From owner-chemistry@ccl.net Mon Jan 17 07:48:00 2011 From: "Dr. Paul Elsinghorst paul.elsinghorst .. gmail.com" To: CCL Subject: CCL: hemiketal formation, transition state optimization Message-Id: <-43659-110117013233-3656-B3NBcWbz8mxnSOEpBNuh6w**server.ccl.net> X-Original-From: "Dr. Paul Elsinghorst" Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 17 Jan 2011 07:32:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Dr. Paul Elsinghorst" [paul.elsinghorst^-^gmail.com] I'm having trouble optimizing a transition state when going from an open ketone/phenol to a cyclic hemiketal. I chose the cyclic hemiketal with a proton still attached to the alcohol oxygen (positive formal charge) and a negatively charged ketone oxygen as the input structure for TS optimization. I preoptimized the structure applying a MMFF94 optimization and subjected that to ORCA giving: ! RKS B3LYP TZVP TightSCF SmallPrint Grid4 NoFinalgrid ! PAL8 NoSOSCF SlowConv OptTS NumFreq COSMO(Water) %geom Calc_Hess true end * xyzfile 0 1 TAXI_6_TS1.xyz Unfortunately ORCA optimizes the structure towards the open ketone/phenol which is obviously not the TS but finally a local minimum. Does someone know what's going wrong here? A further question is: does someone know, whether the proton in hemiketal formation is the one > from the alcohol migrating to the ketone? Is there a rule for this or does it differ depending on solvent? E.g. in protic solvents it might be relayed from solvent and in aprotic solvents it might migrate. I appreciate any ideas/help. Especially if I'm totally wrong in my approach. Thanks, Paul From owner-chemistry@ccl.net Mon Jan 17 08:23:00 2011 From: "Andreas Klamt klamt ~~ cosmologic.de" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43660-110117012358-751-bGPL7hcygXq72fXhx+mVww() server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=ISO-8859-1 Date: Mon, 17 Jan 2011 07:23:41 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt+*+cosmologic.de] Yes that is what we would conclude from a 12 kcal/mol taumtomer energy difference predicted by DFT/COSMO-RS in water.
If there should be any exp. insight contradicting this conclusion I would be happy to learn about it. (Also if there should be soem supporting our conclusion?)

Andreas

Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com:
Using quantum chemical calculations, you found that the diketone form is dominant; does this mean that the enol form predicted by MarvinSketch v3.5.4 in the published article is wrong?

"Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23

Thanks,
Nancy


On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt klamt(a)cosmologic.de <owner-chemistry(~)ccl.net> wrote:
Sent to CCL by: Andreas Klamt [klamt,cosmologic.de]
Hi Nancy,

as I wrote in the previous message, we find by quantum chemical calculations within the COSMO-RS solvation that the diketone form is more stable by abot 12 kcal/mol, that means it absolutely dominates!

Andreas

Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com:
Hi All,

I happened to find a published article where molecular docking simulations of TZDs against a novel protein is detailed:

"Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23

In this paper, the authors, using MarvinSketch v3.5.4, determined that the TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the diketone form (see attached figure).  It appears that the article's tautomer prediction was based only on the pH prior to docking, and had nothing to do with ligand-protein interactions.

Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4?

Thanks in advance.
Nancy



On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de <owner-chemistry(_)ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de]
Hi All,

let me put my 5 cents into the game:
We have done quantum calculations for the heterocyclic ring, with just a methyl group, since electronically the remainder of the compound should have almost no influence on the heterocycle.
DFT/COSMO-RS calculations prove the neutral species
SMILES:CC1C(=O)[NH]C(=O)S1 of the Pioglitazone heterocycle to be favored by 11.3 kcal/mol compared to all other neutral species of the heterocycle, which means that there is no other relvant neutral form.

We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at pH=7 it should be deprotonated with about 25%.
Since the pka of the conj. acid of the pyridine ring according to COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10% in the zwitterionic form.

It will be hard to decide this finally, unless someone measures it, but we are quite confident to be qualitatively right here, because the energy differences for the tautomers should not have more than 5 kcal/mol erro, as we learned in in the SAMPL2 tautomer contest:
see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge, http://www.springerlink.com/content/l577667th758n6h1/

Andreas







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 <http://chemiome.chm.unipg.it>

<owner-chemistry[a]ccl.net <mailto:owner-chemistry[a]ccl.net>> wrote:


   Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it
   <http://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 <http://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,
       Nancy>


   E-mail to subscribers: CHEMISTRY[a]ccl.net
   <mailto:CHEMISTRY[a]ccl.net> or use:>
   E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net
   <mailto:CHEMISTRY-REQUEST[a]ccl.net> or useConferences:

--
Dr. Jens Reinisch
Chemist / Customer Support
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone   +49-2171-363664
mobile  +49-163-7337310
fax     +49-2171-731689
e-mail  reinisch[*]cosmologic.de
web     www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt 



-- 
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt(_)cosmologic.de

web    	www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
CHEMISTRY(~)ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/ 



-- 
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt]~[cosmologic.de
web    	www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
From owner-chemistry@ccl.net Mon Jan 17 08:58:00 2011 From: "Andreas Klamt klamt#cosmologic.de" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43661-110117061749-31780-OANW68yUcmxBgEcS8ZT1Uw%a%server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=ISO-8859-15 Date: Mon, 17 Jan 2011 12:17:32 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt-x-cosmologic.de] I was just pointed by Leif Nørskov-Lauritsen to a stupid error which I made in my first entry on this topic. I wrote that at pH=7 25% would be deprotonated, 75% neutral. That was obviously wrong. It is the other way round: 72% is ionic, 25% neutral. The total amount of zwitterions is then ~3%.

Sorry for my mistake. But the basic message about the most stable neutral form stays valid.
The most stable anionic form is the di-keto anion.

Andreas

Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com:
Using quantum chemical calculations, you found that the diketone form is dominant; does this mean that the enol form predicted by MarvinSketch v3.5.4 in the published article is wrong?

"Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23

Thanks,
Nancy


On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt klamt(a)cosmologic.de <owner-chemistry(~)ccl.net> wrote:
Sent to CCL by: Andreas Klamt [klamt,cosmologic.de]
Hi Nancy,

as I wrote in the previous message, we find by quantum chemical calculations within the COSMO-RS solvation that the diketone form is more stable by abot 12 kcal/mol, that means it absolutely dominates!

Andreas

Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com:
Hi All,

I happened to find a published article where molecular docking simulations of TZDs against a novel protein is detailed:

"Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23

In this paper, the authors, using MarvinSketch v3.5.4, determined that the TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the diketone form (see attached figure).  It appears that the article's tautomer prediction was based only on the pH prior to docking, and had nothing to do with ligand-protein interactions.

Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4?

Thanks in advance.
Nancy



On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de <owner-chemistry(_)ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de]
Hi All,

let me put my 5 cents into the game:
We have done quantum calculations for the heterocyclic ring, with just a methyl group, since electronically the remainder of the compound should have almost no influence on the heterocycle.
DFT/COSMO-RS calculations prove the neutral species
SMILES:CC1C(=O)[NH]C(=O)S1 of the Pioglitazone heterocycle to be favored by 11.3 kcal/mol compared to all other neutral species of the heterocycle, which means that there is no other relvant neutral form.

We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at pH=7 it should be deprotonated with about 25%.
Since the pka of the conj. acid of the pyridine ring according to COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10% in the zwitterionic form.

It will be hard to decide this finally, unless someone measures it, but we are quite confident to be qualitatively right here, because the energy differences for the tautomers should not have more than 5 kcal/mol erro, as we learned in in the SAMPL2 tautomer contest:
see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge, http://www.springerlink.com/content/l577667th758n6h1/

Andreas







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 <http://chemiome.chm.unipg.it>

<owner-chemistry[a]ccl.net <mailto:owner-chemistry[a]ccl.net>> wrote:


   Sent to CCL by: Gabriele Cruciani [gabri##chemiome.chm.unipg.it
   <http://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 <http://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,
       Nancy>


   E-mail to subscribers: CHEMISTRY[a]ccl.net
   <mailto:CHEMISTRY[a]ccl.net> or use:>
   E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net
   <mailto:CHEMISTRY-REQUEST[a]ccl.net> or useConferences:

--
Dr. Jens Reinisch
Chemist / Customer Support
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone   +49-2171-363664
mobile  +49-163-7337310
fax     +49-2171-731689
e-mail  reinisch[*]cosmologic.de
web     www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt 



-- 
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt(_)cosmologic.de

web    	www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
CHEMISTRY(~)ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net or use http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/ 



-- 
PD. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt~~cosmologic.de
web    	www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
From owner-chemistry@ccl.net Mon Jan 17 12:39:00 2011 From: "Aleksey Kuznetsov AlexKuznetsov2007:-:yandex.ru" To: CCL Subject: CCL:G: "Allocation inconsistency in PrSmSU." error in freq calculations Message-Id: <-43662-110117123722-11006-NNcuKTMm5Hn6Q/U/s6rWsg:server.ccl.net> X-Original-From: "Aleksey Kuznetsov" Date: Mon, 17 Jan 2011 12:37:21 -0500 Sent to CCL by: "Aleksey Kuznetsov" [AlexKuznetsov2007_+_yandex.ru] Dear CCLers, I am doing geometry optimizations of ligated quantum dots using the HF/Lanl2dz approach as implemented in Gaussian 03, the quantum dots composition is either Cd33Se33(OPH3)21 or Cd33Se33(SH3)21, bith with 1341 basis functions and C1 symmetry. When I tried to perform frequency calculations of non-completely optimized QDs (to use obtained force constants in order to speed up geometry optimizations), in both cases these calculations interrupted at some point producing the following similar error messages: .. 3 vectors were produced by pass 16. PrismC: NFx= 2048 NFxT= 10 NFxU= 9. PrismC: NFx= 2048 NFxT= 10 NFxU= 8. PrismC: NFx= 2048 NFxT= 10 NFxU= 8. PrismC: NFx= 2048 NFxT= 10 NFxU= 8. PrismC: NFx= 2048 NFxT= 10 NFxU= 9. PrismC: NFx= 2048 NFxT= 10 NFxU= 8. PrismC: NFx= 2048 NFxT= 10 NFxU= 8. PrismC: NFx= 2048 NFxT= 10 NFxU= 8. Inv2: IOpt= 1 Iter= 1 AM= 7.36D-16 Conv= 1.00D-12. Inverted reduced A of dimension 51 with in-core refinement. End of Minotr Frequency-dependent properties file 721 does not exist. Allocation inconsistency in PrSmSU. Error termination via Lnk1e in /home/dbchem/mapete/chem/g03-D.02/g03/l1101.exe at Sat Jan 15 03:09:14 2011. Job cpu time: 0 days 2 hours 56 minutes 59.6 seconds. File lengths (MBytes): RWF= 4869 Int= 0 D2E= 0 Chk= 165 Scr= 1 I intentionally did again single-point calculations of these structures to make sure that chk-files were not lost or corrupted somehow. The memory amount assigned by the %mem keyword is either 320MW or 330MW. What could be the reason of this error and how it could be amended? Any help would be greatly appreciated. With best regards, Aleksey. From owner-chemistry@ccl.net Mon Jan 17 13:49:00 2011 From: "Nancy nancy5villa##gmail.com" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43663-110117134152-17912-GrLzU+N0/v4gWg7BmapThQ:server.ccl.net> X-Original-From: Nancy Content-Type: multipart/mixed; boundary=001636c5b6a5f6342a049a0f219e Date: Mon, 17 Jan 2011 13:41:31 -0500 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa .. gmail.com] --001636c5b6a5f6342a049a0f219e Content-Type: multipart/alternative; boundary=001636c5b6a5f63423049a0f219c --001636c5b6a5f63423049a0f219c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thus, the two major tautomers of pioglitazone are as shown in the attached figure? Also, is there a published article, or other evidence that would confirm that this is indeed the correct tautomeric distribution at pH 7? Thanks you, Nancy On Mon, Jan 17, 2011 at 6:17 AM, Andreas Klamt klamt#cosmologic.de < owner-chemistry++ccl.net> wrote: > Sent to CCL by: Andreas Klamt [klamt-x-cosmologic.de] > I was just pointed by Leif N=F8rskov-Lauritsen to a stupid error which I = made > in my first entry on this topic. I wrote that at pH=3D7 25% would be > deprotonated, 75% neutral. That was obviously wrong. It is the other way > round: 72% is ionic, 25% neutral. The total amount of zwitterions is then > ~3%. > > Sorry for my mistake. But the basic message about the most stable neutral > form stays valid. > The most stable anionic form is the di-keto anion. > > Andreas > > Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com: > > Using quantum chemical calculations, you found that the diketone form is > dominant; does this mean that the enol form predicted by MarvinSketch v3.= 5.4 > in the published article is wrong? > > "Structure-based design of a thiazolidinedione which targets the > mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb > 1;20(3):819-23 > > Thanks, > Nancy > > > On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt klamt(a)cosmologic.de < > owner-chemistry(~)ccl.net > wrote: > >> Sent to CCL by: Andreas Klamt [klamt,cosmologic.de] >> Hi Nancy, >> >> as I wrote in the previous message, we find by quantum chemical >> calculations within the COSMO-RS solvation that the diketone form is mor= e >> stable by abot 12 kcal/mol, that means it absolutely dominates! >> >> Andreas >> >> Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com: >> >> Hi All, >> >> I happened to find a published article where molecular docking simulatio= ns >> of TZDs against a novel protein is detailed: >> >> "Structure-based design of a thiazolidinedione which targets the >> mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb >> 1;20(3):819-23 >> >> In this paper, the authors, using MarvinSketch v3.5.4, determined that t= he >> TZDs would exist predominantly in the enol form at pH 7.4, as opposed to= the >> diketone form (see attached figure). It appears that the article's taut= omer >> prediction was based only on the pH prior to docking, and had nothing to= do >> with ligand-protein interactions. >> >> Does anyone know if the diketone or enol, or perhaps a different tautome= r, >> would be predominant at pH 7.4? >> >> Thanks in advance. >> Nancy >> >> >> >> On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de < >> owner-chemistry(_)ccl.net > wrote: >> >>> >>> Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de] >>> Hi All, >>> >>> let me put my 5 cents into the game: >>> We have done quantum calculations for the heterocyclic ring, with just = a >>> methyl group, since electronically the remainder of the compound should= have >>> almost no influence on the heterocycle. >>> DFT/COSMO-RS calculations prove the neutral species >>> SMILES:CC1C(=3DO)[NH]C(=3DO)S1 of the Pioglitazone heterocycle to be fa= vored >>> by 11.3 kcal/mol compared to all other neutral species of the heterocyc= le, >>> which means that there is no other relvant neutral form. >>> >>> We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. a= t >>> pH=3D7 it should be deprotonated with about 25%. >>> Since the pka of the conj. acid of the pyridine ring according to >>> COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10%= in >>> the zwitterionic form. >>> >>> It will be hard to decide this finally, unless someone measures it, but >>> we are quite confident to be qualitatively right here, because the ener= gy >>> differences for the tautomers should not have more than 5 kcal/mol erro= , as >>> we learned in in the SAMPL2 tautomer contest: >>> see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding t= he >>> predictions of tautomeric equilibria in solution based on the SAMPL2 >>> challenge, http://www.springerlink.com/content/l577667th758n6h1/ >>> >>> Andreas >>> >>> >>> >>> >>> >>> >>>> >>>> Hi All, >>>> >>>> Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value >>>> of the acidic hydrogen on the thiazolidinedione ring of pioglitazone i= s >>>> 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 MarvinSket= ch >>>> 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 wate= r >>>> 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. Ther= e >>>> 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 ca= n >>>> 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 numerou= s >>>> different >>>> tautomeric states; I have attached a figure depicting several o= f >>>> 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, >>>> Nancy> >>>> >>>> >>>> E-mail to subscribers: CHEMISTRY[a]ccl.net >>>> or use:> >>>> E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net >>>> or useConferences: >>>> >>>> http://server.ccl.net/chemistry/announcements/conferences/> >>>> >>>> >>>> >>>> >>> -- >>> Dr. Jens Reinisch >>> Chemist / Customer Support >>> COSMOlogic GmbH & Co. KG >>> Burscheider Strasse 515 >>> D-51381 Leverkusen, Germany >>> >>> phone +49-2171-363664 >>> mobile +49-163-7337310 >>> fax +49-2171-731689 >>> e-mail reinisch[*]cosmologic.de >>> web www.cosmologic.de >>> >>> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt >>> Komplementaer: COSMOlogic Verwaltungs GmbH >>> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt >>> >>> >>> >>> >>> >>> >>> E-mail to subscribers: CHEMISTRY(_)ccl.net o= r >>> use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.netor useConferences: >>> http://server.ccl.net/chemistry/announcements/conferences/>>> >>> >>> >> >> >> -- >> PD. Dr. Andreas Klamt >> CEO / Gesch=E4ftsf=FChrer >> COSMOlogic GmbH & Co. KG >> Burscheider Strasse 515 >> D-51381 Leverkusen, Germany >> >> phone +49-2171-731681 >> fax +49-2171-731689 >> e-mail klamt(_)cosmologic.de >> >> web www.cosmologic.de >> >> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt >> Komplementaer: COSMOlogic Verwaltungs GmbH >> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt >> >> CHEMISTRY(~)ccl.net or use:E-mail to administrators= : >> CHEMISTRY-REQUEST(~)ccl.net or usehttp://www.ccl.net/chemis= try/sub_unsub.shtmlBefore = posting, check wait time at: >> http://www.ccl.netConferences: >> http://server.ccl.net/chemistry/announcements/conferences/ Search >> Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlRTFI: >> http://www.ccl.net/chemistry/aboutccl/instructions/ >> > > > > -- > PD. Dr. Andreas Klamt > CEO / Gesch=E4ftsf=FChrer > COSMOlogic GmbH & Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt:cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt > > -=3D This is automatically added to each message by the mailing script = =3D- To > recover the email address of the author of the message, please change the > strange characters on the top line to the ++ sign. You can also look up th= e > X-Original-From: line in the mail header. E-mail to subscribers: > CHEMISTRY++ccl.net or use:= E-mail to administrators: > CHEMISTRY-REQUEST++ccl.net or useBefore posting, check wait > time at: http://www.ccl.netConferences: > http://server.ccl.net/chemistry/announcements/conferences/ Search > Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail > bounces from CCL with 5.7.1 error, check:= RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > --001636c5b6a5f63423049a0f219c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thus, the two major tautomers of pioglitazone are as shown in the attached = figure?

Also, is there a published article, or other evidence that w= ould confirm that this is indeed the correct tautomeric distribution at pH = 7?

Thanks you,
Nancy



On Mon, = Jan 17, 2011 at 6:17 AM, Andreas Klamt klamt#cosmologic.de <owner-chemistry++ccl.net> wrote:
Sent to CCL by: Andreas Klamt [klamt-x-cosmologic.de] =20 =20 =20
I was just pointed by Leif N=F8rskov-Lauritsen to a stupid error which I made in my first entry on this topic. I wrote that at pH=3D7 25% would be deprotonated, 75% neutral. That was obviously wrong. It is the other way round: 72% is ionic, 25% neutral. The total amount of zwitterions is then ~3%.

Sorry for my mistake. But the basic message about the most stable neutral form stays valid.
The most stable anionic form is the di-keto anion.
=

Andreas

Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com:
Using quantum chemical calculations, you foun= d that the diketone form is dominant; does this mean that the enol form predicted by MarvinSketch v3.5.4 in the published article is wrong?

"Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb 1;20(3):819-23

Thanks,
Nancy


On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt klamt(a)co= smologic.de <owner-chemistry(~)ccl.net> wrote:
Sent to CCL by: Andreas Klamt [klamt,cosmologic.de]
Hi Nancy,

as I wrote in the previous message, we find by quantum chemical calculations within the COSMO-RS solvation that the diketone form is more stable by abot 12 kcal/mol, that means it absolutely dominates!

Andreas

Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com:
Hi All,

I happened to find a published article where molecular docking simulations of TZDs against a novel protein is detailed:

"Structure-based design of a thiazolidinedione which targets the mitochondrial protein mitoNEET" Bioorg M= ed Chem Lett. 2010 Feb 1;20(3):819-23

In this paper, the authors, using MarvinSketch v3.5.4, determined that the TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the diketone form (see attached figure).=A0 It appears that the article's tautomer prediction was based only on the p= H prior to docking, and had nothing to do with ligand-protein interactions.

Does anyone know if the diketone or enol, or perhaps a different tautomer, would be predominant at pH 7.4?

Thanks in advance.
Nancy



On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de <owner-chemistry(_)ccl.net> wrote:

Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de]
Hi All,

let me put my 5 cents into the game:
We have done quantum calculations for the heterocyclic ring, with just a methyl group, since electronically the remainder of the compound should have almost no influence on the heterocycle.
DFT/COSMO-RS calculations prove the neutral species
SMILES:CC1C(=3DO)[NH]C(=3DO)S1 of the Pioglitazone heterocycle to be favored by 11.3 kcal/mol compared to all other neutral species of the heterocycle, which means that there is no other relvant neutral form.

We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at pH=3D7 it should be deprotonated with about 25%.
Since the pka of the conj. acid of the pyridine ring according to COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10% in the zwitterionic form.

It will be hard to decide this finally, unless someone measures it, but we are quite confident to be qualitatively right here, because the energy differences for the tautomers should not have more than 5 kcal/mol erro, as we learned in in the SAMPL2 tautomer contest:
see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the predictions of tautomeric equilibria in solution based on the SAMPL2 challenge, http://www.springerlink.co= m/content/l577667th758n6h1/

Andreas







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"). The= refore, the predominant species
at pH 7.0 predicted by MarvinSketch is the one depicted in
"Figure_2.gif". The different tautomeri= c 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 <http://chemiome.chm.unipg.it>

<owner-chemistry[a]ccl.net <mailto:owner-chemistry[a]ccl.net>> wrote:


=A0 =A0Sent to CCL by: Gabriele Cruciani [gabri##= chemiome.chm.uni= pg.it
=A0 =A0<http://chemiome.chm.unipg.it>]

=A0 =A0Nancy,
=A0 =A0the first form you reported is the most stable in water at pH 7.0.
=A0 =A0However, the fact that one form is more stable than another in water
=A0 =A0does not help you to understand which form will be more 'relevant'
=A0 =A0for docking. In protein the tautomeric equilibria may produce and
=A0 =A0stabilize different forms according to the complementary site. There
=A0 =A0are examples of tautomeric form in protein not stable in water,
=A0 =A0where the energy difference is more than 5 Kcal/mol.

=A0 =A0MoKa software (www.moldiscovery.com <http://www.moldiscovery.com>= ;)

=A0 =A0is fast and accurate to produce tautomer stable in water, but it can
=A0 =A0produce also all the (plausible) tautomeri= c forms.

=A0 =A0Then, a possibility is to dock them into your protein, to see if
=A0 =A0docking methods may differentiate their binding.

=A0 =A0Gabriele Cruciani




=A0 =A0 =A0 =A0Hi All,

=A0 =A0 =A0 =A0I am performing molecular docking = and molecular dynamics
=A0 =A0 =A0 =A0simulations of the
=A0 =A0 =A0 =A0thiazolidinedione pioglitazone bin= ding to the PPAR-gamma
=A0 =A0 =A0 =A0receptor protein
=A0 =A0 =A0 =A0(PDB ID: 1ZGY). The thiazolidinedi= one ring can exist in numerous
=A0 =A0 =A0 =A0different
=A0 =A0 =A0 =A0tautomeric states; I have attached= a figure depicting several of
=A0 =A0 =A0 =A0them.
=A0 =A0 =A0 =A0Which tautomer would be dominant a= t the physiological pH of ~7.0?

=A0 =A0 =A0 =A0Also, are there any software progr= ams that can predict which
=A0 =A0 =A0 =A0tautomer would
=A0 =A0 =A0 =A0be correct?

=A0 =A0 =A0 =A0Thanks in advance,
=A0 =A0 =A0 =A0Nancy>


=A0 =A0E-mail to subscribers: CHEMISTRY[a]ccl.net
=A0 =A0<mailto:CHEMISTRY[a]= ccl.net> or use:>
=A0 =A0E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net
=A0 =A0<mailto:CHEMISTRY-REQUEST[a]ccl.net> or useConferences:

--
Dr. Jens Reinisch
Chemist / Customer Support
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone =A0 +49-2171-363664
mobile =A0+49-163-7337310
fax =A0 =A0 +49-2171-731689
e-mail =A0reinisch[*]cosmologic.de
web =A0 =A0 www.cosmologic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt 



--=20
PD. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klam=
t(_)cosmologic.de

web    	www.cosmolog=
ic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt
CH= EMISTRY(~)ccl.net or use: http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST(~)ccl.net or use h= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/= sub_unsub.shtml Before posting, check wait time at: http://www.ccl.net Job: http:/= /www.ccl.net/jobs Conferences: http://server.ccl.net/chem= istry/announcements/conferences/ Search Messages: http://www.ccl.net/chemistry/searchccl/ind= ex.shtmlh= ttp://www.ccl.net/spammers.txt RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= /a> 



--=20
PD. Dr. Andreas Klamt
CEO / Gesch=E4ftsf=FChrer
COSMOlogic GmbH & Co. KG
Burscheider Strasse 515
D-51381 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt:cosm=
ologic.de
web    	www.cosmolog=
ic.de

HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt

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zd5+v382sMjB2FOOhstOP+R6KC1Hs7eHvetZt7yD5doZJ9dPkOuhtB7N3n7b31nXs53lAtIzkuvB tDWavd3trSga+FmSxYLSM5LroSQbzd5+91/+9Eibg48FpGck10NpbzR7u/fLyd7TJ9lzPodcD6aD 0eztjaC8W32Lx4PSM5LroXQ8mn1jJzhY2njQ55DroTgbzb71thCQnpFcD8bxaPYt+8Kg9Izkeiiu RrNv2iSC0jOS66G4Hc0+3iUGpWck14NJYTR7c8sISs9IrgeT2mj2gekZyfVwyH/NQK6HQx4QuR4O eUDkejjkAZHr4ZAHRK6HQx4QuR4OeUDkejjkAZHr4ZAHRK6HQx4QuR4OeUDkejjkAZHr4ZAHRK6H Qx4QuR4OeUDkejjkAZHr4ZAHRK6HQx4QuR4OeUDkejjkAZHr4ZAHRK6HQx4QuR4OeUDkejjkAZHr 4ZAHRK6HQx4QuR4OeUDkejjkAZHr4ZAHRK6HQx4QuR4OeUDkejjkAZHrhYSEhISEhISEhISEhISE hISEhISEhISEhISEfK75f4JPbl6E9ByBAAAAAElFTkSuQmCC --001636c5b6a5f6342a049a0f219e-- From owner-chemistry@ccl.net Mon Jan 17 14:23:00 2011 From: "Tapas Kar tapas.kar|*|usu.edu" To: CCL Subject: CCL: Energy decomposition programs, such as SAPT Message-Id: <-43664-110117135326-30845-ZdRZW+5ALqi1taBpviT/TQ-,-server.ccl.net> X-Original-From: "Tapas Kar" Date: Mon, 17 Jan 2011 13:53:24 -0500 Sent to CCL by: "Tapas Kar" [tapas.kar[#]usu.edu] Hello, Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or are there others? Also any other Energy decomposition method, besides SAPT (Symmetry-adapted perturbation theory) and Morokuma Energy decomposition method (implemented in GAMESS-US), are developed? Thanks Tapas From owner-chemistry@ccl.net Mon Jan 17 14:58:00 2011 From: "Mehdi Esrafili m_esrafili/a\yahoo.com" To: CCL Subject: CCL: Energy decomposition programs, such as SAPT Message-Id: <-43665-110117143412-22787-8jiVtsqljuZtRc5Gs2Jbrw~~server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="0-813316099-1295292831=:62907" Date: Mon, 17 Jan 2011 11:33:51 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili-#-yahoo.com] --0-813316099-1295292831=:62907 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Tapas; You can use SAPT2008 program (www.physics.udel.edu/~szalewic/SAPT/manual.ht= ml). This program is free of charge.=A0Although there are some differences = between the results of MOLPRO and SAPT2008, but I prefer the former one, be= cause it is more user-friendly. Cheers Mehdi =A0 ---------------------------------------------------------------------------= ---------------------------------------------------=A0=A0 `The man who makes no mistakes does not usually make anything.' =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0 Edward John Phelps (1822-1900) ---------------------------------------------------------------------------= ---------------------------------------------------=20 Mehdi D. Esrafili Assistant Professor of Physical Chemistry=A0 Current address:=A0Department of Chemistry,=20 Faculty of Basic Sciences,University of Margheh, Iran.=20 E-mail 1: m_esrafili:_:yahoo.com=20 E-mail 2: esrafili:_:maragheh.ac.ir ---------------------------------------------------------------------------= ---------------------------------------------------=20 --- On Mon, 1/17/11, Tapas Kar tapas.kar|*|usu.edu wrote: > From: Tapas Kar tapas.kar|*|usu.edu Subject: CCL: Energy decomposition programs, such as SAPT To: "Esrafili, Mehdi D " Date: Monday, January 17, 2011, 10:53 AM Sent to CCL by: "Tapas=A0 Kar" [tapas.kar[#]usu.edu] Hello, Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or are there= others? Also any other Energy decomposition method, besides SAPT (Symmetry-adapted = perturbation theory) and Morokuma Energy decomposition method (implemented = in GAMESS-US), are developed?=A0=20 Thanks=20 Tapas -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-813316099-1295292831=:62907 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Tapas;
You can use SAPT2008 program (www.= physics.udel.edu/~szalewic/SAPT/manual.html). This= program is free of charge. Although there are some differences betwee= n the results of MOLPRO and SAPT2008, but I prefer the former one, because = it is more user-friendly.
Cheers
Mehdi

 
----------------------------------------------------------------------= --------------------------------------------------------  
`The man who makes no mist= akes does not usually make anything.'
    &n= bsp;            = ;            &n= bsp;    Edward John Phelps (1822-1900)
----------------------------------------------------------------------= --------------------------------------------------------
Mehdi D. Esrafili
Assistant Professor of Phy= sical Chemistry 
Current address: Department of Chemistry,
Faculty of Basic Sciences,= University of
Margheh, Iran.
E-mail 1: m_esrafili:_:yahoo.com
E-mail 2: esrafili:_:maragheh.ac.ir
--------------------------= ---------------------------------------------------------------------------= -------------------------


--- On Mon, 1/17/11, Tapa= s Kar tapas.kar|*|usu.edu <owner-chemistry:_:ccl.net> wrote:=

From: Tapas Kar tapas.kar|*|usu.edu <owner-che= mistry:_:ccl.net>
Subject: CCL: Energy decomposition programs, such as = SAPT
To: "Esrafili, Mehdi D " <m_esrafili:_:yahoo.com>
Da= te: Monday, January 17, 2011, 10:53 AM


Sent to CCL by: "Tapas  Kar" [tapas.kar[#]u= su.edu]
Hello,

Is MOLPRO the standard QM program that runs SAPT a= nd SAPT-DFT, or are there others?

Also any other Energy decompositio= n method, besides SAPT (Symmetry-adapted perturbation theory) and Morokuma = Energy decomposition method (implemented in GAMESS-US), are developed? = ;

Thanks
Tapas



-=3D This is automatically added = to each message by the mailing script =3D-
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=0A=0A = --0-813316099-1295292831=:62907-- From owner-chemistry@ccl.net Mon Jan 17 15:33:00 2011 From: "Sergio Emanuel Galembeck segalemb\a/usp.br" To: CCL Subject: CCL: Energy decomposition programs, such as SAPT Message-Id: <-43666-110117151233-27733-ToW7aZkBYRBO6a+hZLMqdQ[]server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Mon, 17 Jan 2011 18:12:17 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb/./usp.br] Dear Tapas, A free of charge SAPT could be obtained in http://www.physics.udel.edu/~szalewic/SAPT/SAPT.html Best regards, Sergio Citando "Tapas Kar tapas.kar|*|usu.edu" : > > Sent to CCL by: "Tapas Kar" [tapas.kar[#]usu.edu] > Hello, > > Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or > are there others? > > Also any other Energy decomposition method, besides SAPT > (Symmetry-adapted perturbation theory) and Morokuma Energy > decomposition method (implemented in GAMESS-US), are developed? > > Thanks > Tapas> > > From owner-chemistry@ccl.net Mon Jan 17 16:08:00 2011 From: "Sriteja Mantha sritejamantha|gmail.com" To: CCL Subject: CCL: Adding missing residues structural data to protein structure file Message-Id: <-43667-110117144208-29525-gA2g4uNoqkx/4DzF8I6arw-,-server.ccl.net> X-Original-From: "Sriteja Mantha" Date: Mon, 17 Jan 2011 14:42:07 -0500 Sent to CCL by: "Sriteja Mantha" [sritejamantha:_:gmail.com] Hi, I am working on a protein structure. I found out that in the pdb file of the corresponding protein, structural data for few of the amino acid residues are not available. I will be thankful to you if someone can suggest me with a software technique/program to add missing residues looking forward for a reply Sriteja Mantha From owner-chemistry@ccl.net Mon Jan 17 16:43:00 2011 From: "Radoslaw Kaminski rkaminski.rk%a%gmail.com" To: CCL Subject: CCL:G: Energy decomposition programs, such as SAPT Message-Id: <-43668-110117162209-29761-hoo+YMTr4CCyMHPK2FDiag-#-server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=0016360e3d306c9c9a049a115f7d Date: Mon, 17 Jan 2011 22:21:52 +0100 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk-.-gmail.com] --0016360e3d306c9c9a049a115f7d Content-Type: text/plain; charset=ISO-8859-1 Hi, As far as I know you can run SAPT with any QM program that performs GTO integrals. You can use GAUSSIAN, GAMESS or DALTON without any problems. For more information try to contact guys from Delawere (USA) or Warsaw (Poland), they will know the best. Radek 2011/1/17 Tapas Kar tapas.kar|*|usu.edu > > Sent to CCL by: "Tapas Kar" [tapas.kar[#]usu.edu] > Hello, > > Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or are there > others? > > Also any other Energy decomposition method, besides SAPT (Symmetry-adapted > perturbation theory) and Morokuma Energy decomposition method (implemented > in GAMESS-US), are developed? > > Thanks > Tapas> > > -- Radoslaw Kaminski, M.Sc. Eng. Ph.D. Student Crystallochemistry Laboratory Department of Chemistry University of Warsaw Pasteura 1, 02-093 Warszawa, Poland http://www.chem.uw.edu.pl/people/RKaminski/ --0016360e3d306c9c9a049a115f7d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

As far as I know you can run SAPT with any QM program that perfo= rms GTO integrals. You can use GAUSSIAN, GAMESS or DALTON without any probl= ems. For more information try to contact guys from Delawere (USA) or Warsaw= (Poland), they will know the best.

Radek


2011/1/17 Tapas Kar tapas.k= ar|*|usu.edu <owner-chemistry[-]ccl.net><= br>

Sent to CCL by: "Tapas =A0Kar" [tapas.kar[#]usu.edu]
Hello,

Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or are there= others?

Also any other Energy decomposition method, besides SAPT (Symmetry-adapted = perturbation theory) and Morokuma Energy decomposition method (implemented = in GAMESS-US), are developed?

Thanks
Tapas



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--
Radoslaw Kaminski, M.Sc= . Eng.
Ph.D. Student
Crystallochemistry Laboratory
Department of C= hemistry
University of Warsaw
Pasteura 1, 02-093 Warszawa, Poland
h= ttp://www.chem.uw.edu.pl/people/RKaminski/
--0016360e3d306c9c9a049a115f7d-- From owner-chemistry@ccl.net Mon Jan 17 17:18:00 2011 From: "Gabriele Cruciani gabri- -chemiome.chm.unipg.it" To: CCL Subject: CCL: Pioglitazone Tautomers Message-Id: <-43669-110117161457-22980-R17FX30mhgMTYdONdglFaQ|a|server.ccl.net> X-Original-From: Gabriele Cruciani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Jan 2011 22:14:31 +0100 MIME-Version: 1.0 Sent to CCL by: Gabriele Cruciani [gabri|a|chemiome.chm.unipg.it] Nancy, you get the same answer from different people, with different background, using different methods, and you keep asking the same question. I think CCL list should be used 'with caution' especially after you get all the answers. What you summarized is not correct. The two forms are not tautomeric forms. They refer to ONE tautomeric form that is in equilibrium with two species, one protonated and one neutral. The percentages you reported refer to the solvent pH and to the specie pKa. Since the pKa of the pioglitazone is 6.3, the relative abundance at pH 7.4 is 85% for the charged and 15% for the neutral one. As told in previous mails, this has nothing to do with the docking into a protein, where the local environment, dielectric, 3D interactions may change the 'form' of the interacting ligand. In this specific case, you cannot say that the charge form may interact better because is more abundant, since the equilibrium between the two forms can be modified by the protein. Precise pKa calculations are very relevant for pharmacokinetic and metabolism studies, but for docking to receptors is better to produce the 'relevant' structures. Do not use too simple methods (like those you reported) since the problem is very complex and require good approaches. Often using the brain is better than using free available software. Gabriele Cruciani > Thus, the two major tautomers of pioglitazone are as shown in the attached > figure? > > Also, is there a published article, or other evidence that would confirm > that this is indeed the correct tautomeric distribution at pH 7? > > Thanks you, > Nancy > > > > On Mon, Jan 17, 2011 at 6:17 AM, Andreas Klamt klamt#cosmologic.de< > owner-chemistry/a\ccl.net> wrote: > >> Sent to CCL by: Andreas Klamt [klamt-x-cosmologic.de] >> I was just pointed by Leif Nørskov-Lauritsen to a stupid error which I made >> in my first entry on this topic. I wrote that at pH=7 25% would be >> deprotonated, 75% neutral. That was obviously wrong. It is the other way >> round: 72% is ionic, 25% neutral. The total amount of zwitterions is then >> ~3%. >> >> Sorry for my mistake. But the basic message about the most stable neutral >> form stays valid. >> The most stable anionic form is the di-keto anion. >> >> Andreas >> >> Am 16.01.2011 19:29, schrieb Nancy nancy5villa**gmail.com: >> >> Using quantum chemical calculations, you found that the diketone form is >> dominant; does this mean that the enol form predicted by MarvinSketch v3.5.4 >> in the published article is wrong? >> >> "Structure-based design of a thiazolidinedione which targets the >> mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb >> 1;20(3):819-23 >> >> Thanks, >> Nancy >> >> >> On Thu, Jan 13, 2011 at 10:31 PM, Andreas Klamt klamt(a)cosmologic.de< >> owner-chemistry(~)ccl.net> wrote: >> >>> Sent to CCL by: Andreas Klamt [klamt,cosmologic.de] >>> Hi Nancy, >>> >>> as I wrote in the previous message, we find by quantum chemical >>> calculations within the COSMO-RS solvation that the diketone form is more >>> stable by abot 12 kcal/mol, that means it absolutely dominates! >>> >>> Andreas >>> >>> Am 13.01.2011 22:25, schrieb Nancy nancy5villa~!~gmail.com: >>> >>> Hi All, >>> >>> I happened to find a published article where molecular docking simulations >>> of TZDs against a novel protein is detailed: >>> >>> "Structure-based design of a thiazolidinedione which targets the >>> mitochondrial protein mitoNEET" Bioorg Med Chem Lett. 2010 Feb >>> 1;20(3):819-23 >>> >>> In this paper, the authors, using MarvinSketch v3.5.4, determined that the >>> TZDs would exist predominantly in the enol form at pH 7.4, as opposed to the >>> diketone form (see attached figure). It appears that the article's tautomer >>> prediction was based only on the pH prior to docking, and had nothing to do >>> with ligand-protein interactions. >>> >>> Does anyone know if the diketone or enol, or perhaps a different tautomer, >>> would be predominant at pH 7.4? >>> >>> Thanks in advance. >>> Nancy >>> >>> >>> >>> On Wed, Jan 12, 2011 at 9:53 AM, Andreas Klamt klamt-*-cosmologic.de< >>> owner-chemistry(_)ccl.net> wrote: >>> >>>> >>>> Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de] >>>> Hi All, >>>> >>>> let me put my 5 cents into the game: >>>> We have done quantum calculations for the heterocyclic ring, with just a >>>> methyl group, since electronically the remainder of the compound should have >>>> almost no influence on the heterocycle. >>>> DFT/COSMO-RS calculations prove the neutral species >>>> SMILES:CC1C(=O)[NH]C(=O)S1 of the Pioglitazone heterocycle to be favored >>>> by 11.3 kcal/mol compared to all other neutral species of the heterocycle, >>>> which means that there is no other relvant neutral form. >>>> >>>> We find with COSMOtherm that the pka of the heterocycle is 6.55, i.e. at >>>> pH=7 it should be deprotonated with about 25%. >>>> Since the pka of the conj. acid of the pyridine ring according to >>>> COSMOtherm (we calculated diethylpyridine) is ~5.6 there should be ~10% in >>>> the zwitterionic form. >>>> >>>> It will be hard to decide this finally, unless someone measures it, but >>>> we are quite confident to be qualitatively right here, because the energy >>>> differences for the tautomers should not have more than 5 kcal/mol erro, as >>>> we learned in in the SAMPL2 tautomer contest: >>>> see Andreas Klamt and Michael Diedenhofen, Some conclusions regarding the >>>> predictions of tautomeric equilibria in solution based on the SAMPL2 >>>> challenge, http://www.springerlink.com/content/l577667th758n6h1/ >>>> >>>> Andreas >>>> >>>> >>>> >>>> >>>> >>>> >>>>> >>>>> 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, >>>>> Nancy> >>>>> >>>>> >>>>> E-mail to subscribers: CHEMISTRY[a]ccl.net >>>>> or use:> >>>>> E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net >>>>> or useConferences: >>>>> >>>>> http://server.ccl.net/chemistry/announcements/conferences/> >>>>> >>>>> >>>>> >>>>> >>>> -- >>>> Dr. Jens Reinisch >>>> Chemist / Customer Support >>>> COSMOlogic GmbH& Co. KG >>>> Burscheider Strasse 515 >>>> D-51381 Leverkusen, Germany >>>> >>>> phone +49-2171-363664 >>>> mobile +49-163-7337310 >>>> fax +49-2171-731689 >>>> e-mail reinisch[*]cosmologic.de >>>> web www.cosmologic.de >>>> >>>> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt >>>> Komplementaer: COSMOlogic Verwaltungs GmbH >>>> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt >>>> >>>> >>>> >>>> >>>> >>>> >>>> E-mail to subscribers: CHEMISTRY(_)ccl.net or >>>> use:>>> >>>> E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.netor useConferences: >>>> http://server.ccl.net/chemistry/announcements/conferences/>>> >>>> >>>> >>> >>> >>> -- >>> PD. Dr. Andreas Klamt >>> CEO / Geschäftsführer >>> COSMOlogic GmbH& Co. KG >>> Burscheider Strasse 515 >>> D-51381 Leverkusen, Germany >>> >>> phone +49-2171-731681 >>> fax +49-2171-731689 >>> e-mail klamt(_)cosmologic.de >>> >>> web www.cosmologic.de >>> >>> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt >>> Komplementaer: COSMOlogic Verwaltungs GmbH >>> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt >>> >>> CHEMISTRY(~)ccl.net or use:E-mail to administrators: >>> CHEMISTRY-REQUEST(~)ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlBefore posting, check wait time at: >>> http://www.ccl.netConferences: >>> http://server.ccl.net/chemistry/announcements/conferences/ Search >>> Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlRTFI: >>> http://www.ccl.net/chemistry/aboutccl/instructions/ >>> >> >> >> >> -- >> PD. Dr. Andreas Klamt >> CEO / Geschäftsführer >> COSMOlogic GmbH& Co. KG >> Burscheider Strasse 515 >> D-51381 Leverkusen, Germany >> >> phone +49-2171-731681 >> fax +49-2171-731689 >> e-mail klamt:cosmologic.de >> web www.cosmologic.de >> >> HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt >> Komplementaer: COSMOlogic Verwaltungs GmbH >> HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas KlamtTo >> recover the email address of the author of the message, please change the >> strange characters on the top line to the /a\ sign. You can also look up the >> X-Original-From: line in the mail header. E-mail to subscribers: >> CHEMISTRY/a\ccl.net or use:E-mail to administrators: >> CHEMISTRY-REQUEST/a\ccl.net or useBefore posting, check wait >> time at: http://www.ccl.netConferences: >> http://server.ccl.net/chemistry/announcements/conferences/ Search >> Messages: http://www.ccl.net/chemistry/searchccl/index.shtml If your mail >> bounces from CCL with 5.7.1 error, check:RTFI: >> http://www.ccl.net/chemistry/aboutccl/instructions/ >> > From owner-chemistry@ccl.net Mon Jan 17 17:53:00 2011 From: "Victor Rosas Garcia rosas.victor(!)gmail.com" To: CCL Subject: CCL: Energy decomposition programs, such as SAPT Message-Id: <-43670-110117171607-3616-lojTyWBmB8MISMWxaLh6Ug-x-server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174bf23e531601049a12201e Date: Mon, 17 Jan 2011 16:15:49 -0600 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor|*|gmail.com] --0015174bf23e531601049a12201e Content-Type: text/plain; charset=ISO-8859-1 There is Natural Energy Decomposition Analysis, in NBO 5.0. Not free but very cheap. Victor 2011/1/17 Tapas Kar tapas.kar|*|usu.edu > > Sent to CCL by: "Tapas Kar" [tapas.kar[#]usu.edu] > Hello, > > Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or are there > others? > > Also any other Energy decomposition method, besides SAPT (Symmetry-adapted > perturbation theory) and Morokuma Energy decomposition method (implemented > in GAMESS-US), are developed? > > Thanks > Tapas> > > --0015174bf23e531601049a12201e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable There is Natural Energy Decomposition Analysis, in NBO 5.0.=A0 Not free but= very cheap.

Victor

2011/1/17 Tapa= s Kar tapas.kar|*|usu.edu = <owner-chemistry[A]ccl.net&= gt;

Sent to CCL by: "Tapas =A0Kar" [tapas.kar[#]usu.edu]
Hello,

Is MOLPRO the standard QM program that runs SAPT and SAPT-DFT, or are there= others?

Also any other Energy decomposition method, besides SAPT (Symmetry-adapted = perturbation theory) and Morokuma Energy decomposition method (implemented = in GAMESS-US), are developed?

Thanks
Tapas



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--0015174bf23e531601049a12201e-- From owner-chemistry@ccl.net Mon Jan 17 18:28:01 2011 From: "Shahar Keinan skeinan+*+gmail.com" To: CCL Subject: CCL: Adding missing residues structural data to protein structure file Message-Id: <-43671-110117174017-29200-cIJXanajna8XTEPZRTYTjQ!^!server.ccl.net> X-Original-From: Shahar Keinan Content-Type: multipart/alternative; boundary=0016e68b68b2d9ee05049a1275e2 Date: Mon, 17 Jan 2011 17:39:44 -0500 MIME-Version: 1.0 Sent to CCL by: Shahar Keinan [skeinan#gmail.com] --0016e68b68b2d9ee05049a1275e2 Content-Type: text/plain; charset=ISO-8859-1 Try WhatIF: http://swift.cmbi.ru.nl/servers/html/index.html The "Build/check/repair model"can repair PDB model. * * *Shahar * On Mon, Jan 17, 2011 at 2:42 PM, Sriteja Mantha sritejamantha|gmail.com < owner-chemistry\a/ccl.net> wrote: > > Sent to CCL by: "Sriteja Mantha" [sritejamantha:_:gmail.com] > Hi, > > I am working on a protein structure. I found out that in the pdb file of > the > corresponding protein, structural data for few of the amino acid residues > are > not available. > I will be thankful to you if someone can suggest me with a software > technique/program to add missing residues > > looking forward for a reply > Sriteja Mantha> > > -- ------------------------------------------------------ Shahar Keinan (919) 357 5319 --0016e68b68b2d9ee05049a1275e2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Try WhatIF:

The "Build/check/repair model"can r= epair PDB model.

=
Shahar

On Mon, Jan 17, 20= 11 at 2:42 PM, Sriteja Mantha sritejamantha|gm= ail.com <owner-chemistry\a/ccl.net> wrote:

Sent to CCL by: "Sriteja =A0Mantha" [sritejamantha:_:gmail.com]
Hi,

I am working on a protein structure. I found out that in the pdb file of th= e
corresponding protein, structural data for few of the amino acid residues a= re
not available.
I will be thankful to you if someone can suggest me with a software
technique/program to add missing residues

looking forward for a reply
Sriteja Mantha



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--
-----------------------= -------------------------------
Shahar Keinan
(919) 357 5319
--0016e68b68b2d9ee05049a1275e2-- From owner-chemistry@ccl.net Mon Jan 17 19:03:00 2011 From: "Vladimir Chupakhin chupvl a gmail.com" To: CCL Subject: CCL: Adding missing residues structural data to protein structure file Message-Id: <-43672-110117180928-25869-cR15Ew3vlUy1Ij69p0eJug ~~ server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 18 Jan 2011 00:08:35 +0100 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl*_*gmail.com] Hi, MODELLER from Sali lab can do this trick - http://salilab.org/modeller/wiki/Missing%20residues Regards, -- Vladimir Chupakhin, Postdoc at joint project between Chemoinformatics laboratory and Structural Chemogenomics group University of Strasbourg, Strasbourg, France On Mon, Jan 17, 2011 at 8:42 PM, Sriteja Mantha sritejamantha|gmail.com wrote: > > Sent to CCL by: "Sriteja  Mantha" [sritejamantha:_:gmail.com] > Hi, > > I am working on a protein structure. I found out that in the pdb file of the > corresponding protein, structural data for few of the amino acid residues are > not available. > I will be thankful to you if someone can suggest me with a software > technique/program to add missing residues > > looking forward for a reply > Sriteja Mantha>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Mon Jan 17 19:38:00 2011 From: "Daniele Gianni daniele.gianni,gmail.com" To: CCL Subject: CCL: COMETS 2011 - 2nd International Track on Collaborative Modeling and Simulation - Call for Papers Message-Id: <-43673-110117171106-31109-dlZC5trj9bUDp7oyYPRYmA/a\server.ccl.net> X-Original-From: Daniele Gianni Content-Type: multipart/alternative; boundary=0016e659f8fe61af89049a120ed2 Date: Mon, 17 Jan 2011 23:10:48 +0100 MIME-Version: 1.0 Sent to CCL by: Daniele Gianni [daniele.gianni ~~ gmail.com] --0016e659f8fe61af89049a120ed2 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Please accept our apologies if you receive multiple copies of this CfP) ################################################################# IEEE WETICE 2011 2nd International Track on Collaborative Modeling and Simulation CALL FOR PAPERS ################################################################# June 27 - June 29, 2011, Paris (France) http://www.sel.uniroma2.it/CoMetS11 ################################################################# # Papers Due: *** March 5, 2011 *** # Accepted papers will be published in the conference proceedings # by the IEEE Computer Society Press and indexed by EI. ################################################################# Modeling and Simulation (M&S) is increasingly becoming a central activity in the design of new systems and in the analysis of existing systems because it enables designers and researchers to investigate systems behavior through virtual representations. For this reason, M&S is gaining a primary role in many industrial and research fields, such as space, critical infrastructures, manufacturing, emergency management, biomedical systems and sustainable future. However, as the complexity of the investigated systems increases and the types of investigations widens, the cost of M&S activities increases for the more complex models and for the communications among a wider number and variety of M&S stakeholders (e.g., sub-domain experts, simulator users, simulator engineers, and final system users). To address the increasing costs of M&S activities, collaborative technologies must be introduced to support these activities by fostering the sharing and reuse of models, by facilitating the communications among M&S stakeholders, and more generally by integrating processes, tools and platforms. Aside from seeking applications of collaborative technologies to M&S activities, the track seeks innovative contributions that deal with the application of M&S practices to the design of collaborative environments. These environments are continuously becoming more complex and therefore their design requires systematic approaches to meet the required quality of collaboration. This is important for two reasons: to reduce rework activities on the actual collaborative environment, and to maximize the productivity and the quality of the process the collaborative environment supports. M&S offers the methodologies and tools for such investigations and therefore it can be used to improve the quality of collaborative environments. A non=96exhaustive list of topics of interest includes: * collaborative environments for M&S * collaborative Systems of Systems M&S * workflow modelling for collaborative environments and processes * agent-based M&S * collaborative distributed simulation * collaborative component-based M&S * net-centric M&S * web-based M&S * model sharing and reuse * model building and evaluation * modeling and simulation of business processes * modeling for collaboration * simulation-based performance evaluation of collaborative networks * model-driven simulation engineering * domain specific languages for the simulation of collaborative environment= s * domain specific languages for collaborative M&S * databases and repositories for M&S * distributed virtual environments * virtual research environment for M&S To stimulate creativity, however, the track maintains a wider scope and invites interested researchers to present contributions that offer original perspectives on collaboration and M&S. +++++++++++++++++++++++++++++++++++ On-Line Submissions and Publication +++++++++++++++++++++++++++++++++++ CoMetS'11 intends to bring together researchers and practitioners to discuss key issues, approaches, open problems, innovative applications and trends in the track research area. Papers should contain original contributions not published or submitted elsewhere. Papers up to six pages (including figures, tables and references) can be submitted. Papers should follow the IEEE format, which is single spaced, two columns, 10 pt Times/Roman font. All submissions should be electronic (in PDF) and will be peer-reviewed by at least three program committee members. Accepted full papers will be included in the proceedings and published by the IEEE Computer Society Press (IEEE approval pending). Please note that at least one author for each accepted paper should register to attend WETICE 2011 to have the paper published in the proceedings. Authors may contact the organizers for expression of interests and content appropriateness at any time. Papers can be submitted in PDF format at the submission site (https://www.easychair.org/conferences/?conf=3Dcomets2011), which is supported by the EasyChair conference management system. Please contact the track chairs (comets2011-#-easychair.org) if you experience problems with the EasyChair Web site. +++++++++++++++ Important Dates +++++++++++++++ * Submission Deadline: March 5, 2011 * Decision to paper authors: April 4, 2011 * Final version of accepted papers due to IEEE: April 29, 2011 * Conference dates: June 27 - June 29, 2011 ++++++++++++++++++++ Organizing Committee ++++++++++++++++++++ * Andrea D'Ambrogio, University of Roma TorVergata, Italy * Daniele Gianni, European Space Agency, The Netherlands * Joachim Fuchs, European Space Agency, The Netherlands * Giuseppe Iazeolla, University of Roma TorVergata, Italy +++++++++++++++++ Program Committee +++++++++++++++++ * Santiago Balestrini, Georgia Institute of Technology, USA * Torsten Bieler, European Space Agency, The Netherlands * Olivier Dalle, University of Nice Sophia Antipolis, CNRS & INRIA, France * Joseph Giampapa, SEI, Carnegie Mellon University, USA * Ralph Huntsinger, Beijng University of Aeronautics and Astronautics, China and California State University, USA * Axel Lehmann, Universitaet der Bundeswehr Muenchen, Germany * Cristiano Leorato, Rhea, The Netherlands * Brian Lewis, Vanguard Software Corporation, USA * Steve McKeever, University of Oxford, UK * David Nickerson, Auckland Bioengineering Institute, NZ * Alfred Park, IBM T.J. Watson Research Center, USA * Wolfgang Prinz, Fraunhofer FIT and RWTH Aachen, Germany * Jos=E9 L. Risco-Martin, Universidad Complutense de Madrid, Spain * Maarten Sierhuis, NASA and Palo Alto Research Center, USA * Hans Vangheluwe, University of Antwerp, Belgium, and McGill University, Canada * Gabriel Wainer, Carleton University, Canada * Quirien Wijnands, European Space Agency, The Netherlands * Heming Zhang, Tsinghua University, China *** Contact Information *** Daniele Gianni (track co-chair) Email: daniele.gianni-#-esa.int --0016e659f8fe61af89049a120ed2 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Please accept our apologies if you receive multiple copies of this CfP= )

################################################= #################=A0
=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 IEEE WETI= CE 2011=A0
=A0=A0 =A0 =A0 =A0 =A0 =A02nd International Track on=A0
=A0=A0 = =A0 =A0 Collaborative Modeling and Simulation=A0
=A0=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 CALL FOR PAPERS=A0
##########################= #######################################=A0

June 27 - June 29, 2011, Paris (France)

#######################################= ##########################=A0
# Papers Due: *** March 5, 2011 ***=A0
# Accepted papers wil= l be published in the conference proceedings=A0
# by the IEEE Com= puter Society Press and indexed by EI.=A0
#######################= ##########################################=A0

Modeling and Simulation (M&S) is increasingly becom= ing a central=A0
activity in the design of new systems and in the= analysis of=A0
existing systems because it enables designers and= researchers to=A0
investigate systems behavior through virtual representations. For=A0
this reason, M&S is gaining a primary role in many industrial = and=A0
research fields, such as space, critical infrastructures,= =A0
manufacturing, emergency management, biomedical systems and=A0
sustainable future. However, as the complexity of the=A0
inves= tigated systems increases and the types of investigations=A0
wide= ns, the cost of M&S activities increases for the more=A0
complex models and for the communications among a wider number and=A0<= /div>
variety of M&S stakeholders (e.g., sub-domain experts, simula= tor=A0
users, simulator engineers, and final system users). To ad= dress=A0
the increasing costs of M&S activities, collaborative=A0
technologies must be introduced to support these activities by=A0
fostering the sharing and reuse of models, by facilitating the=A0 communications among M&S stakeholders, and more generally by=A0integrating processes, tools and platforms.=A0

= Aside from seeking applications of collaborative technologies to=A0
M&S activities, the track seeks innovative contributions that=A0<= div>deal with the application of M&S practices to the design of=A0
collaborative environments. These environments are continuously=A0
becoming more complex and therefore their design requires=A0
systematic approaches to meet the required quality of=A0
collabo= ration. This is important for two reasons: to reduce=A0
rework ac= tivities on the actual collaborative environment, and to=A0
maximize the productivity and the quality of the process the=A0
<= div>collaborative environment supports. M&S offers the methodologies=A0=
and tools for such investigations and therefore it can be used t= o=A0
improve the quality of collaborative environments.=A0

A non=96exhaustive list of topics of interest includes:
=
* collaborative environments for M&S
* collabo= rative Systems of Systems M&S
* workflow modelling for collaborative environments and processes
* agent-based M&S
* collaborative distributed simulatio= n
* collaborative component-based M&S
* net-centric= M&S
* web-based M&S
* model sharing and reuse
* mo= del building and evaluation
* modeling and simulation of business= processes
* modeling for collaboration
* simulation-ba= sed performance evaluation of collaborative networks
* model-driven simulation engineering
* domain specific lang= uages for the simulation of collaborative environments
* domain s= pecific languages for collaborative M&S
* databases and repos= itories for M&S
* distributed virtual environments
* virtual research enviro= nment for M&S

To stimulate creativity, however= , the track maintains a wider=A0
scope and invites interested res= earchers to present contributions=A0
that offer original perspectives on collaboration and M&S.=A0

+++++++++++++++++++++++++++++++++++=A0
On-Li= ne Submissions and Publication=A0
+++++++++++++++++++++++++++++++= ++++=A0

CoMetS'11 intends to bring together researchers and= practitioners=A0
to discuss key issues, approaches, open problem= s, innovative=A0
applications and trends in the track research ar= ea.=A0

Papers should contain original contributions not publis= hed or=A0
submitted elsewhere. Papers up to six pages (including = figures,=A0
tables and references) can be submitted. Papers shoul= d follow the=A0
IEEE format, which is single spaced, two columns, 10 pt=A0
T= imes/Roman font. All submissions should be electronic (in PDF)=A0
and will be peer-reviewed by at least three program committee=A0
members.=A0

Accepted full papers will be included in the proceeding= s and
=A0published by the IEEE Computer Society Press (IEEE=A0
approval pending). Please note that at least one author for each=A0=
accepted paper should register to attend WETICE 2011 to have the=A0
paper published in the proceedings.=A0

Aut= hors may contact the organizers for expression of interests=A0
an= d content appropriateness at any time. Papers can be submitted=A0
in PDF format at the submission site=A0
supported by th= e EasyChair conference management system. Please=A0
contact the track chairs (= comets2011-#-easychair.org) if you=A0
experience problems with = the EasyChair Web site.=A0

+++++++++++++++=A0
Important Dates=A0
+++++++++++++++=A0

* = Submission Deadline: March 5, 2011=A0
* Decision to paper authors= : April 4, 2011=A0
* Final version of accepted papers due to IEEE= : April 29, 2011=A0
* Conference dates: June 27 - June 29, 2011=A0


++++++++++++++++++++=A0
Organizing Committee=A0<= /div>
++++++++++++++++++++=A0

* Andrea D'A= mbrogio, University of Roma TorVergata, Italy=A0
* Daniele Gianni, European Space Agency, The Netherlands=A0
= * Joachim Fuchs, European Space Agency, The Netherlands=A0
* Gius= eppe Iazeolla, University of Roma TorVergata, Italy=A0

=
+++++++++++++++++=A0
Program Committee=A0
+++++++++++++= ++++=A0

* Santiago Balestrini, Georgia Institute o= f Technology, USA
* Torsten Bieler, European Space Agency, The Ne= therlands
* Olivier Dalle, University of Nice Sophia Antipolis, CNRS & INRIA= , France
* Joseph Giampapa, SEI, Carnegie Mellon University, USA<= /div>
* Ralph Huntsinger, Beijng University of Aeronautics and Astronau= tics, China=A0
and = California State University, USA
* Axel Lehmann, Universitaet der= Bundeswehr Muenchen, Germany
* Cristiano Leorato, Rhea, The Neth= erlands
* Brian Lewis, Vanguard Software Corporation, USA
* Steve Mc= Keever, University of Oxford, UK
* David Nickerson, Auckland Bioe= ngineering Institute, NZ
* Alfred Park, IBM T.J. Watson Research = Center, USA
* Wolfgang Prinz, Fraunhofer FIT and RWTH Aachen, Germany
* = Jos=E9 L. Risco-Martin, Universidad Complutense de Madrid, Spain
= * Maarten Sierhuis, NASA and Palo Alto Research Center, USA
* Han= s Vangheluwe, University of Antwerp, Belgium, and McGill University, Canada=
* Gabriel Wainer, Carleton University, Canada
* Quirien Wijn= ands, European Space Agency, The Netherlands
* Heming Zhang, Tsin= ghua University, China

*** Contact Information ***= =A0
Daniele Gianni (track co-chair)=A0
--0016e659f8fe61af89049a120ed2-- From owner-chemistry@ccl.net Mon Jan 17 20:13:00 2011 From: "Francisco Hernandez-Guzman Francisco.Hernandez a accelrys.com" To: CCL Subject: CCL: Adding missing residues structural data to protein structure file Message-Id: <-43674-110117191725-5589-vDRx32rTofxfz+xZIS8+lQ . server.ccl.net> X-Original-From: Francisco Hernandez-Guzman Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 17 Jan 2011 16:16:58 -0800 MIME-Version: 1.0 Sent to CCL by: Francisco Hernandez-Guzman [Francisco.Hernandez=accelrys.com] Hi Sriteja, You can also try using the free Discovery Studio Visualizer from Accelrys. The new 3.0 version comes with new molecular builders amongst other features. http://accelrys.com/products/discovery-studio/visualization-download.php There is also a community site to assist you in case you need help: https://community.accelrys.com/index.jspa Cheers, Francisco Product Manager Accelrys San Diego, CA -----Original Message----- > From: owner-chemistry+francisco.hernandez==accelrys.com{:}ccl.net [mailto:owner-chemistry+francisco.hernandez==accelrys.com{:}ccl.net] On Behalf Of Sriteja Mantha sritejamantha|gmail.com Sent: Monday, January 17, 2011 11:42 AM To: Francisco Hernandez-Guzman Subject: CCL: Adding missing residues structural data to protein structure file Sent to CCL by: "Sriteja Mantha" [sritejamantha:_:gmail.com] Hi, I am working on a protein structure. I found out that in the pdb file of the corresponding protein, structural data for few of the amino acid residues are not available. I will be thankful to you if someone can suggest me with a software technique/program to add missing residues looking forward for a reply Sriteja Manthahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jan 17 20:48:01 2011 From: "Youzhao Lan lyzhao(0)zjnu.cn" To: CCL Subject: CCL: Looking for a source code for calculating Rys Roots and Weights Message-Id: <-43675-110117194842-13609-76LhEpaB9XqRzp7YFwl1Gw/a\server.ccl.net> X-Original-From: "Youzhao Lan" Date: Mon, 17 Jan 2011 19:48:40 -0500 Sent to CCL by: "Youzhao Lan" [lyzhao|a|zjnu.cn] Dear All, Is there a source code for calculating the roots and weights of Rys polynomial? Thanks for your help. Lan