From chemistry-request@ccl.net Fri Jan 21 06:48:28 2005 Received: from shiva.jussieu.fr (shiva.jussieu.fr [134.157.0.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0LBmRi3023859 for ; Fri, 21 Jan 2005 06:48:27 -0500 Received: from ds10.itodys.jussieu.fr (ds10.itodys.jussieu.fr [134.157.24.13]) by shiva.jussieu.fr (8.12.11/jtpda-5.4) with ESMTP id j0LAHMO3008973 for ; Fri, 21 Jan 2005 11:17:22 +0100 (CET) X-Ids: 166 Received: by ds10.itodys.jussieu.fr (8.12.1/1.1.2.11/09Jul02-1200PM) id j0LAHGUi120016; Fri, 21 Jan 2005 11:17:16 +0100 (MET) Date: Fri, 21 Jan 2005 11:17:16 +0100 (MET) From: Michel Petitjean Message-Id: <200501211017.j0LAHGUi120016~at~ds10.itodys.jussieu.fr> To: chemistry~at~ccl.net Subject: CCL:[Re]: orbitals and reality X-Greylist: Sender IP whitelisted, not delayed by milter-greylist-1.7.2 (shiva.jussieu.fr [134.157.0.166]); Fri, 21 Jan 2005 11:17:22 +0100 (CET) X-Miltered: at shiva.jussieu.fr with ID 41F0D6B2.000 by Joe's j-chkmail (http://j-chkmail.ensmp.fr)! X-Antivirus: scanned by sophie at shiva.jussieu.fr X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net To: chemistry~at~ccl.net Subject: CCL:[Re]: orbitals and reality Dear CCLers, I have not read the original paper from which the debate seems to originate, but I have here a naive question for those who think that an orbital is a physical thing rather than a mathematical model: what is the physical reality of a free orbital (i.e. no electron inside) ? Michel Petitjean Email: petitjean~at~itodys.jussieu.fr FIS2005 coordinator http://www.mdpi.org/fis2005 Editor-in-Chief of Entropy http://www.mdpi.org/entropy ITODYS (CNRS, UMR 7086) 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From chemistry-request@ccl.net Fri Jan 21 12:25:04 2005 Received: from day.its.uiowa.edu (day.its.uiowa.edu [128.255.56.107]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0LHP3i3008636 for >ccl.net>; Fri, 21 Jan 2005 12:25:04 -0500 Received: from [128.255.103.199] (dhcp80ff67c7.dynamic.uiowa.edu [128.255.103.199]) by day.its.uiowa.edu (8.12.10/8.12.9/ns-mx-1.16) with ESMTP id j0LHP0km020126; Fri, 21 Jan 2005 11:25:01 -0600 Mime-Version: 1.0 Message-Id: Date: Fri, 21 Jan 2005 11:25:00 -0600 To: chemistry<>ccl.net, gamess<>lists.ciw.edu From: "Jan H. Jensen" >blue.weeg.uiowa.edu> Subject: Ghemical-GMS/GTK-GAMESS available for MacOSX Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.6 required=7.5 tests=FCS_URI_NODOTS,FVGT_s_OBFU_X autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Colleagues: The Ghemical-GMS GUI (http://www.uiowa.edu/~ghemical) and GTK-GAMESS queueing program for the quantum chemistry program GAMESS are now running under MacOSX, in addition to LINUX and Windows as announced previously. The Ghemical-GMS web page now also contains a tutorial on the combined use of the programs as a front-end to GAMESS. -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Professor Department of Chemistry jan-jensen<>uiowa.edu University of Iowa Phone:(319) 335-1108 Iowa City, IA 52242 FAX: (319) 335-1270 http://www.uiowa.edu/~quantum http://www.uiowa.edu/~mbiophys (Molecular Biophysics @ UI) =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@ccl.net Fri Jan 21 11:17:51 2005 Received: from mailhub128.itcs.purdue.edu (mailhub128.itcs.purdue.edu [128.210.5.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0LGHoi3005077 for ; Fri, 21 Jan 2005 11:17:50 -0500 Received: from BPUTNAM3.itap.purdue.edu (bputnam3.rcs.purdue.edu [128.210.189.129]) (authenticated bits=0) by mailhub128.itcs.purdue.edu (8.13.1/8.13.1/scan-smtp) with ESMTP id j0LEEXho017636 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Fri, 21 Jan 2005 09:14:34 -0500 Date: Fri, 21 Jan 2005 09:14:35 -0500 (US Eastern Standard Time) From: Bryan Putnam To: CCL Subject: Building g03 on Opteron64 system with RedHat Enterprise Message-ID: X-X-Sender: bfp*at*mailhub016.itcs.purdue.edu MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by amavisd-new X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, Has anyone had success building gaussian (g03-C.02) on an Opeteron 64 system? We're not using the supported SuSE, but rather RedHat Enterprise Linux AS release 3 (Taroon Update 4) We're using PGI compilers 5.2-4 If I attempt to build using the shared util.so, I get error messages that the libatlas-amd64 and libf77blas-amd64 libraries need to be compiled with the "-fpic" option. So, I successfully recompiled ATLAS (and gaussian) with -fpic, but then I get many undefined references during the link. I also tried building statically, however that results in message: util.a: could not read symbols: Memory exhausted This is in spite of the fact we have plenty of memory. I've tried the obvious things like setting "stacksize", "datasize", etc. to unlimited. Any suggestions or help linking g03 on an Opteron64 system running RedHat Enterprise would be appreciated! Thanks, Bryan Bryan F. Putnam Staff Scientist Rosen Center for Advanced Computing Information Technology at Purdue (ITaP) Young Hall 519 Ph 765-496-8225 Fax 765-494-0566 bfp*at*purdue.edu From chemistry-request@ccl.net Thu Jan 20 23:42:07 2005 Received: from web30806.mail.mud.yahoo.com (web30806.mail.mud.yahoo.com [68.142.200.149]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0L4g4i3002953 for ; Thu, 20 Jan 2005 23:42:04 -0500 Received: (qmail 96291 invoked by uid 60001); 21 Jan 2005 04:42:04 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=WtrM0kPYeTzXPRWgWMVSo28rrhmlBB6jIQckJq3IwLgf90qPyMLOt9FPzkZqG831kPqYvFcJQHJdFiZzVBt95qwEY0qxm0HHBN7Ru0hDat8LKpKrur8NWIgMb6SNSznl3dWQECQ8v6QcnGKBRWC/zTYZMf0eBQ5oiSDnM+MHhDs= ; Message-ID: <20050121044204.96289.qmail[at]web30806.mail.mud.yahoo.com> Received: from [68.46.0.3] by web30806.mail.mud.yahoo.com via HTTP; Thu, 20 Jan 2005 20:42:03 PST Date: Thu, 20 Jan 2005 20:42:03 -0800 (PST) From: Guosheng Wu Subject: Re: CCL:orbitals and reality To: Alan Shusterman , chemistry[at]ccl.net In-Reply-To: <41EFF6D9.40200[at]reed.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=5.6 required=7.5 tests=FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS,FROM_HAS_ULINE_NUMS,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS, SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --- Alan Shusterman wrote: > ... Coming back to the newest experiment in Nature (which I still don't > understand): I don't think it can actually be measuring something about > orbitals because quantum theory says 1) orbitals are not real... Okay, it means you are still interested in the topic b/c you are not deleting it without any reading :-) I still think in some sense that Nature paper did measure something about wave function (or "orbital"=wave function in QM). Wave function psi describes the state of a particle in QM just like r(t) & p(t) for a classical particle, and sometimes it's refered to be probability amplitude(real number), but not the actual probability because of the uncertainty of a phase term [cos(theta)+i*sin(theta)]. ||^2 is the probability density, given psi is normalized. For simplicity, let's forget time varible b/c no interest in dynamics yet. Well, certainly wave function is not "real" mathematically, since it's a complex function and one can easily put a phase term (above) besides it without changing any properties of the system. But how can we observe something not "real", even mathematically? The thing is that Nature paper only mapped the probability amplititude of the wave function, not saying they "observed" the whole wave function. One simple solvable example in QM is hydrogen atom (without any confusion with basis set or multiple electrons). The distribution of its wave function (or probability amplititude) in the 3D space is well-defined and solved analytically. I guess no one needs more explanation for this part. Certainly the probability amplititude of H atom in 3D space could be mapped out experimentally. For example, one could measure its angular distribution of |<1s|1s>|^2 experimentally, then psi(1s) can be got by taking sqrt of(|<1s|1s>|^2), just 0.5/sqrt(pai) since it's a sphere, no exp. needed at all! Again one can add a phase term to it to make it not "REAL", but it does not mean one can not map out ("observe") the wave function's probability amplititude. It's similar for molecule like N2, or even more complicated. I do not think there is any conceptual difference for the above description. We just need more mathematical equations to describe them and solve them. All in all, that Nature paper did not observe the orbital of N2, but mapped out some of its probability amplititudes. If one really likes to argue, then he could simply say: since everything of QM is about wave function, and any wave function is not actually real function, so all QM related stuff has no any reality. Oops, I am almost trapped by myself. -Guosheng --- Alan Shusterman wrote: > My 2 cents (devalued by years of inflation)... > > I read both Nature papers, the original research and the news > perspective. I confess that I couldn't understand the experimental > technique as described in either paper. Therefore, I cannot describe the > > experimental technique in terms of quantum theory. > > So I wrote the authors of both papers for more information. Both of them > > were kind enough to respond to my note and I hope that we will continue > to exchange emails because I have more to learn. I have put their > comments below and added my own thoughts about orbitals at the end. > > #1. Response from David Villeneuve: > > "I don't want to leave you unhappy. We were being somewhat provocative > to > show an orbital wave function, knowing that introductory quantum > mechanics > courses say that you cannot do this. However it is known that one can > measure a quantum state if the system can be repeatedly prepared in the > same > state (see A Royer, Foundations of Physics 19, 3 (1989)). We use an > interference technique of the same electron with itself to record the > phase > of the wave function. > > The other issue is whether a set of single-electron wave functions can > represent the N body quantum system. The answer is no, but quantum > chemists > do it anyway. It is the best that we can do. There is lots of work in > molecular structure that depends on these approximations, such as > GAUSSIAN > ab initio calculations. SO even if orbitals do not exist, they are > extensively used. > > I learned after we published this, that the HOMO of N2 is not that well > known. See Maksic and Vianello, J Phys Chem 106, 6515 (2002), and > Stowasser > and Hoffman, J Am Chem Soc 121, 3414 (1999) for conflicting > calculations. > > Finally, if you are still unhappy, you can just think that we measured a > set > of transition dipole matrix elements from some state to a set of > continuum > plane waves." > > #2. Response from Henrik Stapelfeldt: > > "It is well established that a wave function or an orbital is not > directly > observable for a single quantum system. However, a set of measurements > of > observables (which are real measurable quantities) on a sufficiently > large > number of identically prepared systems may contain enough information to > determine the wave function (or more generally the density matrix) of > the > system considered up to an overall phase. > > This approach has been taken in a large number of works over the past > decade > experimentally as well as theoretically. For instance, using quantum > tomography > the density matrix, or equivalently the Wigner function, has been > reconstructed > for vibrational states of molecules, nonclassical states of light, > trapped > ions, atomic beams and dissociating molecules. I will be happy to send > you > references if you are not familiar with these works. > > In the recent work of Itatani et al. in Nature the molecular orbital is > reconstructed from a large number of measurements of laser induced high > harmonic spectra (the observables) using a mathematical tomography > routine > essentially identical to the one used in medicine CT. This is what I > tried to > explain in my News & Views article in Nature." > > #3. My current thoughts on these emails and orbitals: > > One of the authors admitted that the "measuring an orbital" claim was > deliberately provocative. He also said that one could view the > experiment as only providing information about matrix elements. > Unfortunately, I don't understand the latter, so I can't say whether he > is withdrawing his claim of "measuring an orbital". Perhaps he still > means this? Perhaps not. > > Both of the authors pointed to other publications that describe > experimental techniques for observing wave functions. I have not read > these publications yet and I don't know what they will tell me. I > suspect (but this is only a suspicion) that the maximal claim will be > one can get information about the *full* molecular wave function. The > minimal claim may turn out to be quite a bit less. > > Supposing that one can get information about *full* wave functions, is > it correct to claim that one can "measure orbitals"? (I believe that > this is Sengen Sun's question.) > > This poses interesting questions about what we mean by measurement and > reality. I don't want to get entangled with these deep issues. I will be > > simple-minded and assume experimental measurements are real. > > Some of the emails that I have read so far in this discussion make the > following argument: if an experiment generates data Y that looks like a > familiar entity X, then it is reasonable to say that Y tells us > something useful about X. Other emails have gone farther: since Y comes > > from an experiment ("Y is real" !), it is inappropriate to object to > "Y > tells us about X" on merely theoretical grounds. > > There is something to both of these arguments, but it is important to > recognize their limitations. "Y tells us about X" is an interpretation > of experimental data. It is a mental decision that comes after the > experiment and not an intrinsic property of these data. If we decide to > challenge this interpretation (and this can be done on a variety of > grounds, including theoretical notions about X), we are not jeopardizing > > the status of Y as experimental data. We are only contesting the > interpretation of Y. > > Also, we have to remember that the interpretation "Y tells us about X", > even though it looks reasonable, may be incorrect. Y may be correlated > with our ideas about X, but there may be good reasons for thinking that > X cannot cause Y. > > Let's take a familiar example. Koopmans theorem equates experimental > ionization energies with orbital energies (when the orbitals are defined > > in a certain way). Many experiments have shown that there is rough, > sometimes excellent, agreement between measured energies (Y) and orbital > > energies (X). At this point, we might be tempted to say "Y tells us > about X". Are we correct in doing this? > > I think there is general agreement that Y (experimental ionization > energies) do *not* tell us about X (orbital energies) even though this > is an attractive (and frequently used) interpretation. First, we can > object to this interpretation on purely theoretical grounds: 1) > according to quantum theory, orbitals are not real, so when a molecule > is ionized, we are not "really" changing the occupancy of one orbital > and leaving the other orbitals unchanged, and 2) quantum theory provides > > an alternative description of ionization in terms of molecular states. > The latter description is a) quantitatively more successful than the > "orbital energy" interpretation, and b) is internally consistent with > the rest of quantum theory. > > If one stubbornly insisted that ionization energies tell us about > orbital energies, I would have to ask, "since the task of theory is to > explain experiment, do you plan to revise quantum theory so that it > predicts orbital energies in accord with experiment?" It is interesting > that this hasn't happened. Chemists are largely satisfied with the > current quantum theory (it isn't broken) even when they find the > siren-call of orbitals irresistable. This is an example of the > compartmentalized thinking that we all engage in; different parts of my > mind happily and simultaneously cling to contradictory points of view. > > Coming back to the newest experiment in Nature (which I still don't > understand): I don't think it can actually be measuring something about > orbitals because quantum theory says 1) orbitals are not real, and 2) > the theory always provides a superior orbital-free way to describe the > experiment. I wish I could supply the latter, but I can't (yet). > > If you feel that my inability to provide an orbital-free explanation > proves that the "experiment tells us about orbitals", then I would say > you have two challenges ahead of you. 1) Since current quantum theory > says orbitals are not real, come up with a new quantum theory in which > orbitals are real and have measurable properties. 2) Since your new > theory will say that orbitals are real, accept the theoretical challenge > > of bringing your theory into line with experiment, i.e., modify it so > that it correctly reproduces experimentally measured orbital properties. > > If you are still caught in the middle -- not ready to give up the > current theory, but you find the apparent similarity/correlation of > experimental data and orbital shapes appealing, inspiring, provocative, > and qualitatively useful -- I can sympathize. > > Alan > > -- > Alan Shusterman > Chemistry Department > Reed College > Portland, OR 97202-8199 > 503-517-7699 > http://academic.reed.edu/chemistry/alan/ > "The Way you can go isn't the real Way." Lao Tzu > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Fri Jan 21 05:36:24 2005 Received: from gvedoh01.emea.givaudan.com (mail-external3.givaudan.com [57.66.141.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0LAaKi3019902; Fri, 21 Jan 2005 05:36:23 -0500 To: Nicolas Saettel Cc: chemistry~at~ccl.net, "Computational Chemistry List" Subject: Re: CCL:SMILE to table MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy~at~givaudan.com Date: Fri, 21 Jan 2005 11:36:17 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 21/01/2005 11:36:22, Serialize complete at 21/01/2005 11:36:22 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=2.0 required=7.5 tests=IMPRONONCABLE_1,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j0LAaOi3019909 Try EPI Suite (http://www.epa.gov/oppt/p2framework/docs/epiwin.htm). Regards, Dr. Andras Borosy Seniour Scientist Delivery Systems, Fragrance Research Givaudan Schweiz AG Ueberlandstr. 138 8600 D|bendorf Switzerland tel: + 41-1-8242164 fax: +41-1-8242926 e-mail: andras.borosy~at~givaudan.com Nicolas Saettel Sent by: "Computational Chemistry List" 20.01.2005 18:55 To: chemistry~at~ccl.net cc: Subject: CCL:SMILE to table Hi all, I am looking for a freeware software to translate a text file containing lines with SMILES strings + name of the compounds in a table (HTML, GIF... or a simple view I can print out) with the 2D drawing AND the name of the compounds. mview from Jchem seems to only give me the 2D drawings... Thank you, Nicolas -- Nicolas Saettel, Ph.D., Assistant Professor CERMN - 5, rue Vaubinard - F-14032 CAEN CEDEX Tel. +33.(0)2.31.56.59.10 Fax +33.(0)2.31.93.11.88 UFR des Sciences Pharmaceutiques - Bd Becquerel - F-14032 CAEN CEDEX Tel. +33.(0)2.31.56.60.09 Fax +33.(0)2.31.56.60.20 http://www.cermn.unicaen.fr - http://www.pharmacie.unicaen.fr << Attachment Removed : nicolas.saettel.vcf >> From chemistry-request@ccl.net Fri Jan 21 19:37:03 2005 Received: from fmmailgate04.web.de (fmmailgate04.web.de [217.72.192.242]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0M0b1i3029974 for ; Fri, 21 Jan 2005 19:37:02 -0500 Received: by fmmailgate04.web.de (8.12.10/8.12.10/webde Linux 0.7) with ESMTP id j0LNJh2K014345 for ; Sat, 22 Jan 2005 00:19:43 +0100 Received: from [80.140.11.120] (helo=[192.168.6.2]) by smtp06.web.de with asmtp (TLSv1:RC4-MD5:128) (WEB.DE 4.103 #184) id 1Cs83s-00067s-00; Sat, 22 Jan 2005 00:19:29 +0100 From: Bernd Schubert To: Bryan Putnam Subject: Re: CCL:Building g03 on Opteron64 system with RedHat Enterprise Date: Sat, 22 Jan 2005 00:19:27 +0100 User-Agent: KMail/1.7.2 References: In-Reply-To: Cc: CCL MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200501220019.27978.bernd-schubert[at]web.de> Sender: bernd-schubert[at]web.de X-Sender: bernd-schubert[at]web.de X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Bryan, > We're using PGI compilers 5.2-4 don't use this version! 32bit G03 binaries compiled with this compiler version immediately crash in link101 on our our systems (debian sarge) and 64bit binaries will crash in rather many of the G03 test jobs. We told PGI this and a much worse issue and were told that we either should use version 5.1 or wait until February for version 6. With version 5.1 we could successfully compile G03 and the results of the test jobs are also fine. On the other hand molpro and molcas have issues with 5.1, but for those 5.2 works fine... > > If I attempt to build using the shared util.so, I get error messages that > the libatlas-amd64 and libf77blas-amd64 libraries need to be compiled with G03 has its own atlas libraries, are you using them? Those worked fine for us, though its on a debian biarch64 system. The PGI compiler also asks you during the installation process to install the blas/lapack libraries developed by AMD (ACML). Its rather easy to change the Makefiles to use this library. However, there's another issue with the PGI compiler: You need to specy the full path to the library, the usual options "-Lpath_to_acml -lacml" don't work. Must be something PGI and linker (ld) related, I couldn't find out the reason. Hope it helps, Bernd From chemistry-request@ccl.net Fri Jan 21 13:57:05 2005 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0LIv3i3012661 for ; Fri, 21 Jan 2005 13:57:03 -0500 Received: from Compaq (x2-04-162.goldrush.com [64.162.10.162]) by smtp.goldrush.com (8.12.8/8.12.8) with SMTP id j0LHkYx6024621; Fri, 21 Jan 2005 09:46:43 -0800 From: "Steve Bowlus" To: "Michel Petitjean" , Subject: CCL:RE: [Re]: orbitals and reality Date: Fri, 21 Jan 2005 09:46:33 -0800 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) In-Reply-To: <200501211017.j0LAHGUi120016(at)ds10.itodys.jussieu.fr> X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Importance: Normal X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: chezbowlus(at)goldrush.com X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hmmm ... the tone of this discussion reminds me of my undergraduate philosophy of science course. If my memory serves, there was a school of philosophers which held that "reality" and "real objects" were defined by the operation(s) that measured them. Essentially, an object was "made" real by the process of measuring it, and defined by the measurement. An extreme view within the school held that particular reality was true for only so long as the measuring operation was applied ... Orbitals as mathematical constructs certainly exist (as equations on paper and in the cool, color graphics of which we are so fond); it may be that orbitals as objects could not be realized because we had no means to measure or observe them. There is/was no property defining "orbital-ness." Within this school (and applying the sturdy ignorance of common sense), I would suggest that a "free" (same as "virtual?") orbital does not physically exist until it is populated: it lacks the fundamental property (observability) needed to define it. This is not the same as "What properties would we expect if the orbital were populated?" ... which is how we define virtual orbitals in the first place. The above school of thought gives an interesting perspective on the old saw, "Does a tree falling in the forest make noise if no one is there to here it?" Similarly, do orbitals exist if we have no way to observe them? Maybe someone out there who is a serious student of the philosphy of science could comment on this aspect, or refer the thread to a scientist/philosopher who is ... sb -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request(at)ccl.net]On Behalf Of Michel Petitjean Sent: Friday, January 21, 2005 2:17 AM To: chemistry(at)ccl.net Subject: CCL:[Re]: orbitals and reality To: chemistry(at)ccl.net Subject: CCL:[Re]: orbitals and reality Dear CCLers, I have not read the original paper from which the debate seems to originate, but I have here a naive question for those who think that an orbital is a physical thing rather than a mathematical model: what is the physical reality of a free orbital (i.e. no electron inside) ? Michel Petitjean Email: petitjean(at)itodys.jussieu.fr FIS2005 coordinator http://www.mdpi.org/fis2005 Editor-in-Chief of Entropy http://www.mdpi.org/entropy ITODYS (CNRS, UMR 7086) 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY(at)ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(at)ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow(at)nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Jan 21 17:05:18 2005 Received: from mail.iinet.net.au (mail-05.iinet.net.au [203.59.3.37]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0LM59i3023540 for ; Fri, 21 Jan 2005 17:05:11 -0500 Received: (qmail 13941 invoked from network); 21 Jan 2005 20:52:30 -0000 Received: from unknown (HELO octa4.net.au) (203.217.38.189) by mail.iinet.net.au with SMTP; 21 Jan 2005 20:52:27 -0000 Received: by octa4.net.au (sSMTP sendmail emulation); Sat, 22 Jan 2005 07:51:22 +0930 Date: Sat, 22 Jan 2005 07:51:22 +0930 From: Brian Salter-Duke To: chemistry[at]ccl.net Subject: Re: CCL:orbitals and reality Message-ID: <20050121222122.GA2488[at]monster.ntu.edu.au> Reply-To: Brian Salter-Duke Mail-Followup-To: chemistry[at]ccl.net References: <41EFF6D9.40200[at]reed.edu> <20050121044204.96289.qmail[at]web30806.mail.mud.yahoo.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20050121044204.96289.qmail[at]web30806.mail.mud.yahoo.com> User-Agent: Mutt/1.5.4i X-Spam-Status: No, hits=2.1 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Thu, Jan 20, 2005 at 08:42:03PM -0800, Guosheng Wu wrote: > --- Alan Shusterman wrote: > > ... Coming back to the newest experiment in Nature (which I still don't > > understand): I don't think it can actually be measuring something about > > orbitals because quantum theory says 1) orbitals are not real... > > Okay, it means you are still interested in the topic b/c you are not > deleting it without any reading :-) > > I still think in some sense that Nature paper did measure something about > wave function (or "orbital"=wave function in QM). > > Wave function psi describes the state of a particle in QM just like r(t) & > p(t) for a classical particle, and sometimes it's refered to be > probability amplitude(real number), but not the actual probability because > of the uncertainty of a phase term [cos(theta)+i*sin(theta)]. > ||^2 is the probability density, given psi is normalized. > > For simplicity, let's forget time varible b/c no interest in dynamics yet. > > Well, certainly wave function is not "real" mathematically, since it's a > complex function and one can easily put a phase term (above) besides it > without changing any properties of the system. But how can we observe > something not "real", even mathematically? The thing is that Nature paper > only mapped the probability amplititude of the wave function, not saying > they "observed" the whole wave function. > > One simple solvable example in QM is hydrogen atom (without any confusion > with basis set or multiple electrons). The distribution of its wave > function (or probability amplititude) in the 3D space is well-defined and > solved analytically. I guess no one needs more explanation for this part. > Certainly the probability amplititude of H atom in 3D space could be > mapped out experimentally. For example, one could measure its angular > distribution of |<1s|1s>|^2 experimentally, then psi(1s) can be got by > taking sqrt of(|<1s|1s>|^2), just 0.5/sqrt(pai) since it's a sphere, no > exp. needed at all! Again one can add a phase term to it to make it not > "REAL", but it does not mean one can not map out ("observe") the wave > function's probability amplititude. > > It's similar for molecule like N2, or even more complicated. I do not > think there is any conceptual difference for the above description. We > just need more mathematical equations to describe them and solve them. > > All in all, that Nature paper did not observe the orbital of N2, but > mapped out some of its probability amplititudes. > > If one really likes to argue, then he could simply say: since everything > of QM is about wave function, and any wave function is not actually real > function, so all QM related stuff has no any reality. Oops, I am almost > trapped by myself. > > -Guosheng I have been holding back commenting on this topic because I have not read the Nature paper, but I do want to make one comment that arises in part from the above post but also from others. I think we should make a clear distinction between the total wave function and an orbital. For the H atom, they are the same, but in N2 they are not. I am quite happy about observing something to do with the total wave fuction, but orbitals are another thing. Orbitals are mathematical objects that are "not real" in a quite different way from wave functions being not real. In general orbitals are objects in the Hartree-Fock approximation. They do not approach a "true" orbital as we improve things, but only the orbitals of the Hartree-Fock limit which is still an approximate wave function. However approximate wave functions can be improved to approach the true wave functions, but only by going beyond the Hartree-Fock method and losing any sense of one-electron orbitals. Another post about Koopman's theorem illustrates this. We are confusing ourselves if we think photoelectron spectroscopy observes orbital energies. It observes differences in energies between a molecule and its ion with the latter in various electronic states. Similarly I suspect that this experiment is not observing orbitals but the difference in the wave function for the molecule and its ion, or perhaps just the difference in electron density. The comment about true orbitals from density functional theory is also interesting. This is that if we have the correct functional the DFT orbitals are the same as the difference between the total wave function of the molecule and its ion. The problem is that we do not have the correct functional and no systematic way of moving from present functionals to the correct functional. When we talk about orbitals we are always talking about components of an approximate total wave function not the exact total wave function. We can not observe something that is a componet of an approximate wave function. > --- Alan Shusterman wrote: > > > My 2 cents (devalued by years of inflation)... > > > > I read both Nature papers, the original research and the news > > perspective. I confess that I couldn't understand the experimental > > technique as described in either paper. Therefore, I cannot describe the > > > > experimental technique in terms of quantum theory. > > > > So I wrote the authors of both papers for more information. Both of them > > > > were kind enough to respond to my note and I hope that we will continue > > to exchange emails because I have more to learn. I have put their > > comments below and added my own thoughts about orbitals at the end. > > > > #1. Response from David Villeneuve: > > > > "I don't want to leave you unhappy. We were being somewhat provocative > > to > > show an orbital wave function, knowing that introductory quantum > > mechanics > > courses say that you cannot do this. However it is known that one can > > measure a quantum state if the system can be repeatedly prepared in the > > same > > state (see A Royer, Foundations of Physics 19, 3 (1989)). We use an > > interference technique of the same electron with itself to record the > > phase > > of the wave function. > > > > The other issue is whether a set of single-electron wave functions can > > represent the N body quantum system. The answer is no, but quantum > > chemists > > do it anyway. It is the best that we can do. There is lots of work in > > molecular structure that depends on these approximations, such as > > GAUSSIAN > > ab initio calculations. SO even if orbitals do not exist, they are > > extensively used. > > > > I learned after we published this, that the HOMO of N2 is not that well > > known. See Maksic and Vianello, J Phys Chem 106, 6515 (2002), and > > Stowasser > > and Hoffman, J Am Chem Soc 121, 3414 (1999) for conflicting > > calculations. > > > > Finally, if you are still unhappy, you can just think that we measured a > > set > > of transition dipole matrix elements from some state to a set of > > continuum > > plane waves." > > > > #2. Response from Henrik Stapelfeldt: > > > > "It is well established that a wave function or an orbital is not > > directly > > observable for a single quantum system. However, a set of measurements > > of > > observables (which are real measurable quantities) on a sufficiently > > large > > number of identically prepared systems may contain enough information to > > determine the wave function (or more generally the density matrix) of > > the > > system considered up to an overall phase. > > > > This approach has been taken in a large number of works over the past > > decade > > experimentally as well as theoretically. For instance, using quantum > > tomography > > the density matrix, or equivalently the Wigner function, has been > > reconstructed > > for vibrational states of molecules, nonclassical states of light, > > trapped > > ions, atomic beams and dissociating molecules. I will be happy to send > > you > > references if you are not familiar with these works. > > > > In the recent work of Itatani et al. in Nature the molecular orbital is > > reconstructed from a large number of measurements of laser induced high > > harmonic spectra (the observables) using a mathematical tomography > > routine > > essentially identical to the one used in medicine CT. This is what I > > tried to > > explain in my News & Views article in Nature." > > > > #3. My current thoughts on these emails and orbitals: > > > > One of the authors admitted that the "measuring an orbital" claim was > > deliberately provocative. He also said that one could view the > > experiment as only providing information about matrix elements. > > Unfortunately, I don't understand the latter, so I can't say whether he > > is withdrawing his claim of "measuring an orbital". Perhaps he still > > means this? Perhaps not. > > > > Both of the authors pointed to other publications that describe > > experimental techniques for observing wave functions. I have not read > > these publications yet and I don't know what they will tell me. I > > suspect (but this is only a suspicion) that the maximal claim will be > > one can get information about the *full* molecular wave function. The > > minimal claim may turn out to be quite a bit less. > > > > Supposing that one can get information about *full* wave functions, is > > it correct to claim that one can "measure orbitals"? (I believe that > > this is Sengen Sun's question.) > > > > This poses interesting questions about what we mean by measurement and > > reality. I don't want to get entangled with these deep issues. I will be > > > > simple-minded and assume experimental measurements are real. > > > > Some of the emails that I have read so far in this discussion make the > > following argument: if an experiment generates data Y that looks like a > > familiar entity X, then it is reasonable to say that Y tells us > > something useful about X. Other emails have gone farther: since Y comes > > > from an experiment ("Y is real" !), it is inappropriate to object to > > "Y > > tells us about X" on merely theoretical grounds. > > > > There is something to both of these arguments, but it is important to > > recognize their limitations. "Y tells us about X" is an interpretation > > of experimental data. It is a mental decision that comes after the > > experiment and not an intrinsic property of these data. If we decide to > > challenge this interpretation (and this can be done on a variety of > > grounds, including theoretical notions about X), we are not jeopardizing > > > > the status of Y as experimental data. We are only contesting the > > interpretation of Y. > > > > Also, we have to remember that the interpretation "Y tells us about X", > > even though it looks reasonable, may be incorrect. Y may be correlated > > with our ideas about X, but there may be good reasons for thinking that > > X cannot cause Y. > > > > Let's take a familiar example. Koopmans theorem equates experimental > > ionization energies with orbital energies (when the orbitals are defined > > > > in a certain way). Many experiments have shown that there is rough, > > sometimes excellent, agreement between measured energies (Y) and orbital > > > > energies (X). At this point, we might be tempted to say "Y tells us > > about X". Are we correct in doing this? > > > > I think there is general agreement that Y (experimental ionization > > energies) do *not* tell us about X (orbital energies) even though this > > is an attractive (and frequently used) interpretation. First, we can > > object to this interpretation on purely theoretical grounds: 1) > > according to quantum theory, orbitals are not real, so when a molecule > > is ionized, we are not "really" changing the occupancy of one orbital > > and leaving the other orbitals unchanged, and 2) quantum theory provides > > > > an alternative description of ionization in terms of molecular states. > > The latter description is a) quantitatively more successful than the > > "orbital energy" interpretation, and b) is internally consistent with > > the rest of quantum theory. > > > > If one stubbornly insisted that ionization energies tell us about > > orbital energies, I would have to ask, "since the task of theory is to > > explain experiment, do you plan to revise quantum theory so that it > > predicts orbital energies in accord with experiment?" It is interesting > > that this hasn't happened. Chemists are largely satisfied with the > > current quantum theory (it isn't broken) even when they find the > > siren-call of orbitals irresistable. This is an example of the > > compartmentalized thinking that we all engage in; different parts of my > > mind happily and simultaneously cling to contradictory points of view. > > > > Coming back to the newest experiment in Nature (which I still don't > > understand): I don't think it can actually be measuring something about > > orbitals because quantum theory says 1) orbitals are not real, and 2) > > the theory always provides a superior orbital-free way to describe the > > experiment. I wish I could supply the latter, but I can't (yet). > > > > If you feel that my inability to provide an orbital-free explanation > > proves that the "experiment tells us about orbitals", then I would say > > you have two challenges ahead of you. 1) Since current quantum theory > > says orbitals are not real, come up with a new quantum theory in which > > orbitals are real and have measurable properties. 2) Since your new > > theory will say that orbitals are real, accept the theoretical challenge > > > > of bringing your theory into line with experiment, i.e., modify it so > > that it correctly reproduces experimentally measured orbital properties. > > > > If you are still caught in the middle -- not ready to give up the > > current theory, but you find the apparent similarity/correlation of > > experimental data and orbital shapes appealing, inspiring, provocative, > > and qualitatively useful -- I can sympathize. > > > > Alan > > > > -- > > Alan Shusterman > > Chemistry Department > > Reed College > > Portland, OR 97202-8199 > > 503-517-7699 > > http://academic.reed.edu/chemistry/alan/ > > "The Way you can go isn't the real Way." Lao Tzu > > > > > > > > To send e-mail to subscribers of CCL put the string CCL: on your > > Subject: line > > > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST[at]ccl.net > > > > > > > > > > > > > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY[at]ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow[at]nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > -- Brian Salter-Duke (Brian Duke) b_duke[at]octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-92992847. http://members.iinet.net.au/~linden1/brian/ From chemistry-request@ccl.net Fri Jan 21 15:10:22 2005 Received: from smtp1.kodak.com (smtp1.kodak.com [192.232.121.200]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0LKALi3018014 for ; Fri, 21 Jan 2005 15:10:21 -0500 Received: from roc-us-e1000-111.kodak.com (roc-us-e1000-111.kodak.com [192.232.121.191]) by smtp1.kodak.com (8.11.3/8.11.1) with SMTP id j0LGXuF19269; Fri, 21 Jan 2005 11:33:56 -0500 (EST) Received: from (150.221.122.53) by roc-us-e1000-111.kodak.com via smtp id 3c8e_672ef634_6bcb_11d9_99e1_0002b3efa0be; Fri, 21 Jan 2005 11:42:13 -0500 (EST) To: chemistry~at~ccl.net Cc: schrecke~at~cc.umanitoba.ca Subject: Summary: Silver NMR shifts using PBC X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: leif.olson~at~kodak.com Date: Fri, 21 Jan 2005 11:33:52 -0500 X-MIMETrack: S/MIME Sign by Notes Client on Leif P. Olson/436438/EKC(Release 5.0.5 |September 22, 2000) at 01/21/2005 11:33:53 AM, Serialize by Notes Client on Leif P. Olson/436438/EKC(Release 5.0.5 |September 22, 2000) at 01/21/2005 11:33:53 AM, Serialize complete at 01/21/2005 11:33:53 AM, S/MIME Sign failed at 01/21/2005 11:33:53 AM: The cryptographic key was not found, Serialize by Router on KNOTES2/ISBP/EKC(652HF120|July 29, 2004) at 01/21/2005 11:33:56 AM, Serialize complete at 01/21/2005 11:33:56 AM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 005AFE2E85256F90_=" X-Spam-Status: No, hits=2.8 required=7.5 tests=FREE_TRIAL,HTML_20_30, HTML_MESSAGE,MK_BAD_HTML_04,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multipart message in MIME format. --=_alternative 005AFE2E85256F90_= Content-Type: text/plain; charset="us-ascii" Hello CCL, I received several replies to my question from January 12th, about computing Ag-109 chemical shifts of a crystal, using periodic boundary conditions. The purpose of this is to compare the results to a CP-MAS solid-state NMR spectrum. Thanks to Stan van Gisbergen (SCM), George Fitzgerald (Accelrys), Alex Hofmann (Humboldt-Universitaet Berlin), and Georg Schreckenbach (U. of Manitoba) for their assistance. Their slightly edited replies are pasted at bottom. It seems PARATEC, CPMD, and NMR-CASTEP can do NMR shifts using PBC. Maybe other programs do too, but those are the ones I now know about. Alex suggested that with CPMD, wavefunction convergence with metals could be difficult. Although ADF does not seem to have NMR capability using PBC yet, Georg and his research group are working on this now, based on the ADF-BAND code. Meanwhile I am weighing options, including the idea of cluster vs. PBC. Leif Olson Eastman Kodak Research Laboratories P.S. about using ECPs on metal atoms...though I have not done a lot of basis set testing, I have found that for Ag, the DFT-optimized DZVP (sometimes called "DZVP2", I think?) basis set of Godbout et al. works well in many situations where an all-electron basis set is needed. ***** Dear Dr. Olson, I hope the following commercial information is relevant to your question. Our Amsterdam Density Functional (ADF) program is very well suited for calculating NMR parameters of molecules and clusters [both spin-spin coupling and chemical shifts]. Relativistic effects [scalar and spin-orbit] can be taken into account if needed. All-electron NMR calculations are no problem. The NMR code runs in parallel, so large clusters can be handled with ease. This has been successfully applied to solid-state NMR as well because a [large] cluster description is often sufficient. We can offer you a free trial for ADF if you would like to see how it works for your system(s). I could also send you some NMR references related to ADF and/or the general ADF brochure, and/or provide further details by phone [also on recent developments for solid-state NMR in our periodic structure program BAND], all upon your request. Best regards, Stan van Gisbergen ***** Dear Leif, Accelrys offers the program NMR CASTEP for computing NMR chemical shifts and electric field gradient tensors for solid-state systems. You can find more information on our web site at http://www.accelrys.com/mstudio/ms_modeling/nmrcastep.html. The underlying method is similar to that implemented in PARATEC. The CASTEP interface, however, makes the implementation very easy to use. I will contact you privately with additional information. Sincerley, George Fitzgerald ***** Hi Leif, I think CPMD is in that sense not better than many other plane wave codes. Especially it might be tricke to get wavefunction convergency with metals in CPMD. For this you may consult experts like Ari Seitsonen or somebody connected to the CPMD-group. Another way may be to cut part of the crystal as (highly symmetric) cluster and do that with Gaussian or Turbomole. Hth Alex ***** Dear Leif, Briefly, we are also working on the very subject (to create such a method, that is), and we hope to have a running code (based on ADF-BAND) in about a year -- although I might be optimistic. As to your questions: 1. Gaussian cannot do it at the moment, as you have found out. 2. If you find a code that can do it, you need to be a bit careful because: - to get the metal NMR chemical shift right, you don't normally want a pseudopotential (ECP) at that very atom. Some workarounds have been discussed in the lit. but I am not sure about the latest details. - on the other hand, you probably need a relativistic description of your system, although you MIGHT just barely get by without for a second transition row atom. Best regards, Georg ***** --=_alternative 005AFE2E85256F90_= Content-Type: text/html; charset="us-ascii"
Hello CCL,

I received several replies to my question from January 12th, about computing
Ag-109 chemical shifts of a crystal, using periodic boundary conditions.  The
purpose of this is to compare the results to a CP-MAS solid-state NMR spectrum.

Thanks to Stan van Gisbergen (SCM), George Fitzgerald (Accelrys), Alex
Hofmann (Humboldt-Universitaet Berlin), and Georg Schreckenbach
(U. of Manitoba) for their assistance.  Their slightly edited replies are pasted
at bottom.

It seems PARATEC, CPMD, and NMR-CASTEP can do NMR shifts using PBC.  
Maybe other programs do too, but those are the ones I now know about.
Alex suggested that with CPMD, wavefunction convergence with metals
could be difficult.  

Although ADF does not seem to have NMR capability using PBC yet, Georg
and his research group are working on this now, based on the ADF-BAND code.

Meanwhile I am weighing options, including the idea of cluster vs. PBC.

Leif Olson
Eastman Kodak Research Laboratories

P.S. about using ECPs on metal atoms...though I have not done a lot of
basis set testing, I have found that for Ag, the DFT-optimized DZVP
(sometimes called "DZVP2", I think?) basis set of Godbout et al. works well
in many situations where an all-electron basis set is needed.

*****

Dear Dr. Olson,

I hope the following commercial information is relevant to your
question.

Our Amsterdam Density Functional (ADF) program is very well suited for
calculating NMR parameters
of molecules and clusters [both spin-spin coupling and chemical shifts].
Relativistic effects [scalar and spin-orbit] can be taken into account
if needed.
All-electron NMR calculations are no problem. The NMR code runs in
parallel, so large clusters can
be handled with ease.

This has been successfully applied to solid-state NMR as well because a
[large] cluster description is often
sufficient.

We can offer you a free trial for ADF if you would like to see how it
works for your system(s).
I could also send you some NMR references related to ADF and/or the
general ADF brochure,
and/or provide further details by phone [also on recent developments
for solid-state NMR
in our periodic structure program BAND], all upon your request.

Best regards,
Stan van Gisbergen

*****

Dear Leif,

Accelrys offers the program NMR CASTEP  for computing NMR chemical shifts and
electric field gradient tensors for solid-state systems. You can find more information on our web site at http://www.accelrys.com/mstudio/ms_modeling/nmrcastep.html. The underlying method is similar to that implemented in PARATEC. The CASTEP interface, however, makes the implementation very easy to use.

I will contact you privately with additional information.

Sincerley,
George Fitzgerald

*****

Hi Leif,

I think CPMD is in that sense not better than many other plane wave codes. Especially it might be tricke to get wavefunction convergency with metals in CPMD. For this you may consult experts like Ari Seitsonen or somebody connected to the CPMD-group.

Another way may be to cut part of the crystal as (highly symmetric) cluster and do that with Gaussian or Turbomole.

Hth

Alex

*****

Dear Leif,

Briefly, we are also working on the very subject (to create such a
method, that is), and we hope to have a running code (based on
ADF-BAND) in about a year -- although I might be optimistic.

As to your questions: 1. Gaussian cannot do it at the moment, as you
have found out.
2. If you find a code that can do it, you need to be a bit careful
because:
- to get the metal NMR chemical shift right, you don't normally want a
pseudopotential (ECP) at that very atom. Some workarounds have been
discussed in the lit. but I am not sure about the latest details.
- on the other hand, you probably need a relativistic description of
your system, although you MIGHT just barely get by without for a second
transition row atom.

Best regards, Georg

***** --=_alternative 005AFE2E85256F90_=-- From chemistry-request@ccl.net Fri Jan 21 19:11:58 2005 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0M0Bui3028726 for ; Fri, 21 Jan 2005 19:11:57 -0500 Received: from degas.scripps.edu (degas [137.131.252.44]) by relay1.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id j0LNBSa3000684 for ; Fri, 21 Jan 2005 15:11:28 -0800 (PST) Received: (from lou@localhost) by degas.scripps.edu (8.11.7+Sun/TSRI-4.1.0) id j0LNBKD18424; Fri, 21 Jan 2005 15:11:20 -0800 (PST) Date: Fri, 21 Jan 2005 15:11:20 -0800 (PST) From: Lou Noodleman Message-Id: <200501212311.j0LNBKD18424:at:degas.scripps.edu> To: chemistry:at:ccl.net Subject: Re: CCL:Orbitals and reality Cc: lou:at:scripps.edu X-Sun-Charset: US-ASCII X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Scanned-By: CanIt (www . roaringpenguin . com) on 137.131.200.29 X-Spam-Status: No, hits=2.4 required=7.5 tests=OPT_HEADER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Phil Hultin, Alan Shusterman and CCL group, About May of last year, I sent a post to CCL on this topic. My view then and now (a little more philosophically then) is that "orbitals" are not reality itself, but rather an extremely valuable concept useful for describing reality. That is, the orbital concept is "a map, but not the territory". At that time, I mentioned e-2e inelastic scattering experiments, which report the electron momentum distribution function (orbital densities in momentum space) for individual molecular orbitals and at the same time the experiment reports the ionization potentials IP(n) of the various ion states from the neutral ground state. Roughly speaking, these experiments report the shapes of the molecular orbitals. The cation states can correspond to the main one-hole ionization lines and also to their shakeup satellites. Specifically, these orbitals are well defined and are called Dyson orbitals. For example, see Pang et al., J. Chem. Phys.112, 8043 (2000) for a combined experimental-theoretical/computational study. Typically, the high-lying molecular orbitals are well-defined experimentally (those that lie at less than about 14 eV (IP) for saturated hydrocarbons), while deeper lying orbitals show more mixing and eventually "a breakdown of the orbital picture of ionization" for the inner valence shell C(2s), at about 23 eV and deeper. Also, in work in my own research group, we showed that the delocalized molecular orbital picture of ionization breaks down for inner electron shells and for lone pairs in dimers and for symmetry equivalent groups (examples: N2, O3, Cr(CO)6, Se(CN)2) when electron relaxation from the "passive electrons (and their orbitals)" is stronger than the bonding or antibonding interactions between the symmetry equivalent lone pairs or inner shell electrons. Then a localized excitation dominates, with a much smaller splitting bonding/antibonding for the relaxed hole state. (Noodleman et al., Chem. Phys. 64, 159-166, 1982, and Jonkers et al., Mol. Phys. 46, 609-620, 1982) As in the examples above, these are questions of physics and chemistry, comparing calculations and experiment, and not (mainly) of philosophy. It is true that sets of occupied orbitals can be transformed to other sets (equally valid) under a unitary transformation, for example, delocalized MO's to localized MO's, but this is not true for ionization states or optical excitations. Further, not only electron density, but also kinetic energy matters, and for excited states, transition moments determine intensities. While in principle, electron orbitals can be circumvented in the analysis with reduced density matrices and transition density matrices, but how do you compute, use, and understand these without simpler tools. In practice, orbitals are the simplest way to incorporate both electron kinetic energy and electron density (also spin density) in descriptions of atoms, molecules, and solids. Here I understand that I differ > from Bader's ideas, although I like forces and the virial theorem as much as the next fellow. Also, a "mean field" (orbital) description is always valuable. Niels Bohr has emphasized a number of complementarity relations (as in the Heisenberg Uncertainty Principle). In addition to "position-momentum", "Energy-time", and "particle-wave", the complementary variable to "accuracy" is "clarity". Einstein has recommended that a good theory be "as simple as possible, but no simpler". In my mind, this strongly supports the use of the orbital concept. Louis Noodleman Dept. of Molecular Biology, TPC15 The Scripps Research Institute La Jolla, CA 92037 .