From owner-chemistry@ccl.net Fri Apr 24 05:55:01 2009 From: "Sebastian Kozuch kozuchs^yahoo.com" To: CCL Subject: CCL: Computational Chemistry Wiki Message-Id: <-39153-090424052312-19048-L5MbiNvLYfx2kp/G8NBI0Q%server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-893187826-1240564973=:64364" Date: Fri, 24 Apr 2009 02:22:53 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs,,yahoo.com] --0-893187826-1240564973=:64364 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable The idea of a specific computational chemistry wiki is not to undermine or = compete with Wikipedia. The idea is to complement Wikipedia, blogs, books a= nd papers. Wikipedia is extremely helpful, and if I had the knowledge I wou= ld have loved to contribute there. More than that, as far as I=E2=80=99m co= ncerned if you look for something basic like DFT in the new wiki there shou= ld be only a reference to the entry in Wikipedia.=0ABut I cannot expect Wik= ipedia to have a specific entry on, let=E2=80=99s say, BP86 or UFF. Neither= I suppose we can add there a table with the mean error of the different po= st-HF geometry bond lengths, or a list of the programs that can run M06. Bu= t most of all, I=E2=80=99d like an up to date encyclopedia where if I searc= h for =E2=80=9CMP4=E2=80=9D it won=E2=80=99t appear with a multimedia playe= r.=0AAnd, as Brian says, Wikipedia is not for self-publicity, and most of t= he new methods that appear in computational chemistry cannot enter there un= less they are really fundamental methods. This takes years, and leave most = methods outside. =0AAgain, for those that are real specialists on tradition= al methods, I encourage them to write in Wikipedia. But all the information= that can be useful only for computational chemists, I encourage to put it = in this specific wiki.=0ATake into account that the same people of Wikipedi= a support the creation of specific encyclopedias for specific communities. = =0AAgain, if you like the idea and want to contribute, the page is=0A=C2=A0= =0Ahttp://computationalchemistry.wikia.com=0AMaybe it will work, maybe not.= But for sure it's worth to try it.=0Axxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx= =0A..........Sebastian Kozuch...........=0Axxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx= xxxxx=0A...The Lise Meitner-Minerva Center...=0A.for Computational Quantum = Chemistry.=0A...Hebrew University of Jerusalem....=0A.....kozuchs%yfaat.ch.= huji.ac.il.....=0Ahttp://yfaat.ch.huji.ac.il/kozuch.htm=0Axxxxxxxxxxxxxxxxx= xxxxxxxxxxxxxxxxxxxx =0A=0A=0A=0A=0A________________________________=0AFrom= : Brian Salter-Duke brian.james.duke---gmail.com = =0ATo: "Kozuch, Sebastian " =0ASent: Friday, Apr= il 24, 2009 2:02:53 AM=0ASubject: CCL: Computational Chemistry Wiki=0A=0A= =0ASent to CCL by: Brian Salter-Duke [brian.james.duke:-:gmail.com]=0ALukas= z Cwiklik cwiklik]^[gmail.com wrote:=0A> Sent to CCL by: Lukasz Cwiklik [cw= iklik..gmail.com]=0A> Dear Sebastian,=0A> I do not want to undermine your i= dea of a new wiki, however, this kind=0A> of wiki exist, it is simply in Wi= kipedia (see 'Computational=0A> Chemistry' article which covers a similar r= ange of topics:=0A> http://en.wikipedia.org/wiki/Computational_chemistry). = So maybe it=0A> would be better and easier to encourage CCL-ers to extend t= he existing=0A> Wikipedia articles in this topic. Also, the resulting infor= mation=0A> would be much more accessible for the general audience.=0A> Anyw= ay, your idea to convince people to write something in the wiki=0A> system = is very good.=0A> Best,=0A> Lukasz=0A> =0A=0AI word of caution about using = wikipedia for the purposes proposed by the original poster of this thread, = > from one of the people Henry referred to who tries to upgrade, improve and = protect the wikipedia articles on computational chemistry. Wipedia has its = own policies and guidelines. We are writing an encyclopis based on what oth= ers have said. Everything should be referenced. Original research is not al= lowed. So "new ones, which implies that the authors of those methods are we= lcomed to make self-publicity" is an absolute no-no. Anyone trying to do th= at, would experience serious grief, with the material being promptly remove= d by someone, possibly me.=0A=0AThere is also the science wiki, which was t= he original a computational chemistry wiki, as you can see from the URL it = still has. Here is the main QC entry point:-=0A=0Ahttp://www.compchemwiki.o= rg/index.php?title=3DQuantum_chemistry=0A=0AThe original purpose was rather= different from what is suggested here, as it was to collect together QC re= sults. It also not very active.=0A=0AI would encourage readers of CCL to he= lp maintain and develop the wikipedia pages, but I suggest you move in slow= ly and learn how the place works. One problem with the CC and QC articles i= s that are often dominated by physicists and become almost unintelligible t= o chemists. They need to cover both physics and chemistry viewpoints. I som= etimes give up on these articles and edit something completely different as= a break from CC. I am happy to assist anyone. I am User:Bduke on wikipedia= .=0A=0ABrian.=0A=0A=0A=0A-=3D This is automatically added to each message b= y the mailing script =3D-=0ATo recover the email address of the author of t= he message, please change=0Athe strange characters on the top line to the %= sign. You can also=0A= =0A=0A=0A=C2=A0 =C2=A0 http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: = CHEMISTRY-REQUEST%ccl.net or use=0A=C2=A0 =C2=A0 http://www.ccl.net/cgi-bin= /ccl/send_ccl_message=0A=0ASubscribe/Unsubscribe:=C2=A0 =C2=A0 =C2=A0 http:= //www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait tim= e at: http://www.ccl.net=0A=0AConferences: htt= p://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Message= s: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bou= nces from CCL with 5.7.1 error, check:=0A=C2=A0 =C2=A0 http://www.ccl.net/s= pammers.txt=0A=0A= =0A=0A=0A --0-893187826-1240564973=:64364 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A
=0A

The idea of a specific computational chemistry wik= i is not to undermine or compete with Wikipedia. The idea is to complement Wikipedia, blogs, book= s and papers. Wikipedia is extremely helpful, and if I had the knowledge I = would have loved to contribute there. More than that, as far as I=E2=80=99m= concerned if you look for something basic like DFT in the new wiki there s= hould be only a reference to the entry in Wikipedia.

=0A

But I cannot expec= t Wikipedia to have a specific entry on, let=E2=80=99s say, BP86 or UFF. Ne= ither I suppose we can add there a table with the mean error of the differe= nt post-HF geometry bond leng= ths, or a list of the programs that can run M06. But most of all, I= =E2=80=99d like an up to date encyclopedia where if I search for =E2=80=9CM= P4=E2=80=9D it won=E2=80=99t appear with a multimedia player.

=0A

And, as B= rian says, Wikipedia is not for self-publicity, and most of the new methods= that appear in computational chemistry cannot enter there unless they are = really fundamental methods. This takes years, and leave most methods outsid= e.

=0A

Again, for those that are real specialists on traditional methods, = I encourage them to write in Wikipedia. But all the information that can be= useful only for computational chemists, I encourage to put it in this spec= ific wiki.

=0A

Take into account that the same people of Wikipedia support = the creation of specific encyclopedias for specific communities.

=0A

Again= , if you like the idea and want to contribute, the page is

=0A

 

= =0A

http://computationalchemistry.wikia.com=


Maybe it will work, maybe not. But for sure it's worth to try it.=0A
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch....= .......
xx= xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
...The Lise Meitner-Minerva Center...
.for Computational Qu= antum Chemistry.
...Hebrew University of Jerusalem....
.....kozuchs%yfaat.ch.huji.ac.il.....
http://yfaat.ch.huji.a= c.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx=0A

=0A=
<= BR>=0A
=0A
=0AFrom: Brian Salter-Duke brian.james.duke---gmail.= com <owner-chemistry%ccl.net>
To: "Kozuch, Sebastian " <kozuchs%yahoo.com>
<= B>Sent: Friday, April 24, 2009= 2:02:53 AM
Subject: CCL= : Computational Chemistry Wiki


Sent to CCL by: Brian Salt= er-Duke [brian.james.duke:-:g= mail.com]
Lukasz Cwiklik cwiklik]^[gmail.com wrote:
> Sent to = CCL by: Lukasz Cwiklik [cwiklik..gmail.com]
> Dear Sebastian,
>= I do not want to undermine your idea of a new wiki, however, this kind
= > of wiki exist, it is simply in Wikipedia (see 'Computational
> C= hemistry' article which covers a similar range of topics:
> http://en= .wikipedia.org/wiki/Computational_chemistry). So maybe it
> would be better and easier to encourage CCL-ers to extend the e= xisting
> Wikipedia articles in this topic. Also, the resulting infor= mation
> would be much more accessible for the general audience.
&= gt; Anyway, your idea to convince people to write something in the wiki
= > system is very good.
> Best,
> Lukasz
>

I wo= rd of caution about using wikipedia for the purposes proposed by the origin= al poster of this thread, from one of the people Henry referred to who trie= s to upgrade, improve and protect the wikipedia articles on computational c= hemistry. Wipedia has its own policies and guidelines. We are writing an en= cyclopis based on what others have said. Everything should be referenced. O= riginal research is not allowed. So "new ones, which implies that the autho= rs of those methods are welcomed to make self-publicity" is an absolute no-= no. Anyone trying to do that, would experience serious grief, with the material being promptly removed by someone, possibly me.

There = is also the science wiki, which was the original a computational chemistry = wiki, as you can see from the URL it still has. Here is the main QC entry p= oint:-

http://www.compchemwiki.org/index.php?title=3DQuantum_chemist= ry

The original purpose was rather different from what is suggested = here, as it was to collect together QC results. It also not very active.
I would encourage readers of CCL to help maintain and develop the wiki= pedia pages, but I suggest you move in slowly and learn how the place works= . One problem with the CC and QC articles is that are often dominated by ph= ysicists and become almost unintelligible to chemists. They need to cover b= oth physics and chemistry viewpoints. I sometimes give up on these articles= and edit something completely different as a break from CC. I am happy to = assist anyone. I am User:Bduke on wikipedia.

Brian.



-=3D This is automatically added t= o each message by the mailing script =3D-
To recover the email address o= f the author of the message, please change
the strange characters on the= top line to the % sign. You can also
look up the X-Original-From: line = in the mail header.

E-mail to subscribers: CHEMISTRY%ccl.net or u= se:
   
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=0A=0A --0-893187826-1240564973=:64364-- From owner-chemistry@ccl.net Fri Apr 24 11:11:00 2009 From: "Tobias Kraemer tobiask * chem.gla.ac.uk" To: CCL Subject: CCL:G: Calculation of Redox Potentials Message-Id: <-39154-090424110834-11713-lojTyWBmB8MISMWxaLh6Ug{}server.ccl.net> X-Original-From: Tobias Kraemer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Fri, 24 Apr 2009 16:08:22 +0100 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobiask|chem.gla.ac.uk] Hi.... I'm trying to get experience in calculating some redox potentials of copper complexes to refer these data to experimental values. I have done a number of initial calculations on a test set of organometallic molecules, to get used to the method, using B3LYP/6-31G* and the default PCM model as implemented in Gaussian with methanol as solvent. As expected, deviations from experiment are big (in order of a few hundreds of millivolts). I also applied this protocol to the copper complexes I'm interested in and in a next step increased the basis set to TZVP for copper and ligating atoms, and SVP for remaining ligand atoms. I observed a big difference in the computed value for the redox potential, going from -0.12 (B3LYP/6-31G*) to +0.35 (B3LYP/TZVP). This is surely not so unexpected. There are significant changes in the solvation energy for the reduced form of the complex, Cu(I), whereas the solvation energy of the oxidised form, Cu(II), is uneffected. Also, significant changes in the relative energies of the structures in gas phase contribute to the change in the reduction potential. After reading some papers about the topic, I feel that the use of Jaguar for calculations of this type is preferred. This causes some difficulty in reproducing results, as I'm using Gaussian. So, in order to design some further test calculations, I would like to ask for some advise from people that have experience with this type of calculations using Gaussian and the solvent models therein. Maybe there is some further literature, which would help me as well, that report benchmark calculations using Gaussian. I would especially like to know, if it is advisable to do full optimisations in solvent, to improve the results, and which solvent models yield good results, although I'm aware, that this strongly depends on the system that is being investigated. Your comments are much appreciated. Thanks Tobi -- ____________________________________ dipl.-chem. tobias kraemer westCHEM, department of chemistry university of glasgow joseph black building university avenue glasgow G12 8QQ scotland, uk |phone| +44 (0)141 330 8121 |email| tobiask=chem.gla.ac.uk ____________________________________ From owner-chemistry@ccl.net Fri Apr 24 13:11:00 2009 From: "Andreas Bender, PhD Andreas.Bender*|*cantab.net" To: CCL Subject: CCL: Workshop Invitation: "Optimizing Drug Design", Leiden/NL, 20-23 July 2009 Message-Id: <-39155-090424130728-31542-sqxA6vpKClz7YEbSNPxprQ()server.ccl.net> X-Original-From: "Andreas Bender, PhD" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 24 Apr 2009 19:07:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Andreas Bender, PhD" [Andreas.Bender]^[cantab.net] Dear All, I would like to invite you to our upcoming workshop in Leiden, The Netherlands, from 20-23 July 2009 entitled: "Optimizing Drug Design: Multicriteria Decision Making and Optimization in Drug Discovery and Cheminformatics" http://www.lorentzcenter.nl/lc/web/2009/359/info.php3?wsid=359 This workshop will take place at the Lorentz Center, an international visitors center of Leiden University and intends to promote discussions and foster scientific collaborations. The number of long talks is therefore reduced to a minimum, leaving space for extended debates and constructive discussions. In order to enable participation of as many interested scientists as possible there is no registration fee for the workshop. Also, we can offer 10 travel grants for master's/PhD students and postdocs - please just reply directly to me if you are interested in one of the grants. We will have both oral and poster presentations at the workshop and proceedings of the accepted contributions are planned to be published in the series "Lecture Notes in Bioinformatics". If you intend to present your result at the workshop, please send an abstract to me directly (until the end of May). For further information and registration details please see the workshop website at this address: http://www.lorentzcenter.nl/lc/web/2009/359/info.php3?wsid=359 Best wishes and hoping to see you in The Netherlands! Cheers, Andreas -- Andreas Bender, PhD, Assistant Professor for Cheminformatics Leiden / Amsterdam Center for Drug Research Pharma-IT Platform: http://www.PHARMA-IT.net Division of Medicinal Chemistry: http://www.medchem.leidenuniv.nl Personal Homepage: http://www.andreasbender.de From owner-chemistry@ccl.net Fri Apr 24 14:52:01 2009 From: "Iain Moal Iain.Moal]_[cancer.org.uk" To: CCL Subject: CCL:G: Making movies from molecular vibrations easily Message-Id: <-39156-090424074647-25679-lr/tBxSHL0tZUUqLF7Jzfw[A]server.ccl.net> X-Original-From: "Iain Moal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C9C4C9.AB93243B" Date: Fri, 24 Apr 2009 11:44:40 +0100 MIME-Version: 1.0 Sent to CCL by: "Iain Moal" [Iain.Moal~!~cancer.org.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01C9C4C9.AB93243B Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I=20use=20VMD=20to=20generate=20movies=20of=20molecular=20vibrations.=20=20= First,=20I=20generate=20the=20trajectory=20in=20pdb=20format:=20example=20= http://www.bmm.icnet.uk/~moal01/example.pdb=20which=20I=20generated=20usin= g=20the=20original=20coordinates=20and=20a=20Hessian=20eigenvector. 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Regards, Iain -----Original=20Message----- > From:=20owner-chemistry+iain.moal=3D=3Dcancer.org.uk . ccl.net=20on=20behalf= =20of=20Duy=20Le=20ttduyle*_*gmail.com Sent:=20Thu=2023/04/2009=2020:25 To:=20Iain=20Moal Subject:=20CCL:G:=20Making=20movies=20from=20molecular=20vibrations=20easi= ly =20 Sent=20to=20CCL=20by:=20Duy=20Le=20[ttduyle]![gmail.com] Hello=20there, It=20will=20not=20be=20big=20headache=20if=20we=20just=20use=20simple=20wa= y: -=20make=20pictures=20for=20all=20frames=20we=20want=20to=20display=20in=20= movie -=20Use=20any=20gif=20maker=20or=20movie=20maker=20to=20create=20.GIF=20an= imation=20or=20Movie. *Gif=20maker: Excellent=20one=20http://linux.maruhn.com/sec/whirlgif.html Photoshop *Moviemaker: Simplest=20one=20WINDOWS=20MOVIE=20MAKER Other=20movie=20maker=20which=20can=20make=20movie=20from=20pictures. Regards, D. On=20Wed,=20Apr=2022,=202009=20at=209:13=20AM,=20richard=20apodaca rich_apodaca_._yahoo.com=20=20wrote: > >=20Sent=20to=20CCL=20by:=20richard=20apodaca=20[rich_apodaca=20_=20yahoo.= com] > > >=20Hello=20Thomas, > >=20This=20isn't=20really=20my=20area,=20but=20I=20ran=20across=20this:=20= "Easily=20Make=20a=20Movie=20with=20PyMOL": > >=20http://www.p212121.com/2009/03/24/easily-make-movie-pymol/ > >=20If=20it=20doesn't=20answer=20you=20question=20directly,=20it=20might=20= have=20some=20useful=20leads. > >=20Good=20luck, >=20Rich > >=20___________________________________ > >=20Richard=20L.=20Apodaca > >=20http://depth-first.com=20=A0=20=A0=20=A0Blog >=20http://metamolecular.com=20=A0=20=A0Company > > >=20---=20On=20Wed,=204/22/09,=20Sten=20Nilsson=20Lill=20stenil=20~=20chem= .gu.se=20=20wrote: > >>=20From:=20Sten=20Nilsson=20Lill=20stenil=20~=20chem.gu.se=20 >>=20Subject:=20CCL:G:=20Making=20movies=20from=20molecular=20vibrations=20= easily >>=20To:=20"Apodaca,=20Rich=20"=20 >>=20Date:=20Wednesday,=20April=2022,=202009,=201:59=20AM >> >>=20Sent=20to=20CCL=20by:=20"Sten=20Nilsson=20Lill"=20[stenil|*|chem.gu.s= e] >>=20Dear=20Thomas, >> >>=20Chemcraft=20has=20this=20feature=20and=20it=20works=20perfectly=20OK=20= to=20use >>=20it=20in=20e.g. >>=20PowerPoint=20presentations.=20It=20reads=20Gaussian=20frequency >>=20calculations,=20but >>=20not=20Turbomole=20calculations=20as=20far=20as=20I=20know. >> >>=20Please=20look=20at=20http://www.chemcraftprog.com/=20for=20the >>=20details. >> >>=20Hope=20it=20helps, >> >>=20Sten >> >> >>=20> >>=20>=20Sent=20to=20CCL=20by:=20"Dipl.-Ing.=20Thomas=20Mitterfellner" >>=20>=20[thomas.mitterfellner^^^tugraz.at] >>=20>=20Hello! >>=20> >>=20>=20I've=20been=20searching=20through=20the=20web=20and=20through=20t= he >>=20archives=20but=20I >>=20>=20couldn't=20find=20a=20decent=20solution=20for=20making=20a=20movi= e=20of >>=20a=20molecular >>=20>=20vibration=20one=20gets=20from=20a=20frequency=20calculation=20wit= h >>=20Gaussian=20or >>=20>=20Turbomole.=20While=20Gaussview,=20Molden,=20Molekel=20and=20Jmol >>=20(no=20imaginary >>=20>=20modes,=20as=20it=20seems!),=20are=20able=20to=20display=20the >>=20vibrations,=20there=20is=20no >>=20>=20easy=20option=20to=20create,=20say=20an=20animated=20GIF=20(with >>=20transparency!),=20or=20an >>=20>=20MPEG. >>=20>=20How=20do=20you=20go=20about=20animating=20molecular=20vibrations=20= for >>=20insertion=20into=20a >>=20>=20presentation?=20I'd=20appreciate=20any=20help=20(preferably,=20bu= t >>=20not=20limited=20to >>=20>=20linux/OSS=20solutions)! >>=20> >>=20>=20Thank=20you, >>=20> >>=20>=20Thomas> >>=20> >>=20> >> >> >>=20Ph.=20D.=20Sten=20Nilsson=20Lill >>=20Dep.=20of=20Chemistry >>=20University=20of=20Gothenburg >>=20Kemig=E5rden=204 >>=20S-412=2096=20G=F6teborg,=20Sweden >>=20Phone:=20+46-31-772=202873 >>=20Fax:=20+46-31-772=203840 >>=20E-mail:=20stenil[*]chem.gu.se >>=20Alternative=20e-mail:=20stenil[*]physto.se >> >> >> >>=20-=3D=20This=20is=20automatically=20added=20to=20each=20message=20by=20= the >>=20mailing=20script=20=3D- >>=20To=20recover=20the=20email=20address=20of=20the=20author=20of=20the=20= message, >>=20please=20change >>=20the=20strange=20characters=20on=20the=20top=20line=20to=20the=20_+_=20= sign.=20You >>=20can=20also > >> >>=20E-mail=20to=20subscribers:=20CHEMISTRY_+_ccl.net >>=20or=20use: >>=20=A0=20=A0=20=A0>> >>=20E-mail=20to=20administrators:=20CHEMISTRY-REQUEST_+_ccl.net >>=20or=20use >>=20=A0=20=A0=20=A0>> > >>=20=A0=20=A0=20=A0>> >> >> > > > >=20-=20This=20is=20automatically=20added=20to=20each=20message=20by=20the= =20mailing=20script=20->=20=A0=20=A0=20=A0http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message>=20=A0=20=A0=20=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_= message>=20=A0=20=A0=20=A0http://www.ccl.net/chemistry/sub_unsub.shtml>=20= =A0=20=A0=20=A0http://www.ccl.net/spammers.txt> > > --=20 Men=20don't=20need=20hands=20to=20do=20things! -=3Dhis=20is=20automatically=20added=20to=20each=20message=20by=20the=20ma= iling=20script=20=3D To=20recover=20the=20email=20address=20of=20the=20author=20of=20the=20mess= age,=20please=20change the=20strange=20characters=20on=20the=20top=20line=20to=20the=20 . =20sign.=20= You=20can=20also look=20up=20the=20X-Original-From:=20line=20in=20the=20mail=20header. E-mail=20to=20subscribers:=20CHEMISTRY . ccl.net=20or=20use: =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail=20to=20administrators:=20CHEMISTRY-REQUEST . ccl.net=20or=20use =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=20 =20=20=20=20=20=20http://www.ccl.net/chemistry/sub_unsub.shtml Before=20posting,=20check=20wait=20time=20at:=20http://www.ccl.net Job:=20http://www.ccl.net/jobs=20 Conferences:=20http://server.ccl.net/chemistry/announcements/conferences/ Search=20Messages:=20http://www.ccl.net/chemistry/searchccl/index.shtml If=20your=20mail=20bounces=20from=20CCL=20with=205.7.1=20error,=20check: =20=20=20=20=20=20http://www.ccl.net/spammers.txt RTFI:=20http://www.ccl.net/chemistry/aboutccl/instructions/ This=20communication=20is=20from=20Cancer=20Research=20UK.=20Our=20website= =20is=20at=20www.cancerresearchuk.org.=20We=20are=20a=20charity=20register= ed=20under=20number=201089464=20and=20a=20company=20limited=20by=20guarant= ee=20registered=20in=20England=20&=20Wales=20under=20number=204325234.=20O= ur=20registered=20address=20is=2061=20Lincoln's=20Inn=20Fields,=20London=20= WC2A=203PX.=20Our=20central=20telephone=20number=20is=20020=207242=200200.= =20 This=20communication=20and=20any=20attachments=20contain=20information=20w= hich=20is=20confidential=20and=20may=20also=20be=20privileged.=20=20=20It=20= is=20for=20the=20exclusive=20use=20of=20the=20intended=20recipient(s).=20=20= If=20you=20are=20not=20the=20intended=20recipient(s)=20please=20note=20tha= t=20any=20form=20of=20disclosure,=20distribution,=20copying=20or=20use=20o= f=20this=20communication=20or=20the=20information=20in=20it=20or=20in=20an= y=20attachments=20is=20strictly=20prohibited=20and=20may=20be=20unlawful.=20= =20If=20you=20have=20received=20this=20communication=20in=20error,=20pleas= e=20notify=20the=20sender=20and=20delete=20the=20email=20and=20destroy=20a= ny=20copies=20of=20it. =20 E-mail=20communications=20cannot=20be=20guaranteed=20to=20be=20secure=20or= =20error=20free,=20as=20information=20could=20be=20intercepted,=20corrupte= d,=20amended,=20lost,=20destroyed,=20arrive=20late=20or=20incomplete,=20or= =20contain=20viruses.=20=20We=20do=20not=20accept=20liability=20for=20any=20= such=20matters=20or=20their=20consequences.=20=20Anyone=20who=20communicat= es=20with=20us=20by=20e-mail=20is=20taken=20to=20accept=20the=20risks=20in= =20doing=20so. ------_=_NextPart_001_01C9C4C9.AB93243B-- From owner-chemistry@ccl.net Fri Apr 24 15:28:01 2009 From: "tamer sabry el-shazly t_sabry2005]^[hotmail.com" To: CCL Subject: CCL:G: help needed Message-Id: <-39157-090424103301-8440-W/7UtOzAn43SQzrG96a+0Q++server.ccl.net> X-Original-From: "tamer sabry el-shazly" Date: Fri, 24 Apr 2009 10:32:57 -0400 Sent to CCL by: "tamer sabry el-shazly" [t_sabry2005|-|hotmail.com] dear sir. kindly to help me by answer the following; 1- how can i overcome the abnormal termination of gaussian calculation with G03W\11002exe and 15002exe 2- in spite of presence key word freq in my route input the frequencies not calculated, only optimize the structures without calculating the frequencies , how can i overcome this problem Thanks so much to help recent computational chemist tamer sabry t_sabry2005[A]hotmail.com From owner-chemistry@ccl.net Fri Apr 24 22:38:00 2009 From: "Vincent Xianlong Wang xloongw:-:yahoo.com" To: CCL Subject: CCL:G: Calculation of Redox Potentials Message-Id: <-39158-090424223131-24445-vOmPpP6GxNqDAzwcAwuqhw,+,server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: text/plain; charset=us-ascii Date: Fri, 24 Apr 2009 19:31:18 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw---yahoo.com] Hi Tobias, Is the BSSE (basis set superposition error) relevant to the big deviation you observed? Have you done the correction to check if the results change? Vincent ----- Original Message ---- > From: Tobias Kraemer tobiask * chem.gla.ac.uk To: "Wang, Xianlong " Sent: Friday, April 24, 2009 11:08:22 PM Subject: CCL:G: Calculation of Redox Potentials Sent to CCL by: Tobias Kraemer [tobiask|chem.gla.ac.uk] Hi.... I'm trying to get experience in calculating some redox potentials of copper complexes to refer these data to experimental values. I have done a number of initial calculations on a test set of organometallic molecules, to get used to the method, using B3LYP/6-31G* and the default PCM model as implemented in Gaussian with methanol as solvent. As expected, deviations from experiment are big (in order of a few hundreds of millivolts). I also applied this protocol to the copper complexes I'm interested in and in a next step increased the basis set to TZVP for copper and ligating atoms, and SVP for remaining ligand atoms. I observed a big difference in the computed value for the redox potential, going from -0.12 (B3LYP/6-31G*) to +0.35 (B3LYP/TZVP). This is surely not so unexpected. There are significant changes in the solvation energy for the reduced form of the complex, Cu(I), whereas the solvation energy of the oxidised form, Cu(II), is uneffected. Also, significant changes in the relative energies of the structures in gas phase contribute to the change in the reduction potential. After reading some papers about the topic, I feel that the use of Jaguar for calculations of this type is preferred. This causes some difficulty in reproducing results, as I'm using Gaussian. So, in order to design some further test calculations, I would like to ask for some advise from people that have experience with this type of calculations using Gaussian and the solvent models therein. Maybe there is some further literature, which would help me as well, that report benchmark calculations using Gaussian. I would especially like to know, if it is advisable to do full optimisations in solvent, to improve the results, and which solvent models yield good results, although I'm aware, that this strongly depends on the system that is being investigated. Your comments are much appreciated. Thanks Tobi -- ____________________________________ dipl.-chem. tobias kraemer westCHEM, department of chemistry university of glasgow joseph black building university avenue glasgow G12 8QQ scotland, uk |phone| +44 (0)141 330 8121 |email| tobiask###chem.gla.ac.uk ____________________________________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 Apr 24 23:24:01 2009 From: "Aleksey Kuznetsov AlexKuznetsov2007]~[yandex.ru" To: CCL Subject: CCL: GAMESS: 'PWRT: NODE 0 ENCOUNTERED I/O ERROR WRITING UNIT 24' Error Message-Id: <-39159-090424231312-11852-gJKokDZHWSap5rm98+rrIw ~ server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sat, 25 Apr 2009 06:26:50 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007||yandex.ru] Dear CCL Users, I try to perform single-point calculation using GAMESS on polyoxometalate system containing Ru, W, Si, O and H atoms; here is the beginning of my input file: $contrl scftyp=rhf runtyp=morokuma icharg=-4 mult=1 coord=cart pp=sbkjc units=angs $end $system timlim=2700 mwords=1000 $end $basis gbasis=SBKJC $end $guess guess=huckel $end $scf conv=6 $end $morokm iatm(1)=14 $end $data Ru2H2O2-POM, 1A . . . . The calculation terminates after a few minutes at the step of 2e integrals calculation, giving the following error message: PWRT: NODE 0 ENCOUNTERED I/O ERROR WRITING UNIT 24 EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Fri Apr 24 14:27:50 2009 1193199 WORDS OF DYNAMIC MEMORY USED ON NODE 0, STEP CPU TIME = 306.06 TOTAL CPU TIME = 306.1 ( 5.1 MIN) TOTAL WALL CLOCK TIME= 588.0 SECONDS, CPU UTILIZATION IS 52.06% A fatal error occurred on DDI Process 0. ddikick.x: application process 0 quit unexpectedly. ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). Can anybody please explain me what the reason of this error could be and how to cope with it? I use GAMESS 2006 at Linux machine. Thank you very much! With best regards, Aleksey. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets,+,euch4e.chem.emory.edu -------------------------------------------