From chemistry-request@ccl.net Wed May 28 07:04:59 2003
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From: "Jens Spanget-Larsen" <spanget/at/virgil.ruc.dk>
Organization: Roskilde Universitetscenter
To: CHEMISTRY/at/ccl.net
Date: Wed, 28 May 2003 13:04:50 +0100
Subject: CCL: Orbitals
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Mikael Johansson:

> On Tue, 27 May 2003, Jens Spanget-Larsen wrote:
> 
> > And in principle, MOs are not physical quantities; they are model
> > constructions, and as such they have no physical reality and they
> > cannot be observed experimentally.
> 
> Well, there is a lot of discussion in the literature on this topic.
> A few good examples, biased towards my thinking, could be:
> 
> [1] Stowasser and Hoffmann, "What Do the Kohn-Sham Orbitals and
>     Eigenvalues Mean?", J.Am.Chem.Soc. 121 (1999) 3414-3420.
> [2] Baerends, Theor.Chem.Acc. 103 (2000) 265-269.
> 
> Have a nice day,
>     Mikael J.
>     http://www.helsinki.fi/~mpjohans/


Dear Mikael!

Yes, it is true, there has been some discussion on the status of the
MO concept. But to me, there can be no doubt: In principle, orbitals
are one-electron wavefunctions, and for a many-electron system, they
do by definition NOT correspond to physical reality. However, they 
are extremely useful models, as we all know. The usefulness of the MO
concept in rationalizing a lot of chemistry and spectroscopy 
sometimes leads people to think of MOs as physical quantities, rather 
than simplified models. Do you think my point of view is erroneous?

Yours, Jens >--<


------- End of forwarded message -------
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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 Wed May 28 03:50:08 2003
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Subject: Orbitals
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Mikael Johansson:

> On Tue, 27 May 2003, Jens Spanget-Larsen wrote:
> 
> > And in principle, MOs are not physical quantities; they are model
> > constructions, and as such they have no physical reality and they
> > cannot be observed experimentally.
> 
> Well, there is a lot of discussion in the literature on this topic.
> A few good examples, biased towards my thinking, could be:
> 
> [1] Stowasser and Hoffmann, "What Do the Kohn-Sham Orbitals and
>     Eigenvalues Mean?", J.Am.Chem.Soc. 121 (1999) 3414-3420.
> [2] Baerends, Theor.Chem.Acc. 103 (2000) 265-269.
> 
> Have a nice day,
>     Mikael J.
>     http://www.helsinki.fi/~mpjohans/


Dear Mikael,

Yes, it is true, there has been some discussion on the status of the
MO concept. But to me, there can be no doubt: In principle, orbitals
are one-electron wavefunctions, and for a many-electron system, they
do by definition NOT correspond to physical reality. However, they 
are extremely useful models, as we all know. The usefulness of the MO
concept in rationalizing a lot of chemistry and spectroscopy 
sometimes leads people to think of MOs as physical quantities, rather 
than simplified models. Do you think my point of view is erroneous?

Yours, Jens >--<


=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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 Wed May 28 05:04:16 2003
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From: "Nelson Fonseca" <nfonseca|at|dq.ua.pt>
Subject: mmodgrid
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Experience is what you get when you don't get what you 
want.
        
                      -- Dan Stanford--

hello!

Can anyone point me to where mmodgrid can be downloaded?


Thanks!


Nelson Fonseca
PhD Student
University of Aveiro
Portugal


From chemistry-request@ccl.net Wed May 28 07:53:12 2003
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Hello Jens and All!

On Wed, 28 May 2003, Jens Spanget-Larsen wrote:

> Yes, it is true, there has been some discussion on the status of the
> MO concept. But to me, there can be no doubt: In principle, orbitals
> are one-electron wavefunctions, and for a many-electron system, they
> do by definition NOT correspond to physical reality. However, they
> are extremely useful models, as we all know. The usefulness of the MO
> concept in rationalizing a lot of chemistry and spectroscopy
> sometimes leads people to think of MOs as physical quantities, rather
> than simplified models. Do you think my point of view is erroneous?

I'm not taking sides on which view is more correct, but I am inclined to
like the more physical interpretation of orbitals. Even if they for the
moment are only mathematical constructs, it doesn't rule out the
possibility of a physical foundation to be discovered for them. Orbitals
can also, in a sense, be observed experimentally. See for example:

[1] Vstrvm et.al., "Orbital rehybridization in n-octane adsorbed on
    Cu(110)", JCP 118 (2003) 3782-378
[2] Hasselstrvm et.al., J.Phys.Chem B 104 (2000) 11480-11483

Have a nice day,
    Mikael J.
    http://www.helsinki.fi/~mpjohans/



From chemistry-request@ccl.net Wed May 28 03:01:30 2003
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From: sergiusz.kwasniewski{at}luc.ac.be
To: chemistry{at}ccl.net
Cc: chemistry{at}ccl.net
Subject: CCL:UV spectrum calculation (new question)
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Hi,

I'm curious how well INDO/S-RPA works against INDO/S-CIS for large systems. 
I only remember one article by M. Zerner quite a long time ago..

Probably the calculation takes a lot longer (Hamiltonian matrix is four times 
as big since mixing of particle-hole and hole-particle excitations occurs). 
About the excitation energies: If I'm not mistaken both CIS and RPA are 
consistent methods in electron correlation up to 1st order in one-particle 
excitation energies, but only RPA is up to 1st order for transition dipole 
moments). Two-particle excitations are not accounted for in CIS, and only 
partially in RPA, am I right ?

Are there any problems with numerical instabilities with the implemented RPA 
scheme in a INDO/S-RPA calculation ?

Serge

> > -----Original Message-----
> > From: Mark Thompson [mailto:mark{at}planaria-software.com]
> > Sent: Tuesday, May 27, 2003 1:47 PM
> > To: Jesus Rodriguez-Otero; chemistry{at}ccl.net
> > Subject: CCL: UV spectrum calculation
> 
> 
> 
> Dear Jesus,
> 
> ZINDO does indeed give good results for large organic systems, mainly those
> with low-energy pi-pi* excitations.  As with many semi-empirical methods,
> it
> works best on a series of related molecules where you might be interested
> in
> the effects of certain substitutents.  Also, the effects of solvent can be
> very important and several solvent models have been applied to the ZINDO
> method with good results.
> 
> Here are a couple of my publications where I applied ZINDO to studies of
> photosynthetic pigments:
> 
>  "Excited States of the Bacteriochlorophyll b Dimer
>  of Rhodopseudomonas viridis: A QM/MM Study of the
>  Photosynthetic Reaction Center That Includes MM
>  Polarization" J. Phys. Chem. 1995, 99, 6374-6386.
>  Mark Thompson and Gregory Schenter
> 
>  "Effect of a Polarizable Medium on the Charge-Transfer
>  States of the Photosynthetic Reaction Center from
>  Rhodopseudomonas viridis. " I. Am. Chem. Soc.
>  1990, 112, 7828.  Mark Thompson and Michael Zerner
> 
> 
> ZINDO is available in the ArgusLab 3.1 program.  In addition to the normal
> ZINDO method (based on singles-CI description of the excited state),
> ArgusLab also implements the ZINDO-RPA method which includes contributions
> > from certain low-lying doubles and is particularly good at describing
> rotational spectra and giving good agreement between dipole length and
> dipole velocity transition moments.  ArgusLab also implements the
> Self-Consistent Reaction Field model of Zerner and Karlsson.
> 
> You can obtain ArgusLab at http:://www.arguslab.com
> 
>  Mark Thompson
> 
> =================================
>  Mark Thompson, Ph.D.
>  Planaria Software
>  PO Box 55207
>  Seattle, WA  98155
> 
>  http://www.arguslab.com
>  FAX: 206-440-3305
>  =================================
> 
> 
> -= This is automatically added to each message by mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject:
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> 
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> 
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> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> 
> 
> 
> 
> 





From chemistry-request@ccl.net Wed May 28 10:57:56 2003
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To: <sergiusz.kwasniewski(at)luc.ac.be>, <chemistry(at)ccl.net>
Subject: CCL: UV spectrum calculation (new question)
Date: Wed, 28 May 2003 07:53:51 -0700
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Dear Serge,

> Are there any problems with numerical instabilities with the
> implemented RPA scheme in a INDO/S-RPA calculation ?

There may be, but to date, we've not had any problems running INDO/S-RPA
(aka ZINDO-RPA) on all test systems that we use for standard ZINDO.

An exhaustive reparameterization of ZINDO for RPA is not finished.  For that
matter, an exhaustive parameterization of ZINDO-CIS was also never done, but
Mike Zerner and his students over the years managed to generate a fairly
useful set of parameters for CIS that do well in most cases.  For molecules,
like cyclophanes, where low-lying double excitations may be important, then
one needs to go beyond CIS with ZINDO.  The error for ZINDO-CIS is about
1000 cm^-1 for most systems.

ZINDO-RPA appears to descibe excitations better, and generally requires a
smaller number of active orbitals in the RPA, relative to CIS.

Mark


=================================
Mark Thompson, Ph.D.
Planaria Software
PO Box 55207
Seattle, WA  98155
FAX: 206-440-3305

ArgusLab 3.1 is available at:
http://www.arguslab.com
=================================



From chemistry-request@ccl.net Wed May 28 10:29:46 2003
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Subject: Eigenvalues of hessian
From: "Daniel R. Rohr" <rohrd/at/students.uni-marburg.de>
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Hi CCLers

 Does anybody of you know, why there are more than 3N-6 nonzero
eigenvalues of the hessian? I am especially interested in the question,
whether this error is due to the errors made by differentiation or
whether they are due to an error within the method itself. I usually get
only 3 zero eigenvalues. No matter if the hessian is calculated on a
stationary point or not.

Thanks for your help

Daniel Rohr

-- 
-----------------------------------------------------------------------
 Daniel Rohr                                    Fachbereich Chemie der
                                                Philipps-Universitdt
 Tel.: +49-6421-28-25686                        Hans-Meerwein-Stra_e
 Fax.: +49-6421-28-25566                        D-35043 Marburg
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From chemistry-request@ccl.net Wed May 28 10:14:43 2003
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2003 May 28

Are MOs physically real? This is a meaningful question only if there is some
experiment or observation that could provide an answer _yes_ or _no_.  Is there,
at least in principle, such an experiment or observation?

As J S-L points out, MOs are one-electron functions; does this mean that for
hydrogenlike atoms they _do_ correspond to physical reality?

If MOs have no physical reality for multielectron species, why (a) is Koopmans'
theorem useful,  why (b) do photoelectron spectra match the predictions of MO
energy-level diagrams, and why (c) does the Hueckel 4n+2 rule, which is based on
MO diagrams, work? Of course, it is probably possible to formulate an MO-free
electronic molecular theory that leads to the same predictions a-c, but I suspect
that in some sense (but what sense?) MOs exist--occupied MOs; the meaning of a
virtual MO is harder to see.

E. Lewars
=====



Jens Spanget-Larsen wrote:

> Mikael Johansson:
>
> > On Tue, 27 May 2003, Jens Spanget-Larsen wrote:
> >
> > > And in principle, MOs are not physical quantities; they are model
> > > constructions, and as such they have no physical reality and they
> > > cannot be observed experimentally.
> >
> > Well, there is a lot of discussion in the literature on this topic.
> > A few good examples, biased towards my thinking, could be:
> >
> > [1] Stowasser and Hoffmann, "What Do the Kohn-Sham Orbitals and
> >     Eigenvalues Mean?", J.Am.Chem.Soc. 121 (1999) 3414-3420.
> > [2] Baerends, Theor.Chem.Acc. 103 (2000) 265-269.
> >
> > Have a nice day,
> >     Mikael J.
> >     http://www.helsinki.fi/~mpjohans/
>
> Dear Mikael!
>
> Yes, it is true, there has been some discussion on the status of the
> MO concept. But to me, there can be no doubt: In principle, orbitals
> are one-electron wavefunctions, and for a many-electron system, they
> do by definition NOT correspond to physical reality. However, they
> are extremely useful models, as we all know. The usefulness of the MO
> concept in rationalizing a lot of chemistry and spectroscopy
> sometimes leads people to think of MOs as physical quantities, rather
> than simplified models. Do you think my point of view is erroneous?
>
> Yours, Jens >--<
>
> ------- End of forwarded message -------
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
> -= This is automatically added to each message by mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
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>
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From chemistry-request@ccl.net Wed May 28 10:13:05 2003
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I currently have an undergraduate student who is attempting to compare 
charges of methylated benzene and ferrocene systems using the AIMPAC 
software.  In the case of hexamethyl benzene and the ferrocene analogues he 
is getting very large negative charges on some the ring carbons (-5 to -20) 
and small positive charges on iron (0.5) Can anyone tell me if there is a 
problem with the program or if the ring system can not be treated with this 
method?

Thank you,
Julia Metzker
University of York
Department of Chemistry



From chemistry-request@ccl.net Wed May 28 11:07:55 2003
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E. Lewars:

> Are MOs physically real? This is a meaningful question only if there
> is some experiment or observation that could provide an answer _yes_
> or _no_.  Is there, at least in principle, such an experiment or
> observation?

I don't agree. For a many-electron system, one-electron wavefunctions 
are BY DEFINITION physically unreal. They can only be defined by 
neglecting certain very physical aspects, corresponding to a model 
where electron correlation effects are neglected. According to basic 
Physics, real electrons instantaneously correlate their individual 
movements, but electrons in orbitals don't. Electrons in orbitals are 
'quasi-particles', not 'real particles'.

> As J S-L points out, MOs are one-electron functions; does this mean
> that for hydrogenlike atoms they _do_ correspond to physical reality?

For an isolated hydrogen atom, the orbital wavefunctions, using the 
reduced mass and relativistic quantum mechanics, probably corresponds 
closely to what one might choose to consider as 'reality'. But in the 
end, the question becomes entirely philosophical; for example, no-one 
has ever observed an isolated atom.
 
> If MOs have no physical reality for multielectron species, why (a) is
> Koopmans' theorem useful, why (b) do photoelectron spectra match the
> predictions of MO energy-level diagrams, and why (c) does the Hueckel
> 4n+2 rule, which is based on MO diagrams, work? Of course, it is
> probably possible to formulate an MO-free electronic molecular theory
> that leads to the same predictions a-c, but I suspect that in some
> sense (but what sense?) MOs exist--occupied MOs; the meaning of a
> virtual MO is harder to see.

The MO concept is very useful, forming the basis for excellent models 
of chemical and spectroscopic behaviour. For example, if you adopt 
Koopmans' approximation (neglect of electronic correlation and 
reorganization effects on ionization), Koopmans' well-known theorem 
applies. This is frequently a very good model, largely because the 
different errors introduces by the adoption of Koopmans' 
approximation tend to cancel each other out. But sometimes Koopmans' 
approximation is a bad approximation, and Koopmans' theorem does not 
apply. Or in the other words: The MO picture of ionization is 
sometimes a good model, and sometimes it is not. 

In any case: MOs don't exist in the physical sense. But of course, 
you may say that they 'exist' in our minds!

Jens >--<




=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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 Wed May 28 11:11:54 2003
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From: Jan Labanowski <jkl$at$ccl.net>
To: chemistry$at$ccl.net
cc: Jan Labanowski <jkl$at$ccl.net>
Subject: Spam, CCL, and me...
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The question from subscriber prompted this message to all subscribers.

1) I do understand subscribers concerns that they do not want to post to
   CCL from their company/university e-mail address. Yes, there are policies,
   and liabilities involved. Yes, it is much safer to post from you
   PRIVATE email address. However, there is an advantage to post from
   company/university address.

2) The reason for posting with the company/university address is that
   I very reluctantly put them onto a blacklist. That is, you can post from
   these addresses and your mail will not have "Access denied" bounce.
   The private accounts like on yahoo.com or hotmail.com, etc., often
   have problems posting to CCL since the respective domains are on
   the blacklist (since I get tons of spam from them). 

3) You can post to CCL from ANY address on Earth, assuming that the subnet
   from which you post is not blacklisted. If it is blacklisted (i.e.,
   mail bounces with 'Access denied' from chemistry$at$ccl.net), you need
   to send your message to me: jkl$at$ccl.net so I resend it. The subscription
   list is not checked when deciding if message can be posted. Your
   subscription address is only the address WHERE YOU GET MAIL from CCL. 
   You do not have to use it to POST to CCL. So you can still receive mail to
   your company address, but post to CCL from your private address, or your
   friend's private address, whatever it it. 

4) As I said, many "free e-mail accounts" will have problem posting, since
   the providers of such service also provide a opportunity for spammers.
   Now, if your mail from the private address bounces from CCL, send it to 
   jkl$at$ccl.net (I do not have a blacklist attached to this address, to my
   demise and despair) and  I will resend message to CCL for you.

5) Read the bottom of the messages you receive from CCL. For example,
   when you post to CCL, put the four letter word, CCL:, somewhere on
   the Subject line. It will prevent your message to go to unconditional
   manual review (it may well still end up there if you use some words which
   are often found in spam messages or some other things in your message may
   be "suspisious" to the CCL scripts).   

Please understand that CCL gets about 1000 spam messages a day.
You see only one in a month or less, on average, but it happens because
I work on the principle 'better safe than sorry'. Of course, 
once you have to screen mail manually or automatically, it will
cause delays and often human errors. Oh well... There are people out
there who screwed it up for all of us... We need a new e-mail standard
which authenticates the sender of mail. I will gladly receive all my
spam, if they pay me a $1 per each message. I would be a millionaire by now... 


Jan K. Labanowski         |  phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center |  E-mail: jkl$at$ccl.net 
1224 Kinnear Rd,          |  http://www.ccl.net/~jkl
Columbus, OH 43212-1163   |  http://www.ccl.net/    http://asdn.net/



From chemistry-request@ccl.net Wed May 28 11:34:01 2003
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From: Elmar Gerwalin <elg-.at.-chemie.uni-kl.de>
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Hello !

Would'n it be a good idea to convert the CCL Mailing list to a newsgroup ?

Maybe this would have other disadvantages, but bringing much advantages, too:

Sorted threads, moderation, reading by web interface, ...

Bye
Elmar

On Wednesday 28 May 2003 17:11, Jan Labanowski wrote:
> The question from subscriber prompted this message to all subscribers.
>
> 1) I do understand subscribers concerns that they do not want to post to
>    CCL from their company/university e-mail address. Yes, there are
> policies, and liabilities involved. Yes, it is much safer to post from you
> PRIVATE email address. However, there is an advantage to post from
> company/university address.
>
> 2) The reason for posting with the company/university address is that
>    I very reluctantly put them onto a blacklist. That is, you can post from
>    these addresses and your mail will not have "Access denied" bounce.
>    The private accounts like on yahoo.com or hotmail.com, etc., often
>    have problems posting to CCL since the respective domains are on
>    the blacklist (since I get tons of spam from them).
>
> 3) You can post to CCL from ANY address on Earth, assuming that the subnet
>    from which you post is not blacklisted. If it is blacklisted (i.e.,
>    mail bounces with 'Access denied' from chemistry-.at.-ccl.net), you need
>    to send your message to me: jkl-.at.-ccl.net so I resend it. The subscription
>    list is not checked when deciding if message can be posted. Your
>    subscription address is only the address WHERE YOU GET MAIL from CCL.
>    You do not have to use it to POST to CCL. So you can still receive mail
> to your company address, but post to CCL from your private address, or your
> friend's private address, whatever it it.
>
> 4) As I said, many "free e-mail accounts" will have problem posting, since
>    the providers of such service also provide a opportunity for spammers.
>    Now, if your mail from the private address bounces from CCL, send it to
>    jkl-.at.-ccl.net (I do not have a blacklist attached to this address, to my
>    demise and despair) and  I will resend message to CCL for you.
>
> 5) Read the bottom of the messages you receive from CCL. For example,
>    when you post to CCL, put the four letter word, CCL:, somewhere on
>    the Subject line. It will prevent your message to go to unconditional
>    manual review (it may well still end up there if you use some words
> which are often found in spam messages or some other things in your message
> may be "suspisious" to the CCL scripts).
>
> Please understand that CCL gets about 1000 spam messages a day.
> You see only one in a month or less, on average, but it happens because
> I work on the principle 'better safe than sorry'. Of course,
> once you have to screen mail manually or automatically, it will
> cause delays and often human errors. Oh well... There are people out
> there who screwed it up for all of us... We need a new e-mail standard
> which authenticates the sender of mail. I will gladly receive all my
> spam, if they pay me a $1 per each message. I would be a millionaire by
> now...
>
>
> Jan K. Labanowski         |  phone: 614-292-9279,  FAX: 614-292-7168
> Ohio Supercomputer Center |  E-mail: jkl-.at.-ccl.net
> 1224 Kinnear Rd,          |  http://www.ccl.net/~jkl
> Columbus, OH 43212-1163   |  http://www.ccl.net/    http://asdn.net/
>
>
>
> -= This is automatically added to each message by 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
>
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>
> If your mail is bouncing from CCL.NET domain send it to the maintainer:
> Jan Labanowski,  jkl-.at.-ccl.net (read about it on CCL Home Page)
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

-- 
========================================================
Elmar Gerwalin ,   University of Kaiserslautern,Germany
                   Dept. of Theoretical Chemistry
                   and  IT Service Team
                   elg-.at.-chemie.uni-kl.de    0631-205-2749
========================================================




From chemistry-request@ccl.net Wed May 28 12:31:28 2003
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From: Eric Scerri <scerri.-at-.chem.ucla.edu>
Subject: orbitals
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It seems to me that paper [1] at least makes the elementary 
philosophical error of claiming that if something is useful then it 
must have physical reality.

Stowasser and Hoffmann say virtually as much in this article.


Many scientific concepts have proved useful in the history of science 
but were eventually found to be redundant or non-existent.  For 
example, caloric, phlogiston, the ether etc.

But is there a sense in which the Kohn-Sham orbitals are "more real" 
than the orbitals used in ab initio work?  This seems to be the claim 
of some recent authors.


But then we get into another odd notion, namely that having physical 
reality comes in degrees!



please see,

The Recently Claimed Observation of Atomic Orbitals and Some Related 
Philosophical Issues", Philosophy of Science, 68,(Proceedings) 
S76-S88, N. Koertge, ed. Philosophy of Science Association, East 
Lansing, MI, (2001)


Have Orbitals Really Been Observed?, Journal of Chemical Education, 
77, 1492-1494, (2000)

although neither of these articles discuss the reality of orbitals of 
the DFT variety.


regards,
eric scerri


I would like to invite contibutions of articles or comments on this 
question to the journal Foundations of Chemistry (see below for info).

----------


>  On Tue, 27 May 2003, Jens Spanget-Larsen wrote:
>>
>>  > And in principle, MOs are not physical quantities; they are model
>>  > constructions, and as such they have no physical reality and they
>>  > cannot be observed experimentally.
>>
>>  Well, there is a lot of discussion in the literature on this topic.
>>  A few good examples, biased towards my thinking, could be:
>>
>>  [1] Stowasser and Hoffmann, "What Do the Kohn-Sham Orbitals and
>>      Eigenvalues Mean?", J.Am.Chem.Soc. 121 (1999) 3414-3420.
>>  [2] Baerends, Theor.Chem.Acc. 103 (2000) 265-269.
>
-- 


Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri.-at-.chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.kluweronline.com/issn/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html


From chemistry-request@ccl.net Wed May 28 13:42:45 2003
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Date: Wed, 28 May 2003 17:42:39 -0000
To: "Daniel R. Rohr" <rohrd.-at-.students.uni-marburg.de>,
   "ccl" <chemistry.-at-.ccl.net>
Subject: Re: CCL:Eigenvalues of hessian
From: "Amity Andersen" <andersen.-at-.chem.ucla.edu>
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In-Reply-To: <1054131647.16827.13.camel@charly>

Is your system linear?

"Daniel R. Rohr" <rohrd.-at-.students.uni-marburg.de> said:

> Hi CCLers
> 
>  Does anybody of you know, why there are more than 3N-6 nonzero
> eigenvalues of the hessian? I am especially interested in the question,
> whether this error is due to the errors made by differentiation or
> whether they are due to an error within the method itself. I usually get
> only 3 zero eigenvalues. No matter if the hessian is calculated on a
> stationary point or not.
> 
> Thanks for your help
> 
> Daniel Rohr
> 
> -- 
> -----------------------------------------------------------------------
>  Daniel Rohr                                    Fachbereich Chemie der
>                                                 Philipps-Universitdt
>  Tel.: +49-6421-28-25686                        Hans-Meerwein-Stra_e
>  Fax.: +49-6421-28-25566                        D-35043 Marburg
>  eMail: rohrd.-at-.stud-mailer.uni-marburg.de        Germany
> -----------------------------------------------------------------------
> 
> 
> 
> 
> -= This is automatically added to each message by 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,  jkl.-at-.ccl.net (read about it on CCL Home Page)
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> 
> 
> 
> 
> 



-- 
Amity Andersen
UCLA
Dept. of Chemistry & Biochemistry
Room:  3051 Young Hall
(310) 206-5931
andersen.-at-.chem.ucla.edu




From chemistry-request@ccl.net Wed May 28 11:36:50 2003
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From: James Robinson <prsjjr.-at-.bath.ac.uk>
To: "Daniel R. Rohr" <rohrd.-at-.students.uni-marburg.de>, ccl <chemistry.-at-.ccl.net>
Subject: RE: Eigenvalues of hessian
Date: Wed, 28 May 2003 16:37:04 +0100
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Some numerical methods use small perturbations in the x, y and z planes to compute force constants. Unfortunately this effectively contaminates the calculation with net translations. Could this be happening in your Hessian calc? 

James (if I wrong, do let me know!)

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request.-at-.ccl.net]On
Behalf Of Daniel R. Rohr
Sent: 28 May 2003 15:21
To: ccl
Subject: CCL:Eigenvalues of hessian


Hi CCLers

 Does anybody of you know, why there are more than 3N-6 nonzero
eigenvalues of the hessian? I am especially interested in the question,
whether this error is due to the errors made by differentiation or
whether they are due to an error within the method itself. I usually get
only 3 zero eigenvalues. No matter if the hessian is calculated on a
stationary point or not.

Thanks for your help

Daniel Rohr

-- 
-----------------------------------------------------------------------
 Daniel Rohr                                    Fachbereich Chemie der
                                                Philipps-Universitdt
 Tel.: +49-6421-28-25686                        Hans-Meerwein-Stra_e
 Fax.: +49-6421-28-25566                        D-35043 Marburg
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From chemistry-request@ccl.net Wed May 28 12:46:15 2003
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Date: Wed, 28 May 2003 09:46:14 -0700 (PDT)
From: Guosheng Wu <wu_guosheng2002.-at-.yahoo.com>
Subject: Re: CCL:Orbitals
To: chemistry.-at-.ccl.net
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> > > --- elewars <elewars.-at-.trentu.ca> wrote:
> > > > 2003 May 28
> > > >
> > > > Are MOs physically real? This is a meaningful question only if there is some
> > > > experiment or observation that could provide an answer _yes_ or _no_.  Is there,
> > > > at least in principle, such an experiment or observation?

> > Guosheng Wu wrote:
> > 
> > > MO is just a useful mathematical tool for quantum chemistry/physics, and
> > > it seems to me itself does not have much physical meaning.
> > >
> > > However, many properties from MOs are meaningful and can be observed
> > > by exmperiments: such as the square of absolute MOs (|MO|^2) corresponding
> > > to the electronic density. Things like |MO|^2 of d-orbitals were published
> > > in a Science article last one or a few years.

> --- elewars <elewars.-at-.trentu.ca> wrote:
> > Hello,
> > 
> > Thanks for your ideas. If photoel. spectra (and Koopmans theorem--in this case the
> > second MO is at the ionization limit) really measure the energy difference of two MOs,
> > then MOs exist!
> > 
> > In any case, it is an interesting discussion.
> > 
> > EL
> > =====

The properties from |MO|^2 exist does not really mean MO exists.
 
When we know some properties from x^2 exist and can be measured,
this does not mean x exists and can be measured.
 
For example, what does the complex number(i) mean in the real world?
Measurable? Not really, but obviously it's a useful mathematical tool
for lots of applications. Certainly (i^2=-1) means something. Right?

Related issue for absolute energy: energy difference is measurable 
by many kind of experiments, but not for the absolute energy. 
 
This may lead to some kind of philosophical problem, if one has 
such a taste.

Guosheng

__________________________________
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From chemistry-request@ccl.net Wed May 28 14:24:53 2003
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From: "Leif Laaksonen" <leif.laaksonen_at_csc.fi>
To: <chemistry_at_ccl.net>
Subject: CCL: RE: Orbitals
Date: Wed, 28 May 2003 21:24:41 +0300
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Hi,

I might remember wrong from my primary courses in quantum chemistry
that only obsrvables are the expectation values from the wave
function!

This means that while the wave function (|P>) as such is not
observable the expectation value of property X is (<P|X|P>).

Regards,

-leif  

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request_at_ccl.net] On Behalf Of Guosheng Wu
Sent: Wednesday, May 28, 2003 7:46 PM
To: chemistry_at_ccl.net
Subject: CCL:Orbitals


> > > --- elewars <elewars_at_trentu.ca> wrote:
> > > > 2003 May 28
> > > >
> > > > Are MOs physically real? This is a meaningful question only if there is some
> > > > experiment or observation that could provide an answer _yes_ or _no_.  Is there,
> > > > at least in principle, such an experiment or observation?

> > Guosheng Wu wrote:
> > 
> > > MO is just a useful mathematical tool for quantum chemistry/physics, and
> > > it seems to me itself does not have much physical meaning.
> > >
> > > However, many properties from MOs are meaningful and can be observed
> > > by exmperiments: such as the square of absolute MOs (|MO|^2) corresponding
> > > to the electronic density. Things like |MO|^2 of d-orbitals were published
> > > in a Science article last one or a few years.

> --- elewars <elewars_at_trentu.ca> wrote:
> > Hello,
> > 
> > Thanks for your ideas. If photoel. spectra (and Koopmans theorem--in this case the
> > second MO is at the ionization limit) really measure the energy difference of two MOs,
> > then MOs exist!
> > 
> > In any case, it is an interesting discussion.
> > 
> > EL
> > =====

The properties from |MO|^2 exist does not really mean MO exists.
 
When we know some properties from x^2 exist and can be measured,
this does not mean x exists and can be measured.
 
For example, what does the complex number(i) mean in the real world?
Measurable? Not really, but obviously it's a useful mathematical tool
for lots of applications. Certainly (i^2=-1) means something. Right?

Related issue for absolute energy: energy difference is measurable 
by many kind of experiments, but not for the absolute energy. 
 
This may lead to some kind of philosophical problem, if one has 
such a taste.

Guosheng

__________________________________
Do you Yahoo!?
Yahoo! Calendar - Free online calendar with sync to Outlook(TM).
http://calendar.yahoo.com


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From chemistry-request@ccl.net Wed May 28 13:50:56 2003
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From: Mauricio L Cafiero <mcafiero:at:U.Arizona.EDU>
To: elewars <elewars:at:trentu.ca>
cc: Jens Spanget-Larsen <spanget:at:virgil.ruc.dk>, <chemistry:at:ccl.net>
Subject: CCL:Orbitals
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hello:
     If we take quantum mechanics to be valid, and we accept that the
two particle coulomb interaction is the predominant potential energy term
in the hamitonian, then MO's are physically meaningless. They are simply
artifacts of approximations, a zero-order wavefunction. QM could have
evolved completely without orbitals (except for H-atom of course). I think
the reason we jumped on
orbitals so early in history is that they are a fantastic approximation
and that orthogonal orbitals save a lot of time computationally.

It is the very excellence of the orbital approximation that makes
orbitals out to be more than they are. As was said before, they are
conceptually easy to grasp. As far a Koopmans', it makes no explicilt
reference to orbitals. It is simply that the orbital energy is what
remains when you subtract the energies of the two wave functions
in the single determinant approximation. I also have to say that PES
does not always agree well with orbital diagrams, at least not
quantitatively.

Mauricio Cafiero
Postdoctoral Research Associate
Computational Chemistry Team
National Institute of Standards and Technology
Gaithersburg, Maryland



From chemistry-request@ccl.net Wed May 28 13:49:51 2003
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From: Alan.Shusterman:at:directory.reed.edu (Alan Shusterman)
Subject: CCL: Orbitals
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Some of the postings on this subject have cited *correlations* between orbital properties and physical observables as evidence that orbitals "in some sense" exist.

example: If MOs have no physical reality for multielectron species, why (a) is Koopmans'
theorem useful,  why (b) do photoelectron spectra match the predictions of MO
energy-level diagrams, and why (c) does the Hueckel 4n+2 rule, which is based on
MO diagrams, work? (E. Lewars)

example: Orbitals can also, in a sense, be observed experimentally. (M. Johansson)

I'm sympathetic to these statements, but I prefer Jens' point of view.

I am writing not to cast my vote, but to point out an interesting (to me, anyway) parallel. I teach organic chemistry every fall semester, and every year I must convince my students that *resonance contributors* do not exist even though one can correlate physical observables with the properties of these contributors.

Some may still insist that, "if we routinely think of object X to make a prediction, then object X exists, at least in our minds". This is an interesting idea, but I don't think that it relates well to "existence" in the way chemists use this word.

I'd like to thank everyone who has contributed to this discussion so far. It has been interesting.

-Alan

====
Alan Shusterman
Department of Chemistry
Reed College
Portland, OR
academic.reed.edu/chemistry/alan/



From chemistry-request@ccl.net Wed May 28 14:41:55 2003
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Subject: CCL:Spam, CCL, and me...
In-Reply-To: <200305281733.57663.elg{at}chemie.uni-kl.de>
References: <Pine.GSO.4.21.0305281057490.2983-100000{at}krakow.ccl.net>
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This would not be helpful at all if one is at an
institution lacking decent newsgroup access.
E-mail is a much more generally available to
a wide variety of subscribers.

AJD

At 05:33 PM 5/28/2003 +0200, you wrote:
>Hello !
>
>Would'n it be a good idea to convert the CCL Mailing list to a newsgroup ?
>
>Maybe this would have other disadvantages, but bringing much advantages, too:
>
>Sorted threads, moderation, reading by web interface, ...
>
>Bye
>Elmar
>

Anthony J. Duben
Professor and Chairman
Computer Science Department
Mail Stop 5950
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1 University Plaza
Cape Girardeau MO 63701-4799
phone: 573-651-2194
fax: 573-651-2791\
e-mail: ajduben{at}semo.edu

"When life is very bad, two things make life
   worth living: Mozart and quantum mechanics."
              -- Victor Weisskopf



From chemistry-request@ccl.net Wed May 28 14:45:39 2003
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Hello,
Though I do not know which method you are using to get the wavefunction,
I would blame first to the quality of the wavefunction than to the aimpac
program. Check the boundaries of the carbon atoms to see if the atomic
basin is what you expect to be.
Hope it helps

_-_-_-_-_-_-_-_-_-_-_-_-

   Carlos Silva Lspez
 Dept. Qummica Organica
  Universidade de Vigo
  Phone:0034 986812226
-_-_-_-_-_-_-_-_-_-_-_-_





From chemistry-request@ccl.net Wed May 28 15:11:05 2003
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2003 May 28

Hello,

Good points! Especially the idea that MOs are unreal _by definition_. If you
insist that an MO must be a one-electron function (I know this is in the usual
definition) then I suppose it could be "real" only for a hydrogenlike atom. For
these, as you imply, the exact solutions of the Schroedinger equation evidently
are physically real. As for the point about observing an isolated
system--Heisenberg and Platonic reality....that could lead one far afield,
perhaps.

EL
==================


Jens Spanget-Larsen wrote:

> E. Lewars:
>
> > Are MOs physically real? This is a meaningful question only if there
> > is some experiment or observation that could provide an answer _yes_
> > or _no_.  Is there, at least in principle, such an experiment or
> > observation?
>
> I don't agree. For a many-electron system, one-electron wavefunctions
> are BY DEFINITION physically unreal. They can only be defined by
> neglecting certain very physical aspects, corresponding to a model
> where electron correlation effects are neglected. According to basic
> Physics, real electrons instantaneously correlate their individual
> movements, but electrons in orbitals don't. Electrons in orbitals are
> 'quasi-particles', not 'real particles'.
>
> > As J S-L points out, MOs are one-electron functions; does this mean
> > that for hydrogenlike atoms they _do_ correspond to physical reality?
>
> For an isolated hydrogen atom, the orbital wavefunctions, using the
> reduced mass and relativistic quantum mechanics, probably corresponds
> closely to what one might choose to consider as 'reality'. But in the
> end, the question becomes entirely philosophical; for example, no-one
> has ever observed an isolated atom.
>
> > If MOs have no physical reality for multielectron species, why (a) is
> > Koopmans' theorem useful, why (b) do photoelectron spectra match the
> > predictions of MO energy-level diagrams, and why (c) does the Hueckel
> > 4n+2 rule, which is based on MO diagrams, work? Of course, it is
> > probably possible to formulate an MO-free electronic molecular theory
> > that leads to the same predictions a-c, but I suspect that in some
> > sense (but what sense?) MOs exist--occupied MOs; the meaning of a
> > virtual MO is harder to see.
>
> The MO concept is very useful, forming the basis for excellent models
> of chemical and spectroscopic behaviour. For example, if you adopt
> Koopmans' approximation (neglect of electronic correlation and
> reorganization effects on ionization), Koopmans' well-known theorem
> applies. This is frequently a very good model, largely because the
> different errors introduces by the adoption of Koopmans'
> approximation tend to cancel each other out. But sometimes Koopmans'
> approximation is a bad approximation, and Koopmans' theorem does not
> apply. Or in the other words: The MO picture of ionization is
> sometimes a good model, and sometimes it is not.
>
> In any case: MOs don't exist in the physical sense. But of course,
> you may say that they 'exist' in our minds!
>
> Jens >--<
>
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
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From chemistry-request@ccl.net Wed May 28 16:23:38 2003
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From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" <reynier.-at-.fq.uh.cu>
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 I need to know about the GIAO method' theory to calculate 
chemical shifts in NMR. Does anybody know a site or a paper or 
whatever about this theme that can help me?
 Thanks,
 Reynier.


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This may only show that my mind is *Really* contaminated by the
calculational methods, but I tend to think of the orbitals as the
mathematical building blocks out of which the wave function is =
constructed,
as a linear combination of the determinants thereof.  A multi-electron =
wave
function is just too complicated to comprehend in its entirety. =20

But (I think this is true) if you include the contributions of all
determinants made from the entire set of orbitals--i.e. full CI with no
approximations--the orbitals are not unique and any set of orbitals =
that
"spans the vector space," as a mathematician would put it, can be used.

--David Shobe
S=FCd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe.-at-.sud-chemieinc.com

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

P.S. I wonder if one could define the HOMO at least by reversing =
Koopman's
theorem and calculating the HOMO from the electron density difference
between the molecule and its "vertical" radical cation.  And similarly =
with
the LUMO using the vertical radical anion, if it exists.  Or does one
necessarily run into Guosheng Wu's paradox of knowing X^2  but not =
knowing
X?



-----Original Message-----
From: Alan.Shusterman.-at-.directory.Reed.EDU
[mailto:Alan.Shusterman.-at-.directory.Reed.EDU]
Sent: Wednesday, May 28, 2003 1:50 PM
To: chemistry.-at-.ccl.net
Subject: CCL:Orbitals


Some of the postings on this subject have cited *correlations* between
orbital properties and physical observables as evidence that orbitals =
"in
some sense" exist.

example: If MOs have no physical reality for multielectron species, why =
(a)
is Koopmans'
theorem useful,  why (b) do photoelectron spectra match the predictions =
of
MO
energy-level diagrams, and why (c) does the Hueckel 4n+2 rule, which is
based on
MO diagrams, work? (E. Lewars)

example: Orbitals can also, in a sense, be observed experimentally. (M.
Johansson)

I'm sympathetic to these statements, but I prefer Jens' point of view.

I am writing not to cast my vote, but to point out an interesting (to =
me,
anyway) parallel. I teach organic chemistry every fall semester, and =
every
year I must convince my students that *resonance contributors* do not =
exist
even though one can correlate physical observables with the properties =
of
these contributors.

Some may still insist that, "if we routinely think of object X to make =
a
prediction, then object X exists, at least in our minds". This is an
interesting idea, but I don't think that it relates well to "existence" =
in
the way chemists use this word.

I'd like to thank everyone who has contributed to this discussion so =
far. It
has been interesting.

-Alan

=3D=3D=3D=3D
Alan Shusterman
Department of Chemistry
Reed College
Portland, OR
academic.reed.edu/chemistry/alan/



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charset=3Diso-8859-1">
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<TITLE>CCL: RE: Orbitals</TITLE>
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<BODY>

<P><FONT SIZE=3D2>This may only show that my mind is *Really* =
contaminated by the calculational methods, but I tend to think of the =
orbitals as the mathematical building blocks out of which the wave =
function is constructed, as a linear combination of the determinants =
thereof.&nbsp; A multi-electron wave function is just too complicated =
to comprehend in its entirety.&nbsp; </FONT></P>

<P><FONT SIZE=3D2>But (I think this is true) if you include the =
contributions of all determinants made from the entire set of =
orbitals--i.e. full CI with no approximations--the orbitals are not =
unique and any set of orbitals that &quot;spans the vector space,&quot; =
as a mathematician would put it, can be used.</FONT></P>

<P><FONT SIZE=3D2>--David Shobe</FONT>
<BR><FONT SIZE=3D2>S=FCd-Chemie Inc.</FONT>
<BR><FONT SIZE=3D2>phone (502) 634-7409</FONT>
<BR><FONT SIZE=3D2>fax&nbsp;&nbsp;&nbsp;&nbsp; (502) 634-7724</FONT>
<BR><FONT SIZE=3D2>email&nbsp; dshobe.-at-.sud-chemieinc.com</FONT>
</P>

<P><FONT SIZE=3D2>Don't bother flaming me: I'm behind a =
firewall.</FONT>
</P>

<P><FONT SIZE=3D2>P.S. I wonder if one could define the HOMO at least =
by reversing Koopman's theorem and calculating the HOMO from the =
electron density difference between the molecule and its =
&quot;vertical&quot; radical cation.&nbsp; And similarly with the LUMO =
using the vertical radical anion, if it exists.&nbsp; Or does one =
necessarily run into Guosheng Wu's paradox of knowing X^2&nbsp; but not =
knowing X?</FONT></P>
<BR>
<BR>

<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Alan.Shusterman.-at-.directory.Reed.EDU</FONT>
<BR><FONT SIZE=3D2>[<A =
HREF=3D"mailto:Alan.Shusterman.-at-.directory.Reed.EDU">mailto:Alan.Shusterma=
n.-at-.directory.Reed.EDU</A>]</FONT>
<BR><FONT SIZE=3D2>Sent: Wednesday, May 28, 2003 1:50 PM</FONT>
<BR><FONT SIZE=3D2>To: chemistry.-at-.ccl.net</FONT>
<BR><FONT SIZE=3D2>Subject: CCL:Orbitals</FONT>
</P>
<BR>

<P><FONT SIZE=3D2>Some of the postings on this subject have cited =
*correlations* between orbital properties and physical observables as =
evidence that orbitals &quot;in some sense&quot; exist.</FONT></P>

<P><FONT SIZE=3D2>example: If MOs have no physical reality for =
multielectron species, why (a) is Koopmans'</FONT>
<BR><FONT SIZE=3D2>theorem useful,&nbsp; why (b) do photoelectron =
spectra match the predictions of MO</FONT>
<BR><FONT SIZE=3D2>energy-level diagrams, and why (c) does the Hueckel =
4n+2 rule, which is based on</FONT>
<BR><FONT SIZE=3D2>MO diagrams, work? (E. Lewars)</FONT>
</P>

<P><FONT SIZE=3D2>example: Orbitals can also, in a sense, be observed =
experimentally. (M. Johansson)</FONT>
</P>

<P><FONT SIZE=3D2>I'm sympathetic to these statements, but I prefer =
Jens' point of view.</FONT>
</P>

<P><FONT SIZE=3D2>I am writing not to cast my vote, but to point out an =
interesting (to me, anyway) parallel. I teach organic chemistry every =
fall semester, and every year I must convince my students that =
*resonance contributors* do not exist even though one can correlate =
physical observables with the properties of these =
contributors.</FONT></P>

<P><FONT SIZE=3D2>Some may still insist that, &quot;if we routinely =
think of object X to make a prediction, then object X exists, at least =
in our minds&quot;. This is an interesting idea, but I don't think that =
it relates well to &quot;existence&quot; in the way chemists use this =
word.</FONT></P>

<P><FONT SIZE=3D2>I'd like to thank everyone who has contributed to =
this discussion so far. It has been interesting.</FONT>
</P>

<P><FONT SIZE=3D2>-Alan</FONT>
</P>

<P><FONT SIZE=3D2>=3D=3D=3D=3D</FONT>
<BR><FONT SIZE=3D2>Alan Shusterman</FONT>
<BR><FONT SIZE=3D2>Department of Chemistry</FONT>
<BR><FONT SIZE=3D2>Reed College</FONT>
<BR><FONT SIZE=3D2>Portland, OR</FONT>
<BR><FONT SIZE=3D2>academic.reed.edu/chemistry/alan/</FONT>
</P>
<BR>
<BR>

<P><FONT SIZE=3D2>-=3D This is automatically added to each message by =
mailing script =3D-</FONT>
<BR><FONT SIZE=3D2>To send e-mail to subscribers of CCL put the string =
CCL: on your Subject: line</FONT>
<BR><FONT SIZE=3D2>and send your message to:&nbsp; =
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<P><FONT SIZE=3D2>Send your subscription/unsubscription requests to: =
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From chemistry-request@ccl.net Wed May 28 17:00:06 2003
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Hello CCL members!!
I have a question: 
When Zero-Point Vibration Energy Corrections are necessary? and why?
Thanks 
Rachel




From chemistry-request@ccl.net Wed May 28 16:51:23 2003
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From: Marcos Villarreal <arloa.-at-.dqb.fcq.unc.edu.ar>
To: chemistry.-at-.ccl.net
Subject: phi/psi map
Date: Wed, 28 May 2003 17:57:09 -0300
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Hello,

Is it posible to compute a phi/psi map for a carbohydrate within TINKER?

Thanks in advance,


Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.
http://www.fcq.unc.edu.ar/ciquibic



From chemistry-request@ccl.net Wed May 28 17:04:08 2003
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Date: Wed, 28 May 2003 16:51:44 -0400 (EDT)
From: Rene Fournier - 1999-07-07 <renef.-at-.yorku.ca>
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   Leif Laaksonen makes an important point: only observables
are "real" in QM.  So the question arises: is it possible to
define orbitals as QM observables.  It entirely depends on
how you define the word "orbital".  If one says orbitals are
one-electron functions and nothing more, then of course orbitals
can be made to be QM observables.  For example, just integrate
an exact squared wavefunction over all electron coordinates
but one to get the electron density, then take the square
root, multiply by a phase factor and you get "density orbitals".
[G Hunter, Int J Quantum Chem 9 (1975) 237].   They may not be
very useful as orbitals, but they are "real" in the sense of
QM observables.
    Orbitals are always defined as one-electron functions,
but THAT does not make them "unreal".  The electron density
is a one electron function and very real for any N-electron
system, not only for the H atom.
    One "ab initio" way to define orbitals is to start from
exact wavefunctions and calculate the overlap of a N-electron
wavefunction (neutral) and the ground and various excited
states a (N-1)-electron wavefunction (ion) (Dyson orbitals are
defined in such a way I think).  I'm sure there are definitions
that will make such orbitals unique, but does that make them
QM observables?  I don't think so, but I'd like to hear from
the CCL community on that.  There are other ways to define orbitals
> from exact wavefunctions, I'm sure: are any of them QM observables?
    As for Kohn-Sham orbitals, they may not be real individually
but the N lowest energy ones squared and summed give the true
electron density (an observable) and the negative of the KS HOMO
energy is exactly equal to the first IP (another observable) so
there are at least some bits of reality built in KS orbitals!

Here's some relevant articles:

1) Kohn, Becke, Parr, J Phys Chem 100 (1996) 12974
2) "Kohn-Sham Orbitals and Orbital Energies: Fictitious Constructs but
   Good Approximations All the Same"
   by S. Hamel, P. Duffy, M.E. Casida, and D.R. Salahub
   Journal of Electron Spectroscopy and Related Phenomena (2002?)
3) Chong, Gritsenko, Baerends, J Chem Phys 116 (2002) 1760

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| Chemistry Dpt, York University| Phone: (416) 736 2100 Ext. 30687 |
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To: <Chemistry.-at-.ccl.net>
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Various locations archive mailing lists and allow them to be
read as newsgroups. Some mailing list software allows posting-only access, so
one can read and post via nntp without receiving all the email in addition.
Regular mailing-list users are totally unaffected by this and may ignore its
existence, but those who wish to use newsgroup access may do so instead. See
gmane.org for a good example of this.

> This would not be helpful at all if one is at an
> institution lacking decent newsgroup access.
> E-mail is a much more generally available to
> a wide variety of subscribers.
>
> AJD
>
> At 05:33 PM 5/28/2003 +0200, you wrote:
>>Hello !
>>
>>Would'n it be a good idea to convert the CCL Mailing list to a
>> newsgroup ?
>>
>>Maybe this would have other disadvantages, but bringing much
>> advantages, too:
>>
>>Sorted threads, moderation, reading by web interface, ...
>>
>>Bye
>>Elmar
>>
>
> Anthony J. Duben
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> Computer Science Department
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>
> "When life is very bad, two things make life
>    worth living: Mozart and quantum mechanics."
>               -- Victor Weisskopf
>
>
>
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-- 
Donnie Berkholz
News Editor, The Collegian
University of Richmond
28 Westhampton Way
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From chemistry-request@ccl.net Wed May 28 18:50:08 2003
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> I'm curious how well INDO/S-RPA works against INDO/S-CIS for large 
> systems.
> I only remember one article by M. Zerner quite a long time ago..

A comparison of ZINDO/RPA vs. ZINDO/CIS on various conjugated oligomers 
is included as part of my larger paper (which also compares HF/CIS, 
HF/RPA, TDDFT/CIS and TDDFT/RPA):

J. Phys. Chem. A (2002) 106(44) p. 10596-10605.

At the time, the only ZINDO/RPA I could put my hands on was contributed 
by Sergei Tretiak and Shaul Mukamel, which didn't let me set an active 
space. (In fact, it uses the Lanczos method for a full active space.) A 
parameterization for RPA calculations or a smaller active space would 
probably help.

> Probably the calculation takes a lot longer (Hamiltonian matrix is 
> four times
> as big since mixing of particle-hole and hole-particle excitations 
> occurs).

I think with an efficient implementation, it's not really an issue. 
(It's a semiempirical calc. after all!) I never did timing tests, but I 
can relate that up to 60+ heavy atoms, ZINDO/RPA calculations still 
only took something on the order of minutes (on an 800MHz Pentium III, 
so faster times nowadays).

> Are there any problems with numerical instabilities with the
> implemented RPA scheme in a INDO/S-RPA calculation ?

I'll second Dr. Thompson's comments. I haven't run any extremely 
"strange" molecules, but haven't seen any instabilities.

Cheers,
-Geoff

--
-Geoff Hutchison		<hutchisn=at=chem.northwestern.edu>
Ratner/Marks Groups	(847) 491-3295
Northwestern Chemistry	http://www.chem.northwestern.edu/



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Date: Wed, 28 May 2003 20:18:42 -0400
From: "Renxiao Wang" <renxiao(at)med.umich.edu>
To: <chemistry(at)ccl.net>
Subject: A question on heat of formation
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Hi, CCLers!

Should the heat of formations of two enantiomers of a chiral compound be
identical? I think the answer is yes. Please point out some references
for this. 

A disturbing fact is that, no matter you use QM or MM to calculate the
heat of formation for a given molecule, the number is
conformation-depentdent. I guess this is because of the steric energy
part is conformation-dependent. So, if I really want to compare the
stability of two molecules using heat of formation, how may I calculate
it right?

Best regards,

Renxiao Wang
renxiao(at)med.umich.edu



From chemistry-request@ccl.net Wed May 28 18:52:40 2003
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Date: Thu, 29 May 2003 00:52:34 +0200
From: "Dr. Alexander Hofmann" <ah(at)chemie.hu-berlin.de>
To: ccl <chemistry(at)ccl.net>
Subject: Re: CCL:Eigenvalues of hessian
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In-Reply-To: <NGBBILMDCLJNCGKMLPEEKEHECCAA.prsjjr(at)bath.ac.uk>; from prsjjr(at)bath.ac.uk on Wed, May 28, 2003 at 04:37:04PM +0100

Hi Daniel,

you normally get 3N eigenvalues. 3 are translations and 3 for rotation of the molecule. In solids, it becomes a little more difficult. Please check your modes for these movements.

Hth

Alex

> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request(at)ccl.net]On
> Behalf Of Daniel R. Rohr
> Sent: 28 May 2003 15:21
> To: ccl
> Subject: CCL:Eigenvalues of hessian
> 
> 
> Hi CCLers
> 
>  Does anybody of you know, why there are more than 3N-6 nonzero
> eigenvalues of the hessian? I am especially interested in the question,
> whether this error is due to the errors made by differentiation or
> whether they are due to an error within the method itself. I usually get
> only 3 zero eigenvalues. No matter if the hessian is calculated on a
> stationary point or not.
> 
> Thanks for your help
> 
> Daniel Rohr
> 
> -- 
> -----------------------------------------------------------------------
>  Daniel Rohr                                    Fachbereich Chemie der
>                                                 Philipps-Universitdt
>  Tel.: +49-6421-28-25686                        Hans-Meerwein-Stra_e
>  Fax.: +49-6421-28-25566                        D-35043 Marburg
>  eMail: rohrd(at)stud-mailer.uni-marburg.de        Germany
> -----------------------------------------------------------------------
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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-- 

Dr. Alexander Hofmann

Humboldt-Universitaet zu Berlin
Institut fuer Chemie
Arbeitsgruppe Quantenchemie

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          10099 Berlin              
Visitors: Brook-Taylor-Strasse 2 
          12489 Berlin

ah(at)chemie.hu-berlin.de

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Fax.: +49-30-2093-7136

http://www.chemie.hu-berlin.de/ag_sauer/index.html

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From chemistry-request@ccl.net Wed May 28 18:45:44 2003
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Date: Wed, 28 May 2003 15:45:44 -0700 (PDT)
From: Guosheng Wu <wu_guosheng2002(at)yahoo.com>
Subject: Re: CCL:orbitals
To: chemistry(at)ccl.net
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--- Rene Fournier - 1999-07-07 <renef(at)yorku.ca> wrote:
>    Leif Laaksonen makes an important point: only observables
> are "real" in QM.  So the question arises: is it possible to
> define orbitals as QM observables.  It entirely depends on
> how you define the word "orbital".  If one says orbitals are
> one-electron functions and nothing more, then of course orbitals
> can be made to be QM observables.  For example, just integrate
> an exact squared wavefunction over all electron coordinates
> but one to get the electron density, then take the square
> root, multiply by a phase factor and you get "density orbitals".
> [G Hunter, Int J Quantum Chem 9 (1975) 237].   They may not be
> very useful as orbitals, but they are "real" in the sense of
> QM observables.
 
It's not clear for me how you define "QM observable"?
 
MO is certainly not "observable", if "observable" is defined as something 
can be measured directly or indirectly by an experiment. For example,
electronic density, ionization energy, and so on.
 
The issue is related with the phase factor you mentioned:
  From experimental data, one can get |MO|^2 at a certain position,
  but here "MO" is not unique: MO = |MO|*[cos(theta)+i*sin(theta)], 
  where "theta" can be any arbitary value. 
This may be traced back to the Uncertainty Principles.

Similarly to my original post, 0, 1, 2,... are countable (defined as 
non-negative integers). However, if one do the square of 1, +1 and -1
will come out, not unique --- 2 directions in the 1-D space; 
Do the square of -1, we get +i and -i, 2 direction in the 2-D space...
It seems we can safely say that -1 & i are not countable!?
 
By the way, does it really matter if "MO" is observable or not in any sense?
Maybe useful for teaching.
 
Guosheng
 
 
> --- Rene Fournier - 1999-07-07 <renef(at)yorku.ca> wrote:
> >    Leif Laaksonen makes an important point: only observables
> > are "real" in QM.  So the question arises: is it possible to
> > define orbitals as QM observables.  It entirely depends on
> > how you define the word "orbital".  If one says orbitals are
> > one-electron functions and nothing more, then of course orbitals
> > can be made to be QM observables.  For example, just integrate
> > an exact squared wavefunction over all electron coordinates
> > but one to get the electron density, then take the square
> > root, multiply by a phase factor and you get "density orbitals".
> > [G Hunter, Int J Quantum Chem 9 (1975) 237].   They may not be
> > very useful as orbitals, but they are "real" in the sense of
> > QM observables.
> >     Orbitals are always defined as one-electron functions,
> > but THAT does not make them "unreal".  The electron density
> > is a one electron function and very real for any N-electron
> > system, not only for the H atom.
> >     One "ab initio" way to define orbitals is to start from
> > exact wavefunctions and calculate the overlap of a N-electron
> > wavefunction (neutral) and the ground and various excited
> > states a (N-1)-electron wavefunction (ion) (Dyson orbitals are
> > defined in such a way I think).  I'm sure there are definitions
> > that will make such orbitals unique, but does that make them
> > QM observables?  I don't think so, but I'd like to hear from
> > the CCL community on that.  There are other ways to define orbitals
> > > from exact wavefunctions, I'm sure: are any of them QM observables?
> >     As for Kohn-Sham orbitals, they may not be real individually
> > but the N lowest energy ones squared and summed give the true
> > electron density (an observable) and the negative of the KS HOMO
> > energy is exactly equal to the first IP (another observable) so
> > there are at least some bits of reality built in KS orbitals!
> > 
> > Here's some relevant articles:
> > 
> > 1) Kohn, Becke, Parr, J Phys Chem 100 (1996) 12974
> > 2) "Kohn-Sham Orbitals and Orbital Energies: Fictitious Constructs but
> >    Good Approximations All the Same"
> >    by S. Hamel, P. Duffy, M.E. Casida, and D.R. Salahub
> >    Journal of Electron Spectroscopy and Related Phenomena (2002?)
> > 3) Chong, Gritsenko, Baerends, J Chem Phys 116 (2002) 1760
> > 
> > --------------------------------------------------------------------
> > | Rene Fournier                 | Office:  303 Petrie              |
> > | Chemistry Dpt, York University| Phone: (416) 736 2100 Ext. 30687 |
> > | 4700 Keele Street,  Toronto   | FAX:   (416)-736-5936            |
> > | Ontario, CANADA   M3J 1P3     | e-mail: renef(at)yorku.ca           |
> > --------------------------------------------------------------------
> > |                http://www.chem.yorku.ca/profs/renef/             |
> > --------------------------------------------------------------------
> > 
> > 
> > 
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> > 
> > 
> > 
> > 
> 
> 
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