From owner-chemistry@ccl.net Thu Dec 13 03:22:00 2007 From: "etamar|fh.huji.ac.il" To: CCL Subject: CCL: NBO default structure Message-Id: <-35832-071213031941-19992-UBH7XGzTCl+f5jSnjyxM3Q%%server.ccl.net> X-Original-From: etamar a fh.huji.ac.il Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Thu, 13 Dec 2007 10:21:54 +0200 MIME-Version: 1.0 Sent to CCL by: etamar###fh.huji.ac.il Dear All I wonder if the default structure of an NBO analysis is always the lowest one in energy. Is it possible to choose a different structure which will be lower in energy? and if so- what is the energetic meaning of the default structure? thank you Tamar ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Thu Dec 13 04:29:01 2007 From: "Giuseppina Gini gini!A!elet.polimi.it" To: CCL Subject: CCL: origin of ab initio Message-Id: <-35833-071212134536-15579-FDAHXLtQDd1FvdKyLJQ18A.:.server.ccl.net> X-Original-From: Giuseppina Gini Content-Type: multipart/alternative; boundary="============_-1014640394==_ma============" Date: Wed, 12 Dec 2007 18:55:00 +0100 Mime-Version: 1.0 Sent to CCL by: Giuseppina Gini [gini~!~elet.polimi.it] --============_-1014640394==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" good! there are a lot of possible meanings for expressions in foreign languages. For instance some people says that "nano" is a greek prefix that means "a lot of money from Washington" regards >Actually, Lou Allinger of Molecular Mechanics fame claims that "ab initio" >is a Latin term that means "very expensive." > >Cheers, > >John McKelvey > > >On Dec 12, 2007 4:30 AM, Christoph Etzlstorfer christoph.etzlstorfer >. jku.at ><owner-chemistry]![ccl.net> wrote: > >There is a story about that in Michael J.S. Dewars biography "A >semiempirical life", American Chemical Society, 1992, p. 129. > >Best regards > >Christoph > > >Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ >chemistry.gatech.edu: > >> >Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . >chemistry.gatech.edu] >Dear CCLers; >I would appreciate it if anyone could tell me who used the term of "ab initio >calculations" first. >Thank you very much for your kind attention. > >Best wishes, > >Tommy > > >-- >Tommy Ohyun Kwon, Ph.D >School of Chemistry and Biochemistry >Georgia Institute of Technology >Atlanta Georgia, 30332 >Email: ohyun.kwon]*[chemistry.gatech.edu > > > >the strange characters on the top line to the ,+, sign. You can also > >E-mail to subscribers: CHEMISTRY,+,ccl.net or use: > >http://www.ccl.net/cgi-bin/ccl/send_ccl_message > >E-mail to administrators: >CHEMISTRY-REQUEST,+,ccl.net or >use > >http://www.ccl.net/chemistry/sub_unsub.shtml > >Before posting, check wait time at: http://www.ccl.net > >Job: http://www.ccl.net/jobs >Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > >Search Messages: http://www.ccl.net/htdig >(login: ccl, Password: search) > > http://www.ccl.net/spammers.txt > >RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > > >#################################################### > > www.etzlstorfer.com >*********************************************************** >Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 >Universitaet Linz Fax: *43-732-2468-8747 >A-4040 Linz E-mail: > >christoph.etzlstorfer,+,jku.at >Austria > http://www.orc.uni-linz.ac.at >#################################################### -- - - - - Giuseppina C. Gini DEI, Politecnico di Milano piazza L. da Vinci 32, I-20133 MILANO fax: (+39) 02-2399.3411 phone: (+39) 02-2399.3626 e-mail: gini(!)elet.polimi.it page: http://www.dei.polimi.it/people/gini --============_-1014640394==_ma============ Content-Type: text/html; charset="us-ascii" Re: CCL: origin of ab initio
good!
there are a lot of possible meanings for expressions in foreign languages. For instance some people says that  "nano" is a greek prefix that means "a lot of money from Washington"

regards



Actually, Lou Allinger of Molecular Mechanics fame claims that "ab initio"
is a Latin term that means "very expensive."

Cheers,

John McKelvey


On Dec 12, 2007 4:30 AM, Christoph Etzlstorfer christoph.etzlstorfer . jku.at <owner-chemistry]![ccl.net> wrote:
There is a story about that in Michael J.S. Dewars biography "A semiempirical life", American Chemical Society, 1992, p. 129.

Best regards

Christoph


Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ chemistry.gatech.edu:


Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . chemistry.gatech.edu]
Dear CCLers;
I would appreciate it if anyone could tell me who used the term of "ab initio
calculations" first.
Thank you very much for your kind attention.

Best wishes,

Tommy


--
Tommy Ohyun Kwon, Ph.D
School of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta Georgia, 30332
Email: ohyun.kwon]*[chemistry.gatech.edu



the strange characters on the top line to the ,+, sign. You can also

E-mail to subscribers: CHEMISTRY,+,ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net or use
     

Subscribe/Unsubscribe:
      http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)

      http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



####################################################
                                 www.etzlstorfer.com
***********************************************************
Dr. Christoph Etzlstorfer       Phone:  *43-732-2468-8750
Universitaet Linz              Fax:    *43-732-2468-8747
A-4040 Linz               E-mail: christoph.etzlstorfer,+,jku.at
Austria                   http://www.orc.uni-linz.ac.at
####################################################


--
- - - -
Giuseppina C. Gini
    DEI, Politecnico di Milano
    piazza L. da Vinci 32, I-20133 MILANO
fax:   (+39) 02-2399.3411
phone: (+39) 02-2399.3626
e-mail: gini(!)elet.polimi.it
page:  http://www.dei.polimi.it/people/gini

--============_-1014640394==_ma============-- From owner-chemistry@ccl.net Thu Dec 13 05:51:01 2007 From: "Barabara Jagoda-Cwiklik barbara###fh.huji.ac.il" To: CCL Subject: CCL:G: Convergence failure -- run terminated Message-Id: <-35834-071213045803-30336-PDFeIg+A/R0l5puyy2AnmA,,server.ccl.net> X-Original-From: "Barabara Jagoda-Cwiklik" Content-Type: multipart/alternative; boundary="----=_Part_36044_1610018.1197536537075" Date: Thu, 13 Dec 2007 11:02:17 +0200 MIME-Version: 1.0 Sent to CCL by: "Barabara Jagoda-Cwiklik" [barbara . fh.huji.ac.il] ------=_Part_36044_1610018.1197536537075 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline On Dec 13, 2007 12:50 AM, saif ullah sullah * ruc.dk < owner-chemistry|a|ccl.net> wrote: > Sent to CCL by: "saif ullah" [sullah[a]ruc.dk] > Hi All, > First I would like to introduce my self. My name is Saifullah and > I am a new subscriber to CCL and also just new one to computational > business. I am trying to optimized z-matrix for a part of protein using > gaussian 03. My input job is going stuck with the following termination > message. > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7513, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in /net/node0/g03/l502.exe > Hi Saifullah, You can try to search the CCL archive because the problem was widely discussed here and it's very likely that all the answers are already here... For instance take a look at: http://server.ccl.net/chemistry/resources/messages/2002/10/16.005-dir/index.html http://www.ccl.net/chemistry/resources/messages/2006/01/18.016-dir/index.html Best, Basia -- Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara|a|fh.huji.ac.il ------=_Part_36044_1610018.1197536537075 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline On Dec 13, 2007 12:50 AM, saif ullah sullah * ruc.dk <owner-chemistry|a|ccl.net> wrote:
Sent to CCL by: "saif  ullah" [sullah[a]ruc.dk]
Hi All,
        First I would like to introduce my self. My name is Saifullah and I am a new subscriber to CCL and also just new one to computational business. I am trying to optimized z-matrix for a part of protein using gaussian 03. My input job  is going stuck with the following termination message.
Annihilation of the first spin contaminant:
 S**2 before annihilation     0.7513,   after     0.7500
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /net/node0/g03/l502.exe

Hi Saifullah,

You can try to search the CCL archive because the problem was widely discussed here and it's very likely that all the answers are already here...
For instance take a look at:
http://server.ccl.net/chemistry/resources/messages/2002/10/16.005-dir/index.html
http://www.ccl.net/chemistry/resources/messages/2006/01/18.016-dir/index.html

Best,
Basia

--
Barbara Jagoda-Cwiklik, Ph.D
The Fritz Haber Research Center for Molecular Dynamics
Institute of Chemistry
The Hebrew University of Jerusalem
Jerusalem, ISRAEL
e-mail: barbara|a|fh.huji.ac.il ------=_Part_36044_1610018.1197536537075-- From owner-chemistry@ccl.net Thu Dec 13 05:52:01 2007 From: "Herbert Fruchtl herbert.fruchtl[a]st-andrews.ac.uk" To: CCL Subject: CCL:G: Convergence failure -- run terminated Message-Id: <-35835-071213051204-4316-KfWDD30Xx/DNBQNADrfKhA.@.server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Dec 2007 10:11:32 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl|a|st-andrews.ac.uk] Please don't post complete output files here. A few thousand people get it into their mailbox. A few lines before the actual error message together with some information on the type of calculation are usually enough. Your SCF doesn't converge. Since it is a geometry optimization and it converged in previous steps, it is probably not due to an unreasonable geometry. Try SCF=XQC. This should switch to a more reliable (but slower) convergence mechanism if necessary. Is there a reason for using opt=z-matrix? The default redundant internal coordinates are nearly always better. Herbert saif ullah sullah * ruc.dk wrote: > Sent to CCL by: "saif ullah" [sullah[a]ruc.dk] > Hi All, > First I would like to introduce my self. My name is Saifullah and I am a new subscriber to CCL and also just new one to computational business. I am trying to optimized z-matrix for a part of protein using gaussian 03. My input job is going stuck with the following termination message. > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7513, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in /net/node0/g03/l502.exe at Thu Dec 6 19:12:21 2007. > > Please have a look on the out put file > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Thu Dec 13 08:20:00 2007 From: "Sergio Emanuel Galembeck segalemb^^^usp.br" To: CCL Subject: CCL: NBO default structure Message-Id: <-35836-071213074217-19144-Po7VVrXiOm/fIOnJYe5r7w() server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Thu, 13 Dec 2007 10:41:37 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb/a\usp.br] Dear Tamar, You can choose a different structure using the $choose block. I am not sure about the energetic meaning of the resonance structure choosen by NBO. Best regards, S=C3=A9rgio Citando "etamar|fh.huji.ac.il" : > > Sent to CCL by: etamar###fh.huji.ac.il > Dear All > I wonder if the default structure of an NBO analysis is always > the lowest one in energy. > Is it possible to choose a different structure which will be lower in ener= gy? > and if so- what is the energetic meaning of the default structure? > thank you > Tamar > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > -=3D This is automatically added to each message by the mailing script =3D= -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Thu Dec 13 08:54:01 2007 From: "Rene Fournier renef++yorku.ca" To: CCL Subject: CCL: origin of ab initio/basis set empiricism Message-Id: <-35837-071213083951-32499-NoAsCqW8t55DWgUTMe1OYg:server.ccl.net> X-Original-From: Rene Fournier Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 13 Dec 2007 08:39:36 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Rene Fournier [renef(a)yorku.ca] Hello, I agree on >All commonly used basis >sets, even the Pople-style sets, are generated by optimizing >exponents and contraction coefficients to minimize (ab initio) >energies of atoms and sometimes molecules. That's correct. But there are other problems with choices of basis sets and that's where empiricism can creep in. How many contracted functions is enough? What's the best contraction pattern? (why 6-31G and not 6-21G? or 4-31G? or 9-61G? or 7-1111G?) How many polarization functions? Why not throw in a few bond-centered functions? Many basis sets went into oblivion not because they gave higher energies for atoms or molecules --- adding more functions and keeping them uncontracted always lowers energy. It's that they did not give good agreement with experimental bond lengths, bond energies etc. relative to other basis sets of comparable computational cost. I'm not sure how to call methods where high-level theory is used instead of experiment as the reference to assess goodness of a lower level of theory (maybe a smaller basis). I think it's still empirical because there's the assumption that if the low-level theory reproduces high-level theory to within some accuracy for cases X, Y, Z, it will also reproduce high-level level theory to that accuracy for other cases when we do applications. ( There's also the obvious point that if the high-level theory reference is really, really good, then it IS the experimental result! ) It is possible to take empiricism out of basis set choice by doing many calculations in a sequence with increasingly big basis sets defined by only 1 and maybe 2 parameters, so that one can crank up accuracy smoothly, and extrapolate results to "infinite basis set". Basis sets suitable for that are: - even-tempered fully uncontracted basis sets (K Ruedenberg); - plane-waves (increase energy cut-off and box size); - all-numerical programs (mostly for diatomics, Becke's NUMOL for polyatomics). But I don't see that done very often, even with plane-waves where it would be easy I suppose. Regards, Rene Rene Fournier Office: 303 Petrie Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 4700 Keele Street, Toronto FAX: (416)-736-5936 Ontario, CANADA M3J 1P3 e-mail: renef:+:yorku.ca On Wed, 12 Dec 2007, Kirk Peterson kipeters-*-wsu.edu wrote: > > Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu] > > As a sidebar to this discussion, I have to strongly disagree that > basis set parameters, exponents or contraction coefficients, > use empirical data in their construction. All commonly used basis > sets, even the Pople-style sets, are generated by optimizing > exponents and contraction coefficients to minimize (ab initio) > energies of atoms and sometimes molecules. Some of the Pople-style > basis sets utilize scale factors to apply to atom-optimized exponents, > but these were based on (ab initio) molecular calculations > and not experimental data. > > regards, > > -Kirk > > On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: > > > > > Sent to CCL by: Rene Fournier [renef\a/yorku.ca] > > David Craig and Robert Parr first used "ab initio" in quantum > > chemistry, > > see > > http://www.quantum-chemistry-history.com/Parr1.htm > > Near the middle of that page, Parr recounts: > > > > " Craig and I published this paper on "configuration interaction in > > benzene", where we took the pi-system and did essentially a complete > > configuration interaction calculation on it. > > > > That has some trivial historical interest in that it was there that > > the > > word, the term ab initio was introduced. Craig and Ross had computed > > everything from the start in London and I had personally computed > > everything from start in Pittsburgh. Then we compared our answers > > when we > > were finished- This involved computing of all the integrals as best as > > they could be done and selecting the configurations to mix for the > > ground > > and exited states because there were electronic states that were of > > experimental interest and we checked our answers one against each > > other > > when we were finished. And what the paper says is, that these > > calculations > > were done ab initio by Craig and Ross and by me, independently. And > > Mulliken later said that this was the introduction of the term ab > > initio > > into quantum chemistry. In the short review that you have, I talk > > about > > this and reproduce a picture of a letter from Craig to me where he > > uses > > the term ab initio in a different context. So ab initio was > > introduced in > > the quantum chemistry by Craig in a letter to me and I put it into the > > manuscript. That's where ab initio came from. " > > > > > > Funny thing is Parr later became a champion of Density Functional > > Theory > > and for many years (70's, 80's) DFT practitioners were often > > criticized > > for doing calculations that were not "ab initio". I think views have > > changed now; "first-principles" was introduced probably to say > > "mostly > > not empirical" but without the implications "ab initio" had acquired > > over > > the years. The term "ab initio calculation", as it's commonly used, > > very rarely refers to a calculation "devoid of empiricism", for > > example > > the choice of basis set parameters is almost always empirical, > > see discussion on > > http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html > > > > Rene Fournier Office: 303 Petrie > > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > > 4700 Keele Street, Toronto FAX: (416)-736-5936 > > Ontario, CANADA M3J 1P3 e-mail: renef*_*yorku.ca > > > > > > On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer . > > jku.at wrote: > > > >> There is a story about that in Michael J.S. Dewars biography "A > >> semiempirical life", American Chemical Society, 1992, p. 129. > >> > >> Best regards > >> > >> Christoph > >> > >> > >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ > >> chemistry.gatech.edu: > >> > >>> > >>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . chemistry.gatech.edu] > >>> Dear CCLers; > >>> I would appreciate it if anyone could tell me who used the term of > >>> "ab initio > >>> calculations" first. > >>> Thank you very much for your kind attention. > >>> > >>> Best wishes, > >>> > >>> Tommy > >>> > >>> > >>> -- > >>> Tommy Ohyun Kwon, Ph.D > >>> School of Chemistry and Biochemistry > >>> Georgia Institute of Technology > >>> Atlanta Georgia, 30332 > >>> Email: ohyun.kwon]*[chemistry.gatech.edu > >>> > >>> > >>> > >>> -= This is automatically added to each message by the mailing > >>> script =- > >>> To recover the email address of the author of the message, please > >>> change> Conferences: http://server.ccl.net/chemistry/announcements/ > >>> conferences/ > >>> > >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >>> search)> > >>> > >> > >> #################################################### > >> www.etzlstorfer.com > >> *********************************************************** > >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 > >> Universitaet Linz Fax: *43-732-2468-8747 > >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at > >> Austria http://www.orc.uni-linz.ac.at > >> #################################################### > >> > >> > >> > >> > >> > > > > > > > > -= This is automatically added to each message by the mailing script > > =- > > To recover the email address of the author of the message, please > > change> Conferences: http://server.ccl.net/chemistry/announcements/ > > conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > From owner-chemistry@ccl.net Thu Dec 13 09:45:01 2007 From: "Demetrios Xenides Demetrios.Xenides%%uop.gr" To: CCL Subject: CCL: origin of ab initio Message-Id: <-35838-071213081000-21891-IOI/R7i+6XsUv1C5c7RWSg ~~ server.ccl.net> X-Original-From: Demetrios Xenides Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Dec 2007 14:08:53 +0200 MIME-Version: 1.0 Sent to CCL by: Demetrios Xenides [Demetrios.Xenides:_:uop.gr] If this comment (..."nano" is a greek prefix that means "a lot of money > from Washington") is a joke then do no read the following. In case there are people saying without being jocking, here is the correcting meaning of "nano" from International Scientific Vocabulary, from Greek /nanos/= dwarf. On the other hand it might be true that with nano-* you might have more chances to get funding for your research, thus the reason for the (mis)use of the word. All the best, Demetrios Etymology: International Scientific Vocabulary, from Greek /nanos/ dwarf Giuseppina Gini gini!A!elet.polimi.it wrote: > good! > there are a lot of possible meanings for expressions in foreign > languages. For instance some people says that "nano" is a greek > prefix that means "a lot of money from Washington" > > regards > > > >> Actually, Lou Allinger of Molecular Mechanics fame claims that "ab >> initio" >> is a Latin term that means "very expensive." >> >> Cheers, >> >> John McKelvey >> >> >> On Dec 12, 2007 4:30 AM, Christoph Etzlstorfer christoph.etzlstorfer >> . jku.at > > wrote: >> >> There is a story about that in Michael J.S. Dewars biography "A >> semiempirical life", American Chemical Society, 1992, p. 129. >> >> >> Best regards >> >> >> Christoph >> >> >> >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ >> chemistry.gatech.edu : >> >> >>> >> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . >> chemistry.gatech.edu ] >> >> Dear CCLers; >> >> I would appreciate it if anyone could tell me who used the >> term of "ab initio >> >> calculations" first. >> >> Thank you very much for your kind attention. >> >> >> Best wishes, >> >> >> Tommy >> >> >> >> -- >> >> Tommy Ohyun Kwon, Ph.D >> >> School of Chemistry and Biochemistry >> >> Georgia Institute of Technology >> >> Atlanta Georgia, 30332 >> >> Email: ohyun.kwon]*[chemistry.gatech.edu >> >> >> >> >> >> the strange characters on the top line to the ,+, sign. You >> can also >> >> >> E-mail to subscribers: CHEMISTRY,+,ccl.net >> or use:>> >> >> E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net >> or use >> >> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search) > >> >> >> >> #################################################### >> >> www.etzlstorfer.com >> >> >> *********************************************************** >> >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 >> >> Universitaet Linz Fax: *43-732-2468-8747 >> >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at >> >> >> Austria http://www.orc.uni-linz.ac.at >> >> #################################################### >> > > > -- > > - - - - > *Giuseppina C. Gini > * DEI, Politecnico di Milano > piazza L. da Vinci 32, I-20133 MILANO > *fax:* (+39) 02-2399.3411 > *phone:* (+39) 02-2399.3626 > *e-mail:*_ gini---elet.polimi.it_ > *page:* http://www.dei.polimi.it/people/gini > From owner-chemistry@ccl.net Thu Dec 13 10:19:00 2007 From: "Schrodinger Announcements announce-x-schrodinger.com" To: CCL Subject: CCL: Schrodinger Spring 2008 User Symposium Message-Id: <-35839-071213092500-29416-yWtOyDdA+jwqrcRGcaCv2Q##server.ccl.net> X-Original-From: "Schrodinger Announcements" Date: Thu, 13 Dec 2007 09:24:56 -0500 Sent to CCL by: "Schrodinger Announcements" [announce=schrodinger.com] Schrodinger will hold its third annual Spring User Symposium on June 4th through 6th, 2008, in Portland, Oregon. The Symposium will consist of two full days of scientific presentations by users of Schrodinger software. In addition, there will also be opportunities for social networking, hands-on training, and previews into future product developments. You are invited to submit an abstract for either an oral or a poster presentation - all applicants whose abstracts are accepted for oral presentations will have their registration fees ($600 for the full Symposium) waived; and applicants with accepted posters will receive a 50% discount on the registration fees. Submissions should be e-mailed to conferences|a|schrodinger.com by January 15th, 2008. Please include a short bio, title, and abstract. The presentation should highlight either methods developments or scientific applications using Schrodinger software. Sincerely, Woody Sherman Director, Applications Science From owner-chemistry@ccl.net Thu Dec 13 10:54:01 2007 From: "Saif Ullah sullah-#-ruc.dk" To: CCL Subject: CCL: Convergence failure -- run terminated Message-Id: <-35840-071213095416-16620-+D1IAzVPPgWw3z0cvnJZMg###server.ccl.net> X-Original-From: Saif Ullah Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Dec 2007 15:01:48 +0100 MIME-Version: 1.0 Sent to CCL by: Saif Ullah [sullah||ruc.dk] Hi Kerwin, Thanks for useful suggestions.Yes, I am interested to optimize proton between formamide and amino residue. The system with charge neutral by removing one hydrogen from the Lysine sidechain, does work but I am also interested to optimize the geometry with charge on side chain amine of Lysine. I have set the charge to "1" and also multiplicity to "1", this input job is running at the moment. Saif Quoting Kerwin D Dobbs : > Sullah, > > I'm not a bio person, but it seems that you are looking at > the H-bond between formamide and a much larger molecule. > My guess is that this system should be charge neutral, and > all the electrons should be paired (closed-shell computation > rather than open-shell). Yet you have set the multiplicity > of the system to be a doublet: > > Symbolic Z-matrix: > Charge = 0 Multiplicity = 2 > ^^^ > If you want to see this calculation to completion, you need > to do 2 things. First, set the multiplicity to "1". Next, you > need to alter the structure of your "larger molecule" by > removing a hydrogen from the terminal amino group, i.e.: > > R-CH2-CH2-NH3 change to R-CH2-CH2-NH2 > > Now, if you truly mean for this amino group to have the extra > hydrogen, then the entire system must have a positive charge, > i.e., > > Symbolic Z-matrix: > Charge = 1 Multiplicity = 1 > > From my point-of-view, since you are doing a gas-phase > computation, then you should remove the extra hydrogen and > make the system neutral (Charge = 0). > > Kerwin > ======================================== > Kerwin Dobbs, Computational Chemist > DuPont CR&D > Information & Computing Technologies > Experimental Station, P O Box 80320 > Wilmington DE 19880-0320 > Kerwin.D.Dobbs%x%usa.dupont.com > http://www.linkedin.com/in/kerwindobbs > > This communication is for use by the intended recipient and contains > information that may be Privileged, confidential or copyrighted under > applicable law. If you are not the intended recipient, you are hereby > formally notified that any use, copying or distribution of this e-mail, > in whole or in part, is strictly prohibited. Please notify the sender by > return e-mail and delete this e-mail from your system. Unless explicitly > and conspicuously designated as "E-Contract Intended", this e-mail does > not constitute a contract offer, a contract amendment, or an acceptance > of a contract offer. This e-mail does not constitute a consent to the > use of sender's contact information for direct marketing purposes or for > transfers of data to third parties. > > Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean > > http://www.DuPont.com/corp/email_disclaimer.html > -- From owner-chemistry@ccl.net Thu Dec 13 11:29:01 2007 From: "Marcel Swart marcel.swart_._icrea.es" To: CCL Subject: CCL: origin of ab initio/basis set empiricism Message-Id: <-35841-071213095822-18483-rCtRnQMVaPkJxIugnlCAZQ()server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Thu, 13 Dec 2007 15:58:04 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Marcel Swart [marcel.swart-*-icrea.es] About the basis sets extrapolation, it is done, see for instance: Bak, J=F8rgensen, Olsen, Helgaker, Klopper J. Chem. Phys. 2000, 112, 9229-9242 On Dec 13, 2007, at 2:39 PM, Rene Fournier renef++yorku.ca wrote: > > Sent to CCL by: Rene Fournier [renef(a)yorku.ca] > Hello, > I agree on > >> All commonly used basis >> sets, even the Pople-style sets, are generated by optimizing >> exponents and contraction coefficients to minimize (ab initio) >> energies of atoms and sometimes molecules. > > That's correct. But there are other problems with choices of basis > sets and that's where empiricism can creep in. How many contracted > functions is enough? What's the best contraction pattern? > (why 6-31G and not 6-21G? or 4-31G? or 9-61G? or 7-1111G?) > How many polarization functions? Why not throw in a few bond-=20 > centered functions? > Many basis sets went into oblivion not because they gave higher =20 > energies > for atoms or molecules --- adding more functions and keeping them =20 > uncontracted > always lowers energy. It's that they did not give good agreement =20 > with experimental > bond lengths, bond energies etc. relative to other basis sets of =20 > comparable > computational cost. I'm not sure how to call methods where high-=20 > level theory > is used instead of experiment as the reference to assess goodness =20 > of a lower level > of theory (maybe a smaller basis). I think it's still empirical =20 > because there's > the assumption that if the low-level theory reproduces high-level =20 > theory to > within some accuracy for cases X, Y, Z, it will also reproduce high-=20= > level > level theory to that accuracy for other cases when we do applications. > ( There's also the obvious point that if the high-level theory =20 > reference is > really, really good, then it IS the experimental result! ) > It is possible to take empiricism out of basis set choice by doing > many calculations in a sequence with increasingly big basis sets =20 > defined > by only 1 and maybe 2 parameters, so that one can crank up accuracy =20= > smoothly, > and extrapolate results to "infinite basis set". Basis sets =20 > suitable for > that are: > - even-tempered fully uncontracted basis sets (K Ruedenberg); > - plane-waves (increase energy cut-off and box size); > - all-numerical programs (mostly for diatomics, Becke's NUMOL for =20 > polyatomics). > But I don't see that done very often, even with plane-waves where =20 > it would be > easy I suppose. > > Regards, > Rene > > Rene Fournier Office: 303 Petrie > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > 4700 Keele Street, Toronto FAX: (416)-736-5936 > Ontario, CANADA M3J 1P3 e-mail: renef---yorku.ca > > > > > On Wed, 12 Dec 2007, Kirk Peterson kipeters-*-wsu.edu wrote: > >> >> Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu] >> >> As a sidebar to this discussion, I have to strongly disagree that >> basis set parameters, exponents or contraction coefficients, >> use empirical data in their construction. All commonly used basis >> sets, even the Pople-style sets, are generated by optimizing >> exponents and contraction coefficients to minimize (ab initio) >> energies of atoms and sometimes molecules. Some of the Pople-style >> basis sets utilize scale factors to apply to atom-optimized =20 >> exponents, >> but these were based on (ab initio) molecular calculations >> and not experimental data. >> >> regards, >> >> -Kirk >> >> On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: >> >>> >>> Sent to CCL by: Rene Fournier [renef\a/yorku.ca] >>> David Craig and Robert Parr first used "ab initio" in quantum >>> chemistry, >>> see >>> http://www.quantum-chemistry-history.com/Parr1.htm >>> Near the middle of that page, Parr recounts: >>> >>> " Craig and I published this paper on "configuration interaction in >>> benzene", where we took the pi-system and did essentially a complete >>> configuration interaction calculation on it. >>> >>> That has some trivial historical interest in that it was there that >>> the >>> word, the term ab initio was introduced. Craig and Ross had computed >>> everything from the start in London and I had personally computed >>> everything from start in Pittsburgh. Then we compared our answers >>> when we >>> were finished- This involved computing of all the integrals as =20 >>> best as >>> they could be done and selecting the configurations to mix for the >>> ground >>> and exited states because there were electronic states that were of >>> experimental interest and we checked our answers one against each >>> other >>> when we were finished. And what the paper says is, that these >>> calculations >>> were done ab initio by Craig and Ross and by me, independently. And >>> Mulliken later said that this was the introduction of the term ab >>> initio >>> into quantum chemistry. In the short review that you have, I talk >>> about >>> this and reproduce a picture of a letter from Craig to me where he >>> uses >>> the term ab initio in a different context. So ab initio was >>> introduced in >>> the quantum chemistry by Craig in a letter to me and I put it =20 >>> into the >>> manuscript. That's where ab initio came from. " >>> >>> >>> Funny thing is Parr later became a champion of Density Functional >>> Theory >>> and for many years (70's, 80's) DFT practitioners were often >>> criticized >>> for doing calculations that were not "ab initio". I think views =20 >>> have >>> changed now; "first-principles" was introduced probably to say >>> "mostly >>> not empirical" but without the implications "ab initio" had acquired >>> over >>> the years. The term "ab initio calculation", as it's commonly used, >>> very rarely refers to a calculation "devoid of empiricism", for >>> example >>> the choice of basis set parameters is almost always empirical, >>> see discussion on >>> http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-=20 >>> dir/index.html >>> >>> Rene Fournier Office: 303 Petrie >>> Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 >>> 4700 Keele Street, Toronto FAX: (416)-736-5936 >>> Ontario, CANADA M3J 1P3 e-mail: renef*_*yorku.ca >>> >>> >>> On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer . >>> jku.at wrote: >>> >>>> There is a story about that in Michael J.S. Dewars biography "A >>>> semiempirical life", American Chemical Society, 1992, p. 129. >>>> >>>> Best regards >>>> >>>> Christoph >>>> >>>> >>>> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ >>>> chemistry.gatech.edu: >>>> >>>>> >>>>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . =20 >>>>> chemistry.gatech.edu] >>>>> Dear CCLers; >>>>> I would appreciate it if anyone could tell me who used the term of >>>>> "ab initio >>>>> calculations" first. >>>>> Thank you very much for your kind attention. >>>>> >>>>> Best wishes, >>>>> >>>>> Tommy >>>>> >>>>> >>>>> -- >>>>> Tommy Ohyun Kwon, Ph.D >>>>> School of Chemistry and Biochemistry >>>>> Georgia Institute of Technology >>>>> Atlanta Georgia, 30332 >>>>> Email: ohyun.kwon]*[chemistry.gatech.edu >>>>> >>>>> >>>>> >>>>> -=3D This is automatically added to each message by the mailing >>>>> script =3D- >>>>> To recover the email address of the author of the message, please >>>>> change> Conferences: http://server.ccl.net/chemistry/=20 >>>>> announcements/ >>>>> conferences/ >>>>> >>>>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>>>> search)> >>>>> >>>> >>>> #################################################### >>>> www.etzlstorfer.com >>>> *********************************************************** >>>> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 >>>> Universitaet Linz Fax: *43-732-2468-8747 >>>> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at >>>> Austria http://www.orc.uni-linz.ac.at >>>> #################################################### >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing = script >>> =3D- >>> To recover the email address of the author of the message, please >>> change> Conferences: http://server.ccl.net/chemistry/announcements/ >>> conferences/ >>> >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>> search)> >> >> > > > > -=3D This is automatically added to each message by the mailing =20 > script =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =20 > search)> > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart|-|icrea.es marcel.swart|-|udg.edu web http://www.icrea.es/pag.asp?id=3DMarcel.Swart http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Thu Dec 13 12:07:01 2007 From: "Sergio Emanuel Galembeck segalemb#usp.br" To: CCL Subject: CCL: Strange NBO DEL Calculation Results Message-Id: <-35842-071213102703-7283-F7JWvtaVvBygSrJ0Tcblwg##server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 13 Dec 2007 13:26:37 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb]*[usp.br] Hello, It's a good question: how does NBO choose a resonance structure? I sugges= t that we can ask Professor Weinhold. He is a kind person and always gives helpfull sugestions. Best regards, Sergio Galembeck Citando "Hemant Srivastava hemantkrsri,,gmail.com" = : > > Sent to CCL by: "Hemant Srivastava" [hemantkrsri*o*gmail.com] > Dear Friends, > > I am doing NBO Del calculations, the input file is as follows > > --------------------------------------------------------------------------= --------------------------------- > %chk=3Dc_cyc_6_reac_res1.chk > %mem=3D120MW > # HF/6-31g* scrf=3D(solvent=3Dwater,read,pcm) pop=3D(full,nbodel) > > choose resonance structure-1 > > 0 1 > X=09Y=09Z > > Radii=3DUAHF > > $NBO NBO $END > $Choose > LONE > a 1 > b 2 > end > BOND S 1 2 > =09S 3 5 > end > $END > $del nostar > $End > > --------------------------------------------------------------------------= ------------------------------------------- > > I have made four different resonance structure of the same molecule > and calculated deletion energies. Surprisingly I am getting the NBO > default resonance structure higher in deletion energy than two of the > structures I choose. Does anyone know if it make sense. Following is > the energy of deletions of all four resonance structures. > > Resonance Structure-1=09Energy of deletion : =09-1509.149678811 > Resonance Structure-2=09Energy of deletion :=09-1509.102611727 > Resonance Structure-3=09Energy of deletion : =09-1509.131159010 > Resonance Structure-4=09Energy of deletion : =09-1509.117304249 (Default = =20 > Structure) > > Thanks in advance > > Hemant Srivastava > The Hebrew University of Jerusalem > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Thu Dec 13 12:39:01 2007 From: "Maxim Kholin maxim.kholin!A!q-pharm.com" To: CCL Subject: CCL: New Accurate hERG Inhibition Prediction Software and Services Message-Id: <-35843-071213114559-3695-bEMRMVi0SUDaVAfW5ryP2g++server.ccl.net> X-Original-From: "Maxim Kholin" Date: Thu, 13 Dec 2007 11:45:55 -0500 Sent to CCL by: "Maxim Kholin" [maxim.kholin|q-pharm.com] Dear Colleagues, We invite you to explore new hERG inhibition prediction software and services, which allow you to predict from a molecule structures of compounds their inhibition constants (IC50) for hERG channels. Features: - hERG inhibition prediction is made by docking on Quantum Pharmaceuticals proprietary flexible 3D structure of hERG - No training sets or QSAR methods applied - Docking is based on quantum and molecular physics - Average correlation has RMSD=1.18 pIC50 unit, and correlation coefficient = 0.82 - Output is pIC50 values (-logIC50) for the molecules. The accuracy of prediction is 1.1 pIC50 units. - Easy to use, no special hardware requirements, both Linux/Windows supported - You can also request services based on QUANTUM hERG Screening Assays. Download QUANTUM hERG Screening Assays Brochure at http://www.leadfinding.com/pdf/herg_presentation.pdf Go to http://www.leadfinding.com/herg for DEMO right now. Get promotional price: just $9 k for annual license. Other Quantum Pharmaceuticals technologies: Small molecules drug discovery platform Antibody de novo design: optimization and humanization. ADME/TOX prediction and modeling Mechanism of action. Prediction and modeling More details at www.q-pharm.com Our contact details: Quantum Pharmaceuticals Tel. +7(495) 150 8332 Fax +7(495) 156 156 1 office,+,q-pharm.com www.q-pharm.com From owner-chemistry@ccl.net Thu Dec 13 13:16:01 2007 From: "Pablo Echenique echenique.p_-_gmail.com" To: CCL Subject: CCL: origin of ab initio Message-Id: <-35844-071213120131-14071-Xepe/52SZEji7/uTnHkX+A]=[server.ccl.net> X-Original-From: "Pablo Echenique" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 13 Dec 2007 16:57:27 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Echenique" [echenique.p-#-gmail.com] Oh, man, I cannot believe this. It is the second time. I could not have guessed that irony was so heterogenously distributed. Beware CCLers! Everything you say has high chances of being interpreted literally. :) On Dec 13, 2007 1:08 PM, Demetrios Xenides Demetrios.Xenides%%uop.gr wrote: > > Sent to CCL by: Demetrios Xenides [Demetrios.Xenides:_:uop.gr] > If this comment (..."nano" is a greek prefix that means "a lot of money > > from Washington") is a joke then do no read the following. In case ther= e > are people saying without being jocking, here is the correcting meaning > of "nano" from International Scientific Vocabulary, from Greek /nanos/=3D > dwarf. On the other hand it might be true that with nano-* you might > have more chances to get funding for your research, thus the reason for > the (mis)use of the word. > > All the best, > Demetrios > > Etymology: > International Scientific Vocabulary, from Greek /nanos/ dwarf > > > Giuseppina Gini gini!A!elet.polimi.it wrote: > > good! > > there are a lot of possible meanings for expressions in foreign > > languages. For instance some people says that "nano" is a greek > > prefix that means "a lot of money from Washington" > > > > regards > > > > > > > >> Actually, Lou Allinger of Molecular Mechanics fame claims that "ab > >> initio" > >> is a Latin term that means "very expensive." > >> > >> Cheers, > >> > >> John McKelvey > >> > >> > >> On Dec 12, 2007 4:30 AM, Christoph Etzlstorfer christoph.etzlstorfer > >> . jku.at >> > wrote: > >> > >> There is a story about that in Michael J.S. Dewars biography "A > >> semiempirical life", American Chemical Society, 1992, p. 129. > >> > >> > >> Best regards > >> > >> > >> Christoph > >> > >> > >> > >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ > >> chemistry.gatech.edu : > >> > >> > >>> > >> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . > >> chemistry.gatech.edu ] > >> > >> Dear CCLers; > >> > >> I would appreciate it if anyone could tell me who used the > >> term of "ab initio > >> > >> calculations" first. > >> > >> Thank you very much for your kind attention. > >> > >> > >> Best wishes, > >> > >> > >> Tommy > >> > >> > >> > >> -- > >> > >> Tommy Ohyun Kwon, Ph.D > >> > >> School of Chemistry and Biochemistry > >> > >> Georgia Institute of Technology > >> > >> Atlanta Georgia, 30332 > >> > >> Email: ohyun.kwon]*[chemistry.gatech.edu > >> > >> > >> > >> > >> > >> the strange characters on the top line to the ,+, sign. You > >> can also > >> > >> > >> E-mail to subscribers: CHEMISTRY,+,ccl.net > >> or use:>> > >> > >> E-mail to administrators: CHEMISTRY-REQUEST,+,ccl.net > >> or use > >> > >> Conferences: > >> http://server.ccl.net/chemistry/announcements/conferences/ > >> > >> > >> Search Messages: http://www.ccl.net/htdig (login: ccl, > >> Password: search) > > >> > >> > >> > >> #################################################### > >> > >> www.etzlstorfer.com > >> > >> > >> *********************************************************** > >> > >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 > >> > >> Universitaet Linz Fax: *43-732-2468-8747 > >> > >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at > >> > >> > >> Austria http://www.orc.uni-linz.ac.at > >> > >> #################################################### > >> > > > > > > -- > > > > - - - - > > *Giuseppina C. Gini > > * DEI, Politecnico di Milano > > piazza L. da Vinci 32, I-20133 MILANO > > *fax:* (+39) 02-2399.3411 > > *phone:* (+39) 02-2399.3626 > > *e-mail:*_ gini---elet.polimi.it_ > > *page:* http://www.dei.polimi.it/people/gini > > > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Pablo Echenique Instituto de Biocomputaci=F3n y F=EDsica de los Sistemas Complejos (BIFI) Departamento de F=EDsica Te=F3rica Universidad de Zaragoza Pedro Cerbuna 12, 50009 Zaragoza Spain Tel.: +34 976761260 Fax: +34 976761264 echenique.p(!)gmail.com http://www.pabloechenique.com From owner-chemistry@ccl.net Thu Dec 13 13:49:01 2007 From: "John McKelvey jmmckel:+:gmail.com" To: CCL Subject: CCL: origin of ab initio Message-Id: <-35845-071213094422-9483-VYBosE0dlTprFsCw/qshpg:server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_23328_20650656.1197557043573" Date: Thu, 13 Dec 2007 09:44:03 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel^gmail.com] ------=_Part_23328_20650656.1197557043573 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Kirk, Your comment is correct with respect to construction of basis sets; however in any of the ZDO schemes, or other more elegant schemes, the choice of basis set, the choice of post-SCF treatment, or the choice of a DFT functional [or its construction] to get results that best reproduce experiment is routinely done and is either semi-empirical or purely empirical. Which term suits the best, I do not know. IMHO, "Everybody adjusts something to get the best answer." Regards, John McKelvey On Dec 12, 2007 6:59 PM, Kirk Peterson kipeters-*-wsu.edu < owner-chemistry_-_ccl.net> wrote: > > Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu] > > As a sidebar to this discussion, I have to strongly disagree that > basis set parameters, exponents or contraction coefficients, > use empirical data in their construction. All commonly used basis > sets, even the Pople-style sets, are generated by optimizing > exponents and contraction coefficients to minimize (ab initio) > energies of atoms and sometimes molecules. Some of the Pople-style > basis sets utilize scale factors to apply to atom-optimized exponents, > but these were based on (ab initio) molecular calculations > and not experimental data. > > regards, > > -Kirk > > On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: > > > > > Sent to CCL by: Rene Fournier [renef\a/yorku.ca] > > David Craig and Robert Parr first used "ab initio" in quantum > > chemistry, > > see > > http://www.quantum-chemistry-history.com/Parr1.htm > > Near the middle of that page, Parr recounts: > > > > " Craig and I published this paper on "configuration interaction in > > benzene", where we took the pi-system and did essentially a complete > > configuration interaction calculation on it. > > > > That has some trivial historical interest in that it was there that > > the > > word, the term ab initio was introduced. Craig and Ross had computed > > everything from the start in London and I had personally computed > > everything from start in Pittsburgh. Then we compared our answers > > when we > > were finished- This involved computing of all the integrals as best as > > they could be done and selecting the configurations to mix for the > > ground > > and exited states because there were electronic states that were of > > experimental interest and we checked our answers one against each > > other > > when we were finished. And what the paper says is, that these > > calculations > > were done ab initio by Craig and Ross and by me, independently. And > > Mulliken later said that this was the introduction of the term ab > > initio > > into quantum chemistry. In the short review that you have, I talk > > about > > this and reproduce a picture of a letter from Craig to me where he > > uses > > the term ab initio in a different context. So ab initio was > > introduced in > > the quantum chemistry by Craig in a letter to me and I put it into the > > manuscript. That's where ab initio came from. " > > > > > > Funny thing is Parr later became a champion of Density Functional > > Theory > > and for many years (70's, 80's) DFT practitioners were often > > criticized > > for doing calculations that were not "ab initio". I think views have > > changed now; "first-principles" was introduced probably to say > > "mostly > > not empirical" but without the implications "ab initio" had acquired > > over > > the years. The term "ab initio calculation", as it's commonly used, > > very rarely refers to a calculation "devoid of empiricism", for > > example > > the choice of basis set parameters is almost always empirical, > > see discussion on > > > http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html > > > > Rene Fournier Office: 303 Petrie > > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > > 4700 Keele Street, Toronto FAX: (416)-736-5936 > > Ontario, CANADA M3J 1P3 e-mail: renef*_*yorku.ca > > > > > > On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer . > > jku.at wrote: > > > >> There is a story about that in Michael J.S. Dewars biography "A > >> semiempirical life", American Chemical Society, 1992, p. 129. > >> > >> Best regards > >> > >> Christoph > >> > >> > >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ > >> chemistry.gatech.edu: > >> > >>> > >>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . chemistry.gatech.edu] > >>> Dear CCLers; > >>> I would appreciate it if anyone could tell me who used the term of > >>> "ab initio > >>> calculations" first. > >>> Thank you very much for your kind attention. > >>> > >>> Best wishes, > >>> > >>> Tommy > >>> > >>> > >>> -- > >>> Tommy Ohyun Kwon, Ph.D > >>> School of Chemistry and Biochemistry > >>> Georgia Institute of Technology > >>> Atlanta Georgia, 30332 > >>> Email: ohyun.kwon]*[chemistry.gatech.edu > >>> > >>> > >>> > >>> -= This is automatically added to each message by the mailing > >>> script =- > >>> To recover the email address of the author of the message, please > >>> change> Conferences: http://server.ccl.net/chemistry/announcements/ > >>> conferences/ > >>> > >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > >>> search)> > >>> > >> > >> #################################################### > >> www.etzlstorfer.com > >> *********************************************************** > >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 > >> Universitaet Linz Fax: *43-732-2468-8747 > >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at > >> Austria http://www.orc.uni-linz.ac.at > >> #################################################### > >> > >> > >> > >> > >> > > > > > > > > -= This is automatically added to each message by the mailing script > > =- > > To recover the email address of the author of the message, please > > change> Conferences: http://server.ccl.net/chemistry/announcements/ > > conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > ------=_Part_23328_20650656.1197557043573 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Kirk,

Your comment is correct with respect to construction of basis sets; however in any of the ZDO schemes, or other more elegant schemes, the choice of basis set, the choice of post-SCF treatment, or the choice of a DFT functional [or its construction] to get results that best reproduce experiment is routinely done and is either semi-empirical or purely empirical.  Which term suits the best, I do not know.  IMHO, "Everybody adjusts something to get the best answer."

Regards,

John McKelvey

On Dec 12, 2007 6:59 PM, Kirk Peterson kipeters-*-wsu.edu <owner-chemistry_-_ccl.net> wrote:

Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu]

As a sidebar to this discussion, I have to strongly disagree that
basis set parameters, exponents or contraction coefficients,
use empirical data in their construction.  All commonly used basis
sets, even the Pople-style sets, are generated by optimizing
exponents and contraction coefficients to minimize (ab initio)
energies of atoms and sometimes molecules.  Some of the Pople-style
basis sets utilize scale factors to apply to atom-optimized exponents,
but these were based on (ab initio) molecular calculations
and not experimental data.

regards,

-Kirk

On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote:

>
> Sent to CCL by: Rene Fournier [renef\a/yorku.ca]
> David Craig and Robert Parr first used "ab initio" in quantum
> chemistry,
> see
> http://www.quantum-chemistry-history.com/Parr1.htm
> Near the middle of that page, Parr recounts:
>
> " Craig and I published this paper on "configuration interaction in
> benzene", where we took the pi-system and did essentially a complete
> configuration interaction calculation on it.
>
> That has some trivial historical interest in that it was there that
> the
> word, the term ab initio was introduced. Craig and Ross had computed
> everything from the start in London and I had personally computed
> everything from start in Pittsburgh. Then we compared our answers
> when we
> were finished- This involved computing of all the integrals as best as
> they could be done and selecting the configurations to mix for the
> ground
> and exited states because there were electronic states that were of
> experimental interest and we checked our answers one against each
> other
> when we were finished. And what the paper says is, that these
> calculations
> were done ab initio by Craig and Ross and by me, independently. And
> Mulliken later said that this was the introduction of the term ab
> initio
> into quantum chemistry. In the short review that you have, I talk
> about
> this and reproduce a picture of a letter from Craig to me where he
> uses
> the term ab initio in a different context. So ab initio was
> introduced in
> the quantum chemistry by Craig in a letter to me and I put it into the
> manuscript. That's where ab initio came from.  "
>
>
> Funny thing is Parr later became a champion of Density Functional
> Theory
> and for many years (70's, 80's) DFT practitioners were often
> criticized
> for doing calculations that were not "ab initio".  I think views have
> changed now;  "first-principles" was introduced probably to say
> "mostly
> not empirical" but without the implications "ab initio" had acquired
> over
> the years.  The term "ab initio calculation", as it's commonly used,
> very rarely refers to a calculation "devoid of empiricism", for
> example
> the choice of basis set parameters is almost always empirical,
> see discussion on
> http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html
>
>  Rene Fournier                   Office:  303 Petrie
>  Chemistry Dpt, York University  Phone: (416) 736 2100 Ext. 30687
>  4700 Keele Street,  Toronto     FAX:   (416)-736-5936
>  Ontario, CANADA   M3J 1P3       e-mail: renef*_* yorku.ca
>
>
> On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer .
> jku.at wrote:
>
>> There is a story about that in Michael J.S. Dewars biography "A
>> semiempirical life", American Chemical Society, 1992, p. 129.
>>
>> Best regards
>>
>> Christoph
>>
>>
>> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _
>> chemistry.gatech.edu:
>>
>>>
>>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . chemistry.gatech.edu]
>>> Dear CCLers;
>>> I would appreciate it if anyone could tell me who used the term of
>>> "ab initio
>>> calculations" first.
>>> Thank you very much for your kind attention.
>>>
>>> Best wishes,
>>>
>>> Tommy
>>>
>>>
>>> --
>>> Tommy Ohyun Kwon, Ph.D
>>> School of Chemistry and Biochemistry
>>> Georgia Institute of Technology
>>> Atlanta Georgia, 30332
>>> Email: ohyun.kwon]*[chemistry.gatech.edu
>>>
>>>
>>>
>>> -= This is automatically added to each message by the mailing
>>> script =-
>>> To recover the email address of the author of the message, please
>>> change> Conferences: http://server.ccl.net/chemistry/announcements/
>>> conferences/
>>>
>>> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
>>> search)>
>>>
>>
>> ####################################################
>>                                  www.etzlstorfer.com
>> ***********************************************************
>> Dr. Christoph Etzlstorfer       Phone:  *43-732-2468-8750
>> Universitaet Linz              Fax:    *43-732-2468-8747
>> A-4040 Linz               E-mail: christoph.etzlstorfer,+,jku.at
>> Austria                   http://www.orc.uni-linz.ac.at
>> ####################################################
>>
>>
>>
>>
>>
>
>
>
> -= This is automatically added to each message by the mailing script
> =-
> To recover the email address of the author of the message, please
> change> Conferences: http://server.ccl.net/chemistry/announcements/
> conferences/
>
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
> search)>
>



E-mail to subscribers: CHEMISTRY_-_ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST_-_ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)


------=_Part_23328_20650656.1197557043573-- From owner-chemistry@ccl.net Thu Dec 13 14:24:02 2007 From: "Kirk Peterson kipeters- -wsu.edu" To: CCL Subject: CCL: origin of ab initio/basis set empiricism Message-Id: <-35846-071213134112-25077-FgpsrE6QyLVUcmKZmnBtAA:_:server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Thu, 13 Dec 2007 09:48:39 -0800 Mime-Version: 1.0 (Apple Message framework v915) Sent to CCL by: Kirk Peterson [kipeters%%wsu.edu] Well, I would agree that there can seem to be a lot of choices for the basis set used in a given calculation. But I don't agree that the reliance on experimental data is any worse than the choice of electronic structure method. I would argue that the choice of DFT functional is often much more empirical than the choice of basis set. Experiment is often the gold standard but there are also pitfalls in making those comparisons as well since one has to be very careful to make sure you are comparing to the right quantity, e.g., making sure for bond dissociation energies that you've included at least atomic spin-orbit effects. Also whether you believe that just because a low-level method agrees with a high-level method's result makes the former accurate, that has nothing to do per se with basis sets since the same error cancellations can occur at the complete basis set limit. It's at least a 2-dimensional problem, so any coupling of the errors due to method and basis set can make the analysis of accuracy very difficult if you're not systematic about it. I note that you seem to have forgotten about the family of correlation consistent basis sets first developed in Dunning's group at PNNL (cc-pVDZ, etc.). These are really the only modern set of basis sets that allow one to accurately extrapolate to the basis set limit for HF and correlated methods (even DFT). Including the ones based on relativistic pseudopotentials (cc-pVnZ-PP), they now cover the entire p-block as well as the 1st and 2nd row transition metals (3rd row transition metals to be published soon). Some of the most accurate computational thermochemistry models (Wn of Martin, HEAT, ccCA from the N. Texas group, the composite approach of Feller, Dixon, et al., etc.) hinge on the extrapolation of energies obtained from these sets. With these basis sets the choice is generally much clearer IMHO - choose from a double-, triple-, quadruple- (or higher) zeta level description of the AO's and if you have weak interactions present or negative ion character just use the diffuse-augmented sets (aug-cc-pVDZ, etc.). apologies for the rather long rambling post. -Kirk On Dec 13, 2007, at 5:39 AM, Rene Fournier renef++yorku.ca wrote: > > Sent to CCL by: Rene Fournier [renef(a)yorku.ca] > Hello, > I agree on > >> All commonly used basis >> sets, even the Pople-style sets, are generated by optimizing >> exponents and contraction coefficients to minimize (ab initio) >> energies of atoms and sometimes molecules. > > That's correct. But there are other problems with choices of basis > sets and that's where empiricism can creep in. How many contracted > functions is enough? What's the best contraction pattern? > (why 6-31G and not 6-21G? or 4-31G? or 9-61G? or 7-1111G?) > How many polarization functions? Why not throw in a few bond- > centered functions? > Many basis sets went into oblivion not because they gave higher > energies > for atoms or molecules --- adding more functions and keeping them > uncontracted > always lowers energy. It's that they did not give good agreement > with experimental > bond lengths, bond energies etc. relative to other basis sets of > comparable > computational cost. I'm not sure how to call methods where high- > level theory > is used instead of experiment as the reference to assess goodness of > a lower level > of theory (maybe a smaller basis). I think it's still empirical > because there's > the assumption that if the low-level theory reproduces high-level > theory to > within some accuracy for cases X, Y, Z, it will also reproduce high- > level > level theory to that accuracy for other cases when we do applications. > ( There's also the obvious point that if the high-level theory > reference is > really, really good, then it IS the experimental result! ) > It is possible to take empiricism out of basis set choice by doing > many calculations in a sequence with increasingly big basis sets > defined > by only 1 and maybe 2 parameters, so that one can crank up accuracy > smoothly, > and extrapolate results to "infinite basis set". Basis sets > suitable for > that are: > - even-tempered fully uncontracted basis sets (K Ruedenberg); > - plane-waves (increase energy cut-off and box size); > - all-numerical programs (mostly for diatomics, Becke's NUMOL for > polyatomics). > But I don't see that done very often, even with plane-waves where it > would be > easy I suppose. > > Regards, > Rene > > Rene Fournier Office: 303 Petrie > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > 4700 Keele Street, Toronto FAX: (416)-736-5936 > Ontario, CANADA M3J 1P3 e-mail: renef---yorku.ca > > > > > On Wed, 12 Dec 2007, Kirk Peterson kipeters-*-wsu.edu wrote: > >> >> Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu] >> >> As a sidebar to this discussion, I have to strongly disagree that >> basis set parameters, exponents or contraction coefficients, >> use empirical data in their construction. All commonly used basis >> sets, even the Pople-style sets, are generated by optimizing >> exponents and contraction coefficients to minimize (ab initio) >> energies of atoms and sometimes molecules. Some of the Pople-style >> basis sets utilize scale factors to apply to atom-optimized >> exponents, >> but these were based on (ab initio) molecular calculations >> and not experimental data. >> >> regards, >> >> -Kirk >> >> On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: >> >>> >>> Sent to CCL by: Rene Fournier [renef\a/yorku.ca] >>> David Craig and Robert Parr first used "ab initio" in quantum >>> chemistry, >>> see >>> http://www.quantum-chemistry-history.com/Parr1.htm >>> Near the middle of that page, Parr recounts: >>> >>> " Craig and I published this paper on "configuration interaction in >>> benzene", where we took the pi-system and did essentially a complete >>> configuration interaction calculation on it. >>> >>> That has some trivial historical interest in that it was there that >>> the >>> word, the term ab initio was introduced. Craig and Ross had computed >>> everything from the start in London and I had personally computed >>> everything from start in Pittsburgh. Then we compared our answers >>> when we >>> were finished- This involved computing of all the integrals as >>> best as >>> they could be done and selecting the configurations to mix for the >>> ground >>> and exited states because there were electronic states that were of >>> experimental interest and we checked our answers one against each >>> other >>> when we were finished. And what the paper says is, that these >>> calculations >>> were done ab initio by Craig and Ross and by me, independently. And >>> Mulliken later said that this was the introduction of the term ab >>> initio >>> into quantum chemistry. In the short review that you have, I talk >>> about >>> this and reproduce a picture of a letter from Craig to me where he >>> uses >>> the term ab initio in a different context. So ab initio was >>> introduced in >>> the quantum chemistry by Craig in a letter to me and I put it into >>> the >>> manuscript. That's where ab initio came from. " >>> >>> >>> Funny thing is Parr later became a champion of Density Functional >>> Theory >>> and for many years (70's, 80's) DFT practitioners were often >>> criticized >>> for doing calculations that were not "ab initio". I think views >>> have >>> changed now; "first-principles" was introduced probably to say >>> "mostly >>> not empirical" but without the implications "ab initio" had acquired >>> over >>> the years. The term "ab initio calculation", as it's commonly used, >>> very rarely refers to a calculation "devoid of empiricism", for >>> example >>> the choice of basis set parameters is almost always empirical, >>> see discussion on >>> http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.html >>> >>> Rene Fournier Office: 303 Petrie >>> Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 >>> 4700 Keele Street, Toronto FAX: (416)-736-5936 >>> Ontario, CANADA M3J 1P3 e-mail: renef*_*yorku.ca >>> >>> >>> On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer . >>> jku.at wrote: >>> >>>> There is a story about that in Michael J.S. Dewars biography "A >>>> semiempirical life", American Chemical Society, 1992, p. 129. >>>> >>>> Best regards >>>> >>>> Christoph >>>> >>>> >>>> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ >>>> chemistry.gatech.edu: >>>> >>>>> >>>>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . >>>>> chemistry.gatech.edu] >>>>> Dear CCLers; >>>>> I would appreciate it if anyone could tell me who used the term of >>>>> "ab initio >>>>> calculations" first. >>>>> Thank you very much for your kind attention. >>>>> >>>>> Best wishes, >>>>> >>>>> Tommy >>>>> >>>>> >>>>> -- >>>>> Tommy Ohyun Kwon, Ph.D >>>>> School of Chemistry and Biochemistry >>>>> Georgia Institute of Technology >>>>> Atlanta Georgia, 30332 >>>>> Email: ohyun.kwon]*[chemistry.gatech.edu >>>>> >>>>> >>>>> >>>>> -= This is automatically added to each message by the mailing >>>>> script =- >>>>> To recover the email address of the author of the message, please >>>>> change> Conferences: http://server.ccl.net/chemistry/ >>>>> announcements/ >>>>> conferences/ >>>>> >>>>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>>>> search)> >>>>> >>>> >>>> #################################################### >>>> www.etzlstorfer.com >>>> *********************************************************** >>>> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 >>>> Universitaet Linz Fax: *43-732-2468-8747 >>>> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at >>>> Austria http://www.orc.uni-linz.ac.at >>>> #################################################### >>>> >>>> >>>> >>>> >>>> >>> >>> >>> >>> -= This is automatically added to each message by the mailing script >>> =- >>> To recover the email address of the author of the message, please >>> change> Conferences: http://server.ccl.net/chemistry/announcements/ >>> conferences/ >>> >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >>> search)> >> >> > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Thu Dec 13 15:12:00 2007 From: "Frank Jensen frj : chem.au.dk" To: CCL Subject: CCL: origin of ab initio/basis set empiricism Message-Id: <-35847-071213135127-30302-JNfsBtS0GKXNRP8Fscb4Qg[a]server.ccl.net> X-Original-From: Frank Jensen Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 13 Dec 2007 19:00:08 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj###chem.au.dk] At the risk of being accused for self-promovation, let me add a few =20 comments on the issue of basis sets. A dispropotional number of calculations are done using variations of =20 the 6-31G* or 6-311G* basis sets. The justification is variations of =20 the statement that 'this basis set has been shown to give good =20 results'. Backtracing this leads to some calibration against a set of =20 experimental data for a given set of test systems. Chosing basis sets =20 in this fashion is thus 'empirical' in the sence that it is based on =20 comparison with experiments. A non-empirical way of selecting a basis =20 set must rely on a systematic sequence that smoothly converges towards =20 the basis set limit. Most 'popular' basis sets are of the segmented type, where both =20 exponents and contraction coefficients are optimized based on energy. =20 Unfortunately this leads to the 'multiple minimum' problem. We have =20 for example shown that there are at least 19 different ways of =20 constructing a '6-311' contraction of 11 s-functions. If one also =20 consider possibilities like 7-211, 5-411 and 5-321, the number grows =20 further. Most of these have very similar performances, and there is no =20 unique way of selecting the 'best'. Generating a sequence of segmented =20 basis sets that systematic approach the limit is in my oppinion not =20 possible. A general contracted basis set, on the other hand, separates the =20 optimization of the exponents and the contraction coefficients. As the =20 uncontracted set of functions can be made to converge towards the =20 basis set limit, and the contraction error can be rigorous controlled, =20 this allows construction of a systematic sequence of basis sets, as =20 was first explored by the ANO type basis set. Dunning showed how this could be used to construct the cc-pVXZ =20 sequence for electron correlation methods, and we have used the same =20 idea for constructing the pc-n basis sets for DFT methods. The natural =20 quality parameter in these is the highest angular momentum included. =20 Once this has been selected, the rest of the basis set is in principle =20 unique. These basis sets therefore have a single non-empirical =20 parameter that controls the accuracy. Plane waves have the same single =20 non-empirical parameter quality, but as they usually employe a =20 core-potential, this prevents a rigorous convergence towards the =20 all-electron limit. A notion on the side: while even-tempered basis sets provide a =20 systematic way improving the quality of an atomic calculation, this is =20 not the case for molecular systems. Here increasing the number of =20 functions, even for strictly variational methods like HF and including =20 polarization functions, can increase the energy, and in practise leads =20 to oscillatory behavior. A practical issue is how fast the basis set convergence is. While both =20 the cc-pVXZ and pc-n basis sets provide a controlled convergence, the =20 rate of convergence can for some properties be improved by adding =20 diffuse or tight functions. Both of these options are available for =20 both families of basis sets. My (clearly biased) view is that calculations should always be done =20 using at least a DZP and a TZP quality basis set to identify the =20 pathological cases that always pops up. To illustrate this point: The =20 Ahlrich SVP and the Pople 6-31G* are both of double zeta quality and =20 have typical errors for calculating nuclear magnetic shielding of ~30 =20 ppm. The B3LYP calculated value for oxygen in MgO is +23600 ppm with =20 the SVP and -2960 ppm for 6-31G*. The basis set limiting value is =20 -2440 ppm. Relying on calculations with a single 'empirical' chosen =20 basis set will invariably run into such problems. Using basis sets =20 that belong to families where the error can be controlled allows one =20 to identify such cases, and rigorously remove the basis set error, =20 albeit at a computational cost. Just my 0.02$ (well maybe 0.03$) Frank Citat af "Rene Fournier renef++yorku.ca" : > > Sent to CCL by: Rene Fournier [renef(a)yorku.ca] > Hello, > I agree on > >> All commonly used basis >> sets, even the Pople-style sets, are generated by optimizing >> exponents and contraction coefficients to minimize (ab initio) >> energies of atoms and sometimes molecules. > > That's correct. But there are other problems with choices of basis > sets and that's where empiricism can creep in. How many contracted > functions is enough? What's the best contraction pattern? > (why 6-31G and not 6-21G? or 4-31G? or 9-61G? or 7-1111G?) > How many polarization functions? Why not throw in a few =20 > bond-centered functions? > Many basis sets went into oblivion not because they gave higher energies > for atoms or molecules --- adding more functions and keeping them =20 > uncontracted > always lowers energy. It's that they did not give good agreement =20 > with experimental > bond lengths, bond energies etc. relative to other basis sets of comparabl= e > computational cost. I'm not sure how to call methods where high-level the= ory > is used instead of experiment as the reference to assess goodness of =20 > a lower level > of theory (maybe a smaller basis). I think it's still empirical =20 > because there's > the assumption that if the low-level theory reproduces high-level theory t= o > within some accuracy for cases X, Y, Z, it will also reproduce high-level > level theory to that accuracy for other cases when we do applications. > ( There's also the obvious point that if the high-level theory reference i= s > really, really good, then it IS the experimental result! ) > It is possible to take empiricism out of basis set choice by doing > many calculations in a sequence with increasingly big basis sets defined > by only 1 and maybe 2 parameters, so that one can crank up accuracy smooth= ly, > and extrapolate results to "infinite basis set". Basis sets suitable for > that are: > - even-tempered fully uncontracted basis sets (K Ruedenberg); > - plane-waves (increase energy cut-off and box size); > - all-numerical programs (mostly for diatomics, Becke's NUMOL for =20 > polyatomics). > But I don't see that done very often, even with plane-waves where it would= be > easy I suppose. > > Regards, > Rene > > Rene Fournier Office: 303 Petrie > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > 4700 Keele Street, Toronto FAX: (416)-736-5936 > Ontario, CANADA M3J 1P3 e-mail: renef---yorku.ca > > > > > On Wed, 12 Dec 2007, Kirk Peterson kipeters-*-wsu.edu wrote: > >> >> Sent to CCL by: Kirk Peterson [kipeters-$-wsu.edu] >> >> As a sidebar to this discussion, I have to strongly disagree that >> basis set parameters, exponents or contraction coefficients, >> use empirical data in their construction. All commonly used basis >> sets, even the Pople-style sets, are generated by optimizing >> exponents and contraction coefficients to minimize (ab initio) >> energies of atoms and sometimes molecules. Some of the Pople-style >> basis sets utilize scale factors to apply to atom-optimized exponents, >> but these were based on (ab initio) molecular calculations >> and not experimental data. >> >> regards, >> >> -Kirk >> >> On Dec 12, 2007, at 8:21 AM, Rene Fournier renef+*+yorku.ca wrote: >> >> > >> > Sent to CCL by: Rene Fournier [renef\a/yorku.ca] >> > David Craig and Robert Parr first used "ab initio" in quantum >> > chemistry, >> > see >> > http://www.quantum-chemistry-history.com/Parr1.htm >> > Near the middle of that page, Parr recounts: >> > >> > " Craig and I published this paper on "configuration interaction in >> > benzene", where we took the pi-system and did essentially a complete >> > configuration interaction calculation on it. >> > >> > That has some trivial historical interest in that it was there that >> > the >> > word, the term ab initio was introduced. Craig and Ross had computed >> > everything from the start in London and I had personally computed >> > everything from start in Pittsburgh. Then we compared our answers >> > when we >> > were finished- This involved computing of all the integrals as best as >> > they could be done and selecting the configurations to mix for the >> > ground >> > and exited states because there were electronic states that were of >> > experimental interest and we checked our answers one against each >> > other >> > when we were finished. And what the paper says is, that these >> > calculations >> > were done ab initio by Craig and Ross and by me, independently. And >> > Mulliken later said that this was the introduction of the term ab >> > initio >> > into quantum chemistry. In the short review that you have, I talk >> > about >> > this and reproduce a picture of a letter from Craig to me where he >> > uses >> > the term ab initio in a different context. So ab initio was >> > introduced in >> > the quantum chemistry by Craig in a letter to me and I put it into the >> > manuscript. That's where ab initio came from. " >> > >> > >> > Funny thing is Parr later became a champion of Density Functional >> > Theory >> > and for many years (70's, 80's) DFT practitioners were often >> > criticized >> > for doing calculations that were not "ab initio". I think views have >> > changed now; "first-principles" was introduced probably to say >> > "mostly >> > not empirical" but without the implications "ab initio" had acquired >> > over >> > the years. The term "ab initio calculation", as it's commonly used, >> > very rarely refers to a calculation "devoid of empiricism", for >> > example >> > the choice of basis set parameters is almost always empirical, >> > see discussion on >> > =20 >> http://www.ccl.net/chemistry/resources/messages/2001/11/28.002-dir/index.= html >> > >> > Rene Fournier Office: 303 Petrie >> > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 >> > 4700 Keele Street, Toronto FAX: (416)-736-5936 >> > Ontario, CANADA M3J 1P3 e-mail: renef*_*yorku.ca >> > >> > >> > On Wed, 12 Dec 2007, Christoph Etzlstorfer christoph.etzlstorfer . >> > jku.at wrote: >> > >> >> There is a story about that in Michael J.S. Dewars biography "A >> >> semiempirical life", American Chemical Society, 1992, p. 129. >> >> >> >> Best regards >> >> >> >> Christoph >> >> >> >> >> >> Am 11.12.2007 um 03:13 schrieb Tommy Ohyun Kwon ohyun.kwon _ >> >> chemistry.gatech.edu: >> >> >> >>> >> >>> Sent to CCL by: Tommy Ohyun Kwon [ohyun.kwon . chemistry.gatech.edu] >> >>> Dear CCLers; >> >>> I would appreciate it if anyone could tell me who used the term of >> >>> "ab initio >> >>> calculations" first. >> >>> Thank you very much for your kind attention. >> >>> >> >>> Best wishes, >> >>> >> >>> Tommy >> >>> >> >>> >> >>> -- >> >>> Tommy Ohyun Kwon, Ph.D >> >>> School of Chemistry and Biochemistry >> >>> Georgia Institute of Technology >> >>> Atlanta Georgia, 30332 >> >>> Email: ohyun.kwon]*[chemistry.gatech.edu >> >>> >> >>> >> >>> >> >>> -=3D This is automatically added to each message by the mailing >> >>> script =3D- >> >>> To recover the email address of the author of the message, please >> >>> change> Conferences: http://server.ccl.net/chemistry/announcements/ >> >>> conferences/ >> >>> >> >>> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> >>> search)> >> >>> >> >> >> >> #################################################### >> >> www.etzlstorfer.com >> >> *********************************************************** >> >> Dr. Christoph Etzlstorfer Phone: *43-732-2468-8750 >> >> Universitaet Linz Fax: *43-732-2468-8747 >> >> A-4040 Linz E-mail: christoph.etzlstorfer,+,jku.at >> >> Austria http://www.orc.uni-linz.ac.at >> >> #################################################### >> >> >> >> >> >> >> >> >> >> >> > >> > >> > >> > -=3D This is automatically added to each message by the mailing script >> > =3D- >> > To recover the email address of the author of the message, please >> > change> Conferences: http://server.ccl.net/chemistry/announcements/ >> > conferences/ >> > >> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> > search)> >> >> > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > Frank Jensen http://www.chem.au.dk/~frj ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.