From owner-chemistry@ccl.net Mon May 23 08:16:00 2011
From: "=?UTF-8?B?R8OcTCBBTFRJTkJBxZ4=?= galtinbas=-=gmail.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: UV spectrum
Message-Id: <-44728-110523080717-28686-FePb7F7dQfjC0zgODhJWkw-#-server.ccl.net>
X-Original-From: =?UTF-8?B?R8OcTCBBTFRJTkJBxZ4=?= <galtinbas,gmail.com>
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Date: Mon, 23 May 2011 15:07:06 +0300
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Sent to CCL by: =?UTF-8?B?R8OcTCBBTFRJTkJBxZ4=?= [galtinbas..gmail.com]
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Hi all,


I got UV spectrum (epsilon versus excitation energy (nm)) from
TD-DFTcomputations using Gaussian 09 and I would like to compare
experimental spectrum in the same graph. But experimental spectrum is
absorbance versus wavelength (nm). Does anybody know how to convert
theoretical epsilon values to theoretical absorbance values?

Thanks in advance


Gul

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Hi all,<br><br><br>I got UV spectrum (epsilon versus excitation energy (nm)=
) from=A0 TD-DFTcomputations using Gaussian 09 and I would like to compare =
experimental spectrum in the same graph. But experimental spectrum is absor=
bance versus wavelength (nm). Does anybody know how to convert theoretical =
epsilon values to theoretical absorbance values?<br>
<br>Thanks in advance<br><br><br clear=3D"all">Gul

--001485f878766a294904a3f04f33--


From owner-chemistry@ccl.net Mon May 23 08:51:00 2011
From: "Roman Affentranger roman###douglasconnect.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL: OpenTox Online Seminar: Integrating OpenTox in Bioclipse (Wed, 25 May, 15:00 CEST)
Message-Id: <-44729-110523032320-23975-MXttaBrSQBN0/JG4ts4VBg..server.ccl.net>
X-Original-From: Roman Affentranger <roman(!)douglasconnect.com>
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Date: Mon, 23 May 2011 09:23:01 +0200
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Sent to CCL by: Roman Affentranger [roman_-_douglasconnect.com]
--bcaec501665b73cacf04a3ec57c8
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Dear All

The OpenTox Bioclipse integration seminar/tutorial will take place *Wednesday,
25 May, at 15:00 CEST*, as indicated in the subject. The date in the body
text was wrong. We apologize for that.


Best regards,

Roman Affentranger

On Sat, May 21, 2011 at 6:07 PM, Roman Affentranger <
roman!^!douglasconnect.com> wrote:

> Dear All:
>
> OpenTox recently initiated a series of online seminars and interactive
> tutorials on topics related to predictive toxicology using a virtual
> conferencing system supporting desktop sharing and voice. The tutorials are
> part of the EU FP7 project OpenTox (www.opentox.org), which aims at
> developing an interoperable open source predictive toxicology
> framework which may be used as an enabling platform for the creation of
> predictive toxicology applications.
>
> The next tutorial will be held *Wednesday, 20 April, at 15:00 CEST*, and
> will describe the approach for integrating OpenTox in Bioclipse,
> complemented with hands-on tutorials showing how to take advantage of
> OpenTox functionality from within Bioclipse via the user interface and
> scripts.
>
> The intended audience is people interested in learning how to use OpenTox
> from within Bioclipse, and people interested in how the integration was
> technically implemented. A bleeding-edge release of Bioclipse will be made
> available for the participants before the tutorial.
>
> Participation in these online events involves no registration fee.
> To register for the seminar, visithttp://www.surveymonkey.com/s/opentoxonline.
>
>
> If you have already registered for a previous OpenTox tutorial this spring
> you don't need to register again.
>
>
> Best regards,
> Roman Affentranger
>
>
> --
> Dr. Roman Affentranger
> R&D Activity Coordinator
> Douglas Connect
> Baermeggenweg 14
> 4314 Zeiningen
> Switzerland
>

--bcaec501665b73cacf04a3ec57c8
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear All<br><br>The OpenTox Bioclipse integration seminar/tutorial will tak=
e place <b>Wednesday, 25 May, at 15:00 CEST</b>, as indicated in the subjec=
t. The date in the body text was wrong. We apologize for that.<br><br><br>
Best regards,<br><br>Roman Affentranger<br><br><div class=3D"gmail_quote">O=
n Sat, May 21, 2011 at 6:07 PM, Roman Affentranger <span dir=3D"ltr">&lt;<a=
 href=3D"mailto:roman!^!douglasconnect.com">roman!^!douglasconnect.com</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;"><div class=3D"im">Dear All:<br><br>OpenTox =
recently initiated a series of online seminars and interactive tutorials on=
 topics related to predictive toxicology using a virtual conferencing syste=
m supporting desktop sharing and voice. The tutorials are part of the EU FP=
7 project OpenTox (<a href=3D"http://www.opentox.org/" target=3D"_blank">ww=
w.opentox.org</a>), which aims at developing an interoperable open source p=
redictive toxicology framework=A0which may be used as an enabling=A0platfor=
m for the creation of predictive toxicology applications.<br>


<br></div>The next tutorial will be held <b>Wednesday, 20 April, at 15:00 C=
EST</b>, and will describe the approach for integrating OpenTox in Bioclips=
e, complemented with hands-on tutorials showing how to take advantage of Op=
enTox functionality from within Bioclipse via the user interface and script=
s.<div class=3D"im">
<br>
The intended audience is people interested in learning how to use OpenTox f=
rom within Bioclipse, and people interested in how the integration was tech=
nically implemented.=A0A bleeding-edge release of Bioclipse will be made av=
ailable for the participants before the tutorial.<br>

<br>Participation in these online events involves no registration fee.<br><=
/div>To register for the seminar, visit<a href=3D"http://www.surveymonkey.c=
om/s/opentoxonline" target=3D"_blank"> http://www.surveymonkey.com/s/opento=
xonline</a>. <br>
<div><div></div><div class=3D"h5">
<br>If you have already registered for a previous OpenTox tutorial this spr=
ing you don&#39;t need to register again.<br><font color=3D"#888888"><br><b=
r></font>Best regards,<br>Roman Affentranger<br><font color=3D"#888888"><br=
>

<br></font>-- <br>Dr. Roman Affentranger<br>R&amp;D Activity Coordinator<br=
>Douglas Connect<br>Baermeggenweg 14<br>4314 Zeiningen<br>Switzerland<br>
</div></div></blockquote></div>

--bcaec501665b73cacf04a3ec57c8--


From owner-chemistry@ccl.net Mon May 23 10:02:00 2011
From: "john doe jeffrey.lebowski]*[gmx.de" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL:G: free energy of solvation
Message-Id: <-44730-110523083313-328-oTvewc81qBCHV0axG72MNQ|*|server.ccl.net>
X-Original-From: "john  doe" <jeffrey.lebowski*_*gmx.de>
Date: Mon, 23 May 2011 08:33:12 -0400


Sent to CCL by: "john  doe" [jeffrey.lebowski : gmx.de]
Hi all.

I'm totally new on the field of solvation in QC.

I calculated the free energy of solvation (DeltaG (solv)) with Gaussian03 via:

..
#p BP86/gen/Auto NoSymm SCF=Tight SCRF(COSMO,read,solvent=Toluene)

0 1
..coords...

..basis set...

SCFVAC
Radii=UAHF

The value is positiv.

 (Unpolarized solute)-Solvent             (kcal/mol) =      -1.21
 (Polarized solute)-Solvent               (kcal/mol) =      -1.44
 Solute polarization                      (kcal/mol) =       0.13
 Total electrostatic                      (kcal/mol) =      -1.32
 --------------------------------------------------------------------
 Cavitation energy                        (kcal/mol) =      98.29
 Dispersion energy                        (kcal/mol) =     -76.33
 Repulsion energy                         (kcal/mol) =      14.46
 Total non electrostatic                  (kcal/mol) =      36.43
 DeltaG (solv)                            (kcal/mol) =      35.11


Does this mean the compound should not be soluble in toluene? (In fact it is soluble) Is a positiv value meaningfull at all? It just means that the energy needed to build the cavity is higher than the stabilization on the solute molecule by the polarizable continuum, right? Can one translate that somehow by saying the loss of solvent-solvent interaction is higher than the gain of solvent-solute interaction?

and another thing:

I have read that the best way to calculate (better: to approximate) the free energy of a molecule in solution (without the COSMOtherm software) is to calculate the free energy in the gas phase and to add the free energy of solvation. I ask myself whether the thermal corrections coming from rotational and translational degrees of freedom should be taken into account for the gas-phase free energy as those degrees of freedom are not really present in soltuion, are they?

Thanks for your time to read this and many thanks in advance for any help!

John


From owner-chemistry@ccl.net Mon May 23 11:29:01 2011
From: "Jens Spanget-Larsen spanget%ruc.dk" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL:G: UV spectrum
Message-Id: <-44731-110523111340-15122-crKhOjnm0r7EYABuAM2XJA() server.ccl.net>
X-Original-From: Jens Spanget-Larsen <spanget_-_ruc.dk>
Content-Type: multipart/alternative;
 boundary="------------080205030800070705070305"
Date: Mon, 23 May 2011 17:13:29 +0200
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Sent to CCL by: Jens Spanget-Larsen [spanget(!)ruc.dk]
This is a multi-part message in MIME format.
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Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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Dear Gul,
I wonder how you got epsilon values from a TD-DFT calculation with 
Gaussian09? I think you are mistaken, the Gaussian print-out lists 
dimensionless oscillator strengths, f. The oscillator strength is 
proportional to the observed integrated absorbance, integrating over the 
whole electronic band profile. Consult textbooks on optical 
spectroscopy, or relevant reviews like the one by Stefan Grimme in 
Reviews in Computational Chemistry, Volume 20, Chapter 3, 2004. Grimme 
has a discussion of this matter and a recommendation on how to simulate 
experimental absorbance curves from calculated theoretical transitions 
under the assumption of a Gaussian line shape (pp 168-169 in this chapter).
Yours, Jens >--<

   ------------------------------------------------------
   JENS SPANGET-LARSEN         Office:      +45 4674 2710
   Dept. of Science (18.1)     Fax:         +45 4674 3011
   Roskilde University         Mobile:      +45 2320 6246
   P.O.Box 260                 E-Mail:     spanget.() .ruc.dk
   DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
   ------------------------------------------------------


On 5/23/2011 14:07, GÜL ALTINBAS, galtinbas=-=gmail.com wrote:
> Hi all,
>
>
> I got UV spectrum (epsilon versus excitation energy (nm)) from  
> TD-DFTcomputations using Gaussian 09 and I would like to compare 
> experimental spectrum in the same graph. But experimental spectrum is 
> absorbance versus wavelength (nm). Does anybody know how to convert 
> theoretical epsilon values to theoretical absorbance values?
>
> Thanks in advance
>
>
> Gul 

--------------080205030800070705070305
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
  <head>
    <meta content="text/html; charset=ISO-8859-1"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#ffffff" text="#000000">
    <font size="-1"><font face="Courier New, Courier, monospace"><br>
        Dear Gul,<br>
        I wonder how you got epsilon values from a TD-DFT calculation
        with Gaussian09? I think you are mistaken, the Gaussian
        print-out lists dimensionless oscillator strengths, f. The
        oscillator strength is proportional to the observed integrated
        absorbance, integrating over the whole electronic band profile.
        Consult textbooks on optical spectroscopy, or relevant reviews
        like the one by Stefan Grimme in Reviews in Computational
        Chemistry, Volume 20, Chapter 3, 2004. Grimme has a discussion
        of this matter and a recommendation on how to simulate
        experimental absorbance curves from calculated theoretical
        transitions under the assumption of a Gaussian line shape (pp
        168-169 in this chapter).&nbsp; <br>
        Yours, Jens &gt;--&lt;<br>
      </font></font>
    <pre class="moz-signature" cols="72">  ------------------------------------------------------
  JENS SPANGET-LARSEN         Office:      +45 4674 2710
  Dept. of Science (18.1)     Fax:         +45 4674 3011
  Roskilde University         Mobile:      +45 2320 6246
  P.O.Box 260                 E-Mail:     <a class="moz-txt-link-abbreviated" href="mailto:spanget.() .ruc.dk">spanget.() .ruc.dk</a>
  DK-4000 Roskilde, Denmark   <a class="moz-txt-link-freetext" href="http://www.ruc.dk/~spanget">http://www.ruc.dk/~spanget</a>
  ------------------------------------------------------</pre>
    <br>
    On 5/23/2011 14:07, G&Uuml;L ALTINBA&#350; galtinbas=-=gmail.com wrote:
    <blockquote
cite="mid:-id%233dt-44728-110523080717-28686-oaST1ZfkIX5ERrKFo8gb9g.() .server.ccl.net"
      type="cite">Hi all,<br>
      <br>
      <br>
      I got UV spectrum (epsilon versus excitation energy (nm)) from&nbsp;
      TD-DFTcomputations using Gaussian 09 and I would like to compare
      experimental spectrum in the same graph. But experimental spectrum
      is absorbance versus wavelength (nm). Does anybody know how to
      convert theoretical epsilon values to theoretical absorbance
      values?<br>
      <br>
      Thanks in advance<br>
      <br>
      <br clear="all">
      Gul
    </blockquote>
  </body>
</html>

--------------080205030800070705070305--


From owner-chemistry@ccl.net Mon May 23 12:03:00 2011
From: "ierre Archirel pierre.archirel%a%u-psud.fr" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL:G: Free energy of solvation
Message-Id: <-44732-110523115321-19376-WPWx1/ehrTD+y4VPnCLilQ- -server.ccl.net>
X-Original-From: " ierre  Archirel" <pierre.archirel{}u-psud.fr>
Date: Mon, 23 May 2011 11:53:20 -0400


Sent to CCL by: " ierre  Archirel" [pierre.archirel() u-psud.fr]
This is an answer to John.
You are rising fondamental issues of the reaction field (RF) methods. In a few points:
1- If you consider the solubility of a molecule in the gas phase, the right value of the Standard Free Energy of solvation reads:
DeltaG^0_solv=DeltaG^RF_solv + RTLn 24.5 (i.e. +0.08 eV)
taking account of the different conventions of standard states in gas phase (1atm, ie 1/24.5M) and in solution (1M). You will find this in the Cramer book (Computational Chemistry, Wiley 2004 p. 378). I am afraid this will make your calculated value still more positive.
2- the value of Delta G is very sensitive to the values of the radii you are using. I would say that using DFT you should use radii=uaks. 
3- the translation-rotation is an awful question. Radii values such as UAHF and UAKS have been optimised, so as to reproduce experimental values of the DeltaG_solv of a list of molecules, mainly in water. The RF Delta G is an electrostatic Delta G, that is the RF Delta S gives the entropy variation of the solvent when the solute is present. The translation-rotation entropy of the solute is certainly absent from the RF Delta G_solv.
4- so you are tied up to the fact that the radii have been optimised to yield "good" values with a false formula (without translation-rotation entropy)
5- you may try to add it by your own, taking for the gas phase the usual values (Sackur-Tetrode and rigid rotor) and for the condensed phase some approximated values (look at M. Amzel and X. Siebert papers).
6- if you manage to do it you will introduce the decrease of the translation-rotation entropy when your molecule is dissolved. I am afraid this will give you a DeltaG_solv more positive, again...

This answer is too long, let's wait for other comments!
(by the way if you want to try the SDD radii of gaussian09, you may send me your molecule. SMD cavitation effects are small)

Pierre Archirel
LCP, Universite Paris-Sud
France
pierre.archirel%u-psud.fr


From owner-chemistry@ccl.net Mon May 23 12:38:00 2011
From: "christina jenifer g christinamsc~!~gmail.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate the following?
Message-Id: <-44733-110523121511-14216-OEIu5CZrIEOfxk51gLJLPg\a/server.ccl.net>
X-Original-From: "christina jenifer g" <christinamsc**gmail.com>
Date: Mon, 23 May 2011 12:15:10 -0400


Sent to CCL by: "christina jenifer g" [christinamsc ~ gmail.com]
Dear All,

       I am beginner in computational chemistry. I would like to know how to calculate electron affinity, electron negativity, ionization potential. electron density, ionization energy by using Gaussian.

       if you help in this regards i am really appreciated.

thanking you,

CHRISTINA


From owner-chemistry@ccl.net Mon May 23 13:13:00 2011
From: "christina jenifer g christinamsc,+,gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate the following?
Message-Id: <-44734-110523122542-23685-FgBBO3pa2QpcLDeJyx47FA,+,server.ccl.net>
X-Original-From: "christina jenifer g" <christinamsc##gmail.com>
Date: Mon, 23 May 2011 12:25:40 -0400


Sent to CCL by: "christina jenifer g" [christinamsc(!)gmail.com]
Dear All,

       I am beginner in computational chemistry. 
I would like to know how to calculate electron affinity, 
electron negativity, ionization potential. electron density,
 ionization energy by using Gaussian03/09.

       i am really appreciated your help.

thanking you,

CHRISTINA


From owner-chemistry@ccl.net Mon May 23 13:48:00 2011
From: "Andreas Klamt klamt..cosmologic.de" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: free energy of solvation
Message-Id: <-44735-110523132033-29781-JZV3yXhhXq1GC3vJeEEKiQ^-^server.ccl.net>
X-Original-From: Andreas Klamt <klamt|cosmologic.de>
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Date: Mon, 23 May 2011 19:20:15 +0200
MIME-Version: 1.0


Sent to CCL by: Andreas Klamt [klamt|*|cosmologic.de]
Hi John,

what strange kind of molecule are you treating here? A cavitation energy 
of 96 kcal/mol and a dispersion of -76.33 kcal/mol. These are extremely 
large vales. How can that go along with only
-1.2 kcal solut/solvent interaction? Even the small bond dipoles of 
hexane would give you that order of magnitude.

Something is dramatically wrong here.

Can you send me the compound and solvent? If you like I analyze the 
contributions with COSMOtherm

Andreas

Am 23.05.2011 14:33, schrieb john doe jeffrey.lebowski]*[gmx.de:
> Sent to CCL by: "john  doe" [jeffrey.lebowski : gmx.de]
> Hi all.
>
> I'm totally new on the field of solvation in QC.
>
> I calculated the free energy of solvation (DeltaG (solv)) with Gaussian03 via:
>
> ..
> #p BP86/gen/Auto NoSymm SCF=Tight SCRF(COSMO,read,solvent=Toluene)
>
> 0 1
> ..coords...
>
> ..basis set...
>
> SCFVAC
> Radii=UAHF
>
> The value is positiv.
>
>   (Unpolarized solute)-Solvent             (kcal/mol) =      -1.21
>   (Polarized solute)-Solvent               (kcal/mol) =      -1.44
>   Solute polarization                      (kcal/mol) =       0.13
>   Total electrostatic                      (kcal/mol) =      -1.32
>   --------------------------------------------------------------------
>   Cavitation energy                        (kcal/mol) =      98.29
>   Dispersion energy                        (kcal/mol) =     -76.33
>   Repulsion energy                         (kcal/mol) =      14.46
>   Total non electrostatic                  (kcal/mol) =      36.43
>   DeltaG (solv)                            (kcal/mol) =      35.11
>
>
> Does this mean the compound should not be soluble in toluene? (In fact it is soluble) Is a positiv value meaningfull at all? It just means that the energy needed to build the cavity is higher than the stabilization on the solute molecule by the polarizable continuum, right? Can one translate that somehow by saying the loss of solvent-solvent interaction is higher than the gain of solvent-solute interaction?
>
> and another thing:
>
> I have read that the best way to calculate (better: to approximate) the free energy of a molecule in solution (without the COSMOtherm software) is to calculate the free energy in the gas phase and to add the free energy of solvation. I ask myself whether the thermal corrections coming from rotational and translational degrees of freedom should be taken into account for the gas-phase free energy as those degrees of freedom are not really present in soltuion, are they?
>
> Thanks for your time to read this and many thanks in advance for any help!
>
> John>
>
>


-- 
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