From owner-chemistry@ccl.net Mon Jun  4 05:27:01 2007
From: "Thomas Joseph alabarae+/-yahoo.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: fragment filtering
Message-Id: <-34405-070604051029-32739-/gIB04YMCBgb1IIBmESwiA-#-server.ccl.net>
X-Original-From: "Thomas  Joseph" <alabarae%x%yahoo.com>
Date: Mon, 4 Jun 2007 05:10:24 -0400


Sent to CCL by: "Thomas  Joseph" [alabarae..yahoo.com]
Hi all,

Do any of you know about any FREE softwares which can identify fragments in a chemical database that wil run under Windows?  
I want to identify specific fragments in a chemical database

thank you in advance


From owner-chemistry@ccl.net Mon Jun  4 08:27:00 2007
From: "Szabolcs Csepregi scsepregi ~~ chemaxon.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: fragment filtering
Message-Id: <-34406-070604082429-6244-96WeYYwiG8S+wmNZyZnczw|,|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: Mon, 04 Jun 2007 13:28:23 +0200
MIME-Version: 1.0


Sent to CCL by: Szabolcs Csepregi [scsepregi*|*chemaxon.com]
Hi,

Have a look at Instant JChem: http://www.chemaxon.com/product/ijc.html

Regards,
Szabolcs

Szabolcs Csepregi, PhD
Director of Search Technologies, ChemAxon Ltd.
http://www.chemaxon.com
Skype: szabolcs.csepregi
Tel: +36 1 3878564   Cell: +36 20 4219863   Fax: +36 1 4532659

Thomas Joseph alabarae+/-yahoo.com wrote:
> Sent to CCL by: "Thomas  Joseph" [alabarae..yahoo.com]
> Hi all,
>
> Do any of you know about any FREE softwares which can identify fragments in a chemical database that wil run under Windows?  
> I want to identify specific fragments in a chemical database
>
> thank you in advance>
>
>
>
>


From owner-chemistry@ccl.net Mon Jun  4 09:02:00 2007
From: "Mingyue Zheng myzheng ~ gmail.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: fragment filtering
Message-Id: <-34407-070604082303-6182-IvxeRX2QB0zTrKllGqyAwg|*|server.ccl.net>
X-Original-From: "Mingyue Zheng" <myzheng]![gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_285_7602566.1180956502384"
Date: Mon, 4 Jun 2007 19:28:22 +0800
MIME-Version: 1.0


Sent to CCL by: "Mingyue Zheng" [myzheng++gmail.com]
------=_Part_285_7602566.1180956502384
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

you may try openbabel, good luck!

2007/6/4, Thomas Joseph alabarae+/-yahoo.com <owner-chemistry-$-ccl.net>:
>
>
> Sent to CCL by: "Thomas  Joseph" [alabarae..yahoo.com]
> Hi all,
>
> Do any of you know about any FREE softwares which can identify fragments
> in a chemical database that wil run under Windows?
> I want to identify specific fragments in a chemical database
>
> thank you in advance>
>
>
>


-- 
--------------------------------------------------------------------------------
Dr. Mingyue Zheng
Research Associate, Drug Discovery and Design Center (DDDC)
Box 1201, Shanghai Institute of Materia Medica.
555 Rd. Zuchongzhi, Shanghai, China
Tel:      86-021-50806600-1201
Web:   http://dddc.ac.cn
Email: myzheng-$-mail.shcnc.ac.cn

------=_Part_285_7602566.1180956502384
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

you may try openbabel, good luck!<br><br>
<div><span class="gmail_quote">2007/6/4, Thomas Joseph alabarae+/-<a href="http://yahoo.com">yahoo.com</a> &lt;<a href="mailto:owner-chemistry-$-ccl.net">owner-chemistry-$-ccl.net</a>&gt;:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Sent to CCL by: &quot;Thomas&nbsp;&nbsp;Joseph&quot; [alabarae..yahoo.com]<br>Hi all,<br><br>Do any of you know about any FREE softwares which can identify fragments in a chemical database that wil run under Windows?
<br>I want to identify specific fragments in a chemical database<br><br>thank you in advance<br><br><br><br<br<br<br<br><br>E-mail to subscribers: <a href="mailto:CHEMISTRY-$-ccl.net">CHEMISTRY-$-ccl.net</a> or use:
<br>&nbsp;&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>&nbsp;&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>Subscribe/Unsubscribe:<br>&nbsp;&nbsp;&nbsp;&nbsp; <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">http://www.ccl.net</a><br><br>Job: <a href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a><br>Conferences: <a href="http://server.ccl.net/chemistry/announcements/conferences/">
http://server.ccl.net/chemistry/announcements/conferences/</a><br><br>Search Messages: <a href="http://www.ccl.net/htdig">http://www.ccl.net/htdig</a>&nbsp;&nbsp;(login: ccl, Password: search)<br><br<br>&nbsp;&nbsp;&nbsp;&nbsp; <a href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a><br><br>RTFI: <a href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/
</a><br><br<br><br><br><br></blockquote></div><br><br clear="all"><br>-- <br>--------------------------------------------------------------------------------
<br>Dr. Mingyue Zheng<br>Research Associate, Drug Discovery and Design Center (DDDC)<br>Box 1201, Shanghai Institute of Materia Medica.<br>555 Rd. Zuchongzhi, Shanghai, China<br>Tel:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;86-021-50806600-1201<br>Web:&nbsp;&nbsp; <a href="http://dddc.ac.cn">
http://dddc.ac.cn</a><br>Email: <a href="mailto:myzheng-$-mail.shcnc.ac.cn">myzheng-$-mail.shcnc.ac.cn</a> 

------=_Part_285_7602566.1180956502384--


From owner-chemistry@ccl.net Mon Jun  4 09:58:00 2007
From: "Shobe, David David.Shobe]~[sud-chemie.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL:G: AIM information
Message-Id: <-34408-070604095701-22774-HdX8MIWNneCoXK+O0thGxA:_:server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe-*-sud-chemie.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Mon, 4 Jun 2007 15:56:10 +0200
MIME-Version: 1.0


Sent to CCL by: "Shobe, David" [David.Shobe- -sud-chemie.com]
I've had difficulties with AIM2000 where symmetry-equivalent atoms had
different charges, etc.

Using "nosymm" in the Gaussian calculation to prevent re-orientation of
the coordinates resolved that problem.  (And I got the idea to use
"nosymm" from the CCL list! :-)

--David Shobe

-----Original Message-----
> From: owner-chemistry . ccl.net [mailto:owner-chemistry . ccl.net] 
Sent: Friday, June 01, 2007 5:11 PM
To: Shobe, David
Subject: CCL:G: AIM information


Sent to CCL by: "Guermoune  Abdeladim" [lguermoune]|[hotmail.com]
Hello,  
I am beginner with the program of AIM2000 analysis. First I have create
file wfn from the Gaussian98 using words key P B3LYP/6-311+G**
output=wfn density=current, then I treated file wfn by the AIM2000
program to localize the critical points, the density and laplacian. But
the results don't seem to me coherent, for example when the density
increases laplacian can take a positive value, and it can take a
negative value when the density decrease. In my structure I have
specially a metallic center: iron, and two borons with hydrogens in
bridged position.  
I wish to know if there is another manner to improve my file result wfn
or any others suggestions.  
Thanks.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. 
Thank you.


From owner-chemistry@ccl.net Mon Jun  4 10:35:00 2007
From: "Dr. Ponnadurai Ramasami ramchemi#,#intnet.mu" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: statistical weight
Message-Id: <-34409-070604073241-3176-sJYDay9mv51tSsD60s6f3Q _ server.ccl.net>
X-Original-From: "Dr. Ponnadurai Ramasami" <ramchemi. _ .intnet.mu>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0013_01C7A6B6.B818A4F0"
Date: Mon, 4 Jun 2007 14:43:30 +0400
MIME-Version: 1.0


Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi%x%intnet.mu]
This is a multi-part message in MIME format.

------=_NextPart_000_0013_01C7A6B6.B818A4F0
Content-Type: text/plain;
	charset="Windows-1252"
Content-Transfer-Encoding: quoted-printable

Dear ALL
I have considered the gauche and trans conformers of =
1,2-diisocyanoethane.
I have calculated the equilibrium constant from the free energy =
difference between these two forms.
Then from the equilibrium constant, I have deduced the percentage of =
each conformer.

However one reviewer pointed out that
"Statistical weight of the gauche rotamers (R ln2) was excluded when the =
author estimate the percentage of trans rotamers"
I believe that my method is ok

Can anyone suggest how to include the statistical weight?
Thanks
Ramasami



------=_NextPart_000_0013_01C7A6B6.B818A4F0
Content-Type: text/html;
	charset="Windows-1252"
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=3Dwindows-1252">
<META content=3D"MSHTML 6.00.2600.0" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV>Dear ALL</DIV>
<DIV>I have considered the gauche and trans conformers of=20
1,2-diisocyanoethane.</DIV>
<DIV>I have calculated the equilibrium constant from the free energy =
difference=20
between these two forms.</DIV>
<DIV>Then from the equilibrium constant, I have deduced the percentage =
of each=20
conformer.</DIV>
<DIV>&nbsp;</DIV>
<DIV>However one reviewer pointed out that</DIV>
<DIV>"Statistical weight of the gauche rotamers (R ln2) was excluded =
when the=20
author estimate the percentage of trans rotamers"</DIV>
<DIV>I believe that my method is ok</DIV>
<DIV>&nbsp;</DIV>
<DIV><STRONG><FONT size=3D4>Can anyone suggest how to include the =
statistical=20
weight?</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=3D4>Thanks</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=3D4>Ramasami</FONT></STRONG></DIV>
<DIV><STRONG><FONT size=3D4></FONT></STRONG>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV></BODY></HTML>

------=_NextPart_000_0013_01C7A6B6.B818A4F0--


From owner-chemistry@ccl.net Mon Jun  4 14:01:00 2007
From: "Yingbin Ge yingbin.ge- -gmail.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: statistical weight
Message-Id: <-34410-070604135942-23048-feDgUzJ38M+Qydrk7CresQ(-)server.ccl.net>
X-Original-From: "Yingbin Ge" <yingbin.ge::gmail.com>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 4 Jun 2007 12:59:36 -0500
MIME-Version: 1.0


Sent to CCL by: "Yingbin Ge" [yingbin.ge,+,gmail.com]
I think the author meant that there were 2 degenerate gauche
conformations (and only 1 trans conformation) and probably you might
not have considered the degeneracy factor?

Yingbin

On 6/4/07, Dr. Ponnadurai Ramasami ramchemi#,#intnet.mu
<owner-chemistry[]ccl.net> wrote:
>
>
> Dear ALL
> I have considered the gauche and trans conformers of 1,2-diisocyanoethane.
> I have calculated the equilibrium constant from the free energy difference
> between these two forms.
> Then from the equilibrium constant, I have deduced the percentage of each
> conformer.
>
> However one reviewer pointed out that
> "Statistical weight of the gauche rotamers (R ln2) was excluded when the
> author estimate the percentage of trans rotamers"
> I believe that my method is ok
>
> Can anyone suggest how to include the statistical weight?
> Thanks
> Ramasami
>
>


-- 
Yingbin Ge, Ph. D.
207 Spedding Hall, Ames Lab, Iowa State University
Ames, IA 50011 (Office Phone: 515-294-0540)


From owner-chemistry@ccl.net Mon Jun  4 14:43:00 2007
From: "Grigoriy Zhurko reg_zhurko ~~ chemcraftprog.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Gaussian/PCM/chemical shifts
Message-Id: <-34411-070604125800-17211-Rxiz1FCJZOEgmbCqW6mPKQ%server.ccl.net>
X-Original-From: Grigoriy Zhurko <reg_zhurko/./chemcraftprog.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Mon, 4 Jun 2007 20:58:55 -0700
MIME-Version: 1.0


Sent to CCL by: Grigoriy Zhurko [reg_zhurko]![chemcraftprog.com]
  I suppose, using the calculated TMS carbon shielding is not correct enough, because the TMS standard used in the experiment is not in the gas phase. I tried to calculate the TMS shielding at same level of theory as investigated molecules, but their chemical shifts with it were still overestimated.


> Dear Grigoriy Zhurko,

> in [1] we discuss the importance of the TMS 13C reference values.
> Please find a paragraph which might be relevant to your message
> cited below:

> [..]
> Particular attention should be paid to the case of 
> TMS. For this reference compound in proton and 
> carbon-13 NMR, two structures of Td symmetry exist, 
> as illustrated in ¨gure 1. The one in ¨gure 1 (a) is the 
> global minimum, and the structure of ¨gure 1 (b) is a 
> fourth-order saddle point. The energy of the global 
> minimum (¨gure 1 (a)) , taken from the B3LYP calcula- 
> tion, is 27. 3 kJ molÁ1 lower than the one for structure 
> (b). The corresponding absolute shielding value for 13 C 
> is 200.3 ppm. We chose this value as the reference chemi- 
> cal shift as it corresponds to a true minimum structure. 
> Cheeseman et al. [49] report a 13 C chemical shielding of 
> 195.1 ppm for TMS, whereas our calculation for the 
> non-minimum structure of ¨gure 1 (b) reproduced a 
> value of 195.4 ppm.
> [..]

> There is a little more discussion in the paper.
> Regards,
> Marc Baaden

> [1]  M. Baaden, P. Granger and A. Strich; "Dependence of isotropic
>      shift averages and nuclear shielding tensors on the internal
>      rotation of the functional group X about the C-X bond in seven
>      simple vinylic derivatives H2C=CH-X.", Mol. Phys., 98, 2000,
>      329-342.


>>>> "Grigoriy Zhurko reg_zhurko(!)chemcraftprog.com" said:
 >>> 
 >>> Sent to CCL by: Grigoriy Zhurko [reg_zhurko]*[chemcraftprog.com]
 >>>   This problem is interesting for me too. I have found that computed gas-ph
>      ase 13C chemical shifts (GIAO B3LYP/6-311G(D,P)) correlate very well with
>      the experiment (in CCl4), but the computed values of chemical shifts are s
>      ignificantly overestimated. Maybe the problem is in the reference value fo
>      r converting isotropic shielding into chemical shifts (e.g. with TMS). Wha
>      t value of the TMS shielding on carbon should be used?


  Sincerely,
  Grigoriy Zhurko.


From owner-chemistry@ccl.net Mon Jun  4 15:36:00 2007
From: "Reynier Suardiaz reynier.suardiaz!^!gmail.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: EPR-II, III contraction coefficients
Message-Id: <-34412-070604152635-3883-dV52eDtOJryM05l2RRF0Xw(0)server.ccl.net>
X-Original-From: "Reynier  Suardiaz" <reynier.suardiaz]^[gmail.com>
Date: Mon, 4 Jun 2007 15:26:30 -0400


Sent to CCL by: "Reynier  Suardiaz" [reynier.suardiaz(a)gmail.com]

Dear CCLers
I need the complete set of contraction coefficients for EPR-II and
EPR-III basis sets. If it is possible, in Gaussian format.
Thanks in advance
Reynier


--
http://rincon.uam.es/dir?cw=331069946289062


From owner-chemistry@ccl.net Mon Jun  4 16:11:00 2007
From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= reynier.suardiaz.(-).uam.es" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: EPR-II, III contraction coefficients
Message-Id: <-34413-070604145034-18416-NH0LBnK5uxEEXkmyJeBTqg(-)server.ccl.net>
X-Original-From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" <reynier.suardiaz^^uam.es>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 4 Jun 2007 17:15:51 +0000
MIME-Version: 1.0


Sent to CCL by: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" [reynier.suardiaz_._uam.es]
Dear CCLers
I need the complete set of contraction coefficients for EPR-II and
EPR-III basis sets. If it is possible, in Gaussian format.
Thanks in advance
Reynier


--
http://rincon.uam.es/dir?cw=331069946289062


From owner-chemistry@ccl.net Mon Jun  4 20:15:00 2007
From: "Mustafa Hussein mustafa.hussein86]|[yahoo.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Running GAMESS on Intel Celeron Processors
Message-Id: <-34414-070604201154-17922-SUS4YwTzjYDAT42n+ksySQ^^server.ccl.net>
X-Original-From: "Mustafa  Hussein" <mustafa.hussein86!A!yahoo.com>
Date: Mon, 4 Jun 2007 20:11:51 -0400


Sent to CCL by: "Mustafa  Hussein" [mustafa.hussein86%%yahoo.com]
Hi,

My PC has an Intel Celeron Processor. I have checked the specifications on hardware requirements for running GAMESS. I found no thing stated on Celeron Processors. Does this mean GAMESS can not be run on such processors?

If so, I am gonna change my processor, really.

Any help is appreciated

Thanks

Mustafa


From owner-chemistry@ccl.net Mon Jun  4 23:58:00 2007
From: "Senthil Nathan zenthil03:+:yahoo.co.in" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: Iodide ion optimaization
Message-Id: <-34415-070604235446-26263-4tjI+jegi7Mpd9mm7q3Taw ~~ server.ccl.net>
X-Original-From: "Senthil  Nathan" <zenthil03_._yahoo.co.in>
Date: Mon, 4 Jun 2007 23:54:43 -0400


Sent to CCL by: "Senthil  Nathan" [zenthil03^-^yahoo.co.in]
Dear CCLers

I have used Iodide ion as a nucleophile in my organic reaction. i want to optimaize this ion. please you tell me a best basis setlevel  for this Iodide ion optimaization and energy calculation for DFT level.

regards by
senthil