B')*
  SCF Done:  E(RwB97XD) =  -1656.67122073     A.U. after   16 cycles *E(A)*
  SCF Done:  E(RwB97XD) =  -678.536266897     A.U. after   15 cycles *E(B)*

I hope that has been helpful.

Juan




El 09/06/2011 20:25, Abrash, Sam sabrash~!~richmond.edu escribió:
>
> Hi Folks,
>
> I'm about to do some calculations using the Counterpoise keyword in 
> G09.  I need some help in calculating the binding energy of my complex 
> from the output. I know, for example, how and where to find the 
> counterpoise corrected energy, and I know that the binding energy is
>
> counterpoise corrected energy of complex -- counterpoise corrected 
> energy fragment 1 -- counterpoise corrected energy fragment 2.
>
> What I don't know is where to find the counterpoise corrected energy 
> of the fragments in the Gaussian 09 or Gaussian 03 output.  I would 
> greatly appreciate it if someone could help me with this (the Gaussian 
> User's Reference isn't much help since it doesn't show the output.)  I 
> would especially help if someone could attach at least a portion of an 
> output file which includes the counterpoise corrected energies of the 
> fragments and the complex, so I can see where they are in a real case.
>
> Thank you very much for your help.
>
> Sam
>
> Samuel A. Abrash
> Department of Chemistry
> University of Richmond
> Richmond, VA 23173
> Phone:  804-289-8248
> Fax:  804-287-1897
> E-mail: sabrash:-:richmond.edu <mailto:sabrash:-:richmond.edu>
> Web-page: http://www.richmond.edu/~sabrash 
> <http://oncampus.richmond.edu/%7Esabrash>
>
> "In 1893 Charles Hinton left Japan to become a mathematics instructor 
> at Princeton University, where he invented a baseball-pitching machine 
> that used gunpowder to propel the balls, like a cannon.  After several 
> accidents, the device was abandoned and Hinton lost his job ..." Terry 
> Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III
>
> *From:*owner-chemistry+sabrash==richmond.edu:-:ccl.net 
> [mailto:owner-chemistry+sabrash==richmond.edu:-:ccl.net] *On Behalf Of 
> *Miguel Quiliano Meza rifaximina===gmail.com
> *Sent:* Tuesday, March 22, 2011 6:15 PM
> *To:* Abrash, Sam
> *Subject:* CCL: Carbocation calculations, an approach
>
> Dear colleagues.
>
> My apologies if I disturb you with a couple of questions.
>
> I have never worked with carbocations, but now I have a good case to start
>
> I would like to answer some chemicals questions using computational 
> chemistry, but unfortunately I obtained rare energy values.
>
> Could you tell me please, what should I do? or what kind of chemistry 
> model should I use?.
>
> I want to answer some questions:
>
> *Which reaction is the most probable to happen?
> *What energy is necessary to reach transitional compounds before 
> obtained products?
>
> I have performed some calculations using this:
>
> # opt=tight freq b3lyp/6-31+g scf=qc  with the respect spin 
> multiplicity, but my calculations told me that compound A is most 
> stable than B, besides compound C is most stable than A and B. I 
> stopped here because I think that is impossible.
>
> A: is a carbocation very similar in structure like B
>  B is not a carbocation
> C is a carbocation product of A+B
>
> Final energy for A = -195.60813
>
> Final energy for B = -195.27260
>
> Final energy for C = -390.92315
>
> Thank in advance for your time. Maybe if you don´t have time please 
> recommen me one good paper or good tutorial.
>
> Best regards.
> Miguel.
>

-- 
-------------------------------------------------------------
Juan Aragó March

Universitat de València
Instituto de Ciencia Molecular
Catedrático José Beltrán nº2
E-46980 Paterna (Valencia)
España

Despacho 0.1.6               e-mail: juan.aragó
Phone: +34 963544428         fax: +34 963543274
-------------------------------------------------------------


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    Hi Sam,<br>
    <br>
    I would like to clarify you some points. For instance, in a complex
    formed by two fragments (A and B) counterpoise correction in G09
    uses five single-point energy calculations: <br>
    <ul>
      <li>The energy of the complex AB with the basis set X, E(AB).</li>
      <li>The energy of the fragments A and B with the basis set X, E(A)
        and E(B).</li>
      <li>The energy of the fragments A and B, but now with the basis
        set of the complex, E(A') and E(B').</li>
    </ul>
    With these energies you can compute the counterpoise-corrected
    energy of complex as follows:<br>
    Counterpoise-corrected energy of complex= E(AB)-E(A')-E(B');<br>
    Basis set superposition error (BSSE) energy = E(A)+E(B)-E(A')-E(B');<br>
    <br>
    In this sense, you cannot talk about&nbsp;"<span style="color: blue;">counterpoise
      corrected energy fragment 1 or 2</span>"the only
    counterpoise-corrected energy is the complex one. <br>
    You can find each single-point energy in the output after each SCF.
    For instance, in a dimer computed with wB97X-D the energies follow
    this order: <br>
    &nbsp;SCF Done:&nbsp; E(RwB97XD) =&nbsp; -2335.23274970&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 21
    cycles&nbsp;&nbsp;&nbsp; <b>E(AB)</b><br>
    &nbsp;SCF Done:&nbsp; E(RwB97XD) =&nbsp; -1656.67203385&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 16
    cycles&nbsp;&nbsp;&nbsp;<b> E(A')</b><br>
    &nbsp;SCF Done:&nbsp; E(RwB97XD) =&nbsp; -678.537009287&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 15
    cycles&nbsp;&nbsp;&nbsp; <b>E(B')</b><br>
    &nbsp;SCF Done:&nbsp; E(RwB97XD) =&nbsp; -1656.67122073&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 16
    cycles&nbsp;&nbsp;&nbsp; <b>E(A)</b><br>
    &nbsp;SCF Done:&nbsp; E(RwB97XD) =&nbsp; -678.536266897&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 15
    cycles&nbsp;&nbsp;&nbsp; <b>E(B)</b><br>
    <br>
    I hope that has been helpful.<br>
    <br>
    Juan<br>
    <br>
    &nbsp;&nbsp; <br>
    <br>
    <br>
    El 09/06/2011 20:25, Abrash, Sam sabrash~!~richmond.edu escribi&oacute;:
    <blockquote
cite="mid:-id%233ir-44871-110609142515-10068-NjHFvijdUCvfv4TyvtSghA[]server.ccl.net"
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      <div class="WordSection1">
        <p class="MsoNormal"><span style="color: blue;">Hi Folks,<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;">I&#8217;m about to do
            some calculations using the Counterpoise keyword in G09.&nbsp; I
            need some help in calculating the binding energy of my
            complex from the output. I know, for example, how and where
            to find the counterpoise corrected energy, and I know that
            the binding energy is <o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;">counterpoise
            corrected energy of complex &#8211; counterpoise corrected energy
            fragment 1 &#8211; counterpoise corrected energy fragment 2.<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;">What I don&#8217;t
            know is where to find the counterpoise corrected energy of
            the fragments in the Gaussian 09 or Gaussian 03 output.&nbsp; I
            would greatly appreciate it if someone could help me with
            this (the Gaussian User&#8217;s Reference isn&#8217;t much help since it
            doesn&#8217;t show the output.)&nbsp; I would especially help if
            someone could attach at least a portion of an output file
            which includes the counterpoise corrected energies of the
            fragments and the complex, so I can see where they are in a
            real case.<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;">Thank you very
            much for your help.<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;">Sam<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;">Samuel A. Abrash<br>
            Department of Chemistry<br>
            University of Richmond<br>
            Richmond, VA 23173<br>
            Phone:&nbsp; 804-289-8248<br>
            Fax:&nbsp; 804-287-1897<br>
            E-mail:&nbsp; <a moz-do-not-send="true"
              href="mailto:sabrash:-:richmond.edu"><span style="color:
                blue;">sabrash:-:richmond.edu</span></a><br>
            Web-page:&nbsp; <a moz-do-not-send="true"
              href="http://oncampus.richmond.edu/%7Esabrash"><span
                style="color: blue;">http://www.richmond.edu/~sabrash</span></a><o:p></o:p></span></p>
        <p class="MsoNormal"><span style="font-size: 11pt; font-family:
            &quot;Calibri&quot;,&quot;sans-serif&quot;; color: blue;">"In
            1893&nbsp;Charles Hinton&nbsp;left Japan to become a mathematics
            instructor at Princeton University, where he invented
            a&nbsp;baseball-pitching machine that used gunpowder to propel
            the balls, like a cannon.&nbsp; After several accidents, the
            device was abandoned and Hinton lost his job ..." Terry
            Pratchett, Ian Steward and&nbsp;Jack Cohen, The Science of
            Diskworld III<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color: blue;"><o:p>&nbsp;</o:p></span></p>
        <div style="border-right: medium none; border-width: 1pt medium
          medium; border-style: solid none none; border-color: rgb(181,
          196, 223) -moz-use-text-color -moz-use-text-color; padding:
          3pt 0in 0in;">
          <p class="MsoNormal"><b><span style="font-size: 10pt;
                font-family: &quot;Tahoma&quot;,&quot;sans-serif&quot;;">From:</span></b><span
              style="font-size: 10pt; font-family:
              &quot;Tahoma&quot;,&quot;sans-serif&quot;;">
              owner-chemistry+sabrash==richmond.edu:-:ccl.net
              [<a class="moz-txt-link-freetext" href="mailto:owner-chemistry+sabrash==richmond.edu:-:ccl.net">mailto:owner-chemistry+sabrash==richmond.edu:-:ccl.net</a>] <b>On
                Behalf Of </b>Miguel Quiliano Meza
              rifaximina===gmail.com<br>
              <b>Sent:</b> Tuesday, March 22, 2011 6:15 PM<br>
              <b>To:</b> Abrash, Sam<br>
              <b>Subject:</b> CCL: Carbocation calculations, an approach<o:p></o:p></span></p>
        </div>
        <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
        <p class="MsoNormal" style="margin-bottom: 12pt;">Dear
          colleagues.<br>
          <br>
          My apologies if I disturb you with a couple of questions.<br>
          <br>
          I have never worked with carbocations, but now I have a good
          case to start<br>
          <br>
          I would like to answer some chemicals questions using
          computational chemistry, but unfortunately I obtained rare
          energy values.<br>
          <br>
          Could you tell me please, what should I do? or what kind of
          chemistry model should I use?. <br>
          <br>
          I want to answer some questions:<br>
          <br>
          *Which reaction is the most probable to happen?<br>
          *What energy is necessary to reach transitional compounds
          before obtained products?<br>
          <br>
          I have performed some calculations using this:<br>
          <br>
          # opt=tight freq b3lyp/6-31+g scf=qc&nbsp; with the respect spin
          multiplicity, but my calculations told me that compound A is
          most stable than B, besides compound C is most stable than A
          and B. I stopped here because I think that is impossible.<br>
          <br>
          A: is a carbocation very similar in structure like B<br>
          &nbsp;B is not a carbocation<br>
          C is a carbocation product of A+B<br>
          <br>
          Final energy for A = -195.60813<br>
          <br>
          Final energy for B = -195.27260<br>
          <br>
          Final energy for C = -390.92315<br>
          <br>
          Thank in advance for your time. Maybe if you don&acute;t have time
          please recommen me one good paper or good tutorial.<br>
          <br>
          Best regards.<br>
          Miguel.<br>
          <br>
          <o:p></o:p></p>
      </div>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 
-------------------------------------------------------------
Juan Arag&oacute; March

Universitat de Val&egrave;ncia
Instituto de Ciencia Molecular
Catedr&aacute;tico Jos&eacute; Beltr&aacute;n n&ordm;2
E-46980 Paterna (Valencia)
Espa&ntilde;a

Despacho 0.1.6               e-mail: juan.arag&oacute;
Phone: +34 963544428         fax: +34 963543274
-------------------------------------------------------------</pre>
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--------------000203030601090707080209--


From owner-chemistry@ccl.net Fri Jun 10 09:07:00 2011
From: "Gregorio Garc a gjgarcia[]ujaen.es" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL:G: Problems with Band structure in Gaussian use diffuse functions
Message-Id: <-44876-110610053823-20324-JSlL0+tx6/pH6ePuolj3SQ-,-server.ccl.net>
X-Original-From: "Gregorio   Garc  a" <gjgarcia]~[ujaen.es>
Date: Fri, 10 Jun 2011 05:38:22 -0400


Sent to CCL by: "Gregorio   Garc  a" [gjgarcia(0)ujaen.es]
Hi all
I am trying to obtain band structure  (see keywords below) in Gaussian at level B3LYP/6-31+G* // B3LYP/6-31G*. 

# b3lyp/6-31+g*/Auto PBC=CellRange=5000 pbc=nkpoint=15 iop(5/103=5,5/98=1,5/33=1)

If I use the levels B3LYP/6-31G* // B3LYP/6-31G* and B3LYP/6-311G** // B3LYP/6-31G* (basis set without diffuse functions), there are not problems.
However, when I use diffuse functions I obtain the next problem:
" Possibly not enough cells included in PBC.
 Numerical problems in PBC.
 Error termination via Lnk1e in /home/Gaussian/g09/l502.exe at Fri Jun 10 00:20:58 2011.
 Job cpu time:  0 days 16 hours 21 minutes 59.3 seconds."

In such case, the solution is increase the number of cell (N) by means PBC=CellRange=N (see http://scuseria.rice.edu/gau/g09_pbc/pbc_guide.html).
However, I have used up to PCB=CellRange=2000, and I have obtained the same results. 
I think that it is imposible to calculate band structure using basis sets with diffuse functions.....
Could someone help me?
Someone have calculated bandstructure using diffuse functions?

Thanks in advance


From owner-chemistry@ccl.net Fri Jun 10 09:41:00 2011
From: "Abrash, Sam sabrash]![richmond.edu" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL:G: Correctly Determining Binding Energies Using Counterpoise
Message-Id: <-44877-110610093226-26960-ulm9QKr0DAmt/onxWVyslQ . server.ccl.net>
X-Original-From: "Abrash, Sam" <sabrash~!~richmond.edu>
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Sent to CCL by: "Abrash, Sam" [sabrash]-[richmond.edu]
--_000_DB1DF332AFC21544BA642BA6B7D4654D2ED57C38A0UREXCHANGESCC_
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Thank you.

Sam

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone:  804-289-8248
Fax:  804-287-1897
E-mail:  sabrash-x-richmond.edu<mailto:sabrash-x-richmond.edu>
Web-page:  http://www.richmond.edu/~sabrash<http://oncampus.richmond.edu/~s=
abrash>
"In 1893 Charles Hinton left Japan to become a mathematics instructor at Pr=
inceton University, where he invented a baseball-pitching machine that used=
 gunpowder to propel the balls, like a cannon.  After several accidents, th=
e device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian St=
eward and Jack Cohen, The Science of Diskworld III

> From: owner-chemistry+sabrash=3D=3Drichmond.edu-x-ccl.net [mailto:owner-chemi=
stry+sabrash=3D=3Drichmond.edu-x-ccl.net] On Behalf Of Juan Arag=F3 juan.arag=
o{:}uv.es
Sent: Friday, June 10, 2011 5:06 AM
To: Abrash, Sam
Subject: CCL:G: Correctly Determining Binding Energies Using Counterpoise

Hi Sam,

I would like to clarify you some points. For instance, in a complex formed =
by two fragments (A and B) counterpoise correction in G09 uses five single-=
point energy calculations:

 *   The energy of the complex AB with the basis set X, E(AB).
 *   The energy of the fragments A and B with the basis set X, E(A) and E(B=
).
 *   The energy of the fragments A and B, but now with the basis set of the=
 complex, E(A') and E(B').
With these energies you can compute the counterpoise-corrected energy of co=
mplex as follows:
Counterpoise-corrected energy of complex=3D E(AB)-E(A')-E(B');
Basis set superposition error (BSSE) energy =3D E(A)+E(B)-E(A')-E(B');

In this sense, you cannot talk about "counterpoise corrected energy fragmen=
t 1 or 2"the only counterpoise-corrected energy is the complex one.
You can find each single-point energy in the output after each SCF. For ins=
tance, in a dimer computed with wB97X-D the energies follow this order:
 SCF Done:  E(RwB97XD) =3D  -2335.23274970     A.U. after   21 cycles    E(=
AB)
 SCF Done:  E(RwB97XD) =3D  -1656.67203385     A.U. after   16 cycles    E(=
A')
 SCF Done:  E(RwB97XD) =3D  -678.537009287     A.U. after   15 cycles    E(=
B')
 SCF Done:  E(RwB97XD) =3D  -1656.67122073     A.U. after   16 cycles    E(=
A)
 SCF Done:  E(RwB97XD) =3D  -678.536266897     A.U. after   15 cycles    E(=
B)

I hope that has been helpful.

Juan




El 09/06/2011 20:25, Abrash, Sam sabrash~!~richmond.edu escribi=F3:
Hi Folks,

I'm about to do some calculations using the Counterpoise keyword in G09.  I=
 need some help in calculating the binding energy of my complex from the ou=
tput. I know, for example, how and where to find the counterpoise corrected=
 energy, and I know that the binding energy is

counterpoise corrected energy of complex - counterpoise corrected energy fr=
agment 1 - counterpoise corrected energy fragment 2.

What I don't know is where to find the counterpoise corrected energy of the=
 fragments in the Gaussian 09 or Gaussian 03 output.  I would greatly appre=
ciate it if someone could help me with this (the Gaussian User's Reference =
isn't much help since it doesn't show the output.)  I would especially help=
 if someone could attach at least a portion of an output file which include=
s the counterpoise corrected energies of the fragments and the complex, so =
I can see where they are in a real case.

Thank you very much for your help.

Sam

Samuel A. Abrash
Department of Chemistry
University of Richmond
Richmond, VA 23173
Phone:  804-289-8248
Fax:  804-287-1897
E-mail:  sabrash:-:richmond.edu<mailto:sabrash:-:richmond.edu>
Web-page:  http://www.richmond.edu/~sabrash<http://oncampus.richmond.edu/%7=
Esabrash>
"In 1893 Charles Hinton left Japan to become a mathematics instructor at Pr=
inceton University, where he invented a baseball-pitching machine that used=
 gunpowder to propel the balls, like a cannon.  After several accidents, th=
e device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian St=
eward and Jack Cohen, The Science of Diskworld III

> From: owner-chemistry+sabrash=3D=3Drichmond.edu:-:ccl.net [mailto:owner-che=
mistry+sabrash=3D=3Drichmond.edu:-:ccl.net] On Behalf Of Miguel Quiliano Me=
za rifaximina=3D=3D=3Dgmail.com
Sent: Tuesday, March 22, 2011 6:15 PM
To: Abrash, Sam
Subject: CCL: Carbocation calculations, an approach

Dear colleagues.

My apologies if I disturb you with a couple of questions.

I have never worked with carbocations, but now I have a good case to start

I would like to answer some chemicals questions using computational chemist=
ry, but unfortunately I obtained rare energy values.

Could you tell me please, what should I do? or what kind of chemistry model=
 should I use?.

I want to answer some questions:

*Which reaction is the most probable to happen?
*What energy is necessary to reach transitional compounds before obtained p=
roducts?

I have performed some calculations using this:

# opt=3Dtight freq b3lyp/6-31+g scf=3Dqc  with the respect spin multiplicit=
y, but my calculations told me that compound A is most stable than B, besid=
es compound C is most stable than A and B. I stopped here because I think t=
hat is impossible.

A: is a carbocation very similar in structure like B
 B is not a carbocation
C is a carbocation product of A+B

Final energy for A =3D -195.60813

Final energy for B =3D -195.27260

Final energy for C =3D -390.92315

Thank in advance for your time. Maybe if you don=B4t have time please recom=
men me one good paper or good tutorial.

Best regards.
Miguel.





--

-------------------------------------------------------------

Juan Arag=F3 March



Universitat de Val=E8ncia

Instituto de Ciencia Molecular

Catedr=E1tico Jos=E9 Beltr=E1n n=BA2

E-46980 Paterna (Valencia)

Espa=F1a



Despacho 0.1.6               e-mail: juan.arag=F3

Phone: +34 963544428         fax: +34 963543274

-------------------------------------------------------------

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</o:shapelayout></xml><![endif]--></head><body bgcolor=3Dwhite lang=3DEN-US=
 link=3Dblue vlink=3Dpurple><div class=3DWordSection1><p class=3DMsoNormal>=
<span style=3D'color:blue'>Thank you.<o:p></o:p></span></p><p class=3DMsoNo=
rmal><span style=3D'color:blue'><o:p>&nbsp;</o:p></span></p><p class=3DMsoN=
ormal><span style=3D'color:blue'>Sam<o:p></o:p></span></p><p class=3DMsoNor=
mal><span style=3D'color:blue'><o:p>&nbsp;</o:p></span></p><div><p class=3D=
MsoNormal><span style=3D'color:blue'>Samuel A. Abrash<br>Department of Chem=
istry<br>University of Richmond<br>Richmond, VA 23173<br>Phone:=A0 804-289-=
8248<br>Fax:=A0 804-287-1897<br>E-mail:=A0 <a href=3D"mailto:sabrash-x-richmo=
nd.edu">sabrash-x-richmond.edu</a><br>Web-page:=A0 <a href=3D"http://oncampus=
.richmond.edu/~sabrash">http://www.richmond.edu/~sabrash</a><o:p></o:p></sp=
an></p><p class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:blue'>&quot;In 1893&nbsp;Charles Hinton&nbsp;left=
 Japan to become a mathematics instructor at Princeton University, where he=
 invented a&nbsp;baseball-pitching machine that used gunpowder to propel th=
e balls, like a cannon.&nbsp; After several accidents, the device was aband=
oned and Hinton lost his job ...&quot; Terry Pratchett, Ian Steward and&nbs=
p;Jack Cohen, The Science of Diskworld III<o:p></o:p></span></p></div><p cl=
ass=3DMsoNormal><span style=3D'color:blue'><o:p>&nbsp;</o:p></span></p><div=
><div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in=
 0in 0in'><p class=3DMsoNormal><b><span style=3D'font-size:10.0pt;font-fami=
ly:"Tahoma","sans-serif";color:windowtext'>From:</span></b><span style=3D'f=
ont-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext'> owner-=
chemistry+sabrash=3D=3Drichmond.edu-x-ccl.net [mailto:owner-chemistry+sabrash=
=3D=3Drichmond.edu-x-ccl.net] <b>On Behalf Of </b>Juan Arag=F3 juan.arago{:}u=
v.es<br><b>Sent:</b> Friday, June 10, 2011 5:06 AM<br><b>To:</b> Abrash, Sa=
m<br><b>Subject:</b> CCL:G: Correctly Determining Binding Energies Using Co=
unterpoise<o:p></o:p></span></p></div></div><p class=3DMsoNormal><o:p>&nbsp=
;</o:p></p><p class=3DMsoNormal>Hi Sam,<br><br>I would like to clarify you =
some points. For instance, in a complex formed by two fragments (A and B) c=
ounterpoise correction in G09 uses five single-point energy calculations: <=
o:p></o:p></p><ul type=3Ddisc><li class=3DMsoNormal style=3D'mso-margin-top=
-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'>The energy of=
 the complex AB with the basis set X, E(AB).<o:p></o:p></li><li class=3DMso=
Normal style=3D'mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list=
:l0 level1 lfo1'>The energy of the fragments A and B with the basis set X, =
E(A) and E(B).<o:p></o:p></li><li class=3DMsoNormal style=3D'mso-margin-top=
-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'>The energy of=
 the fragments A and B, but now with the basis set of the complex, E(A') an=
d E(B').<o:p></o:p></li></ul><p class=3DMsoNormal>With these energies you c=
an compute the counterpoise-corrected energy of complex as follows:<br>Coun=
terpoise-corrected energy of complex=3D E(AB)-E(A')-E(B');<br>Basis set sup=
erposition error (BSSE) energy =3D E(A)+E(B)-E(A')-E(B');<br><br>In this se=
nse, you cannot talk about&nbsp;&quot;<span style=3D'color:blue'>counterpoi=
se corrected energy fragment 1 or 2</span>&quot;the only counterpoise-corre=
cted energy is the complex one. <br>You can find each single-point energy i=
n the output after each SCF. For instance, in a dimer computed with wB97X-D=
 the energies follow this order: <br>&nbsp;SCF Done:&nbsp; E(RwB97XD) =3D&n=
bsp; -2335.23274970&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 21 cycle=
s&nbsp;&nbsp;&nbsp; <b>E(AB)</b><br>&nbsp;SCF Done:&nbsp; E(RwB97XD) =3D&nb=
sp; -1656.67203385&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 16 cycles=
&nbsp;&nbsp;&nbsp;<b> E(A')</b><br>&nbsp;SCF Done:&nbsp; E(RwB97XD) =3D&nbs=
p; -678.537009287&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 15 cycles&=
nbsp;&nbsp;&nbsp; <b>E(B')</b><br>&nbsp;SCF Done:&nbsp; E(RwB97XD) =3D&nbsp=
; -1656.67122073&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 16 cycles&n=
bsp;&nbsp;&nbsp; <b>E(A)</b><br>&nbsp;SCF Done:&nbsp; E(RwB97XD) =3D&nbsp; =
-678.536266897&nbsp;&nbsp;&nbsp;&nbsp; A.U. after&nbsp;&nbsp; 15 cycles&nbs=
p;&nbsp;&nbsp; <b>E(B)</b><br><br>I hope that has been helpful.<br><br>Juan=
<br><br>&nbsp;&nbsp; <br><br><br>El 09/06/2011 20:25, Abrash, Sam sabrash~!=
~richmond.edu escribi=F3: <o:p></o:p></p><p class=3DMsoNormal><span style=
=3D'color:blue'>Hi Folks,</span><o:p></o:p></p><p class=3DMsoNormal><span s=
tyle=3D'color:blue'>&nbsp;</span><o:p></o:p></p><p class=3DMsoNormal><span =
style=3D'color:blue'>I&#8217;m about to do some calculations using the Coun=
terpoise keyword in G09.&nbsp; I need some help in calculating the binding =
energy of my complex from the output. I know, for example, how and where to=
 find the counterpoise corrected energy, and I know that the binding energy=
 is </span><o:p></o:p></p><p class=3DMsoNormal><span style=3D'color:blue'>&=
nbsp;</span><o:p></o:p></p><p class=3DMsoNormal><span style=3D'color:blue'>=
counterpoise corrected energy of complex &#8211; counterpoise corrected ene=
rgy fragment 1 &#8211; counterpoise corrected energy fragment 2.</span><o:p=
></o:p></p><p class=3DMsoNormal><span style=3D'color:blue'>&nbsp;</span><o:=
p></o:p></p><p class=3DMsoNormal><span style=3D'color:blue'>What I don&#821=
7;t know is where to find the counterpoise corrected energy of the fragment=
s in the Gaussian 09 or Gaussian 03 output.&nbsp; I would greatly appreciat=
e it if someone could help me with this (the Gaussian User&#8217;s Referenc=
e isn&#8217;t much help since it doesn&#8217;t show the output.)&nbsp; I wo=
uld especially help if someone could attach at least a portion of an output=
 file which includes the counterpoise corrected energies of the fragments a=
nd the complex, so I can see where they are in a real case.</span><o:p></o:=
p></p><p class=3DMsoNormal><span style=3D'color:blue'>&nbsp;</span><o:p></o=
:p></p><p class=3DMsoNormal><span style=3D'color:blue'>Thank you very much =
for your help.</span><o:p></o:p></p><p class=3DMsoNormal><span style=3D'col=
or:blue'>&nbsp;</span><o:p></o:p></p><p class=3DMsoNormal><span style=3D'co=
lor:blue'>Sam</span><o:p></o:p></p><p class=3DMsoNormal><span style=3D'colo=
r:blue'>&nbsp;</span><o:p></o:p></p><p class=3DMsoNormal><span style=3D'col=
or:blue'>Samuel A. Abrash<br>Department of Chemistry<br>University of Richm=
ond<br>Richmond, VA 23173<br>Phone:&nbsp; 804-289-8248<br>Fax:&nbsp; 804-28=
7-1897<br>E-mail:&nbsp; <a href=3D"mailto:sabrash:-:richmond.edu">sabrash:-=
:richmond.edu</a><br>Web-page:&nbsp; <a href=3D"http://oncampus.richmond.ed=
u/%7Esabrash">http://www.richmond.edu/~sabrash</a></span><o:p></o:p></p><p =
class=3DMsoNormal><span style=3D'font-size:11.0pt;font-family:"Calibri","sa=
ns-serif";color:blue'>&quot;In 1893&nbsp;Charles Hinton&nbsp;left Japan to =
become a mathematics instructor at Princeton University, where he invented =
a&nbsp;baseball-pitching machine that used gunpowder to propel the balls, l=
ike a cannon.&nbsp; After several accidents, the device was abandoned and H=
inton lost his job ...&quot; Terry Pratchett, Ian Steward and&nbsp;Jack Coh=
en, The Science of Diskworld III</span><o:p></o:p></p><p class=3DMsoNormal>=
<span style=3D'color:blue'>&nbsp;</span><o:p></o:p></p><div style=3D'border=
:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;border-co=
lor:rgb(181,&#13;&#10;          196, 223) -moz-use-text-color -moz-use-text=
-color'><p class=3DMsoNormal><b><span style=3D'font-size:10.0pt;font-family=
:"Tahoma","sans-serif"'>From:</span></b><span style=3D'font-size:10.0pt;fon=
t-family:"Tahoma","sans-serif"'> owner-chemistry+sabrash=3D=3Drichmond.edu:=
-:ccl.net [<a href=3D"mailto:owner-chemistry+sabrash=3D=3Drichmond.edu:-:cc=
l.net">mailto:owner-chemistry+sabrash=3D=3Drichmond.edu:-:ccl.net</a>] <b>O=
n Behalf Of </b>Miguel Quiliano Meza rifaximina=3D=3D=3Dgmail.com<br><b>Sen=
t:</b> Tuesday, March 22, 2011 6:15 PM<br><b>To:</b> Abrash, Sam<br><b>Subj=
ect:</b> CCL: Carbocation calculations, an approach</span><o:p></o:p></p></=
div><p class=3DMsoNormal>&nbsp;<o:p></o:p></p><p class=3DMsoNormal style=3D=
'margin-bottom:12.0pt'>Dear colleagues.<br><br>My apologies if I disturb yo=
u with a couple of questions.<br><br>I have never worked with carbocations,=
 but now I have a good case to start<br><br>I would like to answer some che=
micals questions using computational chemistry, but unfortunately I obtaine=
d rare energy values.<br><br>Could you tell me please, what should I do? or=
 what kind of chemistry model should I use?. <br><br>I want to answer some =
questions:<br><br>*Which reaction is the most probable to happen?<br>*What =
energy is necessary to reach transitional compounds before obtained product=
s?<br><br>I have performed some calculations using this:<br><br># opt=3Dtig=
ht freq b3lyp/6-31+g scf=3Dqc&nbsp; with the respect spin multiplicity, but=
 my calculations told me that compound A is most stable than B, besides com=
pound C is most stable than A and B. I stopped here because I think that is=
 impossible.<br><br>A: is a carbocation very similar in structure like B<br=
>&nbsp;B is not a carbocation<br>C is a carbocation product of A+B<br><br>F=
inal energy for A =3D -195.60813<br><br>Final energy for B =3D -195.27260<b=
r><br>Final energy for C =3D -390.92315<br><br>Thank in advance for your ti=
me. Maybe if you don=B4t have time please recommen me one good paper or goo=
d tutorial.<br><br>Best regards.<br>Miguel.<br><br><br><o:p></o:p></p><p cl=
ass=3DMsoNormal><br><br><o:p></o:p></p><pre>-- <o:p></o:p></pre><pre>------=
-------------------------------------------------------<o:p></o:p></pre><pr=
e>Juan Arag=F3 March<o:p></o:p></pre><pre><o:p>&nbsp;</o:p></pre><pre>Unive=
rsitat de Val=E8ncia<o:p></o:p></pre><pre>Instituto de Ciencia Molecular<o:=
p></o:p></pre><pre>Catedr=E1tico Jos=E9 Beltr=E1n n=BA2<o:p></o:p></pre><pr=
e>E-46980 Paterna (Valencia)<o:p></o:p></pre><pre>Espa=F1a<o:p></o:p></pre>=
<pre><o:p>&nbsp;</o:p></pre><pre>Despacho 0.1.6=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0 e-mail: juan.arag=F3<o:p></o:p></pre><pre>Phone: +34 963544=
428=A0=A0=A0=A0=A0=A0=A0=A0 fax: +34 963543274<o:p></o:p></pre><pre>-------=
------------------------------------------------------<o:p></o:p></pre></di=
v></body></html>=

--_000_DB1DF332AFC21544BA642BA6B7D4654D2ED57C38A0UREXCHANGESCC_--


From owner-chemistry@ccl.net Fri Jun 10 11:38:01 2011
From: "Devendra Mani devdmani10#%#gmail.com" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate distortion constants
Message-Id: <-44878-110610112206-17932-eSc6C2yCCSce8pLLLmWjCA::server.ccl.net>
X-Original-From: Devendra Mani <devdmani10::gmail.com>
Content-Type: multipart/alternative; boundary=90e6ba3097147e5c0604a55d2166
Date: Fri, 10 Jun 2011 20:51:59 +0530
MIME-Version: 1.0


Sent to CCL by: Devendra Mani [devdmani10{=}gmail.com]
--90e6ba3097147e5c0604a55d2166
Content-Type: text/plain; charset=ISO-8859-1

Dear Abhishek Shahi,
 You can do these calculations on gaussian. Just use freq=vibrot command in
the input line.

Hope it will work for you.

Devendra Mani

On Wed, Jun 8, 2011 at 9:41 AM, ABHISHEK SHAHI shahi.abhishek1984|*|
gmail.com <owner-chemistry^ccl.net> wrote:

> Dear All,
>
>
>    I am looking for a program which can calculate the distortion constants
> (Dj, Djk etc...).Thanks in advance.
>
>
>
> With regards;
>  *ABHISHEK SHAHI*
>
> *Research Scholar
> Inorganic and Physical Chemistry
> Indian Institute Of Science
> Bangalore-12*
> INDIA
>
>
>

--90e6ba3097147e5c0604a55d2166
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Abhishek Shahi, <br>=A0You can do these calculations on gaussian. Just=
 use freq=3Dvibrot command in the input line. <br><br>Hope it will work for=
 you. <br><br>Devendra Mani <br><br><div class=3D"gmail_quote">On Wed, Jun =
8, 2011 at 9:41 AM, ABHISHEK SHAHI shahi.abhishek1984|*|<a href=3D"http://g=
mail.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemi=
stry^ccl.net">owner-chemistry^ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;">Dear All, <br><br><br>=A0=A0 I am looking f=
or a program which can calculate the distortion constants (Dj, Djk etc...).=
Thanks in advance. <br>
<br>=A0<br clear=3D"all"><span style=3D"font-family:times new roman,serif">=
</span><span style=3D"font-family:times new roman,serif"><br>
With regards;</span><br><span style=3D"background-color:rgb(255, 255, 255)"=
>=A0<font style=3D"font-family:trebuchet ms,sans-serif" size=3D"4"><b><span=
 style=3D"color:rgb(51, 51, 255)">ABHISHEK SHAHI</span></b></font></span><b=
r><br>

<i style=3D"font-family:courier new,monospace"><span style=3D"background-co=
lor:rgb(255, 255, 255);color:rgb(0, 102, 0)">Research Scholar</span><br sty=
le=3D"background-color:rgb(255, 255, 255);color:rgb(0, 102, 0)"><span style=
=3D"background-color:rgb(255, 255, 255);color:rgb(0, 102, 0)">Inorganic and=
 Physical Chemistry</span><br style=3D"background-color:rgb(255, 255, 255);=
color:rgb(0, 102, 0)">

<span style=3D"background-color:rgb(255, 255, 255);color:rgb(0, 102, 0)">In=
dian Institute Of Science</span><br style=3D"background-color:rgb(255, 255,=
 255);color:rgb(0, 102, 0)"><span style=3D"background-color:rgb(255, 255, 2=
55);color:rgb(0, 102, 0)">Bangalore-12</span></i> <br>

INDIA<br><span style=3D"font-family:arial black,sans-serif"><span style=3D"=
color:rgb(255, 0, 0)"></span></span><br><br>
</blockquote></div><br>

--90e6ba3097147e5c0604a55d2166--