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To whom may it concerned

I have run an NMR calculation on Gaussian98 using B3LYP/631G*, on a 
compound with C5V symmetry.
But the NMR results i am getting, fit a compound with Cs symmetry, although 
in the computation the full point group is C5v. The Cs symmetry is the 
Abelian subgroup - and i think for some reason this is why i am getting the 
"wrong" results.

Is there a way to bypass this problem?

thank you in advance
................................................................................... 

If you desire peace of soul and happiness, then believe;
If you would be a disciple of truth then inquire. Nietzsche
...................................................................................

Ivan Aprahamian
Department of Organic Chemistry,
The Hebrew University of Jerusalem,
Jerusalem, 91904, Israel.
Tel: ++ 972-2-6586272/258
Fax: ++ 972-2-6527547
E-mail: ivan_at_pob.huji.ac.il



From chemistry-request@ccl.net Sun Feb  6 12:42:14 2005
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Date: Sun, 6 Feb 2005 09:42:10 -0800 (PST)
From: Guosheng Wu <wu_guosheng2002 [] yahoo.com>
Subject: Re: CCL:orbitals and reality
To: Sengen Sun <sengensun [] yahoo.com>, CHEMISTRY [] ccl.net
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"Sorry" is that what I should say first to Dr. Sun, since really I do not
understand much about what he was talking about.  Is it about science or
philosophy, or mystery or whatever, because there seem to be many very
subjective statements about other people and about himself insetead of
pure scientific discussion... 

Please correct me if I am wrong again on the followings:
   In the framework of quantum mechanics, wave function defines the state
of motion for a system. There exists some very simple and well-defined
system, for which the solution to the Schrodinger equation is unique
(beside the arbitary phase component) and accurately sovable, and any
quantum (electron spin) or classical physical properties for the system
can be derived based on the wave function. 

   For example: for a system with 3 energy levels, e1, e2, e3,
corresponding to 3 different channels of an organic reaction, the accurate
solution to its wave function at some time (say t=200 fs, some state for a
dynamic system after scattering/interacting with another system) may be
like this:

   |psi(t=200fs)> = 0.1 |psi_1> + 0.1 |psi_2> + sqrt(0.98) |psi_3>
               (each psi_i is normalized and orthogonal to each other)

what does the wave function at t=200fs tells us?  It tells us that at that
instant time, the probability for the system at state |psi_1> is 1%, at
state |psi_2> is 1% and at state |psi_3> is 98%, any real measurement will
be finally be any of the above eigenstate with corresponding probability,
but for a chemist doing exp. in wet lab, finally he would get about 98%
productivity for channel 3 product.

It is exactly based on the way that Mr. Born would use to calculate
|<psi|psi>|^2, which is the probability density of the system at t=200fs. 

What Born did many years ago?  He provided a statistical explanation for
wave function, by a simple operation |<psi|psi>|^2, saying something like
"what is wave function? its absolute square means the probability density
for the system at some position at some time..."   It does not mean
something like "that wave function itself does not mean anything, unless
we calculate its absolute square", because besides Born's explanation, one
could simply provide other kinds of explanation to wave function, by using
something like <psi|H|psi> and saying that "what is wave function, it
means when one calculte <psi|H|psi>, one would get its energy..."  But why
Born's explanation is more important? I guess it's just because it has
less mathematical operation from |psi> to its absolute square, so more
close to the explanation of wave function itself.

For a classical system, it's equation of motion is also described by some
kind of function, such as f(x,y,z)=x^2+y^2+z^2-R^2 =0, meaning that it's
motion is always limited on a sphere.  Here, the function f(x,y,z) is not
energy, is not position,..., but just the equation of motion for the
system. Does f(x,y,z) have no any kind of physical meaning?  Still, can
not many physically meaningful properties of the system be derived from
that equation? Can not one map the function out but doing experiment?  
... ...

On the other hand, one might want to argue that probability density is
just a property of wave function, and a very important property!  

It's the wave function that determines the probability density, not the
other way, and the former has much more information than the 2nd one,
obviously.  (One can simply make up some different wave functions, but
have exactly the same electron densities. One not perfect example is in
the X-ray data, without the resolution of H atoms or environmenal info,
how could one differentiate if a special density is for OH3+ or NH4+?)
 
Wave function is not just some mad or blind maths, but it defines the
state of motion for a quantum mechanical system, and it defines
essentially everything for that system. 

> I have to say honestly that the authors of the Nature
> papers and some people blindly supporting them are
> scientifically naive on this particular issue and need
> to re-study or re-think of QM. There are no physical
> entities or physical properties directly associated
> with WFs!

Why could not one change the last sentence above into:
  "There are numerous physical entities or physical properties directly
associated with WFs, such as |<psi|psi>|^2, <psi|H|psi>, ... "

Finally, as long as there exists unique solution of wave function for a
system, it's possible to map it out through experiments, partly if not
completely.  In this sense, forgetting about the technical details and
language they used in the Nature paper, the mapping of wave functions 
means much more than what someone would say is nothing but something
made-up from their blind mind.  It's pioneering work, and deserves much
respect.

Thanks for reading.

Sincerely,

-Guosheng Wu 



--- Sengen Sun <sengensun [] yahoo.com> wrote:

> The trajectories or orbits of classical objects have
> well-defined physical meaning, and even a toddler
> could well understand them. Their physical meaning is
> decided by physical reality independant of any
> mathematical equations. I would say they are
> experimentally observable (like force field) although
> we cannot take a snapshot of them. It is also fine to
> me if you say they are not. It is of no point to argue
> for which way you say it. But it is not acceptable to
> say that electrons and nuclei are not observables!
> 
> In contrast, WFs disappear like ghosts outside our
> mathemtical schemes! In fact, the 1954 Nobel prize was
> awarded partially to Born for his interpretation that
> WFs have no physical meaning.  It is also the official
> interpretation in our textbooks that orbitals are not
> observables and have no physical meaning. It could not
> be more clear as shown by Spanget-Larsen's  posting on
> Jan 20, 05. Alan Shusterman, Eric Scerri, many others,
> and I are not creating any new interpretation. We are
> just defending the well-established theory after deep
> thinking for many years and after several years public
> discussion. 
> 
> Dr. Hultin is speculating whether some physical
> properties of electronic structure can lead to some
> information of WFs. This is surely possible for H.
> However, such an activity distinguishes from any
> experimental observation, as it is conducted in
> reference to the pictures in your mind. It is not
> based on any physical interacting relationship. WFs
> are not experimental observable whatever, simply
> because they are not the choice of the nature but
> humans. The choices of the nature are electrons, their
> motion (or density distribution), and the space they
> occupy. The reverse construction of WFs for
> multielectron systems would be extremely hard and is
> impossible to me (or I am not quite sure). Here I do
> share with Dr. N Sukumar's concern with <declaring
> that the experiment has to be wrong because we read in
> some textbook that it cannot be done>. What I am sure
> is that the Nature papers did not produce any relevant
> information for possible mathematical construction of
> WFs. I see myself to be technique-specific. We must be
> very careful to reject any competitive experiements.
> However, what they did is implicit assumptions after
> assumptions without logical connections. 
> 
> I agree well on the two points by Lou Noodleman on
> Jan. 24. It is sure that single WFs carry the
> information of physical reality, even though they are
> human-formulated. That is why they are so useful. It
> is also true that virtual orbitals carry physical
> information one way or the other. WFs are just a
> mathematical tool to dismantle the reality and to wrap
> up the pieces in order to carry them through our math
> procedures. They are just for human convenience and
> cannot be understood until we reach our destination
> where we can re-assemble them together to make sense
> in the reality. 
> 
> I must again emphasize that the electronic structure
> of a quantum system cannot function physically
> according to WFs in chemical reactions. To my best
> knowledge, I am the first person who explicitly states
> so in the public, although this point was implied in
> several occassions by Dewar, Bader, et. al. I also
> wish to emphasize that chemistry is not about orbitals
> but electron density and its reorganization as nuclei
> change their positions. The third important point is
> that chemical reactivity is decided by the easiness of
> electronic reorganization. These three points are very
> valuable in teaching and in scientific research, as
> recognized by two CCL friends recently.
>   
> I have to say honestly that the authors of the Nature
> papers and some people blindly supporting them are
> scientifically naive on this particular issue and need
> to re-study or re-think of QM. There are no physical
> entities or physical properties directly associated
> with WFs!
>  
> --- Eric Scerri <scerri [] chem.ucla.edu> wrote:
> 
> > On Saturday, January 29, 2005, at 12:46  AM,
> > konrad.hinsen [a] laposte.net
> > wrote:
> 
> > > That's my view as well and I have had the same
> > sense of bewilderment
> > > reading the recent discussion. For me the question
> > is not if orbitals
> > > are "real" but if they are useful in understanding
> > molecules. But the
> > > same comment applies to electrons and nuclei.
> > > --
> > > Konrad Hinsen
> > > -------
> > 
> > Many useful things are unobservable!
> > 
> > The question was indeed whether one can observe an
> > orbital.
> > I don't think anybody really doubts the usefulness
> > of the concept.
> > 
> 
> Another problem is what an extent there is that
> orbitals are useful in understanding molecules. They
> cannot be used in such a way that scientists in the
> same field do not understand each other (e.g., on the
> mechanism of a dipolar addition, JPC A 2001, 105,
> 10943; 10946; 10947). This is not just an occassional
> problem. Many claims of explanation based on orbitals
> in the literature turned out to be non-understandable.
> In fact, Dr. Scerri stated in a published paper: <with
> the triumph of QM, there has been an inevitable
> tendency to exaggerate its success, ...>. I can
> support such a statement by giving many examples. The
> claims of orbital observation are just one of them. 
> 
> --- Valentina VETERE <vetere [] esrf.fr> wrote:
> > Sorry I'm still in trouble here..can you please make
> > me understand why an 
> > electron can not be localized in a HOMO. Is the
> > reason that outside the 
> > orbital picture there is a probability different
> > from zero to found the 
> > electron  or are you thinking about a
> > multiconfigurational nature for the 
> > atoms?
> > 
> 
> The uncertainty of a single electron in a
> multi-electron system is not limited to a single
> orbital. This point is well established and documented
> in many textbooks. You may read some textbooks. I
> would recommend Bader's note on web:
> http://www.chemistry.mcmaster.ca/esam/
> 
> 
> Sengen
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 		
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From chemistry-request@ccl.net Sun Feb  6 13:24:13 2005
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On Sat, 5 Feb 2005 22:08:40 -0800 (PST) Sengen Sun wrote:

> In fact, the 1954 Nobel prize was
> awarded partially to Born for his interpretation that
> WFs have no physical meaning.

Not how I would paraphrase the Nobel citation!

> and I are just defending the well-established theory after deep
> thinking for many years and after several years public
> discussion. 
> 
> ... It is sure that single WFs carry the
> information of physical reality, 

Do understand that this is NOT the standard interpretation of quantum
mechanics. This is how hidden variable theories interpret Q.M. The standard
interpretation does not talk about "physical reality."

> I must again emphasize that the electronic structure
> of a quantum system cannot function physically
> according to WFs in chemical reactions.

meaning what?

> I also wish to emphasize that chemistry is not about orbitals
> but electron density and its reorganization as nuclei
> change their positions.

The Copenhagen interpretation denies "physical reality" even to positions
of electrons and nuclei.

>   
> I have to say honestly that the authors of the Nature
> papers and some people blindly supporting them are
> scientifically naive on this particular issue and need
> to re-study or re-think of QM. 
>  

What amazes me about this discussion here is that over 90% of the
argumentation is taking place without any reference to the experimental
setup of the work being disputed! Hence my reference to the story of
determining the number of a horse's teeth. Truly we are proving right some
of the more radical interpretations (a la Heisenberg) that declare that
Q.M.does not deal with the physical world, but rather with what is going on
in the observers' minds! :-)

Dr. N. Sukumar
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute



From chemistry-request@ccl.net Mon Feb  7 11:01:38 2005
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From: "Phil Hultin" <hultin=at=cc.umanitoba.ca>
To: "Computational Chemistry List" <chemistry=at=ccl.net>
Subject: Orbitals yet again
Date: Mon, 7 Feb 2005 10:01:29 -0600
Organization: Dept. of Chemistry, U. of Manitoba
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Two comments:

 

Dr. Sukumar points out that the discussion has veered away from the Nature
paper that stimulated it.  I also have noted that the discussion has
neglected the specifics of Villeneuve et al's paper.  There is a lot of talk
about whether they have actually imaged the difference between N2 and N2+,
but it appears to me that their technique is NOT a difference method at all.
I can't claim to understand everything about their method, and I do feel
very uncomfortable about statements they make about spectroscopic signals
being generated by the interference of two wavefunctions (which are
undeniably human-created and non-physical things).

 

Having said this, I return to my original posting: if Villeneuve et al have
NOT imaged an orbital as they claim (and I believe that strictly speaking
such an image is indeed a QM impossibility), then just what is the physical
origin of the spectroscopic data that they present?  It is fine to deny that
an orbital image is possible, based on theory.  Unless the critics are
claiming that the observation by Villeneuve et al is a fabrication (which
nobody seems to be saying, thank heaven), I really would like to see their
point-by-point explanation of just what actually was observed in
Villeneuve's experiment, or how the processing of the raw data gave rise to
an invalid conclusion.

 

As I understand it, a series of spectra of very high overtones arising from
the laser stimulation of N2 molecules in a set of defined rotational states
with respect to the plane of laser polarization were acquired.  They assert
that this technique selectively excites only the highest-energy electrons in
the sample, which they equate with the HOMO electrons.  The spectra were
found to vary as a function of the rotational orientation of the molecules.
A standard tomographic technique was used to obtain a 3-dimensional plot of
something that the authors assert is the electronic state that gave rise to
the spectral signal.  They quote literature sources to support this claim.
Finally, they note that the topology of this 3-D plot is strikingly similar
to an HF-derived graph of the expected HOMO.

I do not see any point at which the orbital model was used to process the
raw data, but this may be because I have not tracked down the literature
supporting the idea that overtone spectra of this kind do give information
about the electron density of a single state.

 

 

The second comment is this:

 

Dr. Sun remarked:

"Dr. Hultin is speculating whether some physical properties of electronic
structure can lead to some information of WFs. This is surely possible for
H.

However, such an activity distinguishes from any experimental observation,
as it is conducted in reference to the pictures in your mind. It is not
based on any physical interacting relationship. WFs are not experimental
observable whatever, simply because they are not the choice of the nature
but humans. The choices of the nature are electrons, their motion (or
density distribution), and the space they occupy. The reverse construction
of WFs for multielectron systems would be extremely hard and is impossible
to me (or I am not quite sure)."

 

I quite agree that we are not able to deduce a rigorous mathematical
formulation to describe an observation of one among many electrons (if that
is indeed possible).  But I do not think that the only information of
interest is that which can be treated mathematically. Yes, WFs are human
creations and do not have physical reality.  Nevertheless, the inability of
humans to come up with an equation in no way limits our ability to observe
electronic behaviour within the limits of uncertainty.  Just as we can
deduce the concept of a Newtonian trajectory from our observations of balls
in motion, surely we can deduce something orbital-like if we observe that
electron density is concentrated in specific regions of space?  We have the
tools to mathematically describe a Newtonian trajectory, and we do not have
such tools to handle the behaviour of electrons, true.  Does this mean that
we cannot conceptually recognize that there is some systematic behaviour of
electrons?  I hope not.

 

Also, I have remarked that it is possible albeit unlikely that some of our
ab initio mathematical treatments have captured some of this systematic
behaviour, at least superficially.  I do not say that this IS so, I merely
note that it is a possibility.  Does this mean that WFs are "real"?
Absolutely not.  If it were the case that HF or some other theory gave
correspondence to observable electronic behaviour, it would not necessarily
mean that the mechanics of our calculation must reflect the details of how
that behaviour arises.

 

Dr. Philip G. Hultin

Associate Professor of Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

 <mailto:hultin=at=cc.umanitoba.ca> hultin=at=cc.umanitoba.ca

 <http://umanitoba.ca/chemistry/people/hultin>
http://umanitoba.ca/chemistry/people/hultin

 


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<div class=3DSection1>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Two comments:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Dr. Sukumar points out that the discussion has veered away from =
the
Nature paper that stimulated it.&nbsp; I also have noted that the =
discussion
has neglected the specifics of Villeneuve et al&#8217;s paper.&nbsp; =
There is a
lot of talk about whether they have actually imaged the difference =
between N2
and N2+, but it appears to me that their technique is NOT a difference =
method
at all.&nbsp; I can&#8217;t claim to understand everything about their =
method,
and I do feel very uncomfortable about statements they make about =
spectroscopic
signals being generated by the interference of two wavefunctions (which =
are
undeniably human-created and non-physical =
things).<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Having said this, I return to my original posting: if Villeneuve =
et al
have NOT imaged an orbital as they claim (and I believe that strictly =
speaking
such an image is indeed a QM impossibility), then just what is the =
physical
origin of the spectroscopic data that they present?&nbsp; It is fine to =
deny
that an orbital image is possible, based on theory. &nbsp;Unless the =
critics
are claiming that the observation by Villeneuve et al is a fabrication =
(which
nobody seems to be saying, thank heaven), I really would like to see =
their
point-by-point explanation of just what actually was observed in =
Villeneuve&#8217;s
experiment, or how the processing of the raw data gave rise to an =
invalid conclusion.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>As I understand it, a series of spectra of very high overtones =
arising
> from the laser stimulation of N2 molecules in a set of defined =
rotational states
with respect to the plane of laser polarization were acquired.&nbsp; =
They
assert that this technique selectively excites only the highest-energy
electrons in the sample, which they equate with the HOMO =
electrons.&nbsp; The
spectra were found to vary as a function of the rotational orientation =
of the
molecules.&nbsp; A standard tomographic technique was used to obtain a =
3-dimensional
plot of something that the authors assert is the electronic state that =
gave
rise to the spectral signal.&nbsp; They quote literature sources to =
support
this claim.&nbsp; Finally, they note that the topology of this 3-D plot =
is
strikingly similar to an HF-derived graph of the expected =
HOMO.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>I do not see any point at which the orbital model was used to =
process
the raw data, but this may be because I have not tracked down the =
literature
supporting the idea that overtone spectra of this kind do give =
information
about the electron density of a single =
state.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>The second comment is this:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal style=3D'margin-left:0in;text-autospace:none'><font =
size=3D3
face=3D"Times New Roman"><span style=3D'font-size:12.0pt'>Dr. Sun =
remarked:<o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'margin-left:0in;text-autospace:none'><font =
size=3D3
face=3D"Times New Roman"><span =
style=3D'font-size:12.0pt'>&#8220;</span></font><font
size=3D2 face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:
"Courier New"'>Dr. Hultin is speculating whether some physical =
properties of
electronic structure can lead to some information of WFs. This is surely
possible for H.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3D"Courier New"><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:"Courier New"'>However, such an =
activity
distinguishes from any experimental observation, as it is conducted in
reference to the pictures in your mind. It is not based on any physical
interacting relationship. WFs are not experimental observable whatever, =
simply
because they are not the choice of the nature but humans. The choices of =
the
nature are electrons, their motion (or density distribution), and the =
space
they occupy. The reverse construction of WFs for multielectron systems =
would be
extremely hard and is impossible to me (or I am not quite =
sure).&#8221;<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3D"Courier New"><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:"Courier =
New"'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
lang=3DEN-US
style=3D'font-size:12.0pt'>I quite agree that we are not able to deduce =
a rigorous
mathematical formulation to describe an observation of one among many =
electrons
(if that is indeed possible).&nbsp; But I do not think that the only
information of interest is that which can be treated mathematically. =
Yes, WFs
are human creations and do not have physical reality. =
&nbsp;Nevertheless, the
inability of humans to come up with an equation in no way limits our =
ability to
observe electronic behaviour within the limits of uncertainty.&nbsp; =
Just as we
can deduce the concept of a Newtonian trajectory from our observations =
of balls
in motion, surely we can deduce something orbital-like if we observe =
that
electron density is concentrated in specific regions of space?&nbsp; We =
have
the tools to mathematically describe a Newtonian trajectory, and we do =
not have
such tools to handle the behaviour of electrons, true.&nbsp; Does this =
mean
that we cannot conceptually recognize that there is some systematic =
behaviour
of electrons?&nbsp; I hope not.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
lang=3DEN-US
style=3D'font-size:12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
lang=3DEN-US
style=3D'font-size:12.0pt'>Also, I have remarked that it is possible =
albeit
unlikely that some of our ab initio mathematical treatments have =
captured some
of this systematic behaviour, at least superficially.&nbsp; I do not say =
that
this IS so, I merely note that it is a possibility.&nbsp; Does this mean =
that
WFs are &#8220;real&#8221;?&nbsp; Absolutely not.&nbsp; If it were the =
case
that HF or some other theory gave correspondence to observable =
electronic
behaviour, it would not necessarily mean that the mechanics of our =
calculation must
reflect the details of how that behaviour =
arises.</span><o:p></o:p></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Dr. Philip G. Hultin<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Associate Professor of Chemistry,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><u1:place u2:st=3D"on"><u1:PlaceType =
u2:st=3D"on"><st1:place
w:st=3D"on"><st1:PlaceType w:st=3D"on"><font size=3D3 face=3D"Times New =
Roman"><span
  =
style=3D'font-size:12.0pt'>University</span></font></st1:PlaceType></u1:P=
laceType>
 of <u1:PlaceName u2:st=3D"on"><st1:PlaceName =
w:st=3D"on">Manitoba</u1:PlaceName></st1:PlaceName></st1:place></u1:place=
><o:p></o:p></p>

<p class=3DMsoNormal><u1:place u2:st=3D"on"><u1:City =
u2:st=3D"on"><st1:place w:st=3D"on"><st1:City
 w:st=3D"on"><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:12.0pt'>Winnipeg</span></font></st1:City></u1:City>,
 <u1:State u2:st=3D"on"><st1:State =
w:st=3D"on">MB</u1:State></st1:State></st1:place></u1:place><o:p></o:p></=
p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>R3T 2N2<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><a href=3D"mailto:hultin=at=cc.umanitoba.ca"><font size=3D2 =
face=3DArial><span
style=3D'font-size:10.0pt;font-family:Arial'>hultin=at=cc.umanitoba.ca</span=
></font></a><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><a href=3D"http://umanitoba.ca/chemistry/people/hultin"><font =
size=3D2
face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'>http://umanitoba.ca/chemistr=
y/people/hultin</span></font></a><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

</div>

</body>

</html>

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From chemistry-request@ccl.net Mon Feb  7 13:29:20 2005
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Date: Mon, 7 Feb 2005 14:29:13 -0300 (ART)
From: Rodrigo Pontes <pontes_uem ## yahoo.com.br>
Subject: CPU usage
To: chemistry ## ccl.net
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Dear Colleagues,
 
We are running Gaussian on a Windows XP/Pentiun-IV HT 3.2GHz machine. We observed (in the Task manager / performance) that the CPU usage is only around 60%. Have someone noticed the same problem? How could us set the configuration to a 100% CPU usage?
 
Thanks in advance,
 
Rodrigo M. Pontes
Departemanto de Quimica
Universidade Estadual de Maringa
Brazil


		
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<DIV>
<DIV>Dear Colleagues,</DIV>
<DIV>&nbsp;</DIV>
<DIV>We are running Gaussian on a Windows XP/Pentiun-IV HT 3.2GHz&nbsp;machine. We observed (in the Task manager / performance) that the CPU usage is only&nbsp;around 60%. Have&nbsp;someone noticed the same problem? How could us set the configuration to a 100% CPU usage?</DIV>
<DIV>&nbsp;</DIV>
<DIV>Thanks in advance,</DIV>
<DIV>&nbsp;</DIV>
<DIV>Rodrigo M. Pontes</DIV>
<DIV>Departemanto de Quimica</DIV>
<DIV>Universidade Estadual de Maringa</DIV>
<DIV>Brazil</DIV></DIV><p>
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From chemistry-request@ccl.net Mon Feb  7 12:39:14 2005
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Date: Mon, 07 Feb 2005 14:01:52 +0100
To: chemistry ## ccl.net
From: christophe morell <christophe.morell ## ujf-grenoble.fr>
Subject: CCL:orbitals and reality
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	The discussion of Wavefunction and reality is very interesting,
and I would like to comment the last mail of Dr.Sen

1. In contrast (of orbits), WFs disappear like ghosts outside our
mathemtical schemes! In fact, the 1954 Nobel prize was
awarded partially to Born for his interpretation that
WFs have no physical meaning.  It is also the official
interpretation in our textbooks that orbitals are not
observables and have no physical meaning. It could not
be more clear as shown by Spanget-Larsen's  posting on
Jan 20, 05. Alan Shusterman, Eric Scerri, many others,
and I are not creating any new interpretation. We are
just defending the well-established theory after deep
thinking for many years and after several years public
discussion. 


I totally disagree with this claiming. Fortunately Nobel prize
 have not been given to Born for this kind of interpretation.
Beside claiming that WF have no physical meaning is not really
an interpretation. On the contrary Born gave a statistical 
interpretation of the WF, and thus have help us to rationalize 
the wave-particule duality. (Max Born "Atomic Physics")
In Born's book, there is a chapter about "experimental evidence
 of the undulatory  nature of matter" 
My question is : is it possible that wave of matter does exist 
while the corresponding wavefunction have no physical reality?


2. The choices of the nature are electrons, their
motion (or density distribution), and the space they
occupy. 

I partially agree  with this comment. Indeed, the choice of nature
 is electron but what is the nature of electron. I don't know the
 real nature of electrons but I know  that electrons acts sometimes
 like a particule and sometimes like a wave. 
For instance, electronic beam can be scattered. (Davisson and Germer 1927). 
And the compton effect cannot be rationalized through wave mechanic.  
If an electron acts as a wave (De Broglie 1925), it can probably be 
characterized by a wafefunction, even if the wavefunction cannot up to now be
 measured or calculate accurately. 
On the other hand electronic density is human made, and its only the number
 of electron by volume units. This a result of an operation and have nothing
 to do with real nature of electrons even if electronic density can be
measured.
 This is not the choice of the nature but a choice made by the human mind
because
  a density is easier to understand  than a diffuse wave. Beside the
calculation 
using electronic density  are in theory less time consuming.

3. I must again emphasize that the electronic structure
of a quantum system cannot function physically
according to WFs in chemical reactions.

Why??
Do you have experimental or theoretical evidence?

 To my best
knowledge, I am the first person who explicitly states
so in the public, although this point was implied in
several occassions by Dewar, Bader, et. al. I also
wish to emphasize that chemistry is not about orbitals
but electron density and its reorganization as nuclei
change their positions.

This is a amazing statment. Thus the real nature of electron (as a wave)
is denied while the only important variable is electronic density, a human
representation. 
This point of view is common in Density Functional Theory (DFT). 
By the way, the DFT have been justified from wavefunctions (First
Hohenberg-Kohn theorem)
Anyway,  I am not sure that all can be explained from electronic density
and its reorganization.
Some reactions like pericyclics ring closure or Dunitz Burgi attack are
very difficult to rationalize
through DFT, while the interpretation using wavefunction is straightforward

My personal conclusion is that I don't know if wavefunctions are real or
not, but the facts are that electrons acts 
sometimes as wave( even if that hurts my common sense) and I don't think
there is waves without wafefunctions.
The meaning of wavefunction is not clear , but even if we are unable to
understand the meaning of the wavefunction, that does not imply that
wavefunctions are not real.
 

 
I am sorry for the length of my mail.


Best regards

Christophe MORELL 
christophe_morell !! yahoo.fr



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--- "Dr. N. SUKUMAR" <nagams _+_ rpi.edu> wrote:

> On Sat, 5 Feb 2005 22:08:40 -0800 (PST) Sengen Sun
> wrote:
> 
> > In fact, the 1954 Nobel prize was
> > awarded partially to Born for his interpretation
> that
> > WFs have no physical meaning.
> 
> Not how I would paraphrase the Nobel citation!

It is me bad that I did not say it strictly. Forget
the Nobel citation then. The question can be asked
this way: Do we really have a conflict between our
textbooks and the Nature papers? How many people
really think that this is the time to correct our
textbooks based on these Nature papers? The authors of
the current Nature themself are not confident in what
they said. How deep do we need to go if we already see
something evidently wrong with the physical concepts?
If we count the number of a horse's teeth and if we
mix up the first two, do we need continue? :-)

> 
> > I must again emphasize that the electronic
> structure
> > of a quantum system cannot function physically
> > according to WFs in chemical reactions.
> 
> meaning what?
> 

I meant that single electron WFs in multielectron
systems do not have ANY independent physical
functions. Otherwise, they are indeed physical
observables in the content of scientific experiments! 

The evident problem here to me is that some people
support the Nature paper based on how useful the
single WFs are in the mathematical treatments. This is
especially evident in the posting by Guosheng Wu. I do
not wish to address it separately.

I found that the posting by Stefan Bromley on Feb. 2
is very interesting. Based on my rough understanding
of scattering and tunnelling processes, I would say
that WFs are again very useful in mathmatical
treatments of complex physical phenomena. I do not
think that this can change WFs to be physical
observables or to have any observable properties
associated with them. Am I wrong here?


Sengen 





		
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From chemistry-request@ccl.net Mon Feb  7 15:21:16 2005
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Date: Mon,  7 Feb 2005 13:19:50 -0500
From: tminagaw %x% purdue.edu
To: chemistry %x% ccl.net
Subject: Making A Protonated Ligand with ADT
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"How to make A Protonated Ligand"

 I am using ADT(Autodock Tools) with Autodock 3.0.5
 I would like to know the way to make a "protoneted ligand"
 pdbq file.

 As you can see, benA.pdbq in Autodock 3.0.5 example(3PTB)
 has a total charge of 1.001, and I was trying to
 reproduce the same file with an original 3TB.pdb downloaded
 from Protein Data Bank.

 I extracted the ligand part (benA) from 3PTB.pdb,
 added Hydrogens and read this as a ligand molecule using ADT.
 However, ADT has assigned partial charges (Gasteiger charge) with
 a net "total" charge of zero automatically.  I need to assign a
 positive  (+1) total charge to the ligand. How do I request
 ADT to assign non-zero ligand total charges  (e.g., +1 or -1)?
 Thank you.

 Taisuke Minagawa
 Department of Physics
 Purdue University, USA




From chemistry-request@ccl.net Mon Feb  7 06:47:26 2005
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Date: Mon, 07 Feb 2005 11:44:38 +0100
From: Giulio Vistoli <giulio.vistoli :: unimi.it>
Subject: Re: CCL:protein-protein docking program
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Dear Sandro,

You can try EscherNG program (www.ddl.unimi.it, downloadable as 
standalone program or implemented in VEGA) It is a new version of Escher 
program, poposed by Helmer-Citterich and co-workers. This new version  
includes fast rouines for surface calculation and implements 
parallelized code.

Best regards

Giulio Vistoli


