From chemistry-request@ccl.net Tue Jun 14 08:15:37 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5ECFa2p004769 for ; Tue, 14 Jun 2005 08:15:36 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5ECFaNH004768 for chemistry_at_ccl.net; Tue, 14 Jun 2005 08:15:36 -0400 Date: Tue, 14 Jun 2005 08:15:36 -0400 Message-Id: <200506141215.j5ECFaNH004768_at_server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request_at_ccl.net using -f From: "kono, , lemke" To: chemistry_at_ccl.net X-Web-Message-Number: 050614081326-4549 Subject: W:partition functions/gaussian X-Spam-Status: No, score=-0.1 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD,FROM_ENDS_IN_NUMS autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net hello, a question regarding vibrational contributions to the partition function in gaussian. gaussian lists two values for vibrational contribtutions to the partition function, one with zero of energy being the bottom of the well (BOT) , the other for the first vibratonal level (V=0). are both of these values calculated by default for 298.15K and 1bar? thanks kono From chemistry-request@ccl.net Mon Jun 13 23:07:38 2005 Received: from web15107.mail.cnb.yahoo.com (web15107.mail.cnb.yahoo.com [202.165.103.76]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5E37UPB023594 for ; Mon, 13 Jun 2005 23:07:31 -0400 Received: (qmail 91794 invoked by uid 60001); 14 Jun 2005 03:07:28 -0000 Message-ID: <20050614030728.91792.qmail:at:web15107.mail.cnb.yahoo.com> Received: from [61.183.207.52] by web15107.mail.cnb.yahoo.com via HTTP; Tue, 14 Jun 2005 11:07:28 CST Date: Tue, 14 Jun 2005 11:07:28 +0800 (CST) From: renyanliang Subject: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20CCL:formchk=20erro?= To: chemistry:at:ccl.net In-Reply-To: <95fe560c9a7491fd9226b0a91ed12120:at:mayo.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, FROM_ENDS_IN_NUMS autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net thanks, I completely it successfully. --- Jason Thompson P45@: > I believe you need to use the GAUSS_MEMDEF > environment variable, which > allows you to set the memory (in words) available > for G03 utilities > (these utilities use 6 MW by default). For example: > > setenv GAUSS_MEMDEF 1900000 > > for tcsh > > GAUSS_MEMDEF=1900000;export GAUSS_MEMDEF > > for bash, etc. > > See: > > http://www.gaussian.com/g_ur/m_utils.htm > > near the bottom. > > On Jun 12, 2005, at 7:04 AM, renyanliang wrote: > > > Dear everybody > > > > when I used the formchk to convert the file > (gauss > > 03 C02 for sgi), I found one erro as following: > > Read checkpoint file 1prc-pbh-uff-zindo-pop.chk > > Write formatted file 1prc-pbh-uff-zindo-pop.fchk > > Out-of-memory error in routine FChkPn-MO (IEnd= > > 19876291 MxCore= 6291456) > > Use %mem=19MW to provide the minimum amount of > memory > > required to > > complete this step. > > Error termination via Lnk1e at Fri Jun 10 07:34:06 > > 2005. > > Segmentation fault > > hope u can give me some advice. > > > > > > > > > ___________________________________________________________ > > QE;"Cb7QGSJOd#-VP9z5ZR;>xN^@,;xSJ<~I'HE3,4sSJOd > > http://cn.mail.yahoo.com/?id=77071 > > > > > > > > To send e-mail to subscribers of CCL put the > string CCL: on your > > Subject: line > > > > Send your subscription/unsubscription requests to: > > > CHEMISTRY-REQUEST:at:ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > > > If your is mail bouncing from ccl.net domain due > to spam filters, > > please > > use the Web based form from CCL Home Page > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > > +-+ > > > > > > > > > Jason D. Thompson > Molecular Pharmacology and Experimental Therapeutics > Mayo Clinic > Guggenheim 6-93 > 200 First Street SW > Rochester, MN 55905 > (507)-284-1758 > > > -= This is automatically added to each message by > the mailing script =- > To send e-mail to subscribers of CCL put the string > CCL: on your Subject: line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to > spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > __________________________________________________ 8O?lW"2aQE;"3,4sH]A?Cb7QSJOd? http://cn.mail.yahoo.com From chemistry-request@ccl.net Tue Jun 14 04:19:18 2005 Received: from web50405.mail.yahoo.com (web50405.mail.yahoo.com [206.190.38.70]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5E8J2jE004921 for ; Tue, 14 Jun 2005 04:19:06 -0400 Received: (qmail 72189 invoked by uid 60001); 14 Jun 2005 07:18:57 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=M1ecVGNrb8x6XXWe28wjrh2+JmHNaCnhkWRXZw/K066dYe7s08SaJnFv8EBKBm89F+46Jq7061DLtVpm5MFiYi1Af0IZDp3TR9tTpNnDn3MEFJh3RpdtUKV2Bv02/SSmXqRUnfGu1JwbDbKmCkJrshpFBxDCmYvBM9P6a+7iUgA= ; Message-ID: <20050614071857.72187.qmail:at:web50405.mail.yahoo.com> Received: from [193.179.225.19] by web50405.mail.yahoo.com via HTTP; Tue, 14 Jun 2005 00:18:57 PDT Date: Tue, 14 Jun 2005 00:18:57 -0700 (PDT) From: Bruno Sopko Subject: Re: CCL:a secure Xterm emulator To: chemistry:at:ccl.net In-Reply-To: <1D58F94275E4274F8C83B7A880F2D3BE0873F4:at:PVEXCH01.PV.PVPANTHER.NET> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1771939433-1118733537=:71028" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,HTML_40_50,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --0-1771939433-1118733537=:71028 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit And what about cygwin and X11? It is free and can run using ssh protocol. Bruno Sopko "Fan,Huajun" wrote: Hi Dr Borosy May I ask how much ReflextX cost? I am also interested in buying one. Thanks. Huajun Fan Email: hjfan:at:pvamu.edu Tel: (936) 857-2616 Prairie View A&M University Chemistry Department PO Box 4107 Prairie View, TX 77446-4107 --------------------------------- From: Computational Chemistry List on behalf of andras.borosy:at:givaudan.com Sent: Wed 6/8/2005 5:15 AM To: CCL Subject: CCL:a secure Xterm emulator Dear Colleagues, Thank you for the answers. I have ordered Reflection X, because that would be easiest to use for my organic chemist colleagues. Regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy:at:givaudan.com -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY:at:ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1771939433-1118733537=:71028 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
And what about cygwin and X11? It is free and can run using ssh protocol.
 
Bruno Sopko

"Fan,Huajun" <hjfan:at:pvamu.edu> wrote:
Hi Dr Borosy
 
May I ask how much ReflextX cost? I am also interested in buying one.
 
Thanks.
 
Huajun Fan
Email: hjfan@pvamu.edu
Tel: (936) 857-2616
Prairie View A&M University
Chemistry Department
PO Box 4107
Prairie View, TX 77446-4107
 

From: Computational Chemistry List on behalf of andras.borosy:at:givaudan.com
Sent: Wed 6/8/2005 5:15 AM
To: CCL
Subject: CCL:a secure Xterm emulator

Dear Colleagues,

Thank you for the answers. I have ordered Reflection X, because that would
be easiest to use for my organic chemist colleagues.

Regards,

Dr. Andras Borosy
Seniour Scientist
Delivery Systems, Fragrance Research
Givaudan Schweiz AG
Ueberlandstr. 138
8600 D|bendorf
Switzerland
tel: + 41-1-8242164
fax: +41-1-8242926
e-mail: andras.borosy:at:givaudan.com



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http://mail.yahoo.com --0-1771939433-1118733537=:71028-- From chemistry-request@ccl.net Tue Jun 14 10:52:32 2005 Received: from trentu.ca (mxdoug.trentu.ca [192.75.12.132]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5EEqRHn013905 for ; Tue, 14 Jun 2005 10:52:27 -0400 Received: (qmail 17852 invoked by uid 510); 14 Jun 2005 13:52:21 -0000 Received: from 209.42.102.117 by mxdoug (envelope-from , uid 502) with qmail-scanner-1.24 (fsecure: 4.52/2461/libra database 2005-06-09/orion database 2005-06-09/avp(2005-06-13). spamassassin: 3.0.2. Clear:RC:1(209.42.102.117):. Processed in 0.032599 secs); 14 Jun 2005 13:52:21 -0000 X-Qmail-Scanner-Mail-From: elewars:at:trentu.ca via mxdoug X-Qmail-Scanner: 1.24 (Clear:RC:1(209.42.102.117):. Processed in 0.032599 secs) Received: from unknown (HELO trentu.ca) (209.42.102.117) by trentu.ca with SMTP; 14 Jun 2005 13:52:20 -0000 Message-ID: <42AEE122.8060003:at:trentu.ca> Date: Tue, 14 Jun 2005 09:52:34 -0400 From: errol lewars User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: Re: CCL:absorbance spectra or colored compound prediction References: <87328C31E07B9240A019D32F4D4E32865FB196:at:scorreu.IQS.LOCAL> <0D044DE7-12F9-4627-8F92-57917F7410A8:at:geoffhutchison.net> <1118684508.42adc55cd0828:at:www.theorie.physik.uni-muenchen.de> In-Reply-To: <1118684508.42adc55cd0828:at:www.theorie.physik.uni-muenchen.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_RCVD_HELO autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net 2005 June 145 Hello, "DFT-theory only gives something physically meaningful and interpretable for the overall-electron density (and all quantities derivable from that), but not for "single electron"-wavefunctions (=MOs)." Regarding physical interpretations of the Kohn-Sham orbitals: correlations between Kohn-Sham and conventional (ab initio and by implication semiempirical) MOs have been found: 1) R. Stowasser, R. Hoffmann, JACS, 1999, _121_, 3414 2) E. J. Baerends, Theoretical Chemistry Accounts, 2000, _103_, 265. 3) D-P Chong et al., J Phys Chem A, J Chem Phys, 2002, _116_, 1760. 4) C-G Zhan et al., J Phys Chem A, 2003, _107_, 4184. See too: a) H. M. Muchall et al., Can J Chem, 1998, _76_, 221 b) J. Fabian et al., J Mlec Modelling, 2000, _6_, 177. c) T. Kar et al., J Phys Chem A, 2000, _104_, 9953. EL ==== Andreas Serr wrote: >Dear all, > >S. I. Gorelsky and A. B. P. Lever used ZINDO and TD-DFT a lot for calculating >absorption spectra of (charged) transition metal complexes. There are numerous >papers where they used both techniques, but this one might be a good start: > >J Organomet Chem, 635 (2001) 187-196. > >The conclusions are that both methods yield similar results, most interestingly, >that this also applies to the calculated MOs (Kohn-Sham-orbitals vs. >semiempirical ZINDO/s-MOs). I do not know too much about DFT/TD-DFT, but to my >knowledge prior to that publication, DFT-theory only gives something physically >meaningful and interpretable for the overall-electron density (and all >quantities derivable from that), but not for "single electron"-wavefunctions >(=MOs). However, I might be wrong. > >Best wishes, >Andreas > >Geoff Hutchison wrote: > > >>On Jun 13, 2005, at 2:07 AM, Rey Puiggros Oscar wrote: >> >> >> >>>depending on the size of your system my choice would be Time >>>Dependent Density Functional Methods or ZINDO/S. The first one is >>>quite accurate but it is more expensive, while ZINDO/S is semi- >>>empirical and faster but with lower accuracy. >>> >>> >>I'm not sure I'd completely agree with that. For neutral organic >>molecules, I think ZINDO/S does almost as well as TDDFT. Both do well >>with low-lying excited states. >> >>e.g. >>Hutchison, G. R.; et. al. J. Phys. Chem. A 2002, 106, 10596. >>Fabian, J. Theor. Chem. Acc. 2001, 106, 199. >> >>I'm sure there are similar "benchmark" studies too. (Although if anyone >>has similar comparative experiment vs. computed papers for charged >>organic species, I'd be grateful for references.) >> >>-Geoff >> >> > > > From chemistry-request@ccl.net Tue Jun 14 02:19:02 2005 Received: from mail2.cc.huji.ac.il (real-outmail.cc.huji.ac.il [132.64.1.18]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5E6Irkl029861 for ; Tue, 14 Jun 2005 02:18:54 -0400 Received: from mail2.cc.huji.ac.il (localhost [127.0.0.1]) by mail2.cc.huji.ac.il (Postfix) with SMTP id 3F80D1A12A9; Tue, 14 Jun 2005 08:42:17 +0300 (IDT) Received: by mail2.cc.huji.ac.il (Postfix, from userid 31998) id 2DA4F1A12A5; Tue, 14 Jun 2005 08:42:17 +0300 (IDT) Received: from md.huji.ac.il (md.huji.ac.il [132.64.169.2]) by mail2.cc.huji.ac.il (Postfix) with ESMTP id 6B1561A12A9 for ; Tue, 14 Jun 2005 08:42:13 +0300 (IDT) Received: from md.huji.ac.il (shurki.md.huji.ac.il [132.64.165.200]) by md.huji.ac.il (8.12.11/8.12.11) with ESMTP id j5E5gBT6598944 for ; Tue, 14 Jun 2005 08:42:13 +0300 (IDT) Message-ID: <42AE6E32.5080107:at:md.huji.ac.il> Date: Tue, 14 Jun 2005 08:42:10 +0300 From: avital shurki User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030630 X-Accept-Language: en-us, en, he MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: Re: CCL:Defining orbitals References: <9DD56492790889439F731F5BD6DACA0007D78B19:at:srvkyem1.americas.sc-world.com> In-Reply-To: <9DD56492790889439F731F5BD6DACA0007D78B19:at:srvkyem1.americas.sc-world.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed X-Spam-Level: X-Virus: scanned by VAMS 2005 version 8.761 from Mon Jun 13 17:41:29 2005 CEST X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5E6J2kl029868 Using valence bond (VB) theory you can define anything you want (any state and any wavefunction). It is not implemented in gaussian, but in games-uk e.g. it is. Shobe, David wrote: > Yes, but...I think he wants to study what would more correctly be called > a particular state of Li anion triplet. > > I don't remember how Gaussian treats the degeneracy of the three p > orbitals. If Gaussian just arbitrarily picks one of the three p > orbitals, no special manipulation is needed; but if the HOMO is a > mixture of px, py, and pz it's a different story... > > > --David Shobe, Ph.D., M.L.S. > S|d-Chemie, Inc. > phone (502) 634-7409 > fax (502) 634-7724 > > Don't bother flaming me: I'm behind a firewall. > > > ------------------------------------------------------------------------ > *From:* Computational Chemistry List [mailto:chemistry-request:at:ccl.net] > *On Behalf Of *Wayne Steinmetz > *Sent:* Friday, June 10, 2005 4:46 PM > *To:* chemistry:at:ccl.net > *Subject:* CCL:Defining orbitals > > The electrons belong to the entire atom and are not constrained to any > orbital. One uses orbitals to construct the wave function. One must be > sure that the set of orbitals, i.e. the basis set, is sufficiently > flexible to describe completely the molecular species. You are dealing > with an atomic species so a polarization basis set is probably not needed. > > > > Wayne E. Steinmetz > > Carnegie Professor of Chemistry > > Woodbadge Course Director > > Chemistry Department > > Pomona College > > 645 North College Avenue > > Claremont, California 91711-6338 > > USA > > phone: 1-909-621-8447 > > FAX: 1-909-707-7726 > > Email: wsteinmetz:at:pomona.edu > > WWW: pages.pomona.edu/~wsteinmetz > > > > -----Original Message----- > *From:* Computational Chemistry List [mailto:chemistry-request:at:ccl.net] > *On Behalf Of *Christopher Thompson > *Sent:* Thursday, June 09, 2005 6:09 PM > *To:* chemistry:at:ccl.net > *Subject:* CCL:Defining orbitals > > > > Gday, > > > > I would like to do an MP2 calc on a Li- species in triplet state. > > > > With one electron in the s orbital and one in a p orbital, > > how can you constrain the electron to say the px orbital? > > > > Cheers, > > cdth:at:unimelb.edu.au > > > > Christopher Thompson > > Laser Spectroscopy Group > > School of Chemistry > > University of Melbourne > ________________________________________________________________ Dr. Avital Shurki Department of Medicinal Chemistry and natural products, Lise Meitner-Minerva Center for Computational Quantum Chemistry, School of Pharmacy, The Hebrew University of Jerusalem Ein Kerem Campus Jerusalem 91120, Israel Phone +972-2-675-8696 Fax +972-2-675-7076 Email avital:at:md.huji.ac.il http://pharmacy.huji.ac.il/avital/ From chemistry-request@ccl.net Tue Jun 14 02:34:24 2005 Received: from mrbusi1.netcologne.de (mrbusi1.netcologne.de [194.8.194.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5E6YI3s030337 for ; Tue, 14 Jun 2005 02:34:19 -0400 Received: from cosmologic.de (xdsl-213-196-251-206.netcologne.de [213.196.251.206]) by mrbusi1.netcologne.de (Postfix) with ESMTP id 6C2DA1A0005 for ; Tue, 14 Jun 2005 07:28:13 +0200 (CEST) Message-ID: <42AE6AED.8050002:at:cosmologic.de> Date: Tue, 14 Jun 2005 07:28:13 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: Re: CCL:Scientific Conference by Accelrys in London, Nov 14-16 References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Dr. Nauss, is AccelrysWorld really open to anyone, even to vendors of technology competing (or at least not directly connected) with Accelrys software? Regards Andreas Klamt Jeff Nauss wrote: >Accelrys will be hosting AccelrysWorld, a computational chemistry >conference, in London, UK, Nov 14-16. The conference is open to anyone >with an interest in computational chemistry, molecular modeling, and/or >research information technology. Sessions include cheminformatics, >bioinformatics, proteomics, rational drug design, pharmaceutical >development, surface science, and a joint session with the nanotechnology >consortium. Confirmed speakers represent organizations including >AstraZeneca, GSK, IBM, Johnson Matthey, Syngenta, Nerviano >Pharmaceuticals, BNFL, and Astex Technologies. Come along to find out >about the latest computational chemistry solutions, to hear case study >presentations, give feedback and learn from other users in round-table >discussions, and network with your peers. > >More, including agenda and registration details at >http://www.accelrysworld.com. > >-- >Jeffrey L. Nauss, Ph.D. >Lead Training Scientist >Accelrys >10188 Telesis Court, Suite 100 >San Diego, CA 92121-4779 > >Phone: +1-858-799-5555 >Fax: +1-858-799-5100 >http://www.accelrys.com/training > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY:at:ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > -- ----------------------------------------------------------------------------- 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:at:cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From chemistry-request@ccl.net Tue Jun 14 12:01:38 2005 Received: from web33201.mail.mud.yahoo.com (web33201.mail.mud.yahoo.com [68.142.206.99]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5EG1XhV019764 for ; Tue, 14 Jun 2005 12:01:33 -0400 Received: (qmail 24913 invoked by uid 60001); 14 Jun 2005 15:01:30 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=RY4F3c1em5ig7M0qU8bIONMZo10lE0CSk6GpE52m4FNmr2s41kmEGAMmdROBCa3jZ1qL/7LtJgd/PQi4lZf2SKYlPtoW5NyFgH61uart6DN3KiZ/fOd3xcZpysmm4jfnC+If2Wv5yHj/tG4etLxsS5n3x1KNtq8pBCGTIgjrpkw= ; Message-ID: <20050614150130.24911.qmail !=! web33201.mail.mud.yahoo.com> Received: from [139.184.30.16] by web33201.mail.mud.yahoo.com via HTTP; Tue, 14 Jun 2005 08:01:30 PDT Date: Tue, 14 Jun 2005 08:01:30 -0700 (PDT) From: Ricardo Oliveira Subject: RE: TDDFT on G03: negative transition energies To: chemistry !=! ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=3.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FORGED_YAHOO_RCVD autolearn=no version=3.0.3 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear all, Thanks for all the replies. I believe now that the problem is that the structure I am using is not properly optimized. I am trying to do a freq calculation in order to check that. best wishes Ricardo Oliveira Esplugas Dept of Chemistry Sussex University r.o.esplugas !=! susx.ac.uk web: www.hpc.susx.ac.uk/~ricardoe __________________________________ Discover Yahoo! Use Yahoo! to plan a weekend, have fun online and more. Check it out! http://discover.yahoo.com/ __________________________________ Discover Yahoo! Find restaurants, movies, travel and more fun for the weekend. Check it out! http://discover.yahoo.com/weekend.html From chemistry-request@ccl.net Tue Jun 14 11:10:17 2005 Received: from dalal3.rshs.duq.edu (dalal3.rshs.duq.edu [165.190.57.106]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EFAEMc015655 for ; Tue, 14 Jun 2005 11:10:14 -0400 Received: by dalal3.rshs.duq.edu (Postfix, from userid 501) id 5D93513F90; Tue, 14 Jun 2005 10:04:17 -0400 (EDT) Date: Tue, 14 Jun 2005 10:04:17 -0400 From: help = = = gaussian.com To: chemistry = = = ccl.net Subject: Re: CCL:Defining orbitals Message-ID: <20050614140417.GC23927 = = = gaussian.com> References: <9DD56492790889439F731F5BD6DACA0007D78B19 = = = srvkyem1.americas.sc-world.com> <4186c3416e5a95e924f14b43ef31d897 = = = unimelb.edu.au> Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: <4186c3416e5a95e924f14b43ef31d897 = = = unimelb.edu.au> User-Agent: Mutt/1.4i X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dr. Thompson, Doing excited states with MP2 is tricky. The HF reference and the MP2 expansion are done with a single determinant and the SCF procedure solves for the lowest energy of a given point group symmetry. For Li- atom you have nearly degenerate p orbitals, depending on the water(s) around this it will lift the degeneracy but it may also result in fewer than 3 symmetry distinct states. What might be a better approach is to look at TD-DFT which has some effect of correlation, not as good as MP2 for this case, but it will give you a spread of low energy excited state energies based on the ground state orbitals. Pick one of the gradient corrected or hybrid functionals, B3LYP or B3PW86 are well studied, and a fairly large basis set including diffuse functions and polarization, 6-311+G(d,p) or better, and see what you get. If you do have some symmetry you can generally use Guess=(Read,Alter) to flip occupancy and get different states for the MP2 approach. On Tue, Jun 14, 2005 at 11:46:04AM +1000, Christopher Thompson wrote: > David, > > You interpreted my question correctly. Without going into the > experiment in detail ... we generate Li-(H2O)n clusters and record > their infrared spectrum. The source of Li- can potentially create Li- > anions in more than the lowest energy singlet state. It appears that > the symmetry of the clusters is not the same for different e spin > states on the Li- ... an excellent way to differentiate species in > vibrational spectroscopy. It would be nice to characterise the > different triplet states comprehensively. > > Cheers, > Chris > > On 14/06/2005, at 3:40 AM, Shobe, David wrote: > > > > Yes, but...I think he wants to study what would more correctly be > > called a particular state of Li anion triplet. > > > > > > > I don't remember how Gaussian treats the degeneracy of the three p > > orbitals. If Gaussian just arbitrarily picks one of the three p > > orbitals, no special manipulation is needed; but if the HOMO is a > > mixture of px, py, and pz it's a different story... > > > > > > > > > --David Shobe, Ph.D., M.L.S. > > > > > S|d-Chemie, Inc. > > > > > phone (502) 634-7409 > > > > > fax (502) 634-7724 > > > > > > > Don't bother flaming me: I'm behind a firewall. > > > > > > > From: Computational Chemistry List > > [mailto:chemistry-request = = = ccl.net] On Behalf Of Wayne Steinmetz > > > > > Sent: Friday, June 10, 2005 4:46 PM > > > > > To: chemistry = = = ccl.net > > > > > Subject: CCL:Defining orbitals > > > > > > > The electrons belong to the entire atom and are not constrained to > > any orbital. One uses orbitals to construct the wave function. > > One must be sure that the set of orbitals, i.e. the basis set, is > > sufficiently flexible to describe completely the molecular species. > > You are dealing with an atomic species so a polarization basis > > set is probably not needed. > > > > Wayne E. Steinmetz > > Carnegie Professor of Chemistry > > Woodbadge Course Director > > Chemistry Department > > Pomona College > > 645 North College Avenue > > Claremont, California 91711-6338 > > USA > > phone: 1-909-621-8447 > > FAX: 1-909-707-7726 > > Email: wsteinmetz = = = pomona.edu > > WWW: pages.pomona.edu/~wsteinmetz > > > > -----Original Message----- > > From: Computational Chemistry List > > [mailto:chemistry-request = = = ccl.net] On Behalf Of Christopher > > Thompson > > Sent: Thursday, June 09, 2005 6:09 PM > > To: chemistry = = = ccl.net > > Subject: CCL:Defining orbitals > > > > Gday, > > > > I would like to do an MP2 calc on a Li- species in triplet state. > > > > With one electron in the s orbital and one in a p orbital, > > how can you constrain the electron to say the px orbital? > > > > Cheers, > > cdth = = = unimelb.edu.au > > > > Christopher Thompson > > Laser Spectroscopy Group > > School of Chemistry > > University of Melbourne > > > > > > Dr Christopher Thompson > Laser Spectroscopy Group > School of Chemistry > University of Melbourne > VIC, Australia, 3010. > Ph. +61 3 8344 8163 > Fax. +61 3 9347 5180 > > -- Douglas J. Fox Technical Support Gaussian, Inc. help = = = gaussian.com From chemistry-request@ccl.net Tue Jun 14 12:34:51 2005 Received: from iqpc-ms5.iqpc.loc (mail.iqpc.co.uk [195.167.134.86]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EGYlMa021858 for ; Tue, 14 Jun 2005 12:34:47 -0400 Received: from iqpc-ms4.iqpc.loc ([10.10.5.4]) by iqpc-ms5.iqpc.loc with Microsoft SMTPSVC(6.0.3790.211); Tue, 14 Jun 2005 16:50:31 +0100 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C570F8.CB5979EC" Subject: Meeting Hit to Lead Date: Tue, 14 Jun 2005 16:50:31 +0100 Message-ID: <3CCB329C8B224648B4F2E6013B0B62DA1C23A7)at(iqpc-ms4.iqpc.loc> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Meeting Hit to Lead Thread-Index: AcVwP2onw54k2EnYQvajr/xRn/CYmQ== From: "Ricardo Molina" To: X-OriginalArrivalTime: 14 Jun 2005 15:50:31.0818 (UTC) FILETIME=[CB7E4EA0:01C570F8] X-Spam-Status: No, score=0.9 required=5.0 tests=DEAR_SOMETHING, FORGED_RCVD_HELO,HTML_60_70,HTML_MESSAGE autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C570F8.CB5979EC Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Sirs, I would like to bring to your attention a conference we are organising in= London that I am sure would be of interest to the CCL.net readers. We ar= e happy to give a special discount of 10% to all those interested in atte= nding from your site. All they have to do is quote CCL when contacting us= =2E Hit-To-Lead Enhancing lead generation to accelerate quality compounds into lead optim= isation July 18 - 19, 2005 =B7 The Caf=E9 Royal, London, UK http://www.iqpc-pharma.com/GB-2484/SPR4 =20 Increasing pressure to reduce attrition and put forward better quality le= ad compounds is forcing hit-to-lead up the agenda of every pharmaceutical= company. Many are now reducing this major bottleneck by improving decis= ion-making and generating better quality leads faster. And Pharma IQ is = showcasing the most innovative and successful case studies at this year's= Hit-to-Lead conference. Leaders from big pharma including Pfizer, Roche= , Novartis, AstraZeneca, Bayer, Wyeth, Merck, Sanofi-Aventis and Johnson = & Johnson will be revealing their stories of success and failure in lead = generation. By taking a practical and in-depth look at their strategies = and experiences, you can enhance your own practices and ensure you are fo= cussing your resources only on the most promising compounds.=20 If you have any questions or are interested in attending please contact m= e on Ricardo.Molina)at(iqpc.co.uk or giv= e us a call on 0207 368 9300. I am happy to extend a special 10% discount= for all CCL members. There is also a special price for Academia. Simply = quote CCL when contacting us. For full conference agenda visit http://www.iqpc-pharma.com/GB-2484/SPR4 = =20 =20 Thank you very much for your time =20 =20 Ricardo Molina=20 Pharma IQ (a division of IQPC) Anchor House 15-19 Britten Street=20 London SW3 3QL=20 e: Ricardo.Molina)at(iqpc.co.uk =20 w: www.iqpc-pharma.com =20 t: +44 (0) 20 7368 9300=20 ************************************************************************=20= This email is confidential and intended solely for the use of the individ= ual to whom it is addressed. Any views or opinions presented are solely t= hose of the author and do not necessarily represent those of IQPC Ltd or = any of its affiliates. If you are not the intended recipient, be advised = that you have received this email in error and that any use, disseminatio= n, forwarding, printing, or copying of this email is strictly prohibited.= If you have received this email in error please notify us by telephone o= n +44 (0)20 7368 9300.=20 This footnote also confirms that this email message has been checked by a= nti-virus software for the presence of computer virii. However, IQPC Ltd = accepts no responsibility for any virus or defect that might arise from o= pening this e-mail or attachments.=20 ************************************************************************=20= ------_=_NextPart_001_01C570F8.CB5979EC Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear=20= Sirs,

I would like to bring = to your=20 attention a conference we are organising in London that I am sure wo= uld be=20 of interest to the CCL.net=20 readers. We are happy to g= ive a=20 special discount of 10% to all those interested in attending=20 from your site. All they have to do is quote CCL when contacting=20 us.

Hit-To-Lead
Enhanc= ing lead=20 generation to accelerate quality compounds into lead=20 optimisation
July=20 18 - 19, 2005 =B7  The=20 Caf=E9 Royal, London,=20 UK

http://www.iqpc-pharma.com/GB-2484/SPR4

Increasing pressure to reduce attrition and put forward better q= uality=20 lead compounds is forcing hit-to-lead up the agenda of every pharmaceutic= al=20 company.  Many are now redu= cing this=20 major bottleneck by improving decision-making and generating better quality leads=20 faster.  And Pharma = IQ is=20 showcasing the most innovative and successful case studies at this year=92= s=20 Hit-to-Lead conference.  Le= aders=20 > from big pharma including Pfiz= er,=20 Roche, Novartis, AstraZeneca, Bayer, Wyeth, Merck, Sanofi-Aventis and Joh= nson=20 & Johnson will be revealing their stories of success and failu= re in=20 lead generation.  By taking= a=20 practical and in-depth look at their strategies and experiences, you can = enhance=20 your own practices and ensure you are focussing your resources only on th= e most=20 promising compounds.

If=20 you have any questions or are interested in attending please contact me o= n=20 Ricardo.Molina)at(iqpc.co.uk or give us a= call on=20 0207 368 9300. I am happy to extend a special 10% discount for all <= SPAN=20 class=3D054211117-13062005>CCL=20 members. There is also a special price for Academia. Simply quote CCL when contacting=20 us.

For full conference agenda visit http://www.iqpc-pharma.com/GB-2484/SPR4

&n= bsp;

<= SPAN=20 class=3D054211117-13062005>Thank you very much for your=20= time

<= SPAN=20 class=3D054211117-13062005>&nbs= p;

<= SPAN=20 class=3D054211117-13062005>&nbs= p;

<= SPAN=20 class=3D054211117-13062005>

Ricardo=20 Molina=20
Pharma I= Q (a=20 division of IQPC)
Anchor House
15-19 Britten Street=20
London S= W3=20 3QL

e: Ricardo.Molina)at(iqpc.co.uk=20=  
w: www.iqpc-pharma.com
t: +44 (= 0) 20=20 7368 9300=20




= ************************************************************************ =


This email is confidential and intended solely for the use of= the individual to whom it is addressed. Any views or opinions presented = are solely those of the author and do not necessarily represent those of = IQPC Ltd or any of its affiliates. If you are not the intended recipient,= be advised that you have received this email in error and that any use, = dissemination, forwarding, printing, or copying of this email is strictly= prohibited. If you have received this email in error please notify us by= telephone on +44 (0)20 7368 9300.

This footnote also confirms th= at this email message has been checked by anti-virus software for the pre= sence of computer virii. However, IQPC Ltd accepts no responsibility for = any virus or defect that might arise from opening this e-mail or attachme= nts.


********************************************************= **************** ------_=_NextPart_001_01C570F8.CB5979EC-- From chemistry-request@ccl.net Tue Jun 14 12:29:32 2005 Received: from marmot.shef.ac.uk (marmot.shef.ac.uk [143.167.1.4]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EGTTd2021548 for ; Tue, 14 Jun 2005 12:29:29 -0400 Received: from bio5.shef.ac.uk ([143.167.93.147]) by marmot.shef.ac.uk with esmtp (Exim 4.30) envelope-sender id 1DiDRp-00000D-Gl for chemistry)at(ccl.net; Tue, 14 Jun 2005 16:35:29 +0100 Message-ID: <42AEF941.3050302)at(sheffield.ac.uk> Date: Tue, 14 Jun 2005 16:35:29 +0100 From: Nathan Haigh Reply-To: n.haigh)at(sheffield.ac.uk Organization: University of Sheffield User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.8) Gecko/20050513 Debian/1.7.8-1 X-Accept-Language: en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: cactvs csed script request Content-Type: multipart/mixed; boundary="------------020205060404080900020002" X-Sophie-Scan: Yes X-Trusted-Sender-Host: bio5.shef.ac.uk X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. --------------020205060404080900020002 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi, im a bioinformatician working on a metabolomics project. I'm trying to get to grips with representing moleules as smiles for use in a database. I want to be able to convert smiles to unique smiles and have downloaded and installed cactvs. Does anyone have a script that can do this conversion from the command line? Thanks Nathan --------------020205060404080900020002 Content-Type: text/x-vcard; charset=utf-8; name="n.haigh.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="n.haigh.vcf" begin:vcard fn:Nathan Haigh n:Haigh;Nathan org:University of Sheffield;Animal and Plant Sciences adr:;;Western Bank;Sheffield;South Yorkshire;S10 2TN;England email;internet:n.haigh"sheffield.ac.uk title:Mr tel;work:+44 (0)114 22 20112 tel;fax:+44 (0)114 22 20002 tel;home:+44 (0)1484 660 894 tel;cell:+44 (0)7742 533 569 x-mozilla-html:TRUE version:2.1 end:vcard --------------020205060404080900020002-- From chemistry-request@ccl.net Tue Jun 14 12:19:15 2005 Received: from mserv6.dl.ac.uk (mserv6.dl.ac.uk [148.79.80.137]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EGJ9Ax021082 for ; Tue, 14 Jun 2005 12:19:09 -0400 X-DL-MFrom: X-DL-Connect: Received: from [193.62.126.125] (wlandhcp125.dl.ac.uk [193.62.126.125]) by mserv6.dl.ac.uk (8.12.10/8.12.8/[ref postmaster)at(dl.ac.uk]) with ESMTP id j5EFashx019632 for ; Tue, 14 Jun 2005 16:36:54 +0100 Mime-Version: 1.0 (Apple Message framework v622) In-Reply-To: <42AE6E32.5080107)at(md.huji.ac.il> References: <9DD56492790889439F731F5BD6DACA0007D78B19)at(srvkyem1.americas.sc-world.com> <42AE6E32.5080107)at(md.huji.ac.il> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: Joop van Lenthe Subject: Re: CCL:Defining orbitals Date: Tue, 14 Jun 2005 17:36:48 +0200 To: chemistry)at(ccl.net X-Mailer: Apple Mail (2.622) X-CCLRC-SPAM-report: 0 : X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Avital Seeing your emsil, just trioggered by memory. Did you ever get GAMESS-UK ?? Joop On Jun 14, 2005, at 7:42 AM, avital shurki wrote: > > Using valence bond (VB) theory you can define anything you want (any > state and any wavefunction). It is not implemented in gaussian, but in > games-uk e.g. it is. > > > Shobe, David wrote: >> Yes, but...I think he wants to study what would more correctly be >> called a particular state of Li anion triplet. I don't remember how >> Gaussian treats the degeneracy of the three p orbitals. If Gaussian >> just arbitrarily picks one of the three p orbitals, no special >> manipulation is needed; but if the HOMO is a mixture of px, py, and >> pz it's a different story... >> --David Shobe, Ph.D., M.L.S. >> S|d-Chemie, Inc. >> phone (502) 634-7409 >> fax (502) 634-7724 >> Don't bother flaming me: I'm behind a firewall. >> ---------------------------------------------------------------------- >> -- >> *From:* Computational Chemistry List >> [mailto:chemistry-request)at(ccl.net] *On Behalf Of *Wayne Steinmetz >> *Sent:* Friday, June 10, 2005 4:46 PM >> *To:* chemistry)at(ccl.net >> *Subject:* CCL:Defining orbitals >> The electrons belong to the entire atom and are not constrained to >> any orbital. One uses orbitals to construct the wave function. One >> must be sure that the set of orbitals, i.e. the basis set, is >> sufficiently flexible to describe completely the molecular species. >> You are dealing with an atomic species so a polarization basis set is >> probably not needed. >> Wayne E. Steinmetz >> Carnegie Professor of Chemistry >> Woodbadge Course Director >> Chemistry Department >> Pomona College >> 645 North College Avenue >> Claremont, California 91711-6338 >> USA >> phone: 1-909-621-8447 >> FAX: 1-909-707-7726 >> Email: wsteinmetz)at(pomona.edu >> WWW: pages.pomona.edu/~wsteinmetz >> -----Original Message----- >> *From:* Computational Chemistry List >> [mailto:chemistry-request)at(ccl.net] *On Behalf Of *Christopher >> Thompson >> *Sent:* Thursday, June 09, 2005 6:09 PM >> *To:* chemistry)at(ccl.net >> *Subject:* CCL:Defining orbitals >> Gday, >> I would like to do an MP2 calc on a Li- species in triplet state. >> With one electron in the s orbital and one in a p orbital, >> how can you constrain the electron to say the px orbital? >> Cheers, >> cdth)at(unimelb.edu.au >> Christopher Thompson >> Laser Spectroscopy Group >> School of Chemistry >> University of Melbourne > ________________________________________________________________ > > Dr. Avital Shurki > Department of Medicinal Chemistry and natural products, > Lise Meitner-Minerva Center for Computational Quantum Chemistry, > School of Pharmacy, The Hebrew University of Jerusalem > Ein Kerem Campus > Jerusalem 91120, Israel > > Phone +972-2-675-8696 > Fax +972-2-675-7076 > Email avital)at(md.huji.ac.il > http://pharmacy.huji.ac.il/avital/ > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY)at(ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST)at(ccl.net HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > If your is mail bouncing from ccl.net domain due to spam filters, > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > ======================================================== Joop van Lenthe Theoretical Chemistry group Utrecht University joop)at(chem.uu.nl ============================laptop======================= From chemistry-request@ccl.net Tue Jun 14 13:43:18 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EHhHY2025348 for ; Tue, 14 Jun 2005 13:43:18 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 50673324114 for ; Tue, 14 Jun 2005 13:29:16 -0400 (EDT) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 27969-08 for ; Tue, 14 Jun 2005 13:29:12 -0400 (EDT) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 760B9324078 for ; Tue, 14 Jun 2005 13:29:12 -0400 (EDT) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Tue, 14 Jun 2005 13:42:41 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C57108.76292376" x-mimeole: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: Defining orbitals Date: Tue, 14 Jun 2005 13:42:40 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78B1C :: srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Defining orbitals Thread-Index: AcVwkc/4SZvzp0fDQ3K8ikpuHyYQewAdFNiw From: "Shobe, David" To: X-OriginalArrivalTime: 14 Jun 2005 17:42:41.0183 (UTC) FILETIME=[7681EAF0:01C57108] X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_60_70,HTML_MESSAGE, HTML_TITLE_EMPTY autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C57108.76292376 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable ...which means you don't have spherical symmetry and most likely you'll = have near but not exact degeneracy of the three members of the triplet. = This is going to be a difficult calculation. =20 --David Shobe =20 P.S. I never would have guessed Li- would be stable to water. How long = do these clusters last?=20 _____ =20 From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] On = Behalf Of Christopher Thompson Sent: Monday, June 13, 2005 9:46 PM To: chemistry :: ccl.net Subject: CCL:Defining orbitals David,=20 You interpreted my question correctly. Without going into the experiment = in detail ... we generate Li-(H2O)n clusters and record their infrared = spectrum. The source of Li- can potentially create Li- anions in more = than the lowest energy singlet state. It appears that the symmetry of = the clusters is not the same for different e spin states on the Li- ... = an excellent way to differentiate species in vibrational spectroscopy. = It would be nice to characterise the different triplet states = comprehensively.=20 Cheers,=20 Chris=20 On 14/06/2005, at 3:40 AM, Shobe, David wrote:=20 Yes, but...I think he wants to study what would more correctly be = called a particular state of Li anion triplet.=20 I don't remember how Gaussian treats the degeneracy of the three p = orbitals. If Gaussian just arbitrarily picks one of the three p = orbitals, no special manipulation is needed; but if the HOMO is a = mixture of px, py, and pz it's a different story... --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of Wayne Steinmetz Sent: Friday, June 10, 2005 4:46 PM To: chemistry :: ccl.net Subject: CCL:Defining orbitals The electrons belong to the entire atom and are not constrained to any = orbital. One uses orbitals to construct the wave function. One must be = sure that the set of orbitals, i.e. the basis set, is sufficiently = flexible to describe completely the molecular species. You are dealing = with an atomic species so a polarization basis set is probably not = needed.=20 =09 Wayne E. Steinmetz=20 Carnegie Professor of Chemistry=20 Woodbadge Course Director=20 Chemistry Department=20 Pomona College=20 645 North College Avenue=20 Claremont, California 91711-6338=20 USA=20 phone: 1-909-621-8447=20 FAX: 1-909-707-7726=20 Email: wsteinmetz :: pomona.edu=20 WWW: pages.pomona.edu/~wsteinmetz=20 =09 -----Original Message-----=20 From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of Christopher Thompson=20 Sent: Thursday, June 09, 2005 6:09 PM=20 To: chemistry :: ccl.net=20 Subject: CCL:Defining orbitals=20 =09 Gday,=20 =09 I would like to do an MP2 calc on a Li- species in triplet state.=20 =09 With one electron in the s orbital and one in a p orbital,=20 how can you constrain the electron to say the px orbital?=20 =09 Cheers,=20 cdth :: unimelb.edu.au=20 =09 Christopher Thompson=20 Laser Spectroscopy Group=20 School of Chemistry=20 University of Melbourne =09 Dr Christopher Thompson=20 Laser Spectroscopy Group=20 School of Chemistry=20 University of Melbourne=20 VIC, Australia, 3010.=20 Ph. +61 3 8344 8163=20 Fax. +61 3 9347 5180=20 ------_=_NextPart_001_01C57108.76292376 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
...which means you don't have spherical = symmetry and=20 most likely you'll have near but not exact degeneracy of the three = members of=20 the triplet.  This is going to be a difficult=20 calculation.
 
--David Shobe
 
P.S. I never would have guessed Li- would be = stable to=20 water.  How long do these clusters last?

From: Computational Chemistry List=20 [mailto:chemistry-request :: ccl.net] On Behalf Of Christopher=20 Thompson
Sent: Monday, June 13, 2005 9:46 PM
To:=20 chemistry :: ccl.net
Subject: CCL:Defining = orbitals

David,

You interpreted my question correctly. Without going into the = experiment in=20 detail ... we generate Li-(H2O)n clusters and record their infrared = spectrum.=20 The source of Li- can potentially create Li- anions in more than the = lowest=20 energy singlet state. It appears that the symmetry of the clusters is = not the=20 same for different e spin states on the Li- ... an excellent way to=20 differentiate species in vibrational spectroscopy. It would be nice to=20 characterise the different triplet states comprehensively.

Cheers,
Chris

On 14/06/2005, at 3:40 AM, Shobe, David wrote:

Yes, but...I = think he wants=20 to study what would more correctly be called a particular state = of Li=20 anion triplet. 

I don't remember = how Gaussian=20 treats the degeneracy of the three p orbitals.  If Gaussian just=20 arbitrarily picks one of the three p orbitals, no special manipulation = is=20 needed; but if the HOMO is a mixture of px, py, and pz it's a = different=20 story...


--David Shobe, Ph.D.,=20 M.L.S.
S=FCd-Chemie, = Inc.
phone (502)=20 634-7409
fax (502)=20 634-7724

Don't bother flaming me: I'm behind a=20 firewall.

From: Computational Chemistry List=20 [mailto:chemistry-request :: ccl.net] On Behalf Of Wayne=20 Steinmetz

Sent: Friday, June 10, 2005 4:46=20 PM

To: = chemistry :: ccl.net

Subject: CCL:Defining = orbitals


The electrons belong to = the entire=20 atom and are not constrained to any orbital.  One uses orbitals = to=20 construct the wave function.  One must be sure that the set of = orbitals,=20 i.e. the basis set, is sufficiently flexible to describe completely = the=20 molecular species.  You are dealing with an atomic species so a=20 polarization basis set is probably not needed.
Wayne E. = Steinmetz=20
Carnegie Professor of=20 Chemistry
Woodbadge Course=20 Director
Chemistry = Department=20
Pomona = College
645 North College=20 Avenue
Claremont, California=20 91711-6338
USA
phone: = 1-909-621-8447=20
FAX: = 1-909-707-7726=20
Email:=20 wsteinmetz :: pomona.edu
WWW:=20 pages.pomona.edu/~wsteinmetz
-----Original Message-----
From: = Computational=20 Chemistry List [mailto:chemistry-request :: ccl.net] On Behalf Of=20 Christopher Thompson
Sent: = Thursday, June=20 09, 2005 6:09 PM
To:=20 chemistry :: ccl.net
Subject: = CCL:Defining=20 orbitals
Gday,
I would like to do an MP2 = calc on a Li-=20 species in triplet state.
With one electron in the s = orbital and=20 one in a p orbital,
how can you constrain the = electron to=20 say the px orbital?
Cheers,
cdth :: unimelb.edu.au
Christopher Thompson
Laser Spectroscopy Group =
School of Chemistry
University of=20 Melbourne
Dr Christopher Thompson
Laser Spectroscopy Group
School of Chemistry
University of Melbourne
VIC, Australia, 3010.
Ph. +61 3 8344 8163
Fax. +61 3 9347 5180
------_=_NextPart_001_01C57108.76292376-- From chemistry-request@ccl.net Tue Jun 14 13:38:43 2005 Received: from mxsf16.cluster1.charter.net (mxsf16.cluster1.charter.net [209.225.28.216]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EHcb7H025136 for ; Tue, 14 Jun 2005 13:38:38 -0400 Received: from mxip01a.cluster1.charter.net (mxip01a.cluster1.charter.net [209.225.28.131]) by mxsf16.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id j5EHcXev008179 for ; Tue, 14 Jun 2005 13:38:34 -0400 Received: from 24-247-172-122.dhcp.bycy.mi.charter.com (HELO inspiron9100) (24.247.172.122) by mxip01a.cluster1.charter.net with ESMTP; 14 Jun 2005 13:38:34 -0400 Message-Id: <43vth7$qcnlk4 :: mxip01a.cluster1.charter.net> X-IronPort-AV: i="3.93,198,1115006400"; d="scan'208,217"; a="885773956:sNHT52285888" From: "Jim Kress" To: Subject: RE: Defining orbitals Date: Tue, 14 Jun 2005 13:38:33 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0004_01C570E6.5C69BE30" X-Mailer: Microsoft Office Outlook, Build 11.0.6353 In-reply-to: <4186c3416e5a95e924f14b43ef31d897 :: unimelb.edu.au> thread-index: AcVwjwz1OaBeijBgTS+R6awD06BX/gAeKu4w X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0004_01C570E6.5C69BE30 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Why not do an MCSCF calculation? It would solve the single reference = MP2 issues and allow you to examine all the states of interest. =20 Jim _____ =20 From: Christopher Thompson [mailto:cdth :: unimelb.edu.au]=20 Sent: Monday, June 13, 2005 9:46 PM To: chemistry :: ccl.net Subject: CCL:Defining orbitals David, You interpreted my question correctly. Without going into the experiment = in detail ... we generate Li-(H2O)n clusters and record their infrared spectrum. The source of Li- can potentially create Li- anions in more = than the lowest energy singlet state. It appears that the symmetry of the clusters is not the same for different e spin states on the Li- ... an excellent way to differentiate species in vibrational spectroscopy. It = would be nice to characterise the different triplet states comprehensively. Cheers, Chris On 14/06/2005, at 3:40 AM, Shobe, David wrote: Yes, but...I think he wants to study what would more correctly be called = a particular state of Li anion triplet.=20 =20 I don't remember how Gaussian treats the degeneracy of the three p = orbitals. If Gaussian just arbitrarily picks one of the three p orbitals, no = special manipulation is needed; but if the HOMO is a mixture of px, py, and pz = it's a different story... =20 --David Shobe, Ph.D., M.L.S. S=FCd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] On Behalf Of Wayne Steinmetz Sent: Friday, June 10, 2005 4:46 PM To: chemistry :: ccl.net Subject: CCL:Defining orbitals The electrons belong to the entire atom and are not constrained to any orbital. One uses orbitals to construct the wave function. One must be sure that the set of orbitals, i.e. the basis set, is sufficiently = flexible to describe completely the molecular species. You are dealing with an atomic species so a polarization basis set is probably not needed. =20 Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-707-7726 Email: wsteinmetz :: pomona.edu WWW: pages.pomona.edu/~wsteinmetz =20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request :: ccl.net] On Behalf Of Christopher Thompson Sent: Thursday, June 09, 2005 6:09 PM To: chemistry :: ccl.net Subject: CCL:Defining orbitals =20 Gday, =20 I would like to do an MP2 calc on a Li- species in triplet state. =20 With one electron in the s orbital and one in a p orbital, how can you constrain the electron to say the px orbital? =20 Cheers, cdth :: unimelb.edu.au =20 Christopher Thompson Laser Spectroscopy Group School of Chemistry University of Melbourne Dr Christopher Thompson Laser Spectroscopy Group School of Chemistry University of Melbourne VIC, Australia, 3010. Ph. +61 3 8344 8163 Fax. +61 3 9347 5180 ------=_NextPart_000_0004_01C570E6.5C69BE30 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Why not do an MCSCF calculation?  It would = solve the=20 single reference MP2 issues and allow you to examine all the states of=20 interest.
 
Jim

From: Christopher Thompson=20 [mailto:cdth :: unimelb.edu.au]
Sent: Monday, June 13, 2005 = 9:46=20 PM
To: chemistry :: ccl.net
Subject: CCL:Defining=20 orbitals

David,

You interpreted my question correctly. = Without going=20 into the experiment in detail ... we generate Li-(H2O)n clusters and = record=20 their infrared spectrum. The source of Li- can potentially create Li- = anions=20 in more than the lowest energy singlet state. It appears that the = symmetry of=20 the clusters is not the same for different e spin states on the Li- = ... an=20 excellent way to differentiate species in vibrational spectroscopy. It = would=20 be nice to characterise the different triplet states=20 comprehensively.

Cheers,
Chris

On 14/06/2005, at 3:40 = AM,=20 Shobe, David wrote:

Yes,=20 but...I think he wants to study what would more correctly be called = a=20 particular state of Li anion = triplet. 

 
I=20 don't remember how Gaussian treats the degeneracy of the three p=20 orbitals.  If Gaussian just arbitrarily picks one of the three = p=20 orbitals, no special manipulation is needed; but if the HOMO is a = mixture of=20 px, py, and pz it's a different = story...

 

--David=20 Shobe, Ph.D., = M.L.S.

S=FCd-Chemie,=20 Inc.

phone=20 (502) = 634-7409

fax=20 (502) = 634-7724


Don't=20 bother flaming me: I'm behind a = firewall.


From:=20 Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of = Wayne = Steinmetz

Sent:=20 Friday, June 10, 2005 4:46=20 PM

To:=20 = chemistry :: ccl.net

Subject:=20 CCL:Defining = orbitals


The=20 electrons belong to the entire atom and are not constrained to any=20 orbital.  One uses orbitals to construct the wave = function.  One=20 must be sure that the set of orbitals, i.e. the basis set, is = sufficiently=20 flexible to describe completely the molecular species.  You are = dealing=20 with an atomic species so a polarization basis set is probably not = needed.
 
Wayne=20 E. = Steinmetz
Carnegie=20 Professor of = Chemistry
Woodbadge=20 Course = Director
Chemistry=20 = Department
Pomona=20 = College
645=20 North College = Avenue
Claremont,=20 California = 91711-6338
USA
phone:=20 = 1-909-621-8447
FAX:=20 = 1-909-707-7726
Email:=20 = wsteinmetz :: pomona.edu
WWW:=20 = pages.pomona.edu/~wsteinmetz
<= ?fontfamily> 
-----Original=20 = Message-----
From:=20 Computational Chemistry List [mailto:chemistry-request :: ccl.net] = On Behalf Of = Christopher = Thompson
Sent:=20 Thursday, June 09, 2005 6:09 = PM
To:=20 = chemistry :: ccl.net
Subject:=20 CCL:Defining = orbitals
 
Gday,
 
I=20 would like to do an MP2 calc on a Li- species in triplet = state.
 
With=20 one electron in the s orbital and one in a p = orbital,
how=20 can you constrain the electron to say the px = orbital?
 
Cheers,
cdth :: unimelb.edu.au
 
Christopher=20 Thompson
Laser=20 Spectroscopy = Group
School=20 of Chemistry
University=20 of Melbourne

Dr=20 Christopher Thompson
Laser Spectroscopy Group
School of=20 Chemistry
University of Melbourne
VIC, Australia, 3010.
Ph. = +61 3=20 8344 8163
Fax. +61 3 9347=20 5180
------=_NextPart_000_0004_01C570E6.5C69BE30-- From chemistry-request@ccl.net Tue Jun 14 14:07:48 2005 Received: from mta04.mail.t-online.hu (mta04.mail.t-online.hu [195.228.240.57]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EI7iV2026747 for ; Tue, 14 Jun 2005 14:07:45 -0400 Received: from [192.168.0.79] (157.76-182-adsl-pool.axelero.hu [81.182.76.157]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by mail.t-online.hu (Postfix) with ESMTP; Tue, 14 Jun 2005 19:11:09 +0200 (CEST) Message-ID: <42AF0EF2.8050300*&*chemaxon.com> Date: Tue, 14 Jun 2005 19:08:02 +0200 From: Szabolcs Csepregi Organization: Chemaxon Ltd. User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry*&*ccl.net CC: Nathan Haigh , Ferenc Csizmadia Subject: CCL: Re: cactvs csed script request References: <42AEF941.3050302*&*sheffield.ac.uk> In-Reply-To: <42AEF941.3050302*&*sheffield.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Nathan, I don't know how to do it with cactvs, but this is the way to do it with ChemAxon molconvert: molconvert smiles:u in.smiles >unique_out.smiles molconvert, mview and msketch applications are free to everyone. You can download it from here: http://www.chemaxon.com/marvin/download.html For other uses and other ChemAxon products (e.g. the JChem Base might be relevant to you), you can apply for a free academic licence here: http://www.chemaxon.hu/forum/ftopic193.html All the best, Szabolcs Nathan Haigh wrote: > Hi, > > im a bioinformatician working on a metabolomics project. I'm trying to > get to grips with representing moleules as smiles for use in a database. > I want to be able to convert smiles to unique smiles and have downloaded > and installed cactvs. > > Does anyone have a script that can do this conversion from the command > line? > > Thanks > Nathan -- Szabolcs Csepregi, PhD Cheminformatics Scientist, ChemAxon Ltd. http://www.chemaxon.com Skype: szabolcs.csepregi Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 From chemistry-request@ccl.net Tue Jun 14 15:25:00 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EJOtlo029989 for ; Tue, 14 Jun 2005 15:24:56 -0400 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j5EImrJ04615 for ; Tue, 14 Jun 2005 12:48:55 -0600 Message-ID: <42AF2697.1060705)at(eyesopen.com> Date: Tue, 14 Jun 2005 12:48:55 -0600 From: George Vacek Reply-To: vacek)at(eyesopen.com Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: Re: CCL:cactvs csed script request References: <42AEF941.3050302)at(sheffield.ac.uk> In-Reply-To: <42AEF941.3050302)at(sheffield.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net OEChem can create cannonical smiles, among numerous other tasks, and there is an example script for this particular task (cansmi.py). Most academics qualify to use our software at no charge (and with no support). For more information on our philosophy concerning academics, please read http://www.eyesopen.com/business/licensing/commercial.html http://www.eyesopen.com/support/misc/letter_to_academics.html For details of the non-commercial licensing terms, and to apply, please read the terms at http://www.eyesopen.com/forms/academic_license_app.php If you agree to the terms and wish to apply for an academic license, please select the appropriate button and then fill in the form that should automatically appear. Regards, George Vacek VP, Business OpenEye Scientific Software vacek)at(eyesopen.com 505.473.7385 ********************************************************************* OpenEye recently announced the following software releases: FRED 2.1 - accurate and extremely fast docking search for ligand binding within a protein active site OEChem 1.3.3 - cheminformatics and 3D molecular data handling http://www.eyesopen.com/about/news/press_releases/ ********************************************************************* From chemistry-request@ccl.net Tue Jun 14 15:12:46 2005 Received: from mr4.cc.ic.ac.uk (mr4.cc.ic.ac.uk [155.198.5.114]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EJCdJw029616 for ; Tue, 14 Jun 2005 15:12:40 -0400 Received: from icexp3.cc.ic.ac.uk ([155.198.3.43] helo=icex.imperial.ac.uk) by mr4.cc.ic.ac.uk with smtp (Exim 4.44) id 1DiGDY-00068f-60 for chemistry)at(ccl.net; Tue, 14 Jun 2005 19:32:56 +0100 Received: from [155.198.215.23] ([155.198.215.23]) by icex.imperial.ac.uk with Microsoft SMTPSVC(6.0.3790.1830); Tue, 14 Jun 2005 19:32:04 +0100 Message-ID: <42AF22A5.2020001)at(imperial.ac.uk> Date: Tue, 14 Jun 2005 19:32:05 +0100 From: James Kirkpatrick User-Agent: Mozilla Thunderbird 0.9 (Windows/20041103) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: Re: CCL:Defining orbitals References: <43vth7$qcnlk4)at(mxip01a.cluster1.charter.net> In-Reply-To: <43vth7$qcnlk4)at(mxip01a.cluster1.charter.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-OriginalArrivalTime: 14 Jun 2005 18:32:04.0134 (UTC) FILETIME=[5C905C60:01C5710F] X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Jim Kress wrote: > Why not do an MCSCF calculation? It would solve the single reference > MP2 issues and allow you to examine all the states of interest. > also an MCSCF would allow you to calculate specific states only by the use of the IOp(4/72=IJKLMN) keyword > Jim > > ------------------------------------------------------------------------ > *From:* Christopher Thompson [mailto:cdth)at(unimelb.edu.au] > *Sent:* Monday, June 13, 2005 9:46 PM > *To:* chemistry)at(ccl.net > *Subject:* CCL:Defining orbitals > > David, > > You interpreted my question correctly. Without going into the > experiment in detail ... we generate Li-(H2O)n clusters and record > their infrared spectrum. The source of Li- can potentially create > Li- anions in more than the lowest energy singlet state. It > appears that the symmetry of the clusters is not the same for > different e spin states on the Li- >... an excellent way to > differentiate species in vibrational spectroscopy. It would be > nice to characterise the different triplet states comprehensively. > > Cheers, > Chris > > On 14/06/2005, at 3:40 AM, Shobe, David wrote: > > Yes, but...I think he wants to study what would more correctly > be called a particular state of Li anion triplet. > > > > I don't remember how Gaussian treats the degeneracy of the > three p orbitals. If Gaussian just arbitrarily picks one of > the three p orbitals, no special manipulation is needed; but > if the HOMO is a mixture of px, py, and pz it's a different > story... > > > > > --David Shobe, Ph.D., M.L.S. > > > S|d-Chemie, Inc. > > > phone (502) 634-7409 > > > fax (502) 634-7724 > > > > Don't bother flaming me: I'm behind a firewall. > > > > *From:* Computational Chemistry List > [mailto:chemistry-request)at(ccl.net] *On Behalf Of *Wayne Steinmetz > > > *Sent:* Friday, June 10, 2005 4:46 PM > > > *To:* chemistry)at(ccl.net > > > *Subject:* CCL:Defining orbitals > > > > The electrons belong to the entire atom and are not > constrained to any orbital. One uses orbitals to construct > the wave function. One must be sure that the set of orbitals, > i.e. the basis set, is sufficiently flexible to describe > completely the molecular species. You are dealing with an > atomic species so a polarization basis set is probably not needed. > > Wayne E. Steinmetz > Carnegie Professor of Chemistry > Woodbadge Course Director > Chemistry Department > Pomona College > 645 North College Avenue > Claremont, California 91711-6338 > USA > phone: 1-909-621-8447 > FAX: 1-909-707-7726 > Email: wsteinmetz)at(pomona.edu > WWW: pages.pomona.edu/~wsteinmetz > > -----Original Message----- > *From:* Computational Chemistry List > [mailto:chemistry-request)at(ccl.net] *On Behalf Of *Christopher > Thompson > *Sent:* Thursday, June 09, 2005 6:09 PM > *To:* chemistry)at(ccl.net > *Subject:* CCL:Defining orbitals > > Gday, > > I would like to do an MP2 calc on a Li- species in triplet state. > > With one electron in the s orbital and one in a p orbital, > how can you constrain the electron to say the px orbital? > > Cheers, > cdth)at(unimelb.edu.au > > Christopher Thompson > Laser Spectroscopy Group > School of Chemistry > University of Melbourne > > > Dr Christopher Thompson > Laser Spectroscopy Group > School of Chemistry > University of Melbourne > VIC, Australia, 3010. > Ph. +61 3 8344 8163 > Fax. +61 3 9347 5180 > -- James Kirkpatrick ------------------------------------------- Centre for Electronic Materials and devices Imperial College ------------------------------------------- 020 759 47519 From chemistry-request@ccl.net Tue Jun 14 18:39:08 2005 Received: from smtp821.mail.sc5.yahoo.com (smtp821.mail.sc5.yahoo.com [66.163.171.7]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5EMd4nD010302 for ; Tue, 14 Jun 2005 18:39:04 -0400 Received: (qmail 45418 invoked from network); 14 Jun 2005 21:39:02 -0000 Received: from unknown (HELO ?192.168.1.9?) (lbalbes () sbcglobal.net@70.246.132.100 with plain) by smtp821.mail.sc5.yahoo.com with SMTP; 14 Jun 2005 21:39:02 -0000 Mime-Version: 1.0 Message-Id: Date: Tue, 14 Jun 2005 16:35:10 -0500 To: chemistry () ccl.net From: "Lisa M. Balbes, Ph.D." Subject: QSAR Software Content-Type: text/html; charset="us-ascii" X-Spam-Status: No, score=1.2 required=5.0 tests=HTML_40_50,HTML_MESSAGE, MIME_HTML_ONLY autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net QSAR Software
Good Afternoon!

I am evaluating QSAR packages for a client, and am looking for opinions on what's currently available.

I am especially interested in what features people love, hate, can't live without, wish they had, and so on. I would be most appreciative of opinions members of this list would care to share, and of course you will remain anonymous. (Hard data comparisons are also welcome!)

You may respond to me directly, and I will summarize to the list if there is enough interest.

Looking forward to hearing > from you!

Lisa

PS  I tried posting this query on the QSAR society list,  qsar_society () accelrys.com, but did not get anything back.  Does anyone know if that list is active?
--
-------------------------------------------------------------------------------------------------------------------------------
Lisa M. Balbes, Ph.D.    lisa () balbes.com         http://www.balbes.com/
Balbes Consultants                Scientific Documentation Specialist since 1992 
               
American Chemical Society - St Louis Section Treasurer, COMP division WebMaven
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From chemistry-request@ccl.net Tue Jun 14 17:00:33 2005 Received: from zproxy.gmail.com (zproxy.gmail.com [64.233.162.198]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5EL0V5A002221 for ; Tue, 14 Jun 2005 17:00:31 -0400 Received: by zproxy.gmail.com with SMTP id 13so262828nzp for ; Tue, 14 Jun 2005 14:00:31 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:references; b=d32h8Av50iIlHKVWd2OUOK9tNC7Oo6fDUIlpXtDk+JhXB9tvw3uNiyJrlIwxLYHc8qhbmQBz96ZRj6FlBoCbhtzhN2sekLE8swH8UvcjvW6K3X4leeHDeZ8unRSdvYJKvd6yGeJyW9uMGi2UdYVKfQFBHa7lAEjquPg29iRrr/Y= Received: by 10.36.19.10 with SMTP id 10mr3886084nzs; Tue, 14 Jun 2005 14:00:30 -0700 (PDT) Received: by 10.36.7.4 with HTTP; Tue, 14 Jun 2005 14:00:30 -0700 (PDT) Message-ID: Date: Tue, 14 Jun 2005 17:00:30 -0400 From: Gustavo Seabra Reply-To: To: chemistry ~~ ccl.net Subject: Re: CCL:Modifying UFF parameters for an ONIOM calculation In-Reply-To: <211FDB3BAA26EA4782DC2DA769DC0A84071777 ~~ STBEVS04.stb.sun.ac.za> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_21104_9574011.1118782830680" References: <211FDB3BAA26EA4782DC2DA769DC0A84071777 ~~ STBEVS04.stb.sun.ac.za> X-Spam-Status: No, score=1.5 required=5.0 tests=HTML_60_70,HTML_MESSAGE, RCVD_BY_IP,REPLY_TO_EMPTY autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net ------=_Part_21104_9574011.1118782830680 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline On 6/13/05, Crous Werner wrote: >=20 > Dear CCL >=20 > I am a student working with ONIOM in g03. Is it possible to modify the= =20 > UFF-forcefield parameters for an ONIOM calculation in g03 and what is the= =20 > input? If not, can someone perhaps give me advice on how to proceed to do= =20 > this by using other software et cetera? I could not find an answer on the= =20 > internet. I would appreciate any help. Thank you in anticipation. >=20 > Yours sincerely >=20 > Werner Crous >=20 You can specify the parameters you want. Take a look at: http://www.gaussian.com/g_ur/k_mm.htm --=20 ---------------------------------------------------------------------------= ------------------ Gustavo Seabra Postdoctoral Associate Quantum Theory Project University of Florida Registered Linux user number 381680 Say NO! to software patents: http://www.nosoftwarepatents.com ---------------------------------------------------------------------------= ------------------ If at first you don't succeed... ...skydiving is not for you. ------=_Part_21104_9574011.1118782830680 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
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Gustavo Seabra           &nb= sp;            =             Pos= tdoctoral Associate
Quantum Theory Project           &n= bsp;            = ;     University of Florida
Registered Linux user number 381680
Say NO! to = software patents: http://www.n= osoftwarepatents.com
-----------------------------------------------= ----------------------------------------------
If at first you don't succeed...
      = ;            &n= bsp;           ...sk= ydiving is not for you. ------=_Part_21104_9574011.1118782830680-- From chemistry-request@ccl.net Tue Jun 14 17:12:34 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5ELCUKd003013 for ; Tue, 14 Jun 2005 17:12:30 -0400 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j5ELCSJ10951 for ; Tue, 14 Jun 2005 15:12:29 -0600 Message-ID: <42AF4844.7010705 %a% eyesopen.com> Date: Tue, 14 Jun 2005 15:12:36 -0600 From: George Vacek Reply-To: vacek %a% eyesopen.com Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry %a% ccl.net Subject: FRED 2.1 released - fast, effective docking of ligand within an active site Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net OpenEye is pleased to announce FRED 2.1, the latest release of an accurate and extremely fast docking program. For every ligand, FRED systematicly searches all possible poses within a protein active site, filtering for shape complementarity and pharmacophoric features before evaluating with several scoring functions. Key new features in FRED 2.1 include: 7 the use of multiple scoring functions during pose selection. This consensus pose selection significantly improves the likelihood that the ligand is placed in the correct binding mode; 7 a more accurate version of the ChemGauss scoring function with significantly better hydrogen-bond perception; 7 customizable scoring functions and flexible consensus scoring methods; 7 greatly expanded documentation; and 7 docking analysis tools for investigating how various parameter settings affect the reproduction of known structures of ligand-receptor complexes. For further information, please visit www.eyesopen.com or contact business %a% eyesopen.com. Regards, George Vacek VP, Business Development OpenEye Scientific Software -- Regards, George Vacek VP, Business OpenEye Scientific Software vacek %a% eyesopen.com 505.473.7385 ********************************************************************* OpenEye recently announced the following software releases: FRED 2.1 - accurate and extremely fast docking search for ligand binding within a protein active site OEChem 1.3.3 - cheminformatics and 3D molecular data handling http://www.eyesopen.com/about/news/press_releases/ ********************************************************************* From chemistry-request@ccl.net Tue Jun 14 19:12:34 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5ENCWPw018268 for ; Tue, 14 Jun 2005 19:12:32 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5ENCWTM018267 for chemistry !! ccl.net; Tue, 14 Jun 2005 19:12:32 -0400 Date: Tue, 14 Jun 2005 19:12:32 -0400 Message-Id: <200506142312.j5ENCWTM018267 !! server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request !! ccl.net using -f From: "kono, , lemke" To: chemistry !! ccl.net X-Web-Message-Number: 050614150811-29382 Subject: W:isotope calculations X-Spam-Status: No, score=-0.1 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD,FROM_ENDS_IN_NUMS autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net i am running cbs-4 calculations on small deuterated organics and can not get gaussian to rerun for heavier isotopes. does gaussian require a blank line at the input end? any suggestion as how to edit the input below would be appreciated. thanks kono %chk=formaldehyde cbs-4m formaldehyde 0 1 c o 1 oc2 h 1 hc3 2 hco3 h 1 hc4 2 hco4 3 dih4 oc2 1.450000 hc3 1.089000 hco3 109.471 hc4 1.089000 hco4 109.471 dih4 120.000 --link1-- %chk=formaldehyde cbs-4m 0 1 298.16 0.0 0.0 12 16 2 2