From owner-chemistry@ccl.net Fri Apr 20 00:01:00 2012
From: "Nancy nancy5villa---gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: t-Butyl sulfinamide Stability
Message-Id: <-46738-120419235946-31958-GFR7IfsmgSo561jOhS5xdg..server.ccl.net>
X-Original-From: Nancy <nancy5villa|-|gmail.com>
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Date: Thu, 19 Apr 2012 20:59:40 -0700
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Sent to CCL by: Nancy [nancy5villa#%#gmail.com]
--20cf3074b61a62625204be1451ff
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Hello,

Does anyone know how stable sulfinamides are in vivo? Specifically,
molecules such as Ellman's t-butyl sulfinamide. How does their stability
compare to sulfoxides? Do they get oxidized in vivo?  Are they at least
stable in water?

Thanks in advance,
Nancy

--20cf3074b61a62625204be1451ff
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hello,<br><br>Does anyone know how stable sulfinamides are in vivo? Specifi=
cally, molecules such as Ellman&#39;s t-butyl sulfinamide. How does their s=
tability compare to sulfoxides? Do they get oxidized in vivo?=A0 Are they a=
t least stable in water?<br>
<br>Thanks in advance,<br>Nancy<br><br><br><br>

--20cf3074b61a62625204be1451ff--


From owner-chemistry@ccl.net Fri Apr 20 00:35:00 2012
From: "Walid M. I. Hassan walid_m76.:.yahoo.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL:G: Avoided crossing
Message-Id: <-46739-120419193638-7256-NqbpWkqXMbyMWorbU45NQA%%server.ccl.net>
X-Original-From: "Walid M. I. Hassan" <walid_m76]-[yahoo.com>
Date: Thu, 19 Apr 2012 19:36:37 -0400


Sent to CCL by: "Walid M. I. Hassan" [walid_m76|-|yahoo.com]
Dear Scientists

long time since I send email via this list,
my question is very simple does anyone know a software to determine the 
avoided crossing or conical intersection between singlet and triplet states, 
i mean states of different multiplicity

In Gaussian 09 manual, in Opt keyword ,under conical option it is written, 
"Search for a conical intersection or avoided crossing using the state-
averaged CASSCF method. Avoided is a synonym for Conical. Note that 
CASSCF=SlaterDet is needed in order to locate a conical intersection between 
a singlet state and a triplet state." 
I tried this and find it is impossible since in input file you determine a 
singlet or triplet multiplicity but not both

and SlaterDet option just reverse the spin but do not change multiplicity
see this part of output to see the configurations

when I use singlet state with No SLATER DETERMINANT
> I get the following configuration
>        Configuration      1 Symmetry 1 111000
>        Configuration      2 Symmetry 1 11ab00
>        Configuration      3 Symmetry 1 110100
>        Configuration      4 Symmetry 1 1a1b00
> 
> 
> which become as follows with SLATER DETERMINANT
>        Configuration      1 Symmetry 1 111000
>        Configuration      2 Symmetry 1 11ba00
>        Configuration      3 Symmetry 1 11ab00
>        Configuration      4 Symmetry 1 1b1a00
>        Configuration      5 Symmetry 1 11b0a0
> 
> 
> for triplet state in both cases i get the following configuration
>  Configuration      1 Symmetry 1 11aa00
>        Configuration      2 Symmetry 1 11a0a0
>        Configuration      3 Symmetry 1 1a1a00
>        Configuration      4 Symmetry 1 110aa0

as you can see SlaterDet option reverse ab to ba but not to aa
I want to get conical intersection or avoided crossing between
Configuration      1 Symmetry 1 111000 of singlet and
Configuration      1 Symmetry 1 11aa00 of triplet state

I sent this question to Gaussian team and their reply was not convincing to 
me, I will put it here for your reference,
I think they just go around the problem to claim that there is no problem in 
the manual
i think gaussian program can not do it
if i am wrong i will appreciate if you guide me
If i am write so what program can find this conical intersection for me
sorry for long email but i think it won't show my point if it is shorter 

   Dr. Ibrahim,

    Thank you for giving us a chance to comment.

    When you look at those configuration lists you are not actually
looking a lists of identical things.  The singlet without Slater Determinant
is a list of configurations, fixed linear combinations of determinants
giving singlets.  So there will be no triplet terms in this expansion
and the higher roots of the CASSCF equations will all be singlets as
well.

    The second case lists determinants directly and generates singlets
and m(l)=0 triplets.  So configurations 2 and 3 are a pair of determinants
which can contribute to both singlets and triplets with the sign difference
carried on the CI expansion coefficients, not on the determinants
directly.

      The third case correspond to a ground state triplet, m(l)=+/-1 
and no singlet contributions are possible.  Again any excited states will
be triplets so this reference is not suitable for the crossing.

      So the program can compute the crossing you desire by using a 
singlet reference with SlaterDet included in the option list.  You
should still solve for the first few roots to confirm that you have
the second root corresponding to the triplet you expected.


From owner-chemistry@ccl.net Fri Apr 20 04:12:00 2012
From: "Pedro Silva pedros[a]ufp.edu.pt" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: Avoided crossing
Message-Id: <-46740-120420040837-26394-YwSyLB6OeBDL6x7zq6wVEg_+_server.ccl.net>
X-Original-From: Pedro Silva <pedros|a|ufp.edu.pt>
Content-Type: text/plain; charset=ISO-8859-1
Date: Fri, 20 Apr 2012 09:08:31 +0100
MIME-Version: 1.0


Sent to CCL by: Pedro Silva [pedros _ ufp.edu.pt]
Dear Dr. Ibrahim,

It is hard to diagnose your problem and suggest proper fixes without a
sample of the input you have used. I would suggest you sent that to
the Gaussian technical support team, and they will be able to further
help you. Unlike them, CCL members are not paid to answer technical
questions on Gaussian software ;-)

Pedro S.


-- 
Pedro J. Silva
Associate Professor
Universidade Fernando Pessoa
Porto - Portugal
http://homepage.ufp.pt/pedros/science/science.htm
http://biochemicalmatters.blogspot.com


From owner-chemistry@ccl.net Fri Apr 20 08:49:00 2012
From: "Abrash, Sam sabrash{}richmond.edu" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL:G: Avoided crossing
Message-Id: <-46741-120420084731-9906-2Ozon3e3d5AZcBjkFLwqEA]=[server.ccl.net>
X-Original-From: "Abrash, Sam" <sabrash**richmond.edu>
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Content-Transfer-Encoding: 8bit
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Date: Fri, 20 Apr 2012 12:47:19 +0000
MIME-Version: 1.0


Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu]
As far as I understand it, avoided crossings are always between states of the same symmetry, so there wouldn't be an avoided crossing between a singlet and a triplet state.

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
Web-page:  http://www.richmond.edu/~sabrash
"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

-----Original Message-----
> From: owner-chemistry+sabrash==richmond.edu%ccl.net [mailto:owner-chemistry+sabrash==richmond.edu%ccl.net] On Behalf Of Walid M. I. Hassan walid_m76.:.yahoo.com
Sent: Thursday, April 19, 2012 7:37 PM
To: Abrash, Sam
Subject: CCL:G: Avoided crossing


Sent to CCL by: "Walid M. I. Hassan" [walid_m76|-|yahoo.com]
Dear Scientists

long time since I send email via this list,
my question is very simple does anyone know a software to determine the 
avoided crossing or conical intersection between singlet and triplet states, 
i mean states of different multiplicity

In Gaussian 09 manual, in Opt keyword ,under conical option it is written, 
"Search for a conical intersection or avoided crossing using the state-
averaged CASSCF method. Avoided is a synonym for Conical. Note that 
CASSCF=SlaterDet is needed in order to locate a conical intersection between 
a singlet state and a triplet state." 
I tried this and find it is impossible since in input file you determine a 
singlet or triplet multiplicity but not both

and SlaterDet option just reverse the spin but do not change multiplicity
see this part of output to see the configurations

when I use singlet state with No SLATER DETERMINANT
> I get the following configuration
>        Configuration      1 Symmetry 1 111000
>        Configuration      2 Symmetry 1 11ab00
>        Configuration      3 Symmetry 1 110100
>        Configuration      4 Symmetry 1 1a1b00
> 
> 
> which become as follows with SLATER DETERMINANT
>        Configuration      1 Symmetry 1 111000
>        Configuration      2 Symmetry 1 11ba00
>        Configuration      3 Symmetry 1 11ab00
>        Configuration      4 Symmetry 1 1b1a00
>        Configuration      5 Symmetry 1 11b0a0
> 
> 
> for triplet state in both cases i get the following configuration
>  Configuration      1 Symmetry 1 11aa00
>        Configuration      2 Symmetry 1 11a0a0
>        Configuration      3 Symmetry 1 1a1a00
>        Configuration      4 Symmetry 1 110aa0

as you can see SlaterDet option reverse ab to ba but not to aa
I want to get conical intersection or avoided crossing between
Configuration      1 Symmetry 1 111000 of singlet and
Configuration      1 Symmetry 1 11aa00 of triplet state

I sent this question to Gaussian team and their reply was not convincing to 
me, I will put it here for your reference,
I think they just go around the problem to claim that there is no problem in 
the manual
i think gaussian program can not do it
if i am wrong i will appreciate if you guide me
If i am write so what program can find this conical intersection for me
sorry for long email but i think it won't show my point if it is shorter 

   Dr. Ibrahim,

    Thank you for giving us a chance to comment.

    When you look at those configuration lists you are not actually
looking a lists of identical things.  The singlet without Slater Determinant
is a list of configurations, fixed linear combinations of determinants
giving singlets.  So there will be no triplet terms in this expansion
and the higher roots of the CASSCF equations will all be singlets as
well.

    The second case lists determinants directly and generates singlets
and m(l)=0 triplets.  So configurations 2 and 3 are a pair of determinants
which can contribute to both singlets and triplets with the sign difference
carried on the CI expansion coefficients, not on the determinants
directly.

      The third case correspond to a ground state triplet, m(l)=+/-1 
and no singlet contributions are possible.  Again any excited states will
be triplets so this reference is not suitable for the crossing.

      So the program can compute the crossing you desire by using a 
singlet reference with SlaterDet included in the option list.  You
should still solve for the first few roots to confirm that you have
the second root corresponding to the triplet you expected.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Fri Apr 20 09:23:00 2012
From: "Yavuz Dede dede:gazi.edu.tr" <owner-chemistry!A!server.ccl.net>
To: CCL
Subject: CCL:G: Avoided crossing
Message-Id: <-46742-120420045147-18621-kRDTSflb4EVQ/MGSGUOghA!A!server.ccl.net>
X-Original-From: Yavuz Dede <dede#%#gazi.edu.tr>
Content-Type: multipart/alternative;
 boundary="------------080205020204050601040106"
Date: Fri, 20 Apr 2012 11:51:33 +0300
MIME-Version: 1.0


Sent to CCL by: Yavuz Dede [dede(a)gazi.edu.tr]
This is a multi-part message in MIME format.
--------------080205020204050601040106
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 8bit

Dear Ibrahim,
Most MCSCF software (MOLCAS, MOLPRO, GAMESS) calculates what you ask, 
between different space and/or spin states. For example in GAMESS-US 
these crossing searches are named minimum energy crossing (MEX).

Note that, you wouldn't term it an avoided crossing from the beginning. 
Crossings between different states can be true intersections. 
Designation of conical intersection or avoided crossing requires a 
detailed analysis of the relative energies and electronic properties of 
the states under investigation.

Reading works of Dupuis, Schlegel, Robb (among many others) may help.

Best,
Yavuz



On 20.04.2012 02:36, Walid M. I. Hassan walid_m76.:.yahoo.com wrote:
> Sent to CCL by: "Walid M. I. Hassan" [walid_m76|-|yahoo.com]
> Dear Scientists
>
> long time since I send email via this list,
> my question is very simple does anyone know a software to determine the
> avoided crossing or conical intersection between singlet and triplet states,
> i mean states of different multiplicity
>
> In Gaussian 09 manual, in Opt keyword ,under conical option it is written,
> "Search for a conical intersection or avoided crossing using the state-
> averaged CASSCF method. Avoided is a synonym for Conical. Note that
> CASSCF=SlaterDet is needed in order to locate a conical intersection between
> a singlet state and a triplet state."
> I tried this and find it is impossible since in input file you determine a
> singlet or triplet multiplicity but not both
>
> and SlaterDet option just reverse the spin but do not change multiplicity
> see this part of output to see the configurations
>
> when I use singlet state with No SLATER DETERMINANT
>> I get the following configuration
>>         Configuration      1 Symmetry 1 111000
>>         Configuration      2 Symmetry 1 11ab00
>>         Configuration      3 Symmetry 1 110100
>>         Configuration      4 Symmetry 1 1a1b00
>>
>>
>> which become as follows with SLATER DETERMINANT
>>         Configuration      1 Symmetry 1 111000
>>         Configuration      2 Symmetry 1 11ba00
>>         Configuration      3 Symmetry 1 11ab00
>>         Configuration      4 Symmetry 1 1b1a00
>>         Configuration      5 Symmetry 1 11b0a0
>>
>>
>> for triplet state in both cases i get the following configuration
>>   Configuration      1 Symmetry 1 11aa00
>>         Configuration      2 Symmetry 1 11a0a0
>>         Configuration      3 Symmetry 1 1a1a00
>>         Configuration      4 Symmetry 1 110aa0
> as you can see SlaterDet option reverse ab to ba but not to aa
> I want to get conical intersection or avoided crossing between
> Configuration      1 Symmetry 1 111000 of singlet and
> Configuration      1 Symmetry 1 11aa00 of triplet state
>
> I sent this question to Gaussian team and their reply was not convincing to
> me, I will put it here for your reference,
> I think they just go around the problem to claim that there is no problem in
> the manual
> i think gaussian program can not do it
> if i am wrong i will appreciate if you guide me
> If i am write so what program can find this conical intersection for me
> sorry for long email but i think it won't show my point if it is shorter
>
>     Dr. Ibrahim,
>
>      Thank you for giving us a chance to comment.
>
>      When you look at those configuration lists you are not actually
> looking a lists of identical things.  The singlet without Slater Determinant
> is a list of configurations, fixed linear combinations of determinants
> giving singlets.  So there will be no triplet terms in this expansion
> and the higher roots of the CASSCF equations will all be singlets as
> well.
>
>      The second case lists determinants directly and generates singlets
> and m(l)=0 triplets.  So configurations 2 and 3 are a pair of determinants
> which can contribute to both singlets and triplets with the sign difference
> carried on the CI expansion coefficients, not on the determinants
> directly.
>
>        The third case correspond to a ground state triplet, m(l)=+/-1
> and no singlet contributions are possible.  Again any excited states will
> be triplets so this reference is not suitable for the crossing.
>
>        So the program can compute the crossing you desire by using a
> singlet reference with SlaterDet included in the option list.  You
> should still solve for the first few roots to confirm that you have
> the second root corresponding to the triplet you expected.>
>
>
> -- 
> |||||||||||||||||||||||
> Yavuz Dede
> GÜ-Fen Fakültesi
> Kimya Bölümü
> L-128 06500 Ankara
> Tel:  312-202-1386
> Faks: 312-212-2279
> ||||||||||||||||||||
> Yavuz Dede, Ph.D.
> Theoretical/Computational Chemistry
> Gazi University
> Faculty of Science
> Department of Chemistry
> 06500 Ankara TURKEY
> http://w3.gazi.edu.tr/~dede/ydd.htm
> ||||||||||||||||||||||||||||||||||||

--------------080205020204050601040106
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFF99" text="#000000">
    <font face="Courier New, Courier, monospace">Dear Ibrahim,<br>
      Most MCSCF software (MOLCAS, MOLPRO, GAMESS) calculates what you
      ask, between different space and/or spin states. For example in
      GAMESS-US these crossing searches are named minimum energy
      crossing (MEX).<br>
      <br>
      Note that, you wouldn't term it an avoided crossing from the
      beginning. Crossings between different states can be true
      intersections. Designation of conical intersection or avoided
      crossing requires a detailed analysis of the relative energies and
      electronic properties of the states under investigation.<br>
      <br>
      Reading works of Dupuis, Schlegel, Robb (among many others) may
      help.<br>
      <br>
      Best,<br>
      Yavuz<br>
      <br>
      <br>
    </font><br>
    On 20.04.2012 02:36, Walid M. I. Hassan walid_m76.:.yahoo.com wrote:
    <blockquote
cite="mid:-id%234ma-46739-120419193638-7256-9%2FBO6zVaZTSJV6IXPsFC1g[-]server.ccl.net"
      type="cite">
      <pre wrap="">Sent to CCL by: "Walid M. I. Hassan" [walid_m76|-|yahoo.com]
Dear Scientists

long time since I send email via this list,
my question is very simple does anyone know a software to determine the 
avoided crossing or conical intersection between singlet and triplet states, 
i mean states of different multiplicity

In Gaussian 09 manual, in Opt keyword ,under conical option it is written, 
"Search for a conical intersection or avoided crossing using the state-
averaged CASSCF method. Avoided is a synonym for Conical. Note that 
CASSCF=SlaterDet is needed in order to locate a conical intersection between 
a singlet state and a triplet state." 
I tried this and find it is impossible since in input file you determine a 
singlet or triplet multiplicity but not both

and SlaterDet option just reverse the spin but do not change multiplicity
see this part of output to see the configurations

when I use singlet state with No SLATER DETERMINANT
</pre>
      <blockquote type="cite">
        <pre wrap="">I get the following configuration
       Configuration      1 Symmetry 1 111000
       Configuration      2 Symmetry 1 11ab00
       Configuration      3 Symmetry 1 110100
       Configuration      4 Symmetry 1 1a1b00


which become as follows with SLATER DETERMINANT
       Configuration      1 Symmetry 1 111000
       Configuration      2 Symmetry 1 11ba00
       Configuration      3 Symmetry 1 11ab00
       Configuration      4 Symmetry 1 1b1a00
       Configuration      5 Symmetry 1 11b0a0


for triplet state in both cases i get the following configuration
 Configuration      1 Symmetry 1 11aa00
       Configuration      2 Symmetry 1 11a0a0
       Configuration      3 Symmetry 1 1a1a00
       Configuration      4 Symmetry 1 110aa0
</pre>
      </blockquote>
      <pre wrap="">
as you can see SlaterDet option reverse ab to ba but not to aa
I want to get conical intersection or avoided crossing between
Configuration      1 Symmetry 1 111000 of singlet and
Configuration      1 Symmetry 1 11aa00 of triplet state

I sent this question to Gaussian team and their reply was not convincing to 
me, I will put it here for your reference,
I think they just go around the problem to claim that there is no problem in 
the manual
i think gaussian program can not do it
if i am wrong i will appreciate if you guide me
If i am write so what program can find this conical intersection for me
sorry for long email but i think it won't show my point if it is shorter 

   Dr. Ibrahim,

    Thank you for giving us a chance to comment.

    When you look at those configuration lists you are not actually
looking a lists of identical things.  The singlet without Slater Determinant
is a list of configurations, fixed linear combinations of determinants
giving singlets.  So there will be no triplet terms in this expansion
and the higher roots of the CASSCF equations will all be singlets as
well.

    The second case lists determinants directly and generates singlets
and m(l)=0 triplets.  So configurations 2 and 3 are a pair of determinants
which can contribute to both singlets and triplets with the sign difference
carried on the CI expansion coefficients, not on the determinants
directly.

      The third case correspond to a ground state triplet, m(l)=+/-1 
and no singlet contributions are possible.  Again any excited states will
be triplets so this reference is not suitable for the crossing.

      So the program can compute the crossing you desire by using a 
singlet reference with SlaterDet included in the option list.  You
should still solve for the first few roots to confirm that you have
the second root corresponding to the triplet you expected.E-mail to subscribers: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY[-]ccl.net">CHEMISTRY[-]ccl.net</a> or use:
      <a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>

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-- 
|||||||||||||||||||||||
Yavuz Dede
G&Uuml;-Fen Fak&uuml;ltesi
Kimya B&ouml;l&uuml;m&uuml;
L-128 06500 Ankara
Tel:  312-202-1386
Faks: 312-212-2279
||||||||||||||||||||
Yavuz Dede, Ph.D.
Theoretical/Computational Chemistry
Gazi University
Faculty of Science
Department of Chemistry
06500 Ankara TURKEY
<a class="moz-txt-link-freetext" href="http://w3.gazi.edu.tr/~dede/ydd.htm">http://w3.gazi.edu.tr/~dede/ydd.htm</a>
||||||||||||||||||||||||||||||||||||
</pre>
    </blockquote>
  </body>
</html>

--------------080205020204050601040106--


From owner-chemistry@ccl.net Fri Apr 20 09:58:00 2012
From: "Rama Camara ramatoulie.camara,+,live.uwe.ac.uk" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: How to form a protein dimer from the monomer
Message-Id: <-46743-120420085842-26857-K0tjHtO96vva6ELg95eDbw]^[server.ccl.net>
X-Original-From: "Rama  Camara" <ramatoulie.camara-,-live.uwe.ac.uk>
Date: Fri, 20 Apr 2012 08:58:39 -0400


Sent to CCL by: "Rama  Camara" [ramatoulie.camara##live.uwe.ac.uk]
Hi all,

I have a protein monomer which I'd like to reform to its dimer. I was wondering if anyone out there knows of a program (free ones if possible )I can use to do this and how to do it. 

Any tips/suggestions will be highly appreciated. 

Thanks. 

Rama


From owner-chemistry@ccl.net Fri Apr 20 13:44:00 2012
From: "Van Dam, Hubertus J HubertusJJ.vanDam]^[pnnl.gov" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL:G: Avoided crossing
Message-Id: <-46744-120420134304-20545-9uyTKHvY3WMOF07rWY6eDg%x%server.ccl.net>
X-Original-From: "Van Dam, Hubertus J" <HubertusJJ.vanDam%a%pnnl.gov>
Content-Language: en-US
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Date: Fri, 20 Apr 2012 10:42:54 -0700
MIME-Version: 1.0


Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam*_*pnnl.gov]
Dear Walid,

I am afraid the Gaussian folks are right in their comments even if the conventions of the input parameters for quantum chemistry codes may be confusing in your case. The spin of a state is determined by 2 quantum numbers S_z and S^2. For Singlet states S_z is 0. For Triplet states S_z can be either -1, 0 or 1. Normally if you are interested only in the Triplet state it makes sense to specify S_z equals 1 as that also fixes S^2 and allows only determinants that are triplets themselves. Hence there cannot be any confusion about which spin state your wavefunction represents. 

In your case however, you need to be able to describe both singlet and triplet states in the same calculation. You can only achieve this by specifying S_z equals 0 and using a basis of Slater Determinants. In that case you truly only specify S_z and the program can freely represent different spin-states (different S^2) with the same S_z (if you don't use Slater determinants the program seems to generate spin-adapted linear combinations of Slater determinants, so called Configuration State Functions, and you have fixed both S_z and S^2).

So the confusion seems to come from the fact that if you specify a singlet multiplicity in a basis of Slater determinants you do not actually specify the combination of S_z and S^2 quantum numbers of the singlet state. In actual fact you only specify S_z and the program can represent states with different S^2 in that basis. Hence when working in a basis of Slater determinants what you enter for the spin multiplicity is not actually the spin multiplicity but just S_z.

I hope this explains the issue (at least a bit).

Best wishes,

     Huub

-----Original Message-----
> From: owner-chemistry+hubertus.vandam==pnnl.gov() ccl.net [mailto:owner-chemistry+hubertus.vandam==pnnl.gov() ccl.net] On Behalf Of Walid M. I. Hassan walid_m76.:.yahoo.com
Sent: Thursday, April 19, 2012 4:37 PM
To: Van Dam, Hubertus J
Subject: CCL:G: Avoided crossing


Sent to CCL by: "Walid M. I. Hassan" [walid_m76|-|yahoo.com] Dear Scientists

long time since I send email via this list, my question is very simple does anyone know a software to determine the avoided crossing or conical intersection between singlet and triplet states, i mean states of different multiplicity

In Gaussian 09 manual, in Opt keyword ,under conical option it is written, "Search for a conical intersection or avoided crossing using the state- averaged CASSCF method. Avoided is a synonym for Conical. Note that CASSCF=SlaterDet is needed in order to locate a conical intersection between a singlet state and a triplet state." 
I tried this and find it is impossible since in input file you determine a singlet or triplet multiplicity but not both

and SlaterDet option just reverse the spin but do not change multiplicity see this part of output to see the configurations

when I use singlet state with No SLATER DETERMINANT
> I get the following configuration
>        Configuration      1 Symmetry 1 111000
>        Configuration      2 Symmetry 1 11ab00
>        Configuration      3 Symmetry 1 110100
>        Configuration      4 Symmetry 1 1a1b00
> 
> 
> which become as follows with SLATER DETERMINANT
>        Configuration      1 Symmetry 1 111000
>        Configuration      2 Symmetry 1 11ba00
>        Configuration      3 Symmetry 1 11ab00
>        Configuration      4 Symmetry 1 1b1a00
>        Configuration      5 Symmetry 1 11b0a0
> 
> 
> for triplet state in both cases i get the following configuration
>  Configuration      1 Symmetry 1 11aa00
>        Configuration      2 Symmetry 1 11a0a0
>        Configuration      3 Symmetry 1 1a1a00
>        Configuration      4 Symmetry 1 110aa0

as you can see SlaterDet option reverse ab to ba but not to aa I want to get conical intersection or avoided crossing between
Configuration      1 Symmetry 1 111000 of singlet and
Configuration      1 Symmetry 1 11aa00 of triplet state

I sent this question to Gaussian team and their reply was not convincing to me, I will put it here for your reference, I think they just go around the problem to claim that there is no problem in the manual i think gaussian program can not do it if i am wrong i will appreciate if you guide me If i am write so what program can find this conical intersection for me sorry for long email but i think it won't show my point if it is shorter 

   Dr. Ibrahim,

    Thank you for giving us a chance to comment.

    When you look at those configuration lists you are not actually looking a lists of identical things.  The singlet without Slater Determinant is a list of configurations, fixed linear combinations of determinants giving singlets.  So there will be no triplet terms in this expansion and the higher roots of the CASSCF equations will all be singlets as well.

    The second case lists determinants directly and generates singlets and m(l)=0 triplets.  So configurations 2 and 3 are a pair of determinants which can contribute to both singlets and triplets with the sign difference carried on the CI expansion coefficients, not on the determinants directly.

      The third case correspond to a ground state triplet, m(l)=+/-1 and no singlet contributions are possible.  Again any excited states will be triplets so this reference is not suitable for the crossing.

      So the program can compute the crossing you desire by using a singlet reference with SlaterDet included in the option list.  You should still solve for the first few roots to confirm that you have the second root corresponding to the triplet you expected.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Fri Apr 20 14:18:01 2012
From: "Symon Gathiaka sgathiaka!=!gmail.com" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: How to form a protein dimer from the monomer
Message-Id: <-46745-120420141647-32024-wybPYwf/OBXzUgZFIfk4YA/./server.ccl.net>
X-Original-From: Symon Gathiaka <sgathiaka .. gmail.com>
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Sent to CCL by: Symon Gathiaka [sgathiaka(-)gmail.com]
--f46d04428d7639f99004be204aca
Content-Type: text/plain; charset=ISO-8859-1

Hey Rama,

Is the protein from the Protein data bank or a homology model?

If from the PDB, you can use PDBePISA to get the biological assembly (if
thats what the dimer is). You can launch PDBePISA from the EMBL-EBI website
and its straightforward to use.

If its a model, you may have to build it as a dimer.
I hope that helps,
Symon
On Fri, Apr 20, 2012 at 7:58 AM, Rama Camara ramatoulie.camara,+,
live.uwe.ac.uk <owner-chemistry . ccl.net> wrote:

>
> Sent to CCL by: "Rama  Camara" [ramatoulie.camara##live.uwe.ac.uk]
> Hi all,
>
> I have a protein monomer which I'd like to reform to its dimer. I was
> wondering if anyone out there knows of a program (free ones if possible )I
> can use to do this and how to do it.
>
> Any tips/suggestions will be highly appreciated.
>
> Thanks.
>
> Rama>
>
>


-- 
** *As is a tale, so is life: not how long it is, but how good it is, is
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<div>Hey Rama,</div>
<div>=A0</div>
<div>Is the protein from the Protein data bank or a homology model? </div>
<div>=A0</div>
<div>If from the PDB, you can use PDBePISA to get the biological assembly (=
if thats what the dimer is). You can launch=A0PDBePISA from the EMBL-EBI we=
bsite and its straightforward to use.=A0</div>
<div>=A0</div>
<div>If its a model, you may have to build it as a dimer.<br></div>
<div>I hope that helps,</div>
<div>Symon<br></div>
<div class=3D"gmail_quote">On Fri, Apr 20, 2012 at 7:58 AM, Rama Camara ram=
atoulie.camara,+,<a href=3D"http://live.uwe.ac.uk">live.uwe.ac.uk</a> <span=
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<blockquote style=3D"BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PA=
DDING-LEFT:1ex" class=3D"gmail_quote"><br>Sent to CCL by: &quot;Rama =A0Cam=
ara&quot; [ramatoulie.camara##<a href=3D"http://live.uwe.ac.uk/" target=3D"=
_blank">live.uwe.ac.uk</a>]<br>
Hi all,<br><br>I have a protein monomer which I&#39;d like to reform to its=
 dimer. I was wondering if anyone out there knows of a program (free ones i=
f possible )I can use to do this and how to do it.<br><br>Any tips/suggesti=
ons will be highly appreciated.<br>
<br>Thanks.<br><br>Rama<br><br><br><br>-=3D This is automatically added to =
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--f46d04428d7639f99004be204aca--


From owner-chemistry@ccl.net Fri Apr 20 17:20:00 2012
From: "Nikita Matsunaga Nikita.Matsunaga-$-liu.edu" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Avoided crossing
Message-Id: <-46746-120420111633-6972-xbItW1+VDHdwJx0tg2R2Lg**server.ccl.net>
X-Original-From: Nikita Matsunaga <Nikita.Matsunaga(~)liu.edu>
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Date: Fri, 20 Apr 2012 15:16:25 +0000
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Sent to CCL by: Nikita Matsunaga [Nikita.Matsunaga()liu.edu]

You can calculate minimum energy crossing point between two states of different spins, such as singlet and triplet,  in GAMESS. (In $CONTRL RUNTYP=MEX would do the trick.)  The states of the same symmetry and spin can mix, and causes derivative coupling to be non-zero near or at either conical intersection or avoided crossing.  There is no mixing between singlet and triplet states in the non-relativistic quantum chemistry, hence the two states have to cross. The states can mix when spin-orbit coupling is introduced.

Nikita


On Apr 20, 2012, at 8:47 AM, Abrash, Sam sabrash{}richmond.edu wrote:

> 
> Sent to CCL by: "Abrash, Sam" [sabrash**richmond.edu]
> As far as I understand it, avoided crossings are always between states of the same symmetry, so there wouldn't be an avoided crossing between a singlet and a triplet state.
> 
> 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
> Web-page:  http://www.richmond.edu/~sabrash
> "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
> 
> -----Original Message-----
>> From: owner-chemistry+sabrash==richmond.edu|*|ccl.net [mailto:owner-chemistry+sabrash==richmond.edu|*|ccl.net] On Behalf Of Walid M. I. Hassan walid_m76.:.yahoo.com
> Sent: Thursday, April 19, 2012 7:37 PM
> To: Abrash, Sam
> Subject: CCL:G: Avoided crossing
> 
> 
> Sent to CCL by: "Walid M. I. Hassan" [walid_m76|-|yahoo.com]
> Dear Scientists
> 
> long time since I send email via this list,
> my question is very simple does anyone know a software to determine the 
> avoided crossing or conical intersection between singlet and triplet states, 
> i mean states of different multiplicity
> 
> In Gaussian 09 manual, in Opt keyword ,under conical option it is written, 
> "Search for a conical intersection or avoided crossing using the state-
> averaged CASSCF method. Avoided is a synonym for Conical. Note that 
> CASSCF=SlaterDet is needed in order to locate a conical intersection between 
> a singlet state and a triplet state." 
> I tried this and find it is impossible since in input file you determine a 
> singlet or triplet multiplicity but not both
> 
> and SlaterDet option just reverse the spin but do not change multiplicity
> see this part of output to see the configurations
> 
> when I use singlet state with No SLATER DETERMINANT
>> I get the following configuration
>>       Configuration      1 Symmetry 1 111000
>>       Configuration      2 Symmetry 1 11ab00
>>       Configuration      3 Symmetry 1 110100
>>       Configuration      4 Symmetry 1 1a1b00
>> 
>> 
>> which become as follows with SLATER DETERMINANT
>>       Configuration      1 Symmetry 1 111000
>>       Configuration      2 Symmetry 1 11ba00
>>       Configuration      3 Symmetry 1 11ab00
>>       Configuration      4 Symmetry 1 1b1a00
>>       Configuration      5 Symmetry 1 11b0a0
>> 
>> 
>> for triplet state in both cases i get the following configuration
>> Configuration      1 Symmetry 1 11aa00
>>       Configuration      2 Symmetry 1 11a0a0
>>       Configuration      3 Symmetry 1 1a1a00
>>       Configuration      4 Symmetry 1 110aa0
> 
> as you can see SlaterDet option reverse ab to ba but not to aa
> I want to get conical intersection or avoided crossing between
> Configuration      1 Symmetry 1 111000 of singlet and
> Configuration      1 Symmetry 1 11aa00 of triplet state
> 
> I sent this question to Gaussian team and their reply was not convincing to 
> me, I will put it here for your reference,
> I think they just go around the problem to claim that there is no problem in 
> the manual
> i think gaussian program can not do it
> if i am wrong i will appreciate if you guide me
> If i am write so what program can find this conical intersection for me
> sorry for long email but i think it won't show my point if it is shorter 
> 
>   Dr. Ibrahim,
> 
>    Thank you for giving us a chance to comment.
> 
>    When you look at those configuration lists you are not actually
> looking a lists of identical things.  The singlet without Slater Determinant
> is a list of configurations, fixed linear combinations of determinants
> giving singlets.  So there will be no triplet terms in this expansion
> and the higher roots of the CASSCF equations will all be singlets as
> well.
> 
>    The second case lists determinants directly and generates singlets
> and m(l)=0 triplets.  So configurations 2 and 3 are a pair of determinants
> which can contribute to both singlets and triplets with the sign difference
> carried on the CI expansion coefficients, not on the determinants
> directly.
> 
>      The third case correspond to a ground state triplet, m(l)=+/-1 
> and no singlet contributions are possible.  Again any excited states will
> be triplets so this reference is not suitable for the crossing.
> 
>      So the program can compute the crossing you desire by using a 
> singlet reference with SlaterDet included in the option list.  You
> should still solve for the first few roots to confirm that you have
> the second root corresponding to the triplet you expected.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> 
> 

$B?N>kB]_[(B $B>>1J(B
Nikita.Matsunaga]_[liu.edu