From owner-chemistry@ccl.net Fri Aug 29 01:32:00 2008 From: "Bob Clark bclark,+,bcmetrics.com" To: CCL Subject: CCL: tautomerization software Message-Id: <-37678-080829003920-20725-cJ33iu7WORPfWEq0nbDjDQ,+,server.ccl.net> X-Original-From: Bob Clark Content-Type: multipart/mixed; boundary="------------040502020100070109060509" Date: Thu, 28 Aug 2008 22:39:26 -0500 MIME-Version: 1.0 Sent to CCL by: Bob Clark [bclark++bcmetrics.com] This is a multi-part message in MIME format. --------------040502020100070109060509 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi David,

I guess I should have clarified what I meant by "simple" ketones; beta dicarbonyls (and nitro and cyano and...) are exactly the sort of thing I was trying to exclude.  Nor am I unaware of the potential of doing direct calculations.   I did get caught unawares by the delay between sending and posting, both with regard to the earlier e-mail about that and Simon Cross' e-mail about Molecular Discovery's recent work.  

I do have to respectfully disagree about the ease of doing the relevant quantum calculations, though.  Tautomerization is an intermolecular process in almost all cases that I know of, whether it occurs in (near) vacuum or in solution; the underlying changes in orbital symmetry that are involved make that almost unavoidable.   The problem then becomes generally hard.

Either way, it comes back to the point I was trying to make, and that Simon touched on as well: one needs to know whether the ultimate application is going  to be to pick the right tool.

Best regards,

Bob C.


Sent to CCL by: David Gallagher [gallagher.da]=[gmail.com]
Hi Bob,

It seems that you may be unaware that quantum chemistry methods, already proposed by myself and some others, provide the necessary thermodynamic and kinetic information to establish both the equilibrium ratio of the different tautomers and their speed of interconversion at a particular temperature.

It is quite simple to perform a free energy calculation on each tautomer with almost any quantum chemistry package to estimate the free energies (thermodynamics), either gas phase or in an appropriate solvent field.  The ratio of the tautomers can then be determined via a Boltzmann distribution.

The speed of interconversion (kinetics) can be established from the height of the energy barrier to interconversion (activation energy) and the Arrhenius equation.  The height of the energy barrier is simply the free energy of the transition state (between the tautomers) minus the free energy of the appropriate tautomer.  Although, more involved than ground state calculations, characterizing transition states in most cases is relatively straightforward for some quantum chemistry packages (further details on reaction modelling are posted at http://cacheresearch.com/presentations.html )

Far from being 'not relevant for most purposes', the enol tautomer can be the most abundant for some simple ketones such as acetyl-acetone, and even in very low concentrations when the keto-form prevails, the enol tautomer may still be responsible for certain characteristics of a molecules chemistry or reactivity.

Regards,
David


At 07:22 AM 8/28/2008, Bob Clark bclark-x-bcmetrics.com wrote:

The responders so far have failed to distinguish between two kinds of questions: "Could the molecule possibly tautomerize - i.e., do tautomeric structures exist?" (which is what you actually asked)  and "Will the molecule tautomerize?"  Enumerating all possible tautomers is pretty straightforward, but identifying relevant tautomers is often very hard.  Hence the second question is a lot harder to answer, because one has to take kinetic as well as thermodynamic considerations into account.  The enol tautomer of most simple ketones, for example, isn't relevant for most purposes, and there are steroid CH tautomers that are perfectly happy to sit in separate bottles on the shelf for years.

So please provide some context: what do you want to use the information for?
Good luck,
Bob C.

Sent to CCL by: "Arindam  Ganguly" [arindamganguly|gmail.com]
Dear CCL users,
Is there any software out there which can predict the possibility of tautomerism being present in a molecule. Any suggestions and pointers will be really helpful. Thanks in advance.

Arindam
--------------040502020100070109060509 Content-Type: text/x-vcard; charset=utf-8; name="bclark.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="bclark.vcf" begin:vcard fn:Robert D. Clark n:Clark;Robert D. org:Biochemical Infometrics adr:;;PO Box 411431;Creve Coeur;MO;63141;USA email;internet:bclark^_^bcmetrics.com tel;work:+1-314-660-4499 x-mozilla-html:TRUE url:http://www.bcmetrics.com version:2.1 end:vcard --------------040502020100070109060509-- From owner-chemistry@ccl.net Fri Aug 29 06:03:01 2008 From: "Pierre Archirel pierre.archirel],[lcp.u-psud.fr" To: CCL Subject: CCL:G: 5d 7f versus 7d 10f : answer to Guanna Li Message-Id: <-37679-080829060037-19826-iA0gUcbe9Ggzkc2J7w6ojg\a/server.ccl.net> X-Original-From: "Pierre Archirel" Date: Fri, 29 Aug 2008 06:00:33 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel . lcp.u-psud.fr] Dear collegue, Choosing cartesian vs spherical gaussians is not a simple option only changing the size of the basis. You must know with which option the basis you use has been optimised, and keep this option throughout your calculations. More specifically: 1- d cartesian functions include x**2, y**2 and z**2 functions. These functions include the x**2+y**2+z**2=r**2 combination, which has a spherical symmetry and therefore contributes to the s part of the basis. 2- if the basis is optimised with the 6d option it has gaps in the s exponents, which are filled by the r**2 functions of the d part. 3- consequently if you use this basis with the 5d option, you will have a poor s basis. 4- conversely if the basis is optimised with the 5d option the s part of the basis will have no gaps in the exponents 5- if you use it with the 6d option, the r**2 functions of the d part will possibly be redundant with the s part of the basis, and create an overcomplete basis set with numerical difficulties. In conclusion: check how your bases have been optimised: old Pople bases have been optimised with the 5d options, but I do not know with which option the aug-cc bases have been. Sincerely yours, Pierre Archirel, LCP, Orsay, France pierre.archirel[*]lcp.u-psud.fr From owner-chemistry@ccl.net Fri Aug 29 16:55:01 2008 From: "Neelum Seeburrun nseeburrun**gmail.com" To: CCL Subject: CCL: Minima Message-Id: <-37680-080829130711-30487-sHq9EuynC+sl2JkXaX00lA]-[server.ccl.net> X-Original-From: "Neelum Seeburrun" Date: Fri, 29 Aug 2008 13:07:08 -0400 Sent to CCL by: "Neelum Seeburrun" [nseeburrun!=!gmail.com] Dear All The problem I am having is that there are different types of minima: local,global,true and genuine. All of the minima give real values of vibrational frequencies. So how to distingush between them? Your help or references will be appreciated. Neelum nseeburrun(-)gmail.com From owner-chemistry@ccl.net Fri Aug 29 17:30:01 2008 From: "luvish seeb luvish21#,#gmail.com" To: CCL Subject: CCL: valence configuration Message-Id: <-37681-080829122621-25728-IOI/R7i+6XsUv1C5c7RWSg{:}server.ccl.net> X-Original-From: "luvish seeb" Date: Fri, 29 Aug 2008 12:26:17 -0400 Sent to CCL by: "luvish seeb" [luvish21-.-gmail.com] I am working on a theoretical study on clusters. I am to know how the electronic configuration of the clusters is obtained. For example consider the electronic configuration of Ir (subscript 4) which is[(a1)4(e)8(t1)6 (t2)18]. Luvish Seeb luvish21- -gmail.com