From owner-chemistry@ccl.net Fri Jul 12 07:48:00 2013 From: "Peter Bladon p.bladon|a|strath.ac.uk" To: CCL Subject: CCL: Tool to generate conformer database for ligand_like molecules Message-Id: <-48944-130711144745-8410-I9iYQtJMiZjBcH1fEo4lFQ++server.ccl.net> X-Original-From: Peter Bladon Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 11 Jul 2013 19:47:15 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Bladon [p.bladon|a|strath.ac.uk] Dear Sun, The program INTERCHEM has the ability to do what you want. This free program is available by downloading from the Interprobe site. www.interprobe.co.uk using anonymous ftp. Get the latest version install_interchem2013_06_25.exe With a SMILES string you can generate either the minimum energy conformer, or choose to generate a set of 512 conformers, and then sort them according to their energies. Full display and analysis tools are provided. There is also provision to generate conformers of selected chirality. Cheers Peter Dr Peter Bladon Interprobe Chemical Services Gallowhill House, Larch Avenue Lenzie, Kirkintilloch Glasgow G66 4HX Scotland, UK Telephone: 0141-578-1109 Facsimile: 0141-776-7712 URL: www.interprobe.co.uk/inter/interprobe.html ________________________________________ > From: owner-chemistry+cbas25==strath.ac.uk*ccl.net [owner-chemistry+cbas25==strath.ac.uk*ccl.net] On Behalf Of Bin Sun sunbinxod*gmail.com [owner-chemistry*ccl.net] Sent: Saturday, July 06, 2013 4:01 AM To: Bladon, Peter Subject: CCL: Tool to generate conformer database for ligand_like molecules Hello Everyone, I want to achieve all the possible conformations corresponding to the minimums on the potential surface of a ligand_like molecule. To this end, I firstly need to generate as many as possible conformers by rotating the rotatable bonds via some tools or software; Secondly, A sifting stage is performed in which the "bad" conformers having unfavorable energies are excluded. To ensure that there are no important conformations being omitted. the conformer database generated in the first step must be as completed as possible. Is there any tool or software that can generate completed conformer database for ligand_like molecules ? Thanks ! -Sun From owner-chemistry@ccl.net Fri Jul 12 09:32:00 2013 From: "Michel Petitjean petitjean.chiral^_^gmail.com" To: CCL Subject: CCL: Tool to generate conformer database for ligand_like molecules Message-Id: <-48945-130712093104-7972-nM9HDi7z4eLaYBu6Rd7UMw|,|server.ccl.net> X-Original-From: Michel Petitjean Content-Type: multipart/alternative; boundary=20cf302ad7085a5b4f04e15085bd Date: Fri, 12 Jul 2013 15:30:57 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral^gmail.com] --20cf302ad7085a5b4f04e15085bd Content-Type: text/plain; charset=ISO-8859-1 Please have a look at Frog2 (free): http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2 Best regards, Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral]-[gmail.com (preferred), michel.petitjean]-[univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html > Hello Everyone, >> >> I want to achieve all the possible conformations corresponding to the >> minimums on the potential surface of a ligand_like molecule. >> >> To this end, I firstly need to generate as many as possible conformers >> by rotating the rotatable bonds via some tools or software; Secondly, A >> sifting stage is performed in which the "bad" conformers having unfavorable >> energies are excluded. To ensure that there are no important conformations >> being omitted. the conformer database generated in the first step must >> be as completed as possible. >> >> Is there any tool or software that can generate completed conformer >> database for ligand_like molecules ? >> >> Thanks ! >> >> -Sun >> > > --20cf302ad7085a5b4f04e15085bd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Best regards,
Michel.

Michel Petitjean
MTi, INSERM = UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13= , France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral]-[gmail.com (preferred),
=A0= =A0=A0=A0=A0=A0=A0 michel.petitjean]-[univ-paris-diderot.fr
http://pet= itjeanmichel.free.fr/itoweb.petitjean.html

=A0
Hello Everyone,

I want to achieve all the possible conformations correspondin= g to the minimums on the potential surface of a ligand_like mo= lecule.

=A0To this end, I firstly need to ge= nerate as many as possible conformers by rotating the rotatable bond= s via some tools or software; Secondly, A sifting stage is performed in whi= ch the "bad" conformers having unfavorable energies are excluded. To ensure that there are no important conformations being omitted. the conformer database generated in the first step must = =A0be as completed as possible.=A0

Is there any tool or software that can generate c= ompleted conformer database for ligand_like= molecules ?

Thanks !

-Sun

--20cf302ad7085a5b4f04e15085bd-- From owner-chemistry@ccl.net Fri Jul 12 10:07:00 2013 From: "Ailar Badri ailar121242363:-:yahoo.co.uk" To: CCL Subject: CCL:G: Finding the transition state Message-Id: <-48946-130712095401-17794-DlF013i0yH0BS+mmxBYMRQ_._server.ccl.net> X-Original-From: "Ailar Badri" Date: Fri, 12 Jul 2013 09:54:00 -0400 Sent to CCL by: "Ailar Badri" [ailar121242363-.-yahoo.co.uk] Dear CCLers, I'm looking for transition state structure using qst2 command, but I have not been succeed so far. I tried many kinds of reactant/product structures to find the transition state. However, my calculations always terminate with the following error almost immediately after submitting the job: Old curvilinear step not converged, using linear step: SCX= 2.80D+01 DXMaxT= 5.30-317 SCLim= 0.00D+00 Fact= 0.00D+00 RedCar/ORedCr failed for GTrans. Error termination via Lnk1e in /afs/ics.muni.cz/software/g09-D01/em64t.sse4.2/g09/l101.exe at Fri Jul 12 15:31:42 2013. I would be grateful if someone can help me. I am using Gaussian 09 rev. D01. Regards, Ailar Badri From owner-chemistry@ccl.net Fri Jul 12 13:51:01 2013 From: "Alex Allardyce aallardyce*o*chemaxon.com" To: CCL Subject: CCL: ChemAxon's 2013 US UGM Program announced. Message-Id: <-48947-130712043843-14871-zuFBt9uH3taLXj6n3FserA{=}server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="----=_Part_31756_973949382.1373618311748" Date: Fri, 12 Jul 2013 10:38:31 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aallardyce:+:chemaxon.com] ------=_Part_31756_973949382.1373618311748 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Find out how Eli Lilly, NIH, Takeda, Thomson Reuters and 9 other leading R&= D organisations solve problems and accelerate their research with ChemAxon = technology.=20 Refresh your knowledge of features and new products in the JChem version 6 = and 6.1 releases, discuss future product development and catch up with your= peers and colleagues.=20 Monday Sept 23rd - join one of the 3 free satellite sessions; overview of J= Chem integration, working with KNIME and Introducing a new service for IP c= hemistry.=20 UGM Program ( http://www.chemaxon.com/events/ugm-san-diego-2013/#program )= =20 About the meeting ( http://www.chemaxon.com/events/ugm-san-diego-2013/#over= view )=20 Satellite Sessions ( http://www.chemaxon.com/events/ugm-san-diego-2013/#sat= ellite )=20 Hope you can join us=20 Alex=20 ** Satellite Sessions=20 ------------------------------------------------------------=20 Preceding the UGM, on 23rd September, we host 3 concurrent all days session= s, followed by our 1-2-1 discussion session. Attending these sessions is fr= ee of charge for registered UGM attendees.=20 Integration Workshop: For architects, system developers, project managers a= nd leaders of R&D IT, this workshop provides a general overview of ChemAxon= technology and functionality, how easily it fits together and how you can = build and deploy for the desktop, the web or .NET environment. Read more...= ( http://www.chemaxon.com/events/ugm-san-diego-2013/#integration )=20 KNIME Workshop: Relevant to anyone using workflow tools we overview KNIME, = the ChemAxon functionality available using chemistry centric workflows and = then explore downstream processes such as data mining, data transformation = and reporting. Read more... ( http://www.chemaxon.com/events/ugm-san-diego-= 2013/#knime )=20 Markush Open Day: For IP searchers and patent professionals working with ch= emical structures we overview a new service to search and analyse Thomson R= euters Markush content. Read more... ( http://www.chemaxon.com/events/ugm-s= an-diego-2013/#markush )=20 One to One Session: finishing up the day we have an open practice to discus= s your specific scientific, technical or business issues with project owner= s. Read more... ( http://www.chemaxon.com/events/ugm-san-diego-2013/#one-to= -one )=20 ** USUGM User presentation listing:=20 ------------------------------------------------------------=20 01. IJC as a Cloud Hosted LIMS - Adam Idone, Chromocell=20 02. A data analysis platform to work efficiently with CROs Dennis Moccia, C= ognitive Dataworks=20 03. A Chemical Library Design Tool - Tim Parott, Dart Neuroscience 04. Cutt= ing the cord: How Chemaxon technology inspired and enabled our liberation i= nto the cloud - Steven Muskal, Eidogen-Sertanty=20 05. The Lilly Open Innovation Drug Discovery Program (OIDD) - Dan Robertson= , Eli Lilly=20 06. Recent improvements in Marvin v6: Reaction Atom Mapping and its Applica= tion to Reaction Validation in Pharmaceutical ELNs -Daniel Lowe and Roger S= ayle, NextMove Software=20 07. Overview of the NIH Bioassay Research Database (BARD) - Ajit Jadhav, NI= H on behalf of the BARD consortium=20 08. Deltasoft/ChemAxon Tools Empowering Screening, Lead Compound Discovery,= SAR optimization for GPCR Targets in the RTI Drug Discovery Center - Danni= Harris, RTi International=20 09. Keynote - Mark Murcko & Alex Drijver, Schroedinger & ChemAxon=20 10. Machine Learning Applications with JChem - Steve Wilkens, Takeda San Di= ego=20 11. High-Throughput Patent Analysis With D2S - Steve Wilkens, Takeda San Di= ego=20 12. Patent analytics - what can Markush data tell us? - Steve Hajkowski, Th= omson Reuters=20 13. LIFE, LIFEwrx and the Library of Integrated Network-Based Cellular Sign= atures - Christopher Mader, U. Miami=20 14. Chemical mixture fingerprints and applications - Oleg Ursu, U. New Mexi= co Cancer Center=20 ** Related: 2013 European UGM Archive Opens=20 ------------------------------------------------------------=20 ** Program - videos & Slides ( http://www.chemaxon.com/ugm-archive/2013-eu/= #program )=20 Meeting Report by Yvonne Martin ( http://www.chemaxon.com/ugm-archive/2013-= eu/#report )=20 All UGMs Archive: ( http://www.chemaxon.com/ugm-archive/ )=20 Alex Allardyce=20 Marketing Dir.=20 ChemAxon Ltd=20 Z=C3=A1hony u. 7. Building HX, Budapest, 1031 Hungary=20 http://www.chemaxon.com=20 Tel: + 361 453 0435=20 Fax: + 361 4532659=20 mailto:aa(!)chemaxon.com=20 ------=_Part_31756_973949382.1373618311748 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Find out how Eli Lilly, NIH= , Takeda, Thomson Reuters and 9 other leading R&D organisations solve p= roblems and accelerate their research with ChemAxon technology.
Refresh your knowledge of features and new products in the JChem ver= sion 6 and 6.1 releases, discuss future product development and catch up wi= th your peers and colleagues.
Monday Sept 23rd - join one of the 3 free = satellite sessions;  overview of JChem integration, working with KNIME= and Introducing a new service for IP chemistry.

UGM Prog= ram (http://www.chemax= on.com/events/ugm-san-diego-2013/#program)    
About = the meeting (http:/= /www.chemaxon.com/events/ugm-san-diego-2013/#overview)   &nbs= p;
Satellite Sessions (http://www.chemaxon.com/events/ugm-san-diego-2013/#satellite)=

Hope you can join us
Alex

** Sat= ellite Sessions
--------------------------------------------------------= ----
Preceding the UGM, on 23rd September, we host 3 concurrent all days= sessions, followed by our 1-2-1 discussion session. Attending these sessio= ns is free of charge for registered UGM attendees.

Integr= ation Workshop: For architects, system developers, project managers and lea= ders of R&D IT, this workshop provides a general overview of ChemAxon t= echnology and functionality, how easily it fits together and how you can bu= ild and deploy for the desktop, the web or .NET environment. Read more... (= http://www= .chemaxon.com/events/ugm-san-diego-2013/#integration)

KNIME Workshop: Relevant to anyone using workflow tools we overview KNIME,= the ChemAxon functionality available using chemistry centric workflows and= then explore downstream processes such as data mining, data transformation= and reporting. Read more... (http://www.chemaxon.com/events/ugm-san-diego-2013/#knime)
Markush Open Day: For IP searchers and patent professionals working = with chemical structures we overview a new service to search and analyse Th= omson Reuters Markush content. Read more... (http://www.chemaxon.com/events/ugm-san-diego-2013/#= markush)

One to One Session: finishing up the day we = have an open practice to discuss your specific scientific, technical or bus= iness issues with project owners. Read more... (http://www.chemaxon.com/events/ugm-san-d= iego-2013/#one-to-one)


** USUGM User presentation= listing:
------------------------------------------------------------01. IJC as a Cloud Hosted LIMS - Adam Idone, Chromocell
02. A data ana= lysis platform to work efficiently with CROs Dennis Moccia, Cognitive Dataw= orks
03. A Chemical Library Design Tool - Tim Parott, Dart Neuroscience= 04. Cutting the cord: How Chemaxon technology inspired and enabled our lib= eration into the cloud - Steven Muskal, Eidogen-Sertanty
05. The Lilly = Open Innovation Drug Discovery Program (OIDD) - Dan Robertson, Eli Lilly 06. Recent improvements in Marvin v6: Reaction Atom Mapping and its Appli= cation to Reaction Validation in Pharmaceutical ELNs -Daniel Lowe and Roger= Sayle, NextMove Software
07. Overview of the NIH Bioassay Research Dat= abase (BARD) - Ajit Jadhav, NIH on behalf of the BARD consortium
08. De= ltasoft/ChemAxon Tools Empowering Screening, Lead Compound Discovery, SAR o= ptimization for GPCR Targets in the RTI Drug Discovery Center - Danni Harri= s, RTi International
09. Keynote - Mark Murcko & Alex Drijver, Schr= oedinger & ChemAxon
10. Machine Learning Applications with JChem - = Steve Wilkens, Takeda San Diego
11. High-Throughput Patent Analysis Wit= h D2S - Steve Wilkens, Takeda San Diego
12. Patent analytics - what can= Markush data tell us? - Steve Hajkowski, Thomson Reuters
13. LIFE, LIF= Ewrx and the Library of Integrated Network-Based Cellular Signatures - Chri= stopher Mader, U. Miami
14. Chemical mixture fingerprints and applicati= ons - Oleg Ursu, U. New Mexico Cancer Center

** Related: = 2013 European UGM Archive Opens
----------------------------------------= --------------------
** Program - videos & Slides (http://www.chemaxon.com/ugm-archive/2013-eu/#program)=       
Meeting Report by Yvonne Martin (http://www.chemaxon.com/ugm-archive/2013-eu/#repor= t)
All UGMs Archive: (http://www.chemaxon.com/ugm-archive/) 
<= br>
Alex Allardyce
<= span style=3D"color: #666666; font-size: xx-small;" data-mce-style=3D"color= : #666666; font-size: xx-small;">Marketing Dir.
ChemAxon Ltd
Z=C3=A1hony= u. 7. Building HX, Budapest, 1031 Hungary
http://www.chemaxon.com=
Tel: +361 453 0435
Fax: +361 4532659
mailt= o:aa(!)chemaxon.com
------=_Part_31756_973949382.1373618311748-- From owner-chemistry@ccl.net Fri Jul 12 14:26:00 2013 From: "Zahra Alimohammadi Keyvani fahimea76[a]gmail.com" To: CCL Subject: CCL: exertation of potential barrier in guassian 09 package Message-Id: <-48948-130712062025-24944-91hvcVxES2j2P6rxArT8WA#server.ccl.net> X-Original-From: "Zahra Alimohammadi Keyvani" Date: Fri, 12 Jul 2013 06:20:24 -0400 Sent to CCL by: "Zahra Alimohammadi Keyvani" [fahimea76+*+gmail.com] Dear all; I want to do my computations under external potential like particle in box model . How can i exert such potential barrier in my jobs in guassian? thanks for your help. Best Regards; Alimohammadi From owner-chemistry@ccl.net Fri Jul 12 15:01:00 2013 From: "Theodore S. Dibble tsdibble]_[esf.edu" To: CCL Subject: CCL:G: Singlet Dioxygen Optimization Failure at MP2/6-31G Message-Id: <-48949-130712140304-11234-wZ0ZLq3Wx7kQi8adX3wzPQ%x%server.ccl.net> X-Original-From: "Theodore S. Dibble" Date: Fri, 12 Jul 2013 14:03:03 -0400 Sent to CCL by: "Theodore S. Dibble" [tsdibble^^esf.edu] The previous comments are correct: 1) the ground state state of O2 is a triplet 2) standard single reference methods like DFT and MP2 are not appropriate for the singlet excited states (plural!) of O2 ...but they omit some relevant points a) your basis set (6-31G) is too small to expect good relative energies b) the dissociation of the molecule that you observed often happens when the program has found the wavefunction of an dissociative excited state (the singlet excited states of O2 are bound). Dissociation like this should prompt you to check that the program found the right state. Regards, Ted Dibble Theodore S. Dibble Professor of Chemistry SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/faculty/dibble/ > "Hao-Bo Guo guohaobo[#]gmail.com" wrote: > > Sent to CCL by: Hao-Bo Guo [guohaobo===gmail.com] > --e89a8f923e7886055904e14707fd > Content-Type: text/plain; charset=ISO-8859-1 > > He's trying to optimize the singlet O2 in the 1Sigma excited state, for > which theory such as EOM-CCSD may be required. > > Hao-Bo Guo > > > On Thu, Jul 11, 2013 at 7:54 PM, Cu Phung cphung::methodist.edu < > owner-chemistry|,|ccl.net> wrote: > > > Diatomic oxygen is not a singlet state but a triplet state. That is why > > it won't optimize. Change the line > > 0 1 > > to > > 0 3 > > and it should work. > > > > CGP > > > > Sent > from my iPad > > > > On Jul 11, 2013, at 1:04 PM, "Jiabo Li jiaboli{=}yahoo.com" < > > owner-chemistry]-[ccl.net> wrote: > > > > O2 has a triplet ground state, not singlet. > > > > *From:* "Anon anon,example.none" > > > > *To:* "Li, Jiabo " > > *Sent:* Thursday, July 11, 2013 6:54 AM > > *Subject:* CCL:G: Singlet Dioxygen Optimization Failure at MP2/6-31G > > > > > > Sent to CCL by: "Anon" [anon : example.none] > > I am trying to optimize singlet dioxygen at the MP2/6-31G level of theory > > but it is not working. Increasing the number of optimization steps does no > > good either. After the number of steps are used up, I see that the final > > length of the unoptimized molecule is about 50 Angstroms. At each > > optimization step Gaussian keeps increasing the bond length, failing to > > realize that the bond length is much smaller. > > > > Here is the input that I am using: > > > > # MP2/6-31G OPT > > > > 0 1 > > O > > O 1 R1 > > > > R1=1.2 > > > > Could someone add any insight to this issue? Why can't I optimize > > dioxygen, which is such a simple molecule? Can a specific keyword help this > > problem?**the > > strange characters on the top line to the (_) sign. You can also** > > E-mail to subscribers: CHEMISTRY(_)ccl.net or use: > > = > > > > E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net or use> **> ****Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > **> > > > > > > > > ********** > > > > > > --e89a8f923e7886055904e14707fd > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > >
He's trying to optimize the singlet O2 in the 1Sigma e= > xcited state, for which theory such as EOM-CCSD may be required.

div>
Hao-Bo Guo


v class=3D"gmail_quote"> > On Thu, Jul 11, 2013 at 7:54 PM, Cu Phung cphung:: st.edu">methodist.edu < mistry|,|ccl.net" target=3D"_blank">owner-chemistry|,|ccl.net> wr= > ote:
>
x #ccc solid;padding-left:1ex">
Diatomic oxygen is no= > t a singlet state but a triplet state. =A0That is why it won't optimize= > . =A0Change the line
>
=A0 0 1
to
=A0 0 3
and it should work. div>

CGP

Sent > from my iPad

On = > Jul 11, 2013, at 1:04 PM, "Jiabo Li jiaboli{=3D} o.com" target=3D"_blank">yahoo.com" < emistry]-[ccl.net" target=3D"_blank">owner-chemistry]-[ccl.net> wrot= > e:
>
family:Courier New,courier,monaco,monospace,sans-serif">
O2 has a= > triplet ground state, not singlet.
>

>
ce,sans-serif"> >
if"> >
>
-RIGHT:#ccc 1px solid;BORDER-BOTTOM:#ccc 1px solid;PADDING-BOTTOM:0px;PADDI= > NG-TOP:0px;PADDING-LEFT:0px;MARGIN:5px 0px;BORDER-LEFT:#ccc 1px solid;LINE-= > HEIGHT:0;PADDING-RIGHT:0px" readonly> >
From:= > "Anon anon, "_blank">dal.ca" <owner-chemistry(_) target=3D"_blank">ccl.net>
> To: "Li, Jiabo " &= > lt;jiaboli(_)yahoo.com&g= > t;
Sent: Thursday, July = > 11, 2013 6:54 AM
> Subject: CCL:G: Singlet Diox= > ygen Optimization Failure at MP2/6-31G
>


Sent to CCL by: "Anon" [anon := > dal.ca]
I am trying to= > optimize singlet dioxygen at the MP2/6-31G level of theory but it is not w= > orking. Increasing the number of optimization steps does no good either. Af= > ter the number of steps are used up, I see that the final length of the uno= > ptimized molecule is about 50 Angstroms. At each optimization step Gaussian= > keeps increasing the bond length, failing to realize that the bond length = > is much smaller.
>
Here is the input that I am using:

# MP2/6-31G OPT

0 1 >O
O 1 R1

R1=3D1.2

Could someone add any insight to this i= > ssue? Why can't I optimize dioxygen, which is such a simple molecule? C= > an a specific keyword help this problem?
>


-=3D This is automatically added to each message by the mailing= > script =3D-the strange characters on the top line to the (_) sign. = > You can also
E-mail to subscribers: )ccl.net" target=3D"_blank">CHEMISTRY(_)ccl.net or use:
> =A0 =A0 =A0 =3D

E-mail to administrators: Y-REQUEST(_)ccl.net" target=3D"_blank">CHEMISTRY-REQUEST(_)ccl.net or u= > se
=A0 =A0 =A0 e" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message > > =A0 =A0 =A0 target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml
<= > /u>Conferences: ents/conferences/" target=3D"_blank">http://server.ccl.net/chemistry/announ= > cements/conferences/
> =A0 = > =A0 =A0 http:= > //www.ccl.net/spammers.txt

RTFI: hemistry/aboutccl/instructions/" target=3D"_blank">http://www.ccl.net/chemi= > stry/aboutccl/instructions/
>



= >
>

> > --e89a8f923e7886055904e14707fd-- > > From owner-chemistry@ccl.net Fri Jul 12 16:05:00 2013 From: "Frank Jensen frj^chem.au.dk" To: CCL Subject: CCL:G: Singlet Dioxygen Optimization Failure at MP2/6-31G Message-Id: <-48950-130712160208-7003-6bMS+wX9iVwceDkLuyeMvw^server.ccl.net> X-Original-From: Frank Jensen Content-Language: da-DK Content-Type: multipart/alternative; boundary="_000_9110095E4E5E466FBE8EEFC87726225Fchemaudk_" Date: Fri, 12 Jul 2013 20:02:00 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj^_^chem.au.dk] --_000_9110095E4E5E466FBE8EEFC87726225Fchemaudk_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Just to clarify the recent rant on O2. The ground state is a triplet, can be run with any of your favorite single = determinant methods. There are two low-lying singlet states. The lowest is a singlet delta state. It can be described by a two-determina= nt casscf, or a single determinant with complex orbitals. The latter is an = option in Gaussian, and can be done at the MP2 level. Equilibrium geometry = and singlet-triplet splitting is quite good at this level. The next excited state is a singlet sigma. You need a 2e-2o casscf to descr= ice this. These are low-lying valence states and basis set requirements are as usual = for 'ground state' systems. Specifying a singlet (real orbital) determinant will get you a mixture of t= he singlet delta and sigma state. Go figure how relevant that is for your a= pplication. Frank Sendt fra min iPad Den 12/07/2013 kl. 03.55 skrev "Bradley Welch bwelch5[-]slu.edu" >: Singlet Oxygen does in fact exist as an excited state in the oxygen diatomi= c molecule. I think the O2 singlet needs to a more powerful method besides = MP2 for an excited state calculation. I ran it through Gaussian 09 with CCS= D(T)/6-311G** and it successfully completed. You might want to use a more r= obust basis set depending on what you are planning on doing, especially for= an excited state. On Thu, Jul 11, 2013 at 6:54 PM, Cu Phung cphung::methodist.edu > wr= ote: Diatomic oxygen is not a singlet state but a triplet state. That is why it= won't optimize. Change the line 0 1 to 0 3 and it should work. CGP Sent > from my iPad On Jul 11, 2013, at 1:04 PM, "Jiabo Li jiaboli{=3D}yahoo.com" > wrote: O2 has a triplet ground state, not singlet. > From: "Anon anon,example.none" > To: "Li, Jiabo " > Sent: Thursday, July 11, 2013 6:54 AM Subject: CCL:G: Singlet Dioxygen Optimization Failure at MP2/6-31G Sent to CCL by: "Anon" [anon : example.none] I am trying to optimize singlet dioxygen at the MP2/6-31G level of theory b= ut it is not working. Increasing the number of optimization steps does no g= ood either. After the number of steps are used up, I see that the final len= gth of the unoptimized molecule is about 50 Angstroms. At each optimization= step Gaussian keeps increasing the bond length, failing to realize that th= e bond length is much smaller. Here is the input that I am using: # MP2/6-31G OPT 0 1 O O 1 R1 R1=3D1.2 Could someone add any insight to this issue? Why can't I optimize dioxygen,= which is such a simple molecule? Can a specific keyword help this problem? -=3D This is automatically added to each message by the mailing script =3D-= the strange characters on the top line to the (_) sign. You can also E-mail to subscribers: CHEMISTRY(_)ccl.net or u= se: =3D E-mail to administrators: CHEMISTRY-REQUEST(_)ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Bradley Welch Saint Louis University Monsanto Hall Room 218 --_000_9110095E4E5E466FBE8EEFC87726225Fchemaudk_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Just to clarify the recent rant on O2.
The ground state is a triplet, can be run with any of your favorite si= ngle determinant methods.
There are two low-lying singlet states.
The lowest is a singlet delta state. It can be described by a two-dete= rminant casscf, or a single determinant with complex orbitals. The latter i= s an option in Gaussian, and can be done at the MP2 level. Equilibrium geom= etry and singlet-triplet splitting is quite good at this level.
The next excited state is a singlet sigma. You need a 2e-2o casscf to = descrice this.
These are low-lying valence states and basis set requirements are as u= sual for 'ground state' systems.
Specifying a singlet (real orbital) determinant will get you a mixture= of the singlet delta and sigma state. Go figure how relevant that is for y= our application.

Frank

Sendt fra min iPad

Den 12/07/2013 kl. 03.55 skrev "Bradley Welch bwelch5[-]slu.edu" <owner-chemistry..ccl.net>:

Singlet Oxygen does in fact exist as an excited state in t= he oxygen diatomic molecule. I think the O2 singlet needs to a more powerfu= l method besides MP2 for an excited state calculation. I ran it through Gau= ssian 09 with CCSD(T)/6-311G** and it successfully completed. You might want to use a more robust basis set d= epending on what you are planning on doing, especially for an excited state= . 


On Thu, Jul 11, 2013 at 6:54 PM, Cu Phung cphung= ::methodist.edu <owner-chemistry|,|ccl.net> wrote:
Diatomic oxygen is not a singlet state but a triplet state.  That= is why it won't optimize.  Change the line
  0 1
to
  0 3
and it should work.

CGP

Sent > from my iPad

On Jul 11, 2013, at 1:04 PM, "Jiabo Li jiaboli{=3D}yahoo.com" <owner-chemistry]-[ccl.net> w= rote:

O2 has a triplet ground state, not singlet.

From: &= quot;Anon anon,dal.ca" <owner-chemistry(_)ccl.net>
To: "Li, Jiabo " &= lt;jiaboli(_)yahoo.com&g= t;
Sent: Thursday, July 11, 201= 3 6:54 AM
Subject: CCL:G: Singlet Diox= ygen Optimization Failure at MP2/6-31G


Sent to CCL by: "Anon" [sp= : xxx.ca]
I am trying to optimize singlet dioxygen at the MP2/6-31G level of theory b= ut it is not working. Increasing the number of optimization steps does no g= ood either. After the number of steps are used up, I see that the final len= gth of the unoptimized molecule is about 50 Angstroms. At each optimization step Gaussian keeps increasing= the bond length, failing to realize that the bond length is much smaller.<= br>
Here is the input that I am using:

# MP2/6-31G OPT

0 1
O
O 1 R1

R1=3D1.2

Could someone add any insight to this issue? Why can't I optimize dioxygen,= which is such a simple molecule? Can a specific keyword help this problem?=



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Monsanto Hall Room 218
--_000_9110095E4E5E466FBE8EEFC87726225Fchemaudk_-- From owner-chemistry@ccl.net Fri Jul 12 17:27:00 2013 From: "shawn wong subchap.sp4]=[gmail.com" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48951-130712165407-13780-Jfy4fiweqo+jfho+dqgbsw * server.ccl.net> X-Original-From: shawn wong Content-Type: multipart/alternative; boundary=001a11c3a94ce1a02204e156b532 Date: Fri, 12 Jul 2013 16:54:01 -0400 MIME-Version: 1.0 Sent to CCL by: shawn wong [subchap.sp4,,gmail.com] --001a11c3a94ce1a02204e156b532 Content-Type: text/plain; charset=ISO-8859-1 You may use www.sciencing.net. You can add your own keywords and receive email notifications when new papers are published. It's very convenient. Best wishes, Shawn 2013/7/9 Lucus White lucus.white2000,gmail.com > >> >> Sent to CCL by: "Lucus White" [lucus.white2000[]gmail.com] >> Hi All, >> >> I'm just curious about what the best way is to check the latest papers. >> For instance, I want to see the >> most recent issues and the ASAP papers in the major journals. I normally >> visit the journal websites one >> by one, but is there any better way to do it? >> >> Any suggestions would be appreciated. >> >> Best wishes, >> Lucus >> lucus.white2000,,gmail.com** >> E-mail to subscribers: CHEMISTRY\a/ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST\a/ccl.net or use>> **>> >> >> > --001a11c3a94ce1a02204e156b532 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
You may use www.sciencing.net. You can add your own keywords and receive email no= tifications when new papers are published. It's very convenient.
<= div style>
Best wishes,
Shawn

=
2013/7/9 Lucus White lucus.white2000,gmail.com <owner-chemistry\a/ccl.net>=

Sent to CCL by: "Lucus =A0White" [lucus.white2000[]gmail.com]
Hi All,

I'm just curious about what the best way is to check the latest papers.= For instance, I want to see the
most recent issues and the ASAP papers in the major journals. I normally vi= sit the journal websites one
by one, but is there any better way to do it?

Any suggestions would be appreciated.

Best wishes,
Lucus
lucus.white2000,,gmail.com



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