"At least Loria = gave something back to Canada with this trade." "Taking from = Montreal and giving back to Toronto is not really a recipe for = peace = or goodwill."

<= /div>

= --Apple-Mail=_19C52917-78F2-46D9-AEDD-9C6FE2E11502-- From owner-chemistry@ccl.net Sun Mar 10 12:38:00 2013 From: "Errol Lewars elewars[]trentu.ca" To: CCL Subject: CCL: Anybody have pointers for protomer/tautomer ranking articles? Message-Id: <-48397-130310121252-28163-yj41I0he3mUeXjdJN4yGkQ\a/server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 10 Mar 2013 12:12:20 -0400 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars * trentu.ca] 2013 March 10 "evaluating the likelihood of particular protonization or tautomerization states" If you mean calculating which of two or more protonated species (ditto for tautomers) you will end up predominantly, you have a thermodynamics problem, and need to calculate the relative stabilities of the conjugate acids. These refs may be of some help: "Assigning absolute values to proton affinities: a differentiation between competing sites" B J Smith, L Radom, JACS, 1993, 115, 4885-4888 "N-Protonation vs. O-protonation..." S J Cho et al, JOC, 1997, 62, 4068-4071 "...Prediction of the Relative Basicities and Preferred Protonation Sites" J F Sanz et al, J Comp Chem, 1988, 9, 784-789 "On the Relationaship between the preferred sites of Hydrogen Bonding and Protonation" B Chan et al, J Phys Chem A, 2005, 109(24), 5509-5517 You are likely interested in the situation in solution, and will probably use a continuum solvent model. Two papers relevnt to tautomers and solvent are: K Lammertsma, B V Prasad, JACS, 1994, 116, 642-650 B Balta, V Aviyente, J Comp Chem, 2003, 24(14), 1789 Thermodynamic basicity/tautomer stability may not reflect kinetic basicity/rate of tautomer formation; fortunately rate is usually not what we seek, for calculating it would be more of a problem. E. Lewars == Joe Leonard jleonard42~~gmail.com wrote: > Folks, I am interesting in learning of any preferably recent articles > discussing the state of the art of evaluating the likelihood of > particular protonization or tautomerization states of molecules. I > will do a Google Scholar search as well, but pinging CCL tends to be > more rewarding, as I sometimes find Google like "drinking from a > firehose". In this case, I hope that some of the authors of these > articles peruse CCL... > > Thanks in advance! > > Joe Leonard > jleonard42\a/gmail.com > -- > "At least Loria gave something back to Canada with this trade." > "Taking from Montreal and giving back to Toronto is not really a > recipe for peace or goodwill." > > > From owner-chemistry@ccl.net Sun Mar 10 15:38:00 2013 From: "mark andrew blitz m.blitz%x%leeds.ac.uk" To: CCL Subject: CCL: MESMER 2.0 Message-Id: <-48398-130310135545-18243-R5yhVjSN3QD3cGxMFS2cAA+/-server.ccl.net> X-Original-From: "mark andrew blitz" Date: Sun, 10 Mar 2013 13:55:44 -0400 Sent to CCL by: "mark andrew blitz" [m.blitz/./leeds.ac.uk] On behalf of the MESMER team, I am delighted to announce that MESMER 2.0 (Master Equation Solver for Multi Energy-well Reactions) is now available for download. MESMER is a Master Equation Solver that can be used to determined the outcome of reactions whose potential energy surface is characterized by one or more potential wells (local minima), connected by transition-states , before forming products. It bridges the gap between kinetic experiments and calculated ab initio potential energy surfaces, hence can be used by either practitioner to test the validity of their results. MESMER attempts to incorporate various facilities that make it easy to apply ME analysis to gas kinetics, e.g. data inputted using XML and Firefox PES viewer to aid in the construction of input files. The Windows installer and Linux tar file are located at: http://sourceforge.net/projects/mesmer/ The source can also be viewed and downloaded from this site. There are also bug and feature request tracking facilities which we encourage you to use. The following features have been incorporated: Implementation of the Marquardt non-linear least squares algorithm so the ME input parameters can be fitted to experimental data, rate coefficients and yields. The range of adjustable parameters that can be used in data fitting includes transition state imaginary frequency and the exponential temperature dependence parameter of DEdown. Hindered rotations, including asymmetric rotors. The reaction types have been extended to include bimolecular sink reactions. A plug-in class has been implemented that allows transition state sums of states to be input as a function of E or E and J. A plug-in class has been implemented that calculates the prior distribution. Species evolution charts. Calculation of microcanonical rate coefficients for non-adiabatic transitions. WKB tunnelling method. For those that download and use Mesmer, we encourage the user to provide feedback. We can provide some help and we are receptive to suggestions for future developments of the code. Please direct your comments or suggestions either through the above site or by email (Mark Blitz (M.Blitz\a/leeds.ac.uk)) We have recently published an article that describes some of the implementation details of MESMER (Journal of Physical Chemistry A, 95459560, 116 (2012)). More information is available at the MESMER website: http://www.chem.leeds.ac.uk/mesmer.html The MESMER team also participate in the MEIC (Master Equation Inter- Comparison), details of which are available from Prof. John Barker (jrbarker\a/umich.edu). Regards, on behalf of the MESMER team: Struan H Robertson, Chris Morley, David Glowacki, Robin Shannon, Chi-Hsiu Liang, Michael Pilling, Mark Blitz and Paul Seakins, Mark Blitz School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT. U.K. Tel 0113 343 6594 Email: M.Blitz\a/leeds.ac.uk From owner-chemistry@ccl.net Sun Mar 10 19:21:00 2013 From: "Christopher Cramer cramer#umn.edu" To: CCL Subject: CCL: Anybody have pointers for protomer/tautomer ranking articles? Message-Id: <-48399-130310171529-25265-m8lXXb/GjNTeJzAkirBL3w{:}server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-2-243303323 Date: Sun, 10 Mar 2013 17:14:36 -0400 Mime-Version: 1.0 (Apple Message framework v1085) Sent to CCL by: Christopher Cramer [cramer * umn.edu] --Apple-Mail-2-243303323 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Joe, As part of the SAMPL09 challenge sponsored by OpenEye, many groups = competed in predicting tautomer ratios. The results were published in a = special issue of J. Comput. Aid. Mol. Des. Our contribution was Ribeiro, R. F.; Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. = "Prediction of SAMPL2 aqueous solvation free energies and tautomeric = ratios using the SM8, SM8AD, and SMD solvation models" J. Comput.-Aid. = Mol. Des. 2010, 24, 317-333. but several others were also published, and I recall an overview article = by one of the OpenEye scientists. Best, Chris On Mar 10, 2013, at 9:54 AM, Joe Leonard jleonard42~~gmail.com wrote: > Folks, I am interesting in learning of any preferably recent articles = discussing the state of the art of evaluating the likelihood of = particular protonization or tautomerization states of molecules. I will = do a Google Scholar search as well, but pinging CCL tends to be more = rewarding, as I sometimes find Google like "drinking from a firehose". = In this case, I hope that some of the authors of these articles peruse = CCL... >=20 > Thanks in advance! >=20 > Joe Leonard > jleonard42\a/gmail.com > -- > "At least Loria gave something back to Canada with this trade." = "Taking from Montreal and giving back to Toronto is not really a recipe = for peace or goodwill." >=20 >=20 >=20 -- Christopher J. Cramer Elmore H. Northey Professor University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 Phone: (612) 624-0859 || FAX: (612) 626-7541 -------------------------- Faculty Liaison for eLearning Initiatives Office of the Senior Vice President for Academic Affairs and Provost 236 Morrill Hall Phone: (612) 626-1215 -------------------------- Mobile: (952) 297-2575 Email: cramer%x%umn.edu Twitter: %x%ChemProfCramer Website: http://pollux.chem.umn.edu --Apple-Mail-2-243303323 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii J. = Comput.-Aid. Mol. Des. 2010, 24, = 317-333.

but several others were also = published, and I recall an overview article by one of the OpenEye = scientists.

Best,

Chris<= /div>

On Mar 10, 2013, at 9:54 AM, Joe Leonard = jleonard42~~gmail.com wrote:

Folks, I am interesting in = learning of any preferably recent articles discussing the state of the = art of evaluating the likelihood of particular protonization or = tautomerization states of molecules. I will do a Google Scholar = search as well, but pinging CCL tends to be more rewarding, as I = sometimes find Google like "drinking from a firehose". In this = case, I hope that some of the authors of these articles peruse = CCL...

Thanks in = advance!

Joe Leonard
jleonard42\a/gmail.com
=
--
"At least Loria gave something back = to Canada with this trade." "Taking from Montreal and giving = back to Toronto is not really a recipe for peace = or goodwill."

<= /div>
=

Christopher J. Cramer

Elmore H. Northey = Professor

Department of Chemistry

207 Pleasant St. = SE

Phone: (612) 624-0859 || = FAX: (612) 626-7541

Faculty Liaison = for eLearning Initiatives

Office of the Senior Vice = President for Academic Affairs and Provost

236 = Morrill = Hall

Phone: (612) 626-1215

Mobile: (952) = 297-2575

cramer%x%umn.edu

Twitter: %x%ChemProfCramer

Website: http://pollux.chem.umn.edu<= /div>

= --Apple-Mail-2-243303323--