From owner-chemistry@ccl.net Thu Oct 24 00:44:00 2013 From: "Tymofii Nikolaienko tim_mail^^^ukr.net" To: CCL Subject: CCL: software for population analysis Message-Id: <-49268-131024003320-22770-5bfWgs+2+qaXZkfLGqB96A[]server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1251; format=flowed Date: Thu, 24 Oct 2013 07:33:12 +0300 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail:-:ukr.net] Dear CCLers, Could someone please suggest a freeware program for performing natural population analysis? All the best, Tim From owner-chemistry@ccl.net Thu Oct 24 01:18:00 2013 From: "Salma bibi salmachemist88|*|gmail.com" To: CCL Subject: CCL:G: Bandwidth estimation of valence and conduction band Message-Id: <-49269-131024010710-32767-gtvYJwapujSrFo5NB0D/7w#,#server.ccl.net> X-Original-From: Salma bibi Content-Type: multipart/alternative; boundary=047d7b4724a2d4afad04e9759a4c Date: Thu, 24 Oct 2013 10:07:04 +0500 MIME-Version: 1.0 Sent to CCL by: Salma bibi [salmachemist88*_*gmail.com] --047d7b4724a2d4afad04e9759a4c Content-Type: text/plain; charset=ISO-8859-1 Dear CCL members, Can anyone please guide me how to estimate Bandwidth of valence and conduction band.I am working with D-A copolymer used in solar cells.And for D-A concept it is necessary to take into consideration the bandwidths.but i am unaware of its calculation using Gaussian 09.Any help in this regard will be highly acknowledged. Best regards. --047d7b4724a2d4afad04e9759a4c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL members,
Can anyone please gui= de me how to estimate Bandwidth=A0 of valence and conduction band.I am work= ing with D-A copolymer used in solar cells.And for D-A concept it is necess= ary to take into consideration the bandwidths.but i am unaware of its calcu= lation using Gaussian 09.Any help in this regard will be highly acknowledge= d.
Best regards.
--047d7b4724a2d4afad04e9759a4c-- From owner-chemistry@ccl.net Thu Oct 24 02:38:00 2013 From: "John Keller jwkeller:-:alaska.edu" To: CCL Subject: CCL:G: software for population analysis Message-Id: <-49270-131024023644-20945-FZTTgN0XTxTZiNiJgQRmpg=-=server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=047d7b2e087312cd7104e976db92 Date: Wed, 23 Oct 2013 22:36:37 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller===alaska.edu] --047d7b2e087312cd7104e976db92 Content-Type: text/plain; charset=ISO-8859-1 Hi Tim, As far as I know, there is no free version of NBO. However, you can use the WebMO website (www.webmo.net) as a guest user. Optimize your molecule on your local system, upload the .log or .out output file to www.webmo.net, select New Job with this Geometry, select Gaussian, enter the method and basis set (presumably the same as your optimization..), choose NBO, and click the Continue arrow. The MO and NBO surfaces are calculated on your local machine using JAVA. The .log file will have the NBO details. NB: Gaussian runs only NBO v 3.0, but this contains most of the basic NBO functions. The time limit for guest account is 60 sec, which will limit the number of atoms and basis set size significantly. However, I was able to complete a default NBO job on 4-chloropyridine at the B3LYP/6-31+G(d,p) level of theory in 54 sec of cpu time. See job 138823. Best, John Keller, University of Alaska Fairbanks On Wed, Oct 23, 2013 at 8:33 PM, Tymofii Nikolaienko tim_mail^^^ukr.net < owner-chemistry:-:ccl.net> wrote: > > Sent to CCL by: Tymofii Nikolaienko [tim_mail:-:ukr.net] > Dear CCLers, > > Could someone please suggest a freeware program for performing natural > population analysis? > > All the best, > Tim> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --047d7b2e087312cd7104e976db92 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Tim,
As far as I know, there is no f= ree version of NBO. However, you can use the WebMO website (www.webmo.net) as a guest user. Optimize your molecul= e on your local system, upload the .log or .out output file to www.webmo.net, select New Job with this Geometry, = select Gaussian, enter the method and basis set (presumably the same as you= r optimization..), choose NBO, and click the Continue arrow. The MO and NBO= surfaces are calculated on your local machine using JAVA. The .log file wi= ll have the NBO details. NB: Gaussian runs only NBO v 3.0, but this contain= s most of the basic NBO functions.
The time limit for guest account is 60 sec, which will limit the= number of atoms and basis set size significantly. However, I was able to c= omplete a default NBO job on 4-chloropyridine at the B3LYP/6-31+G(d,p) leve= l of theory in 54 sec of cpu time. See job=A0 138823.
Best,
John Keller, University of Alaska Fairbanks



On Wed, Oct 23, = 2013 at 8:33 PM, Tymofii Nikolaienko tim_mail^^^= ukr.net <owner-chemistry:-:ccl.net> wrote:

Sent to CCL by: Tymofii Nikolaienko [tim_mail:-:ukr.net]
Dear CCLers,

Could someone please suggest a freeware program for performing natural
population analysis?

All the best,
Tim



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--047d7b2e087312cd7104e976db92-- From owner-chemistry@ccl.net Thu Oct 24 04:54:00 2013 From: "Shaumik Ray rayshaumik*gmail.com" To: CCL Subject: CCL:G: DFT Simulation of Ionic bonding in GaussView and Gaussian09 software Message-Id: <-49271-131024045251-806-8ljlRIh6mwTIORMEjY+i+w.:.server.ccl.net> X-Original-From: "Shaumik Ray" Date: Thu, 24 Oct 2013 04:52:50 -0400 Sent to CCL by: "Shaumik Ray" [rayshaumik===gmail.com] I have a background o f simulating organic molecules in GaussView and Gaussian09 software package. However, when I am trying to do DFT simulations (Frequency and Optimisation) with B3LYP and 6-31G (d) basis set combinations (giving an overall charge of 0 and Spin - Singlet) OF Ionic Bond structures like Calcium Silicate, Calcium Hydroxide etc, I am getting an error message. For Calcium Silicate, I am connecting SO4 and keeing 2 Ca atoms on either side. Can someone help me to simulate ionic bonds in Gaussian software. Do I have to connect all the molecules in some way? Please help. From owner-chemistry@ccl.net Thu Oct 24 08:18:01 2013 From: "niveditha surukonti nivs916||gmail.com" To: CCL Subject: CCL: how to calculate phosphorescence in g09? Message-Id: <-49272-131024032800-11086-ZhcOyNEMt7ZcUhuppo7I5w(~)server.ccl.net> X-Original-From: "niveditha surukonti" Date: Thu, 24 Oct 2013 03:27:59 -0400 Sent to CCL by: "niveditha surukonti" [nivs916*gmail.com] i want to calculate phosphorescence for triphenylamine and also for triphenyle benzene based molecules. can anybody please tell me how to calculate and what are the important steps to follow? thanks in advance. From owner-chemistry@ccl.net Thu Oct 24 09:59:00 2013 From: "Abhinav Tathe goldenabhi{:}gmail.com" To: CCL Subject: CCL: how to calculate phosphorescence in g09? Message-Id: <-49273-131024095648-9238-Xw92UGia7mZ4AtJGa7vVuA^^^server.ccl.net> X-Original-From: Abhinav Tathe Content-Type: multipart/alternative; boundary=047d7beb90a6a0b52404e97d00e8 Date: Thu, 24 Oct 2013 19:26:37 +0530 MIME-Version: 1.0 Sent to CCL by: Abhinav Tathe [goldenabhi a gmail.com] --047d7beb90a6a0b52404e97d00e8 Content-Type: text/plain; charset=ISO-8859-1 Dear Niveditha, It will be helpful to suggest you about calculating the phosphorescence if you specify which parameters/values you want to calculate related to phosphorescence. Abhinav Tathe | Research Scholar | Dyestuff Tech.Dept, ICT,Mumbai. | Mobile : +91 7666110210 | goldenabhi**gmail.com *The Department of Dyestuff Technology, Institute of Chemical Technology, cordially invites you to attend and participate in the National Symposium on Functional Applications of Colorants (NSFAC-2013) on October 29-30, 2013. * * * On Thu, Oct 24, 2013 at 12:57 PM, niveditha surukonti nivs916||gmail.com < owner-chemistry**ccl.net> wrote: > > Sent to CCL by: "niveditha surukonti" [nivs916*gmail.com] > i want to calculate phosphorescence for triphenylamine and also for > triphenyle benzene based molecules. can anybody please tell me how to > calculate and what are the important steps to follow? > thanks in advance.> > > --047d7beb90a6a0b52404e97d00e8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Niveditha,

It will be helpful to s= uggest you about calculating the phosphorescence if you specify which param= eters/values you want to calculate related to phosphorescence.

Abhinav Tathe |= Research Scholar | Dyestuff Tech.Dept, ICT,Mumbai.=
| Mobile : +91=A07666110210 | goldenabhi**gmail.com

The Department of= Dyestuff Technology, Institute of Chemical Technology, cordially invites y= ou to attend and participate in the=A0Na= tional Symposium on Functional Applications of Colorants=A0 (NSFAC-2013)= on October 29-30, 2013.
=A0
=A0


On Thu, Oct 24, 2013 at 12:57 PM, nivedi= tha surukonti nivs916||gmail.com <o= wner-chemistry**ccl.net> wrote:

Sent to CCL by: "niveditha =A0surukonti" [nivs916*gmail.com]
i want to calculate phosphorescence for triphenylamine and also for triphen= yle benzene based molecules. can anybody please tell me how to calculate an= d what are the important steps to follow?
thanks in advance.



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--047d7beb90a6a0b52404e97d00e8-- From owner-chemistry@ccl.net Thu Oct 24 16:37:00 2013 From: "Michael K Gilson mgilson__ucsd.edu" To: CCL Subject: CCL: New Protein-Ligand Binding Validation Sets Available at BindingDB Message-Id: <-49274-131024163237-6201-hXK9gq9tkMHHpzy6TvlSpA-#-server.ccl.net> X-Original-From: "Michael K Gilson" Date: Thu, 24 Oct 2013 16:32:36 -0400 Sent to CCL by: "Michael K Gilson" [mgilson : ucsd.edu] Dear CCL Colleagues, I thought you might be interested a set of about 750 different protein-ligand docking/binding validation sets that were automatically extracted from the larger BindingDB dataset: http://www.bindingdb.org/validation_sets/ Each Set is a congeneric series of ligands with measured affinities (IC50 or Ki) for a single protein target, where at least one compound in the series has a known co-crystal structure in the PDB. In many cases, we were able to use Surflex* to generate plausible docked poses of the ligands without a crystal structure. You can download each compound set as an SDfile, and you can also add your own comments about a set ("loved it!" "problematic") on the web-site. There are also linked literature references, and it's a good idea to check the data before relying on them, since we don't have the personnel to check them all in detail. I hope you find this useful. Please feel free to contact me if you have any questions, or suggestions for improving the site! Best regards, Mike Gilson UCSD *Thanks to Ajay Jain and Russell Spitzer for help with Surflex. From owner-chemistry@ccl.net Thu Oct 24 18:06:00 2013 From: "Joseph Leonard jleonard42- -gmail.com" To: CCL Subject: CCL: Comparison of qm-derived force fields Message-Id: <-49275-131024180415-6858-ewP6+t5sa4wd4z+6VdIvMg-.-server.ccl.net> X-Original-From: Joseph Leonard Content-Type: multipart/alternative; boundary=047d7beb90a623c61504e983d0b0 Date: Thu, 24 Oct 2013 18:04:08 -0400 MIME-Version: 1.0 Sent to CCL by: Joseph Leonard [jleonard42|*|gmail.com] --047d7beb90a623c61504e983d0b0 Content-Type: text/plain; charset=ISO-8859-1 Folks, does anybody have references where people have compared "old" force fields derived from HF/6-31g* (maybe mp2) with "new" force fields derived > from larger-basis DFT calculations? I'm interested in learning how the state of the art has progressed and lack a better lit searching engine than google. Given the qm experience in ccl's readership I hope some ff developers are reading. Thanks in advance for pointers! Joe Leonard -- I live in a science fiction fantasy, except it's all real now. You guys grew up with computers. Computers grew up with me. --047d7beb90a623c61504e983d0b0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks, does=A0anybody have references where people have compared "old&= quot; force fields derived from HF/6-31g* (maybe mp2) with "new" = force fields derived from larger-basis DFT calculations? =A0I'm=A0interested in learning how the state of the art has progressed and = lack a better lit searching engine than google. Given the qm experience in = ccl's readership I hope some ff developers are reading. Thanks in advan= ce for pointers!

Joe Leonard


--
I live in a scienc= e fiction fantasy, except it's all real now. =A0You guys grew up=A0with= computers. =A0Computers grew up with me.


--047d7beb90a623c61504e983d0b0--