From owner-chemistry@ccl.net Fri Jan 13 00:14:00 2006 From: "Kalju Kahn kalju . chem.ucsb.edu" To: CCL Subject: CCL: Semiempirical examples for teaching: success stories Message-Id: <-30480-060112235242-23794-+MyldeUb1JWBi4kJodIfFg*server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 12 Jan 2006 20:52:30 -0800 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju\a/chem.ucsb.edu] Dear CCL members, I am teaching computational chemistry this quarter, and are looking for several examples on successful applications of semiempirical methods in chemistry. The examples ideally: a) Involve chemistry that is normally taught in undergraduate OChem or Biochem. b) Can be reproduced in less than a day/processor on modern hardware c) Have (or had at one time) clear value in advancing our understanding of chemistry (as opposed to just predicting correctly some energy difference or spectral property) d) Give quantitatively accurate results when compared to experiment or much higher level computational results. I am planning to make brief tutorials for select examples and will post the link with summary early next month. Thanks, Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Fri Jan 13 04:03:03 2006 From: "Egon Willighagen egonw^_^sci.kun.nl" To: CCL Subject: CCL: VHTS software Message-Id: <-30481-060113035542-8092-JreSi3nAslcdyDEdyKto3A/a\server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Fri, 13 Jan 2006 07:59:28 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egonw]![sci.kun.nl] On Thursday 12 January 2006 22:06, you wrote: > Does anyone know if there is free (OpenSource) software available for = > virtual high-throughput screening? We're interested in screening = > virtual compound libraries and would like to use OpenSource applications = > if they are available. Depending on what you exactly want to screen on, CDK [1] provides good tools for this. QSAR and ADMETox models can be build with it, e.g. using R [2] as backend [3,4]. Additionally, things like the Rule-of-Five are implemented. There are options in implementing them in your environment as well: 1. write a custom program 2. embed the screening in a workflow, like PipeLine Pilot (tm) or the open source Taverna [5] Support is available in real-time (IRC: #cdk at irc.freenode.net) and by email on one of the many mailing lists. Egon 1.http://cdk.sf.net/ 2.http://www.r-project.org/ 3.R.Guha, Using R to provide statistical functionality for QSAR modeling in CDK, CDK News, 2005, 2(1), 7-13 4.http://almost.cubic.uni-koeln.de/cdk/cdk_top/cdk_news/ 5.http://taverna.sf.net/ -- e.willighagen[*]science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Fri Jan 13 05:07:02 2006 From: "Peter W. Thulstrup pwt~!~kvl.dk" To: CCL Subject: CCL: Systematic DFT study of spin states for (first row transition metal) coordination compounds? Message-Id: <-30482-060113042936-17429-oi5U55ZMI6MpbsYRzXcN3w*server.ccl.net> X-Original-From: "Peter W. Thulstrup" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01C61824.A5D00300" Date: Fri, 13 Jan 2006 09:35:10 +0100 MIME-Version: 1.0 Sent to CCL by: "Peter W. Thulstrup" [pwt|kvl.dk] This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C61824.A5D00300 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello CCL, Are any of you aware of systematic studies evaluating the performance of = DFT for the prediction of the ground state of transition metal complexes = (e.g. high-, intermediate- and low spin state energies)? Thank you for any help! Peter W. Thulstrup pwt|a|kvl.dk (I haven't been following the threads lkately so I apologize if this = subject has been up recently) ------=_NextPart_000_0031_01C61824.A5D00300 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello CCL,
 
Are any of you aware of systematic = studies=20 evaluating the performance of DFT for the prediction of the ground = state of=20 transition metal complexes (e.g. high-, intermediate- and low spin state = energies)?
 
Thank you for any help!
 
Peter W. Thulstrup
pwt|a|kvl.dk
 
(I haven't been following the threads = lkately so I=20 apologize if this subject has been up = recently)
------=_NextPart_000_0031_01C61824.A5D00300-- From owner-chemistry@ccl.net Fri Jan 13 06:18:01 2006 From: "Marcel Swart m.swart:+:few.vu.nl" To: CCL Subject: CCL: Systematic DFT study of spin states for (first row transition metal) coordination compounds? Message-Id: <-30483-060113060926-6309-7dTr0ypoI29Ksm/XxS3uXg]*[server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-2--70490752 Date: Fri, 13 Jan 2006 12:08:19 +0100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Marcel Swart [m.swart-,-few.vu.nl] --Apple-Mail-2--70490752 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Hello Peter, yes, I know of such a study. We have recently performed and reported=20 such a study in: M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma "Validation of exchange-correlation functionals for spin states of=20 iron-complexes" J. Phys. Chem. A 2004, 108, 5479-5483 On Jan 13, 2006, at 11:24 AM, Peter W. Thulstrup pwt~!~kvl.dk wrote: > Hello CCL, > > Are any of you aware of systematic studies evaluating the performance=20= > of =3D > DFT for the prediction of the ground state of transition metal=20 > complexes =3D > (e.g. high-, intermediate- and low spin state energies)? > > Thank you for any help! > > Peter W. Thulstrup > pwt:kvl.dk > > (I haven't been following the threads lkately so I apologize if this =3D= > subject has been up recently) > =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 dr. Marcel Swart Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart- -few.vu.nl W http://www.few.vu.nl/~swart =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 Starting May 1, 2006: ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2--70490752 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Hello Peter, yes, I know of such a study. We have recently performed and reported such a study in: Times M. Swart, A.R. Groenhof, A.W. Ehlers and K. Lammertsma=20 "Validation of exchange-correlation functionals for spin states of iron-complexes"=20 J. Phys. Chem. A 2004, 108, 5479-5483 On Jan 13, 2006, at 11:24 AM, Peter W. Thulstrup pwt~!~kvl.dk wrote: Hello CCL, Are any of you aware of systematic studies evaluating the performance of =3D DFT for the prediction of the ground state of transition metal complexes =3D (e.g. high-, intermediate- and low spin state energies)? Thank you for any help! Peter W. Thulstrup pwt:kvl.dk (I haven't been following the threads lkately so I apologize if this =3D subject has been up recently) = Helvetica=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Courierdr. Marcel Swart = Courier Theoretische Chemie (kamer R152) Vrije Universiteit Amsterdam Faculteit der Exacte Wetenschappen De Boelelaan 1083 1081 HV Amsterdam The Netherlands T +31-(0)20-5987619 F +31-(0)20-5987629 E m.swart- -few.vu.nl W http://www.few.vu.nl/~swart = Helvetica=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96 = Courier0000,4040,8080Starting May 1, 2006: = Courier0000,4040,8080 ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) = Helvetica<= color>0000,4040,8080=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96=96= =96=96=96=96=96=96=96=96=96=96=96 --Apple-Mail-2--70490752-- From owner-chemistry@ccl.net Fri Jan 13 06:52:01 2006 From: "=?ISO-8859-1?Q?Miquel_Sol=E0?= miquel.sola\a/udg.es" To: CCL Subject: CCL: Systematic DFT study of spin states for (first row transition metal) coordination compounds? Message-Id: <-30484-060113063829-24663-8ioe+jfcGJnTQQtXcplU3w**server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Miquel_Sol=E0?= Content-Type: multipart/alternative; boundary="------------090807090009020003040007" Date: Fri, 13 Jan 2006 11:42:08 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Miquel_Sol=E0?= [miquel.sola(a)udg.es] This is a multi-part message in MIME format. --------------090807090009020003040007 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear Peter, For a particular case (not a systematic study), take a look at the following reference: <>J. Poater, M. Solà, A. Rimola, L. Rodríguez-Santiago and M. Sodupe J. Phys. Chem. A, 108 (2004) 6072-6078. Best regards, Miquel Peter W. Thulstrup pwt~!~kvl.dk wrote: >Sent to CCL by: "Peter W. Thulstrup" [pwt|kvl.dk] >This is a multi-part message in MIME format. > >------=_NextPart_000_0031_01C61824.A5D00300 >Content-Type: text/plain; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > >Hello CCL, > >Are any of you aware of systematic studies evaluating the performance of = >DFT for the prediction of the ground state of transition metal complexes = >(e.g. high-, intermediate- and low spin state energies)? > >Thank you for any help! > >Peter W. Thulstrup >pwt:kvl.dk > >(I haven't been following the threads lkately so I apologize if this = >subject has been up recently) >------=_NextPart_000_0031_01C61824.A5D00300 >Content-Type: text/html; > charset="iso-8859-1" >Content-Transfer-Encoding: quoted-printable > > > >charset=3Diso-8859-1"> > > > > >
Hello CCL,
>
 
>
Are any of you aware of systematic = >studies=20 >evaluating the performance of DFT for the prediction of the ground = >state of=20 >transition metal complexes (e.g. high-, intermediate- and low spin state = > >energies)?
>
 
>
Thank you for any help!
>
 
>
Peter W. Thulstrup
>
href=3D"mailto:pwt:kvl.dk">pwt:kvl.dk
>
 
>
(I haven't been following the threads = >lkately so I=20 >apologize if this subject has been up = >recently)
> >------=_NextPart_000_0031_01C61824.A5D00300--> > > > > > -- -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- Miquel Solà Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona, CATALONIA (Spain) Phone +34.972.41.89.12 Cellular-Phone: +34.626.163.580 FAX +34.972.41.83.56 World Wide Web: http://iqc.udg.es/~miquel/mike.html e-mail: miquel.sola-,-udg.es -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- --------------090807090009020003040007 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit
Dear Peter,

For a particular case (not a systematic study), take a look at the following reference:

<>J. Poater, M. Solà, A. Rimola, L. Rodríguez-Santiago and M. Sodupe
J. Phys. Chem. A, 108 (2004) 6072-6078.

Best regards,

Miquel


Peter W. Thulstrup pwt~!~kvl.dk wrote: 
Sent to CCL by: "Peter W. Thulstrup" [pwt|kvl.dk]
This is a multi-part message in MIME format.

------=_NextPart_000_0031_01C61824.A5D00300
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hello CCL,

Are any of you aware of systematic studies evaluating the performance of =
DFT for the prediction of the ground state of transition metal complexes =
(e.g. high-, intermediate- and low spin state energies)?

Thank you for any help!

Peter W. Thulstrup
pwt:kvl.dk

(I haven't been following the threads lkately so I apologize if this =
subject has been up recently)
------=_NextPart_000_0031_01C61824.A5D00300
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2900.2802" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Hello CCL,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Are any of you aware of systematic =
studies=20
evaluating the performance of DFT for the prediction of the&nbsp;ground =
state of=20
transition metal complexes (e.g. high-, intermediate- and low spin state =

energies)?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thank you for any help!</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Peter W. Thulstrup</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><A=20
href=3D"mailto:pwt:kvl.dk">pwt:kvl.dk</A></FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>(I haven't been following the threads =
lkately so I=20
apologize if this subject has been up =
recently)</FONT></DIV></BODY></HTML>

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-- 

 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
 Miquel Solà                           
 Institut de Química Computacional         
 Universitat de Girona                   
 Campus Montilivi
 17071 Girona, CATALONIA (Spain)          
 Phone +34.972.41.89.12
 Cellular-Phone:  +34.626.163.580
 FAX   +34.972.41.83.56                               
 World Wide Web: http://iqc.udg.es/~miquel/mike.html   
 e-mail: miquel.sola-,-udg.es                         
 -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
--------------090807090009020003040007-- From owner-chemistry@ccl.net Fri Jan 13 08:00:00 2006 From: "Hrusak Jan hrusak::kav.cas.cz" To: CCL Subject: CCL: Systematic DFT study of spin states for (first row transition metal) coordination compounds? Message-Id: <-30485-060113072225-14073-EbehKq4ZMINKcP/qQbFjeA\a/server.ccl.net> X-Original-From: "Hrusak Jan" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Jan 2006 12:35:06 +0100 MIME-Version: 1.0 Sent to CCL by: "Hrusak Jan" [hrusak,kav.cas.cz] Have a look to papers published by Holthausen M. C. and Koch W. Hrusak ________________________ RNDr. Jan H R U S A K, CSc. Member of the Presidium of the Academy Council Academy of Sciences of the Czech Republic Narodni 3, 110 00 Prague 1, Czech Republic tel. +420 221 403 258, fax +420 221 403 476 http://www.cas.cz/en/ar_medailonek_en_old.php?m=2-03&ID=5 hrusak(0)kav.cas.cz -----Original Message----- > From: owner-chemistry(0)ccl.net [mailto:owner-chemistry(0)ccl.net] Sent: Friday, January 13, 2006 11:46 AM To: Hrusak, Jan Subject: CCL: Systematic DFT study of spin states for (first row transition metal) coordination compounds? Sent to CCL by: "Peter W. Thulstrup" [pwt|kvl.dk] This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C61824.A5D00300 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello CCL, Are any of you aware of systematic studies evaluating the performance of = DFT for the prediction of the ground state of transition metal complexes = (e.g. high-, intermediate- and low spin state energies)? Thank you for any help! Peter W. Thulstrup pwt:kvl.dk (I haven't been following the threads lkately so I apologize if this = subject has been up recently) ------=_NextPart_000_0031_01C61824.A5D00300 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello CCL,
 
Are any of you aware of systematic = studies=20 evaluating the performance of DFT for the prediction of the ground = state of=20 transition metal complexes (e.g. high-, intermediate- and low spin state = energies)?
 
Thank you for any help!
 
Peter W. Thulstrup
pwt:kvl.dk
 
(I haven't been following the threads = lkately so I=20 apologize if this subject has been up = recently)
------=_NextPart_000_0031_01C61824.A5D00300--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jan 13 09:40:01 2006 From: "Ian Hovell HOVELL===cetem.gov.br" To: CCL Subject: CCL:G: RES: G: Gaussian 03 optimizatio restart Message-Id: <-30486-060113061537-7497-mwU0qLwcQgyqhL4oiidzPA ~ server.ccl.net> X-Original-From: Ian Hovell Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 13 Jan 2006 08:27:22 -0300 MIME-Version: 1.0 Sent to CCL by: Ian Hovell [HOVELL%x%cetem.gov.br] Marius, Thats a simple one. Open the out file using Gausview, using the option to load all the optimization steps, use the viewer to show the required geometry step and go > from there. Hope this helps Ian -----Mensagem original----- De: Marius Retegan retegan.marius+/-gmail.com [mailto:owner-chemistry(_)ccl.net] Enviada em: quinta-feira, 12 de janeiro de 2006 12:10 Para: Hovell, Ian Assunto: CCL:G: Gaussian 03 optimizatio restart Sent to CCL by: Marius Retegan [retegan.marius a gmail.com] Hello First of all I would like to say Happy New Year to all subscribers of CCL. I have a short question. Lets say that I have a completed optimization and I want to use the geometry and the guess from a intermediate step to start another job. It's this possible? I've search the Gaussian 03 manual but I couldn't find find somethig related to my problem. Any help would be appriciated. Thank you very much.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jan 13 10:15:00 2006 From: "Frank Neese neese%x%mpi-muelheim.mpg.de" To: CCL Subject: CCL: Systematic DFT study of spin states for (first row transition metal) coordination compounds? Message-Id: <-30487-060113075743-23614-ar9tBHsI5oWy8YJEwBLwzw]=[server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Fri, 13 Jan 2006 13:20:11 +0100 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese^mpi-muelheim.mpg.de] Dear Peter, for example, Fouqeau, A.; Casida, M.E.; Lawson, L.M.; Hauser, A.; Neese, F. (2005) Comparison of Density Functionals for Energy and Structural Differences Between the High-[5T2g: (t2g4)(eg2)] and Low-[1A1g: (t2g6)(eg0)] Spin States of Iron(II) Coordination Compounds : II. Comparison of Results for More than Ten Modern Functionals with Ligand Field Theory and Ab Initio Results for Hexaquoferrous Dication, [Fe(H2O)6]2+ and Hexaminoferrous Dication [Fe(NH3)6]2+, J. Chem. Phys., 122, 044110/1-13 Fouqueau, A.; Mer, S.; Casida, M.E.; Daku, L.M.L.; Hauser, A.; Mieva, T.; Neese, F. (2004) Comparison of Density Functionals for Energy and Structural Differences between the High [5T2g: t2g4eg2] and Low [1A1g: t2g6] Spin States of the Hexaquo-Ferrous Ion, [Fe(H2O)6]2+, J. Chem. Phys., 120, 9473-9486. Schöneboom, J.; Neese, F.; Thiel, W. (2005) Towards Identification of the Compound I Reactive Intermediate in Cytochrome P450 Chemistry: A QM/MM Study of its EPR and Mössbauer Parameters, J. Am. Chem. Soc., 127, 5840-5853 and references therein. There have been quite a few studies. DFT tends to be biased in favour of low spin states. Hope that helps, all the best, Frank From owner-chemistry@ccl.net Fri Jan 13 10:50:00 2006 From: "Eduardo Lemos de Sa edulsa . mkem.uu.se" To: CCL Subject: CCL: software for solving mathematics equations Message-Id: <-30488-060113034106-6448-Y3QEVQEVoowf8wwUTYbDkQ]![server.ccl.net> X-Original-From: Eduardo Lemos de Sa Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 13 Jan 2006 08:41:52 +0100 MIME-Version: 1.0 Sent to CCL by: Eduardo Lemos de Sa [edulsa]=[mkem.uu.se] Hello Patrick Mupad is a very good software and it is free. Of course, you can use octave (open source). Regards Eduardo skpang,ctimail.com wrote: >Sent to CCL by: skpang|*|ctimail.com >Dear all, > >Is there any free software for doing calculus,and it can solve the >symbolic equation like MathCAD? > >Regards, > >Patrick > >My e-mail address : skpang ~ ctimail.com> > > > > -- Eduardo Lemos de Sa Materials Chemistry Department - Uppsala University (Licensed by Departamento de Quimica - Universidade Federal do Parana) edulsa|-|mkem.uu.se or edulsa|-|quimica.ufpr.br phone: ++46 (18) 471 3747 From owner-chemistry@ccl.net Fri Jan 13 11:52:00 2006 From: "Nuno A.G. Bandeira nuno.bandeira===ist.utl.pt" To: CCL Subject: CCL: Systematic DFT study of spin states for (first row transition Message-Id: <-30489-060113115114-30358-4FCZf+o18et87gL/qlDHkQ _ server.ccl.net> X-Original-From: "Nuno A.G. Bandeira" Sent to CCL by: "Nuno A.G. Bandeira" [nuno.bandeira[-]ist.utl.pt] Peter W. Thulstrup pwt~!~kvl.dk wrote: > Hello CCL, > > Are any of you aware of systematic studies evaluating the performance of = > DFT for the prediction of the ground state of transition metal complexes = > (e.g. high-, intermediate- and low spin state energies)? Check out the following references: Deeth et al J. Comput. Chem. 2004,25,1840 Harvey, J. N. Structure and Bonding 2004,112,151 Slomon et al, J. Chem. Phys. 2002,117,4729 Reiher et al, Theor. Chem. Acc. 2001,107,48 The Structure and Bonding article is an extremely good review for the deltaSCF approach. A very recent methodology called spin-flipping TDDFT is available in the ADF package. The relevant articles are: Wang, F. Ziegler, T. J. Chem. Phys. 2005,122,074109 Seth, M. Ziegler, T. J. Chem Phys. 2005,123,144105 The latter attempts to alleviate the problem of the multi-reference character and degeneracies in transition metal complexes. hope this helps, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student %x% IST,Lisbon -- From owner-chemistry@ccl.net Fri Jan 13 13:25:00 2006 From: "James J. P. Stewart mrmopac##worldnet.att.net" To: CCL Subject: CCL: Semiempirical examples for teaching: success stories Message-Id: <-30490-060113113430-20325-ohWL70m/3Suc6btpUelkKg:+:server.ccl.net> X-Original-From: "James J. P. Stewart" Content-Type: multipart/alternative; boundary="=====================_164548978==.ALT" Date: Fri, 13 Jan 2006 08:58:05 -0700 Mime-Version: 1.0 Sent to CCL by: "James J. P. Stewart" [mrmopac]*[worldnet.att.net] --=====================_164548978==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dr Kahn requested examples of where semiempirical methods provide useful results. The heats of formation of compounds in the NIST WebBook were compared with the results of semiempirical and DFT calculations, and many severe errors were found in the reference data. Here is a list of the compounds for which the reported HoF was in error: * 5-Hepten-2-one, 6-methyl- (C8H14O) * Benzene, hexafluoro- (C6F6) * 4-Hydroxy-4-methylpentan-2-one (C6H12O2) * Thietane (C3H6S) * Propanedioic acid, diethyl ester (C7H12O4) * Benzene, pentafluoro(trifluoromethyl)- (C7F8) * 2-Propanone, 1,1,1,3,3,3-hexafluoro- (C3F6O) * Ethane, 1,1'-oxybis[2-methoxy- (C6H14O3) * p-Hydroxybiphenyl (C12H10O) * Perfluoro-n-butane (C4F10) * Cyclohexane, dodecafluoro- (C6F12) * 2,6,6-Trimethyl-2-cyclohexen-1-one (C9H14O) * Benzene, bromopentafluoro- (C6BrF5) * Benzene, pentafluoroiodo- (C6F5I) * 5,6-Dibutyl-5,6-bis(4-tert-butylphenyl)decane (C38H62) * 1,3,5-Triazine, 2,4,6-trimethoxy- (C6H9N3O3) * Phenol, 2-(1,1-dimethylethyl)-4-methyl- (C11H16O) * 2,2'-Biquinoline (C18H12N2) * Pentacyclo[18.2.2.2(9,12).0(4,15).0(6,17)]hexacosa-4,6(17),9,11,15,20,22,23,25-nonane (C26H26) * 1,2,3,6-Tetrahydropyridine (C5H9N) * Bis(n-perfluoropropyl ether) (C6F14O) * Dioxybismethanol (C2H6O4) * Benzenamine, 3-chloro-4-methyl- (C7H8ClN) * Pyrazine, 1,4-dioxide (C4H4N2O2) * Terephthalamide (C8H8N2O2) * Isophthalamide (C8H8N2O2) * Cyclohexane, undecyl- (C17H34) * 1,3-Butadiene, 1,1,2,3,4,4-hexafluoro- (C4F6) * 2,4,6-Trimethylphenyl isocyanide (C10H11N) * Fluorodinitrophenylmethane (C7H5FN2O4) * 1H-Indene, 6-(1,1-dimethylethyl)-2,3-dihydro-1,1-dimethyl- (C15H22) * Perfluoro-2-butene (C4F8) * DL-3,4-Di(1-cyclohexen-1-yl)-2,2,5,5-tetramethylhexane (C22H38) * 1,3,5-Tricyanobenzene (C9H3N3) For details, please see: Stewart, J.J.P., Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, J. Mol. Model, 2004, 10, 1, 6-10. Jimmy. At 04:19 AM 1/13/2006, Kalju Kahn kalju . chem.ucsb.edu wrote: >Sent to CCL by: Kalju Kahn [kalju\a/chem.ucsb.edu] >Dear CCL members, > >I am teaching computational chemistry this quarter, and are looking >for several examples on successful applications of semiempirical >methods in chemistry. The examples ideally: > >a) Involve chemistry that is normally taught in undergraduate OChem or >Biochem. >b) Can be reproduced in less than a day/processor on modern hardware >c) Have (or had at one time) clear value in advancing our >understanding of chemistry (as opposed to just predicting correctly >some energy difference or spectral property) >d) Give quantitatively accurate results when compared to experiment or >much higher level computational results. > >I am planning to make brief tutorials for select examples and will >post the link with summary early next month. > >Thanks, > >Kalju > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Dr. Kalju Kahn >Department of Chemistry and Biochemistry >University of California, Santa Barbara > ( _+_ _+_ ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry LLC | E-mail: mrmopac_+_worldnet.att.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .------------------------\ (----( )--------------------------------------. \_) ) / (_/ --=====================_164548978==.ALT Content-Type: text/html; charset="us-ascii" Dr Kahn requested examples of where semiempirical methods provide useful results.

The heats of formation of compounds in the NIST WebBook were compared with the results of semiempirical and DFT calculations, and many severe errors were found in the reference data.  Here is a list of the compounds for which the reported HoF was in error:
  1. 5-Hepten-2-one, 6-methyl- (C8H14O)
  2. Benzene, hexafluoro- (C6F6)
  3. 4-Hydroxy-4-methylpentan-2-one (C6H12O2)
  4. Thietane (C3H6S)
  5. Propanedioic acid, diethyl ester (C7H12O4)
  6. Benzene, pentafluoro(trifluoromethyl)- (C7F8)
  7. 2-Propanone, 1,1,1,3,3,3-hexafluoro- (C3F6O)
  8. Ethane, 1,1'-oxybis[2-methoxy- (C6H14O3)
  9. p-Hydroxybiphenyl (C12H10O)
  10. Perfluoro-n-butane (C4F10)
  11. Cyclohexane, dodecafluoro- (C6F12)
  12. 2,6,6-Trimethyl-2-cyclohexen-1-one (C9H14O)
  13. Benzene, bromopentafluoro- (C6BrF5)
  14. Benzene, pentafluoroiodo- (C6F5I)
  15. 5,6-Dibutyl-5,6-bis(4-tert-butylphenyl)decane (C38H62)
  16. 1,3,5-Triazine, 2,4,6-trimethoxy- (C6H9N3O3)
  17. Phenol, 2-(1,1-dimethylethyl)-4-methyl- (C11H16O)
  18. 2,2'-Biquinoline (C18H12N2)
  19. Pentacyclo[18.2.2.2(9,12).0(4,15).0(6,17)]hexacosa-4,6(17),9,11,15,20,22,23,25-nonane (C26H26)
  20. 1,2,3,6-Tetrahydropyridine (C5H9N)
  21. Bis(n-perfluoropropyl ether) (C6F14O)
  22. Dioxybismethanol (C2H6O4)
  23. Benzenamine, 3-chloro-4-methyl- (C7H8ClN)
  24. Pyrazine, 1,4-dioxide (C4H4N2O2)
  25. Terephthalamide (C8H8N2O2)
  26. Isophthalamide (C8H8N2O2)
  27. Cyclohexane, undecyl- (C17H34)
  28. 1,3-Butadiene, 1,1,2,3,4,4-hexafluoro- (C4F6)
  29. 2,4,6-Trimethylphenyl isocyanide (C10H11N)
  30. Fluorodinitrophenylmethane (C7H5FN2O4)
  31. 1H-Indene, 6-(1,1-dimethylethyl)-2,3-dihydro-1,1-dimethyl- (C15H22)
  32. Perfluoro-2-butene (C4F8)
  33. DL-3,4-Di(1-cyclohexen-1-yl)-2,2,5,5-tetramethylhexane (C22H38)
  34. 1,3,5-Tricyanobenzene (C9H3N3)

For details, please see:

Stewart, J.J.P., Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, J. Mol. Model, 2004, 10, 1, 6-10.


Jimmy.

 At 04:19 AM 1/13/2006, Kalju Kahn kalju . chem.ucsb.edu wrote:
Sent to CCL by: Kalju Kahn [kalju\a/chem.ucsb.edu]
Dear CCL members,

I am teaching computational chemistry this quarter, and are looking
for several examples on successful applications of semiempirical
methods in chemistry.  The examples ideally:

a) Involve chemistry that is normally taught in undergraduate OChem or
Biochem.
b) Can be reproduced in less than a day/processor on modern hardware
c) Have (or had at one time) clear value in advancing our
understanding of chemistry (as opposed to just predicting correctly
some energy difference or spectral property)
d) Give quantitatively accurate results when compared to experiment or
much higher level computational results.

I am planning to make brief tutorials for select examples and will
post the link with summary early next month.

Thanks,

Kalju

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
University of California, Santa Barbara


                         ( _+_ _+_ )
 .-----------------oOOo----(_)----oOOo--------------------------------------.
 | James J. P. Stewart                 |                                    |
 | Stewart Computational Chemistry LLC | E-mail:  mrmopac_+_worldnet.att.net  |
 | 15210 Paddington Circle             |  39/03/15 N, 104/49/29 W           |
 | Colorado Springs CO 80921-2512      |                                    |
 | USA                   .ooo0         | Phone: USA +(719) 488-9416         |
 |                       (   )   Oooo. |                                    |
 .------------------------\ (----(   )--------------------------------------.
                           \_)    ) /
                                 (_/ --=====================_164548978==.ALT-- From owner-chemistry@ccl.net Fri Jan 13 14:12:01 2006 From: "Elaine Meng meng%%cgl.ucsf.edu" To: CCL Subject: CCL: Simple molecular graphics Message-Id: <-30491-060113135622-8280-sXSWC3dbpvxYvVTv4UH7+A]|[server.ccl.net> X-Original-From: Elaine Meng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Fri, 13 Jan 2006 10:17:12 -0800 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Elaine Meng [meng(_)cgl.ucsf.edu] > I know this is similar to previous questions that have been sent to > the list in the past. But I am going to ask it anyway...I keep > searching for a program that will make simple publication quality > molecular graphics pictures (usually black-and-white), but with a > couple of added features, and runs on Windows or Linux. > > Vast numbers of molecular graphics programs are advertised for their > capability to make "publication quality" images. But what this always > seems to refer to is the ability to create stunning color pictures > complete with shadows, fog effects, dramatic backgrounds, etc., > perhaps rendered with the help of POV-Ray. Nice, but not what I > usually need for figures to put into journal articles or technical > reports. I usually just want ball-and-stick, black-and-white (or a > simple color scheme to highlight heteroatoms), maybe some > cross-hatching to suggest depth, and some labeling capability, with > the end result a high-resolution image or vector output. UCSF Chimera can save images at arbitrarily high resolutions. Also available: various representations including ball-and-stick, coloring with shades of gray, any color background, atom/bond deletion, "pseudobonds" to show distance measurements or hydrogen bonding, and more uniquely, a 2D Labels feature for placing arbitrary labels in the x,y coordinate system of the graphics window. Available for Wiindows, Mac, Linux, etc. and free for noncommercial use, http://www.cgl.ucsf.edu/chimera ----- Elaine C. Meng, Ph.D. meng~~cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html > An example of a program that comes pretty close to what I would like > is XChemEdit, where I can read in a structure, and quickly > rotate/translate it to a desired orientation. Then, with a few mouse > clicks I can remove undesired bonds, make dashed bonds (e.g. for > hydrogen bonds or transition states), label bond > distances/angles/dihedrals, resize and move labels, etc. This only > takes a minute or two, unfortunately the resulting images are not, in > my opinion, good enough for external publication. They are nicely > labeled and clear, but low-resolution. > > As an alternative, I have tried Schakal99, which can make excellent > publication-quality b/w molecular graphics, and it seems that one has > extensive control over the final image. But I find it difficult to > use even after studying the manual and going through quite a few > examples, and I am not sure that certain things like labeling bond > angles can even be done. > > I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they > aren't quite what I am looking for either. We don't own Cache, > Chem3D, or Gaussview, so I haven't tried them...what about those or > other software? Is it best to just put in the time to really learn > Schakal usage? Would you agree that fancy photorealistic "publication > quality" graphics are often discouraged by journal editors anyway? > > Thanks! > > Leif Olson > Eastman Kodak Research Laboratories > From owner-chemistry@ccl.net Fri Jan 13 14:46:01 2006 From: "Jim Pfaendtner pfaendtner^northwestern.edu" To: CCL Subject: CCL:G: internal rotation in hydrocarbons Message-Id: <-30492-060113141236-13087-QTSK6M3f/1F8NgNs+FMNPg###server.ccl.net> X-Original-From: "Jim Pfaendtner" Sent to CCL by: "Jim Pfaendtner" [pfaendtner[-]northwestern.edu] Hi, I am trying to develop a short code which will take a 1-D relaxed PES scan of my dihedral angles and allow me to calculate the energy levels from the 1D schrodinger equation. I'm obtaining the PES as a full fourier fit from Gaussian simulations. Can anyone recommend a good method to obtain the lowest eigenvalues from the 1D schrodinger equation? The PES scans are fit to full Fourier series because because my molecules are somewhat irregular. I have been trying to use a grid-based method but haven't had much luck. If people know of any public-domain codes which can help me with this, I would greatly appreciate it. Regards, Jim Pfaendtner From owner-chemistry@ccl.net Fri Jan 13 15:21:00 2006 From: "Jim Pfaendtner pfaendtner..northwestern.edu" To: CCL Subject: CCL:G: internal rotation hydrocarbons Message-Id: <-30493-060113141131-11900-uvQzj3GqZ5FEXaaNlnanjA{}server.ccl.net> X-Original-From: "Jim Pfaendtner" Sent to CCL by: "Jim Pfaendtner" [pfaendtner[]northwestern.edu] Hi, I am trying to develop a short code which will take a 1-D relaxed PES scan of my dihedral angles and allow me to calculate the energy levels from the 1D schrodinger equation. I'm obtaining the PES as a full fourier fit from Gaussian simulations. Can anyone recommend a good method to obtain the lowest eigenvalues from the 1D schrodinger equation? The PES scans are fit to full Fourier series because because my molecules are somewhat irregular. I have been trying to use a grid-based method but haven't had much luck. If people know of any public-domain codes which can help me with this, I would greatly appreciate it. Regards, Jim Pfaendtner From owner-chemistry@ccl.net Fri Jan 13 15:56:00 2006 From: "James J. P. Stewart mrmopac:worldnet.att.net" To: CCL Subject: CCL: Semiempirical examples for teaching: success stories Message-Id: <-30494-060113143100-26236-NYAd8w2awG3ZSdlhihae2g^_^server.ccl.net> X-Original-From: "James J. P. Stewart" Content-Type: multipart/alternative; boundary="=====================_177286794==.ALT" Date: Fri, 13 Jan 2006 12:30:34 -0700 Mime-Version: 1.0 Sent to CCL by: "James J. P. Stewart" [mrmopac||worldnet.att.net] --=====================_177286794==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed My apologies: My last message re semiempirical methods contained invalid URLs. Here is a "cleaner" version: Dr Kahn requested examples of where semiempirical methods provide useful results. The heats of formation of compounds in the NIST WebBook were compared with the results of semiempirical and DFT calculations, and many severe errors were found in the reference data. Here is a list of the compounds for which the reported HoF was in error: 5-Hepten-2-one, 6-methyl- (C8H14O) Benzene, hexafluoro- (C6F6) 4-Hydroxy-4-methylpentan-2-one (C6H12O2) Thietane (C3H6S) Propanedioic acid, diethyl ester (C7H12O4) Benzene, pentafluoro(trifluoromethyl)- (C7F8) 2-Propanone, 1,1,1,3,3,3-hexafluoro- (C3F6O) Ethane, 1,1'-oxybis[2-methoxy- (C6H14O3) p-Hydroxybiphenyl (C12H10O) Perfluoro-n-butane (C4F10) Cyclohexane, dodecafluoro- (C6F12) 2,6,6-Trimethyl-2-cyclohexen-1-one (C9H14O) Benzene, bromopentafluoro- (C6BrF5) Benzene, pentafluoroiodo- (C6F5I) 5,6-Dibutyl-5,6-bis(4-tert-butylphenyl)decane (C38H62) 1,3,5-Triazine, 2,4,6-trimethoxy- (C6H9N3O3) Phenol, 2-(1,1-dimethylethyl)-4-methyl- (C11H16O) 2,2'-Biquinoline (C18H12N2) Pentacyclo[18.2.2.2(9,12).0(4,15).0(6,17)]hexacosa-4,6(17),9,11,15,20,22,23,25-nonane (C26H26) 1,2,3,6-Tetrahydropyridine (C5H9N) Bis(n-perfluoropropyl ether) (C6F14O) Dioxybismethanol (C2H6O4) Benzenamine, 3-chloro-4-methyl- (C7H8ClN) Pyrazine, 1,4-dioxide (C4H4N2O2) Terephthalamide (C8H8N2O2) Isophthalamide (C8H8N2O2) Cyclohexane, undecyl- (C17H34) 1,3-Butadiene, 1,1,2,3,4,4-hexafluoro- (C4F6) 2,4,6-Trimethylphenyl isocyanide (C10H11N) Fluorodinitrophenylmethane (C7H5FN2O4) 1H-Indene, 6-(1,1-dimethylethyl)-2,3-dihydro-1,1-dimethyl- (C15H22) Perfluoro-2-butene (C4F8) DL-3,4-Di(1-cyclohexen-1-yl)-2,2,5,5-tetramethylhexane (C22H38) 1,3,5-Tricyanobenzene (C9H3N3) For details, please see Stewart, J.J.P., Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, J. Mol. Model, 2004, 10, 1, 6-10. Here is the URL: http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mask=1 Jimmy. At 04:19 AM 1/13/2006, Kalju Kahn kalju . chem.ucsb.edu wrote: >Sent to CCL by: Kalju Kahn [kalju\a/chem.ucsb.edu] >Dear CCL members, > >I am teaching computational chemistry this quarter, and are looking >for several examples on successful applications of semiempirical >methods in chemistry. The examples ideally: > >a) Involve chemistry that is normally taught in undergraduate OChem or >Biochem. >b) Can be reproduced in less than a day/processor on modern hardware >c) Have (or had at one time) clear value in advancing our >understanding of chemistry (as opposed to just predicting correctly >some energy difference or spectral property) >d) Give quantitatively accurate results when compared to experiment or >much higher level computational results. > >I am planning to make brief tutorials for select examples and will >post the link with summary early next month. > >Thanks, > >Kalju > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >Dr. Kalju Kahn >Department of Chemistry and Biochemistry >University of California, Santa Barbara ( ]_[ ]_[ ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry LLC | E-mail: mrmopac]_[worldnet.att.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .------------------------\ (----( )--------------------------------------. \_) ) / (_/ --=====================_177286794==.ALT Content-Type: text/html; charset="us-ascii" My apologies: My last message re semiempirical methods contained invalid URLs.

Here is a "cleaner" version:

Dr Kahn requested examples of where semiempirical methods provide useful results.

The heats of formation of compounds in the NIST WebBook were compared with the results of semiempirical and DFT calculations, and many severe errors were found in the reference data.  Here is a list of the compounds for which the reported HoF was in error:

5-Hepten-2-one, 6-methyl- (C8H14O)
Benzene, hexafluoro- (C6F6)
4-Hydroxy-4-methylpentan-2-one (C6H12O2)
Thietane (C3H6S)
Propanedioic acid, diethyl ester (C7H12O4)
Benzene, pentafluoro(trifluoromethyl)- (C7F8)
2-Propanone, 1,1,1,3,3,3-hexafluoro- (C3F6O)
Ethane, 1,1'-oxybis[2-methoxy- (C6H14O3)
p-Hydroxybiphenyl (C12H10O)
Perfluoro-n-butane (C4F10)
Cyclohexane, dodecafluoro- (C6F12)
2,6,6-Trimethyl-2-cyclohexen-1-one (C9H14O)
Benzene, bromopentafluoro- (C6BrF5)
Benzene, pentafluoroiodo- (C6F5I)
5,6-Dibutyl-5,6-bis(4-tert-butylphenyl)decane (C38H62)
1,3,5-Triazine, 2,4,6-trimethoxy- (C6H9N3O3)
Phenol, 2-(1,1-dimethylethyl)-4-methyl- (C11H16O)
2,2'-Biquinoline (C18H12N2)
Pentacyclo[18.2.2.2(9,12).0(4,15).0(6,17)]hexacosa-4,6(17),9,11,15,20,22,23,25-nonane (C26H26)
1,2,3,6-Tetrahydropyridine (C5H9N)
Bis(n-perfluoropropyl ether) (C6F14O)
Dioxybismethanol (C2H6O4)
Benzenamine, 3-chloro-4-methyl- (C7H8ClN)
Pyrazine, 1,4-dioxide (C4H4N2O2)
Terephthalamide (C8H8N2O2)
Isophthalamide (C8H8N2O2)
Cyclohexane, undecyl- (C17H34)
1,3-Butadiene, 1,1,2,3,4,4-hexafluoro- (C4F6)
2,4,6-Trimethylphenyl isocyanide (C10H11N)
Fluorodinitrophenylmethane (C7H5FN2O4)
1H-Indene, 6-(1,1-dimethylethyl)-2,3-dihydro-1,1-dimethyl- (C15H22)
Perfluoro-2-butene (C4F8)
DL-3,4-Di(1-cyclohexen-1-yl)-2,2,5,5-tetramethylhexane (C22H38)
1,3,5-Tricyanobenzene (C9H3N3)

For details, please see

Stewart, J.J.P., Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation, J. Mol. Model, 2004, 10, 1, 6-10.

Here is the URL:

http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mask=1


Jimmy.

 At 04:19 AM 1/13/2006, Kalju Kahn kalju . chem.ucsb.edu wrote:

Sent to CCL by: Kalju Kahn [kalju\a/chem.ucsb.edu]
Dear CCL members,

I am teaching computational chemistry this quarter, and are looking
for several examples on successful applications of semiempirical
methods in chemistry.  The examples ideally:

a) Involve chemistry that is normally taught in undergraduate OChem or
Biochem.
b) Can be reproduced in less than a day/processor on modern hardware
c) Have (or had at one time) clear value in advancing our
understanding of chemistry (as opposed to just predicting correctly
some energy difference or spectral property)
d) Give quantitatively accurate results when compared to experiment or
much higher level computational results.

I am planning to make brief tutorials for select examples and will
post the link with summary early next month.

Thanks,

Kalju

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
University of California, Santa Barbara


                         ( ]_[ ]_[ )
 .-----------------oOOo----(_)----oOOo--------------------------------------.
 | James J. P. Stewart                 |                                    |
 | Stewart Computational Chemistry LLC | E-mail:  mrmopac]_[worldnet.att.net  |
 | 15210 Paddington Circle             |  39/03/15 N, 104/49/29 W           |
 | Colorado Springs CO 80921-2512      |                                    |
 | USA                   .ooo0         | Phone: USA +(719) 488-9416         |
 |                       (   )   Oooo. |                                    |
 .------------------------\ (----(   )--------------------------------------.
                           \_)    ) /
                                 (_/ --=====================_177286794==.ALT-- From owner-chemistry@ccl.net Fri Jan 13 20:10:00 2006 From: "Lukasz Cwiklik lukasz.cwiklik:_:uochb.cas.cz" To: CCL Subject: CCL: software for solving mathematics equations Message-Id: <-30495-060113174345-2335-Y43T7QKpP4tzckOQKIuedQ(_)server.ccl.net> X-Original-From: Lukasz Cwiklik Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Jan 2006 22:40:51 +0100 MIME-Version: 1.0 Sent to CCL by: Lukasz Cwiklik [lukasz.cwiklik(a)uochb.cas.cz] On 1/12/06, skpang,ctimail.com wrote: > Sent to CCL by: skpang|*|ctimail.com > Is there any free software for doing calculus,and it can solve the > symbolic equation like MathCAD? Maxima: http://maxima.sourceforge.net/ Best regards, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Fri Jan 13 20:45:00 2006 From: "Steve Williams willsd::appstate.edu" To: CCL Subject: CCL:G: internal rotation in hydrocarbons Message-Id: <-30496-060113185823-17998-qg7wiMGDx65Y0TFj817OWw!=!server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Fri, 13 Jan 2006 16:53:31 -0500 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd*o*appstate.edu] Jim Pfaendtner pfaendtner^northwestern.edu wrote: >Sent to CCL by: "Jim Pfaendtner" [pfaendtner[-]northwestern.edu] >Hi, > >I am trying to develop a short code which will take a 1-D relaxed PES scan of my dihedral angles and allow me to calculate the energy levels from the 1D schrodinger equation. I'm obtaining the PES as a full fourier fit from Gaussian simulations. > >Can anyone recommend a good method to obtain the lowest eigenvalues from the 1D schrodinger equation? The PES scans are fit to full Fourier series because because my molecules are somewhat irregular. > >I have been trying to use a grid-based method but haven't had much luck. If people know of any public-domain codes which can help me with this, I would greatly appreciate it. > >Regards, >Jim Pfaendtner> > > > > I think there is a windows code called fgh that will do this. I think I have a zip install file for it somewhere, but it might be best to google fgh or fgh.exe or fgh.zip and get it from its distributor. Let me know if you have trouble finding it. Steve Williams From owner-chemistry@ccl.net Fri Jan 13 22:44:00 2006 From: "Terry Frankcombe T.Frankcombe^^chem.leidenuniv.nl" To: CCL Subject: CCL: Semiempirical examples for teaching: success stories Message-Id: <-30497-060113210721-23824-ZybRhjhzkf1PcfbBeBGiIw++server.ccl.net> X-Original-From: Terry Frankcombe Content-Type: text/plain; charset=us-ascii Date: Sat, 14 Jan 2006 02:15:06 +0100 Mime-Version: 1.0 Sent to CCL by: Terry Frankcombe [T.Frankcombe[]chem.leidenuniv.nl] *cough* *splutter* Sorry James, but that's complete nonsense (to put it politely). Since when have semiempirical extrapolations* been taken over experimental data? Complete codswallop. A lot of the claims you make in that paper are questionable at best. What you have shown are best interpreted as FAILURES of semiempirical and DFT methods, not wins. Terry *I say extrapolations to highlight that semiempirical methods applied outside their training set are not much more than guesses. Informed guesses, but guesses nonetheless. -- Dr Terry Frankcombe LIC / Theoretical Chemistry University of Leiden Postbus 9502, 2300 RA Leiden, The Netherlands Ph. +31 71 527 4533 Fax +31 71 527 4397 > Sent to CCL by: "James J. P. Stewart" [mrmopac||worldnet.att.net] > --=====================_177286794==.ALT > Content-Type: text/plain; charset="us-ascii"; format=flowed > > My apologies: My last message re semiempirical methods contained invalid URLs . > > Here is a "cleaner" version: > > Dr Kahn requested examples of where semiempirical methods provide > useful results. > > The heats of formation of compounds in the NIST WebBook were compared > with the results of semiempirical and DFT calculations, and many > severe errors were found in the reference data. Here is a list of > the compounds for which the reported HoF was in error: > > 5-Hepten-2-one, 6-methyl- (C8H14O) > Benzene, hexafluoro- (C6F6) > 4-Hydroxy-4-methylpentan-2-one (C6H12O2) > Thietane (C3H6S) > Propanedioic acid, diethyl ester (C7H12O4) > Benzene, pentafluoro(trifluoromethyl)- (C7F8) > 2-Propanone, 1,1,1,3,3,3-hexafluoro- (C3F6O) > Ethane, 1,1'-oxybis[2-methoxy- (C6H14O3) > p-Hydroxybiphenyl (C12H10O) > Perfluoro-n-butane (C4F10) > Cyclohexane, dodecafluoro- (C6F12) > 2,6,6-Trimethyl-2-cyclohexen-1-one (C9H14O) > Benzene, bromopentafluoro- (C6BrF5) > Benzene, pentafluoroiodo- (C6F5I) > 5,6-Dibutyl-5,6-bis(4-tert-butylphenyl)decane (C38H62) > 1,3,5-Triazine, 2,4,6-trimethoxy- (C6H9N3O3) > Phenol, 2-(1,1-dimethylethyl)-4-methyl- (C11H16O) > 2,2'-Biquinoline (C18H12N2) > Pentacyclo[18.2.2.2(9,12).0(4,15).0(6,17)]hexacosa-4,6(17),9,11,15,20,22,23,2 5-nonane > (C26H26) > 1,2,3,6-Tetrahydropyridine (C5H9N) > Bis(n-perfluoropropyl ether) (C6F14O) > Dioxybismethanol (C2H6O4) > Benzenamine, 3-chloro-4-methyl- (C7H8ClN) > Pyrazine, 1,4-dioxide (C4H4N2O2) > Terephthalamide (C8H8N2O2) > Isophthalamide (C8H8N2O2) > Cyclohexane, undecyl- (C17H34) > 1,3-Butadiene, 1,1,2,3,4,4-hexafluoro- (C4F6) > 2,4,6-Trimethylphenyl isocyanide (C10H11N) > Fluorodinitrophenylmethane (C7H5FN2O4) > 1H-Indene, 6-(1,1-dimethylethyl)-2,3-dihydro-1,1-dimethyl- (C15H22) > Perfluoro-2-butene (C4F8) > DL-3,4-Di(1-cyclohexen-1-yl)-2,2,5,5-tetramethylhexane (C22H38) > 1,3,5-Tricyanobenzene (C9H3N3) > > For details, please see > > Stewart, J.J.P., Comparison of the accuracy of semiempirical and some > DFT methods for predicting heats of formation, J. Mol. Model, 2004, > 10, 1, 6-10. > > Here is the URL: > > http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mask=1 > > > Jimmy. > > At 04:19 AM 1/13/2006, Kalju Kahn kalju . chem.ucsb.edu wrote: > >Sent to CCL by: Kalju Kahn [kalju\a/chem.ucsb.edu] > >Dear CCL members, > > > >I am teaching computational chemistry this quarter, and are looking > >for several examples on successful applications of semiempirical > >methods in chemistry. The examples ideally: > > > >a) Involve chemistry that is normally taught in undergraduate OChem or > >Biochem. > >b) Can be reproduced in less than a day/processor on modern hardware > >c) Have (or had at one time) clear value in advancing our > >understanding of chemistry (as opposed to just predicting correctly > >some energy difference or spectral property) > >d) Give quantitatively accurate results when compared to experiment or > >much higher level computational results. > > > >I am planning to make brief tutorials for select examples and will > >post the link with summary early next month. > > > >Thanks, > > > >Kalju > > > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >Dr. Kalju Kahn > >Department of Chemistry and Biochemistry > >University of California, Santa Barbara > > > ( || || ) > .-----------------oOOo----(_)----oOOo-------------------------------------- . > | James J. P. Stewart | | > | Stewart Computational Chemistry LLC | E-mail: mrmopac||worldnet.att.net | > | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | > | Colorado Springs CO 80921-2512 | | > | USA .ooo0 | Phone: USA +(719) 488-9416 | > | ( ) Oooo. | | > .------------------------\ (----( )-------------------------------------- . > \_) ) / > (_/ > --=====================_177286794==.ALT > Content-Type: text/html; charset="us-ascii" > > > > My apologies: My last message re semiempirical methods contained invalid > URLs.

> Here is a "cleaner" version:

> Dr Kahn requested examples of where semiempirical methods provide useful > results.

> The heats of formation of compounds in the NIST WebBook were compared > with the results of semiempirical and DFT calculations, and many severe > errors were found in the reference data.  Here is a list of the > compounds for which the reported HoF was in error:

> 5-Hepten-2-one, 6-methyl- (C8H14O)
> Benzene, hexafluoro- (C6F6)
> 4-Hydroxy-4-methylpentan-2-one (C6H12O2)
> Thietane (C3H6S)
> Propanedioic acid, diethyl ester (C7H12O4)
> Benzene, pentafluoro(trifluoromethyl)- (C7F8)
> 2-Propanone, 1,1,1,3,3,3-hexafluoro- (C3F6O)
> Ethane, 1,1'-oxybis[2-methoxy- (C6H14O3)
> p-Hydroxybiphenyl (C12H10O)
> Perfluoro-n-butane (C4F10)
> Cyclohexane, dodecafluoro- (C6F12)
> 2,6,6-Trimethyl-2-cyclohexen-1-one (C9H14O)
> Benzene, bromopentafluoro- (C6BrF5)
> Benzene, pentafluoroiodo- (C6F5I)
> 5,6-Dibutyl-5,6-bis(4-tert-butylphenyl)decane (C38H62)
> 1,3,5-Triazine, 2,4,6-trimethoxy- (C6H9N3O3)
> Phenol, 2-(1,1-dimethylethyl)-4-methyl- (C11H16O)
> 2,2'-Biquinoline (C18H12N2)
> Pentacyclo[18.2.2.2(9,12).0(4,15).0(6,17)]hexacosa-4,6(17),9,11,15,20,22,23,2 5-nonane > (C26H26)
> 1,2,3,6-Tetrahydropyridine (C5H9N)
> Bis(n-perfluoropropyl ether) (C6F14O)
> Dioxybismethanol (C2H6O4)
> Benzenamine, 3-chloro-4-methyl- (C7H8ClN)
> Pyrazine, 1,4-dioxide (C4H4N2O2)
> Terephthalamide (C8H8N2O2)
> Isophthalamide (C8H8N2O2)
> Cyclohexane, undecyl- (C17H34)
> 1,3-Butadiene, 1,1,2,3,4,4-hexafluoro- (C4F6)
> 2,4,6-Trimethylphenyl isocyanide (C10H11N)
> Fluorodinitrophenylmethane (C7H5FN2O4)
> 1H-Indene, 6-(1,1-dimethylethyl)-2,3-dihydro-1,1-dimethyl- (C15H22)
> Perfluoro-2-butene (C4F8)
> DL-3,4-Di(1-cyclohexen-1-yl)-2,2,5,5-tetramethylhexane (C22H38)
> 1,3,5-Tricyanobenzene (C9H3N3)

> For details, please see

> Stewart, J.J.P., Comparison of the accuracy of semiempirical and some DFT > methods for predicting heats of formation, J. Mol. Model, 2004, 10, 1, > 6-10.

> Here is the URL:

> > > http://webbook.nist.gov/cgi/cbook.cgi?Source=2004STE6-10&Units=SI&Mas k=1
>
>
> Jimmy.

>  At 04:19 AM 1/13/2006, Kalju Kahn kalju . chem.ucsb.edu wrote:
>

Sent to CCL by: Kalju Kahn > [kalju\a/chem.ucsb.edu]
> Dear CCL members,

> I am teaching computational chemistry this quarter, and are looking
> for several examples on successful applications of semiempirical
> methods in chemistry.  The examples ideally:

> a) Involve chemistry that is normally taught in undergraduate OChem > or
> Biochem.
> b) Can be reproduced in less than a day/processor on modern hardware
> c) Have (or had at one time) clear value in advancing our
> understanding of chemistry (as opposed to just predicting correctly
> some energy difference or spectral property)
> d) Give quantitatively accurate results when compared to experiment > or
> much higher level computational results.

> I am planning to make brief tutorials for select examples and will
> post the link with summary early next month.

> Thanks,

> Kalju

> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Kalju Kahn
> Department of Chemistry and Biochemistry
> University of California, Santa Barbara
>
>

>
>               ;            > ( || || )
>  .-----------------oOOo----(_)----oOOo---------------------------------- ----.
>  | James J. P. > Stewart           &nbs p;     > |            &nbs p;              ;          > |
>  | Stewart Computational Chemistry LLC | E-mail:  > mrmopac||worldnet.att.net  |
>  | 15210 Paddington > Circle             ; > |  39/03/15 N, 104/49/29 > W           |
>  | Colorado Springs CO 80921-2512      > |            &nbs p;              ;          > |
>  | > USA            &n bsp;      > .ooo0         | Phone: USA +(719) > 488-9416         |
>  |           &nbs p;           > (   )   Oooo. > |            &nbs p;              ;          > |
>  .------------------------\ (----(   > )--------------------------------------.
>               ;              > \_)    ) /
>               ;                     > (_/ > > > --=====================_177286794==.ALT--> >