From owner-chemistry@ccl.net Sat Sep 11 05:52:01 2010
From: "Boes, Fabian Fabian.Boes,+,certara.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Free European Tripos Symposium and Workshop, 2nd (and/or 3rd) November 2010, Frankfurt, Germany
Message-Id: <-42737-100910191404-3165-YpTkGrkpK+OLp4Fhu0z+dw * server.ccl.net>
X-Original-From: "Boes, Fabian" <Fabian.Boes^certara.com>
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Date: Fri, 10 Sep 2010 17:17:38 -0500
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Sent to CCL by: "Boes, Fabian" [Fabian.Boes,+,certara.com]
You are cordially invited to join us for a one day symposium and/or a SYBYL-X hands-on workshop.

Hear colleagues from industry speak about:

* Employing virtual screening with web technologies to empower scientists (Bayer CropScience)
* Structure and ligand-based molecular invention workflows using Muse (JOHNSON & JOHNSON)
* Easily identifying closely related analogs with property examination (Elara Pharmaceuticals)

Further topics covered by Tripos scientists include:

* Substructural filtering to eradicate frequent hitters in biochemical high throughput screens
* Torsional profiling effects when starting with multi-conformers in 3D pharmacophore searching
* Enhanced docking utilizing protein flexibility, tuned scoring functions and fragment placement

The workshop will conclude with a special free networking culinary event where we can take a rest from generating ideas for chemists to make and physically create ourselves something great. So join us for this gastronomy workshop to prepare and enjoy a 3-5 course gourmet meal.

In addition or alternatively, attend a hands-on workshop the following day on the 3rd November to experience:

* Improved docking workflows, with easy access to fragment-guided docking and improved scoring via protein pocket adaptation
* Getting introduced and instantly familiar with the new easy to use QSAR workflow
* Employing pharmacophore searching with SYBYL-X’s UNITY, creating pharmacophores, running database searches, and using tips and tricks to improve results

Attendees to the workshop are asked to bring their own laptops if available - Tripos will install SYBYL-X on you laptop for use during the workshop and each attendee will receive a license for an additional 30 day trial period.

To register for this free event and read the full agenda, please click on the link below.

http://bit.ly/9AxwsU

Kind regards
Fabian
_________________________________________________________________
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From owner-chemistry@ccl.net Sat Sep 11 09:40:00 2010
From: "Partha Biswas partha361*gmail.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL:G: grid=ultrafine command in Q-Chem package
Message-Id: <-42738-100911075212-1568-cj9X1MRkMVAZGFxIFBODbw(!)server.ccl.net>
X-Original-From: "Partha  Biswas" <partha361{=}gmail.com>
Date: Sat, 11 Sep 2010 07:52:10 -0400


Sent to CCL by: "Partha  Biswas" [partha361(0)gmail.com]
Dear all,

Can anyone suggest how to use grid=ultrafine command in the geometry optimization job using Q-Chem pachkge? int(grid=ultrafine)---- this specification is avaliable in G03 package especially when you are using DFT method for geometry optimization.

Thanks in advance.

Regards,
Partha Biswas


From owner-chemistry@ccl.net Sat Sep 11 10:15:00 2010
From: "Andreas Klamt klamt]|[cosmologic.de" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Gsolv - pKa - Frequency
Message-Id: <-42739-100911101332-5111-WaVp+qXFl8iENqxW61+LEw]*[server.ccl.net>
X-Original-From: Andreas Klamt <klamt]-[cosmologic.de>
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Date: Sat, 11 Sep 2010 16:13:25 +0200
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Sent to CCL by: Andreas Klamt [klamt()cosmologic.de]
  Dear Toomas,

indeed, I have submitted such a paper recently together with a group in 
Australia.
I hope it appears soon.

Andreas

Am 10.09.2010 12:01, schrieb Toomas Tamm tt-ccl2(0)yki.ttu.ee:
> Sent to CCL by: Toomas Tamm [tt-ccl2,,yki.ttu.ee]
> On Sun, 2010-09-05 at 10:45 -0500, Christopher Cramer cramer..umn.edu
> wrote:
>
>>   At that point, the "best" (in my opinion) way to define the free
>> energy in solution is to do a continuum calculation and add the
>> derived free energy of solvation to the gas phase free energy.
> I have been using this (or similar) schemes and trying to very briefly
> justify them in the resulting papers. This has led to questions from
> reviewers about the approximations, and I have had no better place to
> refer them to than the CCL archives.
>
> Is there a research paper (or book) which could be referenced which
> would explain and justify this way of calculating free energies in
> solution? If there is none, here is a suggestion to someone
> authoritative (Chris, Andreas, ...) to write one.
>


-- 
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH&  Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt|-|cosmologic.de
web    	www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt


From owner-chemistry@ccl.net Sat Sep 11 13:09:01 2010
From: "Marcel Swart marcel.swart- -icrea.es" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Gsolv - pKa - Frequency
Message-Id: <-42740-100911130738-22552-qg7wiMGDx65Y0TFj817OWw]*[server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart*icrea.es>
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Date: Sat, 11 Sep 2010 19:07:25 +0200
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Sent to CCL by: Marcel Swart [marcel.swart**icrea.es]
See e.g.

Thirty years of continuum solvation chemistry: a review, and prospects for the near future
Jacopo Tomasi
Theor Chem Acc (2004) 112: 184–203

Quantum Mechanical Continuum Solvation Models
Jacopo Tomasi, Benedetta Mennucci, and Roberto Cammi
Chem. Rev. 2005, 105, 2999−3093

On Sep 10, 2010, at 12:01 PM, Toomas Tamm tt-ccl2(0)yki.ttu.ee wrote:

> I have been using this (or similar) schemes and trying to very briefly
> justify them in the resulting papers. This has led to questions from
> reviewers about the approximations, and I have had no better place to
> refer them to than the CCL archives.
> 
> Is there a research paper (or book) which could be referenced which
> would explain and justify this way of calculating free energies in
> solution? If there is none, here is a suggestion to someone
> authoritative (Chris, Andreas, ...) to write one. 


===================================
dr. Marcel Swart

ICREA Research Professor at
Institut de Química Computacional
Universitat de Girona

Parc Científic i Tecnològic
Edifici Jaume Casademont (despatx A-27)
Pic de Peguera 15
17003 Girona
Catalunya (Spain)

tel
+34-972-183240
fax
+34-972-183241
e-mail
marcel.swart-x-icrea.es
marcel.swart-x-udg.edu
web
http://www.marcelswart.eu
===================================


From owner-chemistry@ccl.net Sat Sep 11 15:15:00 2010
From: "Eric B. Isaacs ebisaacs*o*gmail.com" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL:G: grid=ultrafine command in Q-Chem package
Message-Id: <-42741-100911151249-4738-VoP6GyFL90BNUTMsL2JyWQ(!)server.ccl.net>
X-Original-From: "Eric B. Isaacs" <ebisaacs{:}gmail.com>
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Sent to CCL by: "Eric B. Isaacs" [ebisaacs:+:gmail.com]
Hi Partha,

The density of the grid can be controlled with the "xc_grid" keyword  
in the $rem section, with the Euler-Maclaurin scheme for radial points  
and the Lebedev or Gauss-Legendre schemes for angular points (see  
section 4.3.6 of the Q-Chem manual). I believe Grid=UltraFine requests  
a (99, 590) grid.

Also, I'm not sure if this feature is current, but you might try to  
run Q-Chem with a Gaussian input file that has the ultrafine grid with  
the "-g" flag in the Q-Chem command line, which as I understand it  
converts Gaussian input format to that of Q-Chem.

Regards,
Eric



On Sep 11, 2010, at 4:52 AM, Partha Biswas partha361*gmail.com wrote:

>
> Sent to CCL by: "Partha  Biswas" [partha361(0)gmail.com]
> Dear all,
>
> Can anyone suggest how to use grid=ultrafine command in the geometry  
> optimization job using Q-Chem pachkge? int(grid=ultrafine)---- this  
> specification is avaliable in G03 package especially when you are  
> using DFT method for geometry optimization.
>
> Thanks in advance.
>
> Regards,
> Partha Biswas
>
>
>
> -= This is automatically added to each message by the mailing script  
> =-
> To recover the email address of the author of the message, please  
> change> Conferences: http://server.ccl.net/chemistry/announcements/ 
> conferences/>
>


From owner-chemistry@ccl.net Sat Sep 11 15:49:00 2010
From: "Ernst-Walter Knapp knapp[-]chemie.fu-berlin.de" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Gsolv - pKa - Frequency
Message-Id: <-42742-100911111814-31671-9vYtzCEF0CDgFjgyTXpMHg]~[server.ccl.net>
X-Original-From: Ernst-Walter Knapp <knapp|*|chemie.fu-berlin.de>
Content-Type: multipart/alternative;
 boundary="------------030003030905070906090009"
Date: Sat, 11 Sep 2010 17:07:36 +0200
MIME-Version: 1.0


Sent to CCL by: Ernst-Walter Knapp [knapp===chemie.fu-berlin.de]
This is a multi-part message in MIME format.
--------------030003030905070906090009
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Content-Transfer-Encoding: 7bit

  Dear Toomas,

Your view is completely right.
We recently showed how one can compute pKas
and redox potentials for a number of different chemical compounds.
The RMSDs with measured values are about half a pH unit and
50 mV, respectively.
See
M. Schmidt am Busch and E.W. Knapp: Accurate pK_a determination for a 
heterogeneous set of organic molecules, ChemPhysChem *5* (2004) 1513--1522.
and
M. Schmidt am Busch and E.W. Knapp: One-electron reduction potential for 
oxygen- and sulfur-centered organic radicals in protic and aprotic 
solvents, J. Am. Chem. Soc. *127* (2005) 15730-15737.

By alternating the DFT functional and combining it with a post SCF corretion
we could also compute redox potentials of single nuclear transition 
metal complexes
involving Fe, Ni, Mn with RMSDs to measured values of about 60 mV.
See:
A. Galstyan and E.W. Knapp: Accurate redox potential computations of 
mononuclear iron, manganese and nickel model complexes, J. Comp. Chem. 
*30* (2009) 203-211.

Best wishes, Walter

-- 

|---------------------------------------------------------------------|
|  Dr. Ernst-Walter Knapp            email: knapp_-_chemie.fu-berlin.de |
|  Free University of Berlin                   Tel.: +49 30 838 54387 |
|  Department of Biology, Chemistry, Pharmacy  Fax.: +49 30 838 56921 |
|  Institute of Chemistry&  Biochemistry                              |
|  Macromolecular Modeling and Simulation of Biomolecular Systems     |
|  Fabeckstrasse 36A                                                  |
|  D-14195 Berlin                                                     |
|  Germany                    www: http://agknapp.chemie.fu-berlin.de |
|---------------------------------------------------------------------|




Am 11.09.2010 16:13, schrieb Andreas Klamt klamt]|[cosmologic.de:
>
> Sent to CCL by: Andreas Klamt [klamt()cosmologic.de]
>  Dear Toomas,
>
> indeed, I have submitted such a paper recently together with a group 
> in Australia.
> I hope it appears soon.
>
> Andreas
>
> Am 10.09.2010 12:01, schrieb Toomas Tamm tt-ccl2(0)yki.ttu.ee:
>> Sent to CCL by: Toomas Tamm [tt-ccl2,,yki.ttu.ee]
>> On Sun, 2010-09-05 at 10:45 -0500, Christopher Cramer cramer..umn.edu
>> wrote:
>>
>>>   At that point, the "best" (in my opinion) way to define the free
>>> energy in solution is to do a continuum calculation and add the
>>> derived free energy of solvation to the gas phase free energy.
>> I have been using this (or similar) schemes and trying to very briefly
>> justify them in the resulting papers. This has led to questions from
>> reviewers about the approximations, and I have had no better place to
>> refer them to than the CCL archives.
>>
>> Is there a research paper (or book) which could be referenced which
>> would explain and justify this way of calculating free energies in
>> solution? If there is none, here is a suggestion to someone
>> authoritative (Chris, Andreas, ...) to write one.
>>
>
>



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    Dear Toomas, <br>
    <br>
    Your view is completely right. <br>
    We recently showed how one can compute pKas <br>
    and redox potentials for a number of different chemical compounds. <br>
    The RMSDs with measured values are about half a pH unit and <br>
    50 mV, respectively. <br>
    See <br>
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<![endif]--><span style="font-size: 11pt; font-family: Helvetica;"
      lang="EN-US">M.
      Schmidt am Busch and E.W. Knapp: Accurate pK<sub>a</sub>
      determination for a
      heterogeneous set of organic molecules, ChemPhysChem <b>5</b>
      (2004) 1513</span><span style="font-size: 11pt; font-family:
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<![endif]--><span style="font-size: 11pt; font-family: Helvetica;"
      lang="EN-US">M.
      Schmidt am Busch and E.W. Knapp: One-electron reduction potential
      for oxygen-
      and sulfur-centered organic radicals in protic and aprotic
      solvents, </span><span style="font-size: 11pt; font-family:
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    <br>
    By alternating the DFT functional and combining it with a post SCF
    corretion<br>
    we could also compute redox potentials of single nuclear transition
    metal complexes <br>
    involving Fe, Ni, Mn with RMSDs to measured values of about 60 mV. <br>
    See: <br>
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<![endif]--><span style="font-size: 11pt; font-family: Helvetica;"
      lang="EN-GB">A.
      Galstyan and E.W. Knapp: Accurate redox potential computations of
      mononuclear
      iron, manganese and nickel model complexes, </span><span
      style="font-size: 11pt; font-family: Helvetica;" lang="EN-US">J.
      Comp. Chem. <b style="">30</b> </span><st1:phone o:ls="trans"
      w:st="on"><span style="font-size: 11pt; font-family: Helvetica;"
        lang="EN-GB">(2009) 203-211</span></st1:phone><span
      style="font-size: 11pt; font-family: Helvetica;" lang="EN-GB">.</span><br>
    <br>
    Best wishes, Walter <br>
    <br>
    <pre class="moz-signature" cols="72">-- 

|---------------------------------------------------------------------|
|  Dr. Ernst-Walter Knapp            email: <a class="moz-txt-link-abbreviated" href="mailto:knapp_-_chemie.fu-berlin.de">knapp_-_chemie.fu-berlin.de</a> |                  
|  Free University of Berlin                   Tel.: +49 30 838 54387 |
|  Department of Biology, Chemistry, Pharmacy  Fax.: +49 30 838 56921 |
|  Institute of Chemistry &amp; Biochemistry                              |
|  Macromolecular Modeling and Simulation of Biomolecular Systems     |
|  Fabeckstrasse 36A                                                  |
|  D-14195 Berlin                                                     |
|  Germany                    www: <a class="moz-txt-link-freetext" href="http://agknapp.chemie.fu-berlin.de">http://agknapp.chemie.fu-berlin.de</a> |
|---------------------------------------------------------------------|</pre>
    <br>
    <br>
    <br>
    Am 11.09.2010 16:13, schrieb Andreas Klamt klamt]|[cosmologic.de:
    <blockquote
cite="mid:-id%234dg-42739-100911101332-5111-cISwCrpdtj1+sFWQsg6kXg_-_server.ccl.net"
      type="cite">
      <br>
      Sent to CCL by: Andreas Klamt [klamt()cosmologic.de]
      <br>
       Dear Toomas,
      <br>
      <br>
      indeed, I have submitted such a paper recently together with a
      group in Australia.
      <br>
      I hope it appears soon.
      <br>
      <br>
      Andreas
      <br>
      <br>
      Am 10.09.2010 12:01, schrieb Toomas Tamm tt-ccl2(0)yki.ttu.ee:
      <br>
      <blockquote type="cite">Sent to CCL by: Toomas Tamm
        [tt-ccl2,,yki.ttu.ee]
        <br>
        On Sun, 2010-09-05 at 10:45 -0500, Christopher Cramer
        cramer..umn.edu
        <br>
        wrote:
        <br>
        <br>
        <blockquote type="cite">  At that point, the "best" (in my
          opinion) way to define the free
          <br>
          energy in solution is to do a continuum calculation and add
          the
          <br>
          derived free energy of solvation to the gas phase free energy.
          <br>
        </blockquote>
        I have been using this (or similar) schemes and trying to very
        briefly
        <br>
        justify them in the resulting papers. This has led to questions
        from
        <br>
        reviewers about the approximations, and I have had no better
        place to
        <br>
        refer them to than the CCL archives.
        <br>
        <br>
        Is there a research paper (or book) which could be referenced
        which
        <br>
        would explain and justify this way of calculating free energies
        in
        <br>
        solution? If there is none, here is a suggestion to someone
        <br>
        authoritative (Chris, Andreas, ...) to write one.
        <br>
        <br>
      </blockquote>
      <br>
      <br>
    </blockquote>
    <br>
    <br>
    <pre class="moz-signature" cols="72">
</pre>
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