From owner-chemistry@ccl.net Fri Aug 20 02:55:01 2010 From: "Sayan Mondal sayanmondal.ncbs{=}gmail.com" To: CCL Subject: CCL: Which Basis Set to use for compound containing Zn Message-Id: <-42568-100820021959-30232-malEkA3q5VwCf9KS/idkIw---server.ccl.net> X-Original-From: Sayan Mondal Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 20 Aug 2010 11:49:41 +0530 MIME-Version: 1.0 Sent to CCL by: Sayan Mondal [sayanmondal.ncbs-$-gmail.com] Hi all, Can anybody please tell me which pseudo potential and what density functional are the best suited for computing thermochemical properties of compounds having Zinc (Zn). Please tell me the reference paper too, if you know. thanks, Sayan -- Sayan Mondal Graduate Student Dr. Mrinalini Puranik's Lab National Centre for Biological Sciences, TIFR Bangalore - 560065 INDIA Ph: +91-080-2366 6161 Fax: +91-080-2363 6662 From owner-chemistry@ccl.net Fri Aug 20 04:49:00 2010 From: "Gerald Knizia knizia.:.theochem.uni-stuttgart.de" To: CCL Subject: CCL: Which Basis Set to use for compound containing Zn Message-Id: <-42569-100820044628-31402-ydE9fsujSd52x5eWAw+jrw-x-server.ccl.net> X-Original-From: Gerald Knizia Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 20 Aug 2010 10:46:20 +0200 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia(_)theochem.uni-stuttgart.de] On Friday 20 August 2010 08:19, Sayan Mondal wrote: > Can anybody please tell me which pseudo potential and what density > functional are the best suited for computing thermochemical properties > of compounds having Zinc (Zn). The best pseudopotential would be ECP10MDF (D. Figgen, G. Rauhut, M. Dolg, H. Stoll, Chem. Phys. 311, 227 (2005).) and the best basis set the corresponding VnZ-PP/AVnZ-PP family (K.A. Peterson, C. Puzzarini, Theor. Chem. Acc. 114, 283 (2005).) -- Gerald Knizia From owner-chemistry@ccl.net Fri Aug 20 07:30:00 2010 From: "Sayed Mesa elsayed.elmes]=[yahoo.com" To: CCL Subject: CCL: T delta S or delta S Message-Id: <-42570-100820072849-27662-qA9v7MuNM4xnCzcTXoRekQ:_:server.ccl.net> X-Original-From: "Sayed Mesa" Date: Fri, 20 Aug 2010 07:28:48 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes() yahoo.com] Dear CCL community Might these questions be simple and silly but I would like to understand this confused issue at least for me. I observe that some papers used (T delta S) parameter and others used the (delta S) parameter for complexation reaction using QC methods. (i)I would like to know what the privilege of using TS instead (delta S)? (ii) And what are information could be drown from these parameters for a complexation reaction between transition metal ion and macrocycle ligand? (iii) Some papers calculate only deltaH and deltaG and do not care with (T delta S) or (delta S)? I do not know why? Thanks in advance, Sayed From owner-chemistry@ccl.net Fri Aug 20 08:40:01 2010 From: "john furr john.furr^^gmail.com" To: CCL Subject: CCL: T delta S or delta S Message-Id: <-42571-100820083938-24955-6l8OPyqulokhrBtE7fwGfg:server.ccl.net> X-Original-From: john furr Content-Type: multipart/alternative; boundary=00c09f93d5db37a03a048e4097d1 Date: Fri, 20 Aug 2010 08:39:32 -0400 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr+/-gmail.com] --00c09f93d5db37a03a048e4097d1 Content-Type: text/plain; charset=ISO-8859-1 T just stands for temperature. In the event the paper referenced only gives Delta S then you should probably assume they are working with standard conditions. http://en.wikipedia.org/wiki/Standard_conditions_for_temperature_and_pressure That would be my initial take on it. Bullet point number 2: Ultimately you are interested in the total free energy of binding (Delta G). However it's sometimes very useful to think in terms of entropic gains/losses (Delta S). Usually when I'm thinking about entropic contributions to binding I'm thinking about conformational freedom > from the receptor and the ligand. I find that in general you want the smallest most rigid molecule that will get the job done. Some targets require larger molecules (For example trying to disrupt protein protein interactions) while most seem to require smaller rule of 5 like compounds. Beyond that many other factors will come into play during the life cycle of a drug discovery program like bioavailability, toxicity, metabolism, etc. I'm sure others will chime in with other rules of thumb here as well. As for bullet point number there. Some papers are interested in the total free energy difference (Delta G). Some papers are interested in the enthalpic contributions (Delta H) and some groups are only interested in measuring entropic contributions (Delta S). It's really hard to say why one group chooses one over the other without reading the content of the paper. On Fri, Aug 20, 2010 at 7:28 AM, Sayed Mesa elsayed.elmes]=[yahoo.com < owner-chemistry(-)ccl.net> wrote: > > Sent to CCL by: "Sayed Mesa" [elsayed.elmes() yahoo.com] > Dear CCL community > > Might these questions be simple and silly but I would like to understand > this confused issue at least for me. I observe that some papers used (T > delta S) parameter and others used the (delta S) parameter for complexation > reaction using QC methods. > > (i)I would like to know what the privilege of using TS instead (delta S)? > (ii) And what are information could be drown from these parameters for a > complexation reaction between transition metal ion and macrocycle ligand? > (iii) Some papers calculate only deltaH and deltaG and do not care with (T > delta S) or (delta S)? I do not know why? > > Thanks in advance, > Sayed> > > --00c09f93d5db37a03a048e4097d1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable T just stands for temperature.=A0 In the event the paper referenced only gi= ves Delta S then you should probably assume they are working with standard = conditions.

http://en.wikipedia.org/wiki/Standard_con= ditions_for_temperature_and_pressure

That would be my initial take on it.

Bullet point number 2:=A0 U= ltimately you are interested in the total free energy of binding (Delta G).= However it's sometimes very useful to think in terms of entropic gains= /losses (Delta S).=A0 Usually when I'm thinking about entropic contribu= tions to binding I'm thinking about conformational freedom from the rec= eptor and the ligand.=A0 I find that in general you want the smallest most = rigid molecule that will get the job done.=A0 Some targets require larger m= olecules (For example trying to disrupt protein protein interactions) while= most seem to require smaller rule of 5 like compounds.=A0 Beyond that many= other factors will come into play during the life cycle of a drug discover= y program like=A0 bioavailability, toxicity, metabolism, etc.=A0 I'm su= re others will chime in with other rules of thumb here as well.

As for bullet point number there. Some papers are interested in the tot= al free energy difference (Delta G).=A0 Some papers are interested in the e= nthalpic contributions (Delta H) and some groups are only interested in mea= suring entropic contributions (Delta S).=A0 It's really hard to say why= one group chooses one over the other without reading the content of the pa= per.=A0

On Fri, Aug 20, 2010 at 7:28 AM, Sayed Mesa = elsayed.elmes]=3D[yahoo.com <owner-chemistry(-)ccl.net<= /a>> wrote:

Sent to CCL by: "Sayed =A0Mesa" [elsayed.elmes() yahoo.com]
Dear CCL community

Might these questions be simple and silly but I would like to understand th= is confused issue at least for me. I observe that some papers used (T delta= S) parameter =A0and others used the (delta S) parameter for complexation r= eaction using QC methods.

(i)I would like to know what the privilege of using TS instead (delta S)? (ii) And what are information could be drown from these parameters for a co= mplexation reaction between transition metal ion and macrocycle ligand?
(iii) Some papers calculate only deltaH and deltaG and do not care with (T = delta S) or (delta S)? I do not know why?

Thanks in advance,
Sayed



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--00c09f93d5db37a03a048e4097d1-- From owner-chemistry@ccl.net Fri Aug 20 13:29:00 2010 From: "neranjan perera neranjan007],[gmail.com" To: CCL Subject: CCL:G: bader chargers Message-Id: <-42572-100820132748-20129-pU1W81ccLlMQcAjzV1T3fA!=!server.ccl.net> X-Original-From: neranjan perera Content-Type: multipart/alternative; boundary=00032555bb5a82651f048e449dea Date: Fri, 20 Aug 2010 13:27:38 -0400 MIME-Version: 1.0 Sent to CCL by: neranjan perera [neranjan007[#]gmail.com] --00032555bb5a82651f048e449dea Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Thank you very much for the help given to understand how it is calculated= , I do have a another question concerning the bader charges, I used to create a cube file using gaussian, and converted it to bader charges. I used b3lyp theory and lanl2dz basis set for Au atoms and 6-31g*= * for the other atoms. To calculate the partial chargers using , subtracting the Bader charge fro= m the Valance number of electrons gives me a good result for the atoms which basis 6-31g** was used. But not for the Au (gold) atoms. The bader charge for the gold atoms are around 18.8~18.9 How can I calculate the partial charge for the Au atoms when lanl2dz basis is used? Thank you very much. Regards, Neranjan Perera The numbers have simply been substracted from their atomic numbers, as is done in population analysis schemes PKI On Wed, Aug 18, 2010 at 2:33 AM, Robert McGibbon rmcgibbo{=3D}princeton.edu wrote: > Seems very simple. They just subtract the number of electrons in the Bade= r > region from the number of protons. Thus, the partial charge on oxygen is = 8 > - 9.1566 =3D -1.157, and in the hydrogen region it's 1 - 0.4238 =3D +0.57= 6. > > Here's the relevant section of the paper: > > =3D=3D=3D=3D > > Three Bader regions were found, each containing one atom. The total charg= e > in each one of the regions around the hydrogen atoms contained 0.4238 > electrons and the oxygen region contained 9.1566 electrons, which gives a > sum of 10.0041 electrons. The atomic partial charges are the same as foun= d > by Bader [2](= see Table > 1), > showing that these two different algorithms yield the same results. > ------------------------------ > > Table 1. > > Partial charge of oxygen and hydrogen in an isolated water molecule > Partial charge > ------------------------------ > O atomH atoms Bader's original work-1.16+0.58 This work-1.157+0.576 > > > ---- > Robert McGibbon > Princeton University > Undergraduate Class of 2011 > > On Tue, Aug 17, 2010 at 11:32 PM, neranjan perera neranjan007]*[gmail.com > > wrote: > >> Hi, >> In the paper " G. Henkelman et al. / Computational Materials Science 36 >> (2006) 354-360" , they have got bader chargers for water (H2O) as, >> For Hydrogen 0.4238 e >> Oxygen 9.1566 e >> >> and then converted these Bader chargers into atomic partial charges; >> Hydrogen +0.58 >> Oxygen -1.16 >> >> So I want to know how to do the above conversion ? >> >> >> Thanks >> Neranjan Perera. >> >> >> >> >> On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kaminski rkaminski.rk[#] >> gmail.com > wrote: >> >>> What do you understand by these 'atomic partial charges'? >>> >>> Radek >>> >>> >>> 2010/8/17 neranjan perera neranjan007!A!gmail.com < >>> owner-chemistry|,|ccl.net > >>> >>> Hi, >>>> how can i convert "bader chargers" to "atomic partial chargers"? >>>> >>>> Thanks. >>>> >>>> >>>> Neranjan Perera. >>>> neranjan007 *-* gmail.com >>>> >>>> -- >>>> Graduate Student >>>> Department of Chemistry >>>> University of Connecticut >>>> >>>> >>>> >>> >>> >>> -- >>> Radoslaw Kaminski, M.Sc. Eng. >>> Ph.D. Student >>> Crystallochemistry Laboratory >>> Department of Chemistry >>> University of Warsaw >>> Pasteura 1, 02-093 Warszawa, Poland >>> http://acid.ch.pw.edu.pl/~rkaminski/ >> >> --=20 Graduate Student Department of Chemistry University of Connecticut --00032555bb5a82651f048e449dea Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
  Thank you very much for the help given to understand how it i= s calculated,

I do have a another question concerning the bader char= ges,
I used to create a cube file using gaussian, and converted it to ba= der charges. I used b3lyp theory and  lanl2dz basis set for Au atoms a= nd 6-31g** for the other atoms.

 To calculate the partial chargers using , subtracting the Bader c= harge from the Valance number of electrons gives me a good result for the a= toms which basis 6-31g** was used.  But not for the Au (gold) atoms. <= br>The bader charge for the gold atoms are around 18.8~18.9

How can I calculate the partial charge for the Au atoms when lanl2dz ba= sis is used?

Thank you very much.

Regards,
Neranjan Perer= a





The numbers have simply been substracted from the= ir atomic numbers, as is done in population analysis schemes
PKI


On Wed, Aug 18, 2010 at 2:33 AM, = Robert McGibbon rmcgibbo{=3D}princeton.edu= <owner-chemistry*-*ccl= .net> wrote:

Seems very simple. They just subtract the n= umber of electrons in the Bader region from the number of protons. Thus, th= e partial charge on oxygen is 8 - 9.1566 =3D -1.157, and in the hydrog= en region it's 1 - 0.4238 =3D +0.576. 

Here's the relevant section of the paper:

<= p>=3D=3D=3D=3D

Three Bader regions were found, each containing one atom. The total charge in each one of the regions around the hydrogen atoms contained 0.4238=20 electrons and the oxygen region contained 9.1566 electrons, which gives a sum of 10.0041 electrons. The atomic partial charges are the same as=20 found by Bader [2] (see Table 1), s= howing that these two different algorithms yield the same results.


Table 1.

Partial charge of oxygen and hyd= rogen in an isolated water molecule

Partial charge
O atomH atoms
Bader’s original work−1.16+0.58
This work&= minus;1.157+0.576

<= /div>


----
Robert McGibbon
Princeton Universit= y
Undergraduate Class of 2011

On Tue, Aug 17, 2010 at 11:32 PM, neranjan perera neranjan007]*[gmail.com <owner-chemis= try()ccl.net> wrote:
Hi,
 In the paper " G. Henkelman et al. / Computational Materi= als Science 36 (2006) 354–360" , they have got bader chargers fo= r water (H2O) as,
For   Hydrogen   0.4238 e
&nb= sp;       Oxygen     9.15= 66 e
 
and then converted these Bader chargers into atomic partial charg= es;
       Hydrogen   +0.58
=        Oxygen      -= 1.16

So I want to know how to do the above conversion ?

Thanks
Neranjan Perera.


            = ;            &n= bsp;            = ;            &n= bsp;            = ;         

On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kaminski rkamins= ki.rk[#]gmail.com <owner-chemistry|ccl.net> wrote:
What do you under= stand by these 'atomic partial charges'?

Radek


2010/8/17 neranjan perera neranjan007!A!gmail.com <owner-chemistry|,|ccl.net>

Hi,
 &nbs= p; how can i convert "bader chargers" to "atomic partial cha= rgers"?

Thanks.


Neranjan Perera.
neranjan007 *-* gmail.com

--
Graduate Student
Department of Chemistry
University of Connecticut




--
Radoslaw Kaminski, M.Sc. Eng.
Ph.D. Student
Cryst= allochemistry Laboratory
Department of Chemistry
University of Warsaw=
Pasteura 1, 02-093 Warszawa, Poland
http:/= /acid.ch.pw.edu.pl/~rkaminski/



--
Graduate St= udent
Department of Chemistry
University of Connecticut


--00032555bb5a82651f048e449dea-- From owner-chemistry@ccl.net Fri Aug 20 17:06:00 2010 From: "Dr. Xiaofeng (Frank) Duan duanx.ctr]~[afrl.hpc.mil" To: CCL Subject: CCL: FP-LMTO Message-Id: <-42573-100820165311-25252-CAfKjtVpmJwveByaswjyhg*server.ccl.net> X-Original-From: "Dr. Xiaofeng (Frank) Duan" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Aug 2010 16:53:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Xiaofeng (Frank) Duan" [duanx.ctr,,afrl.hpc.mil] Hi all, Can anyone tell me which software packages (free or cost) has the FP-LMTO method implemented for MD similations? Thanks, Frank Duan -- From owner-chemistry@ccl.net Fri Aug 20 18:45:01 2010 From: "Mihaly Mezei Mihaly.Mezei-$-mssm.edu" To: CCL Subject: CCL: Dockres update Message-Id: <-42574-100820184111-31505-6XIs3LqWxGf1ZimdIfkx+w,server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Fri, 20 Aug 2010 18:41:04 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei===mssm.edu] Greetings, The program Dockres that analyzes/filters the virtual screening results and the asssociated set of utilities Fullscreen that sets up virtual screening has recently been updated. Besides screening with Autodock (http://autodock.scripps.edu/) it now includes virtual screening with eHiTS (http://www.simbiosys.ca/ehits/index.html). Furthermore, Dockres has been parallelized using MPI. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Fri Aug 20 19:49:00 2010 From: "Alex Allardyce aa{}chemaxon.com" To: CCL Subject: CCL: ChemAxon extends chemicalize.org free service with predicted data and user customization Message-Id: <-42575-100820104105-10174-mftjc8BDWH/BhG7dMFkxZA[#]server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------050608050009070405070106" Date: Fri, 20 Aug 2010 16:40:53 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa!=!chemaxon.com] This is a multi-part message in MIME format. --------------050608050009070405070106 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excuse cross postings. We announce some developments (below) of a free service we started a year or so back. The functionality has been greatly improved and feedback is excellent so we make this announcement to bring this to your attention. Hope you like it Cheers Alex ************* ChemAxon extends chemicalize.org free service with predicted data and user customization: More predictions added to chemistry browsing service ChemAxon announces the addition of major new functionality in it's chemicalize.org web based service. The new features help users understand better the chemical structure with more predicted properties and a customizable layout to be of most use. chemicalize.org is a service to add chemistry and chemical information to a users web browsing experience by identifying chemical structure names from Web page text and adding structure images within a 'chemicalized' version of the Web page. Users can also 'chemicalize' chemical names or structure files directly through the service. Beyond structure recognition and generation users can explore individual structures to see structure related properties and other calculations. The latest release sees improvements in chemical name recognition, potential to upload chemical structure files and the addition of a new 'Data page', which generates many structure based predictions for each molecule and presents these in a customizable form (open, close, move and re-size individual calculation panels). Major calculations include logP, logD, pKa, topology analysis and charge. Other calculations are to be added in the future. To try the service, paste a URL at the site (http://www.chemicalize.org/) or mouse over the dotted underline text on this chemicalized wikipedia page, http://www.chemicalize.org/?q=http%3A%2F%2Fen.wikipedia.org%2Fwiki%2FList_of_organic_compounds or visit a Data page, for example: http://www.chemicalize.org/?mol=lipitor The service is to be presented during ChemAxon's User Group Meeting being held at Boston's Omni Parker House, September 14-15, the complete program is here: http://www.chemaxon.com/events/2010-us-ugm/ About chemicalize.org chemicalize.org is a public website created by ChemAxon for adding chemical resolution to web browsing, chemical names and structure files. The service is free and will be useful to anyone wishing to add chemical structures and data to their web experience. About ChemAxon ChemAxon is a leader in providing cheminformatics software development platforms and applications for the biotechnology, pharmaceutical and agrochemical industries. With core capabilities for structure visualization, search and management, property prediction, virtual synthesis, screening and drug design, ChemAxon focuses upon active interaction with users and software portability to create powerful, cost effective cross platform solutions and programming interfaces to power modern cheminformatics and chemical communication. For more information please visit www.chemaxon.com. ************* -- *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa{:}chemaxon.com --------------050608050009070405070106 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Excuse cross postings.

We announce some developments (below) of a free service we started a year or so back. The functionality has been greatly improved and feedback is excellent so we make this announcement to bring this to your attention. Hope you like it

Cheers
Alex

*************
ChemAxon extends chemicalize.org free service with predicted data and user customization: More predictions added to chemistry browsing service

ChemAxon announces the addition of major new functionality in it's chemicalize.org web based service. The new features help users understand better the chemical structure with more predicted properties and a customizable layout to be of most use.

chemicalize.org is a service to add chemistry and chemical information to a users web browsing experience by identifying chemical structure names from Web page text and adding structure images within a 'chemicalized' version of the Web page. Users can also 'chemicalize' chemical names or structure files directly through the service. Beyond structure recognition and generation users can explore individual structures to see structure related properties and other calculations.

The latest release sees improvements in chemical name recognition, potential to upload chemical structure files and the addition of a new ‘Data page’, which generates many structure based predictions for each molecule and presents these in a customizable form (open, close, move and re-size individual calculation panels). Major calculations include logP, logD, pKa, topology analysis and charge. Other calculations are to be added in the future.

To try the service, paste a URL at the site (http://www.chemicalize.org/) or mouse over the dotted underline text on this chemicalized wikipedia page, http://www.chemicalize.org/?q=http%3A%2F%2Fen.wikipedia.org%2Fwiki%2FList_of_organic_compounds or visit a Data page, for example: http://www.chemicalize.org/?mol=lipitor

The service is to be presented during ChemAxon’s User Group Meeting being held at Boston’s Omni Parker House, September 14-15, the complete program is here: http://www.chemaxon.com/events/2010-us-ugm/

About chemicalize.org
chemicalize.org is a public website created by ChemAxon for adding chemical resolution to web browsing, chemical names and structure files. The service is free and will be useful to anyone wishing to add chemical structures and data to their web experience.

About ChemAxon
ChemAxon is a leader in providing cheminformatics software development platforms and applications for the biotechnology, pharmaceutical and agrochemical industries. With core capabilities for structure visualization, search and management, property prediction, virtual synthesis, screening and drug design, ChemAxon focuses upon active interaction with users and software portability to create powerful, cost effective cross platform solutions and programming interfaces to power modern cheminformatics and chemical communication. For more information please visit www.chemaxon.com.

*************
--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa{:}chemaxon.com
--------------050608050009070405070106--