From chemistry-request@ccl.net Wed Jan 19 10:28:46 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0JFSiYr017871 for ; Wed, 19 Jan 2005 10:28:44 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id BCDE33241D3 for ; Wed, 19 Jan 2005 10:23:00 -0500 (EST) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 31691-03 for ; Wed, 19 Jan 2005 10:23:00 -0500 (EST) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id E5C8C3241D2 for ; Wed, 19 Jan 2005 10:22:59 -0500 (EST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Wed, 19 Jan 2005 10:25:27 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C4FE3B.19CFEA27" Subject: RE: orbitals and reality Date: Wed, 19 Jan 2005 10:25:26 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78A4A)at(srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: orbitals and reality Thread-Index: AcT+LdcCeQvYjPRpSkSBFrX9Fn7gBQACPQTg From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 19 Jan 2005 15:25:27.0327 (UTC) FILETIME=[1A6FB2F0:01C4FE3B] X-Spam-Status: No, hits=4.1 required=7.5 tests=HTML_20_30,HTML_FONTCOLOR_BLUE, HTML_MESSAGE,HTML_TITLE_EMPTY,NO_RDNS2,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 This is a multi-part message in MIME format. ------_=_NextPart_001_01C4FE3B.19CFEA27 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Demetrios, and CCL readers: =20 I wouldn't read anything into Sengen's use of this forum (CCL) rather = than a letter to the editor, to discuss his disagreement with the = conclusions of the Scerri "orbitals" paper. He may have intended this = to be a philosophical discussion among friends, whereas a letter to the = editor might be considered a direct confrontation. And not everyone = likes to make direct confrontations. =20 =20 On the other hand [Dear Sengen]: Writing a "Comment on..." letter to the = Journal of Chemical Education may be an opportunity to start a debate on = "orbitals and reality--and what should we teach our students?" among = teachers of chemistry. Not to mention a way to lengthen your = publications list. ;-) =20 =20 --David Shobe, Ph.D., M.L.S.=20 S=FCd-Chemie, Inc.=20 phone (502) 634-7409=20 fax (502) 634-7724=20 Don't bother flaming me: I'm behind a firewall.=20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net]On = Behalf Of Demetrios Xenides Sent: Wednesday, January 19, 2005 4:53 AM To: chemistry)at(ccl.net Subject: CCL:orbitals and reality Wouldn't also be a good idea to see something published (comment or = another paper) by the guy (Sengen Sun) who has started the discussion? = If he is so very much determined that the authors have not made an = important step forward on the (possible) mapping of MOs then his = comments would be highly appreciated by the "misleaded" scientific = community. Cheers Demetrios p.s. respect to the people who not only performed a study but they = published it as well. From: Computational Chemistry List on behalf of Sengen Sun Sent: Mon 1/17/2005 4:46 PM To: chemistry)at(ccl.net Subject: CCL:orbitals and reality=20 I have been asked to make a summary on this year discussion on this subject. I received responces from 10 this year. 3 of them are neutral, 5 agree, and 2 disagree. I am specially interested in the disagreements and therefore post them here. I would think the first one might be meaningful. And we will have to see. I would be much happier if Mikael P Johansson and any one else could also critisize my earlier postings on the List as well :-). Here are two examples: http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+07+28+001; http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+06+02+016; The second disagreement is not specific enough. But I will address it later after Mikael P Johansson's next message or posting. Cheers! Sengen =20 --- Mikael P Johansson = wrote: =20 Well, if it helps, I disagree with you :-) I will write up a "pro-orbital" mail for CCL as soon as my work load permits. Happy New Year, Mikael J. http://www.helsinki.fi/~mpjohans/ =20 =20 --- @yahoo.com> wrote: =20 Hello Dr. Sun, It's interesting to see your posts about that paper. Since I am very busy I have not read the details of the paper. However it looks like what they did in the paper is very important and meaningful. I think they derived some information about the orbital from experiments and data analysis, similar to the X-ray data analysis in some sense. Also they mentioned that the phase component of the wave function is arbitary. Very likely they derived the real part or the imaginative part, or at least some of either. So it's still very meaningful =20 =20 =20 __________________________________ Do you Yahoo!? Yahoo! Mail - 250MB free storage. Do more. Manage less. http://info.mail.yahoo.com/mail_250 Send your subscription/unsubscription requests to: = CHEMISTRY-REQUEST)at(ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs and send your message to: CHEMISTRY)at(ccl.net Send your subscription/unsubscription requests to: = CHEMISTRY-REQUEST)at(ccl.net=20 HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs=20 Jan Labanowski, jlabanow)at(nd.edu (read about it on CCL Home Page) =20 ------_=_NextPart_001_01C4FE3B.19CFEA27 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 Demetrios, and CCL readers:
 
I=20 wouldn't read anything into Sengen's use of this forum (CCL) rather than = a=20 letter to the editor, to discuss his disagreement with the conclusions = of the=20 Scerri "orbitals" paper.  He may have intended this to be a = philosophical=20 discussion among friends, whereas a letter to the editor might be = considered a=20 direct confrontation.  And not everyone likes to make direct=20 confrontations. 
 
On the=20 other hand [Dear Sengen]: Writing a "Comment on..." letter to = the Journal=20 of Chemical Education may be an opportunity to start a debate = on=20 "orbitals and reality--and what should we teach our students?" among = teachers of=20 chemistry.  Not to mention a way to lengthen your publications = list.=20 ;-) 
 

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

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

-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request)at(ccl.net]On Behalf Of Demetrios=20 Xenides
Sent: Wednesday, January 19, 2005 4:53 = AM
To:=20 chemistry)at(ccl.net
Subject: CCL:orbitals and=20 reality

Wouldn't also be a good idea to see = something=20 published (comment or another paper) by the guy (Sengen Sun) who has = started=20 the discussion? If he is so very much determined that the authors have = not=20 made an important step forward on the (possible) mapping of MOs then = his=20 comments would be highly appreciated by the "misleaded" scientific=20 community.

Cheers
Demetrios

p.s. respect to the = people who=20 not only performed a study but they published it as = well.



From: Computational Chemistry List on =
behalf of Sengen Sun
Sent: Mon 1/17/2005 4:46 PM
To: chemistry)at(ccl.net
Subject: CCL:orbitals and reality=20




I have been asked to make a summary on this year
discussion on this subject. I received responces from
10 this year. 3 of them are neutral, 5 agree, and 2
disagree. I am specially interested in the
disagreements and therefore post them here. I would
think the first one might be meaningful. And we will
have to see.

I would be much happier if Mikael P Johansson and any
one else could also critisize my earlier postings on
the List as well :-). Here are two examples:

http:/=
/www.ccl.net/cgi-bin/ccl/message.cgi?2003+07+28+001;

http:/=
/www.ccl.net/cgi-bin/ccl/message.cgi?2003+06+02+016;

The second disagreement is not specific enough. But I
will address it later after Mikael P Johansson's next
message or posting.

Cheers!

Sengen
=20
--- Mikael P Johansson <mikael.johansson@helsink=
i.fi>
wrote:


  
Well, if it helps, I =
disagree with you :-) I will
write up a "pro-orbital"
mail for CCL as soon as my work load permits.

Happy New Year,
    Mikael J.
    http://www.helsinki.fi/~mpjoha=
ns/
    

  
--- @yahoo.com> wrote:

  
Hello Dr. Sun,

It's interesting to see your posts about that paper.


Since I am very busy I have not read the details of
the paper. However it
looks like what they did in the paper is very
important and meaningful.

I think they derived some information about the
orbital from experiments
and data analysis, similar to the X-ray data
analysis in some sense. Also
they mentioned that the phase component of the wave
function is arbitary.
Very likely they derived the real part or the
imaginative part, or at
least some of either.  So it's still very meaningful

    

  





              =20
__________________________________
Do you Yahoo!?
Yahoo! Mail - 250MB free storage. Do more. Manage less.
http://info.mail.yahoo.com/m=
ail_250



Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs











and send your message to:  CHEMISTRY)at(ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net=20
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs=20

Jan Labanowski,  jlabanow)at(nd.edu (read about it on =
CCL Home Page)
------_=_NextPart_001_01C4FE3B.19CFEA27-- From chemistry-request@ccl.net Wed Jan 19 11:14:07 2005 Received: from web30803.mail.mud.yahoo.com (web30803.mail.mud.yahoo.com [68.142.200.146]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0JGE6Yr019157 for ; Wed, 19 Jan 2005 11:14:06 -0500 Received: (qmail 14118 invoked by uid 60001); 19 Jan 2005 16:14:02 -0000 Message-ID: <20050119161402.14116.qmail..at..web30803.mail.mud.yahoo.com> Received: from [67.110.18.100] by web30803.mail.mud.yahoo.com via HTTP; Wed, 19 Jan 2005 08:14:02 PST Date: Wed, 19 Jan 2005 08:14:02 -0800 (PST) From: Guosheng Wu Subject: Re: CCL:orbitals and reality To: Demetrios Xenides , chemistry..at..ccl.net In-Reply-To: <41EE2DEC.9030100..at..uibk.ac.at> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=3.0 required=7.5 tests=FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS,FROM_HAS_ULINE_NUMS,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 >--- @yahoo.com> wrote: > Hello Dr. Sun, > > It's interesting to see your posts about that paper. > Since I am very busy I have not read the details of the paper. However it > looks like what they did in the paper is very important and meaningful. > > I think they derived some information about the orbital from experiments > and data analysis, similar to the X-ray data analysis in some sense. Also > they mentioned that the phase component of the wave function is arbitary. > Very likely they derived the real part or the imaginative part, or at > least some of either. So it's still very meaningful. The above short message was actually from me. Later Dr. Sun suggested I post some "rigorous" message on CCL, so just say a few more words, but not necessarily rigorous: (1)What we usually mean "experimental observed" has still been transformed in this or that way from original signals into the final data we called experimental results, and many times mathematical operations are applied to get more meaningful results, such experiments like FT-IR, X-ray for structure... Even what we see with our naked eyes is still just some information transformed by our eyes, brain, lots of neural cells, where lots of mathematical calculations are involved, for example, we know the difference of a sphere and a cube with a glance. (2)Almost all of the current experiments only measure some components of the properties of some object: we either get the mass, the size, electron density, pH,... or whatever, but not everything at a time with a single instrument. That Nature paper did observe some properties of molecular orbital (or molecular wave function), and they did get them with the help of deatiled mathematical operations. It's a wonderful experimental results, and will certainly be very useful in helping us understand many details of chemical reactivity. Of course, it deserves a Nature paper, although there may be some confusing Quantum mechanics terms used in the paper. Well, maybe Dr. Sun is more interested in discussing some kind of philosophy, not the scientific or technical components of the paper. That is more elusive, and maybe not interested to most of the listers. Maybe that's why there has been not many responses to his original post. I strongly suggest Dr. Sun write to the Nature magazine. Hopefully they will publish it with/without any response from the authors, if that discussion is meaningful and interesting to the general scientific public. Thanks for reading, -Guosheng --- Demetrios Xenides wrote: > Wouldn't also be a good idea to see something published (comment or > another paper) by the guy (Sengen Sun) who has started the discussion? > If he is so very much determined that the authors have not made an > important step forward on the (possible) mapping of MOs then his > comments would be highly appreciated by the "misleaded" scientific > community. > > Cheers > Demetrios > > p.s. respect to the people who not only performed a study but they > published it as well. > > > > >From: Computational Chemistry List on behalf of Sengen Sun > >Sent: Mon 1/17/2005 4:46 PM > >To: chemistry..at..ccl.net > >Subject: CCL:orbitals and reality > > > >I have been asked to make a summary on this year > >discussion on this subject. I received responces from > >10 this year. 3 of them are neutral, 5 agree, and 2 > >disagree. I am specially interested in the > >disagreements and therefore post them here. I would > >think the first one might be meaningful. And we will > >have to see. > > > >I would be much happier if Mikael P Johansson and any > >one else could also critisize my earlier postings on > >the List as well :-). Here are two examples: > > > >http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+07+28+001; > > > >http://www.ccl.net/cgi-bin/ccl/message.cgi?2003+06+02+016; > > > >The second disagreement is not specific enough. But I > >will address it later after Mikael P Johansson's next > >message or posting. > > > >Cheers! > > > >Sengen > > > >--- Mikael P Johansson > >wrote: > > > >>Well, if it helps, I disagree with you :-) I will > >>write up a "pro-orbital" > >>mail for CCL as soon as my work load permits. > >> > >>Happy New Year, > >> Mikael J. > >> http://www.helsinki.fi/~mpjohans/ > > > >--- @yahoo.com> wrote: > > > >>Hello Dr. Sun, > >> > >>It's interesting to see your posts about that paper. > >> > >> > >>Since I am very busy I have not read the details of > >>the paper. However it > >>looks like what they did in the paper is very > >>important and meaningful. > >> > >>I think they derived some information about the > >>orbital from experiments > >>and data analysis, similar to the X-ray data > >>analysis in some sense. Also > >>they mentioned that the phase component of the wave > >>function is arbitary. > >>Very likely they derived the real part or the > >>imaginative part, or at > >>least some of either. So it's still very meaningful > >> __________________________________ Do you Yahoo!? Yahoo! Mail - Find what you need with new enhanced search. http://info.mail.yahoo.com/mail_250 From chemistry-request@ccl.net Wed Jan 19 10:26:53 2005 Received: from oceanite.ens-lyon.fr (oceanite.ens-lyon.fr [140.77.1.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0JFQkYr017744 for >ccl.net>; Wed, 19 Jan 2005 10:26:52 -0500 Received: from localhost (oceanite.ens-lyon.fr [127.0.0.1]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id 5DA59320A02 for >ccl.net>; Wed, 19 Jan 2005 16:18:40 +0100 (CET) Received: from oceanite.ens-lyon.fr ([127.0.0.1]) by localhost (oceanite [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 31486-02 for >ccl.net>; Wed, 19 Jan 2005 16:18:40 +0100 (CET) Received: from [140.77.2.67] (mambo.ens-lyon.fr [140.77.2.67]) by oceanite.ens-lyon.fr (Postfix) with ESMTP id 274C0320421 for >ccl.net>; Wed, 19 Jan 2005 16:18:40 +0100 (CET) Message-ID: <41EE7BEA.1090802<>ens-lyon.fr> Date: Wed, 19 Jan 2005 16:25:30 +0100 From: Paul Fleurat-Lessard >ens-lyon.fr> Reply-To: Paul.Fleurat-Lessard<>ens-lyon.fr User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.8a4) Gecko/20040927 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 Cc: chemistry<>ccl.net Subject: Re: CCL:orbitals and reality References: <7E64C424A9A62B4592CC505FD28982074A4348<>KC-MAIL6.kc.umkc.edu> In-Reply-To: <7E64C424A9A62B4592CC505FD28982074A4348<>KC-MAIL6.kc.umkc.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed X-Virus-Scanned: by amavisd-new-20030616-p10 (Debian) at ens-lyon.fr X-Spam-Status: No, hits=3.7 required=7.5 tests=NO_RDNS2,RM_tl_ToNone 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 j0JFQrYr017750 Dear CCLers, I have read the original paper, and I am a bit confused about it. Unfortunately, the last discussions around it in the list have not succeeded in convincing me about the results. First, I have to say that I am quite excited about the idea of 'seeing' orbitals... BUT like some of us, I was taught that the MO are a mathematical construction. Some 'proofs' of this being: 1) Should I take the HF or CASSCF orbitals ? A more interesting case: should I take canonical, natural or localized orbitals ? They all give the same total energy and total density but are associated to different shapes and orbital energies. 2) Some ways of solving the Schrodinger equation do not involve orbitals at all. For example, the Quantum Monte Carlo approaches. So, I must admit that I have some difficulties to understand how one can 'see' something that is not well defined (at least for me). Can't it be that what they have seen if the total density of N2+ ? which has basically the shape of the HOMO of N2 ? Just my 2 cents, Regards, Paul. PS: Despite the fact that I fully respect the work of all researchers, I think that it is our _duty_ to criticize our work. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard<>ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07 Si vous ne pouvez expliquer un concept ` un enfant de six ans, c'est que vous ne le comprenez pas complhtement. Albert Einstein From chemistry-request@ccl.net Wed Jan 19 09:10:47 2005 Received: from seas.marine.usf.edu (seas.marine.usf.edu [131.247.136.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0JEAlYr015440 for ; Wed, 19 Jan 2005 09:10:47 -0500 Received: from yluo (ms136dhcp239.marine.usf.edu [131.247.136.239]) by seas.marine.usf.edu (8.13.1/8.13.1) with SMTP id j0JE6D2O023640 for ; Wed, 19 Jan 2005 09:06:13 -0500 (EST) Message-ID: <002201c4fe30$08e04fa0$ef88f783[at]marine.usf.edu> From: "luo" To: Subject: Geometry Optimization of Gadolinium Complex Date: Wed, 19 Jan 2005 09:06:13 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001F_01C4FE06.1FF4C3D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-USFCMS-MailScanner-Information: Please contact the postmaster[at]marine.usf.edu for more information X-USFCMS-MailScanner: Scanned X-MailScanner-From: luo[at]seas.marine.usf.edu X-Spam-Status: No, hits=0.0 required=7.5 tests=HTML_MESSAGE 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 multi-part message in MIME format. ------=_NextPart_000_001F_01C4FE06.1FF4C3D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All, I want to make the geometry optimization of the complex. Which software = can do that? Company name? Many thanks in advance. Yu-Ran Luo, Ph. D. ------=_NextPart_000_001F_01C4FE06.1FF4C3D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 All,
 
I=20 want to make=20 the geometry optimization of the complex. Which software can do = that?=20 Company name?
 
Many=20 thanks in advance.
 
Yu-Ran=20 Luo, Ph. D.
 
------=_NextPart_000_001F_01C4FE06.1FF4C3D0-- From chemistry-request@ccl.net Thu Jan 20 06:55:03 2005 Received: from chemail.tamu.edu (CHENOV3.tamu.edu [165.91.142.133]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KBt3i3010759 for ; Thu, 20 Jan 2005 06:55:03 -0500 Received: from suntur jms9668 [172.16.48.9] by chemail.tamu.edu with NetMail SMTP Agent $Revision: 1.1.1.1 $ on Novell NetWare; Thu, 20 Jan 2005 04:37:14 -0600 Message-ID: <004d01c4fedb$f5869f70$093010ac@suntur> Reply-To: "Jorge Seminario" From: "Jorge Seminario" To: References: <20050112053422.66343.qmail[at]web51304.mail.yahoo.com> Subject: Re: CCL:orbitals and reality Date: Thu, 20 Jan 2005 04:36:48 -0600 Organization: Texas A&M University MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 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, I understand the problem is whether MO's have any physical reality or not to be observable. Certainly, the goal of any model we create to explain a feature of nature is to explain such feature the best it can; needless to say, some models are better than others. Let's assume, as many agree, that the molecular densities can be measured, so we can get rho(r) at any point r for the neutral of N2 and also for its vertical cation, N2+. Let me define the difference of these two densities as the "experimental density of the HOMO" (just a definition). This density difference corresponds to a one-electron density, it certainly corresponds to the ejected electron, and therefore has correspondence to a one-electron wavefunction; this should be trivial to accept (well, to same extent...) Now, if you read the papers of my dear friends Levy and Perdew several years ago, this experimental HOMO should correspond "exactly" to the HOMO in DFT (provided you have the "exact" functional, any way it will be a good approximation otherwise). Thus, my point is that if we can observe one-electron densities of molecules, we certainly can observe the HOMO (at least indirectly). For sure, we can have another long discussion to decide which of the theoretical HOMOs is the best but that is another problem. Cordially Jorge Jorge M. Seminario Professor of Chemical Engineering and Professor of Electrical Engineering Texas A&M University 3122 TAMU College Station, TX 77843-3122 Phone and Fax 979-845-3301 seminario[at]tamu.edu http://cheweb.tamu.edu/faculty/seminario/ From chemistry-request@ccl.net Thu Jan 20 09:56:27 2005 Received: from web30808.mail.mud.yahoo.com (web30808.mail.mud.yahoo.com [68.142.200.151]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j0KEuPi3019634 for ; Thu, 20 Jan 2005 09:56:25 -0500 Received: (qmail 49156 invoked by uid 60001); 20 Jan 2005 13:56:25 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=edj+n6GAKpiWlGOWoUEyggPcJRKEla+Bj+HNRCnJhAiHV6PfvMhqscI3vX7hl4TkDClsHYF08V3C4QdPJjizjrwo59CqEVWyEQ7Wmfch6DJ7GPrqb5dWIpeil+k6mBuC6DD2M1VRWJC5GXrM9zGUZcsYEeioal2ySpTfIrw4LMM= ; Message-ID: <20050120135625.49154.qmail^at^web30808.mail.mud.yahoo.com> Received: from [67.110.18.100] by web30808.mail.mud.yahoo.com via HTTP; Thu, 20 Jan 2005 05:56:24 PST Date: Thu, 20 Jan 2005 05:56:24 -0800 (PST) From: Guosheng Wu Subject: Re: CCL:orbitals and reality To: Paul Fleurat-Lessard , sensengen^at^yahoo.com Cc: chemistry^at^ccl.net In-Reply-To: <41EE7BEA.1090802^at^ens-lyon.fr> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=4.5 required=7.5 tests=FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS,FROM_HAS_ULINE_NUMS,IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The molecular orbital(wave function) is a mathematical tool, and also useful and meaningful physical concept. I guess if they had published the results ("map" of wave function) of 1S(n=1, l=0, sphere, right?) for hydrogen atom, who else would have asked so many questions? Is there anything wrong with the shape of H(1S) wave function? By the way, that is accurate solution even without any basis set? So what's wrong with more complicated wave function of N2? Nothing is wrong conceptly, right? -Guosheng --- Paul Fleurat-Lessard wrote: > Dear CCLers, > > I have read the original paper, and I am a bit confused about it. > Unfortunately, the last discussions around it in the list have not > succeeded in convincing me about the results. > First, I have to say that I am quite excited about the idea of 'seeing' > orbitals... BUT like some of us, I was taught that the MO are a > mathematical construction. Some 'proofs' of this being: > 1) Should I take the HF or CASSCF orbitals ? > A more interesting case: should I take canonical, natural or localized > orbitals ? They all give the same total energy and total density but > are associated to different shapes and orbital energies. > 2) Some ways of solving the Schrodinger equation do not involve orbitals > > at all. For example, the Quantum Monte Carlo approaches. > > So, I must admit that I have some difficulties to understand how one can > > 'see' something that is not well defined (at least for me). > > Can't it be that what they have seen if the total density of N2+ ? which > > has basically the shape of the HOMO of N2 ? > > Just my 2 cents, > Regards, > Paul. > > PS: Despite the fact that I fully respect the work of all researchers, I > > think that it is our _duty_ to criticize our work. > > -- > Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard^at^ens-lyon.fr > Laboratoire de Chimie > Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 > 46, Allie d'Italie Fax: + 33 (0)4 72 72 88 60 > 69364 Lyon Cedex 07 > > Si vous ne pouvez expliquer un concept ` un enfant de six ans, > c'est que vous ne le comprenez pas complhtement. > Albert Einstein > > > > > -= 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 Thu Jan 20 11:07:09 2005 Received: from wasp.am.qub.ac.uk ([143.117.23.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KG76i3023798 for ; Thu, 20 Jan 2005 11:07:06 -0500 Received: (qmail 5659 invoked from network); 20 Jan 2005 15:07:04 -0000 Received: from onslaught.am.qub.ac.uk (mail@143.117.23.180) by wasp.am.qub.ac.uk with SMTP; 20 Jan 2005 15:07:04 -0000 Received: from ssen (helo=localhost) by onslaught.am.qub.ac.uk with local-esmtp (Exim 3.35 #1 (Debian)) id 1Crdto-0008IY-00 for ; Thu, 20 Jan 2005 15:07:04 +0000 Date: Thu, 20 Jan 2005 15:07:04 +0000 (GMT) From: Sanjay Kumar Sen X-Wasp-Original-From: Sanjay Kumar Sen To: chemistry)at(ccl.net Subject: CCP6 Workshop in Belfast Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net CCP6 Workshop Announcement "Semiclassical and Other Methods for Understanding Molecular Collisions and Chemical Reactions" Belfast, UK 2-5 April 2005 Dear Colleagues, This specialist workshop is sponsored by CCP6 (the UK Collaborative Computational Project on Molecular Quantum Dynamics). The workshop will focus on the challenging problems associated with the interpretation and understanding of the molecular scattering data obtained both experimentally and in numerical simulations. * The conference fee is estimated to be 160 pounds (including the conference dinner). * The meeting will take place at the Stranmillis University College in central Belfast. The list of confirmed overseas speakers includes: Prof. V.Aquilanti (Italy) Prof. B.Kendrick (USA) Prof. G.Lendvay (Hungary) Prof. W.H.Miller (USA) Prof. A.Z.Msezane (USA) Prof. H.Nakamura (Japan) Prof. G.Schatz (USA) Prof. R.Skodje (USA) Prof. J.Zhang (USA) Prof. J. Aoiz (Spain) Prof. L. Bonnet (France) The list of confirmed UK speakers includes: Prof. A.S. Dickinson Prof. M.S. Child Prof. J.N.L. Connor Prof. D.S.F. Crothers Prof. G.G. Balint-Kurti Prof. G. Gribakin Dr. J. McCann Dr. M. P. de Miranda Dr. S. C. Althorpe Dr. D. Sokolovski Organising committee: Dr. D. Sokolovski Prof. J.N.L. Connor Dr. S. Sen. CCP6 will publish a booklet of short articles by people who attend the workshop. Each participant in the workshop is requested to provide a short review-style article (400 - 2000 words) outlining their recent work in the area of the workshop. We will need the articles in by 15th March 2005. If you will be able to come, please let us have provisional titles for your talk and article as soon as possible. The booklet will be edited electronically, in LaTeX, and ONLY email submissions will be accepted. We look forward to see you in Belfast. Yours sincerely, Dr. Dmitri Sokolovski (Belfast) Prof. J.N.L. Connor (Manchester) Dr. Sanjay Sen (Belfast) NB: For further information please consult Dr. Dmitri Sokolovski d.sokolovski)at(qub.ac.uk Tel: 0044 (0)28 9097 3199 From chemistry-request@ccl.net Thu Jan 20 11:03:37 2005 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KG3ai3023619 for ; Thu, 20 Jan 2005 11:03:36 -0500 Received: from Fledermaus (net05.chem.umanitoba.ca [130.179.48.85]) (authenticated bits=0) by electra.cc.umanitoba.ca (8.13.0/8.13.0) with ESMTP id j0KEwi75001005 for ; Thu, 20 Jan 2005 08:58:44 -0600 (CST) Message-Id: <200501201458.j0KEwi75001005..at..electra.cc.umanitoba.ca> Reply-To: From: "Phil Hultin" To: "Computational Chemistry List" Subject: RE: orbitals and reality Date: Thu, 20 Jan 2005 08:58:39 -0600 Organization: Dept. of Chemistry, U. of Manitoba MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 In-Reply-To: <20050117224622.17167.qmail..at..web51304.mail.yahoo.com> Thread-Index: AcT88ILMibIaDKhnSt2LKiOpr0iqVwADrJow 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 This is a copy of a note I sent to Sengen Sun. I am posting it now because there does seem to have been some interest in the issue he raised on CCL - at the time there had been no response. Dr. Sun has promised to respond to my comments in the future. ==================================== Dr. Sun: I noted your request for further response to the "orbital debate" that has arisen from the Nature paper by Villeneuve et al. The orbital model is undeniably a key part of modern electronic structure theory, and it is therefore understandable that experimentalists would seek physical confirmation (if not proof) of its validity. On the other hand, it is equally true that theoreticians have always maintained that orbitals are "merely" mathematical constructs, that any arbitrary set of orbitals does not represent a unique solution to the Schroedinger equation, and that orbitals are therefore non-physical and non-observable. So, to get to the argument over Villeneuve et al: Having read the paper I must confess that I do not fully understand the experiment that they did. They assert that the overtone spectra that they acquire encode symmetry information about the electronic state (which they call an orbital) from which the electron is ejected and to which it returns. Since they cite literature support for this assertion I am prepared to accept it for the sake of argument until someone provides a persuasive counter argument. So, the question is, what did they actually observe and how should it be interpreted? I suggest that denying their experiment on theoretical grounds is scientifically inappropriate. Observation must have priority over theory, or we are talking about religion instead of science. This doesn't mean that they actually observed an orbital - but rather, if you are going to criticise their interpretation of the data you should present an alternative explanation of the origin of their spectra that is consistent with your view of electronic theory as well as with their observations. While the fact that orbitals are "only a model" means we must not assume that they are "real", I suggest that it is inappropriate to take it as axiomatic that the orbital model cannot embody at least some aspect of physical "reality". It is entirely possible that electronic structure behaves under certain specific probes as if orbitals were real, that is, that our artifical model fortuitously captures an observable aspect of electrons. I don't want to argue that Villeneuve et al are correct. But please, if you really want to conduct a scientific debate, address their experimental observations directly and don't simply say that "because they are inconsistent with theory they must be false". Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin..at..cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin From chemistry-request@ccl.net Thu Jan 20 08:18:19 2005 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KDIIi3014616 for ; Thu, 20 Jan 2005 08:18:18 -0500 Received: by smtp2.ruc.dk (Postfix, from userid 1005) id E09CD238008; Thu, 20 Jan 2005 12:15:58 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 69419238020 for ; Thu, 20 Jan 2005 12:15:55 +0100 (CET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 20 Jan 05 12:15:55 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 20 Jan 05 12:15:48 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry=at=ccl.net Date: Thu, 20 Jan 2005 12:15:20 +0100 Subject: CCL:orbitals and reality Reply-To: spanget=at=ruc.dk Message-ID: <41EFA0DD.19043.4DBFF8F@localhost> Priority: normal In-reply-to: <20050119161402.14116.qmail=at=web30803.mail.mud.yahoo.com> References: <41EE2DEC.9030100=at=uibk.ac.at> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Spam-Status: No, hits=0.2 required=7.5 tests=BAD_X_HEADERS autolearn=no version=2.61 X-Spam-Level: Dear CCL-community! I became curious whether the disagreement in the current discussion on 'Orbitals and Reality' might originate in misleading or unclear presentations in introductory chemistry textbooks. Is the confusion introduced here, leading perhaps to the use of improper language in scientific articles, even by frontline researchers in leading journals? First I looked up Zumdahl's "Chemical Principles" and found the following careful explanation of the situation. Can it be stated more clearly? Yours, Jens >--< Steven S. Zumdahl: "Chemical Principles", Fourth Edition, Houghton Mifflin, Boston 2004. pp673-675: "14.6 Orbitals: Human Inventions "In the treatment of the bonding and structure in molecules we have stressed that the descriptions we have given are models - and simple ones, at that. These models are extraordinarily valuable because they provide pictures in our minds of what molecules might look like and how they might behave. This helps us decide what questions to ask (what experiments to do) as we try to understand more completely the complicated behavior of matter. However, as valuable these pictures are, we must remember that they greatly oversimplify a very complex situation. We must realize that these models can give us a rather superficial view that is often highly misleading. "For example, after all of the talk about orbitals in the last several chapters, you probably have the distinct impression that orbitals actually exist. The truth is, they do not - at least not in the physical sense. Orbitals are mathematical functions - solutions to a modified Schrvdinger equation (the changes made to allow separation into independent electron equations). "Thus orbitals are mathematical tools we use to describe atoms and molecules. However, they have no physical reality in the sense that if you could look at the water molecule you would probably not "see" anything like the pictures we have shown in this book. These pictures merely help us visualize the theoretical imformation we have accumulated for water. (...) "The point made here is ... to make sure that you appreciate the nature of models and that you recognize the difference between the information learned about matter from experiments and the information learned from theories. Because matter is so complex, we often tailor our theories to explain a limited area of nature so as to keep the theories simple enough to understand and use. However, it is very dangerous to assume that such a limited theory can then be used in a wider sense. We must be very careful to ask proper questions of our theories or we face the danger of being greatly misled." =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget=at=ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Thu Jan 20 09:24:48 2005 Received: from smtp4.dti.ne.jp (smtp4.dti.ne.jp [202.216.228.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KEOki3017947 for ; Thu, 20 Jan 2005 09:24:47 -0500 Received: from oemcomputer (PPP154.fukuoka-ip.dti.ne.jp [211.132.92.154]) by smtp4.dti.ne.jp (3.10s) with SMTP id j0KDNVYB019909 for ; Thu, 20 Jan 2005 22:23:31 +0900 (JST) Message-ID: <002001c4fef2$bf50c9a0$9a5c84d3@oemcomputer> From: "Telkuni Tsuru" To: Subject: Summary) DBs for RNA Date: Thu, 20 Jan 2005 22:20:00 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello, CCLers. I had posted following question 3 days ago. Then I received one good reply ----- Original Question ----- > I'm looking for DBs and web-sites which describe the relationship between > RNA sequence and structure(including calculated structure). > > Although I know "Nucleic Acid Database" http://ndbserver.rutgers.edu/ , > the site's sequence number is few to me. I can't find suitable data from > "PDB" http://www.rcsb.org/pdb/ . And I don't know calculated structure DBs. The Reply: >>> from Dr. Sukumar >>> Have you tried: RNABase (The RNA Structure Database) - http://www.rnabase.org/ The RNA World Website - http://www.imb-jena.de/RNA.html and for RNA Folding prediction: Mfold - http://www.bioinfo.rpi.edu/applications/mfold/ Sfold - http://sfold.wadsworth.org/index.pl Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute ---------------------------------------------------- Telkuni Tsuru telkuni(at)venus.dti.ne.jp From chemistry-request@ccl.net Thu Jan 20 05:42:39 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 j0KAgbi3006857; Thu, 20 Jan 2005 05:42:38 -0500 To: chemistry*at*ccl.net Cc: "Computational Chemistry List" Subject: PQS-Chem MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: andras.borosy*at*givaudan.com Date: Thu, 20 Jan 2005 10:12:13 +0100 X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12 |February 13, 2003) at 20/01/2005 11:42:38, Serialize complete at 20/01/2005 11:42:38 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=3.7 required=7.5 tests=FVGT_m_MULTI_ODD2, FVGT_s_OBFU_Q0,FVGT_s_OBFU_Q1,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 j0KAgdi3006862 Dear Colleagues, Do you have any experience with PQS-Chem software (http://www.pqs-chem.com)? Is it worth buying? 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 From chemistry-request@ccl.net Thu Jan 20 14:23:24 2005 Received: from imap.reed.edu (imap.reed.edu [134.10.2.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KJNLi3003094 for ; Thu, 20 Jan 2005 14:23:21 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by imap.reed.edu (8.12.10/8.12.10) with ESMTP id j0KIJaHr013275 for ; Thu, 20 Jan 2005 10:19:36 -0800 Received: from imap.reed.edu ([127.0.0.1]) by localhost (imap [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 12822-08 for ; Thu, 20 Jan 2005 10:19:36 -0800 (PST) Received: from [127.0.0.1] (dsl-206-103-41-215.dsl.easystreet.com [206.103.41.215]) (authenticated bits=0) by imap.reed.edu (8.12.10/8.12.10) with ESMTP id j0KIJXxQ013272 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 20 Jan 2005 10:19:33 -0800 Message-ID: <41EFF6D9.40200[at]reed.edu> Date: Thu, 20 Jan 2005 10:22:17 -0800 From: Alan Shusterman User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: CCL:orbitals and reality Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at imap.reed.edu X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_DSL,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net 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 From chemistry-request@ccl.net Thu Jan 20 16:31:23 2005 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KLVLi3008860 for ; Thu, 20 Jan 2005 16:31:21 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 22ED63241D6 for ; Thu, 20 Jan 2005 15:21:09 -0500 (EST) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 30774-10 for ; Thu, 20 Jan 2005 15:21:08 -0500 (EST) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 6DDFE3241B4 for ; Thu, 20 Jan 2005 15:21:08 -0500 (EST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Thu, 20 Jan 2005 15:23:45 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: orbitals and reality Date: Thu, 20 Jan 2005 15:23:45 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78A57{at}srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: orbitals and reality Thread-Index: AcT88ILMibIaDKhnSt2LKiOpr0iqVwADrJowAIt9PTA= From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 20 Jan 2005 20:23:45.0742 (UTC) FILETIME=[F122D6E0:01C4FF2D] X-Spam-Status: No, hits=2.5 required=7.5 tests=NO_RDNS2,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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j0KLVNi3008865 Since I've stepped into this discussion, perhaps I ought to at least look at the paper that started this. :-) Does anyone have a usable citation? I'm seeing different authors and different journals mentioned...which probably means there is more than one article. The article I am interested in is the one which describes how the "orbitals" were observed "experimentally". --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. From chemistry-request@ccl.net Thu Jan 20 13:57:44 2005 Received: from postin.uv.es (postin.uv.es [147.156.1.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KIvgi3001892 for ; Thu, 20 Jan 2005 13:57:43 -0500 Received: from sello.uv.es (sello.ci.uv.es [147.156.1.112]) by postin.uv.es (8.12.11/8.12.11) with ESMTP id j0KHrUU8009561 for ; Thu, 20 Jan 2005 18:53:30 +0100 Received: from [147.156.100.119] (nebot3.icmol.uv.es [147.156.100.119]) (authenticated bits=0) by sello.uv.es (8.12.2/8.12.2) with ESMTP id j0KHrRoi012952 for ; Thu, 20 Jan 2005 18:53:28 +0100 Mime-Version: 1.0 (Apple Message framework v619) Content-Transfer-Encoding: 7bit Message-Id: <2FF1550B-6B0C-11D9-A386-000A959EAD5A_at_uv.es> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed To: chemistry_at_ccl.net From: Ignacio Nebot-Gil Subject: Fwd: CCL:orbitals and reality Date: Thu, 20 Jan 2005 18:53:27 +0100 X-Mailer: Apple Mail (2.619) 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 Begin forwarded message: > From: Ignacio Nebot-Gil > Date: 20 de enero de 2005 17:32:12 GMT+01:00 > To: "Jorge Seminario" > Subject: Re: CCL:orbitals and reality > > Dear all > > I do'nt agree. > > Orbital, following McWeeny and Sutcliffe definition (Methods of > Molecular Quantum Mechanics) is the wavefunction obtained from a > monoelectronic hamiltonian operator, actual or effective. > > If the hamiltonian operator is actually monoelectronic, no other > electrons are present. If it is effective, then, the electron > interaction is averaged in some way, as in the majority of systems > (all but H atom and H2+ molecule and some other ions). Then, orbital > is only the result of an approximate calculation, although it can be > used to establish models and to interpret experimental facts, as many > chemists do. > > But my main objection is that orbital is a wavefunction (no physical > meaning according to the Bohr interpretation of the wavefunction) and > electron density is related not with the orbitals but with its SQUARE > (probabilistic meaning, Bohr again). Hence, the difference between the > experimental electron density of N2 and N2+ cannot be related with the > HOMO, but, in any case, with its square. > Even that will not be right, because the electron density difference > is experimental, and then the ACTUAL electron interaction is involved. > This interaction is not taken in consideration in the orbital concept > (see definition above). In other words, if we calculate the N2 HOMO, > even using an infinite basis set, and we obtain its square, the > result, which can be considered as the exact HOMO, will not be > identical to the electron density difference between N2 and N2+. The > electron interactions taken into account in these two situations are > DIFFERENT. > > Ignacio Nebot-Gil > > On 20/01/2005, at 11:36, Jorge Seminario wrote: > >> Dear All, >> I understand the problem is whether MO's have any physical >> reality or not to be observable. Certainly, the goal of any model we >> create >> to explain a feature of nature is to explain such feature the best it >> can; >> needless to say, some models are better than others. >> Let's assume, as many agree, that the molecular densities can be >> measured, >> so we can get rho(r) at any point r for the neutral of N2 >> and also for its vertical cation, N2+. >> Let me define the difference of these two densities as the >> "experimental density of the HOMO" (just a definition). >> This density difference corresponds to a one-electron density, >> it certainly corresponds to the ejected electron, >> and therefore has correspondence to a one-electron wavefunction; >> this should be trivial to accept (well, to same extent...) >> Now, if you read the papers of my dear friends Levy and Perdew >> several years ago, this experimental HOMO should correspond "exactly" >> to the HOMO in DFT (provided you have the "exact" functional, any way >> it will be a good approximation otherwise). >> Thus, my point is that if we can observe one-electron densities of >> molecules, we certainly can observe the HOMO (at least indirectly). >> For sure, we can have another long discussion to decide >> which of the theoretical HOMOs is the best but that is another >> problem. >> Cordially >> Jorge >> Jorge M. Seminario >> Professor of Chemical Engineering and >> Professor of Electrical Engineering >> Texas A&M University >> 3122 TAMU >> College Station, TX 77843-3122 >> Phone and Fax 979-845-3301 >> seminario:at:tamu.edu >> http://cheweb.tamu.edu/faculty/seminario/ >> >> >> -= 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) >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- >> +-+ >> >> >> >> >> >> > > Prof. Ignacio Nebot-Gil > > ----------------------------------------------------------------------- > --------------------------- > Instituto de Ciencia Molecular & Dept. Quimica Fisica > Univ. Valencia E-mail: Ignacio.Nebot:at:uv.es > Dr. Moliner, 50 Phone: 34 96 354 4333 > 46100 - Burjassot (Valencia), Spain FAX: 34 96 354 3156 > ----------------------------------------------------------------------- > --------------------------- > From chemistry-request@ccl.net Thu Jan 20 13:56:42 2005 Received: from evalingui.unicaen.fr (evalingui.unicaen.fr [193.55.130.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KIuei3001834 for ; Thu, 20 Jan 2005 13:56:41 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by evalingui.unicaen.fr (Postfix) with ESMTP id 2E0451635F0 for ; Thu, 20 Jan 2005 18:55:44 +0100 (CET) Received: from evalingui.unicaen.fr ([127.0.0.1]) by localhost (evalingui [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 01306-01 for ; Thu, 20 Jan 2005 18:55:43 +0100 (CET) Received: from baligan.unicaen.fr (baligan2-2.unicaen.fr [10.14.32.2]) by evalingui.unicaen.fr (Postfix) with ESMTP id 6FC59163511 for ; Thu, 20 Jan 2005 18:55:43 +0100 (CET) Received: from [193.55.134.48] (station-MCI.cermn.unicaen.fr [193.55.134.48]) by baligan.unicaen.fr (8.12.11/jtpda-5.4) with ESMTP id j0KHthRe1179659 for ; Thu, 20 Jan 2005 18:55:43 +0100 (MET) Message-ID: <41EFF09F.8060507$at$pharmacie.unicaen.fr> Date: Thu, 20 Jan 2005 18:55:43 +0100 From: Nicolas Saettel Organization: UFR de Pharmacie de Caen - CERMN User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: fr, en MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: SMILE to table Content-Type: multipart/mixed; boundary="------------040903010202040309050409" X-Virus-Scanned: by amavisd-new-20030616-p10 (Debian) at unicaen.fr X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. --------------040903010202040309050409 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi all, I am looking for a freeware software to translate a text file containing lines with SMILES strings + name of the compounds in a table (HTML, GIF... or a simple view I can print out) with the 2D drawing AND the name of the compounds. mview from Jchem seems to only give me the 2D drawings... Thank you, Nicolas -- Nicolas Saettel, Ph.D., Assistant Professor CERMN - 5, rue Vaubinard - F-14032 CAEN CEDEX Tel. +33.(0)2.31.56.59.10 Fax +33.(0)2.31.93.11.88 UFR des Sciences Pharmaceutiques - Bd Becquerel - F-14032 CAEN CEDEX Tel. +33.(0)2.31.56.60.09 Fax +33.(0)2.31.56.60.20 http://www.cermn.unicaen.fr - http://www.pharmacie.unicaen.fr --------------040903010202040309050409 Content-Type: text/x-vcard; charset=utf-8; name="nicolas.saettel.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="nicolas.saettel.vcf" begin:vcard fn:Nicolas Saettel n:Saettel;Nicolas org:CERMN;Molecular Modelling adr;quoted-printable:;;5, rue Vaub=C3=A9nard;Caen;;14032;FRANCE email;internet:nicolas.saettel$at$pharmacie.unicaen.fr title:Ph.D. tel;work:+33 (0)2 31 56 59 10 tel;fax:+33 (0)2 31 93 11 88 tel;cell:+33 (0)6 73 73 68 66 x-mozilla-html:FALSE url:http://www.cermn.unicaen.fr/ version:2.1 end:vcard --------------040903010202040309050409-- From chemistry-request@ccl.net Thu Jan 20 17:15:19 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 j0KMFHi3011830 for ; Thu, 20 Jan 2005 17:15:17 -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 j0KL1Akm018064 for ; Thu, 20 Jan 2005 15:01:10 -0600 Mime-Version: 1.0 Message-Id: Date: Thu, 20 Jan 2005 15:01:09 -0600 To: chemistry|at|ccl.net From: "Jan H. Jensen" Subject: on-line protein pKa predictor Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.3 required=7.5 tests=FCS_URI_NODOTS 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 I am happy to announce the on-line version of the PROPKA program (v. 1.00) for the rapid prediction and structural rationalization of pKa values of ionizable amino acid residues in proteins: http://ghemical.chem.uiowa.edu -- =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Jan H. Jensen Associate Professor Department of Chemistry jan-jensen|at|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 Thu Jan 20 17:20:34 2005 Received: from mailTM.sued-chemie.de (mailtm.sued-chemie.de [195.145.99.198]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KMKWi3012354 for ; Thu, 20 Jan 2005 17:20:33 -0500 Received: from mailtm2.sued-chemie.com (unknown [172.16.1.15]) by mailTM.sued-chemie.de (Postfix) with SMTP id E6AB6177466 for ; Thu, 20 Jan 2005 21:25:48 +0100 (CET) Received: from srv49003.scag.sc-world.com (srv49003.scag.sc-world.com [10.100.2.201]) by scmuc08.sued-chemie.de (8.11.1/8.11.1) with ESMTP id j0KKJjP31252 for ; Thu, 20 Jan 2005 21:19:49 +0100 (MET) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srv49003.scag.sc-world.com with Microsoft SMTPSVC(5.0.2195.5329); Thu, 20 Jan 2005 21:17:16 +0100 X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: orbitals and reality Date: Thu, 20 Jan 2005 15:17:14 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0007D78A56|at|srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: orbitals and reality Thread-Index: AcT88ILMibIaDKhnSt2LKiOpr0iqVwADrJowAIsp0QA= From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 20 Jan 2005 20:17:16.0921 (UTC) FILETIME=[09617690:01C4FF2D] X-Spam-Status: No, hits=4.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS,NO_RDNS2 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 j0KMKYi3012359 Here's an interesting and related question: Are symmetry groups (point and space groups) real? These are also "mathematical constructs". (As for myself, I tend to "reify" mathematical objects, but relegate them to a separate "math world.") --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. From chemistry-request@ccl.net Thu Jan 20 18:05:38 2005 Received: from electra.cc.umanitoba.ca (electra.cc.umanitoba.ca [130.179.16.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0KN5bi3016120 for ; Thu, 20 Jan 2005 18:05:37 -0500 Received: from Fledermaus (net05.chem.umanitoba.ca [130.179.48.85]) (authenticated bits=0) by electra.cc.umanitoba.ca (8.13.0/8.13.0) with ESMTP id j0KN5aqI013090 for ; Thu, 20 Jan 2005 17:05:36 -0600 (CST) Message-Id: <200501202305.j0KN5aqI013090=at=electra.cc.umanitoba.ca> Reply-To: From: "Phil Hultin" To: "Computational Chemistry List" Subject: Orbitals and reality Date: Thu, 20 Jan 2005 17:05:30 -0600 Organization: Dept. of Chemistry, U. of Manitoba MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_005A_01C4FF12.421EDE70" X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcT/RIk+evUJ6yprT8aGr62i9RVd5w== X-Spam-Status: No, hits=0.5 required=7.5 tests=HTML_60_70,HTML_MESSAGE,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 This is a multi-part message in MIME format. ------=_NextPart_000_005A_01C4FF12.421EDE70 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I think Alan Shusterman's comments are very much to the point regarding this discussion. On the other hand, he is perhaps taking the argument that I and others have made a little bit narrowly. "since Y comes > from an experiment ("Y is real" !), it is inappropriate to object to > "Y tells us about X" on merely theoretical grounds." What I (at least) actually said was: "if you are going to criticise their interpretation of the data you should present an alternative explanation of the origin of their spectra that is consistent with your view of electronic theory as well as with their observations. While the fact that orbitals are "only a model" means we must not assume that they are "real", I suggest that it is inappropriate to take it as axiomatic that the orbital model cannot embody at least some aspect of physical "reality". It is entirely possible that electronic structure behaves under certain specific probes as if orbitals were real, that is, that our artificial model fortuitously captures an observable aspect of electrons." That is, theory is indeed the lens through which data are interpreted, but that to object to an interpretation you must do more than simply say "no, it cannot be so". It is at least possible as I remarked that one indeed cannot observe orbitals or wavefunctions, but that nonetheless the spatial distribution of electronic density in a simple molecule can be probed as the authors assert in the Nature paper. The way to criticize this is, in my opinion, to say "you are not observing orbitals, neither are you observing the interference pattern between two electronic wavefunctions. The reasons for this are X, Y, Z. On the other hand, you are observing something, and based on your description of your experiment, I believe that the origin of the spectra you obtain and their angular dependence lies in phenomena A, B and C." I for one am glad that a serious discussion of this topic has evolved. I was beginning to think that CCL was going to be nothing but technical questions about how to make programs work ;-). Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin=at=cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_005A_01C4FF12.421EDE70 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Normal Document Template

I think Alan Shusterman’s comments are very = much to the point regarding this discussion.  On the other hand, he is = perhaps taking the argument that I and others have made a little bit = narrowly.

 

“since Y comes

> = > from an experiment ("Y is real" !), it is inappropriate to object to =

> = "Y

tells = us about X" on merely theoretical = grounds.”

 

What I (at least) actually = said was:

“if you are going to criticise their interpretation of the data you should = present an alternative explanation of the origin of their spectra that is = consistent with your view of electronic theory as well as with their = observations.

 

While = the fact that orbitals are "only a model" means we must not assume that = they are "real", I suggest that it is inappropriate to take it as axiomatic that the orbital model cannot embody at least some aspect of = physical "reality".  It is entirely possible that electronic = structure behaves under certain specific probes as if orbitals were real, that is, = that our artificial model fortuitously captures an observable aspect of = electrons.”

 

That is, = theory is indeed the lens through which data are interpreted, but that to object to an interpretation you must do more than simply say “no, it cannot be = so”.  It is at least possible as I remarked that one indeed cannot observe = orbitals or wavefunctions, but that nonetheless the spatial distribution of = electronic density in a simple molecule can be probed as the authors assert in the = Nature paper.  The way to criticize this is, in my opinion, to say = “you are not observing orbitals, neither are you observing the interference = pattern between two electronic wavefunctions.  The reasons for this are X, = Y, Z.  On the other hand, you are observing something, and based on your = description of your experiment, I believe that the origin of the spectra you obtain = and their angular dependence lies in phenomena A, B and = C.”

 

I for one am = glad that a serious discussion of this topic has evolved.  I was beginning to = think that CCL was going to be nothing but technical questions about how to = make programs work ;-).

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin=at=cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

------=_NextPart_000_005A_01C4FF12.421EDE70-- From chemistry-request@ccl.net Thu Jan 20 19:18:04 2005 Received: from chemaxon.hu (90.156-228-195.hosting.adatpark.hu [195.228.156.90]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0L0I2i3021443 for ; Thu, 20 Jan 2005 19:18:03 -0500 Received: from [192.168.0.2] (ktv32-211-77.catv-pool.axelero.hu [62.201.77.211]) (authenticated bits=0) by chemaxon.hu (8.13.1/8.13.1) with ESMTP id j0KMrtvu031433 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO); Thu, 20 Jan 2005 23:53:55 +0100 Message-ID: <41F036CF.5020708*at*chemaxon.com> Date: Thu, 20 Jan 2005 23:55:11 +0100 From: Ferenc Csizmadia User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.5) Gecko/20041217 X-Accept-Language: en-us, en, hu, zh-cn MIME-Version: 1.0 To: Nicolas Saettel CC: chemistry*at*ccl.net Subject: Re: CCL:SMILE to table References: <41EFF09F.8060507*at*pharmacie.unicaen.fr> In-Reply-To: <41EFF09F.8060507*at*pharmacie.unicaen.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=5.4 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS,RCVD_IN_SORBS_WEB autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Nicolas, > 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... MarvinView (mview) can do what you want! You have 2 choices: - Select the Table >> Show fields menu option - mview -f field_0 input.smiles See command-line options at http://www.chemaxon.com/marvin/doc/user/mview.html If you want more freedom, you can combine MolConverter and MarvinView. For example displaying the structures in 3D and showing their names: molconvert mrv -3 1.smi | mview -f field_0 - MolConverter and MarvinSketch are free (if not used in an application or if you are an academic user) and portable just like MarvinView. (They are included in both Marvin Beans and JChem) http://www.chemaxon.com/marvin/doc/user/molconvert.html http://www.chemaxon.com/marvin/doc/user/msketch.html Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com