From owner-chemistry@ccl.net Thu Aug 28 01:15:00 2008
From: "Arindam Ganguly arindamganguly###gmail.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37650-080828011314-1038-FTXi51Bp2IOE0vnDhT/gXA[A]server.ccl.net>
X-Original-From: "Arindam  Ganguly" <arindamganguly^^^gmail.com>
Date: Thu, 28 Aug 2008 01:13:08 -0400


Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
Dear CCL users,
Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.

Arindam


From owner-chemistry@ccl.net Thu Aug 28 01:49:01 2008
From: "Isabelle Navizet navizet-*-univ-mlv.fr" <owner-chemistry:+:server.ccl.net>
To: CCL
Subject: CCL:G: ONIOM calculation errors. Help!
Message-Id: <-37651-080828010424-32626-5tBYLYcZd0BnUHkvkyUIfg:+:server.ccl.net>
X-Original-From: Isabelle Navizet <navizet]![univ-mlv.fr>
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Date: Thu, 28 Aug 2008 11:59:44 +0800
Mime-Version: 1.0


Sent to CCL by: Isabelle Navizet [navizet a univ-mlv.fr]
Hello YuanYuan Cui, 

May I try to give some information which can help you.

First, in the line of multiplicity and charges, you should have in total
6 numbers (see manual of Gaussian):
chrgreal-low  spinreal-low [chrgmodel-high spinmodel-high [chrgmodel-low
spinmodel-low ]]
where real-low is the whole system described in MM, model-high is for
you the 2 Zn described in QM, model-low is for you the 2 Zn described in
MM
Did you put this numbers correctly ?

Second, I guess that you atom number 204 is Zn ? You should add VDW
amber parameters for Zn at the end of the input file (see in Gaussian
Manual the amber page, key word VDW).

Hope that will help you.

Isabelle Navizet


From owner-chemistry@ccl.net Thu Aug 28 03:29:00 2008
From: "rosi ombrato r.ombrato=angelini.it" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: apo enzyme
Message-Id: <-37652-080828031926-27936-z8pnQTGwwNoiwVNyniHaqQ:-:server.ccl.net>
X-Original-From: "rosi  ombrato" <r.ombrato+/-angelini.it>
Date: Thu, 28 Aug 2008 03:19:21 -0400


Sent to CCL by: "rosi  ombrato" [r.ombrato~~angelini.it]
Hi Elaine,

thank you so much for your answer.
I have an apo structure but the binding site isn't defined. Can I use some tecnique (Sitemap sw) to identify the potential binding sites? Can I to be sure ot the binding site identified to do docking?
regards
rosella
  


> "Elaine Meng meng|,|cgl.ucsf.edu"  wrote:
> 
> Sent to CCL by: "Elaine  Meng" [meng:+:cgl.ucsf.edu]
> > I would like to known if it's possible to use apo structure to do virtual
> > screening. holo strucutre doesn't esist.
> 
> Hi Rosella,
> Of course it is possible, but success depends on the individual protein
> (especially how much the conformation changes) and docking protocol.  
> You can take a look at papers comparing results of docking to the
> complexed and uncomplexed protein conformations.  Here is one such paper:
> 
> McGovern SL, Shoichet BK.
> Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes.
> J Med Chem. 2003 Jul 3;46(14):2895-907.
> PMID: 12825931
> 
> Good luck,
> Elaine
> 
> -----
> Elaine C. Meng, Ph.D.                          meng__cgl.ucsf.edu
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 
>


From owner-chemistry@ccl.net Thu Aug 28 04:04:00 2008
From: "Mikko Vainio mivainio^^^abo.fi" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37653-080828031945-27986-WDkPbahUhko+qyysdXN49g ~~ server.ccl.net>
X-Original-From: Mikko Vainio <mivainio*|*abo.fi>
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Date: Thu, 28 Aug 2008 09:27:55 +0300
MIME-Version: 1.0


Sent to CCL by: Mikko Vainio [mivainio(!)abo.fi]
There are plenty:
http://www.molecular-networks.com/software/tautomer/index.html
http://tautgen.sourceforge.net/
http://www.chemaxon.com/product/calc_pl_land.html
http://www.chemcomp.com/journal/sdtools.htm#Wash
http://www.molinspiration.com/docu/mib/
http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/tautomers/
http://www.schrodinger.com/ProductDescription.php?mID=6&sID=7
and probably more - almost each chemoinformatics software vendor has one.

/Mikko

Arindam Ganguly arindamganguly###gmail.com wrote:
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
> 
> Arindam> 
> 
> 

-- 
:: Mikko Vainio <mikko.vainio%abo.fi> tel + 358 2 215 4600
:: Structural Bioinformatics Laboratory
:: Department of Biochemistry and Pharmacy
:: Abo Akademi University, Tykistokatu 6A, FI-20520 Turku Finland


From owner-chemistry@ccl.net Thu Aug 28 04:43:00 2008
From: "rosella ombrato r.ombrato!^!angelini.it" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37654-080828034749-10217-AvL1uvvrFpGm3f0cBUM5GQ#,#server.ccl.net>
X-Original-From: "rosella  ombrato" <r.ombrato-*-angelini.it>
Date: Thu, 28 Aug 2008 03:47:45 -0400


Sent to CCL by: "rosella  ombrato" [r.ombrato%a%angelini.it]
Hi Arindam,

I use Ligprep (schodinger suite) to do 3D structure conversions by including tautomeric, stereochemical, and ionization variations, as well as energy minimization and flexible filters to generate fully customized ligand libraries that are optimized for further computational analyses




> "Arindam Ganguly arindamganguly###gmail.com"  wrote:
> 
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
> 
> Arindam
> 
>


From owner-chemistry@ccl.net Thu Aug 28 05:16:01 2008
From: "Szabolcs Csepregi scsepregi]~[chemaxon.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37655-080828042733-3632-tf95/L6URAONwJYYxRFMTw^server.ccl.net>
X-Original-From: Szabolcs Csepregi <scsepregi++chemaxon.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=UTF-8; format=flowed
Date: Thu, 28 Aug 2008 09:37:59 +0200
MIME-Version: 1.0


Sent to CCL by: Szabolcs Csepregi [scsepregi[#]chemaxon.com]
Hi Arindam,

You can try the Tautomerization plugin of Marvin:
http://www.chemaxon.com/product/tautomer.html

Please note that although Marvin is free to use on the desktop, the 
plugins are licensed separately.
(You may also qualify for the academic license: 
http://www.chemaxon.com/forum/ftopic193.html )

I hope this helps,
Szabolcs

Szabolcs Csepregi, PhD
Director of Search Technologies, ChemAxon Ltd.
http://www.chemaxon.com
Skype: szabolcs.csepregi
Tel: +36 1 4532661  Cell: +36 20 4219863  Fax: +36 1 4532659


Arindam Ganguly arindamganguly###gmail.com wrote:
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
>
> Arindam>
>
>
>


From owner-chemistry@ccl.net Thu Aug 28 05:49:00 2008
From: "Tamas Gunda tgunda2:_:puma.unideb.hu" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: 2nd time Chemdraw2002
Message-Id: <-37656-080828052238-9935-9PcOrK2zyLmdHhbN1FNiHA##server.ccl.net>
X-Original-From: "Tamas Gunda" <tgunda2,puma.unideb.hu>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_003F_01C90900.57D9C7B0"
Date: Thu, 28 Aug 2008 11:22:23 +0200
MIME-Version: 1.0


Sent to CCL by: "Tamas Gunda" [tgunda2!A!puma.unideb.hu]
This is a multi-part message in MIME format.

------=_NextPart_000_003F_01C90900.57D9C7B0
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Tif images are bitmaps. If you open a bitmap image in ChemDraw (from =
file or via the clipboard), they will be exactly the same as the =
original. But on resizing in  ChemDraw, they quality will suffer. So you =
must ensure prior to exporting to ChemDraw that the physical resolution =
of the image and its DPI settings are appropriate and the image can be =
used in ChemDraw without resizing. You can use a number of image editing =
softwares to change the DPI of a tif image.

Tamas Gunda
  ----- Original Message -----=20
  From: irfan ahmad irfaahmad#,#gmail.com=20
  To: Gunda, Tamas E =20
  Sent: Wednesday, August 27, 2008 21:35 PM
  Subject: CCL: 2nd time Chemdraw2002


  Thanks to reply as you told, its right but our problem is that when we =
insert TIFF or any other format picture in chemdraw,=20
  picture chages its quality in other words we want to paste pictrure =
into chemdraw (and it should have its original form ).=20
  waiting for suggestions




  =20
  On 8/28/08, Kaliappan Muthukumar muthukumar2k3[-]gmail.com =
<owner-chemistry]_[ccl.net> wrote:=20
    Try this,

    Cut the picture from Chemdraw

    Go to Word --> Edit ---> Paste special ----> Choose 'enhanced meta =
file' ----> and OK

    It will be in your word document as a Picture file, and you cant =
take it back to chemdraw, once you paste it.=20

    Best regards,
    MK



    On Wed, Aug 27, 2008 at 9:30 AM, Tamas Gunda tgunda2..puma.unideb.hu =
<owner-chemistry]*[ccl.net> wrote:


      Sent to CCL by: "Tamas Gunda" [tgunda2,puma.unideb.hu]
      Transfer to where? Do you mean that a drawing from ChemDraw into =
another application (such Word?). Or simply pasting a drawing from one =
ChemDraw window to another one?

      In the latter case, there is a bug even in the latest ChemDraw =
that if the settings of the two windows are not the same, not all of =
properties are converted properly. One has to reapply the settings as =
nevessary. On the other hand, a chemdraw document can contain & use max. =
22 colors. (foreground, background + 20 others). If all colors are used =
in both documents, then on copy/pasting a structure the colors might =
tget mixed up. Especially color #20 can behave oddly, obviously a bug.

      What do you mean "some bad spots apear on it."?


      T. Gunda


      ----- Original Message -----=20

        From: "Mr shabbir shabbir!^!nenu.edu.cn" =
<owner-chemistry/a\ccl.net>

      To: "Gunda, Tamas E " <tgunda2/a\puma.unideb.hu>
      Sent: Tuesday, August 26, 2008 14:31 PM
      Subject: CCL: 2nd time Chemdraw2002




        Sent to CCL by: "Mr  shabbir" [shabbir * nenu.edu.cn]
        Hi
        I am using chemdraw2002.When I trasferred by pasting a figure to =
chemdraw window that figure changes its color and some bad spots apear =
on it.I used many ways but no effect.Any body now how to paste figure in =
chmdraw so that it can not change its orginality.
        Highly appreciating the answer

        Mr Shabbir
        shabbir(!)nenu.edu.cn






      E-mail to subscribers: CHEMISTRY]*[ccl.net or use:E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: =
http://server.ccl.net/chemistry/announcements/conferences/

      Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: =
search)--=20
    ----------------------------------------------------------
    ... UNTIL SCIENCE IS MIXED WITH EMOTION AND APPEALS TO THE HEART AND
    IMAGINATION , IT IS LIKE DEAD INORGANIC MATTER; AND WHEN IT IS SO =
MIXED
    AND SO TRANSFORMED IT IS LITERATURE.

    -- JOHN BURROUGHS

    With My Best Wishes,
    Kaliappan Muthukumar,=20
    ------------------------------------------------------------
    =20


------=_NextPart_000_003F_01C90900.57D9C7B0
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.6000.16674" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#feecd3>
<DIV><FONT face=3DArial size=3D2>Tif images are bitmaps. If you open a =
bitmap image=20
in ChemDraw (from file or via the clipboard), they will be exactly the =
same as=20
the original. But on resizing in&nbsp; ChemDraw, they quality will =
suffer. So=20
you must ensure prior to exporting to ChemDraw that the physical =
resolution of=20
the image and&nbsp;its DPI settings are appropriate and the image can be =
used in=20
ChemDraw without resizing. You can use a number of image editing =
softwares to=20
change the DPI of a tif image.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Tamas Gunda</FONT></DIV>
<BLOCKQUOTE=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Downer-chemistry()ccl.net =
href=3D"mailto:owner-chemistry()ccl.net">irfan=20
  ahmad irfaahmad#,#gmail.com</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Dtgunda2()puma.unideb.hu=20
  href=3D"mailto:tgunda2()puma.unideb.hu">Gunda, Tamas E </A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Wednesday, August 27, =
2008 21:35=20
  PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL: 2nd time =
Chemdraw2002</DIV>
  <DIV><BR></DIV>
  <DIV><STRONG>Thanks to reply as you told, its right but our problem is =
that=20
  when we insert TIFF or any other format&nbsp;picture in chemdraw,=20
  </STRONG></DIV>
  <DIV><STRONG>picture chages its quality in other words we want to =
paste=20
  pictrure into chemdraw (and it should have its original form ).=20
</STRONG></DIV>
  <DIV><STRONG>waiting for suggestions</STRONG></DIV>
  <DIV><STRONG></STRONG>&nbsp;</DIV>
  <DIV>&nbsp;</DIV>
  <DIV><BR><BR>&nbsp;</DIV>
  <DIV><SPAN class=3Dgmail_quote>On 8/28/08, <B =
class=3Dgmail_sendername>Kaliappan=20
  Muthukumar muthukumar2k3[-]<A =
href=3D"http://gmail.com">gmail.com</A></B> &lt;<A=20
  =
href=3D"mailto:owner-chemistry]_[ccl.net">owner-chemistry]_[ccl.net</A>&g=
t;=20
  wrote:</SPAN>=20
  <BLOCKQUOTE class=3Dgmail_quote=20
  style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: =
#ccc 1px solid">
    <DIV dir=3Dltr>
    <DIV>Try this,</DIV>
    <DIV>&nbsp;</DIV>
    <DIV>Cut the picture from Chemdraw</DIV>
    <DIV>&nbsp;</DIV>
    <DIV>Go to Word --&gt; Edit ---&gt; Paste special ----&gt; Choose =
'enhanced=20
    meta file' ----&gt; and OK</DIV>
    <DIV>&nbsp;</DIV>
    <DIV>It will be&nbsp;in your word document as a Picture file, and =
you cant=20
    take it back to chemdraw, once you paste it. </DIV>
    <DIV>&nbsp;</DIV>
    <DIV>Best regards,</DIV>
    <DIV>MK</DIV>
    <DIV>&nbsp;</DIV>
    <DIV>&nbsp;</DIV>
    <DIV>&nbsp;</DIV>
    <DIV class=3Dgmail_quote><SPAN class=3Dq>On Wed, Aug 27, 2008 at =
9:30 AM, Tamas=20
    Gunda tgunda2..<A onclick=3D"return =
top.js.OpenExtLink(window,event,this)"=20
    href=3D"http://puma.unideb.hu/" target=3D_blank>puma.unideb.hu</A> =
<SPAN=20
    dir=3Dltr>&lt;<A onclick=3D"return =
top.js.OpenExtLink(window,event,this)"=20
    href=3D"mailto:owner-chemistry]*[ccl.net"=20
    target=3D_blank>owner-chemistry]*[ccl.net</A>&gt;</SPAN> =
wrote:<BR></SPAN>
    <BLOCKQUOTE class=3Dgmail_quote=20
    style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: =
#ccc 1px solid"><SPAN=20
      class=3Dq><BR>Sent to CCL by: "Tamas Gunda" [tgunda2,<A=20
      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://puma.unideb.hu/"=20
      target=3D_blank>puma.unideb.hu</A>]<BR>Transfer to where? Do you =
mean that a=20
      drawing from ChemDraw into another application (such Word?). Or =
simply=20
      pasting a drawing from one ChemDraw window to another =
one?<BR><BR>In the=20
      latter case, there is a bug even in the latest ChemDraw that if =
the=20
      settings of the two windows are not the same, not all of =
properties are=20
      converted properly. One has to reapply the settings as nevessary. =
On the=20
      other hand, a chemdraw document can contain &amp; use max. 22 =
colors.=20
      (foreground, background + 20 others). If all colors are used in =
both=20
      documents, then on copy/pasting a structure the colors might tget =
mixed=20
      up. Especially color #20 can behave oddly, obviously a =
bug.<BR><BR>What do=20
      you mean "some bad spots apear on it."?<BR><BR><BR>T.=20
      Gunda<BR><BR><BR>----- Original Message ----- <BR>
      <BLOCKQUOTE class=3Dgmail_quote=20
      style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; =
BORDER-LEFT: #ccc 1px solid">From:=20
        "Mr shabbir shabbir!^!<A=20
        onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
        href=3D"http://nenu.edu.cn/" target=3D_blank>nenu.edu.cn</A>"=20
        &lt;owner-chemistry/a\<A=20
        onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
        href=3D"http://ccl.net/" =
target=3D_blank>ccl.net</A>&gt;<BR></BLOCKQUOTE>To:=20
      "Gunda, Tamas E " &lt;tgunda2/a\<A=20
      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://puma.unideb.hu/"=20
      target=3D_blank>puma.unideb.hu</A>&gt;<BR>Sent: Tuesday, August =
26, 2008=20
      14:31 PM<BR>Subject: CCL: 2nd time Chemdraw2002<BR><BR><BR>
      <BLOCKQUOTE class=3Dgmail_quote=20
      style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; =
BORDER-LEFT: #ccc 1px solid"><BR>Sent=20
        to CCL by: "Mr &nbsp;shabbir" [shabbir * <A=20
        onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
        href=3D"http://nenu.edu.cn/" =
target=3D_blank>nenu.edu.cn</A>]<BR>Hi<BR>I am=20
        using chemdraw2002.When I trasferred by pasting a figure to =
chemdraw=20
        window that figure changes its color and some bad spots apear on =
it.I=20
        used many ways but no effect.Any body now how to paste figure in =
chmdraw=20
        so that it can not change its orginality.<BR>Highly appreciating =
the=20
        answer<BR><BR>Mr Shabbir<BR>shabbir(!)<A=20
        onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
        href=3D"http://nenu.edu.cn/"=20
      =
target=3D_blank>nenu.edu.cn</A><BR><BR><BR></BLOCKQUOTE><BR><BR><BR></SPA=
N><SPAN=20
      class=3Dq>E-mail to subscribers: <A=20
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      use:<BR>&nbsp; &nbsp; <A=20
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efore=20
      posting, check wait time at: <A=20
      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://www.ccl.net/" target=3D_blank><A=20
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      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://www.ccl.net/htdig"=20
      target=3D_blank>http://www.ccl.net/htdig</A></A> &nbsp;(login: =
ccl,=20
      Password: search)<BR></SPAN><SPAN class=3Dq>&nbsp; &nbsp; <A=20
      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://www.ccl.net/spammers.txt" target=3D_blank><A=20
      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://www.ccl.net/spammers.txt"=20
      =
target=3D_blank>http://www.ccl.net/spammers.txt</A></A><BR><BR>RTFI: <A=20
      onclick=3D"return top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/"=20
      target=3D_blank><A onclick=3D"return =
top.js.OpenExtLink(window,event,this)"=20
      href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/"=20
      =
target=3D_blank>http://www.ccl.net/chemistry/aboutccl/instructions/</A></=
A><BR><BR><BR></SPAN></BLOCKQUOTE></DIV><BR><BR=20
    clear=3Dall><BR>--=20
    =
<BR>----------------------------------------------------------<BR>... =
UNTIL=20
    SCIENCE IS MIXED WITH EMOTION AND APPEALS TO THE HEART =
AND<BR>IMAGINATION ,=20
    IT IS LIKE DEAD INORGANIC MATTER; AND WHEN IT IS SO MIXED<BR>AND SO=20
    TRANSFORMED IT IS LITERATURE.<BR><BR>-- JOHN BURROUGHS<BR><BR>With =
My Best=20
    Wishes,<BR>Kaliappan Muthukumar,=20
    =
<BR>------------------------------------------------------------<BR>&nbsp=
;</DIV></BLOCKQUOTE></DIV><BR></BLOCKQUOTE></BODY></HTML>

------=_NextPart_000_003F_01C90900.57D9C7B0--


From owner-chemistry@ccl.net Thu Aug 28 06:27:00 2008
From: "Mikael Johansson mpjohans%chem.au.dk" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Open-shell spin-orbit NMR shielding software
Message-Id: <-37657-080828062425-6424-Au/qAxHII6T7fQd6R7/4Ng%x%server.ccl.net>
X-Original-From: Mikael Johansson <mpjohans---chem.au.dk>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Thu, 28 Aug 2008 12:24:13 +0200
MIME-Version: 1.0


Sent to CCL by: Mikael Johansson [mpjohans=-=chem.au.dk]

Hello All!

Is anyone aware of a program that would be capable of doing NMR shielding 
calculations (NICS at least) for open-shell systems, including spin-orbit 
effects? Also, the ability to use ECP's or other frozen core formalisms would 
be very useful, as I'd like to apply it to reasonably large heavy metal 
systems.

Have a nice day,
     Mikael J.
     http://www.iki.fi/~mpjohans


From owner-chemistry@ccl.net Thu Aug 28 07:14:00 2008
From: "Adil R Zhugralin zhugrali:bc.edu" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL:G: Difficulties with Hirshfeld Population Analysis
Message-Id: <-37658-080828070404-7099-uYiJq6mEfAsf4SDpCfpCXw|server.ccl.net>
X-Original-From: "Adil R Zhugralin" <zhugrali+*+bc.edu>
Date: Thu, 28 Aug 2008 07:04:01 -0400


Sent to CCL by: "Adil R Zhugralin" [zhugrali:_:bc.edu]
Dear all,

I have been trying to calculate Hirshfeld charges (from HPA) in Gaussian03 with iop(6/79=1), and I've been getting unrealistically large charges even in a neutral molecule (Sum of Hirshfeld charges=-79.225986). Both cation and anion HPA gave me ******** for the "Sum of Hirshfeld charges". I need HPA to estimate fukui indices/atomic softness indices through finite difference approximation for an organometallic complex, containing Mo(VI) atom (opt and freq were done as a separate job at B3PW91/6-31+G(d,p) and SDD on Mo). 

I wonder if HPA does not handle ECPs well or are there any other ways for me to get HPA working? Different level of theory or charge method? I did try to use Mulliken, Lowdin, charges, but I get negative f- functions for atoms of interest (gross atomic charges of the cation are higher than those of the neutral molecule). Is Voronoi Deformation Density (VDD) method available in Gaussian?

All responses would be appreciated, thanks in advance,

Adil R. Zhugralin
Boston College, Department of Chemistry


From owner-chemistry@ccl.net Thu Aug 28 07:40:01 2008
From: "Andreas Klamt klamt-#-cosmologic.de" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37659-080828064539-27556-2X83GAVIEedvRl+Xn+blrQ[]server.ccl.net>
X-Original-From: Andreas Klamt <klamt^cosmologic.de>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=UTF-8; format=flowed
Date: Thu, 28 Aug 2008 12:08:23 +0200
MIME-Version: 1.0


Sent to CCL by: Andreas Klamt [klamt]=[cosmologic.de]
Just for completion:
The COSMOfrag software of COSMOlogic also has a tautomer generator as 
side functionality.

Andreas

Mikko Vainio mivainio^^^abo.fi schrieb:
>
> Sent to CCL by: Mikko Vainio [mivainio(!)abo.fi]
> There are plenty:
> http://www.molecular-networks.com/software/tautomer/index.html
> http://tautgen.sourceforge.net/
> http://www.chemaxon.com/product/calc_pl_land.html
> http://www.chemcomp.com/journal/sdtools.htm#Wash
> http://www.molinspiration.com/docu/mib/
> http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/tautomers/
> http://www.schrodinger.com/ProductDescription.php?mID=6&sID=7
> and probably more - almost each chemoinformatics software vendor has one.
>
> /Mikko
>
> Arindam Ganguly arindamganguly###gmail.com wrote:
>> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
>> Dear CCL users,
>> Is there any software out there which can predict the possibility of 
>> tautomerism being present in a molecule. Any suggestions and pointers 
>> will be really helpful. Thanks in advance.
>>
>> Arindam>
>>
>


-- 
--------------------------------------------------------------------------
Dr. habil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
e-mail: klamt-$-cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------
COSMOlogic
       Your Competent Partner for
       Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------
Please note our COSMO-RS Symposium in 2009 
(For details see: http://www.cosmologic.de/Symposium/symposium.html)


From owner-chemistry@ccl.net Thu Aug 28 08:29:01 2008
From: "Kamalakar Jadhav kjadhav-*-vlifesciences.com" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37660-080828080649-25116-jbfNAMLfSI56+91Euys0Aw]~[server.ccl.net>
X-Original-From: Kamalakar Jadhav <kjadhav]^[vlifesciences.com>
Content-Type: multipart/alternative;
 boundary="------------000905060709020106060302"
Date: Thu, 28 Aug 2008 17:11:18 +0530
MIME-Version: 1.0


Sent to CCL by: Kamalakar Jadhav [kjadhav+/-vlifesciences.com]
This is a multi-part message in MIME format.
--------------000905060709020106060302
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit

VLifeMDS software has this facility
Look at www.vlifesciences.com

Hope this helps.

Kamalakar


Arindam Ganguly arindamganguly###gmail.com wrote:
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
>
> Arindam>
>
>
>
>   

--------------000905060709020106060302
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">
VLifeMDS software has this facility<br>
Look at <a class="moz-txt-link-abbreviated"
 href="http://www.vlifesciences.com">www.vlifesciences.com</a>
<br>
<br>
Hope this helps.
<br>
<br>
<div class="moz-signature">
</div>
Kamalakar
<div class="moz-signature">
<meta http-equiv="Content-Type" content="text/html; ">
<title>Untitled Document</title>
<style type="text/css">
<!--
.style1 {	font-family: Arial, Helvetica, sans-serif;
	font-size: 10px;
	color: #666666;
}
.style3 {	font-size: 11px;
	font-weight: bold;
	color: #666666;
	font-family: Arial, Helvetica, sans-serif;
}
--></style></div>
<br>
<br>
Arindam Ganguly arindamganguly###gmail.com wrote:
<blockquote
 cite="mid:-id%234hb-37650-080828011314-1038-81+17j4dScK9Hg7UX0c+Ew,,server.ccl.net"
 type="cite">
  <pre wrap="">Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
Dear CCL users,
Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.

ArindamE-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>

E-mail to administrators: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY-REQUEST,,ccl.net">CHEMISTRY-REQUEST,,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<a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a>

Before posting, check wait time at: <a class="moz-txt-link-freetext" href="http://www.ccl.net">http://www.ccl.net</a>

Job: <a class="moz-txt-link-freetext" href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a> 
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RTFI: <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a>




  </pre>
</blockquote>
</body>
</html>

--------------000905060709020106060302--


From owner-chemistry@ccl.net Thu Aug 28 08:59:01 2008
From: "Jonathan Brecher jsb%x%cambridgesoft.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: 2nd time Chemdraw2002
Message-Id: <-37661-080827171656-31893-Pe1f1CwbacbqxiJyirWugg:_:server.ccl.net>
X-Original-From: Jonathan Brecher <jsb[#]cambridgesoft.com>
Content-Type: multipart/alternative; boundary="============_-992252499==_ma============"
Date: Wed, 27 Aug 2008 16:46:34 -0400
Mime-Version: 1.0


Sent to CCL by: Jonathan Brecher [jsb,cambridgesoft.com]
--============_-992252499==_ma============
Content-Type: text/plain; charset="us-ascii" ; format="flowed"

As an employee of CambridgeSoft, I have to say that it is extremely 
frustrating to read this thread.  We have an award-winning support 
department, and we would very likely have solved the problem reported 
by the original poster within hours (or at most a day or two) if he 
had contacted when he found the problem in the first place.  The 
support department can be contacted at support###cambridgesoft.com or 
via a web for at http://www.cambridgesoft.com/services/  The web form 
is actually a little better because it captures a bit more 
information that will sometimes provide an accurate answer more 
quickly.

I strongly encourage the original poster (and anyone else with 
questions about the behavior of CambridgeSoft products) to contact 
our support department with a full description of the problem 
including sample files when possible, and get answers direct from the 
source.


Jonathan Brecher
CambridgeSoft Corporation
jsb###cambridgesoft.com




>Thanks to reply as you told, its right but our problem is that when 
>we insert TIFF or any other format picture in chemdraw,
>picture chages its quality in other words we want to paste pictrure 
>into chemdraw (and it should have its original form ).
>waiting for suggestions
>
>
>
>
>
>On 8/28/08, Kaliappan Muthukumar 
>muthukumar2k3[-]<http://gmail.com>gmail.com 
><<mailto:owner-chemistry]_[ccl.net>owner-chemistry]_[ccl.net> wrote:
>
>Try this,
>
>Cut the picture from Chemdraw
>
>Go to Word --> Edit ---> Paste special ----> Choose 'enhanced meta 
>file' ----> and OK
>
>It will be in your word document as a Picture file, and you cant 
>take it back to chemdraw, once you paste it.
>
>Best regards,
>MK
>
>
>
>On Wed, Aug 27, 2008 at 9:30 AM, Tamas Gunda 
>tgunda2..<http://puma.unideb.hu/>puma.unideb.hu 
><<mailto:owner-chemistry]*[ccl.net>owner-chemistry]*[ccl.net> wrote:
>
>
>Sent to CCL by: "Tamas Gunda" [tgunda2,<http://puma.unideb.hu/>puma.unideb.hu]
>Transfer to where? Do you mean that a drawing from ChemDraw into 
>another application (such Word?). Or simply pasting a drawing from 
>one ChemDraw window to another one?
>
>In the latter case, there is a bug even in the latest ChemDraw that 
>if the settings of the two windows are not the same, not all of 
>properties are converted properly. One has to reapply the settings 
>as nevessary. On the other hand, a chemdraw document can contain & 
>use max. 22 colors. (foreground, background + 20 others). If all 
>colors are used in both documents, then on copy/pasting a structure 
>the colors might tget mixed up. Especially color #20 can behave 
>oddly, obviously a bug.
>
>What do you mean "some bad spots apear on it."?
>
>
>T. Gunda
>
>
>----- Original Message -----
>
>From: "Mr shabbir shabbir!^!<http://nenu.edu.cn/>nenu.edu.cn" 
><owner-chemistry/a\<http://ccl.net/>ccl.net>
>
>To: "Gunda, Tamas E " <tgunda2/a\<http://puma.unideb.hu/>puma.unideb.hu>
>Sent: Tuesday, August 26, 2008 14:31 PM
>Subject: CCL: 2nd time Chemdraw2002
>
>
>Sent to CCL by: "Mr  shabbir" [shabbir * <http://nenu.edu.cn/>nenu.edu.cn]
>Hi
>I am using chemdraw2002.When I trasferred by pasting a figure to 
>chemdraw window that figure changes its color and some bad spots 
>apear on it.I used many ways but no effect.Any body now how to paste 
>figure in chmdraw so that it can not change its orginality.
>Highly appreciating the answer
>
>Mr Shabbir
>shabbir(!)<http://nenu.edu.cn/>nenu.edu.cn
>
>
>
>
>E-mail to subscribers: <mailto:CHEMISTRY]*[ccl.net>CHEMISTRY]*[ccl.net or use:
> 
><http://www.ccl.net/cgi-bin/ccl/send_ccl_message>http://www.ccl.net/cgi-bin/ccl/send_ccl_message
>
>E-mail to administrators: 
><mailto:CHEMISTRY-REQUEST]*[ccl.net>CHEMISTRY-REQUEST]*[ccl.net or 
>use
> 
><http://www.ccl.net/cgi-bin/ccl/send_ccl_message>http://www.ccl.net/cgi-bin/ccl/send_ccl_message
><http://www.ccl.net/chemistry/sub_unsub.shtml>http://www.ccl.net/chemistry/sub_unsub.shtml
>
>Before posting, check wait time at: <>http://www.ccl.net
>
>Job: <>http://www.ccl.net/jobs Conferences: 
><>http://server.ccl.net/chemistry/announcements/conferences/
>
>Search Messages: <>http://www.ccl.net/htdig  (login: ccl, Password: search)
>     <>http://www.ccl.net/spammers.txt
>
>RTFI: <>http://www.ccl.net/chemistry/aboutccl/instructions/
>
>
>
>
>--
>----------------------------------------------------------
>... UNTIL SCIENCE IS MIXED WITH EMOTION AND APPEALS TO THE HEART AND
>IMAGINATION , IT IS LIKE DEAD INORGANIC MATTER; AND WHEN IT IS SO MIXED
>AND SO TRANSFORMED IT IS LITERATURE.
>
>-- JOHN BURROUGHS
>
>With My Best Wishes,
>Kaliappan Muthukumar,
>------------------------------------------------------------
>

--============_-992252499==_ma============
Content-Type: text/html; charset="us-ascii"

<!doctype html public "-//W3C//DTD W3 HTML//EN">
<html><head><style type="text/css"><!--
blockquote, dl, ul, ol, li { padding-top: 0 ; padding-bottom: 0 }
 --></style><title>Re: CCL: 2nd time Chemdraw2002</title></head><body>
<div>As an employee of CambridgeSoft, I have to say that it is
extremely frustrating to read this thread.&nbsp; We have an
award-winning support department, and we would very likely have solved
the problem reported by the original poster within hours (or at most a
day or two) if he had contacted when he found the problem in the first
place.&nbsp; The support department can be contacted at
support###cambridgesoft.com or via a web for at
http://www.cambridgesoft.com/services/&nbsp; The web form is actually
a little better because it captures a bit more information that will
sometimes provide an accurate answer more quickly.</div>
<div><br></div>
<div>I strongly encourage the original poster (and anyone else with
questions about the behavior of CambridgeSoft products) to contact our
support department with a full description of the problem including
sample files when possible, and get answers direct from the
source.</div>
<div><br></div>
<div><br></div>
<div>Jonathan Brecher</div>
<div>CambridgeSoft Corporation</div>
<div>jsb###cambridgesoft.com</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<blockquote type="cite" cite><b>Thanks to reply as you told, its right
but our problem is that when we insert TIFF or any other
format&nbsp;picture in chemdraw,</b></blockquote>
<blockquote type="cite" cite><b>picture chages its quality in other
words we want to paste pictrure into chemdraw (and it should have its
original form ).</b></blockquote>
<blockquote type="cite" cite><b>waiting for
suggestions</b></blockquote>
<blockquote type="cite" cite>&nbsp;</blockquote>
<blockquote type="cite" cite>&nbsp;</blockquote>
<blockquote type="cite" cite><br>
<br>
&nbsp;</blockquote>
<blockquote type="cite" cite>On 8/28/08,<b> Kaliappan Muthukumar
muthukumar2k3[-]</b><a href="http://gmail.com"><b>gmail.com</b></a> &lt;<a
href="mailto:owner-chemistry]_[ccl.net">owner-chemistry]_[ccl.net</a>&gt;
wrote:<br>
<blockquote>Try this,</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>Cut the picture from Chemdraw</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>Go to Word --&gt; Edit ---&gt; Paste special ----&gt;
Choose 'enhanced meta file' ----&gt; and OK</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>It will be&nbsp;in your word document as a Picture file,
and you cant take it back to chemdraw, once you paste it.</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>Best regards,</blockquote>
<blockquote>MK</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>&nbsp;</blockquote>
<blockquote>On Wed, Aug 27, 2008 at 9:30 AM, Tamas Gunda tgunda2..<a
href="http://puma.unideb.hu/">puma.unideb.hu</a> &lt;<a
href="mailto:owner-chemistry]*[ccl.net">owner-chemistry]*[ccl.net</a>&gt;
wrote:<br>
<blockquote><br>
Sent to CCL by: &quot;Tamas Gunda&quot; [tgunda2,<a
href="http://puma.unideb.hu/">puma.unideb.hu</a>]<br>
Transfer to where? Do you mean that a drawing from ChemDraw into
another application (such Word?). Or simply pasting a drawing from one
ChemDraw window to another one?<br>
<br>
In the latter case, there is a bug even in the latest ChemDraw that if
the settings of the two windows are not the same, not all of
properties are converted properly. One has to reapply the settings as
nevessary. On the other hand, a chemdraw document can contain &amp;
use max. 22 colors. (foreground, background + 20 others). If all
colors are used in both documents, then on copy/pasting a structure
the colors might tget mixed up. Especially color #20 can behave oddly,
obviously a bug.<br>
<br>
What do you mean &quot;some bad spots apear on it.&quot;?<br>
<br>
<br>
T. Gunda<br>
<br>
<br>
----- Original Message -----<br>
<blockquote>From: &quot;Mr shabbir shabbir!^!<a
href="http://nenu.edu.cn/">nenu.edu.cn</a>&quot;
&lt;owner-chemistry/a\<a href="http://ccl.net/">ccl.net</a>&gt;<br>
</blockquote>
</blockquote>
<blockquote>To: &quot;Gunda, Tamas E &quot; &lt;tgunda2/a\<a
href="http://puma.unideb.hu/">puma.unideb.hu</a>&gt;<br>
Sent: Tuesday, August 26, 2008 14:31 PM<br>
Subject: CCL: 2nd time Chemdraw2002<br>
<blockquote><br>
Sent to CCL by: &quot;Mr &nbsp;shabbir&quot; [shabbir * <a
href="http://nenu.edu.cn/">nenu.edu.cn</a>]<br>
Hi<br>
I am using chemdraw2002.When I trasferred by pasting a figure to
chemdraw window that figure changes its color and some bad spots apear
on it.I used many ways but no effect.Any body now how to paste figure
in chmdraw so that it can not change its orginality.<br>
Highly appreciating the answer<br>
<br>
Mr Shabbir<br>
shabbir(!)<a href="http://nenu.edu.cn/">nenu.edu.cn</a><br>
</blockquote>
</blockquote>
<blockquote><br>
<br>
<br>
E-mail to subscribers: <a
href="mailto:CHEMISTRY]*[ccl.net">CHEMISTRY]*[ccl.net</a> or use:<br>
&nbsp;&nbsp;&nbsp; <a
href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message"
>http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a
href="mailto:CHEMISTRY-REQUEST]*[ccl.net">CHEMISTRY-REQUEST]*[ccl.net</a
> or use<br>
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href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message"
>http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<a
href="http://www.ccl.net/chemistry/sub_unsub.shtml"
>http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a
href="">http://www.ccl.net</a><br>
<br>
Job: <a href="">http://www.ccl.net/jobs</a> Conferences: <a
href="">http://server.ccl.net/chemistry/announcements/conferences/</a
></blockquote>
<blockquote><br>
Search Messages: <a href="">http://www.ccl.net/htdig</a> &nbsp;(login:
ccl, Password: search)<br>
&nbsp;&nbsp;&nbsp; <a href="">http://www.ccl.net/spammers.txt</a><br>
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RTFI: <a
href="">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
</blockquote>
</blockquote>
<blockquote><br>
<br>
<br>
--<br>
----------------------------------------------------------<br>
... UNTIL SCIENCE IS MIXED WITH EMOTION AND APPEALS TO THE HEART
AND<br>
IMAGINATION , IT IS LIKE DEAD INORGANIC MATTER; AND WHEN IT IS SO
MIXED<br>
AND SO TRANSFORMED IT IS LITERATURE.<br>
<br>
-- JOHN BURROUGHS<br>
<br>
With My Best Wishes,<br>
Kaliappan Muthukumar,<br>
------------------------------------------------------------<br>
&nbsp;</blockquote>
</blockquote>
<div><br></div>
</body>
</html>
--============_-992252499==_ma============--


From owner-chemistry@ccl.net Thu Aug 28 09:33:01 2008
From: "Ramon Crehuet rcsqtc|*|iiqab.csic.es" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: Transition State question
Message-Id: <-37662-080828084714-18714-0DlqCL3CwjWzN888pzCA4Q]-[server.ccl.net>
X-Original-From: Ramon Crehuet <rcsqtc]=[iiqab.csic.es>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Thu, 28 Aug 2008 13:53:50 +0200
MIME-Version: 1.0


Sent to CCL by: Ramon Crehuet [rcsqtc_+_iiqab.csic.es]
Dear Mark,
You have come across an interesting problem. Let me extend a little what
Justin Finnerty explained. If you follow the IRC from TS_1 to TS_2 you
will find interesting things... At TS_1 the IRC curve is a maximum along
its vector, but following the curve, at TS_2 this direction will be a
minimum (it has to be so, you cannot have two maxima connected by a
continous smooth curve without a minimum in between).
So the transition vector at TS_2 is not the IRC vector that comes from
TS_1, but an orthogonal direction. This direction had to be a minimum in
the TS_1 (by definition), so somewhere along the IRC it changed from a
minimum to a maximum. Following the IRC you are in a valley before that
point and on a ridge, after the point (concerning only that direction).
Hence the name valley-ridge inflection point.
Because at this point the curvature is zero, and afterwards it is
negative, it costs no energy to go astray from the IRC: the IRC is no
longer a valley, so molecules can fall out of the ridge. Therefore
kinetic theories based on the IRC may fail and product distributions may
be difficult to estimate, except for very symmetric cases. This is true
even if the valley-ridge inflection point is not on the IRC but close to
it, which may be even more difficult to detect.
For more details, check this work and the references therein:
http://www.springerlink.com/content/y174850737714t65/

Cheers,
Ramon



Dr.Wolfgang Quapp quappa/rz.uni-leipzig.de wrote:
> 
> Sent to CCL by: "Dr.Wolfgang Quapp" [quapp-x-rz.uni-leipzig.de]
> Zitat von "Mark Zottola mzottola^^gmail.com" <owner-chemistry(!)ccl.net>:
> 
>> In examining a potential energy surface of a species of interest, I have
>> come across something unique to my experience.  I have, apparently, run
>> across a system which an intermediate connects to a transition state via
>> *another* transition state.  The IRC calculations validate this
>> connection.
>> The second transition state connects two other species.  In other words
>>
>> A ---->   B (TS_1) -----> C (TS_2) ;
>>
>> D ----> C (TS_2) -----> F
>>
>> The second TS (TS_2)  is a first order saddle point.  Has anyone run
>> across
>> this before?  Or am I missing something fundamental in these
>> calculations?
>> I have come across a Schlegel reference where a transition state connects
>> three different species.  Yet this communication was for an open-shell
>> system.
>>
>> Thanks for any helpful comments, references, etc.
>>
>>
>> Mark
>>
> 
> Hallo Mark,
> 
> see, for example, model surfaces for your problem in:
> 
> Theoret Chem Acc 112 (2004) 40-51,  or
> J Molec struct 695-696 (2004) 95-101
> 
> Greetings
> Dr.Wolfgang Quapp
> 
> 
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> 
> 
> 
> -=his is automatically added to each message by the mailing script =-http://www.ccl.net/chemistry/sub_unsub.shtml> 
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/> 
> 
>


From owner-chemistry@ccl.net Thu Aug 28 10:09:01 2008
From: "Ol Ga eurisco1%a%pochta.ru" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL:G: Difficulties with Hirshfeld Population Analysis
Message-Id: <-37663-080828093600-22565-03mAG6gF/d1xZLt3CHWgYQ.:.server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1^_^pochta.ru>
Date: Thu, 28 Aug 2008 09:35:55 -0400


Sent to CCL by: "Ol  Ga" [eurisco1_+_pochta.ru]
Dear Adil R. Zhugralin!

It is necessary to use _all-electronic_ basis set, e.g. DGDZVP , and explicitly define in the route section 6D 10F.

VDD is not avaiable in Gaussian 03.


Sincerely,

Ol Ga



----- Original Message ----- 
> From: "Adil R Zhugralin zhugrali:bc.edu" <owner-chemistry=-=ccl.net>
To: "Ga, Ol " <eurisco1=-=pochta.ru>
Sent: Thursday, August 28, 2008 3:04 PM
Subject: CCL:G: Difficulties with Hirshfeld Population Analysis


> 
> 
> Sent to CCL by: "Adil R Zhugralin" [zhugrali:_:bc.edu]
> Dear all,
> 
> I have been trying to calculate Hirshfeld charges (from HPA) in Gaussian03 with iop(6/79=1), and I've been getting unrealistically large charges even in a neutral molecule (Sum of Hirshfeld charges=-79.225986). Both cation and anion HPA gave me ******** for the "Sum of Hirshfeld charges". I need HPA to estimate fukui indices/atomic softness indices through finite difference approximation for an organometallic complex, containing Mo(VI) atom (opt and freq were done as a separate job at B3PW91/6-31+G(d,p) and SDD on Mo). 
> 
> I wonder if HPA does not handle ECPs well or are there any other ways for me to get HPA working? Different level of theory or charge method? I did try to use Mulliken, Lowdin, charges, but I get negative f- functions for atoms of interest (gross atomic charges of the cation are higher than those of the neutral molecule). Is Voronoi Deformation Density (VDD) method available in Gaussian?
> 
> All responses would be appreciated, thanks in advance,
> 
> Adil R. Zhugralin
> Boston College, Department of Chemistry
>


From owner-chemistry@ccl.net Thu Aug 28 10:42:01 2008
From: "Lothar Terfloth lothar.terfloth.:.molecular-networks.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37664-080828035628-13987-SvKBXgkL+JJVX8o0YDeVGg^server.ccl.net>
X-Original-From: Lothar Terfloth <lothar.terfloth|-|molecular-networks.com>
Content-Transfer-Encoding: 7bit
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Date: Thu, 28 Aug 2008 09:06:29 +0200
MIME-Version: 1.0


Sent to CCL by: Lothar Terfloth [lothar.terfloth*molecular-networks.com]
Dear Arindam,

I would suggest to consider our software Tautomer for this purpose.
More detailed information about Tautomer is available at the URL:

http://www.molecular-networks.com/software/tautomer/index.html

Demo-versions of Tautomer are available for evaluation from our
download area (http://www.molecular-networks.com/php/profile.php).

Tautomer explicitly enumerates the tautomers.

The following types of tautomerism are supported:
     *  keto-enol and thioenol exchange
     * imine exchange
     * nonsubstitued heteroaromatic exchange
     * hetero atom hydrogen exchange
     * keten / inol exchange
     * nitro form / aci form of nitro compounds
     * nitroso / oxim exchange
     * cyanuric acid, formamidinsulfon acid, hydrogen cyanide

With best regards,

  Lothar Terfloth

Arindam Ganguly arindamganguly###gmail.com wrote:
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
> 
> Arindam
> 
> 
> 
-- 
--------------------------------------------------------
  Dr. Lothar Terfloth              Tel. +49-9131-9790623
  Molecular Networks GmbH          Fax: +49-9131-815 669

      Henkestr. 91
      D-91052 Erlangen
      Germany

      email:  Lothar.Terfloth.^.mol-net.com
      www:    http://www.mol-net.com
--------------------------------------------------------


From owner-chemistry@ccl.net Thu Aug 28 11:24:00 2008
From: "Simon Cross simon++moldiscovery.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37665-080828060420-26392-g/hHM0zXYbU0/cDjQSbwcA-#-server.ccl.net>
X-Original-From: Simon Cross <simon],[moldiscovery.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Thu, 28 Aug 2008 10:05:16 +0100
MIME-Version: 1.0


Sent to CCL by: Simon Cross [simon[#]moldiscovery.com]
Hi Arindam, there are several programs available for enumerating 
tautomers, however many do not estimate the stability of tautomer, so 
you don't know which to focus on. Recently we released MoKa 
(http://www.moldiscovery.com/soft_moka.php), that is based on GRID 
molecular interaction fields, for pKa modelling and also deals with 
tautomerism. Key features relevant to tautomerism include:

- MoKa will warn you if your structure is an unstable tautomer in the 
graphical interface
- you can convert structures to their most stable tautomer (using rules 
such as aromaticity as well as the predicted atomic pKas)
- you can enumerate all tautomers that exist above a specified abundance

If you would like more information then I would recommend you contact 
our sales_at_moldiscovery_dot_com address.

All the best,

Simon

---
Dr Simon Cross
Snr Scientist & Product Manager
Molecular Discovery Ltd

Arindam Ganguly arindamganguly###gmail.com wrote:
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
>
> Arindam>
>
>   


-- 
Simon Cross
Snr Scientist & Product Manager
Molecular Discovery Ltd
Tel 07980 572278
www.moldiscovery.com


From owner-chemistry@ccl.net Thu Aug 28 11:53:00 2008
From: "Serguei Patchkovskii ps^-^ned.sims.nrc.ca" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: Open-shell spin-orbit NMR shielding software
Message-Id: <-37666-080828102915-16278-WzPAl+q2ObipMAJqZsUfWA:-:server.ccl.net>
X-Original-From: Serguei Patchkovskii <ps|a|ned.sims.nrc.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Thu, 28 Aug 2008 09:43:13 -0400 (EDT)
MIME-Version: 1.0


Sent to CCL by: Serguei Patchkovskii [ps-#-ned.sims.nrc.ca]
On Thu, 28 Aug 2008, Mikael Johansson mpjohans%chem.au.dk wrote:

> Is anyone aware of a program that would be capable of doing NMR shielding
> calculations (NICS at least) for open-shell systems, including spin-orbit
> effects? Also, the ability to use ECP's or other frozen core formalisms would
> be very useful, as I'd like to apply it to reasonably large heavy metal
> systems.

Michael,

NMR shielding tensors in open-shell systems are a statistical property,
which makes them considerably harder to compute than for closed-shell
species. In particular, you need a fair understanding of the electronic
structure of the molecule, including the multiplet splittings, g-tensors,
and hyperfine coupling constants. You may also need these quantities
for some of the excited electronic states, especially in transition-metal
complexes. As a result of the complexity of the open-shell NMR shielding
tensors, you are much less likely to get sensible results from a black-box
program.

For some simpler special cases, you can get open-shell NMR parameters
> from ADF, Dalton, or MAG-Respect - but you should be very much aware
that you need to understand what you are doing in order to trust the
results (or even to _get_ the results in the first place).

Some more or less random references:

- A detailed overview of the theory of NMR shielding tensors in 
  paramagnetic molecular systems can be found in:  S. Moon and 
  S. Patchkovskii, "First-Principles Calculations of Paramagnetic 
  NMR Shifts", chapter 20 in M. Kaupp, M. Buhl, and V.G. Malkin, 
  "Calculation of NMR and EPR Parameters" (Wiley, Winheim, 2004)

- Z. Rinkevicius, J. Vaara, L. Telyatnik, and O. Vahtras, "Calculations 
  of nuclear magnetic shielding in paramagnetic molecules", JCP 118, 
  2550 (2003).

- P. Hrobarik, R. Reviakine, A. V. Arbuznikov, O. L. Malkina, 
  V. G. Malkin, F. H. Kohler, and M. Kaupp, "Density functional 
  calculations of NMR shielding tensors for paramagnetic systems 
  with arbitrary spin multiplicity: Validation on 3d metallocenes", 
  JCP 126, 024107 (2007).

Have fun,

Serguei

---
Dr. Serguei Patchkovskii

Tel: +1-(613)-990-0945
Fax: +1-(613)-947-2838
E-mail: Serguei.Patchkovskii[#]nrc.ca

Coordinator of Modelling Software
Theory and Computation Group
Steacie Institute for Molecular Sciences
National Research Council Canada
Room 2011, 100 Sussex Drive
Ottawa, Ontario
K1A 0R6 Canada


From owner-chemistry@ccl.net Thu Aug 28 12:27:01 2008
From: "Elaine Meng meng++cgl.ucsf.edu" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: apo enzyme
Message-Id: <-37667-080828114509-18336-0+JoP4+mMH46tBI8hzVvvw(0)server.ccl.net>
X-Original-From: "Elaine  Meng" <meng,cgl.ucsf.edu>
Date: Thu, 28 Aug 2008 11:45:04 -0400


Sent to CCL by: "Elaine  Meng" [meng++cgl.ucsf.edu]
Hi Rosella,
There are probably >100 different methods for predicting the active or binding site given a 3D structure - you really should search for some papers and Web servers, it is too much to cover in an e-mail.  Also you could use any biochemical data such as mutations known to affect activity.  I would guess none of the methods allow you to be completely "sure" of the binding site, but you could just dock to the top few predictions.

For example, the CASTp server
<http://sts-fw.bioengr.uic.edu/castp/calculation.php>
identifies pockets, and the few largest pockets could be used.  That is just an example because there are so many different methods.
Elaine
-----
Elaine C. Meng, Ph.D.                          meng/a\cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html


From owner-chemistry@ccl.net Thu Aug 28 13:03:01 2008
From: "David Gallagher gallagher.da() gmail.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37668-080828120533-3864-qFv0TIJHhIxwjjZSkARjOA-x-server.ccl.net>
X-Original-From: David Gallagher <gallagher.da]|[gmail.com>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Thu, 28 Aug 2008 08:09:20 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da(a)gmail.com]
Hi Arindam,

Perhaps the definitive method would be to calculate the free energy 
of each tautomer, and the height of the activation barrier to 
interconversion using quantum mechanics.  This is essentially a 
simple reaction modelling exercise and can be done with many quantum 
chemistry packages.  From the barrier height and the Arrhenius 
equation it is possible to estimate the interconversion rates.

A water-catalyzed keto-enol tautomerization 'movie' is posted at:

     http://cacheresearch.com/presentations.html

This particular reaction path is the MOPAC Intrinsic Reaction 
Coordinate (IRC) which is computed from the transition state.  There 
are also some notes posted on the same page on how to perform the 
reaction modelling:

     GuideToTransitionStateModeling.pdf
     Reaction Modeling Lab-61.pdf

Although, MOPAC does an excellent job with thermodynamic properties 
of ground state molecules, it tends to systematically overestimate 
activation energy barriers and so, needs calibrating.  Alternatively, 
a high-level ab initio method, though much slower, may provide a more 
accurate estimate of the activation energy.

Regards,
David


At 10:13 PM 8/27/2008, Arindam Ganguly arindamganguly###gmail.com wrote:

>Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
>Dear CCL users,
>Is there any software out there which can predict the possibility of 
>tautomerism being present in a molecule. Any suggestions and 
>pointers will be really helpful. Thanks in advance.
>
>Arindam


From owner-chemistry@ccl.net Thu Aug 28 13:38:01 2008
From: "Rajarshi Guha rguha**indiana.edu" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: apo enzyme
Message-Id: <-37669-080828132937-23526-LnR0S+3HH49EQBSgbQGOUg _ server.ccl.net>
X-Original-From: Rajarshi Guha <rguha(~)indiana.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Date: Thu, 28 Aug 2008 13:29:04 -0400
Mime-Version: 1.0 (Apple Message framework v753.1)


Sent to CCL by: Rajarshi Guha [rguha(a)indiana.edu]

On Aug 28, 2008, at 11:45 AM, Elaine Meng meng++cgl.ucsf.edu wrote:
>
> Sent to CCL by: "Elaine  Meng" [meng++cgl.ucsf.edu]
>
>
> For example, the CASTp server
> <http://sts-fw.bioengr.uic.edu/castp/calculation.php>
> identifies pockets, and the few largest pockets could be used.   
> That is just an example because there are so many different methods.

Do you have any pointers to comparisons of performance (accuracy etc)  
of various methods? I recently had cause to use a binding site  
prediction server - in the end I used two and used a consensus  
prediction, since it wasn't clear which one would be better.

-------------------------------------------------------------------
Rajarshi Guha  <rguha]*[indiana.edu>
GPG Fingerprint: D070 5427 CC5B 7938 929C  DD13 66A1 922C 51E7 9E84
-------------------------------------------------------------------
So the Zen master asked the hot-dog vendor,
"Can you make me one with everything?"
         - TauZero on Slashdot


From owner-chemistry@ccl.net Thu Aug 28 14:13:01 2008
From: "Elaine Meng meng:cgl.ucsf.edu" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: apo enzyme
Message-Id: <-37670-080828140351-30956-HpAarxX1s+5x3Snd3ApjBg-*-server.ccl.net>
X-Original-From: "Elaine  Meng" <meng^cgl.ucsf.edu>
Date: Thu, 28 Aug 2008 14:03:48 -0400


Sent to CCL by: "Elaine  Meng" [meng^cgl.ucsf.edu]
Hi Rajarshi,
This isn't my main area of work nowadays, so I don't know of a good review off the top of my head.
However, I tried searching PubMed using

("binding site"[tiab] OR "active site"[tiab]) AND prediction[tiab] AND review[pt]

which yielded some possibly useful articles including

Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA.
Free resources to assist structure-based virtual ligand screening experiments.
Curr Protein Pept Sci. 2007 Aug;8(4):381-411. Review.

Laurie AT, Jackson RM.
Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening.
Curr Protein Pept Sci. 2006 Oct;7(5):395-406. Review.

Flower DR.
Receptor-binding sites: bioinformatic approaches.
Methods Mol Biol. 2006;316:291-358. Review.

Also, publications describing the many various individual methods usually include some estimate of success rate based on comparison to a set of knowns, sometimes relative to other similar methods.  I remember the CASTp papers saying that in some high percentage of cases, the largest pocket is the active or binding site of a protein.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng*_*cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html


From owner-chemistry@ccl.net Thu Aug 28 14:47:00 2008
From: "Kristin Robinson krobinson|a|schrodinger.com" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL: apo enzyme
Message-Id: <-37671-080828140646-32389-wsnrIz4h9JBtcKiA0WIDVg.:.server.ccl.net>
X-Original-From: "Kristin  Robinson" <krobinson^^^schrodinger.com>
Date: Thu, 28 Aug 2008 14:06:42 -0400


Sent to CCL by: "Kristin  Robinson" [krobinson-*-schrodinger.com]
Sent to CCL by: Rajarshi Guha [rguha(a)indiana.edu]

>Do you have any pointers to comparisons of performance (accuracy etc) of >various methods? I recently had cause to use a binding site prediction server >- in the end I used two and used a consensus prediction, since it wasn't clear >which one would be better. 


Hi Rajarshi,

There is a paper on SiteMap that includes a validation study of known binding sites. Here is the reference:

Halgren, T., "New Method for Fast and Accurate Binding-site Identification and Analysis", Chem. Biol. Drug Des., 2007, 69, 146148.

I hope that is helpful.

Kristin


From owner-chemistry@ccl.net Thu Aug 28 15:23:00 2008
From: "zborowsk _ chemia.uj.edu.pl" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37672-080828060747-29155-FWLMdzf50W7buyiUUMCtIg,+,server.ccl.net>
X-Original-From: zborowsk__chemia.uj.edu.pl
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-2
Date: Thu, 28 Aug 2008 11:24:07 +0200 (CEST)
MIME-Version: 1.0


Sent to CCL by: zborowsk]_[chemia.uj.edu.pl
Hi
Maybe there is any software that can perform calculations in the "black
box" mode. But in general you need any quantum mechanical program (or even
molecular mechanic one, it depends on your molecules) in order to obtain
free energies and later you have to perform some elementary calculations
by yourself.

If you have some problems you can contact me

Regards



>
> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of
> tautomerism being present in a molecule. Any suggestions and pointers will
> be really helpful. Thanks in advance.
>
> Arindam>
>
>


-- 
Krzysztof Zborowski
Faculty of Chemistry
Jagiellonian University
3 Ingardena Street
30-060 Krakow
Poland
phone: +48(12)632-4888 ext. 2064 or 2067
fax:  +48(12)634-05-15
email: zborowsk^-^chemia.uj.edu.pl
gg 3817259
skype kzys70
www.chemia.uj.edu.pl/~zborowsk


From owner-chemistry@ccl.net Thu Aug 28 16:04:01 2008
From: "Bob Clark bclark-x-bcmetrics.com" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37673-080828123449-26425-P0GL1OO8xxROfCAbCpILZA|server.ccl.net>
X-Original-From: Bob Clark <bclark#bcmetrics.com>
Content-Type: multipart/mixed;
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Date: Thu, 28 Aug 2008 09:22:04 -0500
MIME-Version: 1.0


Sent to CCL by: Bob Clark [bclark!=!bcmetrics.com]
This is a multi-part message in MIME format.
--------------070409020202050002090505
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The responders so far have failed to distinguish between two kinds of 
questions: "Could the molecule possibly tautomerize - i.e., do 
tautomeric structures exist?" (which is what you actually asked)  and 
"Will the molecule tautomerize?"  Enumerating all possible tautomers is 
pretty straightforward, but identifying relevant tautomers is often very 
hard.  Hence the second question is a lot harder to answer, because one 
has to take kinetic as well as thermodynamic considerations into 
account.  The enol tautomer of most simple ketones, for example, isn't 
relevant for most purposes, and there are steroid CH tautomers that are 
perfectly happy to sit in separate bottles on the shelf for years.

So please provide some context: what do you want to use the information for?

Good luck,

Bob C.

> Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
> Dear CCL users,
> Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.
>
> Arindam


--------------070409020202050002090505
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begin:vcard
fn:Robert D. Clark
n:Clark;Robert D.
org:Biochemical Infometrics
adr:;;PO Box 411431;Creve Coeur;MO;63141;USA
email;internet:bclark.|.bcmetrics.com
tel;work:+1-314-660-4499
x-mozilla-html:TRUE
url:http://www.bcmetrics.com
version:2.1
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--------------070409020202050002090505--


From owner-chemistry@ccl.net Thu Aug 28 19:38:00 2008
From: "Gonzalo Jimenez-Oses gjimenez**unizar.es" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Bimolecular reactions under pseudo-first order conditions
Message-Id: <-37674-080828193530-20811-bLHr8ftGhfwSK+wGYgxfQQ__server.ccl.net>
X-Original-From: "Gonzalo  Jimenez-Oses" <gjimenez(!)unizar.es>
Date: Thu, 28 Aug 2008 19:35:25 -0400


Sent to CCL by: "Gonzalo  Jimenez-Oses" [gjimenez-$-unizar.es]
Dear CCL'ers,

Maybe my question is somewhat silly, but I wonder if there is any possible way to determine the unimolecular or bimolecular character of a given reaction by carrying out its kinetic study only under pseudo-first order conditions. I have read somewhere that, for bimolecular reactions, "a plot of the observed rate constant versus the concentration of the reagent being varied will result in a linear relationship if pseudo-first order conditions are met. The slope of this plot yields the apparent bimolecular rate constant for the reaction, under the chosen experimental conditions."

Particularly, I refer to those reactions which only take place when one of the reactants is used as a solvent, and one wants to know if this reaction is intrisically unimolecular or bimolecular (i.e. the reaction could be bimolecular in nature but it can only take place if the concentration of one reactant is huge...). 

Many thanks in advance,

Gonzalo


From owner-chemistry@ccl.net Thu Aug 28 20:12:00 2008
From: "David Gallagher gallagher.da-*-gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: tautomerism software
Message-Id: <-37675-080828192926-20283-pCLu+6gKjFDIg5igb/zJAQ%%server.ccl.net>
X-Original-From: David Gallagher <gallagher.da- -gmail.com>
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Date: Thu, 28 Aug 2008 15:57:17 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da]=[gmail.com]
Hi Bob,

It seems that you may be unaware that quantum chemistry methods, 
already proposed by myself and some others, provide the necessary 
thermodynamic and kinetic information to establish both the 
equilibrium ratio of the different tautomers and their speed of 
interconversion at a particular temperature.

It is quite simple to perform a free energy calculation on each 
tautomer with almost any quantum chemistry package to estimate the 
free energies (thermodynamics), either gas phase or in an appropriate 
solvent field.  The ratio of the tautomers can then be determined via 
a Boltzmann distribution.

The speed of interconversion (kinetics) can be established from the 
height of the energy barrier to interconversion (activation energy) 
and the Arrhenius equation.  The height of the energy barrier is 
simply the free energy of the transition state (between the 
tautomers) minus the free energy of the appropriate 
tautomer.  Although, more involved than ground state calculations, 
characterizing transition states in most cases is relatively 
straightforward for some quantum chemistry packages (further details 
on reaction modelling are posted at 
http://cacheresearch.com/presentations.html )

Far from being 'not relevant for most purposes', the enol tautomer 
can be the most abundant for some simple ketones such as 
acetyl-acetone, and even in very low concentrations when the 
keto-form prevails, the enol tautomer may still be responsible for 
certain characteristics of a molecules chemistry or reactivity.

Regards,
David


At 07:22 AM 8/28/2008, Bob Clark bclark-x-bcmetrics.com wrote:

>The responders so far have failed to distinguish between two kinds 
>of questions: "Could the molecule possibly tautomerize - i.e., do 
>tautomeric structures exist?" (which is what you actually 
>asked)  and "Will the molecule tautomerize?"  Enumerating all 
>possible tautomers is pretty straightforward, but identifying 
>relevant tautomers is often very hard.  Hence the second question is 
>a lot harder to answer, because one has to take kinetic as well as 
>thermodynamic considerations into account.  The enol tautomer of 
>most simple ketones, for example, isn't relevant for most purposes, 
>and there are steroid CH tautomers that are perfectly happy to sit 
>in separate bottles on the shelf for years.
>
>So please provide some context: what do you want to use the information for?
>Good luck,
>Bob C.
>
>>Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
>>Dear CCL users,
>>Is there any software out there which can predict the possibility 
>>of tautomerism being present in a molecule. Any suggestions and 
>>pointers will be really helpful. Thanks in advance.
>>
>>Arindam
>
>
>


From owner-chemistry@ccl.net Thu Aug 28 21:44:01 2008
From: "Thanh Truong ttruong^^^astonis.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry made Simple by Avisto
Message-Id: <-37676-080828095036-49-MsQdj6iF0iSRSe4zI28JXw%a%server.ccl.net>
X-Original-From: "Thanh Truong" <ttruong- -astonis.com>
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	boundary="----=_Part_14611_24271496.1219949155368"
Date: Thu, 28 Aug 2008 18:45:55 -0600
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Sent to CCL by: "Thanh Truong" [ttruong ~ astonis.com]
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Dear CCL Members:

Avisto (Astonis Virtual Studio) is now available free at
   http://Astonis.com<https://www.umail.utah.edu/exchweb/bin/redir.asp?URL=http://Astonis.com>
Please download it and try.

Avisto represents a paradigm shift in computational chemistry. It makes
computational chemistry SIMPLE. Avisto allows for seamless integrations
of applications into workflows, transparently accessing remote computing
resources and data sources.  It makes the cloud computing a reality.

The current version of Avisto demonstrates its main features.
With a few mouse clicks you can create workflows that connect molecular
mechanics force field tool with several different run types (MM
optimization,
PM6 optimization and/or PM6 Vibrational analysis) of MOPAC2007,
a semiempirical molecular orbital package. More options and
applications will be available
soon, though it is already a very useful tool not only for education but
also for your own research.

Please try it and if you like it, spread the news. If you do not like
it, tell us.

Hoping to hear your comments soon,

-- 
Thanh N. Truong and the Avisto Development Team

Astonis LLC
4347 South 1100 East
Salt Lake City, Utah 84124
Phone: (801) 809-6996

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<div dir="ltr"><div><br clear="all">Dear CCL Members:<br><br>Avisto (Astonis Virtual Studio) is now available free at<br>&nbsp;&nbsp; <a href="https://www.umail.utah.edu/exchweb/bin/redir.asp?URL=http://Astonis.com" target="_blank">http://Astonis.com</a><br>
Please download it and try.<br><br>Avisto represents a paradigm shift in computational chemistry. It makes<br>computational chemistry SIMPLE. Avisto allows for seamless integrations<br>of applications into workflows, transparently accessing remote computing<br>
resources and data sources.&nbsp; It makes the cloud computing a reality.<br><br>The current version of Avisto demonstrates its main features.<br>With a few mouse clicks you can create workflows that connect molecular<br>mechanics force field tool with several different run types (MM optimization,<br>
PM6 optimization and/or PM6 Vibrational analysis) of MOPAC2007,<br>a semiempirical molecular orbital package. More options and applications&nbsp;will be available<br>soon, though it is already a very useful tool not only for education but<br>
also for your own research.<br><br>Please try it and if you like it, spread the news. If you do not like<br>it, tell us.<br><br>Hoping to hear your comments soon,<br><br>-- <br>Thanh N. Truong and the Avisto Development Team</div>

<div><br>Astonis LLC<br>4347 South 1100 East<br>Salt Lake City, Utah 84124<br>Phone: (801) 809-6996<br></div></div>

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From owner-chemistry@ccl.net Thu Aug 28 22:18:01 2008
From: "gnli gnli,dicp.ac.cn" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Pure vs. Cartesian Basis Functions
Message-Id: <-37677-080828221357-23743-uwJjxEtvE2mKvXIJ7Xrolw(_)server.ccl.net>
X-Original-From: "gnli" <gnli~~dicp.ac.cn>
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Date: Fri, 29 Aug 2008 10:15:36 +0800
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Sent to CCL by: "gnli" [gnli\a/dicp.ac.cn]
This is a multi-part message in MIME format.

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Dear CCLer,

Please forgive me for my simple question.

Is it necessary to keep the basis set to be Pure or Cartesian type during
all the calculate step in one system?

For example, we optimize a molecule using  "hf/3-21g  hf/6-31g  b3lyp/6-31g
b3lyp/6-31++g(d,p)  b3lyp/aug-cc-pvdz" gradually,  need we define the Basis
Functions all in 5D 7F or 6D 10F in the route section consistently, or just
using default? Is the difference serious?    

Thanks!

best wishes
Guanna Li
 <mailto:gnli{:}dicp.ac.cn> gnli{:}dicp.ac.cn





 


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<p class=3DMsoNormal><b><font size=3D2 face=3D"Times New Roman"><span =
lang=3DEN-US
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CCLer,<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><b><font size=3D2 face=3D"Times New Roman"><span =
lang=3DEN-US
style=3D'font-size:10.5pt;font-weight:bold'>Please forgive me for my =
simple
question.<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><b><font size=3D2 face=3D"Times New Roman"><span =
lang=3DEN-US
style=3D'font-size:10.5pt;font-weight:bold'>Is it necessary to keep the =
basis set
to be Pure or Cartesian type during all the calculate step in one =
system?<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><b><font size=3D2 face=3D"Times New Roman"><span =
lang=3DEN-US
style=3D'font-size:10.5pt;font-weight:bold'>For example, we optimize a =
molecule
using &nbsp;&#8220;hf/3<st1:chmetcnv TCSC=3D"0" NumberType=3D"1" =
Negative=3D"True"
HasSpace=3D"False" SourceValue=3D"21" UnitName=3D"g" =
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hf/6<st1:chmetcnv TCSC=3D"0" NumberType=3D"1" Negative=3D"True" =
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SourceValue=3D"31" UnitName=3D"g" w:st=3D"on">-31g</st1:chmetcnv> =
&nbsp;b3lyp/6<st1:chmetcnv
TCSC=3D"0" NumberType=3D"1" Negative=3D"True" HasSpace=3D"False" =
SourceValue=3D"31"
UnitName=3D"g" w:st=3D"on">-31g</st1:chmetcnv> =
&nbsp;b3lyp/6-31++g(d,p)&nbsp;
b3lyp/aug-cc-pvdz&#8221; gradually, &nbsp;need we define the Basis =
Functions
all in 5D <st1:chmetcnv TCSC=3D"0" NumberType=3D"1" Negative=3D"False"
HasSpace=3D"False" SourceValue=3D"7" UnitName=3D"F" =
w:st=3D"on">7F</st1:chmetcnv> or 6D
<st1:chmetcnv TCSC=3D"0" NumberType=3D"1" Negative=3D"False" =
HasSpace=3D"False"
SourceValue=3D"10" UnitName=3D"F" w:st=3D"on">10F</st1:chmetcnv> in the =
route section
consistently, or just using default? Is the difference serious? =
&nbsp;&nbsp;&nbsp;<o:p></o:p></span></font></b></p>

<p class=3DMsoNormal><b><font size=3D2 face=3D"Times New Roman"><span =
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style=3D'font-size:10.5pt;font-weight:bold'>Thanks!<o:p></o:p></span></fo=
nt></b></p>

<p><font size=3D2 face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
Arial'>best wishes<br>
Guanna Li<br>
</span></font><span lang=3DEN-US><a =
href=3D"mailto:gnli{:}dicp.ac.cn"><font size=3D2
face=3DArial><span =
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