From owner-chemistry@ccl.net Wed Dec 7 02:13:01 2005 From: "Sengen Sun sengensun() yahoo.com" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30209-051207020025-21946-WvFt4MyVgp7uy6bjdvGOOA!^!server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 6 Dec 2005 23:00:22 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun]_[yahoo.com] I regret for my last posting to respond to Alan Shusterman. It is not friendly and looks very ugly to me after I posted it. There I just wanted to say that every CCL-member should be free to discuss any CC-related topics. For the last several days, I have been supported by a number of CCL-friends, while I have also been described by others using these interesting words: "aimed at", "jealous", "attack","ox-grinning" in a few private e-mails. It is fine to me. But I still must emphasize that science and philosophy should be fairly discussed as if a driver must be free > from alcohol. All scientists must be equal to express their scientific opinions. This is why CCL is such a symbol of the modern human civilization that nothing else could match, not Nature, not JACS, not C & EN News.... I would give up the battle against orbital observability if we don't correct our evident mistakes in the fundamental description of the orbital concept. Generally, metaphors and daul meaning languages should not be used in the descriptions of science and philosophy, and are destructive when there is a need to be clear and concise. For example: "Orbital interaction control of chemical reactions" is strictly false and misleading. But if we add some constraints like: "orbital interaction control is a mathematical language and has no physical meaning and reality", it is then fine to me. All students can then understand. It is because of a general lack of the contraints that "orbital interaction" has been so exagerated in literature that some folks claimed its possible experimental measurements. Orbital observation claims are exactly the fatality of our vague theoretical languages. To me, the Hoffmann's quote is exactly equivalent to "orbitals are observable" no matter what he really thinks, while Dr. Alan Shusterman repeated his opposite position in both his public and private communications. I apologize that I did not answer him in time due to the time constraint. But what we can do is to keep the difference and move forward. As I remember, Hoffmann also said in a JACS paper about 6 or 7 years ago that orbitals are both real and unreal or something like that. If such a scientific giant makes such vague remarks from time to time, the claims for orbital orbservation will be waiting in a line to come out. I really do not mean to attack or blame any one here. I mean that we do have a choice to make science more consistent and move forward. I hope these are my final remarks under this thread. Sengen __________________________________________ Yahoo! DSL – Something to write home about. Just $16.99/mo. or less. dsl.yahoo.com From owner-chemistry@ccl.net Wed Dec 7 03:38:01 2005 From: "Alan Shusterman alan#%#reed.edu" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30210-051207033526-12756-MPAhSLEouPjNNFECenVanA#,#server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 07 Dec 2005 00:34:54 -0800 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan##reed.edu] Sengen Sun should not worry that he has offended me. I do not take any offense from his email and I am glad to read many of his ideas. In this regard, it may help to draw a distinction between the two halves of his last post. The first part of his post refers to his ideas about what controls organic reactions. I think this kind of material is interesting. It is just the kind of thing I like to see on the CCL when I check my email each day. I learn a lot from the CCL discussions of how one might *use* orbitals to explain chemical phenomena. The second part of his post returns to the original "orbitals are observable" debate. This part describes my views correctly; I don't think "orbitals are observable". I also disagree with his interpretation of Hoffmann's statement, but I have to admit that I can't be sure of any interpretation. So I will point out the obvious: Hoffmann is alive, a nice fellow, and usually happy to explain himself. Why not just ask him??? In the meantime, I don't think my objections to "orbitals are observable" have been addressed (see "Orbitals & CI" in my previous post). I am not an atomic physicist and do not have deep training in this area. My arguments may be bogus. If anyone can show me a mistake, I would be grateful because I have given this argument to my students more than once, and I'd like to improve my teaching if I can. Finally, my opposition to "orbitals are observable" should not be interpreted as "orbitals are not useful" or "orbitals are not interesting". I think they are useful and interesting. I hope that my previous post does not discourage anyone from writing about orbitals. That was not my intention at all. My apologies for any misunderstandings that I have caused. -Alan Sengen Sun sengensun() yahoo.com wrote: >Sent to CCL by: Sengen Sun [sengensun]_[yahoo.com] > >I regret for my last posting to respond to Alan >Shusterman. It is not friendly and looks very ugly to >me after I posted it. > -- Alan Shusterman Chemistry Department Reed College Portland, OR 97202-8199 503-517-7699 http://academic.reed.edu/chemistry/alan/ "Yield and overcome; Bend and be straight." Lao Tzu 22 From owner-chemistry@ccl.net Wed Dec 7 06:33:01 2005 From: "Pradipta Bandyopadhyay pradipta_._iitg.ernet.in" To: CCL Subject: CCL: Intel 9.0 C compiler installation ! Message-Id: <-30211-051207061637-18590-sqxA6vpKClz7YEbSNPxprQ/./server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 7 Dec 2005 16:36:31 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta*_*iitg.ernet.in] Apologies for not being a true computational chemistry question. While installing intel l_cc 9.0 compiler I am supposed to see several options (after running install.sh) 1,2,3 etc. But I am just seeing only 1 (1(a),1(b),1(c), 1(d), 1(e)) and exit option. Option 1 seems only for information regarding the product. Has anyone faced the same problem? Thanks. Pradipta ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Wed Dec 7 08:01:00 2005 From: "Ulrike Salzner salzner#fen.bilkent.edu.tr" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30212-051207042752-2210-7+/FsjijJ+2kxAHZs6YdbA=-=server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 07 Dec 2005 11:27:40 +0200 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner(_)fen.bilkent.edu.tr] I am following the debate with interest. At this point I would like take up only the "CI" argument of Alan. Clearly HF wave functions of molecules are approximations and the correlation problem can only be fixed with post HF treatments that do not produce orbitals. For one- electron systems, however, hydrogen-like orbitals are exact solutions and describes states. The properties of states can be observed experimentally. Is it conceivable that phases of the orbitals of one- electron systems can be observed? Moving to Helium, orbitals are no longer exact but extremely good numerical solutions are available, which, to my knowledge are very similar to hydrogens orbitals. What I am asking myself: are orbitals not observable in principle, or do we just face technical problems when multi-electron systems are considered? > In the meantime, I don't think my objections to "orbitals are > observable" have been addressed (see "Orbitals & CI" in my previous > post). I am not an atomic physicist and do not have deep training in > this area. My arguments may be bogus. If anyone can show me a mistake, I > would be grateful because I have given this argument to my students more > than once, and I'd like to improve my teaching if I can. > -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Wed Dec 7 08:48:00 2005 From: "Brian Salter-Duke b_duke./a\.octa4.net.au" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30213-051207060626-10257-PO8CTpabol4ulIBys8l2QA/a\server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 7 Dec 2005 22:06:12 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke|a|octa4.net.au] On Wed, Dec 07, 2005 at 03:41:02AM -0500, Alan Shusterman alan#%#reed.edu wrote: > Sent to CCL by: Alan Shusterman [alan##reed.edu] > Sengen Sun should not worry that he has offended me. I do not take any > offense from his email and I am glad to read many of his ideas. In this > regard, it may help to draw a distinction between the two halves of his > last post. > > The first part of his post refers to his ideas about what controls > organic reactions. I think this kind of material is interesting. It is > just the kind of thing I like to see on the CCL when I check my email > each day. I learn a lot from the CCL discussions of how one might *use* > orbitals to explain chemical phenomena. > > The second part of his post returns to the original "orbitals are > observable" debate. This part describes my views correctly; I don't > think "orbitals are observable". I also disagree with his interpretation > of Hoffmann's statement, but I have to admit that I can't be sure of any > interpretation. So I will point out the obvious: Hoffmann is alive, a > nice fellow, and usually happy to explain himself. Why not just ask him??? > > In the meantime, I don't think my objections to "orbitals are > observable" have been addressed (see "Orbitals & CI" in my previous > post). I am not an atomic physicist and do not have deep training in > this area. My arguments may be bogus. If anyone can show me a mistake, I > would be grateful because I have given this argument to my students more > than once, and I'd like to improve my teaching if I can. > > Finally, my opposition to "orbitals are observable" should not be > interpreted as "orbitals are not useful" or "orbitals are not > interesting". I think they are useful and interesting. I hope that my > previous post does not discourage anyone from writing about orbitals. > That was not my intention at all. If my views have been misintepreted, let me say that I entirely agree with Alan here - orbitals are usefull, but they cannot possibly be real. Keep the argument going. Brian. > My apologies for any misunderstandings that I have caused. > -Alan > > Sengen Sun sengensun() yahoo.com wrote: > > >Sent to CCL by: Sengen Sun [sengensun]_[yahoo.com] > > > >I regret for my last posting to respond to Alan > >Shusterman. It is not friendly and looks very ugly to > >me after I posted it. > > > > -- > Alan Shusterman > Chemistry Department > Reed College > Portland, OR 97202-8199 > 503-517-7699 > http://academic.reed.edu/chemistry/alan/ > "Yield and overcome; Bend and be straight." Lao Tzu 22> > > -- Brian Salter-Duke (Brian Duke) b_duke _ octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. From owner-chemistry@ccl.net Wed Dec 7 09:23:00 2005 From: "Loan Huynh huynhkl2000],[yahoo.ca" To: CCL Subject: CCL: measurement of energy of solvation experimentaly Message-Id: <-30214-051207004732-18092-qJrEoFBxocpog82paPG/BQ!A!server.ccl.net> X-Original-From: "Loan Huynh" Sent to CCL by: "Loan Huynh" [huynhkl2000- -yahoo.ca] Hi all, I am currently do the simulation to calculated the cohesive energy density (CED). I want to compare the in silico and in vitro CED. Does everyone know the technique (or reference) for evaluating the energy of solvation experimentaly (in vitro experiment. Any advice would be greatly appreciated. Many thanks, LH From owner-chemistry@ccl.net Wed Dec 7 09:58:00 2005 From: "Irilenia Nobeli irilenia.nobeli\a/kcl.ac.uk" To: CCL Subject: CCL: ADT installation on Mac OS X Message-Id: <-30215-051207035338-26806-rcRRmzEPqNgFcY5EVzbQ2Q * server.ccl.net> X-Original-From: Irilenia Nobeli Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 7 Dec 2005 07:52:18 +0000 Mime-Version: 1.0 (Apple Message framework v728) Sent to CCL by: Irilenia Nobeli [irilenia.nobeli]![kcl.ac.uk] > Hi, I posted the following message at the Autodock mailing list but have not received an answer so I'm trying my luck here.... > Hi, > Looking quickly through the archives I could not find an answer to > this, so I'm hoping that someone has solved it by now. After > installing a binary version of autodock tools > (complete2.3_binary_ppcDarwin7_acad_1-3alpha2) on a MacOS X 10.4, > I get the following error when trying to start either pmv or adt: > > Traceback (most recent call last): > File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- > packages/AutoDockTools/bin/runAdt.py", line 51, in ? > from Pmv.moleculeViewer import MoleculeViewer > File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- > packages/Pmv/moleculeViewer.py", line 18, in ? > from DejaVu.Geom import Geom > File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- > packages/DejaVu/__init__.py", line 66, in ? > raise RuntimeError('FATAL ERROR: opengltk.OpenGL Package not > found') > RuntimeError: FATAL ERROR: opengltk.OpenGL Package not found > > Does anyone know how to solve this? > > Thanks, > > Irilenia > ----------------------------- Irilenia (Irene) Nobeli Randall Division of Cell and Molecular Biophysics New Hunt's House (room 3.14) King's College London, Guy's Campus London, SE1 1UL U.K. irilenia.nobeli*kcl.ac.uk +44(0)207-8486329 From owner-chemistry@ccl.net Wed Dec 7 10:33:01 2005 From: "David F. Green dfgreen[#]ams.sunysb.edu" To: CCL Subject: CCL: measurement of energy of solvation experimentaly Message-Id: <-30216-051207095643-6888-CKS0VqUfz2aLyMMKMN6vvw : server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 07 Dec 2005 09:56:16 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen+*+ams.sunysb.edu] Try: Wolfenden et. al. "Affinities of amino acid side chains for solvent water" Biochemistry 20(4): 849-855 (1981). ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Loan Huynh huynhkl2000],[yahoo.ca wrote: > Sent to CCL by: "Loan Huynh" [huynhkl2000- -yahoo.ca] > Hi all, > > I am currently do the simulation to calculated the cohesive energy density (CED). I want to compare the in silico and in vitro CED. Does everyone know the technique (or reference) for evaluating the energy of solvation experimentaly (in vitro experiment. Any advice would be greatly appreciated. > > Many thanks, > LH> > > From owner-chemistry@ccl.net Wed Dec 7 11:08:00 2005 From: "Jeff Nauss jnauss!=!accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for January Message-Id: <-30217-051207105801-12189-HT3IpxE/RrOiBdFIqoQQeA|a|server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Wed, 7 Dec 2005 07:57:43 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss%x%accelrys.com] Accelrys Inc. are holding the following training workshops during January 2006. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs for the scheduled workshops are $500 per day for all customers. For the on-line presentations, the price is $175 per three hour session for all customers. CAMBRIDGE, UK Introduction to Life Science Modeling with InsightII 10-11 Jan Homology-Based Protein Design 12-13 Jan CHARMm 16-17 Jan Structure Based Drug Design with InsightII 18-19 Jan ONLINE TRAINING DS Gene 24 Jan (3pm PST) Protein-Protein Docking 25 Jan (7am PST) DS Gene 25 Jan (7am PST) DS ViewerPro 26 Jan (7am PST) MacVector 26 Jan (3pm PST) MacVector 27 Jan (7am PST) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html and http://www.accelrys.com/services/training/general/calendar_online.html. Questions regarding scheduling and content should be directed to workshops_._accelrys.com. -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From owner-chemistry@ccl.net Wed Dec 7 11:42:00 2005 From: "Rajarshi Guha rxg218(!)psu.edu" To: CCL Subject: CCL: Intel 9.0 C compiler installation ! Message-Id: <-30218-051207101833-21353-HUxe212LcWIrK3mOVXVbIA^^^server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 07 Dec 2005 10:18:39 -0500 Mime-Version: 1.0 Sent to CCL by: Rajarshi Guha [rxg218]|[psu.edu] On Wed, 2005-12-07 at 06:33 -0500, Pradipta Bandyopadhyay pradipta_._iitg.ernet.in wrote: > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta*_*iitg.ernet.in] > > Apologies for not being a true computational chemistry question. > > While installing intel l_cc 9.0 compiler I am supposed to see several options > (after running install.sh) 1,2,3 etc. > > But I am just seeing only 1 (1(a),1(b),1(c), 1(d), 1(e)) and exit option. > Option 1 seems only for information regarding the product. > > Has anyone faced the same problem? Thanks. Do you have an older version installed? I have 9.0 installed and running the installer shows the above options ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- A beer delayed is a beer denied. From owner-chemistry@ccl.net Wed Dec 7 12:17:00 2005 From: "Luciano Costa ltcnikit]~[gmail.com" To: CCL Subject: CCL: Intel 9.0 C compiler installation ! Message-Id: <-30219-051207110529-15468-B10U4LYyCmLfYRoqqkkpdw~!~server.ccl.net> X-Original-From: Luciano Costa Content-Type: multipart/alternative; boundary="----=_Part_31067_10327586.1133967986735" Date: Wed, 7 Dec 2005 13:06:26 -0200 MIME-Version: 1.0 Sent to CCL by: Luciano Costa [ltcnikit.:.gmail.com] ------=_Part_31067_10327586.1133967986735 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear pradipta, do you installed with sucess ?! You could detail your question, because I don't understand if you installed or not ?! Best regards, Luciano On 12/7/05, Pradipta Bandyopadhyay pradipta_._iitg.ernet.in < owner-chemistry]*[ccl.net> wrote: > > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta*_*iitg.ernet.in] > > Apologies for not being a true computational chemistry question. > > While installing intel l_cc 9.0 compiler I am supposed to see several > options > (after running install.sh) 1,2,3 etc. > > But I am just seeing only 1 (1(a),1(b),1(c), 1(d), 1(e)) and exit option. > Option 1 seems only for information regarding the product. > > Has anyone faced the same problem? Thanks. > > Pradipta > > > > -------------------------------------------------------------------------= ---------- > This email was sent from IIT Guwahati Webmail. If you are not the > intended recipient, please contact the sender by email and delete all > copies; your cooperation in this regard is appreciated. > http://www.iitg.ernet.in > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > -- ### Luciano Tavares da Costa ### ## MSc. Eng. Qu=EDmico ## 100 % Linux ############################# ------=_Part_31067_10327586.1133967986735 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
 Dear pradipta,

do you installed  with sucess ?! You could detail your question, because I  don't understand  if you  installed or not ?!

Best regards,

Luciano

On 12/7/05, Pradipta Bandyopadhyay pradipta_.= _iitg.ernet.in <owner-che= mistry]*[ccl.net> wrote:
Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta*_*iitg.ernet.in]

Apologies for not being a tr= ue computational chemistry question.

While installing intel l_cc 9.0 compiler I am supposed to see several options
(after running install.sh= ) 1,2,3 etc.

But I am just seeing only 1 (1(a),1(b),1(c), 1(d), 1(e)= ) and exit option.
Option 1 seems only for information regarding the pro= duct.

Has anyone faced the same problem? Thanks.

   = ; Pradipta


------------------------------------------------= -----------------------------------
This email was sent from IIT Guwahati Webmail. If you are not  the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated.
http://www.iitg.ernet.in



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--
### Luc= iano Tavares da Costa ###
##       MSc. En= g. Qu=EDmico
##       100 % Linux
#####= ######################## ------=_Part_31067_10327586.1133967986735-- From owner-chemistry@ccl.net Wed Dec 7 12:52:00 2005 From: "Phil Hultin hultin[a]cc.umanitoba.ca" To: CCL Subject: CCL: Orbitals and Philosophy Message-Id: <-30220-051207112849-2488-J9pkSqFr45Mr7lNj4nZb3g=-=server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C5FB18.FFAAAED0" Date: Wed, 7 Dec 2005 10:28:37 -0600 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin. * .cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C5FB18.FFAAAED0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit In the context of the discussion of whether orbitals are real/observable/measurable, it might be worth pointing out that philosophy has struggled with the concept of "reality" under its various guises since, well, since forever. I doubt very much that any of us can honestly claim to know what is "real" when pressed to provide a completely rigorous and universally applicable definition. Plato of course suggested that we were the inhabitants of a cave, watching only the shadows on the walls cast by "real" objects in the doorway of our cave. Orbitals are rather like shadows of a reality that we struggle to understand, and our debate about their reality is like asking about the reality of a cave-dweller's perceptions. As an organic chemist, I find the orbital model very useful to predict a variety of experimental outcomes, and to rationalize them after the fact as well. But lately I have been cautioning my students to remember that orbitals are only a model, that we talk of sigma and pi bonds, of bonding and antibonding MOs etc out of convenience and as a matter of utility. I also point out to them that it would make no sense whatsoever to abandon the simple models at this stage of chemical knowledge, because there is no alternative model yet available that can provide the practical guidance that has led to the great successes of synthetic organic chemistry. The time to abandon orbital theories will be when the total synthesis of taxol can be rationalized, guided, designed and implemented by arguments based only on observable electron density etc. This is in a sense akin to Samuel Johnson's refutation of Bishop Berkely (http://www.samueljohnson.com/refutati.html) - I accept a working definition of reality on a provisional basis because it helps me to navigate through the world as I presently perceive it, orbitals and all. Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin * cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_0007_01C5FB18.FFAAAED0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

In the context of the discussion of whether orbitals = are real/observable/measurable, it might be worth pointing out that = philosophy has struggled with the concept of “reality” under its various = guises since, well, since forever.  I doubt very much that any of us can = honestly claim to know what is “real” when pressed to provide a = completely rigorous and universally applicable = definition.

 

Plato of course suggested that we were the = inhabitants of a cave, watching only the shadows on the walls cast by “real” = objects in the doorway of our cave.  Orbitals are rather like shadows of a = reality that we struggle to understand, and our debate about their reality is = like asking about the reality of a cave-dweller’s = perceptions.

 

As an organic chemist, I find the orbital model very = useful to predict a variety of experimental outcomes, and to rationalize them = after the fact as well.  But lately I have been cautioning my students to remember that orbitals are only a model, that we talk of sigma and pi = bonds, of bonding and antibonding MOs etc out of convenience and as a matter of = utility.  I also point out to them that it would make no sense whatsoever to abandon = the simple models at this stage of chemical knowledge, because there is no = alternative model yet available that can provide the practical guidance that has led = to the great successes of synthetic organic chemistry.  The time to = abandon orbital theories will be when the total synthesis of taxol can be = rationalized, guided, designed and implemented by arguments based only on observable = electron density etc.  This is in a sense akin to Samuel Johnson’s = refutation of Bishop Berkely (http://www.samueljohn= son.com/refutati.html) – I accept a working definition of reality on a provisional basis = because it helps me to navigate through the world as I presently perceive it, = orbitals and all.

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin * cc.umanitoba.ca

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

 

------=_NextPart_000_0007_01C5FB18.FFAAAED0-- From owner-chemistry@ccl.net Wed Dec 7 13:49:00 2005 From: "Jens Thomas j.m.h.thomas===dl.ac.uk" To: CCL Subject: CCL: ADT installation on Mac OS X Message-Id: <-30221-051207124416-5677-A3TtUm85YtBF5a0cHoyqOA|-|server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 07 Dec 2005 16:53:35 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas++dl.ac.uk] Irilenia Nobeli irilenia.nobelia/kcl.ac.uk wrote: >Sent to CCL by: Irilenia Nobeli [irilenia.nobeli]![kcl.ac.uk] > > >Hi, > >I posted the following message at the Autodock mailing list but have >not received an answer so I'm trying my luck here.... > > >>Hi, >>Looking quickly through the archives I could not find an answer to >>this, so I'm hoping that someone has solved it by now. After >>installing a binary version of autodock tools >>(complete2.3_binary_ppcDarwin7_acad_1-3alpha2) on a MacOS X 10.4, >>I get the following error when trying to start either pmv or adt: >> >>Traceback (most recent call last): >> File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- >>packages/AutoDockTools/bin/runAdt.py", line 51, in ? >> from Pmv.moleculeViewer import MoleculeViewer >> File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- >>packages/Pmv/moleculeViewer.py", line 18, in ? >> from DejaVu.Geom import Geom >> File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- >>packages/DejaVu/__init__.py", line 66, in ? >> raise RuntimeError('FATAL ERROR: opengltk.OpenGL Package not >>found') >>RuntimeError: FATAL ERROR: opengltk.OpenGL Package not found >> >>Does anyone know how to solve this? >> >>Thanks, >> >>Irilenia >> >> Hi Irilenia It looks like you need to install the Python bindings for GTK. There's a link here that I hope will help: http://www.async.com.br/faq/pygtk/index.py?req=show&file=faq01.019.htp Best wishes, Jens From owner-chemistry@ccl.net Wed Dec 7 16:12:00 2005 From: "Axel Mathieu AMathieu^^tranzyme.com" To: CCL Subject: CCL: Comparison of Distance geometry algorithms Message-Id: <-30222-051207153504-31871-Fjz65oWU2/Tg9JAo7PKtaQ%server.ccl.net> X-Original-From: "Axel Mathieu" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5FB60.3D0B9F72" Date: Wed, 7 Dec 2005 13:58:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Axel Mathieu" [AMathieu===tranzyme.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C5FB60.3D0B9F72 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable =20 =20 Dear CCLer's, =20 Planning an NMR structure elucidation project, I was wondering if any of you have compared different DG codes to see if similar results are obtained. In particular, I'm interested in your experience using the TINKER DistGeom module and/or DGEOM(95) found on QCPE. If others are freely (cheaply) available, I would also appreciate hearing about them. =20 Thank you for taking the time to read this request, APM ------_=_NextPart_001_01C5FB60.3D0B9F72 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

 

 

Dear CCLer’s,

 

Planning an NMR structure elucidation project, I was wondering if any of you have compared different DG codes to see if = similar results are obtained. In particular, I’m interested in your = experience using the TINKER DistGeom module and/or = DGEOM(95) found on QCPE. If others are freely = (cheaply) available, I would also appreciate hearing about them.

 

Thank you for taking the time to read this = request,

APM

------_=_NextPart_001_01C5FB60.3D0B9F72-- From owner-chemistry@ccl.net Wed Dec 7 17:41:00 2005 From: "Michael K Gilson gilson~!~umbi.umd.edu" To: CCL Subject: CCL: Virtual Screening and New Search Tools on BindingDB Message-Id: <-30223-051207174007-25686-pWuOQY6hNzcEJYDSBVGa7g|-|server.ccl.net> X-Original-From: "Michael K Gilson" Sent to CCL by: "Michael K Gilson" [gilson,umbi.umd.edu] Dear Colleagues, BindingDB now provides on-line tools for virtual compound screening by your choice of three methods: - maximum similarity - binary kernel discrimation - support vector machine You can build a set of "actives" for your target of interest with a BindingDB search, then upload an SDfile of compounds and rank them according to the likelihood of being active. In order to build your active set, you can search BindingDB for compounds with a desired range of affinities across one or multiple drug-targets, by using the "Targets & Ki IC50" and "Targets & DG" links on the left-hand side of the homepage. When you have the compounds you want, click on Make Data Set to start virtual screening. Alternatively, you can upload your own set of "actives" instead of building it with a BindingDB search. To do this, click on Virtual Screening on the homepage. If you try these new features, we would greatly appreciate your feedback. Best regards, Mike -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu From owner-chemistry@ccl.net Wed Dec 7 19:34:00 2005 From: "Alan Shusterman alan,,reed.edu" To: CCL Subject: CCL: question on molecular orbitals in CO and NO Message-Id: <-30224-051207193045-18101-vIWXtALq11HKvK9kGOehSg _ server.ccl.net> X-Original-From: Alan Shusterman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 07 Dec 2005 16:30:09 -0800 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan.:.reed.edu] This post combines responses to Ulrike Salzner (see below) and Phil Hultin. Phil describes some of the difficulties associated with the "reality" concept. He also describes his preference for "model" as a term to use with orbitals. I agree with both points, and, like Phil, I use "model" when I lecture on orbitals to my organic chemistry class. The physics textbooks that I've looked at in the last few days mention a whole host of philosophical problems connected with reality. Then, after making this brief nod to philosophy, they spend the rest of the book showing us how to make numerical predictions that can be compared with experiment. I think Phil's ideas are completely consistent with this point of view. I've been typing "orbitals are real" instead of "orbitals are experimentally observable" because I'm a lazy typist. I don't think the ideas are identical and I only meant to deal with experimental observability. Now on to Ulrike's questions... Ulrike Salzner salzner#fen.bilkent.edu.tr wrote: >Is it conceivable that phases of the orbitals of one- >electron systems can be observed? > > > This question goes waaay beyond my expertise. I'm a consumer of quantum mechanics, not an authority. Sorry. >Moving to Helium, orbitals are no longer exact but extremely good >numerical solutions are available, which, to my knowledge are very >similar to hydrogens orbitals. What I am asking myself: are orbitals not >observable in principle, or do we just face technical problems when >multi-electron systems are considered? > > > > I'm curious about the assumption that underlies Ulrike's question. I was taught that the "extremely good numerical solutions" for helium (and I'm thinking of the Hylleraas models) did not use one-electron orbitals, but like all lazy students, I did not read the original paper(s). I was also taught (e.g. Karplus and Porters' treatment of helium) that orbital models of helium do *not* provide "extremely good" estimates of the atomic energy. Maybe someone else can shed more light on these issues? Turning to Ulrike's actual question, my answer has already been given: orbitals are not observable in principle. But I believe this because various physicists have taught me to believe this. Alan -- Alan Shusterman Chemistry Department Reed College Portland, OR 97202-8199 503-517-7699 http://academic.reed.edu/chemistry/alan/ "Yield and overcome; Bend and be straight." Lao Tzu 22 From owner-chemistry@ccl.net Wed Dec 7 21:35:00 2005 From: "John Bushnell bushnell .. chem.ucsb.edu" To: CCL Subject: CCL: ADT installation on Mac OS X Message-Id: <-30225-051207205957-22851-xMFnDSYB5PWkSHn8UzDnNw**server.ccl.net> X-Original-From: John Bushnell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 7 Dec 2005 17:08:08 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: John Bushnell [bushnell##chem.ucsb.edu] Actually, this doesn't look (to me) to be related to pygtk, though I can see how it might look like that :-) It seems to be looking for a module named opengltk, which I would guess would be something that would somehow take advantage of openGL acceleration for tk widgets. I don't use either, but happen to be a big fan of pygtk... - John On Wed, 7 Dec 2005, Jens Thomas j.m.h.thomas===dl.ac.uk wrote: > Sent to CCL by: Jens Thomas [j.m.h.thomas++dl.ac.uk] > Irilenia Nobeli irilenia.nobelia/kcl.ac.uk wrote: >> Sent to CCL by: Irilenia Nobeli [irilenia.nobeli]![kcl.ac.uk] >> >> >> Hi, >> >> I posted the following message at the Autodock mailing list but have >> not received an answer so I'm trying my luck here.... >> >> >>> Hi, >>> Looking quickly through the archives I could not find an answer to >>> this, so I'm hoping that someone has solved it by now. After >>> installing a binary version of autodock tools >>> (complete2.3_binary_ppcDarwin7_acad_1-3alpha2) on a MacOS X 10.4, >>> I get the following error when trying to start either pmv or adt: >>> >>> Traceback (most recent call last): >>> File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- >>> packages/AutoDockTools/bin/runAdt.py", line 51, in ? >>> from Pmv.moleculeViewer import MoleculeViewer >>> File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- >>> packages/Pmv/moleculeViewer.py", line 18, in ? >>> from DejaVu.Geom import Geom >>> File "/Users/irilenia/apps/src/mglTools/share/lib/python2.3/site- >>> packages/DejaVu/__init__.py", line 66, in ? >>> raise RuntimeError('FATAL ERROR: opengltk.OpenGL Package not >>> found') >>> RuntimeError: FATAL ERROR: opengltk.OpenGL Package not found >>> >>> Does anyone know how to solve this? >>> >>> Thanks, >>> >>> Irilenia >>> >>> > Hi Irilenia > > It looks like you need to install the Python bindings for GTK. There's a > link here that I hope will help: > > http://www.async.com.br/faq/pygtk/index.py?req=show&file=faq01.019.htp > > Best wishes, > > Jens >