From owner-chemistry@ccl.net Wed Mar 25 03:30:01 2009
From: "Benjamin Roberts benjamincharlesroberts_._gmail.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: Flory-Huggins chi parameters for strongly interacting ionic species
Message-Id: <-38922-090325032818-28833-uLKFsMDRELJaYPQRwkrGLA##server.ccl.net>
X-Original-From: Benjamin Roberts <benjamincharlesroberts++gmail.com>
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Date: Wed, 25 Mar 2009 16:28:07 +0900
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Sent to CCL by: Benjamin Roberts [benjamincharlesroberts(!)gmail.com]
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Dear list,

I am using computational methods to calculate Flory-Huggins chi parameters
(for input into DPD simulations) via the energy of mixing E(mix). I have
used fragment based approaches (Materials Studio "Blends") and also,
separately, molecular dynamics simulations of condensed phases of the pure
and mixed components to determine E(mix) from cohesive energy densities.

My problem is the my system includes polycations and polyanions that
interact strongly by Coloumbic forces. The chi parameters I obtain are
extremely large and negative (in some cases in the negative hundreds or
thousands). These values cannot be used to generate meaningful DPD repulsion
parameters by the commonly used Groot & Warren approach, because the
repulsions have a negative sign and the DPD simulation physics are no longer
meaningful.

Has anyone parameterised a similar system for DPD using chi parameters, or
can suggest an alternative approach?

Thanks for your consideration,

Benjamin.

--000e0cd18264e4073c0465ec7021
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<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Dear
list,</span></p>

<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">I am
using computational methods to calculate Flory-Huggins chi parameters (for
input into DPD simulations) via the energy of mixing E(mix). I have used
fragment based approaches (Materials Studio &quot;Blends&quot;) and also,
separately, molecular dynamics simulations of condensed phases of the pure and
mixed components to determine E(mix) from cohesive energy densities.</span></p>

<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">My
problem is the my system includes polycations and polyanions that interact
strongly by Coloumbic forces. The chi parameters I obtain are extremely large
and negative (in some cases in the negative hundreds or thousands). These
values cannot be used to generate meaningful DPD repulsion parameters by the commonly
used Groot &amp; Warren approach, because the repulsions have a negative sign
and the DPD simulation physics are no longer meaningful.</span></p>

<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Has
anyone parameterised a similar system for DPD using chi parameters, or can
suggest an alternative approach?</span></p>

<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Thanks
for your consideration,</span></p>

<p class="MsoNormal" style="mso-pagination:none;mso-layout-grid-align:none;
text-autospace:none"><span style="font-size:10.0pt;font-family:Arial">Benjamin.</span></p>

--000e0cd18264e4073c0465ec7021--


From owner-chemistry@ccl.net Wed Mar 25 06:14:01 2009
From: "Ting Li Ting.Li_+_chem.kuleuven.be" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: Flory-Huggins chi parameters for strongly interacting ionic species
Message-Id: <-38923-090325060926-4237-ZbkFe/8ZcJbPugo9kFNaLg ~~ server.ccl.net>
X-Original-From: Ting Li <Ting.Li .. chem.kuleuven.be>
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Date: Wed, 25 Mar 2009 11:09:00 +0100
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Sent to CCL by: Ting Li [Ting.Li ~ chem.kuleuven.be]
Hi, Benjamin,

According to my experience, method like that used in "Blends" is not 
suitable for a system
with strong specific interaction, such as hydrogen-bonding, dipole 
interaction or electrostatic,
although it's reasonably good for some system composed by apolar 
molecules. the reason is
some interaction is long ranged (like electrostatic) or highly 
directional (like HBoding), and these
are not handled correctly or applicable in that "fragment based 
algorithm". Therefore, you should
not expect good results. In addition, in this kind of algorithm 
molecules are kept rigid, which is another
critical approximation for some molecule to form favorite interaction by 
adapting themselves.

Furthermore, I doubt if you could simply apply the original 
Flory-Huggins theory in a highly charged
system. Try to look for modified versions or other theory.

Best regards,
Ting Li

---------------------------------------------------------
Molecular and Nanomaterials, Department of Chemistry
Katholieke Universiteit Leuven (KULeuven)
Celestijnenlaan 200F, B-3001 Heverlee, Belgium

Email: Ting.Li:_:chem.kuleuven.be
Tel: 32-16-327614 or 327481
---------------------------------------------------------



Benjamin Roberts benjamincharlesroberts_._gmail.com wrote:
>
> Dear list,
>
> I am using computational methods to calculate Flory-Huggins chi 
> parameters (for input into DPD simulations) via the energy of mixing 
> E(mix). I have used fragment based approaches (Materials Studio 
> "Blends") and also, separately, molecular dynamics simulations of 
> condensed phases of the pure and mixed components to determine E(mix) 
> from cohesive energy densities.
>
> My problem is the my system includes polycations and polyanions that 
> interact strongly by Coloumbic forces. The chi parameters I obtain are 
> extremely large and negative (in some cases in the negative hundreds 
> or thousands). These values cannot be used to generate meaningful DPD 
> repulsion parameters by the commonly used Groot & Warren approach, 
> because the repulsions have a negative sign and the DPD simulation 
> physics are no longer meaningful.
>
> Has anyone parameterised a similar system for DPD using chi 
> parameters, or can suggest an alternative approach?
>
> Thanks for your consideration,
>
> Benjamin.
>

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm


From owner-chemistry@ccl.net Wed Mar 25 09:08:00 2009
From: "mi yang shabbir3790 ~ hotmail.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: missing reply Enthalpy Vs Thermal Stability
Message-Id: <-38924-090325025532-23768-2MWc9WhrMRRngvTCuTsHKA%x%server.ccl.net>
X-Original-From: "mi  yang" <shabbir3790 : hotmail.com>
Date: Wed, 25 Mar 2009 02:55:28 -0400


Sent to CCL by: "mi  yang" [shabbir3790%hotmail.com]


 Dear ccl users,
 I have calculated the enthalpy of a reaction of the formation an alkali metal
 complex A+B=C. Now my value is higher than previous similar complexes enthalpy
 of formation values, Let say previous is positive 8 kalCal/mol and mine is 15
 Kalcal/mol.
 Now can I say my design complex can be more thermally stable than the previous
 ones.?
 thanx for answer...


From owner-chemistry@ccl.net Wed Mar 25 10:53:00 2009
From: "taner atalar taneratalar|*|gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: softwares for catalyst subject
Message-Id: <-38925-090325105144-2049-LlVmcsOIAH5Q0wDNKujL+Q]*[server.ccl.net>
X-Original-From: taner atalar <taneratalar[#]gmail.com>
Content-Type: multipart/alternative; boundary=0015174be6d28631db0465f2a251
Date: Wed, 25 Mar 2009 16:51:30 +0200
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Sent to CCL by: taner atalar [taneratalar[*]gmail.com]
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Dear CCL users,

I  plan to work on some homogeneous and heterogeneus catalyst (their design
and/or mechanisms).

So can you recommend me any programmes which are especially good for this
purpose ?

I am waiting your recommendations

Thank you very much for your valuable advices ...


Note:

I prefer softawares which are working in windows operating system
"Also easy to use" is another important factor for me

Taner Atalar

--0015174be6d28631db0465f2a251
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Content-Transfer-Encoding: quoted-printable

<div>Dear CCL users,</div>
<div>=A0</div>
<div>I=A0 plan to=A0work on=A0some homogeneous and heterogeneus catalyst=A0=
(their design and/or mechanisms).</div>
<div>=A0</div>
<div>So can you=A0recommend me any=A0programmes which are especially good f=
or this purpose ?</div>
<div>=A0</div>
<div>I am waiting your recommendations</div>
<div>=A0</div>
<div>Thank you very much for your valuable advices ...</div>
<div>=A0</div>
<div>=A0</div>
<div>Note:</div>
<div>=A0</div>
<div>I prefer=A0softawares which are working in windows=A0operating system=
=A0</div>
<div>&quot;Also easy to use&quot; is another important factor for me</div>
<div>=A0</div>
<div>Taner Atalar</div>

--0015174be6d28631db0465f2a251--


From owner-chemistry@ccl.net Wed Mar 25 12:48:01 2009
From: "Nir London nir+/-rosettadesigngroup.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Rosetta Academic Training Webinar
Message-Id: <-38926-090325124701-7389-k3+WSptwuVJkeLT9rOkTpw() server.ccl.net>
X-Original-From: "Nir  London" <nir[a]rosettadesigngroup.com>
Date: Wed, 25 Mar 2009 12:46:58 -0400


Sent to CCL by: "Nir  London" [nir_._rosettadesigngroup.com]
The Rosetta Design Group is proud to present the first webinar in the Rosetta Academic Workshop 
Series. For the first webinar, we have selected to focus on Protein-Protein Docking based on the 
answers to the interest poll. We hope this will be the first in a line of helpful and inspiring webinars to 
kick-off our Rosetta Academic Workshop Series.

What: Protein-Protein Docking
When: May 4th 2009, 0800-1000 AM EST

Where: Your office!

Visit here for more details and registration:
http://rosettadesigngroup.com/RDGLS/index.php?sid=54479&lang=en

Pleas note: This is not a promotional webinar. Rosetta is open-source and freeware for academic and 
non-profit organizations and can be downloaded here from University of Washington's TechTransfer 
Digital Ventures. The majority of the webinar is concerned with Rosetta 2.3.0. Rosetta 3.0 is still a beta 
version.

Hope to see you there,

Nir London.

Rosetta Design Group | http://rosettadesigngroup.com/


From owner-chemistry@ccl.net Wed Mar 25 13:29:01 2009
From: "Johannes Pfister pfister]^[chemie.uni-wuerzburg.de" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: electrostatic potentials of excited states
Message-Id: <-38927-090325093245-10280-ZJlsyfeNbMsydqnUonUZig**server.ccl.net>
X-Original-From: "Johannes  Pfister" <pfister__chemie.uni-wuerzburg.de>
Date: Wed, 25 Mar 2009 09:32:41 -0400


Sent to CCL by: "Johannes  Pfister" [pfister_+_chemie.uni-wuerzburg.de]
Hi

I try to get electrostatic potentials of excited states, but so far I failed.
My approaches so far:
I used Turbomole5.10 with the option "$pointval pot" which genereates a file called tp.plt, which I should be able to visualize with gopenmole. But if I try to do the same for the excited state I get the groundstate again, since this file is generated during the dscf step, and not during escf. So even if I could visualize the electrostatic potential with gopenmole, it will simply look the same as the one for the ground state.
I also tried Gaussian 03 Revision B.04. First I calculated for a sample molecule ground and excited state (HF/TDHF) and added the option pop=reg to get the electrostatic pot. That works fine and I can get the picture using gaussview (open .chk file; results; surfaces; new cube -> total density; dscf matrix; new mapped surfaces; ESP; dscf matrix). But it doesn't matter if I use the .chk file of the ground or excited state, the electrostat.pot. always looks identical. I even tried to switch the density matrix from dscf to CI using not only TD-HF but CIS, but still I can only apply the dscf-matrix. I even tried to calculate this gaussian job by gaussview directly, but that didn't change anything for the better.

So my question is: Is it in principle possible to get an electrostatic potential for the excited state with either Turbomole or Gaussian, and can someone tell me how exactly I must do this?

Best regards

                         Johannes Pfister

email: pfister~~chemie.uni-wuerzburg.de


From owner-chemistry@ccl.net Wed Mar 25 14:04:01 2009
From: "Bora karasulu bkarasulu+*+ku.edu.tr" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL:G: G03: l103 link error
Message-Id: <-38928-090325061150-4479-MER7+ERLzZINH5Lwsbh+gA#,#server.ccl.net>
X-Original-From: "Bora  karasulu" <bkarasulu(a)ku.edu.tr>
Date: Wed, 25 Mar 2009 06:11:47 -0400


Sent to CCL by: "Bora  karasulu" [bkarasulu^-^ku.edu.tr]
Hi everybody,
I am a new user of CCL and using Gaussian03 to carry out reaction path calculations for an ONIOM layer system.
As far as I know, for the ONIOM systems, people use opt=path keyword for IRC (or reaction path) calculations. Is this the correct method for doing IRC with ONIOM layered systems, or is there some other methods (or keywords).

On the other hand, when I apply the opt=path with optreactant and optproduct keywords with uff=qeq basis set, I get the error message that is "Point 1 is the highest energy point". Is there something to prevent this error. I have some other problems with opt=path method I will ask them later, if I can fix this problem.

Thanks in advance,

Best regrads,
Bora Karasulu


From owner-chemistry@ccl.net Wed Mar 25 15:57:01 2009
From: "Sebastian Kozuch kozuchs _ yahoo.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: softwares for catalyst subject
Message-Id: <-38929-090325130142-14246-4hPUVTgXOF6FXrfBj3gHyA ~~ server.ccl.net>
X-Original-From: Sebastian Kozuch <kozuchs ~~ yahoo.com>
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Date: Wed, 25 Mar 2009 09:01:29 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Sebastian Kozuch [kozuchs(_)yahoo.com]

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Content-Type: text/plain; charset=us-ascii

To calculate the TOF or compare catalysts by their efficiency from the energies of intermediates and transition states there is an excel file in the supporting information of J Phys Chem A 2008, 112, 6032. This is based on the energetic span model. But of course you need to have the energies calculated by a QM program. 

 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
...The Lise Meitner-Minerva Center...
.for Computational Quantum Chemistry.
...Hebrew University of Jerusalem....
.....kozuchs_._yfaat.ch.huji.ac.il.....
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx




________________________________
> From: taner atalar taneratalar|*|gmail.com <owner-chemistry_._ccl.net>
To: "Kozuch, Sebastian " <kozuchs_._yahoo.com>
Sent: Wednesday, March 25, 2009 4:51:30 PM
Subject: CCL: softwares for catalyst subject


Dear CCL users,
 
I  plan to work on some homogeneous and heterogeneus catalyst (their design and/or mechanisms).
 
So can you recommend me any programmes which are especially good for this purpose ?
 
I am waiting your recommendations
 
Thank you very much for your valuable advices ...
 
 
Note:
 
I prefer softawares which are working in windows operating system 
"Also easy to use" is another important factor for me
 
Taner Atalar


      
--0-628992724-1237996889=:50694
Content-Type: text/html; charset=us-ascii

<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt">To calculate the TOF or compare catalysts by their efficiency from the energies of intermediates and transition states there is an excel file in the supporting information of J Phys Chem A 2008, 112, 6032. This is based on the energetic span model. But of course you need to have the energies calculated by a QM program. <br><div>&nbsp;</div><span style="font-family: courier,monaco,monospace,sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">..........Sebastian Kozuch...........</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style="font-family:
 courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">...The Lise Meitner-Minerva Center...</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">.for Computational Quantum Chemistry.</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">...Hebrew University of Jerusalem....</span><br style="font-family: courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">.....kozuchs_._yfaat.ch.huji.ac.il.....</span><br style="font-family: courier,monaco,monospace,sans-serif;"><a rel="nofollow" target="_blank" href="http://yfaat.ch.huji.ac.il/kozuch.htm"><span style="font-family: courier,monaco,monospace,sans-serif;">http://yfaat.ch.huji.ac.il/kozuch.htm</span></a><br style="font-family:
 courier,monaco,monospace,sans-serif;"><span style="font-family: courier,monaco,monospace,sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><div><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> taner atalar taneratalar|*|gmail.com &lt;owner-chemistry_._ccl.net&gt;<br><b><span style="font-weight: bold;">To:</span></b> "Kozuch, Sebastian " &lt;kozuchs_._yahoo.com&gt;<br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, March 25, 2009 4:51:30 PM<br><b><span style="font-weight: bold;">Subject:</span></b> CCL: softwares for catalyst subject<br></font><br>
<div>Dear CCL users,</div>
<div>&nbsp;</div>
<div>I&nbsp; plan to&nbsp;work on&nbsp;some homogeneous and heterogeneus catalyst&nbsp;(their design and/or mechanisms).</div>
<div>&nbsp;</div>
<div>So can you&nbsp;recommend me any&nbsp;programmes which are especially good for this purpose ?</div>
<div>&nbsp;</div>
<div>I am waiting your recommendations</div>
<div>&nbsp;</div>
<div>Thank you very much for your valuable advices ...</div>
<div>&nbsp;</div>
<div>&nbsp;</div>
<div>Note:</div>
<div>&nbsp;</div>
<div>I prefer&nbsp;softawares which are working in windows&nbsp;operating system&nbsp;</div>
<div>"Also easy to use" is another important factor for me</div>
<div>&nbsp;</div>
<div>Taner Atalar</div>
</div></div></div><br>



      </body></html>
--0-628992724-1237996889=:50694--


From owner-chemistry@ccl.net Wed Mar 25 16:58:01 2009
From: "Christos S Garoufalis garoufal],[physics.upatras.gr" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL:G: electrostatic potentials of excited states
Message-Id: <-38930-090325164736-12883-rQYIQSi8imYFWOIGX7I61g~~server.ccl.net>
X-Original-From: "Christos S Garoufalis" <garoufal[]physics.upatras.gr>
Date: Wed, 25 Mar 2009 16:47:32 -0400


Sent to CCL by: "Christos S Garoufalis" [garoufal^physics.upatras.gr]
Dear Johannes

As for the turbomole program it might be helpful to check out the end of 
paragraph 9.3.3 of the manual which
discusses the ricc2 module...

As for the gaussian program, perhaps you should try a CIS(root=n) 
calculation using the DENSITY
keyword accordingly. The CIS implementation provides excited state 
densities.

cheers
Christos

> "Johannes Pfister pfister]^[chemie.uni-wuerzburg.de"  wrote:
> 
> Sent to CCL by: "Johannes  Pfister" [pfister_+_chemie.uni-wuerzburg.de]
> Hi
> 
> I try to get electrostatic potentials of excited states, but so far I failed.
> My approaches so far:
> I used Turbomole5.10 with the option "$pointval pot" which genereates a file called tp.plt, which I should be able to visualize with gopenmole. But if I try to do the same for the excited state I get the groundstate again, since this file is generated during the dscf step, and not during escf. So even if I could visualize the electrostatic potential with gopenmole, it will simply look the same as the one for the ground state.
> I also tried Gaussian 03 Revision B.04. First I calculated for a sample molecule ground and excited state (HF/TDHF) and added the option pop=reg to get the electrostatic pot. That works fine and I can get the picture using gaussview (open .chk file; results; surfaces; new cube -> total density; dscf matrix; new mapped surfaces; ESP; dscf matrix). But it doesn't matter if I use the .chk file of the ground or excited state, the electrostat.pot. always looks identical. I even tried to switch the density matrix from dscf to CI using not only TD-HF but CIS, but still I can only apply the dscf-matrix. I even tried to calculate this gaussian job by gaussview directly, but that didn't change anything for the better.
> 
> So my question is: Is it in principle possible to get an electrostatic potential for the excited state with either Turbomole or Gaussian, and can someone tell me how exactly I must do this?
> 
> Best regards
> 
>                          Johannes Pfister
> 
> email: pfister~~chemie.uni-wuerzburg.de
> 
>


From owner-chemistry@ccl.net Wed Mar 25 20:41:01 2009
From: "Babak Khalili khalili.babak**gmail.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL:G: L101 error
Message-Id: <-38931-090325020842-20682-ZsxcWKXTt4YFD/so/1XTvA ~~ server.ccl.net>
X-Original-From: "Babak  Khalili" <khalili.babak]![gmail.com>
Date: Wed, 25 Mar 2009 02:08:38 -0400


Sent to CCL by: "Babak  Khalili" [khalili.babak-,-gmail.com]
Dear all,
How can I solve the problem of L101 (Reads title and molecule specification), in Gaussian 98 to run it. 
Thanks, 
Babak