On the other hand it doesn't cover more recent deve= lopments like DFT and =C2=A0CC.=C2=A0For a pragmatic introduction to DFT I = would recommend Holthausen and Kochs "A Chemists Guide to DFT".

Best regards / Johannes

20= 11/1/12 neeraj misra neerajmisra:hotmail.com= <owner= -chemistry[#]ccl.net>

Sent to CCL by: "neeraj =C2=A0misra" [neerajmisra()hotmail.com]
Dear CCL'ers,
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Although we do have a lot= of very good literature on "electronic structure theory" availab= le but i am looking for a sigle source of the best possible treatment on th= is topic..Any help in this regard would be gratefully acknowledged.

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--00163630f337e985e80499a1ae9f-- From owner-chemistry@ccl.net Wed Jan 12 07:50:01 2011 From: "Shirin Seifert shirin.seifert-#-gmail.com" To: CCL Subject: CCL: Linux .CHK Message-Id: <-43607-110112072052-23177-kAEBiMLp7edpIBtzYlPIgw(_)server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=0016e659fd08a6a8950499a5386f Date: Wed, 12 Jan 2011 15:50:05 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert=gmail.com] --0016e659fd08a6a8950499a5386f Content-Type: text/plain; charset=ISO-8859-1 Hello! How can I open a .chk file generated in linux with GaussView in windows? How to convert? Thanks --0016e659fd08a6a8950499a5386f Content-Type: text/html; charset=ISO-8859-1 Hello!
How can I open a .chk file generated in linux with GaussView in windows?
How to convert?

Thanks
--0016e659fd08a6a8950499a5386f-- From owner-chemistry@ccl.net Wed Jan 12 08:24:00 2011 From: "Kalju Kahn kalju[#]chem.ucsb.edu" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43608-110112075852-4880-uXPi43NC3TTbL0aCjTxPPg[*]server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 12 Jan 2011 04:58:39 -0800 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju*o*chem.ucsb.edu] Nancy, I may be old-fashioned but I recall that a book with a title "Beilstein" used to have all sorts of wonderful chemical data, including pKa values that someone had measured, usually with a considerably better accuracy than many modern pKa prediction programs provide. If you take time to hunt it down from your local library, you may find that the pKa for thiazolidinedione is about 6.7. I would expect that the alkyl substituent, and the distal protonated pyridinium moiety will lower this value a bit but it should be above 6.4. In my bias to trust experiments, I also take an opportunity to point out that collecting a couple of 13C NMR spectra of thiazolidinedione in aqueous solution (10% D2O for lock) in the pH range from 5 to 8 would reveal not only the pKa but also the tautomeric forms of the acid and the anion. A related and well studied model here is allantoin; see (shameless self-promotion follows) Kahn, K.; Serfozo, P.; Tipton, P. A. Identification of the true product of the urate oxidase reaction. J. Am. Chem. Soc. 1997, 119, 5435-5442. I would be highly surprised if the acid is anything else than the expected CO-NH-CO. However, as others have nicely explained already, the dominant tautomer in the protein binding pocket may be different than the one in the water. In addition to what has already been said here, you could also calculate relative energies of tautomers using a respectable QM method, and analyze the effect of solvent polarity on the relative energies to judge if hydrogen bonding to the putative OH form would be sufficient to stabilize such a structure. Cheers, Kalju > Hi All, > > Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value of > the acidic hydrogen on the thiazolidinedione ring of pioglitazone is 4.57 > (see attached "Figure_1.gif"). Therefore, the predominant species at pH > 7.0 > predicted by MarvinSketch is the one depicted in "Figure_2.gif". The > different tautomeric forms predicted by MarvinSketch are shown in > "Figure_3.gif". > > Can anyone explain where these predictions come from, and if they are > correct? > > Thanks, > Nancy > > > On Mon, Jan 10, 2011 at 4:16 AM, Gabriele Cruciani gabri(0) > chemiome.chm.unipg.it wrote: > >> >> Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it] >> Nancy, >> the first form you reported is the most stable in water at pH 7.0. >> However, the fact that one form is more stable than another in water >> does >> not help you to understand which form will be more 'relevant' for >> docking. >> In protein the tautomeric equilibria may produce and stabilize different >> forms according to the complementary site. There are examples of >> tautomeric >> form in protein not stable in water, where the energy difference is more >> than 5 Kcal/mol. >> >> MoKa software (www.moldiscovery.com) is fast and accurate to produce >> tautomer stable in water, but it can produce also all the (plausible) >> tautomeric forms. >> >> Then, a possibility is to dock them into your protein, to see if docking >> methods may differentiate their binding. >> >> Gabriele Cruciani >> >> >> >> >> Hi All, >>> >>> I am performing molecular docking and molecular dynamics simulations of >>> the >>> thiazolidinedione pioglitazone binding to the PPAR-gamma receptor >>> protein >>> (PDB ID: 1ZGY). The thiazolidinedione ring can exist in numerous >>> different >>> tautomeric states; I have attached a figure depicting several of them. >>> Which tautomer would be dominant at the physiological pH of ~7.0? >>> >>> Also, are there any software programs that can predict which tautomer >>> would >>> be correct? >>> >>> Thanks in advance, >>> Nancyhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/> >> >> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Wed Jan 12 09:00:00 2011 From: "Gkourmpis, Thomas Thomas.Gkourmpis_._borealisgroup.com" To: CCL Subject: CCL:G: Linux .CHK Message-Id: <-43609-110112083728-15070-hmBQyYzyn33IWQ2ywAWb+g^server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_2BD27C21A5B53C4AB53F403FC915A18216C07E3120CMS02mignetwo_" Date: Wed, 12 Jan 2011 14:37:11 +0100 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis]^[borealisgroup.com] --_000_2BD27C21A5B53C4AB53F403FC915A18216C07E3120CMS02mignetwo_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Here you go http://www=2Egaussian=2Ecom/g_whitepap/remote=2Ehtm check this = tutorial from the official Gaussian web page=2E I think it will be useful= =2E=0D=0A=0D=0AThomas=0D=0A=0D=0AFrom: owner-chemistry+thomas=2Egkourmpis= =3D=3Dborealisgroup=2Ecom:+:ccl=2Enet [mailto:owner-chemistry+thomas=2Egkourm= pis=3D=3Dborealisgroup=2Ecom:+:ccl=2Enet] On Behalf Of Shirin Seifert shirin= =2Eseifert-#-gmail=2Ecom=0D=0ASent: Wednesday, January 12, 2011 1:20 PM=0D= =0ATo: Gkourmpis, Thomas=0D=0ASubject: CCL: Linux =2ECHK=0D=0A=0D=0AHello!= =0D=0AHow can I open a =2Echk file generated in linux with GaussView in win= dows?=0D=0AHow to convert?=0D=0A=0D=0AThanks=0D=0A=0D=0A=0D=0A --_000_2BD27C21A5B53C4AB53F403FC915A18216C07E3120CMS02mignetwo_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Here you go http://www=2Egaussian=2Ecom/g_whitepa= p/remote=2Ehtm check this tutorial from the official Gaussian web page= =2E I think it will be useful=2E

Thomas<= /o:p>

From: owner-che= mistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom:+:ccl=2Enet [mailto:owner-= chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom:+:ccl=2Enet] On Beha= lf Of Shirin Seifert shirin=2Eseifert-#-gmail=2Ecom
Sent: Wed= nesday, January 12, 2011 1:20 PM
To: Gkourmpis, Thomas
Subj= ect: CCL: Linux =2ECHK

Hello!
How can I open a =2Echk= file generated in linux with GaussView in windows?
How to convert?
<= br>Thanks