From chemistry-request@ccl.net Mon Jun 2 02:04:58 2003 Received: from lac.chem.nagoya-u.ac.jp (lac.chem.nagoya-u.ac.jp [133.6.84.199]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5264vgC014817 for ; Mon, 2 Jun 2003 02:04:58 -0400 Received: from lac2.chem.nagoya-u.ac.jp (lac2.chem.nagoya-u.ac.jp [133.6.84.36]) by lac.chem.nagoya-u.ac.jp (Postfix) with ESMTP id 5D43AD9DC4 for ; Mon, 2 Jun 2003 15:04:56 +0900 (JST) From: Hannes Loeffler Organization: Nagoya University To: chemistry:at:ccl.net Subject: CCL: how to do umbrella sampling/PMF in CHARMM Date: Mon, 2 Jun 2003 15:05:50 +0900 User-Agent: KMail/1.5 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200306021505.50637.hloeffler:at:lac.chem.nagoya-u.ac.jp> Hi, I want to do some tests with umbrella sampling/PMF but seem to have some troubles how to do it. I first tried the "Umbrella Sampling along a Reaction Coordinate" (umbrel.doc) but the CHARMM testcase obviously doesn't sample anything. Next I tried the QM/MM example from the MAMD workshop (MMFP module) but even after some days there is no further output (seems to be stuck in the minimization step). Could anybody give me some hints how to proceed (maybe a simple example input). I just want to sample along a single distance. Hannes. From chemistry-request@ccl.net Sun Jun 1 21:14:48 2003 Received: from sungoddess.ccs.yorku.ca (sungoddess.ccs.yorku.ca [130.63.236.144]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h521EmgC007681 for ; Sun, 1 Jun 2003 21:14:48 -0400 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungoddess.ccs.yorku.ca (8.12.9/8.12.8) with ESMTP id h521El0O011583 for ; Sun, 1 Jun 2003 21:14:47 -0400 (EDT) Received: (from chan@localhost) by curl.gkcl.yorku.ca (8.10.0/8.10.0) id h521Ei102277 for chemistry:at:ccl.net; Sun, 1 Jun 2003 21:14:44 -0400 (EDT) From: Wai-To Chan Message-Id: <200306020114.h521Ei102277:at:curl.gkcl.yorku.ca> Subject: Re: calculating atomic charges with AIMPAC To: chemistry:at:ccl.net Date: Sun, 1 Jun 2003 21:14:44 -0400 (EDT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit <<<<<<<<<<<<<<<, What "chemical intuition"? The one that comes from looking for many years to Mulliken populations in gaussian outputs? That is not science, it is prejudgment. Whatever interpretation we want to give to them, Bader charges are unique and well defined properties of the electron density of the molecule or solid under study. Both experimental and good theoretical electron densities agree on the calculated Bader charges of hundreths of compounds well characterized so far. On the other hand, Bader charges >>>>>>>>>>>>>>>>>>>>>>>>>>>> Mulliken charges could indeed give counterintuitive results. I remember it has a serious problem related to basis-set sensitivity. I am not sure what experimental measurements you referred to. Bader chages, bond paths, lone pairs and so forth are defined in terms of the topology of electron density a measurable qauntity. So it is only natural that theoretical AIM properties should match experimental measurements. If you were referring to the transferability of the properties of atoms or molecular fragments as defined by Bader then AIM may be said to be a predictor of experimental measurement in certain respect. For the purpose of calculating partial atomic charges AIM is not always a good choice. For large size molecules containing elements of ring structures the code in Gaussian is very vulnerable to error. PROAIMV is more reliable but it could be very time consuming. For organometallic systems I suspect that the use of ECP would cause problems in the analysis of Laplacian and perhaps bond critical points as well. Use AIM in cases where it provides better prediction or correlation of whatever you are calculationg. Off the top of my head I remember AIM does give good correlation with proton affinity for some carbonyl system. I have done calculations on systems for which the Natural population charges analysis methods also gave reliable results for interpretation of site-specific reactivies on small metal clusters. Wai-To Chan <<<<<<<<<<<<<<<<<<<<<<<<< are not enough to analyze the electron densities. The whole multipolar series (charges are nothing but the zero order poles) should be considered instead. Several recent works by Popelier, for instance, would made a good reading in this respect. In any case, the charges quoted in the original question look like if the wavefunction is wrong by some reason. Perhaps a calculation not converged. Regards, Victor Lua~na >>>>>>> From chemistry-request@ccl.net Mon Jun 2 03:14:02 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h527DugC017458 for ; Mon, 2 Jun 2003 03:13:59 -0400 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id PAA22030 for ; Mon, 2 Jun 2003 15:10:08 +0800 Message-Id: <200306020710.PAA22030(at)mx1.ustc.edu.cn> Date: Mon, 2 Jun 2003 15:12:2 +0800 From: 6!Q8@W Reply-To: dxl(at)mail.ustc.edu.cn To: CCls Subject: G98 help--opt failed. Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon302344156336_=====" This is a multi-part message in MIME format. --=====000_Dragon302344156336_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xzQ0NMc6O6DQoJDQoJV2hhdCBzaG91bGQgSSBkbyB3aGVuIHRoZSBvcHQgaXMgZmFp bGVkIHdpdGggDQoJIiBTZWFyY2ggZGlkIG5vdCBsb3dlciB0aGUgZW5lcmd5IHNpZ25pZmljYW50 bHkuDQogTm8gbG93ZXIgcG9pbnQgZm91bmQgLS0gcnVuIGFib3J0ZWQuIg0KCVRoZXJlIGlzIG9u ZSBTQ0YgRG9uZSBiZWZvcmUgdGhlIGZhaWx1cmUuDQoJQW5kIHRoZSB3b3JrIGlzIGRvbmUgYWZ0 ZXIgYSBjb21wbGV0ZWQgb3B0IHdvcmsgd2l0aCBhIHNtYWxsZXIgYmFzaXMgc2V0LA0KCXdpdGgg I1BXOTFQVzkxL0dlbiBQc2V1ZG89UmVhZCBndWVzcz1yZWFkIGdlb209Y2hlY2sgb3B0IFNDRj0o cWMsY29udmVyPTgpLg0KCQ0KICAgIFRoYW5rIHlvdSBmb3IgeW91ciBoZWxwIaGhoaGhoaGhoaGh oaGhoaENCiAJCQkJDQqhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhRGluZyBYdW5sZWkNCqGh oaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaEyMDAzLTA2LTAyDQpfX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fDQpEaW5nIFh1bmxlaSwgUGguRC4gQ2FuZGlkYXRl DQpPcGVuIExhYm9yYXRvcnkgb2YgQm9uZCBTZWxlY3RpdmUgQ2hlbWlzdHJ5DQpVbml2ZXJzaXR5 IG9mIFNjaWVuY2UgJiBUZWNobm9sb2d5IG9mIENoaW5hDQpIZWZlaSwgQW5odWkgMjMwMDI2LCBQ LlIuQ2hpbmENClRlbC46IDAwODYtNTUxLTM2MDM0MTgNCkZheC46IDAwODYtNTUxLTM2MDI5NjkN CkUtbWFpbDogZHhsQG1haWwudXN0Yy5lZHUuY24NCkh0dHA6Ly93d3cuYnNjLnVzdGMuZWR1LmNu L35keGwNCg== --=====000_Dragon302344156336_===== Content-Type: image/gif; name="LittleBoy.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy.GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon302344156336_=====-- From chemistry-request@ccl.net Mon Jun 2 02:37:59 2003 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h526bwgC015621 for ; Mon, 2 Jun 2003 02:37:59 -0400 Received: from [128.97.147.213] (ch-13.psnet.ucla.edu [128.97.147.213]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id h526bo7s015240; Sun, 1 Jun 2003 23:37:52 -0700 Mime-Version: 1.0 X-Sender: scerri(at)chlorine.chem.ucla.edu (Unverified) Message-Id: In-Reply-To: <200306012009.h51K92iI009416(at)smtp3.server.rpi.edu> References: <200306012009.h51K92iI009416(at)smtp3.server.rpi.edu> Date: Fri, 6 Jun 2003 23:37:27 -0700 To: "Dr. N. SUKUMAR" From: Eric Scerri Subject: Re: CCL:orbitals Cc: ccl Content-Type: multipart/alternative; boundary="============_-1157154642==_ma============" --============_-1157154642==_ma============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" >On Fri, 30 May 2003 16:07:46 -0700 Eric Scerri wrote: > >> >> >> As somebody working in philosophy of science and more specifically >> philosophy of chemistry I have found the recent discussion very >> interesting. >> > >While for my part, I have always been a "working computational chemist", >I've studied with great interest the debates between Bohr, Einstein, Bohm >and others. > >> >> There is a long-standing debate in philosophy of science going back >> for hundreds of years which in modern terminology is referred to as >> the realism versus anti-realism debate... >> >> Finally, it should also be recalled that the most widely held >> interpretation of quantum mechanics, the Copenhagen interpretation, >> is essentially an anti-realistic interpretation regardless of what >> people like Einstein and David Bohm may have wanted... > >While I agree that this is indeed a long-standing debate, the problem was >exacerbated by the insistence of some, like Bohr and Heisenberg, that >science is concerned not with the physical universe ("physical reality") >per se, but with human knowledge/awareness of the physical universe. While >we might agree that the latter does fall within the purview of science, >most scientists today would opine that it falls within the discipline of >cognitive science rather than physics. Few are the physicists who are able >to get grants to study human cognition using acceleraters rather than EEGs >and MRIs! But far more obviously the anti-realistic view was adopted because so many QM concepts seem to defy a realistic interpretation. Is the electron a wave or a particle? The electron has no definite trajectory. Electron spin is not really spin, Collapse of the wavefunction issue etc etc. Anti-realism in QM does not depend on holding the view that physical theory is somehow concerned with physical awareness. > > >> For example >> phlogiston was initially quite useful and successful in explaining >> many chemical facts. Some people may even have believed that this >> meant that phlogiston was a real physical entity and yet as everybody >> knows it turned out to be a mistake. > >Perhaps a better example might be the aether and spacetime. You did not explain why you felt that your example was "better" than phlogiston. >While most >people today might say that the aether theory was a big mistake, I regard >spacetime as simply a modified version of the aether concept, in the same >way that modern DFT helped reformulate the concepts of hardness and >electronegativity. So does spacetime "exist"? Or do orbitals have "physical >reality" (to distinguish it from the real/imaginary/complex >classification)? To me, questions like this are inherently unanswerable, or >at least unanswerable at the level of science. Such questions belong in the >realm of philosophy and religion. > >Science can ask: is the phlogiston concept still useful? The answer there >is no! Is the orbital concept still useful? Here the answer is that, within >bounds, yes! But is it absolute? Can it explain all observations? Certainly >not! Now a more difficult question (and one that calls for subjective >judgements): is it a reasonable working model? Here opinions seem to >differ. > >It is possible to formulate and rationalize most of our observations >entirely without reference to orbitals. Several successful theories, such >as the variational formulation of density functional theory and some >Green's function theories, do just this. Does this make the orbital concept >any less valid? No, but it does argue against religious beliefs of orbital >reality. Does this make orbitals any less useful? Again, no. The most >widely used theoretical formulations (Hartree-Fock, CI, Kohn-Sham DFT) are >still constructed in terms of orbital expansions. But I would argue that it >makes little sense to try to "explain" all our observations in terms of >orbitals, a practice which is still widely prevalent. > >> >> except in the general sense that all scientific >> theories and approaches are eventually refuted. This view, called > > the pessimistic meta-induction, ... >> >> > >There seems to be an inconsistency here: that of extrapolating beyond the >known range of validity of the model. I would modify this to say that all >scientific theories should be, in principle, falsifiable or refutable. A >theory that isn't so is not science, but religion. No inconsistency. I am making a different point from the elementary Popperian demarcation criterion between science and pseudo-science which you seem to want want to substitute. Incidentally that criterion has been thoroughly criticized by subsequent philosophers of science to the point that it is not really a contender these days. But that's another story. My point is a separate one. As Popper himself stated, "All theories are born refuted", meaning that sooner or later they will all be refuted. Scientific theories are only provisionally useful. Every single one of them will eventually be refuted. This is a meta-induction based on the fate of all past and now defunct theories > from the history of science. This notion in itself should be a warning against taking too seriously any of the entities postulated by theories, especially those that are unobservable. Of course one may argue that induction from past instances is not a reliable path to knowledge and that it just so happens that our cherished current theories have finally reached the point where they are refutable but will never actually be refuted. But that would be plain stupid of course. eric scerri -- 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 --============_-1157154642==_ma============ Content-Type: text/html; charset="us-ascii" Re: CCL:orbitals
On Fri, 30 May 2003 16:07:46 -0700 Eric Scerri wrote:

>
>
> As somebody working in philosophy of science and more specifically
> philosophy of chemistry I have found the recent discussion very
> interesting.
>

While for my part, I have always been a "working computational chemist",
I've studied with great interest the debates between Bohr, Einstein, Bohm
and others.

>
> There is a long-standing debate in philosophy of science going back
> for hundreds of years which in modern terminology is referred to as
> the realism versus anti-realism debate...
>
> Finally, it should also be recalled that the most widely held
> interpretation of quantum mechanics, the Copenhagen interpretation,
> is essentially an anti-realistic interpretation regardless of what
> people like Einstein and David Bohm may have wanted...

While I agree that this is indeed a long-standing debate, the problem was
exacerbated by the insistence of some, like Bohr and Heisenberg, that
science is concerned not with the physical universe ("physical reality")
per se, but with human knowledge/awareness of the physical universe. While
we might agree that the latter does fall within the purview of science,
most scientists today would opine that it falls within the discipline of
cognitive science rather than physics. Few are the physicists who are able
to get grants to study human cognition using acceleraters rather than EEGs
and MRIs!



But far more obviously the anti-realistic view was adopted because so many QM concepts seem to defy a realistic interpretation.  Is the electron a wave or a particle?  The electron has no definite trajectory.  Electron spin is not really spin, Collapse of the wavefunction issue etc etc. 

Anti-realism in QM does not depend on holding the view that physical theory is somehow concerned with physical awareness. 



>
> For example
> phlogiston was initially quite useful and successful in explaining
> many chemical facts.        Some people may even have believed that this
> meant that phlogiston was a real physical entity and yet as everybody
> knows it turned out to be a mistake.

Perhaps a better example might be the aether and spacetime.


You did not explain why you felt that your example was "better" than phlogiston. 


While most
people today might say that the aether theory was a big mistake, I regard
spacetime as simply a modified version of the aether concept, in the same
way that modern DFT helped reformulate the concepts of hardness and
electronegativity. So does spacetime "exist"? Or do orbitals have "physical
reality" (to distinguish it from the real/imaginary/complex
classification)? To me, questions like this are inherently unanswerable, or
at least unanswerable at the level of science. Such questions belong in the
realm of philosophy and religion.

Science can ask: is the phlogiston concept still useful? The answer there
is no! Is the orbital concept still useful? Here the answer is that, within
bounds, yes! But is it absolute? Can it explain all observations? Certainly
not! Now a more difficult question (and one that calls for subjective
judgements): is it a reasonable working model? Here opinions seem to
differ.

It is possible to formulate and rationalize most of our observations
entirely without reference to orbitals. Several successful theories, such
as the variational formulation of density functional theory and some
Green's function theories, do just this. Does this make the orbital concept
any less valid? No, but it does argue against religious beliefs of orbital
reality. Does this make orbitals any less useful? Again, no. The most
widely used theoretical formulations (Hartree-Fock, CI, Kohn-Sham DFT) are
still constructed in terms of orbital expansions. But I would argue that it
makes little sense to try to "explain" all our observations in terms of
orbitals, a practice which is still widely prevalent.

>
>  except in the general sense that all scientific
> theories and approaches are eventually refuted.  This view, called
> the pessimistic meta-induction, ...
>
>

There seems to be an inconsistency here: that of extrapolating beyond the
known range of validity of the model. I would modify this to say that all
scientific theories should be, in principle, falsifiable or refutable. A
theory that isn't so is not science, but religion.


No inconsistency.  I am making a different point from the elementary Popperian demarcation criterion between science and pseudo-science which you seem to want want to substitute.  Incidentally that criterion has been thoroughly criticized by subsequent philosophers of science to the point that it is not really a contender these days.  But that's another story. 

My point is a separate one.  As Popper himself stated, "All theories are born refuted", meaning that sooner or later they will all be refuted.  Scientific theories are only provisionally useful.  Every single one of them will eventually be refuted.  This is a meta-induction based on the fate of all past and now defunct theories > from the history of science.  This notion in itself should be a warning against taking too seriously any of the entities postulated by theories, especially those that are unobservable. 

Of course one may argue that induction > from past instances is not a reliable path to knowledge and that it just so happens that our cherished current theories have finally reached the point where they are refutable but will never actually be refuted.  But that would be plain stupid of course. 


eric scerri
--


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
--============_-1157154642==_ma============-- From chemistry-request@ccl.net Mon Jun 2 09:57:45 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52DvhgC030941 for ; Mon, 2 Jun 2003 09:57:45 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3p2/8.9.3) with ESMTP id QAA345574 for ; Mon, 2 Jun 2003 16:57:40 +0300 (EEST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Mon, 2 Jun 2003 16:57:40 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans_at_soul.helsinki.fi To: chemistry_at_ccl.net Subject: CCL: Summary: pdm97 or other general ESP-fitting programs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! Some two weeks ago, I posted a question regarding the fate of the pdm97 ESP charge fitting program. No luck in that respect, but I got some other good suggestions. The rest is somewhat Turbomole specific. Andreas Klamt pointed out that it could be an idea to use the COSMO-output, as it prints out the ESP on the COSMO-surface. Konrad Hinsen recommended the MMTK toolkit, as it has a module for charge fitting. MMTK is available at http://starship.python.net/crew/hinsen/MMTK/ Artem Masunov informed me that Molden has charge fitting option (from G98/Gamess output): http://www.cmbi.kun.nl/~schaft/molden/manual.html#Ref10 Also, AMBER offers a free charge-fitting program, RESP, available at: http://www.amber.ucsf.edu/amber/amber.html I combined the first two suggestions and wrote a small script that uses the Turbomole COSMO-output and the MMTK toolkit to fit ESP charges. If anyone is interested, it's available (turboesp.py): http://www.helsinki.fi/~mpjohans/scripts/ Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@ccl.net Mon Jun 2 11:24:22 2003 Received: from cirse.saclay.cea.fr (cirse.saclay.cea.fr [132.166.192.127]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52FOLgC000734 for ; Mon, 2 Jun 2003 11:24:22 -0400 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.saclay.cea.fr (8.12.9/CEAnet-Internet.1.0) with ESMTP id h52FOLeL013823 for ; Mon, 2 Jun 2003 17:24:21 +0200 (MEST) Received: from muguet.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.6) with ESMTP id for ; Mon, 2 Jun 2003 17:22:29 +0200 Received: from petunia.bruyeres.cea.fr (petunia.bruyeres.cea.fr [132.165.64.1]) by muguet.saclay.cea.fr (8.12.9/CEAnet-Interne.1.0) with ESMTP id h52FOKcR015695 for ; Mon, 2 Jun 2003 17:24:20 +0200 (MEST) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by petunia.bruyeres.cea.fr (8.9.3+Sun/jtpda-5.3.2) with ESMTP id RAA18893 for ; Mon, 2 Jun 2003 17:20:43 +0200 (MET DST) Received: by styx.bruyeres.cea.fr; id RAA03169; Mon, 2 Jun 2003 17:24:19 +0200 (MET DST) Message-Id: <200306021524.RAA03169=at=styx.bruyeres.cea.fr> Sender: mathieu=at=indre.ripault.cea.fr Date: Mon, 02 Jun 2003 16:52:51 +0200 From: Didier MATHIEU Organization: CEA X-Mailer: Mozilla 4.72 [fr] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry=at=ccl.net Subject: MM parameters from ab initio Content-Type: multipart/alternative; boundary="------------1681929DFEF16C530FA59302" --------------1681929DFEF16C530FA59302 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Is there any available program that could fit intramolecular force field parameters (to be used in a standard molecular mechanics energy expression) from the equilibrium geometry and cartesian force constants of the system ? Or more generally, any tools to derive a specific (non-transferable) intramolecular force field from ab initio data ? Thanks -- Didier Mathieu CEA - Le Ripault BP 16 37260 Monts Didier.Mathieu=at=cea.fr Tel +33 02 47 34 41 85 Fax +33 02 47 34 51 42 --------------1681929DFEF16C530FA59302 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hello,

Is there any available program that could fit intramolecular force field parameters (to be used in a standard molecular mechanics energy expression) > from the equilibrium geometry and cartesian force constants of the system ?
Or more generally, any tools to derive a specific (non-transferable) intramolecular force field from ab initio data ?
Thanks 

-- 
Didier Mathieu
CEA - Le Ripault
BP 16
37260 Monts
Didier.Mathieu=at=cea.fr
Tel +33 02 47 34 41 85
Fax +33 02 47 34 51 42
  --------------1681929DFEF16C530FA59302-- From chemistry-request@ccl.net Mon Jun 2 10:17:40 2003 Received: from sal.ahpcrc.org (sal.ahpcrc.org [144.34.1.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52EHegC031510 for ; Mon, 2 Jun 2003 10:17:40 -0400 Received: from mycroft.ahpcrc.org (mycroft.ahpcrc.org [144.34.9.34]) by sal.ahpcrc.org (8.11.6/8.11.6) with ESMTP id h52EHMb12156; Mon, 2 Jun 2003 09:17:22 -0500 Received: (from rbw@localhost) by mycroft.ahpcrc.org (8.11.6/8.11.6) id h52EHGn21136; Mon, 2 Jun 2003 09:17:16 -0500 Date: Mon, 2 Jun 2003 09:17:16 -0500 From: Richard Walsh Message-Id: <200306021417.h52EHGn21136=at=mycroft.ahpcrc.org> To: nagams=at=rpi.edu, scerri=at=chem.ucla.edu Subject: Re: CCL:orbitals Cc: chemistry=at=ccl.net On Sun, 01 Jun 2003 16:09:02 EDT, Dr. N. Sukumar: >There seems to be an inconsistency here: that of extrapolating beyond the >known range of validity of the model. I would modify this to say that all >scientific theories should be, in principle, falsifiable or refutable. A >theory that isn't so is not science, but religion. The only exceptions are >axioms and they are to be regarded as merely working hypotheses. Axioms are >not falsifiable, but they can cease to be useful. In science there are no >self-evident truths. Problems arise when axioms are confused for facts. >Replacement of one set of fundamental axioms (as for example, the >centrality of the earth) for another often leads to a major paradigm shift >in science. "Problems arise when axioms (models) are confused for facts (realities)" ... and axioms/models that have long dominated the contemporary culture of the mind are likely to be confused in just this way ... and in forgetting what they are, we can over extend ... "the known validity of the model." This would seem to be at the heart of the matter and the issue arises at a deeper level than orbitals. Perhaps the most primitive axiom is the principle of identity upon which the concept of counting is based. Who would argue against its usefulness? As Poncaire said, "If everyting springs from the principle of identity, then everything must be reducible to it." Yet, how can truly identical things be distinguished? What risks do we run when we assume the reality/usefulness of "two-ness" ... ;-) ... forgetting mere orbitals for the moment ... Who is ready to discard counting and all that flows from it (it seems to continue to be useful and is the most interesting game in town), but are we all aware of the risks we are taking in over extending this axiom and in relying on the countableness of the Universe ... ;-) ... as scientists, we must find it "in principle" discardable or falsifiable, oui? ... are we left with anything that is irrefutable? ... for any given scientist, the first reality and only irrefutable model or non-discardable axiom would seem to have to be "I am" which I think precedes "I think" regardless of what Descartes thought. Given existence, identity, counting, and ... their less palpable consequences ... orbitals (while they are useful) ... computational chemistry remains an interesting game of both discovery and creation. ;-) ... rbw #--------------------------------------------------- # Richard Walsh # Project Manager, Cluster Computing, Computational # Chemistry and Finance # netASPx, Inc. # 1200 Washington Ave. So. # Minneapolis, MN 55415 # VOX: 612-337-3467 # FAX: 612-337-3400 # EMAIL: rbw=at=networkcs.com, richard.walsh=at=netaspx.com # rbw=at=ahpcrc.org # #--------------------------------------------------- # "What you can do, or dream you can, begin it; # Boldness has genius, power, and magic in it." # -Goethe #--------------------------------------------------- # "Without mystery, there can be no authority." # -Charles DeGaulle #--------------------------------------------------- # "Why waste time learning when ignornace is # instantaneous?" -Thomas Hobbes #--------------------------------------------------- From chemistry-request@ccl.net Mon Jun 2 10:04:42 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52E4fgC031177 for ; Mon, 2 Jun 2003 10:04:42 -0400 Expiry-Date: Fri, 29 Aug 2003 -1:-1:-1 +0000 To: CHEMISTRY=at=ccl.net Cc: Elizabeth Crookenden Subject: CCL: Accelrys Training Workshops for August MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Reply-To: Elizabeth Crookenden Message-ID: From: Jeff Nauss Date: Mon, 2 Jun 2003 07:04:40 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.1CF1|March 04, 2003) at 06/02/2003 07:04:42, Serialize complete at 06/02/2003 07:04:42 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h52E4ggC031178 Accelrys Inc. are holding the following training workshops at locations in the US and Europe during August 2003. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. Costs are $600 per day for commercial, $520 per day for government and $380 per day for academic plus appropriate taxes. Rational Drug Design: Introduction to Cerius2 for Life Sciences 5th b 6th August 2003, San Diego, CA Pharmacophore Generation with Catalyst 7th b 8th August 2003, San Diego, CA For course details and registration see: http://www.accelrys.com/training/rdd/schedule.html Bioinformatics: Wisconsin Package and SeqLab 18th b 19th August 2003, Burlington, MA SeqWeb 20th b 21st August 2003, Burlington, MA DS Gene 22nd August 2003, Burlington, MA For course details and registration see: http://www.accelrys.com/training/bioinf/schedule.html Macromolecular Modeling: Introduction Life Science Modeling with InsightII, 19th b 20th August 2003, San Diego, CA Homology-Based Protein Design 21st b 22nd August 2003, San Diego, CA For course details and registration see: http://www.accelrys.com/training/macro/schedule.html -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss=at=accelrys.com http://www.accelrys.com/training From chemistry-request@ccl.net Mon Jun 2 09:47:16 2003 Received: from srvus010.unitedcatalysts.com (srvus010.unitedcatalysts.com [208.23.162.8] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with SMTP id h52DlGgC030684 for ; Mon, 2 Jun 2003 09:47:16 -0400 Received: by lvlxch02.ntdomain.americas.sc-world.com with Internet Mail Service (5.5.2653.19) id ; Mon, 2 Jun 2003 09:45:11 -0400 Message-ID: <5CF08BBFE6DE97478C1E76E654CAF90801BC0C05(at)lvlxch02.ntdomain.americas.sc-world.com> From: "Shobe, Dave" To: "'CCL'" Subject: RE: Orbitals Date: Mon, 2 Jun 2003 09:45:11 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/mixed; boundary="----=_NextPartTM-000-93ac11e8-b8e1-4e8b-b6e3-04bdac561061" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------=_NextPartTM-000-93ac11e8-b8e1-4e8b-b6e3-04bdac561061 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3290D.303AA810" ------_=_NextPart_001_01C3290D.303AA810 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable That's an interesting observation. Structures of main-group (including organic) compounds are often rationalized in terms of hybridization, which because it relies on = orbitals implies a small role for interelectron repulsion. However, these same structures are often rationalized using VSEPR = theory, which is 100% based on interelectron repulsion, at least if you ignore = the underlying assumption that electrons, for mysterious reasons, come in = pairs. --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. -----Original Message----- From: Avijit Ghosh [mailto:avijit(at)physics.drexel.edu] Sent: Friday, May 30, 2003 7:01 PM To: chemistry(at)ccl.net Subject: CCL:Orbitals ....... > (2) Does the single e- wavefunction density have any > meaning? Let me decompose this a bit. To me the fact that > organic chemists can "hybridize" orbitals (aka "handwaving > quantum mechanics") is a testament to the contribution of > e-e- correlation as actually not being that much at least > for the first part of the periodic table. In fact that elements have = > the properties that they do is also a testament to this. ....... ------_=_NextPart_001_01C3290D.303AA810 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: Orbitals

That's an interesting observation.

Structures of main-group (including organic) = compounds are often rationalized in terms of hybridization, which = because it relies on orbitals implies a small role for interelectron = repulsion.

However, these same structures are often rationalized = using VSEPR theory, which is 100% based on interelectron repulsion, at = least if you ignore the underlying assumption that electrons, for = mysterious reasons, come in pairs.

--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.



-----Original Message-----
From: Avijit Ghosh [mailto:avijit(at)physics.drexel.e= du]
Sent: Friday, May 30, 2003 7:01 PM
To: chemistry(at)ccl.net
Subject: CCL:Orbitals

.......

>       (2) Does the = single e- wavefunction density have any
> meaning? Let me decompose this a bit. To me the = fact that
> organic chemists can "hybridize" = orbitals (aka "handwaving
> quantum mechanics") is a testament to the = contribution of
> e-e- correlation as actually not being that = much at least
> for the first part of the periodic table. In = fact that  elements have
> the properties that they do is also a testament = to this.

.......

------_=_NextPart_001_01C3290D.303AA810-- ------=_NextPartTM-000-93ac11e8-b8e1-4e8b-b6e3-04bdac561061-- From chemistry-request@ccl.net Mon Jun 2 10:07:08 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52E76gC031240 for ; Mon, 2 Jun 2003 10:07:07 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3p2/8.9.3) with ESMTP id RAA349313 for ; Mon, 2 Jun 2003 17:07:06 +0300 (EEST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Mon, 2 Jun 2003 17:07:06 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans(at)soul.helsinki.fi To: chemistry(at)ccl.net Subject: CCL: Summary: History of atomic shell labels Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id h52E78gC031241 Hello All! The recent discussion on orbitals reminded me that I never posted a summary on a few questions I posed two years ago. As it's some time ago, and I didn't get an answer for everything, here comes the questions again. The summary part is further below: 1.) Who came up with the idea of starting labeling of the atomic shells from K, L, M..., and more interestingly; why start from K? 2.) The subshell labels came from the spectral lines of alkali metals, but where Sharp, Principal and Diffuse lines are quite self explanatory, I have some difficulty of picturing a "Fundamental" spectral line :-) Any help? 3.) Was there a good reason for leaving out j from the labels for subshells? So far I've managed to get a definitive answer on the origin of K, L, M, etc., which was introduced by Barkla, 'K' coming from German "K|rzere Wellenldngen" and 'L' from "Ldngere Wellenldngen". This was suggested by Eric Scerri (see below) and I also found it in a book by V. Trkal, Electronic Structure of Atoms and Molecules (1969). j was apparently left out just to avoid confusion. No definitive answer on that though. No-one has had any idea of the origin of the "fundamental" spectral line. Below is a list of the replies I've got. The book by Trkal was recommended to me by Dr. Henrik Konschin of our lab. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ ===================================== From: Steve Williams [...] >3.) Was there a good reason for leaving out j from the labels for > subshells? The story I have heard about this is that since j and J are used both as general angular momentum quantum number symbols, as well as for total (spin + orbital) angular momentum, it was thought too likely to cause confusion if j and J were used as orbital angular momentum symbols as well. Good luck with your search... Steve Williams ASU Chemistry Boone, NC 28608 USA ======================================== From: Eric Scerri [...] (1) The historical origin of K, L, M etc dates back to the work of the British X-ray spectroscopist George Barkla who was later awarded a Nobel Prize. If I recall his key article was in 1911 in the Philosophical Magazine. He is mentioned in all standard historical accounts such as the books by Pais for example. Title: Inner Bound. It was his work which led to van den Broek's suggestion that the ordering principle for the periodic system might be atomic number rather than atomic weight which in turn inspired Moseley to experimentally verify this idea in 1914. van den Broek also cited Geiger and Marsden's famous experiements on the scattering of alpha radiation. More about all these episodes appears in my forthcoming book on the Story of the Periodic System to be published by McGraw-Hill as a 'trade book'. (2) no idea! (3) Presumably because j or even J is used for the vectorial sum of l and s and L and S respectively. Having an orbital labeled j would just confuse matters. regards, -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA ======================================== From: Michael Nolan Hi, I can answer number 1 for you: K = kurz L = lang and after that it's alphabetical. kurz is german for short lang is german for long. The early spectroscopists were german! regards Mick [...] -- ******************************************************** Michael Nolan Computational Modelling, NMRC Lee Maltings, Prospect Row, Cork, IRELAND ======================================== From: Huub van Dam [...] > 3.) Was there a good reason for leaving out j from the labels for > subshells? I would think it was thought that j could be mistaken for being an i too easily. However, I have authorative information on this one. [...] -- ======================================================================== Huub van Dam E-mail: CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ======================================================================== From chemistry-request@ccl.net Mon Jun 2 07:15:28 2003 Received: from mail-gate (uni-paderborn.de [131.234.22.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52BFRgC025566 for ; Mon, 2 Jun 2003 07:15:28 -0400 Received: from oc34 ([131.234.240.94]:3550 "EHLO upb.de") by mail.uni-paderborn.de with ESMTP id ; Mon, 2 Jun 2003 13:13:28 +0200 Message-ID: <3EDB31B5.2000500*at*upb.de> Date: Mon, 02 Jun 2003 13:15:01 +0200 From: Edgar Luttmann User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-DE; rv:1.0.1) Gecko/20020823 Netscape/7.0 (BDP) X-Accept-Language: de-de, de MIME-Version: 1.0 CC: ccl Subject: CD spectrum simulation? References: <200306012009.h51K92iI009416*at*smtp3.server.rpi.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit To: unlisted-recipients:; (no To-header on input) Hi, I would like to know if there is any method to simulate (at least a rough) CD spectrum of a small peptide. I do have a PDB file (so I have 3D coordinates) and it would be great to predict a spectrum from this. Any hints are welcome and I will give a summary. Thanks in advance Edgar -- Edgar Luttmann University of Paderborn, Germany Department of organic chemistry From chemistry-request@ccl.net Mon Jun 2 10:11:30 2003 Received: from chem.ch.huji.ac.il (chem.ch.huji.ac.il [132.64.90.35]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52EBTgC031351 for ; Mon, 2 Jun 2003 10:11:30 -0400 Received: from baikal (baikal.ch.huji.ac.il [132.64.98.52]) by chem.ch.huji.ac.il (8.9.3/8.9.3) with SMTP id RAA11357 for ; Mon, 2 Jun 2003 17:11:28 +0300 (IDT) Message-ID: <058201c32910$dba44fa0$34624084*at*ch.huji.ac.il> From: "David Danovich" To: Subject: NBO problem Date: Mon, 2 Jun 2003 17:11:27 +0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-8-i" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear CCl's One of my friends tries to calculate few natural charges and in some systems it works and in other it does not. He gets the following answer from the program: "Here are some natural charge. Some compounds could not be calculated. There is a message in the Gaussian output as follows. "NBO cannot handle linearly dependant basis sets." Somebody knows what can be done in this situation and what exactly the program means? Thank you David From jkl@ccl.net Sun Jun 1 10:35:21 2003 -0400 Return-Path: Message-ID: <3EDA0FBF.1010009_at_tesla.jci.tju.edu> Date: Sun, 01 Jun 2003 10:37:51 -0400 From: Xiaobing Tian Reply-To: xiaobing_at_tesla.jci.tju.edu Organization: TJU To: jkl_at_ccl.net Subject: AutoDock install Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, I recently downloaded the autodock program. The download was for version 3.0, which unzipped to 3.05. I'm trying to install on a Red Hat Linux 8.0 PC. I tried to follow the instruction under FAQ for editing the autodock makefile and the autogrid makefile. The lines to delete in the autodock makefile correspond as stated, but in the autogrid makefile the lines to remove do not correspond. When I compiled the autodock makefile, it was compiled with just warnings, so I assume it's okay. But the autogrid makefile had errors when I tried to compile after attempting delete the lines I was instructed to change even though the line numbers don't match up. Where there changes to the autogrid makefile recently that cause the linux install tutorial intstructions to not correspond correctly with the autogrid makefile? Would you be able to write out the text for the first and last line of the section to delete in the autogrid makefile? Xiaobing. -- Xiaobing Tian, Ph.D. Department of Biochemistry & Molecular Pharmacology Thomas Jefferson University 233 South 10th Street, Suite 219 Philadelphia PA19107 voice: 215-955-1364 fax: 215-955-4580, 215-923-9214 website: http://tesla.jci.tju.edu From jkl@ccl.net Sat May 31 11:17:49 2003 -0400 Date: Sat, 31 May 2003 10:59:29 -0400 (EDT) From: Steve Heller To: chemistry*at*ccl.net Subject: ADMET I Conference, Feb 11-23, 2004, San Diego In-Reply-To: Message-ID: ADMET I Conference February 11-23, 2004 Town & Country Hotel San Diego, CA www.scherago.com/admet Co- Organizers: Stephen R. Heller, NIST, USA (srheller*at*nist.gov) Tony Hopfinger, University of Illinois at Chicago, USA (hopfingr*at*uic.edu) Organizing Committee: Susan Bassett, Bioreason, USA (bassett*at*bioreason.com) Osman Gunar, Accelyrs, USA (osman*at*accelrys.com) Peter Gund, IBM Life Sciences Pharmaceutical R&D Solutions, USA (petegund*at*us.ibm.com) Philip Judson, LHASA/University of Leeds, UK (judson*at*dircon.co.uk) D.J. Livingstone, ChemQuest, UK (davel*at*chmqst.demon.co.uk) Edward Matthews, Food & Drug Administration, USA (matthewsse*at*cder.fda.gov) Donna Morrall, Proctor & Gamble, USA (morrall.dd*at*pg.com) Ann M Richard, US Environmental Protection Agency, USA (richard.ann*at*epa.gov) Patrick Sinko, Rutgers, The State University of New Jersey, USA (sinko*at*rci.rutgers.edu) Sung-Sau So , Hoffmann-La Roche, USA (sung-sau.so*at*roche.com) Gil Veith, US Environmental Protection Agency, USA (veith.gilman*at*epa.gov) David A. Winkler, CSIRO Molecular Science, Australia (dave.winkler*at*csiro.au) Antony Williams, ACD/Labs, Canada (antony.williams*at*acdlabs.com) Chihae Yang, Leadscope, USA (cyang*at*leadscope.com) Session Topics: Computational Toxicology Computational Metabolism/Excretion Experimental ADMET Computational Absorption/Distribution Meeting Focus: ADMET I will be an international meeting bringing together leaders in the computational and experimental areas of ADMET. The meeting will consist of invited lectures, poster talks, scientific and vendor workshop presentations. The lectures will focus on theory and application of both computational and experimental ADMET approaches. In addition, lecturers will be asked to mention explicitly how they handle structural diversity and noisy data characteristic of ADMET problems. ____________________________________________________________________________________________ Please forward additional information about: Registration_ Sponsorship_ Exhibiting_ Name:___________________________________________Title:________________________________ Company/Institution____________________________________________________________________ Address:______________________________________________________________________________ City:_______________________ State:_______ Country______________ Postal Code:_____________ Phone:____________________________________ Fax:_______________________________________ Email:________________________________________________________________________________ SCHERAGO INTERNATIONAL ? 11 Penn Plaza, Ste 1003, New York, NY 10001 Tel: 212-643-1750 x20 / Fax: 212-643-1758 Email: admet*at*scherago.com / Website: www.scherago.com/admet From chemistry-request@ccl.net Mon Jun 2 14:32:27 2003 Received: from smtp1.server.rpi.edu (smtp1.server.rpi.edu [128.113.2.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52IWRgC006893 for ; Mon, 2 Jun 2003 14:32:27 -0400 Received: from webmail.rpi.edu (webmail.rpi.edu [128.113.26.21]) by smtp1.server.rpi.edu (8.12.9/8.12.9) with ESMTP id h52IWQCR022260; Mon, 2 Jun 2003 14:32:26 -0400 Message-Id: <200306021832.h52IWQCR022260/at/smtp1.server.rpi.edu> Content-Type: text/plain Content-Disposition: inline To: scerri/at/chem.ucla.edu From: "Dr. N. SUKUMAR" Organization: Rensselaer Polytechnic Institute Cc: chemistry/at/ccl.net X-Originating-Ip: 128.113.135.209 Mime-Version: 1.0 Reply-To: "Dr. N. SUKUMAR" Date: Mon, 02 Jun 2003 14:32:26 EDT X-Mailer: EMUmail 4.00 Subject: Re: CCL:orbitals X-Scanned-By: MIMEDefang 2.28 On Fri, 6 Jun 2003 23:37:27 -0700 Eric Scerri wrote: > > But far more obviously the anti-realistic view was adopted because so > many QM concepts seem to defy a realistic interpretation. Is the > electron a wave or a particle? The electron has no definite > trajectory. Electron spin is not really spin, Collapse of the > wavefunction issue etc etc. > This is again a meaningless classification in this day and age. Which Almighty Being declared that everything has to be a particle or a wave? An electron is an electron, just as an elephant is an elephant. Is an elephant a pillar or a rope? It has a massive leg like a pillar, but a flexible tail like a rope. This does not imply any pillar-rope duality. The closest I can think of to such an Almighty Being was Neils Bohr, the Creator of the Copenhagen Interpretation. But waves and particles were just everyday objects to give early 20th century physicists an intuitive feel for difficult quantum mechanical concepts, to "explain" these concepts to people of that generation (but I use this term rather warily, because many consider an "explanation" as something absolute, rather than tentative: one way of seeing things). Now two or more generations of students have grown up "seeing" electrons on their TV screens and computer monitors, whereas many are the inner city youth who have never seen a water wave in a lake or sea. Bohr held the view that quantum objects always had to be formulated in terms of classical everyday language. But as we all know, the everyday language of today is not Bohr's classical language. Isn't it time to rework these tired 20th century laymen's analogies? Now in terms of mathematics, of course, we have Newtonian mechanics under one set of limiting conditions and Newtonian (physical) optics under another. But this does not mean that an electron is a particle or a wave or a particle when you look and a wave when you don't. > > > You did not explain why you felt that your example was "better" than > phlogiston. > > OK, not "better"; just more convenient for my argument :-) > > ... As Popper himself stated, "All theories > are born refuted", meaning that sooner or later they will all be > refuted. Scientific theories are only provisionally useful. Every > single one of them will eventually be refuted. This is a > meta-induction based on the fate of all past and now defunct theories > from the history of science... But this itself is only a theory and hence is "born refuted". That makes it a self-refuting argument. > > Of course one may argue that induction from past instances is not a > reliable path to knowledge and that it just so happens that our > cherished current theories have finally reached the point where they > are refutable but will never actually be refuted. But that would be > plain stupid of course. > > I myself donot disagree with your belief, but it is just that: a BELIEF. Those who believe otherwise and seek the "ultimate" Theory of Everything or Hoheberg and Kohn's Universal Functional are NOT plain stupid. 150 years ago, one could have said that all attempts by humans to achieve powered flight had failed and thus, by meta-induction, all future attempts would be doomed to failure. Likewise for all attempts throughout human history to transmute elements. There are so many variables. If the federal governments stop funding high energy physics altogether, as they are quite likely to sooner or later, or if humanity does not survive into the next century, then the Standard Model of physics may never be refuted (with apologies to Popper). Does any of this make the Standard Model any more "true"? A meaningless question, in my opinion. The fact that all theories may (or may not) be "born refuted" does not make all theories equal. Some theories are more useful than others. Some explain more observations than earlier ones. In that limited sense, it IS fair to say that these theories are perhaps more "true" or closer to "reality". But we are straying far afield from orbitals, I'm afraid. Dr. N. Sukumar http://www.drugmining.com/ Visiting Scientist Rensselaer Department of Chemistry and Wadsworth Center, New York State Dept.of Health From chemistry-request@ccl.net Mon Jun 2 14:04:03 2003 Received: from web20605.mail.yahoo.com (web20605.mail.yahoo.com [216.136.226.163]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h52I43gC006288 for ; Mon, 2 Jun 2003 14:04:03 -0400 Message-ID: <20030602180402.99282.qmail/at/web20605.mail.yahoo.com> Received: from [206.111.112.115] by web20605.mail.yahoo.com via HTTP; Mon, 02 Jun 2003 11:04:02 PDT Date: Mon, 2 Jun 2003 11:04:02 -0700 (PDT) From: Sengen Sun Subject: CCL: Do MOs explain chemistry? To: chemistry/at/ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Clearly, most people recognize no physical reality for MOs. It is perfectly fine to me that we can think it real in our minds as suggested by Jens Spanget-Larsen. But we should be very careful to attribute MOs extra power that they don t really have. We should not exaggerate the role of MOs in scientific explanations because they are very valuable for predictions. We do need conceptual clearance in scientific descriptions without passion or we made mistakes How good MOs in explanations of chemistry? In order to answer this question, we must know what the criteria are for scientific explanations. The issue of SCIENTIFIC EXPLANATION has been discussed in many occasions (e.g., Scerri, E. R. Chem. Education: Research and Practice in Europe 2001, 2, 165; Science & Education 9, 405, 2000). Based on my understanding, there are two groups of people with different criteria of EXPLANATION and UNDERSTANDING. First, natural phenomena should be explained based on very fundamental factors that really control the nature. At least, the fundamental factors should be roughly or qualitatively sorted that are responsible for a specific event. An understanding is achieved if we can roughly describe how the control factors work competitively or cooperatively. In some very complex situation, the responsible factors can not be sorted or clearly partitioned. But we know how many control factors are involved. In this case, we may say the natural event is too complicated and we can not fully explain it. I am a person in this group. But I know I am not alone. In the second group, a natural event is not necessarily explained by fundamental factors. A mathematical index embodying all the factors can be used conveniently for the explanation. This is the very popular view on the List. This group of people is represented by Roald Hoffmann (see his recent discussions on this topic, American Scientist 2003, 91, 9-11). A friend on this List responded to a posting of mine the other day this way: "Dmitro Khoroshun" : [As many things around, it ultimately boils down to Coulombic law and some annoying other things, but the combinations of the trivial physical effects are enormous even in simple molecules, let along in solutions or living organisms. Currently, some questions are beyond the realm of computational chemistry, and there are professionals who might be able to deal with them in a more ad hoc, but hopefully more efficient manner.] Dmitro s and the second group of people s views deserve my high respect. Philosophically, I think that these 2 groups of people are actually one unified group in the sense of science. There are no reasons that two groups should criticize each other. But we should get down to the specifics what we should say and what we should not on a particular natural event. I would like to give a specific example of many contradictions since the birth of QM, - the secondary MO interaction (SMOI). As I discussed with my former supervisors, schoolmates and colleagues, an agreement was never reached. In the literature, some authors refused the existence of SMOI (Acc. Chem. Res. 2000, 33, 658). Some others conducted some mathematical treatments and produced some numbers, claiming the existence (JOC 2001, 66, 6178). Some authors even implied that the SMOI could someday be directly measured (JOC 2002, 67, 9153). Should we ask what the produced numbers mean for an understanding? Or science has advanced to such a stage that numbers mean understanding and no question should be asked? The MO concept surely embodies many fundamental factors. Fukui & Hoffmann well deserved 1981 Nobel prize due to their discovery of the correlation between MOs and chemical reactivity. But I don t think that everything they said is correct. We must criticize their mistakes hard without mercy. Their mistakes could have too much negative impacts on our scientific community due to their high profiles, especially on experimental chemists with little theoretical knowledge. Few chemists (none in my opinion) really understand MO explanations of chemical reaction mechanism! Hoffmann admitted that some prominent scientists don t agree with him (Theochem 1998, 424:1-6). It is simply necessary that experimental chemists TRUST theoretical chemists. The problem is that even there is no agreement among some renowned theoretical chemists. Chemical reactions are about to overcome resisting forces. In another scientific term, the resistance can be described by potential energy barriers. You are creating magic at the advanced level if you say that chemistry is about stabilization and destabilization of MOs. The MO explanations of chemical reactions are good ones only if UNDERSTANDING could mean TRUST and FOLLOW! What does it mean if a chemical reaction theory can not be understood by the people who actually do the chemical reactions? Another philosophical question: How does a good correlation relationship NECESSARILY mean understanding and explanations? Please advise me if any one knows any references on this question. Now come back to my Subject question. If MOs are used appropriately, they explain. Otherwise, they mystify! __________________________________ Do you Yahoo!? Yahoo! Calendar - Free online calendar with sync to Outlook(TM). http://calendar.yahoo.com From chemistry-request@ccl.net Mon Jun 2 17:45:42 2003 Received: from mx3.trentu.ca (mx3.trentu.ca [192.75.12.4]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h52LjggC011365 for ; Mon, 2 Jun 2003 17:45:42 -0400 Received: (qmail 31253 invoked by uid 504); 2 Jun 2003 21:45:42 -0000 Received: from elewars/at/trentu.ca by mx3.trentu.ca by uid 501 with qmail-scanner-1.14 (fsecure: 4.15/4370/2003-05-30/2003-05-30. 2003-05-27/ Clear:. Processed in 0.321447 secs); 02 Jun 2003 21:45:42 -0000 X-Qmail-Scanner-Mail-From: elewars/at/trentu.ca via mx3.trentu.ca X-Qmail-Scanner: 1.14 (Clear:. Processed in 0.321447 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx3.trentu.ca with SMTP; 2 Jun 2003 21:45:41 -0000 Message-ID: <3EDBC646.604C269A/at/trentu.ca> Date: Mon, 02 Jun 2003 17:48:54 -0400 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Shobe, Dave" , chemistry/at/ccl.net Subject: Re: CCL:hybrid/VSEPR References: <5CF08BBFE6DE97478C1E76E654CAF90801BC0C05/at/lvlxch02.ntdomain.americas.sc-world.com> Content-Type: multipart/alternative; boundary="------------DE2EBAAB135F692D3721CACB" --------------DE2EBAAB135F692D3721CACB Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit 2003 June 2 Hello, re hybridization vs. VSEPR: Hybridization is purely a mathematical procedure, whereby electron density is resolved into components, rather than a physically real phenomenon that occurs before bonding. It "...is _never_ necessary" (J. Simons and J. Nichols, "Quantum Mechanics in Chemistry", Oxford U Press, New York, 1997, p. 133). I view it as being analogous to resolving a force into components, and indeed, like forces, orbitals are mathematically vectors (in Hilbert space); so it legitimate to take linear combinations of them. The VSEPR model, on the other hand, seems to me to be an attempt to provide a _physical_ explanation of the shape of molecules, namely electrostatic repulsion. Actually, I suspect that Pauling (a popularizer, if indeed not the originator of the concept) thought of hybridization as "real", and staunchly championed the bent bonds model of the C/C double bond over the sigma/pi view. (About 5 years ago someone posted an amusing anecdote about Pauling to the CCL: asked if orbitals are real, he is supposed to have said "They must be real, because Mulliken and I have been using them for the past [30 or whatever] years".) E. Lewars ==== "Shobe, Dave" wrote: > > > That's an interesting observation. > > Structures of main-group (including organic) compounds are often > rationalized in terms of hybridization, which because it relies on > orbitals implies a small role for interelectron repulsion. > > However, these same structures are often rationalized using VSEPR > theory, which is 100% based on interelectron repulsion, at least if > you ignore the underlying assumption that electrons, for mysterious > reasons, come in pairs. > > --David Shobe > S|d-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. > > > -----Original Message----- > From: Avijit Ghosh [mailto:avijit/at/physics.drexel.edu] > Sent: Friday, May 30, 2003 7:01 PM > To: chemistry/at/ccl.net > Subject: CCL:Orbitals > > ....... > > > (2) Does the single e- wavefunction density have any > > meaning? Let me decompose this a bit. To me the fact that > > organic chemists can "hybridize" orbitals (aka "handwaving > > quantum mechanics") is a testament to the contribution of > > e-e- correlation as actually not being that much at least > > for the first part of the periodic table. In fact that elements > have > > the properties that they do is also a testament to this. > > ....... --------------DE2EBAAB135F692D3721CACB Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 2003 June 2

Hello, re hybridization vs. VSEPR:

Hybridization is purely a mathematical procedure, whereby electron density is resolved into components, rather than a physically real phenomenon that occurs before bonding. It "...is _never_  necessary" (J. Simons and J. Nichols, "Quantum Mechanics in Chemistry", Oxford U Press, New York, 1997, p. 133). I view it as being analogous to resolving a force into components, and indeed, like forces, orbitals are mathematically vectors (in Hilbert space); so it legitimate to take linear combinations of them. The VSEPR model, on the other hand, seems to me to be an attempt to provide a _physical_ explanation of the shape of molecules, namely electrostatic repulsion.

Actually, I suspect that Pauling (a popularizer, if indeed not the originator of the concept) thought of hybridization as "real", and staunchly championed the bent bonds model of the C/C double bond over the sigma/pi view. (About 5 years ago someone posted an amusing anecdote about Pauling to the CCL: asked if orbitals are real, he is supposed to have said "They must be real, because Mulliken and I have been using them for the past [30 or whatever] years".)

E. Lewars
====

"Shobe, Dave" wrote:

 

That's an interesting observation.

Structures of main-group (including organic) compounds are often rationalized in terms of hybridization, which because it relies on orbitals implies a small role for interelectron repulsion.

However, these same structures are often rationalized using VSEPR theory, which is 100% based on interelectron repulsion, at least if you ignore the underlying assumption that electrons, for mysterious reasons, come in pairs.

--David Shobe
Süd-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.
 

-----Original Message-----
From: Avijit Ghosh [mailto:avijit/at/physics.drexel.edu]
Sent: Friday, May 30, 2003 7:01 PM
To: chemistry/at/ccl.net
Subject: CCL:Orbitals

.......

>       (2) Does the single e- wavefunction density have any
> meaning? Let me decompose this a bit. To me the fact that
> organic chemists can "hybridize" orbitals (aka "handwaving
> quantum mechanics") is a testament to the contribution of
> e-e- correlation as actually not being that much at least
> for the first part of the periodic table. In fact that  elements have
> the properties that they do is also a testament to this.

.......

--------------DE2EBAAB135F692D3721CACB-- From chemistry-request@ccl.net Mon Jun 2 11:46:15 2003 Received: from mserv7.dl.ac.uk (mail.dl.ac.uk [148.79.80.138]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h52FkFgC001827 for ; Mon, 2 Jun 2003 11:46:15 -0400 X-DL-MFrom: X-DL-Connect: Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv7.dl.ac.uk (8.12.9/8.12.8/[ref postmaster/at/dl.ac.uk]) with ESMTP id h52Fk9NR006303 for ; Mon, 2 Jun 2003 16:46:09 +0100 Message-ID: <3EDB6B4C.1050307/at/dl.ac.uk> Date: Mon, 02 Jun 2003 16:20:44 +0100 From: "Van Dam, HJJ (Huub)" Organization: CCLRC Daresbury Laboratory User-Agent: Mozilla/5.0 (X11; U; OSF1 alpha; en-US; rv:0.9.4.1) Gecko/20020517 Netscape6/6.2.3 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry/at/ccl.net Subject: Accuracy of RPA linear response calculations Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers, I am planning to do some large scale calculations of excitation spectra in the Random Phase Approximation (RPA). However, before I burn fast amounts of CPU cycles I would like to have a good idea of how sensible I can expect the results to be (in comparison to experimental results). Could you suggest some recent review papers on applications of this theory, please? I will summarize the responses of course. If you choose to respond but do not want your response to appear in the summary please let me know. Many thanks, Huub van Dam -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam/at/dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK mobile: +44-7739-330511 WA4 4AD ========================================================================