From owner-chemistry@ccl.net Thu Nov 9 05:16:01 2006 From: "Mahesh Menon mahesh_menon71#yahoo.com" To: CCL Subject: CCL:G: anharmonic constant Message-Id: <-32976-061108135703-13421-B6iIRa4vPvLxYAGv1Hxl9Q+/-server.ccl.net> X-Original-From: Mahesh Menon Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1631463099-1163008611=:28442" Date: Wed, 8 Nov 2006 09:56:51 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Mahesh Menon [mahesh_menon71[A]yahoo.com] --0-1631463099-1163008611=:28442 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Ramasami, You did not mention which software you use for anharmonic calculation. If you are using Gaussian03, then there is no way we can do the anhamonic calculations for linear (e.g. CO), spherically symmetrical molecules (Oh symmetry like SF6) and other highly symmetrical molecules (e.g. C60). You have to use other softwares. Regards, Mahesh "Dr. Ponnadurai Ramasami ramchemi,+,intnet.mu" wrote: Dear All I did a frequency calculation for carbon monoxide. #P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3DVibRot maxdisk=3D2gb or #P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3Danharm maxdisk=3D2gb However for this diatomic molecule, the anharmonic constant does not = appear in the output, although it appears for a triatomic molecule. Can anyone help? Thanks Ramasami --------------------------------- Sponsored Link Get an Online or Campus degree - Associate's, Bachelor's, or Master's - in less than one year. --0-1631463099-1163008611=:28442 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Ramasami,
You did not mention which software you use for anharmonic calculation.
 
If you are using Gaussian03, then there is no way we can do the anhamonic calculations for linear (e.g. CO), spherically symmetrical molecules (Oh symmetry like SF6) and other highly symmetrical molecules (e.g. C60). You have to use other softwares.
 
Regards,
Mahesh
 
 
 


"Dr. Ponnadurai Ramasami ramchemi,+,intnet.mu" <owner-chemistry-#-ccl.net> wrote:

Dear All

I did a frequency calculation for carbon monoxide.

#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3DVibRot maxdisk=3D2gb
or
#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3Danharm maxdisk=3D2gb


However for this diatomic molecule, the anharmonic constant does not =
appear in the output, although it appears for a triatomic molecule.

Can anyone help?

Thanks

Ramasami

Sponsored Link

Get an Online or Campus degree - Associate's, Bachelor's, or Master's - in less than one year. --0-1631463099-1163008611=:28442-- From owner-chemistry@ccl.net Thu Nov 9 06:25:01 2006 From: "Cory Pye cpye#%#crux.smu.ca" To: CCL Subject: CCL:G: Gaussian calculation Message-Id: <-32977-061108200757-26301-uFk3d5/DKPc6uy8VrtaSqQ|-|server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 8 Nov 2006 20:07:56 -0400 (AST) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye---crux.smu.ca] Hello Emi, I have done this for phosphate for some small and medium-sized basis sets at the HF and MP2 levels. See C. C. Pye and W. W .Rudolph, J. Phys. Chem. A, 107, 8746 (2003). I also have some unpublished results up to aug-cc-pVQZ. If you are talking about PO4 3-, the multiplicity is 1. The anion is not electronically stable and will spontaneously lose an electron (and probably then an O- to give PO3 -). This would probably show itself by an RHF->UHF instability. You would need a very large basis set to see this happen. On Wed, 8 Nov 2006, Emi Psachoulia efthymia.psachoulia^-^merton.ox.ac.uk wrote: > Sent to CCL by: "Emi Psachoulia" [efthymia.psachoulia!A!merton.ox.ac.uk] > Hi, > > I tried to use Gaussian03 to do geometrical optimization of a phosphate anion and then to calculate its charges. > I used for the geometry calculation HF/6-31G(d) Opt NoSymm and HF/6-31G(d,p) Opt NoSymm and then for the charge HF/6-31G* pop=mk iop(6/33=2) and HF/6-31G** pop=mk iop(6/33=2) respectively. > I had an output for the geometry calculations, but not for the charges. > I would like to ask you what the multiplicity is for system given that electrons delocalised. > Also, what basis set shall I use? > > Thank you, > > Emi Psachoulia > efthymia.psachoulia{}merton.ox.ac.uk > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye{}crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Thu Nov 9 08:52:00 2006 From: "Alex Henderson Alex.Henderson(a)manchester.ac.uk" To: CCL Subject: CCL: Looking for structure enumeration code Message-Id: <-32978-061108150259-31987-7jq+J5JjBhj9qQY+IcucEw::server.ccl.net> X-Original-From: "Alex Henderson" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Wed, 8 Nov 2006 18:24:50 +0000 MIME-Version: 1.0 Sent to CCL by: "Alex Henderson" [Alex.Henderson() manchester.ac.uk] Hi, (Apologies for cross-posting) Does anyone know of any available source code (any language, but prefer Java, C/C++, Perl) that can enumerate chemically correct structures given a molecular formula? For example; if I have C4H10 I could have the linear CCCC or the branched CC(C)C (in SMILES notation). I appreciate that for larger molecular formulae we will get a huge number of structures, but that's OK. Many thanks, Alex From owner-chemistry@ccl.net Thu Nov 9 09:27:01 2006 From: "Wolf-D. Ihlenfeldt wdi]~[xemistry.com" To: CCL Subject: CCL: Looking for structure enumeration code Message-Id: <-32979-061109091022-16831-maYe11csnha/6085ZzFx5A[#]server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 9 Nov 2006 09:10:07 -0500 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi]_[xemistry.com] I suggest you investigate Molgen: http://www.mathe2.uni-bayreuth.de/molgen4/ I do not know about source code availability, though. W. D. Ihlenfeldt Xemistry GmbH wdi,xemistry.com > -----Original Message----- > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net] > Sent: Thursday, November 09, 2006 9:00 AM > To: Ihlenfeldt, W.d. > Subject: CCL: Looking for structure enumeration code > > Sent to CCL by: "Alex Henderson" [Alex.Henderson() manchester.ac.uk] > > > Hi, > > (Apologies for cross-posting) > > Does anyone know of any available source code (any language, > but prefer Java, C/C++, Perl) that can enumerate chemically > correct structures given a molecular formula? > > For example; if I have C4H10 I could have the linear CCCC or > the branched CC(C)C (in SMILES notation). > > I appreciate that for larger molecular formulae we will get a > huge number of structures, but that's OK. > > Many thanks, > Alex > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, > please change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > From owner-chemistry@ccl.net Thu Nov 9 10:27:00 2006 From: "Kai Hartmann Kai.Hartmann|uni-koeln.de" To: CCL Subject: CCL: Looking for structure enumeration code Message-Id: <-32980-061109102454-27932-cgIPmmfnc+Fc+zA9DbKefg#,#server.ccl.net> X-Original-From: "Kai Hartmann" Date: Thu, 9 Nov 2006 10:24:54 -0500 Sent to CCL by: "Kai Hartmann" [Kai.Hartmann|a|uni-koeln.de] Hi Alex, if I understood correctly, given one specific sum formula you would like to create all isomeric structures. You can use the Chemistry Development Kit for this. It is a java library for Chem-/Bioinformatics (http://cdk.sf.net/) and licensed LGPL (open source). The relevant part is in the package structgen. You may want to use the deterministic version. Alternatively, to get an overview of the space in case of a large number of structures, you can use the stochastic algorithm. Kai Alex Henderson Alex.Henderson(a)manchester.ac.uk schrieb: > Sent to CCL by: "Alex Henderson" [Alex.Henderson() manchester.ac.uk] > > > Hi, > > (Apologies for cross-posting) > > Does anyone know of any available source code (any language, but prefer Java, C/C++, Perl) that can enumerate chemically correct structures given a molecular formula? > > For example; if I have C4H10 I could have the linear CCCC or the branched CC(C)C (in SMILES notation). > > I appreciate that for larger molecular formulae we will get a huge number of structures, but that's OK. > > Many thanks, > Alex > From owner-chemistry@ccl.net Thu Nov 9 13:09:01 2006 From: "Jennifer Clare Brookes ucapjcb]^[ucl.ac.uk" To: CCL Subject: CCL:G: Infra Red Absorbancies Message-Id: <-32981-061109104615-16445-JBb64Pl/HNn5YSkNgEs4oQ ~~ server.ccl.net> X-Original-From: "Jennifer Clare Brookes" Date: Thu, 9 Nov 2006 10:46:14 -0500 Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb#ucl.ac.uk] Hi, I am using Gaussian 03 to calculate the vibrational frequencies of small molecules and would like to understand how the program calculates the infra-red intensities. I find the values in kmmol-1 can differ by factors of 10 when method and basis set is changed. The relative values make sense and agree with experiment but I would like to know exactly how the absolute numbers are found. As I understand it the values given are based on the derivative of dipole moment with respect to displacement squared, but how is this found? ie are partial charges used and how are these calculated (mulliken?). Thanks, any help is much appreciated. From owner-chemistry@ccl.net Thu Nov 9 13:44:01 2006 From: "Philippe Carbonniere philippe.carbonniere!A!univ-pau.fr" To: CCL Subject: CCL:G: anharmonic constant Message-Id: <-32982-061109104104-15661-rIiCCnFuDsqIIdIWZd4AHQ() server.ccl.net> X-Original-From: Philippe Carbonniere Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 09 Nov 2006 15:43:48 +0100 MIME-Version: 1.0 Sent to CCL by: Philippe Carbonniere [philippe.carbonniere]![univ-pau.fr] Dear all, Concerning the anharmonic calculations in G03 for linear or spherically symmetrical molecules : optimize the molecule in a lower symmetry (no more than two-fold axis), starting with a corresponding geometry. It works well. Best regards, Philippe Carbonniere Mahesh Menon mahesh_menon71#yahoo.com a écrit : >Sent to CCL by: Mahesh Menon [mahesh_menon71[A]yahoo.com] > >--0-1631463099-1163008611=:28442 >Content-Type: text/plain; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >Dear Ramasami, > You did not mention which software you use for anharmonic calculation. > > If you are using Gaussian03, then there is no way we can do the anhamonic calculations for linear (e.g. CO), spherically symmetrical molecules (Oh symmetry like SF6) and other highly symmetrical molecules (e.g. C60). You have to use other softwares. > > Regards, > Mahesh > > > > > >"Dr. Ponnadurai Ramasami ramchemi,+,intnet.mu" wrote: > >Dear All > >I did a frequency calculation for carbon monoxide. > >#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3DVibRot maxdisk=3D2gb >or >#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3Danharm maxdisk=3D2gb > > >However for this diatomic molecule, the anharmonic constant does not = >appear in the output, although it appears for a triatomic molecule. > >Can anyone help? > >Thanks > >Ramasami > > > >--------------------------------- >Sponsored Link > >Get an Online or Campus degree - Associate's, Bachelor's, or Master's - in less than one year. >--0-1631463099-1163008611=:28442 >Content-Type: text/html; charset=iso-8859-1 >Content-Transfer-Encoding: 8bit > >
Dear Ramasami,
You did not mention which software you use for anharmonic calculation.
 
If you are using Gaussian03, then there is no way we can do the anhamonic calculations for linear (e.g. CO), spherically symmetrical molecules (Oh symmetry like SF6) and other highly symmetrical molecules (e.g. C60). You have to use other softwares.
 
Regards,
Mahesh
 
 
 


"Dr. Ponnadurai Ramasami ramchemi,+,intnet.mu" <owner-chemistry^-^ccl.net> wrote:

Dear All

I did a frequency calculation for carbon monoxide.

#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3DVibRot maxdisk=3D2gb
or
#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3Danharm maxdisk=3D2gb


However for > this diatomic molecule, the anharmonic constant does not =
appear in the output, although it appears for a triatomic molecule.

Can anyone help?

Thanks

Ramasami

> > >

Sponsored Link

>Get an Online or Campus degree - Associate's, Bachelor's, or Master's - in less than one year. >--0-1631463099-1163008611=:28442--> > > > > > From owner-chemistry@ccl.net Thu Nov 9 14:19:01 2006 From: "Jan Labanowski janl^speakeasy.net" To: CCL Subject: CCL: Few comments from CCL Manager Message-Id: <-32983-061109130502-15074-njT3KtWNZeCtjSWrXTHl4Q:+:server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 09 Nov 2006 18:04:54 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl[*]speakeasy.net] Dear CCL Members, You cannot complain that I am swamping the list with "messages to members" too often, but I need to do it occasionally so you remember that I am still here... I would like to start from thanking CCL Supporters: American Chemical Society COMP Division: http://membership.acs.org/C/COMP/ Please visit the COMP division page periodically to learn about new symposia, awards, and competitions, and if you are a member of ACS, make sure that you sign up for the membership of COMP Division. It offers numerous benefits, discounts on publications and participation in ACS COMP sponsored meetings and timely information. Computational Science and Engineering Online (CSE-Online) http://cse-online.net/ that provides and excellent environment for many research domains where computational chemistry is used (reaction engineering, molecular biology, material science and data archiving and visualization and more). It is free, extensible, grid-enabled, secure, and runs on many platforms. Sunset Molecular Discovery, LLC http://sunsetmolecular.com/ where you can acquire important tools for drug discovery: WOMBAT and WOMBAT-PK databases of biological activities and Pharmacokinetics and ChemGPS (Chemical Global Positionin System). Sunset Molecular Discovery also provides consulting in the area of Lead Discovery. Please visit the site to learn more about their offering. You or your company is more than welcome to "adopt the CCL page" and have their logo there. It will not only say: "I care!" but will give a better ranking for your Web site on Google. I also thank all of you who support CCL by submitting interesting questions and valuable answers to CCL and submit materials to its archives. Many of you also use the CCL paid services that keep CCL running. Please check how you and/or your organization can become the CCL Supporter by visiting: http://server.ccl.net/chemistry/aboutccl/supporting/ WHAT IS NEW? CCL is now indexed by the new service from ISI (ISI Web of Knowledge) which gives it a certain status of recognition as a valuable site. I proudly display their logo on the CCL Home page: http://www.ccl.net Thank you for all your contributions and discussions -- I did not have anything to do with it. Keep the level of discussions high since it is an award to all of you. Job page: --------- http://www.ccl.net/chemistry/announcements/jobs/ was visited more than 300,000 times within last year. From comments that I receive, it is a good place to post your announcement about the open position. Some people report finding a suitable candidate within days > from posting the ad. For those who look for jobs in the "ChemComp" field this is a valuable resource to find a job on any level. Use this resource to your advantage!!! Conference page: ---------------- Please submit workshops and conferences there. It is a free service and will get your announcement on Google. This page is also visited frequently by CCL Membership. Even if you are not associated with the organizer, please include there information on events that you consider interesting. FEW REMINDERS: Please read occasionally the Instructions to the list: http://www.ccl.net/chemistry/aboutccl/instructions/ Some mistakes that I see made sometimes: a) If you reply to the message from CCL the mail DOES NOT GO TO THE AUTHOR. The author's address is obfuscated on the From: line of the message and you need to see the header of the message to recover it and type it in manually. Why? Many of you have spyware/virus on your computers that automatically extracts the email addresses from the incoming messages. This is done to protect the authors of the messages. Humans can easily guess the correct address and malware cannot do it. The list has a Reply-To: field set to point to chemistry a ccl.net and when you click on Reply, this is where the message should go. But... It depends on the software you use to compose the mail. To make sure that bounces do not go to the CCL distribution, the messages come to you from the address owner-chemistry a ccl.net If you reply to this address (i.e., your email agent does not honor the Reply-To: field) your message goes to the same place that bounces go: TRASH. Sorry... So, before you click on [Send] check that the To: says: CHEMISTRY a CCL.NET. Since I do not read the bounces, I cannot redirect them to the list. There are just too many of them and most of them are the responses from your spyware/virus. Only the automatic scripts process the owner-chemistry mailbox and if you sent your message there, it will be lost. b) If you send message to CCL either to chemistry a ccl.net or by using the WEB Interface at: http://server.ccl.net/cgi-bin/ccl/send_ccl_message you will be send a message requesting the confirmation. This is the only way to verify that the author's address is valid and real. If you do not see the confirmation request (it may take sometimes an hour for it to get to you), check your SPAMBOX. The confirmation request contains links and may have been stopped by your spam filter. The other possibility is that you sent your message to a wrong address (as described in "a" above) or that you did not enter a valid address on the form. Note, you DO NOT HAVE TO BE SUBSCRIBED to post to CCL, but you will be verified. On your first posting to CCL the moderator has to approve your address for posting. If you do not see your message posted, bug the moderator (jkl a ccl.net). c) MIME attachments, like images and application/SOMETHING, are not allowed on CCL. I really prefer to be safe than sorry with all new exploits being designed daily. So, mail with attachments is rejected. I am trying to clean the winmail.dat attachment that is added by Microsoft software and this is a nuisance. Please make sure your mail is set not to attach the winmail.dat. It is TOTALLY useless, bulky, and is often rejected by spam filters since being an application (i.e., executable entity) it is a potential risk. For the good of all of us, please send PLAIN TEXT messages to CCL. d) I myself (and you too, most likely) get mail that apparently comes from CCL but is a virus or spam. This is a common practice of the "scum of Internet" to disguise themselves as some respectable entity. It is easy to see that such mail is a fake by examining the header of your message. The CCL server IP address is: 66.93.212.15 and if it does not appear on the top Received: line of your message header, the message did not come from CCL and is a fake. While I cannot say that CCL will NEVER spam you (if they can hack banks and CIA, they can hack me too), but so far, CCL is lucky. But if you see spam/virus from CCL, please alert me ASAP, since it would mean that my luck ran away... e) Please upload interesting stuff to CCL and share: http://server.ccl.net/chemistry/aboutccl/contributing/ CCL is not only a discussion forum but also archives, and uploading material there gives it some "permanence" (CCL Archives are 15 years old). Please encourage others to "save" their software, information, write-ups, data, examples, educational materials, demos, etc in the CCL archives and make it publicly available. Since CCL site is actively indexed by many search engines this material will be easier to find for everyone. Thank you for your patience and understanding... Jan Labanowski CCL Manager jkl a ccl.net http://www.ccl.net From owner-chemistry@ccl.net Thu Nov 9 15:06:00 2006 From: "Alex Henderson Alex.Henderson:+:manchester.ac.uk" To: CCL Subject: CCL: Looking for structure enumeration code Message-Id: <-32984-061109150512-31491-fCiHbvz5e6DiYC1IRTpWYQ|server.ccl.net> X-Original-From: "Alex Henderson" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 9 Nov 2006 20:05:02 +0000 MIME-Version: 1.0 Sent to CCL by: "Alex Henderson" [Alex.Henderson%%manchester.ac.uk] Hi Kai, Thanks for the information on CDK. This seems to be a very powerful package. Alex - > -----Original Message----- > From: owner-chemistry#,#ccl.net [mailto:owner-chemistry#,#ccl.net] On Behalf Of Kai > Hartmann Kai.Hartmann|uni-koeln.de > Sent: 09 November 2006 15:29 > To: Henderson, Alex > Subject: CCL: Looking for structure enumeration code > > Sent to CCL by: "Kai Hartmann" [Kai.Hartmann|a|uni-koeln.de] > Hi Alex, > > if I understood correctly, given one specific sum formula you would like > to create all isomeric structures. > > You can use the Chemistry Development Kit for this. It is a java library > for Chem-/Bioinformatics (http://cdk.sf.net/) and licensed LGPL (open > source). The relevant part is in the package structgen. You may want to > use the deterministic version. Alternatively, to get an overview of the > space in case of a large number of structures, you can use the > stochastic algorithm. > > Kai > > Alex Henderson Alex.Henderson(a)manchester.ac.uk schrieb: > > Sent to CCL by: "Alex Henderson" [Alex.Henderson() manchester.ac.uk] > > > > > > Hi, > > > > (Apologies for cross-posting) > > > > Does anyone know of any available source code (any language, but prefer Java, > C/C++, Perl) that can enumerate chemically correct structures given a molecular > formula? > > > > For example; if I have C4H10 I could have the linear CCCC or the branched CC(C)C > (in SMILES notation). > > > > I appreciate that for larger molecular formulae we will get a huge number of > structures, but that's OK. > > > > Many thanks, > > Alex> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > From owner-chemistry@ccl.net Thu Nov 9 16:03:00 2006 From: "Alex Henderson Alex.Henderson() manchester.ac.uk" To: CCL Subject: CCL: Looking for structure enumeration code Message-Id: <-32985-061109155919-23161-yyiaQa/TLlivRPq0zoEFUw^server.ccl.net> X-Original-From: "Alex Henderson" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 9 Nov 2006 20:02:21 +0000 MIME-Version: 1.0 Sent to CCL by: "Alex Henderson" [Alex.Henderson+/-manchester.ac.uk] Thanks for the information on Molgen; it looks interesting. Maybe I don't need to write any code at all! Alex - > -----Original Message----- > From: owner-chemistry[*]ccl.net [mailto:owner-chemistry[*]ccl.net] On Behalf Of Wolf- > D. Ihlenfeldt wdi]~[xemistry.com > Sent: 09 November 2006 14:40 > To: Henderson, Alex > Subject: CCL: Looking for structure enumeration code > > Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi]_[xemistry.com] > > I suggest you investigate Molgen: > > http://www.mathe2.uni-bayreuth.de/molgen4/ > > I do not know about source code availability, though. > > W. D. Ihlenfeldt > Xemistry GmbH > wdi+/-xemistry.com > > > > -----Original Message----- > > From: owner-chemistry+/-ccl.net [mailto:owner-chemistry+/-ccl.net] > > Sent: Thursday, November 09, 2006 9:00 AM > > To: Ihlenfeldt, W.d. > > Subject: CCL: Looking for structure enumeration code > > > > Sent to CCL by: "Alex Henderson" [Alex.Henderson() manchester.ac.uk] > > > > > > Hi, > > > > (Apologies for cross-posting) > > > > Does anyone know of any available source code (any language, > > but prefer Java, C/C++, Perl) that can enumerate chemically > > correct structures given a molecular formula? > > > > For example; if I have C4H10 I could have the linear CCCC or > > the branched CC(C)C (in SMILES notation). > > > > I appreciate that for larger molecular formulae we will get a > > huge number of structures, but that's OK. > > > > Many thanks, > > Alex > > > > > > > > -= This is automatically added to each message by the mailing > > script =- > > To recover the email address of the author of the message, > > please change> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/ > > > > Search Messages: http://www.ccl.net/htdig (login: ccl, > > Password: search)> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -+-+-+-+-+> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > From owner-chemistry@ccl.net Thu Nov 9 21:16:00 2006 From: "Zhuofeng KE \(Jonathan Kerr\) jorphancore=yahoo.com.cn" To: CCL Subject: CCL: =?gb2312?q?=BB=D8=B8=B4=A3=BA=20CCL:=20Starter=20in=20computational=20cat?= =?gb2312?q?alysis?= Message-Id: <-32986-061108212623-5824-qi1ge2ZI+DZPzU53kGFffg]![server.ccl.net> X-Original-From: "Zhuofeng KE \(Jonathan Kerr\)" Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1392713895-1163035574=:1579" Date: Thu, 9 Nov 2006 09:26:14 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: "Zhuofeng KE \(Jonathan Kerr\)" [jorphancore|*|yahoo.com.cn] --0-1392713895-1163035574=:1579 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear Kaci T. Ziegler and K. Morokuma have done many nice works on the polymerization reactions catalyzed by homo- or heterogeneous catalyst systems. Maybe their papers are helpful for your study. Zhuofeng KE (Jonathan Kerr) Theoretical and Computational Laboratory of Chemistry SUN YAT-SEN University, Guangzhou,510275 R.P. China Email: jorphancore++yahoo.com.cn --------------------------------- ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ£¡ --0-1392713895-1163035574=:1579 Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: 8bit
Dear Kaci
 
T. Ziegler and K. Morokuma have done many nice works on the polymerization reactions catalyzed by homo- or heterogeneous catalyst systems. Maybe their papers are helpful for your study.


Zhuofeng KE  (Jonathan Kerr)  
Theoretical and Computational Laboratory of Chemistry   
SUN YAT-SEN University,
Guangzhou,510275
R.P. China
Email: jorphancore++yahoo.com.cn

ÇÀ×¢ÑÅ»¢Ãâ·ÑÓÊÏä-3.5GÈÝÁ¿£¬20M¸½¼þ£¡ --0-1392713895-1163035574=:1579-- From owner-chemistry@ccl.net Thu Nov 9 21:51:00 2006 From: "tie jun cheng tjcheng^_^mail.sioc.ac.cn" To: CCL Subject: CCL: ask for a logP dataset Message-Id: <-32987-061109205430-12800-22G/Rq5f0xbq5PJ/13cigw .. server.ccl.net> X-Original-From: "tie jun cheng" Date: Thu, 9 Nov 2006 20:54:29 -0500 Sent to CCL by: "tie jun cheng" [tjcheng[*]mail.sioc.ac.cn] Dear CCLers recently I am going to do some work on a logP (partition coefficient in water and 1-octanol) predicting algorithm. My training set was constructed from Hansch's compilation (Hansch C, Leo A, 1995. Exploring QSAR: Hydrophobic, electronic, and steric constants. ACS.), I need a seperate testset to test this algorithm. Who kindly can tell me where i can find such dataset? Thanks in advance for your help JAY From owner-chemistry@ccl.net Thu Nov 9 22:25:00 2006 From: "tie jun cheng ccl!^!mail.sioc.ac.cn" To: CCL Subject: CCL: ask for a logP dataset Message-Id: <-32988-061109205722-13004-6bGMPAXmeivE5Zxarqjj4w-,-server.ccl.net> X-Original-From: "tie jun cheng" Date: Thu, 9 Nov 2006 20:57:22 -0500 Sent to CCL by: "tie jun cheng" [ccl|a|mail.sioc.ac.cn] Dear CCLers recently I am going to do some work on a logP (partition coefficient in water and 1-octanol) predicting algorithm. My training set was constructed from Hansch's compilation (Hansch C, Leo A, 1995. Exploring QSAR: Hydrophobic, electronic, and steric constants. ACS.), I need a seperate testset to test this algorithm. Who kindly can tell me where i can find such dataset? Thanks in advance for your help JAY From owner-chemistry@ccl.net Thu Nov 9 23:00:00 2006 From: "T. Daniel Crawford crawdad|,|exchange.vt.edu" To: CCL Subject: CCL:G: Infra Red Absorbancies Message-Id: <-32989-061109210649-12345-6n0+YjoQTuQNmRhFA/1GxQ a server.ccl.net> X-Original-From: "T. Daniel Crawford" Date: Thu, 09 Nov 2006 16:31:27 -0500 Sent to CCL by: "T. Daniel Crawford" [crawdad-#-exchange.vt.edu] Jennifer, You can find a relatively complete explanation of the theory of infrared "intensities" (which are more accurately referred to as "integrated absorption coefficients") in the book "Molecular Vibrations", by Wilson, Decius, and Cross, Dover, 1980, pp. 162-168. The values are indeed determined from derivative dipole moments, which, for most ab initio methods, can be calculated either analytically or via finite differences. Here's a single-page explanation of the relationship between vibrational transition moments and dipole derivatives that I give to my graduate students. I hope this will help. -TDC [** CCL Moderator: The document was detached from the message and placed on the CCL Web site as: http://www.ccl.net/cca/documents/ir_intensities-1.pdf **] On 11/9/06 1:21 PM, "Jennifer Clare Brookes ucapjcb]^[ucl.ac.uk" > Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb#ucl.ac.uk] > > Hi, I am using Gaussian 03 to calculate the vibrational frequencies of small > molecules and would like to understand how the program calculates the > infra-red intensities. I find the values in kmmol-1 can differ by factors of > 10 when method and basis set is changed. The relative values make sense and > agree with experiment but I would like to know exactly how the absolute > numbers are found. As I understand it the values given are based on the > derivative of dipole moment with respect to displacement squared, but how is > this found? ie are partial charges used and how are these calculated > (mulliken?). Thanks, any help is much appreciated. > -- T. Daniel Crawford Department of Chemistry crawdad*vt.edu Virginia Tech www.chem.vt.edu/faculty/crawford.php Voice: 540-231-7760 FAX: 540-231-3255 -------------------- PGP Public Key at: http://www.chem.vt.edu/chem-dept/crawford/publickey.txt From owner-chemistry@ccl.net Thu Nov 9 23:35:00 2006 From: "James Robinson James.Robinson() prosonix.co.uk" To: CCL Subject: CCL:G: Enforcing Symmetry in Gaussian03 Message-Id: <-32990-061109205430-121234-EjjkVOMaJJhYl8vZB4KiOw+*+server.ccl.net> X-Original-From: "James Robinson" Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C701DD.481E8E6A" Date: Mon, 6 Nov 2006 19:53:51 -0000 MIME-Version: 1.0 Sent to CCL by: "James Robinson" [James.Robinson++prosonix.co.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01C701DD.481E8E6A Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Soren, the simple way to force gaussian to maintain point group symmetry is to = build symmetrical z-matrices. That is if one was optimising say ethylene = (H2C=3DCH2) one would simple use the same variable for the C-H = distances.=20 %nproc=3D? %mem=3D? %chk=3Detsym.chk #p opt=3D(z-matrix) nosymm b3lyp/6-31+G(d) # gfinput iop(6/7=3D3) pop=3Dfull=20 symmetrical ethylene optmz 0 1 C =20 C 1 r21 =20 H 1 r31 2 a312 =20 H 1 r31 2 a312 3 d4123 0 H 2 r31 1 a312 3 d4123 0 H 2 r31 1 a312 3 d6213 0 =20 r21 1.321967 r31 1.086117 a312 123.097821 d4123 179.999993 d6213 -0.000214 I often write z-matrices like these by hand. Sometimes one has to use = dihedral angles that are opposite in sign to symmetrical dihedrals. I = also use the opt=3Dz-matrix and nosymm keywords together whenever I have = had to run calculations like these. Hope this helps. Dr James Robinson Senior Scientist -----Original Message----- From: Soren Eustis soren|-|jhu.edu [mailto:owner-chemistry ~ ccl.net] Sent: Mon 06/11/2006 16:44 To: James Robinson Subject: CCL: Enforcing Symmetry in Gaussian03 =20 -----Original Message----- From: Soren Eustis soren|-|jhu.edu [mailto:owner-chemistry ~ ccl.net] Sent: Mon 06/11/2006 16:44 To: James Robinson Subject: CCL: Enforcing Symmetry in Gaussian03 =20 Sent to CCL by: "Soren Eustis" [soren:+:jhu.edu] This seems to be a simple question, but I am having some difficulties. = I want to calculate the optimized geometry of a molecule but wish to keep = the point group of the molecule intact. How can I do this? Do I need to = use the symm=3Dfollow keyword??? Soren Eustis ------_=_NextPart_001_01C701DD.481E8E6A Content-Type: test/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable removed by moderator ------_=_NextPart_001_01C701DD.481E8E6A--