From owner-chemistry@ccl.net Thu May 7 05:54:01 2009 From: "Mahmoud Korani Abdel-Latif mkkhedr(a)hotmail.com" To: CCL Subject: CCL: Cartesian Reaction Surface (CRS) Message-Id: <-39243-090507055147-26512-o5moCMx3dJUWM+94kI7o/g- -server.ccl.net> X-Original-From: "Mahmoud Korani Abdel-Latif" Date: Thu, 7 May 2009 05:51:43 -0400 Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr(~)hotmail.com] Dear CCL'ers, Thanks in advance. I want to construct the PES for certain molecule using Cartesian reaction Surface method. I am asking about any free software for CRS. And the method to do that. Any hints Should be appreciated. Cheers, Mahmoud From owner-chemistry@ccl.net Thu May 7 09:29:00 2009 From: "Chunhui Li baotogo2004]*[gmail.com" To: CCL Subject: CCL: Need help with photolysis Message-Id: <-39244-090507092631-32274-EWczmJ5prg3hlF3oD9C7tg%a%server.ccl.net> X-Original-From: "Chunhui Li" Date: Thu, 7 May 2009 09:26:27 -0400 Sent to CCL by: "Chunhui Li" [baotogo2004 .. gmail.com] Hi, Dear all, I am studying the photodegradation of certain pigments. I calculated the UV spectrum by Spartan. If there are peaks indicating the adsorption, how to interpret these regarding to its photodegradation capability? Is it possible to do further calculation to find out the photodegradation products? Could anybody point me some review-type papers? Thanks in advance! Lily From owner-chemistry@ccl.net Thu May 7 10:40:00 2009 From: "matthew john tassell mtassell\a/gmail.com" To: CCL Subject: CCL:G: AIM2000 in G03 Message-Id: <-39245-090507103759-30090-Dz/DSR6zbs1p1wuH+j+Abw%a%server.ccl.net> X-Original-From: "matthew john tassell" Date: Thu, 7 May 2009 10:37:56 -0400 Sent to CCL by: "matthew john tassell" [mtassell,+,gmail.com] Dear CCL forum I have recently purchased aim2000 and have been having problems locating some 3,-1 critical points. I am looking at actinide cyclopentadienyl systems and what is very strange is that when i have chemically identical (symmetry equivalent)(M-C) bonds there appears to be critical points missing so that between the M and Cp there are only 2 and in some cases 1 3,-1 points present when each C is the same. I have tried using nosymm to no avail and changing the intergration grid in the calculation but the quality seems to be unimportant. I read on ccl that G03 rev d has a problem with outputting coordinates to the .wfn file and it turns out that i am using rev d and was wondering what coordinates i should be using because it was mentioned that they are IIRC ? If anybody has exsperienced any of these problems i would be extremly grateful for any advice or assistance Thank you Matt From owner-chemistry@ccl.net Thu May 7 11:15:01 2009 From: "luca bertini luca.bertini-#-unimib.it" To: CCL Subject: CCL: Need help with photolysis Message-Id: <-39246-090507104135-30874-WHMdOwdiAMMuaDJQp+4Mzg-,-server.ccl.net> X-Original-From: "luca bertini" Content-Transfer-Encoding: 8bit Content-Type: text/html;charset=iso-8859-1 Date: Thu, 07 May 2009 16:03:40 +0200 MIME-Version: 1.0 Sent to CCL by: "luca bertini" [luca.bertini[A]unimib.it]
Hi Lily

briefly, you have to analyze the MOs involved in each excitations that you believe could be active in the  photodegradation process.  If you have any suggestions about the mechanism of this photochemical process, you could sample the corresponding excited PES along the suggested path.

To establish the chemical nature of the photoproducts is not an easy task. Once you know which is the excited state involved in your process and you have informations about the photochemical path you might try to relax the geometry of the one of the structure you found during the PES sampling.     

Luca Bertini 

On Thu, 7 May 2009 09:26:27 -0400
 "Chunhui Li baotogo2004]*[gmail.com" <owner-chemistry-*-ccl.net> wrote:
>
> Sent to CCL by: "Chunhui  Li" [baotogo2004 .. gmail.com]
> Hi, Dear all,
>
> I am studying the photodegradation of certain pigments.
>I calculated the UV spectrum by Spartan. If there are
>peaks indicating the adsorption, how to interpret these
>regarding to its photodegradation capability? Is it
>possible to do further calculation to find out the
>photodegradation products? Could anybody point me some
>review-type papers?
>
> Thanks in advance!
>
> Lily
>
>
>
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From owner-chemistry@ccl.net Thu May 7 14:58:00 2009 From: "Carlos F. Lagos carlos . cbuc.cl" To: CCL Subject: CCL: docking Message-Id: <-39247-090507135403-859-PfZ1xEZNe/RXbdly124K3w-$-server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 7 May 2009 13:14:25 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos..cbuc.cl] You can also use Accelrys Discovery Studio, they a have a free trial for = a month, and it allows docking and MD. =20 QF Carlos F. Lagos =20 Centre for Bioinformatics, Faculty of Biological Sciences Medicinal Chemistry Laboratory, Faculty of Chemistry P. Universidad Catolica de Chile I Portugal # 49, Zocalo ZIP 8330025 I Santiago =96 Chile Phone: + 56 2 6862376 - 3541911 I http://www.cbuc.cl =20 -----Mensaje original----- De: owner-chemistry+carlos=3D=3Dcbuc.cl-#-ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl-#-ccl.net] En nombre de Vincent.Leroux{}loria.fr Enviado el: Mi=E9rcoles, 06 de Mayo de 2009 10:16 Para: Lagos, Carlos F Asunto: CCL: docking Sent to CCL by: Vincent.Leroux\a/loria.fr Hello, No need to SHOUT OUT LOUD... GOLD, Glide and ICM-Docking are fine docking packages. You can also =20 use DOCK or AutoDock if your institution cannot afford them. I would recommend NAMD for MD simulations. VL "neeraj misra neerajmisra!=3D!hotmail.com" a = =E9crit=A0: > > Sent to CCL by: "neeraj misra" [neerajmisra[-]hotmail.com] > PLEASE SUGGEST SOME GOOD PACKAGE FOR DOCKING STUDIES AND MD = SIMULATION. > > -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt__________ Information from ESET NOD32 Antivirus, version of virus = signature database 4056 (20090506) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 __________ Information from ESET NOD32 Antivirus, version of virus = signature database 4060 (20090507) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com =20 From owner-chemistry@ccl.net Thu May 7 15:32:00 2009 From: "Rzepa, Henry h.rzepa+/-imperial.ac.uk" To: CCL Subject: CCL: AIM2000 in G03 Message-Id: <-39248-090507151207-11793-Usu0dEtqcuEEaU8x86m3Dw++server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Thu, 7 May 2009 20:11:48 +0100 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa^-^imperial.ac.uk] >Sent to CCL by: "matthew john tassell" [mtassell,+,gmail.com] >Dear CCL forum > >I have recently purchased aim2000 and have been having problems locating > >some 3,-1 critical points. I am looking at actinide cyclopentadienyl systems and > AIM2000 does not deal with pseudopotentials, or I believe higher than f functions. Its quite probable that the Poincare Hopf condition cannot be met for such systems, and that the core region of the actinide is quite wrong. -- +44 (020) 7594 5774 (Voice); FOAF: http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Thu May 7 16:07:00 2009 From: "L E Johnson lejohn07.[A].louisville.edu" To: CCL Subject: CCL:G: AIM2000 in G03 Message-Id: <-39249-090507125704-28223-7fC7NX8NTvcbdFZAU2qSAA[A]server.ccl.net> X-Original-From: L E Johnson Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Thu, 7 May 2009 12:25:44 -0400 MIME-Version: 1.0 Sent to CCL by: L E Johnson [lejohn07~!~louisville.edu] Hey Matt, As far as the G03 version D, if you use the nosymm keyword to generate your= wavefunction file, the coordinates should be ok. Also, depending on which = basis set you're using, you may need density=3Dcurrent in the route line. I= f using HF or DFT, don't include it. If you have a symmetrical eta-5 coordinated cyclopentadienyl ring, you may = only get one (3,-1) CP from the M to the center of the Cp. If this is the c= ase, the bond path will likely lead to the ring CP, and veer off towards on= e carbon just before reaching the RCP- the 3,-1 has to connect two (3,-3) n= uclear attractors. So you may be ok with just having one BCP. Is this what = you're seeing, or do the CPs make no sense? Another issue may be the actinide- I'm not too familiar with basis sets for= it, but if you're using an effective core potential basis set, you will ge= t some strange and often bad results with AIM2000 because you have too many= (3,-3) attractors in the wfn. Hope this is some help. If you can't get it to run with AIM2000, you could = try Todd Keith's AIMAll (free download)- there's no graphic interface, but = you could compare the CP results. Plus AIMAll is a lot faster. Lucius ---------------------------------------- Lucius Johnson Department of Chemistry University of Louisville Louisville, Kentucky 40292 (502) 852-0192 lejohn07**louisville.edu >>> "matthew john tassell mtassella/gmail.com" 05= /07/09 11:00 AM >>> Sent to CCL by: "matthew john tassell" [mtassell,+,gmail.com] Dear CCL forum I have recently purchased aim2000 and have been having problems locating=20 some 3,-1 critical points. I am looking at actinide cyclopentadienyl system= s and=20 what is very strange is that when i have chemically identical (symmetry=20 equivalent)(M-C) bonds there appears to be critical points missing so that= =20 between the M and Cp there are only 2 and in some cases 1 3,-1 points=20 present when each C is the same. I have tried using nosymm to no avail and changing the intergration grid in= =20 the calculation but the quality seems to be unimportant.=20 I read on ccl that G03 rev d has a problem with outputting coordinates to= =20 the .wfn file and it turns out that i am using rev d and was wondering what= =20 coordinates i should be using because it was mentioned that they are IIRC ? If anybody has exsperienced any of these problems i would be extremly=20 grateful for any advice or assistance Thank you=20 Matt -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu May 7 17:31:00 2009 From: "S. Bill s_bill36()yahoo.co.uk" To: CCL Subject: CCL: TD-DFT Keyword Message-Id: <-39250-090507172945-26128-sA5rEy3tm3NHcv2v4dP91g===server.ccl.net> X-Original-From: "S. Bill" Date: Thu, 7 May 2009 17:29:41 -0400 Sent to CCL by: "S. Bill" [s_bill36===yahoo.co.uk] Dear CCL I am a beginner in TD-DFT Calculation and I need a help. I have a couple of questions related to TD-DFT method. I did a couple of jobs using TD-DFT, as following: Td=(nstate=10) Td=(nstate=20) Td=(nstate=10,root=10) I found that Td=(nstate=10,root=10) Gaussum UV graph is the same exactly as that of Td=(nstate=10), is it correct? becasue I was wondering Td=(nstate=10,root=10) means to start from state number 10 and do other more 10 states, as a result, the last output should be the output of 20 state, doesn't it? The second question, how can I determine the correct number of nstate? The last question is related to EqSolv, I did TD-DFT with EqSolv keyword, and WITHOUT specifying and PCM model (NO PCM keyword in the route). And I found that the job is working normally without any complaining, how? and in this case, which model did it use? Thanks in advance From owner-chemistry@ccl.net Thu May 7 21:40:00 2009 From: "Duy Le ttduyle]-[gmail.com" To: CCL Subject: CCL:G: TD-DFT Keyword Message-Id: <-39251-090507213842-17280-R+cGRUVs23IT0Nk32uXaVA . server.ccl.net> X-Original-From: Duy Le Content-Type: multipart/alternative; boundary=001636af022e7ff85604695caf03 Date: Thu, 7 May 2009 21:38:09 -0400 MIME-Version: 1.0 Sent to CCL by: Duy Le [ttduyle::gmail.com] --001636af022e7ff85604695caf03 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit I think you should read this part of manual http://www.gaussian.com/g_ur/k_td.htm Good luck! On Thu, May 7, 2009 at 5:29 PM, S. Bill s_bill36()yahoo.co.uk < owner-chemistry]|[ccl.net> wrote: > > Sent to CCL by: "S. Bill" [s_bill36===yahoo.co.uk] > Dear CCL > I am a beginner in TD-DFT Calculation and I need a help. I have a couple of > questions related to TD-DFT method. I did a couple of jobs using TD-DFT, as > following: > Td=(nstate=10) > Td=(nstate=20) > Td=(nstate=10,root=10) > > I found that Td=(nstate=10,root=10) Gaussum UV graph is the same exactly as > that of Td=(nstate=10), is it correct? becasue I was wondering > Td=(nstate=10,root=10) means to start from state number 10 and do other more > 10 states, as a result, the last output should be the output of 20 state, > doesn't it? > > The second question, how can I determine the correct number of nstate? > > The last question is related to EqSolv, I did TD-DFT with EqSolv keyword, > and WITHOUT specifying and PCM model (NO PCM keyword in the route). And I > found that the job is working normally without any complaining, how? and in > this case, which model did it use? > Thanks in advance> > > -- Men don't need hands to do things! --001636af022e7ff85604695caf03 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I think you should read this part of manual
http://www.gaussian.com/g_ur/k_td.htm
Good luc= k!

On Thu, May 7, 2009 at 5:29 PM, S. Bil= l s_bill36()yahoo.co.uk <owner-chemistry]|[ccl.net> wrote:

Sent to CCL by: "S. =A0Bill" [s_bill36=3D=3D=3Dyahoo.co.uk]
Dear CCL
I am a beginner in TD-DFT Calculation and I need a help. I have a couple of= questions related to TD-DFT method. I did a couple of jobs using TD-DFT, a= s following:
Td=3D(nstate=3D10)
Td=3D(nstate=3D20)
Td=3D(nstate=3D10,root=3D10)

I found that Td=3D(nstate=3D10,root=3D10) Gaussum UV graph is the same exac= tly as that of Td=3D(nstate=3D10), is it correct? becasue I was wondering T= d=3D(nstate=3D10,root=3D10) means to start from state number 10 and do othe= r more 10 states, as a result, the last output should be the output of 20 s= tate, doesn't it?

The second question, how can I determine the correct number of nstate?

The last question is related to EqSolv, I did TD-DFT with EqSolv keyword, a= nd WITHOUT specifying and PCM model (NO PCM keyword in the route). And I fo= und that the job is working normally without any complaining, how? and in t= his case, which model did it use?
Thanks in advance



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--001636af022e7ff85604695caf03-- From owner-chemistry@ccl.net Thu May 7 23:12:00 2009 From: "Mannan K malie_03_._yahoo.co.in" To: CCL Subject: CCL: Is there any free combinatorial libray design tool Message-Id: <-39252-090507220839-29121-cvVUcXUZO/34WaMbA+9/TQ ~ server.ccl.net> X-Original-From: "Mannan K" Date: Thu, 7 May 2009 22:08:35 -0400 Sent to CCL by: "Mannan K" [malie_03|a|yahoo.co.in] Hi CCLers, I would like to design a set of compounds (ie combinatorial library) for virtual screening on a particular core molecule. Is there any free tool available for designing a specific library. Thank you, Mannan