From owner-chemistry@ccl.net Sat Oct 30 02:34:00 2010 From: "Brian Salter-Duke b_duke-*-bigpond.net.au" To: CCL Subject: CCL: question on Born-Oppenheimer approx. Message-Id: <-43039-101030013515-9213-75ebEpd6uPUe0w/xVHY//g() server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Sat, 30 Oct 2010 16:32:47 +1100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke ~ bigpond.net.au] On Fri, Oct 29, 2010 at 05:20:33PM -0700, Eric Scerri scerri.:.chem.ucla.edu wrote: > > Dear CCL'ers > > For many years now a few theoretical chemists (Primas, Woolley, > Sutcliffe) have claimed that there is something significant going on in > connection with the Born-Oppenheimer approximation. > > They claim that applying the approximation amounts to writing the > structure of a molecule in 'by hand' rather than the structure being > inherent in the quantum formalism. > > They cite examples such as C2H5OH and CH3OCH3 which share the same > Hamiltonian and conclude that structure cannot therefore be deduced > from QM in an ab initio fashion. > > Some philosophers of chemistry have taken this a good deal further as a > sign that chemistry (molecular structure) cannot be strictly reduced to > quantum mechanics. Some even claim that there is 'emergence' taking > place. > > Most chemists I have discussed this issue with claim that these > philosophers and even the theoretical chemists mentioned above are > reaching incorrect conclusions. Most chemists claim that structure does > really exist as a matter of fact and that we could in principle solve the > Schrodinger equation without fixing the position of the nuclei by solving > the equation for every conceivable arrangement and would thereby recover > the inherent structure. That is still using the B-O approximation as each arrangement is fixing the nuclei. To me the most worrying feature of the notion of structure is that we are looking at a set of n indistiguishable electrons in the field of m distinguishable (because they are at different points in space) nuclei. However, the proper QM position is that we have n indistiguishable electrons in the field of m nuclei some of which should be indistinguishable - the 2 C atoms (if both C12) in C2H5OH and CH3OCH3 for example. > I would be interested in comments and have a follow-up question if there > is any interest in this topic. > > all the best, > eric scerri > > Eric Scerri, The Periodic Table, Its Story and Its Significance, Oxford > University Press, 2007 > http://www.oup.com/us/catalog/general/subject/Chemistry/?view=usa&ci=9780195305739 > -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke:monash.edu Honorary Researcher Fellow Monash Institute of Pharmaceutical Sciences, Monash University Parkville Campus, VIC 3052, Australia. From owner-chemistry@ccl.net Sat Oct 30 15:50:01 2010 From: "Ahmet Koseoglu naclcys__hotmail.com" To: CCL Subject: CCL: Autodock Tools error - Undefined atom type Hm Message-Id: <-43040-101030151914-23945-sGUO2sZgdih+gQ+9RbyHhg---server.ccl.net> X-Original-From: "Ahmet Koseoglu" Date: Sat, 30 Oct 2010 15:19:12 -0400 Sent to CCL by: "Ahmet Koseoglu" [naclcys ~ hotmail.com] Dear CCL members, I have been trying to run Autodock for the first time using AutoDock Tools and Autodock4. I want to define flexible residues for the receptor molecule but when I try to choose the residue by opening the receptor first (no probem up to here) and following the command Flexible Residues -> Input -> Choose Macromolecule it gives the following error: ERROR ********************************************* Traceback (most recent call last): File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\ViewerFramework\VF.py", line 735, in tryto result = apply( command, args, kw ) File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\AutoDockTools\autoflexCommands.py", line 235, in doit ad4_typer.setAutoDockElements(mol) File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\AutoDockTools\atomTypeTools.py", line 369, in setAutoDockElements ah.assignHybridization(mol.allAtoms) File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\PyBabel\atomTypes.py", line 127, in assignHybridization a.babel_atomic_number = self.get_atomic_number(a.babel_type) File "C:\Program Files\MGLTools 1.5.4\MGLToolsPckgs\PyBabel\atomTypes.py", line 103, in get_atomic_number (name,_name) ) ValueError: Could not find atomic number for Hm Hm Now I figured these hydrogens are the the ones on the methyl groups that are attached to the HEME group and are written as HMA1, HMA2, HMA3, HMB1,... so on in the PDB file. As far as I understand the progam does not recognize the hydrogen type "HM". I don't know with which symbol I can replace HM in the PDB input or if there is any other solution. Any help is appreciated. Regards, Ahmet Koseoglu From owner-chemistry@ccl.net Sat Oct 30 17:21:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek+/-few.vu.nl" To: CCL Subject: CCL: question on Born-Oppenheimer approx. Message-Id: <-43041-101030035806-6556-NObekvkw8PtvcC2CnVWvvw],[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 30 Oct 2010 09:57:59 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek*few.vu.nl] On Sat, Oct 30, 2010 at 2:20 AM, Eric Scerri scerri.:.chem.ucla.edu wrote: > They claim that applying the approximation amounts to writing the structure > of a molecule in 'by hand' rather than the structure being inherent in the > quantum formalism. > They cite examples such as C2H5OH and CH3OCH3 which share the same > Hamiltonian and conclude that structure cannot therefore be deduced from QM > in an ab initio fashion. Does this analysis properly take the environment into account? I would expect that if the tunneling time between the isomers is long enough then the "classical" structures would be superselected by the environment (i.e. quantum mechanical decoherence). If the isomers would have similar energies this would be a kind of spontaneous symmetry breaking. Sincerely, Ulf Ekstrom From owner-chemistry@ccl.net Sat Oct 30 19:42:00 2010 From: "Eric Scerri scerri^-^chem.ucla.edu" To: CCL Subject: CCL: question on Born-Oppenheimer approx. Message-Id: <-43042-101030191145-20740-pqbhfQEqxZxmF/sa/3T4bg]^[server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-1-932297535 Date: Sat, 30 Oct 2010 15:19:02 -0700 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Eric Scerri [scerri:-:chem.ucla.edu] --Apple-Mail-1-932297535 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Thanks for all the responses so far. Ulf, please say a little more about super-selection rules etc. The =20 last time I spoke about this topic at a conference in London on =20 "Emergence", a philosopher of physics also brought up super-selection =20= but did not go into any detail. And what is the difference in the energies of these two isomers? Can =20= anyone help? eric scerri --------------- ------------------------------------------------------------------------=20= ------------------------------------------------------------------------=20= ------------------------------------------------------------------------=20= -------------------- The Periodic Table: Its Story and Its Significance, by Eric Scerri, =20 Oxford University Press, 2007. named as an "outstanding academic book of 2007" by Choice Library =20 magazine. Reviews: "An absolutely gorgeous book. I put it on my bedside table and then =20 stayed up half the night reading it - it is immensely readable." ---Oliver Sacks, author of The Man Who Mistook his wife for a Hat, =20 Awakenings etc. =93As the author of "The Periodic System of Chemical Elements: A =20 History of the First Hundred Years" (1969), I consider Scerri's "The =20 Periodic Table: Its Story and Its Significance" a worthy successor. I =20= declare his new book a must, not only for all historians of chemistry =20= and the other natural sciences, but also for the scientists and =20 pupils thereof.--- Jan W. van Spronsen, author of "The Periodic =20 System of Chemical Elements: A History of the First Hundred Years" =93Few concepts are more important in chemistry than the periodic =20 table, and Eric Scerri's book offers a wonderfully thorough, lucid, =20 and provocative introduction for both chemists and the scientifically =20= literate to this major cultural contribution. Anyone interested in =20 the foundations of chemistry will take delight, inspiration, and =20 information from this highly approachable book.=94 ----- Peter Atkins, =20= author of "The Periodic Kingdom", "Molecules" etc. On Oct 30, 2010, at 12:57 AM, Ulf Ekstr=F6m ulfek+/-few.vu.nl wrote: > > Sent to CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek*few.vu.nl] > > On Sat, Oct 30, 2010 at 2:20 AM, Eric Scerri scerri.:.chem.ucla.edu > wrote: >> They claim that applying the approximation amounts to writing the =20 >> structure >> of a molecule in 'by hand' rather than the structure being =20 >> inherent in the >> quantum formalism. >> They cite examples such as C2H5OH and CH3OCH3 which share the same >> Hamiltonian and conclude that structure cannot therefore be =20 >> deduced from QM >> in an ab initio fashion. > > Does this analysis properly take the environment into account? I =20 > would expect > that if the tunneling time between the isomers is long enough then the > "classical" > structures would be superselected by the environment (i.e. quantum =20 > mechanical > decoherence). If the isomers would have similar energies this would =20= > be a kind of > spontaneous symmetry breaking. > > Sincerely, > Ulf Ekstrom > > > > -=3D This is automatically added to each message by the mailing =20 > script =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/> > --Apple-Mail-1-932297535 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252


Thanks for all the responses so = far.

Ulf, please say a little more about = super-selection rules etc.  The last time I spoke about this topic = at a conference in London on "Emergence", a philosopher of physics also = brought up super-selection but did not go into any = detail.

And what is the difference in the = energies of these two isomers?  Can anyone = help?


eric = scerri

---------------

<= span class=3D"Apple-style-span" style=3D"font-size: 16px; = ">
The Periodic Table: Its Story and = Its Significance, by Eric Scerri, Oxford University Press, = 2007.

named as an "outstanding = academic book of 2007" by Choice Library magazine.

 I put it on my bedside = table and then stayed up half the night reading it - it is immensely = readable."---Oliver Sacks, author of The Man Who Mistook his = wife for a Hat, Awakenings = etc.

=93As the = author of "The Periodic System of Chemical Elements: A History of the = First Hundred Years" (1969), I consider Scerri's "The Periodic Table: = Its Story and Its Significance" a worthy successor. I declare his new = book a must, not only for all historians of chemistry and the other = natural sciences, but also for the scientists and pupils = thereof.--- Jan W. = van Spronsen, author of "The Periodic System of Chemical Elements: A = History of the First Hundred = Years"

=93Few concepts are more important in chemistry than = the periodic table, and Eric Scerri's book offers a wonderfully = thorough, lucid, and provocative introduction for both chemists and the = scientifically literate to this major cultural contribution. Anyone = interested in the foundations of chemistry will take delight, = inspiration, and information from this highly approachable = book.=94 ----- Peter Atkins, author of "The Periodic Kingdom", = "Molecules" = etc.


Sent to = CCL by: =3D?ISO-8859-1?Q?Ulf_Ekstr=3DF6m?=3D [ulfek*few.vu.nl]

On Sat, = Oct 30, 2010 at 2:20 AM, Eric Scerri scerri.:.chem.ucla.edu
<owner-chemistry.{=}.ccl.net> wrote:
=
They claim that applying = the approximation amounts to writing the structure
of a molecule in 'by hand' rather than the structure = being inherent in the
quantum = formalism.
They cite examples such as = C2H5OH and CH3OCH3 which share the same
in an ab initio fashion.
=

Does this analysis properly take the environment = into account? I would expect
that if the = tunneling time between the isomers is long enough then the
"classical"
structures = would be superselected by the environment (i.e. quantum = mechanical
decoherence). If the isomers = would have similar energies this would be a kind of
spontaneous symmetry breaking.

Ulf Ekstrom



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